@article{eirin-lopez_marine_2019, title = {Marine {Environmental} {Epigenetics}}, volume = {11}, issn = {1941-1405, 1941-0611}, url = {https://www.annualreviews.org/doi/10.1146/annurev-marine-010318-095114}, doi = {10.1146/annurev-marine-010318-095114}, abstract = {Marine organisms’ persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics—mechanisms that facilitate phenotypic variation through genotype–environment interactions—are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.}, language = {en}, number = {1}, urldate = {2023-12-14}, journal = {Annual Review of Marine Science}, author = {Eirin-Lopez, Jose M. and Putnam, Hollie M.}, month = jan, year = {2019}, pages = {335--368}, file = {Eirin-Lopez and Putnam - 2019 - Marine Environmental Epigenetics.pdf:C\:\\Users\\Owner\\Zotero\\storage\\GYNCDISQ\\Eirin-Lopez and Putnam - 2019 - Marine Environmental Epigenetics.pdf:application/pdf}, } @article{gleason_multi-omics_2023, title = {Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel}, volume = {226}, issn = {0022-0949, 1477-9145}, url = {https://journals.biologists.com/jeb/article/226/22/jeb245962/335437/Multi-omics-reveals-largely-distinct-transcript}, doi = {10.1242/jeb.245962}, abstract = {ABSTRACT Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.}, language = {en}, number = {22}, urldate = {2023-12-14}, journal = {Journal of Experimental Biology}, author = {Gleason, Lani U. and Fekete, Florian J. and Tanner, Richelle L. and Dowd, W. Wesley}, month = nov, year = {2023}, pages = {jeb245962}, file = {Gleason et al. - 2023 - Multi-omics reveals largely distinct transcript- a.pdf:C\:\\Users\\Owner\\Zotero\\storage\\29HDMM2T\\Gleason et al. - 2023 - Multi-omics reveals largely distinct transcript- a.pdf:application/pdf}, } @article{huang_identification_2017, title = {Identification of long non-coding {RNAs} in two anthozoan species and their possible implications for coral bleaching}, volume = {7}, copyright = {2017 The Author(s)}, issn = {2045-2322}, url = {https://www.nature.com/articles/s41598-017-02561-y}, doi = {10.1038/s41598-017-02561-y}, abstract = {Long non-coding RNAs (lncRNAs) have been shown to play regulatory roles in a diverse range of biological processes and are associated with the outcomes of various diseases. The majority of studies about lncRNAs focus on model organisms, with lessened investigation in non-model organisms to date. Herein, we have undertaken an investigation on lncRNA in two zoanthids (cnidarian): Protolpalythoa varibilis and Palythoa caribaeorum. A total of 11,206 and 13,240 lncRNAs were detected in P. variabilis and P. caribaeorum transcriptome, respectively. Comparison using NONCODE database indicated that the majority of these lncRNAs is taxonomically species-restricted with no identifiable orthologs. Even so, we found cases in which short regions of P. caribaeorum’s lncRNAs were similar to vertebrate species’ lncRNAs, and could be associated with lncRNA conserved regulatory functions. Consequently, some high-confidence lncRNA-mRNA interactions were predicted based on such conserved regions, therefore revealing possible involvement of lncRNAs in posttranscriptional processing and regulation in anthozoans. Moreover, investigation of differentially expressed lncRNAs, in healthy colonies and colonial individuals undergoing natural bleaching, indicated that some up-regulated lncRNAs in P. caribaeorum could posttranscriptionally regulate the mRNAs encoding proteins of Ras-mediated signal transduction pathway and components of innate immune-system, which could contribute to the molecular response of coral bleaching.}, language = {en}, number = {1}, urldate = {2023-12-14}, journal = {Scientific Reports}, author = {Huang, Chen and Morlighem, Jean-Étienne R. L. and Cai, Jing and Liao, Qiwen and Perez, Carlos Daniel and Gomes, Paula Braga and Guo, Min and Rádis-Baptista, Gandhi and Lee, Simon Ming-Yuen}, month = jul, year = {2017}, note = {Number: 1 Publisher: Nature Publishing Group}, keywords = {Gene regulatory networks, Sequence annotation}, pages = {5333}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\G4HHFMFL\\Huang et al. - 2017 - Identification of long non-coding RNAs in two anth.pdf:application/pdf}, } @article{todd_power_2016, title = {The power and promise of {RNA}-seq in ecology and evolution}, volume = {25}, copyright = {© 2016 John Wiley \& Sons Ltd}, issn = {1365-294X}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13526}, doi = {10.1111/mec.13526}, abstract = {Reference is regularly made to the power of new genomic sequencing approaches. Using powerful technology, however, is not the same as having the necessary power to address a research question with statistical robustness. In the rush to adopt new and improved genomic research methods, limitations of technology and experimental design may be initially neglected. Here, we review these issues with regard to RNA sequencing (RNA-seq). RNA-seq adds large-scale transcriptomics to the toolkit of ecological and evolutionary biologists, enabling differential gene expression (DE) studies in nonmodel species without the need for prior genomic resources. High biological variance is typical of field-based gene expression studies and means that larger sample sizes are often needed to achieve the same degree of statistical power as clinical studies based on data from cell lines or inbred animal models. Sequencing costs have plummeted, yet RNA-seq studies still underutilize biological replication. Finite research budgets force a trade-off between sequencing effort and replication in RNA-seq experimental design. However, clear guidelines for negotiating this trade-off, while taking into account study-specific factors affecting power, are currently lacking. Study designs that prioritize sequencing depth over replication fail to capitalize on the power of RNA-seq technology for DE inference. Significant recent research effort has gone into developing statistical frameworks and software tools for power analysis and sample size calculation in the context of RNA-seq DE analysis. We synthesize progress in this area and derive an accessible rule-of-thumb guide for designing powerful RNA-seq experiments relevant in eco-evolutionary and clinical settings alike.}, language = {en}, number = {6}, urldate = {2023-12-14}, journal = {Molecular Ecology}, author = {Todd, Erica V. and Black, Michael A. and Gemmell, Neil J.}, year = {2016}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13526}, keywords = {biological replication, differential expression, experimental design, power analysis, RNA sequencing}, pages = {1224--1241}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\QY6CJN5N\\Todd et al. - 2016 - The power and promise of RNA-seq in ecology and ev.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\KLA8SNCX\\mec.html:text/html}, } @article{gajigan_microrna_2017, title = {A {microRNA} regulates the response of corals to thermal stress}, volume = {26}, copyright = {© 2017 John Wiley \& Sons Ltd}, issn = {1365-294X}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14130}, doi = {10.1111/mec.14130}, abstract = {Coral reefs are diverse ecosystems of great ecological and economic importance. However, corals are vulnerable to a variety of stressors, including rising seawater temperatures, and yet little is known about the genetic mechanisms underlying their survival and adaptation to stress. Like other animals, corals possess genes for key members of the microRNA (miRNA) machinery. miRNAs are short RNAs that regulate diverse cellular processes, including organismal stress response, through post-transcriptional repression of gene transcripts. Through small RNA sequencing, we identified 26 miRNAs in the coral, Acropora digitifera. Many of the identified miRNAs are novel, while eight are conserved with miRNAs previously identified in other cnidarians. One of the identified miRNAs is differentially expressed in coral tissues exposed to acute thermal stress. This thermally responsive miRNA putatively regulates multiple pathways of the organismal stress response, DNA/RNA expression regulation, repair mechanisms, tissue morphogenesis, and signalling. We propose a model by which miRNA regulation allows the coral to mount a robust stress response through sequestration of a pool of nontranslated transcripts encoding stress response proteins. Release of miRNA-mediated repression under stress conditions may result in rapid and abundant translation of proteins that help the coral maintain cellular homoeostasis. These findings highlight the potential importance of miRNAs in the thermal resilience of corals.}, language = {en}, number = {13}, urldate = {2023-12-14}, journal = {Molecular Ecology}, author = {Gajigan, Andrian P. and Conaco, Cecilia}, year = {2017}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14130}, keywords = {Acropora digitifera, Cnidaria, coral resilience, microRNA}, pages = {3472--3483}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\6ACEIF9Z\\Gajigan and Conaco - 2017 - A microRNA regulates the response of corals to the.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\MEIDKBT3\\mec.html:text/html}, } @article{moran_cnidarian_2014, title = {Cnidarian {microRNAs} frequently regulate targets by cleavage}, volume = {24}, doi = {10.1101/gr.162503.113}, abstract = {In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA "seed") to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.}, journal = {Genome research}, author = {Moran, Yehu and Fredman, David and Praher, Daniela and Li, Xin and Wee, Liang and Rentzsch, Fabian and Zamore, Phillip and Technau, Ulrich and Seitz, Hervé}, month = mar, year = {2014}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\GWQLI4VR\\Moran et al. - 2014 - Cnidarian microRNAs frequently regulate targets by.pdf:application/pdf}, } @article{zhu_symbiodiniaceae_2022, title = {Symbiodiniaceae {microRNAs} and their targeting sites in coral holobionts: {A} transcriptomics-based exploration}, volume = {114}, issn = {0888-7543}, shorttitle = {Symbiodiniaceae {microRNAs} and their targeting sites in coral holobionts}, url = {https://www.sciencedirect.com/science/article/pii/S0888754322001495}, doi = {10.1016/j.ygeno.2022.110404}, abstract = {Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-Symbiodiniaceae holobionts, and contributes valuable data for further coral research.}, number = {4}, urldate = {2023-12-14}, journal = {Genomics}, author = {Zhu, Yunchi and Liao, Xin and Han, Tingyu and Chen, J. -Y. and He, Chunpeng and Lu, Zuhong}, month = jul, year = {2022}, keywords = {microRNA, Reef-building coral, Symbiodiniaceae, Transcriptome}, pages = {110404}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\5V9WJ6SQ\\S0888754322001495.html:text/html;Zhu et al. - 2022 - Symbiodiniaceae microRNAs and their targeting site.pdf:C\:\\Users\\Owner\\Zotero\\storage\\NUQXR6D6\\Zhu et al. - 2022 - Symbiodiniaceae microRNAs and their targeting site.pdf:application/pdf}, } @article{liew_identification_2014, title = {Identification of {MicroRNAs} in the {Coral} {Stylophora} pistillata}, volume = {9}, issn = {1932-6203}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091101}, doi = {10.1371/journal.pone.0091101}, abstract = {Coral reefs are major contributors to marine biodiversity. However, they are in rapid decline due to global environmental changes such as rising sea surface temperatures, ocean acidification, and pollution. Genomic and transcriptomic analyses have broadened our understanding of coral biology, but a study of the microRNA (miRNA) repertoire of corals is missing. miRNAs constitute a class of small non-coding RNAs of ∼22 nt in size that play crucial roles in development, metabolism, and stress response in plants and animals alike. In this study, we examined the coral Stylophora pistillata for the presence of miRNAs and the corresponding core protein machinery required for their processing and function. Based on small RNA sequencing, we present evidence for 31 bona fide microRNAs, 5 of which (miR-100, miR-2022, miR-2023, miR-2030, and miR-2036) are conserved in other metazoans. Homologues of Argonaute, Piwi, Dicer, Drosha, Pasha, and HEN1 were identified in the transcriptome of S. pistillata based on strong sequence conservation with known RNAi proteins, with additional support derived from phylogenetic trees. Examination of putative miRNA gene targets indicates potential roles in development, metabolism, immunity, and biomineralisation for several of the microRNAs. Here, we present first evidence of a functional RNAi machinery and five conserved miRNAs in S. pistillata, implying that miRNAs play a role in organismal biology of scleractinian corals. Analysis of predicted miRNA target genes in S. pistillata suggests potential roles of miRNAs in symbiosis and coral calcification. Given the importance of miRNAs in regulating gene expression in other metazoans, further expression analyses of small non-coding RNAs in transcriptional studies of corals should be informative about miRNA-affected processes and pathways.}, language = {en}, number = {3}, urldate = {2023-12-14}, journal = {PLOS ONE}, author = {Liew, Yi Jin and Aranda, Manuel and Carr, Adrian and Baumgarten, Sebastian and Zoccola, Didier and Tambutté, Sylvie and Allemand, Denis and Micklem, Gos and Voolstra, Christian R.}, month = mar, year = {2014}, note = {Publisher: Public Library of Science}, keywords = {RNA sequencing, Coral reefs, Corals, Gene regulation, MicroRNAs, RNA interference, Sequence alignment, Transcriptome analysis, unread}, pages = {e91101}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\8735KY2B\\Liew et al. - 2014 - Identification of MicroRNAs in the Coral Stylophor.pdf:application/pdf}, } @article{gallardo-escarate_caligus_2017, title = {The {Caligus} rogercresseyi {miRNome}: {Discovery} and transcriptome profiling during the sea lice ontogeny}, volume = {4}, issn = {2352-2151}, shorttitle = {The {Caligus} rogercresseyi {miRNome}}, url = {https://www.sciencedirect.com/science/article/pii/S2352215117300041}, doi = {10.1016/j.aggene.2017.03.002}, abstract = {Small RNA sequencing in the copepod ectoparasite Caligus rogercresseyi was conducted to evidence putative roles of non-coding RNAs during the sea louse ontogeny. Here, differentially expressed miRNAs and mRNAs for each developmental stage were analyzed in parallel with bioinformatic gene target predictions. Based on sequence analysis, C. rogercresseyi miRNome comprises 673 conserved miRNAs, including precursors, 5′ and 3′ isomiRs. The conserved miRNAs include 40 families found in twelve different arthropods species. The results also showed that C. rogercresseyi miRNome exhibit stage-specific expression patterns, with miRNA-996-4 and miRNA-124 displaying sex-biased expression. Target prediction of these miRNAs identifies possible silencing mechanism of sex-related genes. Furthermore, bantam isomiRs were highly transcribed during the infective stage of copepodid and target prediction using differentially expressed genes in Atlantic salmon infested with sea lice, suggests a putative role of these miRNAs in the host-pathogen interaction. This is the first study reporting a miRNA repertoire in a marine copepod ectoparasite that affects the salmon aquaculture worldwide.}, urldate = {2023-12-14}, journal = {Agri Gene}, author = {Gallardo-Escárate, C. and Valenzuela-Muñoz, V. and Boltaña, S. and Nuñez-Acuña, G. and Valenzuela-Miranda, D. and Gonçalves, A. T. and Détrée, C. and Tarifeño-Saldivia, E. and Farlora, R. and Roberts, S. and Putnam, H. M.}, month = jun, year = {2017}, keywords = {gene target prediction, miRNAs, small RNA sequencing, unread}, pages = {8--22}, file = {Gallardo-Escárate et al. - 2017 - The Caligus rogercresseyi miRNome Discovery and t.pdf:C\:\\Users\\Owner\\Zotero\\storage\\MFVXYTLJ\\Gallardo-Escárate et al. - 2017 - The Caligus rogercresseyi miRNome Discovery and t.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\PT8ZCFSH\\S2352215117300041.html:text/html}, } @article{huttenhofer_non-coding_2005, title = {Non-coding {RNAs}: hope or hype?}, volume = {21}, issn = {0168-9525}, shorttitle = {Non-coding {RNAs}}, url = {https://www.sciencedirect.com/science/article/pii/S0168952505000831}, doi = {10.1016/j.tig.2005.03.007}, abstract = {The past four years have seen an explosion in the number of detected RNA transcripts with no apparent protein-coding potential. This has led to speculation that non-protein-coding RNAs (ncRNAs) might be as important as proteins in the regulation of vital cellular functions. However, there has been significantly less progress in actually demonstrating the functions of these transcripts. In this article, we review the results of recent experiments that show that transcription of non-protein-coding RNA is far more widespread than was previously anticipated. Although some ncRNAs act as molecular switches that regulate gene expression, the function of many ncRNAs is unknown. New experimental and computational approaches are emerging that will help determine whether these newly identified transcription products are evidence of important new biochemical pathways or are merely ‘junk’ RNA generated by the cell as a by-product of its functional activities.}, number = {5}, urldate = {2023-12-14}, journal = {Trends in Genetics}, author = {Hüttenhofer, Alexander and Schattner, Peter and Polacek, Norbert}, month = may, year = {2005}, keywords = {ncRNA, review, read}, pages = {289--297}, file = {Hüttenhofer et al. - 2005 - Non-coding RNAs hope or hype.pdf:C\:\\Users\\Owner\\Zotero\\storage\\IRUMZK9B\\Hüttenhofer et al. - 2005 - Non-coding RNAs hope or hype.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\B8NLDCNI\\S0168952505000831.html:text/html}, } @article{pham_epigenetic_2023, title = {Epigenetic analytical approaches in ecotoxicological aquatic research}, volume = {330}, issn = {0269-7491}, url = {https://www.sciencedirect.com/science/article/pii/S026974912300739X}, doi = {10.1016/j.envpol.2023.121737}, abstract = {Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016–2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15\%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.}, urldate = {2023-12-15}, journal = {Environmental Pollution}, author = {Pham, Kim and Ho, Long and D'Incal, Claudio Peter and De Cock, Andrée and Berghe, Wim Vanden and Goethals, Peter}, month = aug, year = {2023}, keywords = {Aquatic animal, DNA methylation, environmental Epigenetics, Environmental stress, Histone modification, Pollution, unread}, pages = {121737}, file = {Pham et al. - 2023 - Epigenetic analytical approaches in ecotoxicologic.pdf:C\:\\Users\\Owner\\Zotero\\storage\\5658SFQ8\\Pham et al. - 2023 - Epigenetic analytical approaches in ecotoxicologic.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\FGZG2PMF\\S026974912300739X.html:text/html}, } @misc{putnam_dynamic_2022, title = {Dynamic {DNA} methylation contributes to carryover effects and beneficial acclimatization in geoduck clams}, copyright = {© 2022, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, url = {https://www.biorxiv.org/content/10.1101/2022.06.24.497506v2}, doi = {10.1101/2022.06.24.497506}, abstract = {Given the rapidly changing global climate, there is a growing need to understand the acclimatory basis of animal response to environmental change. To investigate the role of DNA methylation in environmental acclimatization, we generated a reference genome and surveyed the physiology and DNA methylomes of juvenile geoduck clams, Panopea generosa, under differing seawater pH regimes. Juveniles were initially exposed to one of three seawater pH conditions, followed by ambient common-garden conditions, then a second reciprocal exposure to ambient pH or pH 7.4. Within 10 days of the initial low pH exposure, juvenile clams showed decreased shell size relative to ambient pH with corresponding differential DNA methylation. Following four months of ambient common-garden conditions, juveniles initially exposed to low pH compensatorily grew larger, with DNA methylation indicative of these phenotypic differences, demonstrating epigenetic carryover effects persisted months after initial exposure. Functional enrichment analysis of differentially methylated genes revealed regulation of signal transduction through widespread changes in the Wnt signaling pathways that influence cell growth, proliferation, tissue and skeletal formation, and cytoskeletal change. After 10 days of secondary exposure to pH 7.4, naive juvenile clams were more sensitive to low pH compared to those initially exposed, showing reduced growth and having nearly a 2-fold greater change in DNA methylation. Collectively, this new genomic resource and coordinated phenotypic and methylomic response support that epigenetic mechanisms underlie acclimatization to provide beneficial phenotypes.}, language = {en}, urldate = {2023-12-15}, publisher = {bioRxiv}, author = {Putnam, Hollie M. and Trigg, Shelly A. and White, Samuel J. and Spencer, Laura H. and Vadopalas, Brent and Natarajan, Aparna and Hetzel, Jonathan and Jaeger, Erich and Soohoo, Jonathan and Gallardo-Escárate, Cristian and Goetz, Frederick W. and Roberts, Steven B.}, month = aug, year = {2022}, note = {Pages: 2022.06.24.497506 Section: New Results}, keywords = {unread}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YDGIGJJ3\\Putnam et al. - 2022 - Dynamic DNA methylation contributes to carryover e.pdf:application/pdf}, } @article{buckley_characterizing_2023, title = {Characterizing biological responses to climate variability and extremes to improve biodiversity projections}, volume = {2}, issn = {2767-3200}, url = {https://journals.plos.org/climate/article?id=10.1371/journal.pclm.0000226}, doi = {10.1371/journal.pclm.0000226}, abstract = {Projecting ecological and evolutionary responses to variable and changing environments is central to anticipating and managing impacts to biodiversity and ecosystems. Current modeling approaches are largely phenomenological and often fail to accurately project responses due to numerous biological processes at multiple levels of biological organization responding to environmental variation at varied spatial and temporal scales. Limited mechanistic understanding of organismal responses to environmental variability and extremes also restricts predictive capacity. We outline a strategy for identifying and modeling the key organismal mechanisms across levels of biological organization that mediate ecological and evolutionary responses to environmental variation. A central component of this strategy is quantifying timescales and magnitudes of climatic variability and how organisms experience them. We highlight recent empirical research that builds this information and suggest how to design future experiments that can produce more generalizable principles. We discuss how to create biologically informed projections in a feasible way by combining statistical and mechanistic approaches. Predictions will inform both fundamental and practical questions at the interface of ecology, evolution, and Earth science such as how organisms experience, adapt to, and respond to environmental variation at multiple hierarchical spatial and temporal scales.}, language = {en}, number = {6}, urldate = {2023-12-15}, journal = {PLOS Climate}, author = {Buckley, Lauren B. and Carrington, Emily and Dillon, Michael E. and García-Robledo, Carlos and Roberts, Steven B. and Wegrzyn, Jill L. and Urban, Mark C.}, month = jun, year = {2023}, note = {Publisher: Public Library of Science}, keywords = {Biodiversity, Body temperature, Climate change, Ecological niches, Evolutionary genetics, Genetic polymorphism, Mussels, Organismal evolution, unread}, pages = {e0000226}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\PQAJ2TEZ\\Buckley et al. - 2023 - Characterizing biological responses to climate var.pdf:application/pdf}, } @misc{spencer_population-specific_2023, title = {Population-specific effects of ocean acidification in the {Olympia} oyster}, copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/}, url = {https://www.biorxiv.org/content/10.1101/2023.09.08.556443v1}, doi = {10.1101/2023.09.08.556443}, abstract = {Populations of marine species that respond differently to ocean acidification offer natural reservoirs of biodiversity that can be leveraged for conservation efforts and to sustain marine food systems. The molecular and physiological traits associated with tolerance to acidification must first be identified. This study leveraged oysters from three phenotypically distinct populations of the Olympia oyster, Ostrea lurida, but that were bred and reared in common conditions for four years. We assessed their growth, reproductive development, and transcriptional response to acidification within and across generations. Responses reveal energetic trade-offs that reflect unique physiotypes previously observed among populations. The population with the slowest growth but high survival rates, oysters from Dabob Bay, mounted the largest transcriptional response to acidification without effects to growth and reproduction. A moderate response was observed in the population with fastest growth rate but lowest fecundity (Fidalgo Bay). Oyster Bay, the population with highest fecundity but lowest survival rates, did not respond at the transcript level. Oyster Bay was also the only population for which acidification negatively affected growth and reproductive development. While exposure to acidification did not affect gene expression in the next generation’s larval stage, it did result in larger larvae in the Oyster Bay population, which could partially alleviate negative effects of acidification in the wild for that population. Given the distinct transcriptional response of the Dabob Bay population to acidification and its high survival rates in previous studies, we then identified genes that were uniquely expressed in Dabob Bay oysters compared to the other populations. Genes involved in antibacterial and antiviral processes, metabolism, growth, and reproduction were uniquely expressed in Dabob Bay, and many similar functions were identified in both adults and larvae, which provides insight into the mechanisms behind a stress-tolerant oyster population. The population-specific physiotypes and responses to acidification illustrate the diversity of physiological strategies in O. lurida that balance the energetic demands of growth, reproduction, cellular maintenance, and offspring viability. Taken together this study reveals that there are distinct physiotypes among marine invertebrate populations on small geographic scales with implications for species resilience to acidification and other environmental stressors.}, language = {en}, urldate = {2023-12-15}, publisher = {bioRxiv}, author = {Spencer, Laura H. and Silliman, Katherine and Roberts, Steven}, month = sep, year = {2023}, note = {Pages: 2023.09.08.556443 Section: New Results}, keywords = {unread}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\LBBENQSV\\Spencer et al. - 2023 - Population-specific effects of ocean acidification.pdf:application/pdf}, } @article{gurr_repeat_2021, title = {Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam}, volume = {224}, issn = {0022-0949}, url = {https://doi.org/10.1242/jeb.233932}, doi = {10.1242/jeb.233932}, abstract = {Although low levels of thermal stress, irradiance and dietary restriction can have beneficial effects for many taxa, stress acclimation remains little studied in marine invertebrates, even though they are threatened by climate change stressors such as ocean acidification. To test the role of life-stage and stress-intensity dependence in eliciting enhanced tolerance under subsequent stress encounters, we initially conditioned pediveliger Pacific geoduck (Panopea generosa) larvae to ambient and moderately elevated PCO2 (920 µatm and 2800 µatm, respectively) for 110 days. Then, clams were exposed to ambient, moderate or severely elevated PCO2 (750, 2800 or 4900 µatm, respectively) for 7 days and, following 7 days in ambient conditions, a 7-day third exposure to ambient (970 µatm) or moderate PCO2 (3000 µatm). Initial conditioning to moderate PCO2 stress followed by second and third exposure to severe and moderate PCO2 stress increased respiration rate, organic biomass and shell size, suggesting a stress-intensity-dependent effect on energetics. Additionally, stress-acclimated clams had lower antioxidant capacity compared with clams under ambient conditions, supporting the hypothesis that stress over postlarval-to-juvenile development affects oxidative status later in life. Time series and stress intensity-specific approaches can reveal life-stages and magnitudes of exposure, respectively, that may elicit beneficial phenotypic variation.}, number = {13}, urldate = {2023-12-15}, journal = {Journal of Experimental Biology}, author = {Gurr, Samuel J. and Wanamaker, Shelly A. and Vadopalas, Brent and Roberts, Steven B. and Putnam, Hollie M.}, month = jul, year = {2021}, keywords = {Bivalve, unread}, pages = {jeb233932}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\HALDPF5A\\Gurr et al. - 2021 - Repeat exposure to hypercapnic seawater modifies g.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\V9BTEI8S\\Repeat-exposure-to-hypercapnic-seawater-modifies.html:text/html}, } @article{venkataraman_differential_2022, title = {Differential {DNA} methylation in {Pacific} oyster reproductive tissue in response to ocean acidification}, volume = {23}, issn = {1471-2164}, url = {https://doi.org/10.1186/s12864-022-08781-5}, doi = {10.1186/s12864-022-08781-5}, abstract = {There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- {\textgreater} T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization.}, number = {1}, urldate = {2023-12-15}, journal = {BMC Genomics}, author = {Venkataraman, Yaamini R. and White, Samuel J. and Roberts, Steven B.}, month = aug, year = {2022}, keywords = {DNA methylation, Bivalve, Gonad development, Ocean acidification, Pacific oyster, unread, Crassostrea gigas}, pages = {556}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\332TKNEZ\\Venkataraman et al. - 2022 - Differential DNA methylation in Pacific oyster rep.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\SW3ZECZ2\\s12864-022-08781-5.html:text/html}, } @article{dang_epigenetic-associated_2023, title = {Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment}, volume = {32}, copyright = {© 2022 John Wiley \& Sons Ltd.}, issn = {1365-294X}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16751}, doi = {10.1111/mec.16751}, abstract = {For marine invertebrates with a pelagic–benthic life cycle, larval exposure to ocean acidification (OA) can affect adult performance in response to another environmental stressor. This carry-over effect has the potential to alter phenotypic traits. However, the molecular mechanisms that mediate “OA”-triggered carry-over effects have not been explored despite such information being key to improving species fitness and management strategies for aquafarming. This study integrated the genome-wide DNA methylome and transcriptome to examine epigenetic modification-mediated carry-over OA impacts on phenotypic traits of the ecologically and commercially important oyster species Crassostrea hongkongensis under field conditions. Larvae of C. hongkongensis were exposed to control pH 8.0 and low pH 7.4 conditions, mimicking near future OA scenario in their habitat, before being outplanted as post-metamorphic juveniles at two mariculture field sites with contrasting environmental stressors for 9 months. The larval carry-over OA effect was found to have persistent impacts on the growth and survival trade-off traits on the outplanted juveniles, although the beneficial or adverse effect depended on the environmental conditions at the outplanted sites. Site-specific plasticity was demonstrated with a diverse DNA methylation-associated gene expression profile, with signal transduction and the endocrine system being the most common and highly enriched functions. Highly methylated exons prevailed in the key genes related to general metabolic and endocytic responses and these genes are evolutionarily conserved in various marine invertebrates in response to OA. These results suggest that oysters with prior larval exposure history to OA had the ability to trigger rapid local adaptive responses via epigenetic modification to cope with multiple stressors in the field.}, language = {en}, number = {2}, urldate = {2023-12-15}, journal = {Molecular Ecology}, author = {Dang, Xin and Lim, Yong-Kian and Li, Yang and Roberts, Steven B. and Li, Li and Thiyagarajan, Vengatesen}, year = {2023}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16751}, keywords = {DNA methylation, carry-over capacity, methylRAD, ocean acidification, oysters, phenotypic plasticity, tradeoff traits, transcriptome, unread}, pages = {412--427}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YTYW97KB\\Dang et al. - 2023 - Epigenetic-associated phenotypic plasticity of the.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\IN9ICRF5\\mec.html:text/html}, } @article{gaiti_origin_2017, title = {Origin and evolution of the metazoan non-coding regulatory genome}, volume = {427}, issn = {00121606}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0012160616305735}, doi = {10.1016/j.ydbio.2016.11.013}, abstract = {Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa. High-throughput next-generation sequencing, largely in bilaterian model species, has led to the discovery of tens of thousands of non-coding RNA genes (ncRNAs), including short, long and circular forms, and uncovered the central roles they play in development. Based on the analysis of non-bilaterian metazoan, unicellular holozoan and fungal genomes, the evolution of some ncRNAs, such as Piwi-interacting RNAs, correlates with the emergence of metazoan multicellularity, while others, including microRNAs, long non-coding RNAs and circular RNAs, appear to be more ancient. Analysis of non-coding regulatory DNA and histone post-translational modifications have revealed that some cis-regulatory mechanisms, such as those associated with proximal promoters, are present in non-animal holozoans, while others appear to be metazoan innovations, most notably distal enhancers. In contrast, the cohesin-CTCF system for regulating higher-order chromatin structure and enhancerpromoter long-range interactions appears to be restricted to bilaterians. Taken together, most bilaterian noncoding regulatory mechanisms appear to have originated before the divergence of crown metazoans. However, differential expansion of non-coding RNA and cis-regulatory DNA repertoires in bilaterians may account for their increased regulatory and morphological complexity relative to non-bilaterians.}, language = {en}, number = {2}, urldate = {2023-12-15}, journal = {Developmental Biology}, author = {Gaiti, Federico and Calcino, Andrew D. and Tanurdžić, Miloš and Degnan, Bernard M.}, month = jul, year = {2017}, keywords = {unread}, pages = {193--202}, file = {Gaiti et al. - 2017 - Origin and evolution of the metazoan non-coding re.pdf:C\:\\Users\\Owner\\Zotero\\storage\\6XCS6WP2\\Gaiti et al. - 2017 - Origin and evolution of the metazoan non-coding re.pdf:application/pdf}, } @misc{admoni_target_2023, title = {Target complementarity in cnidarians supports a common origin for animal and plant {microRNAs}}, copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, url = {https://www.biorxiv.org/content/10.1101/2023.01.08.523153v2}, doi = {10.1101/2023.01.08.523153}, abstract = {microRNAs (miRNAs) are important post-transcriptional regulators that activate silencing mechanisms by annealing to mRNA transcripts. While plant miRNAs match their targets with nearly-full complementarity leading to mRNA cleavage, miRNAs in most animals require only a short sequence called ‘seed’ to inhibit target translation. Recent findings showed that miRNAs in cnidarians, early-branching metazoans, act similarly to plant miRNAs, by exhibiting full complementarity and target cleavage; however, it remained unknown if seed- based regulation was possible in cnidarians. Here, we investigate the miRNA-target complementarity requirements for miRNA activity in the cnidarian Nematostella vectensis. We show that bilaterian-like complementarity of seed-only or seed and supplementary 3’ matches are insufficient for miRNA-mediated knockdown. Furthermore, miRNA-target mismatches in the cleavage site decrease knockdown efficiency. Finally, miRNA silencing of a target with three seed binding sites in the 3’ untranslated region that mimics typical miRNA targeting was repressed in zebrafish but not in Nematostella and Hydractinia symbiolongicarpus. Altogether, these results unravel striking similarities between plant and cnidarian miRNAs consolidating the evidence for common evolutionary origin of miRNAs in plants and animals.}, language = {en}, urldate = {2023-12-15}, publisher = {bioRxiv}, author = {Admoni, Yael and Fridrich, Arie and Razin, Talya and Salinas-Saavedra, Miguel and Rabani, Michal and Frank, Uri and Moran, Yehu}, month = oct, year = {2023}, note = {Pages: 2023.01.08.523153 Section: New Results}, keywords = {unread}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\KPFCPXGE\\Admoni et al. - 2023 - Target complementarity in cnidarians supports a co.pdf:application/pdf}, } @article{kang_mirtrace_2018, title = {{miRTrace} reveals the organismal origins of {microRNA} sequencing data}, volume = {19}, issn = {1474-760X}, url = {https://doi.org/10.1186/s13059-018-1588-9}, doi = {10.1186/s13059-018-1588-9}, abstract = {We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately ({\textgreater} 99\%) assigns real and simulated data to 14 important animal and plant groups, sensitively detects parasitic infection in mammals, and discovers the primate origin of single cells. Applying our algorithm to over 700 public datasets, we find evidence that over 7\% are cross-contaminated and present a novel solution to clean these computationally, even after sequencing has occurred. miRTrace is freely available at https://github.com/friedlanderlab/mirtrace.}, number = {1}, urldate = {2023-12-15}, journal = {Genome Biology}, author = {Kang, Wenjing and Eldfjell, Yrin and Fromm, Bastian and Estivill, Xavier and Biryukova, Inna and Friedländer, Marc R.}, month = dec, year = {2018}, keywords = {unread, Cross-species Contamination, miRNA Sequencing Data, miRTrace, Original Taxonomy, Plant Clades}, pages = {213}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\HIREVKH3\\Kang et al. - 2018 - miRTrace reveals the organismal origins of microRN.pdf:application/pdf}, } @article{asgari_epigenetic_2014, title = {Epigenetic modifications underlying symbiont-host interactions}, volume = {86}, issn = {0065-2660}, doi = {10.1016/B978-0-12-800222-3.00010-3}, abstract = {The development, existence, and functioning of numerous animals and plants depend on their symbiotic interactions with other organisms, mainly microorganisms. In return, the symbionts benefit from safe habitats and nutrient-rich environments provided by their hosts. In these interactions, genetic changes in either of the partners may provide fitness advantages and become subjects to natural selection. Recent findings suggest that epigenetic changes, heritable or within the organism's life time, in either of the partners play significant roles in the establishment of symbiotic relationships. In this review, a variety of epigenetic effects underlying the most common host-symbiont interactions will be examined to determine to what extent these effects are shared in various interactions and how the epigenetic pathways could possibly be manipulated to benefit the interacting symbionts.}, language = {eng}, journal = {Advances in Genetics}, author = {Asgari, Sassan}, year = {2014}, pmid = {25172352}, keywords = {microRNA, Gene regulation, unread, Animals, Epigenesis, Genetic, Epigenetics, Humans, Methylation, Microbiota, Plants, Selection, Genetic, Symbiont, Symbiosis}, pages = {253--276}, } @article{leitao_interspecies_2020, title = {Interspecies {Communication} in {Holobionts} by {Non}-{Coding} {RNA} {Exchange}}, volume = {21}, issn = {1422-0067}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7177868/}, doi = {10.3390/ijms21072333}, abstract = {Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.}, number = {7}, urldate = {2023-12-15}, journal = {International Journal of Molecular Sciences}, author = {Leitão, Ana Lúcia and Costa, Marina C. and Gabriel, André F. and Enguita, Francisco J.}, month = mar, year = {2020}, pmid = {32230931}, pmcid = {PMC7177868}, keywords = {unread}, pages = {2333}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YMUWJIBL\\Leitão et al. - 2020 - Interspecies Communication in Holobionts by Non-Co.pdf:application/pdf}, } @article{stocks_uea_2018, title = {The {UEA} {sRNA} {Workbench} (version 4.4): a comprehensive suite of tools for analyzing {miRNAs} and {sRNAs}}, volume = {34}, issn = {1367-4803}, shorttitle = {The {UEA} {sRNA} {Workbench} (version 4.4)}, url = {https://doi.org/10.1093/bioinformatics/bty338}, doi = {10.1093/bioinformatics/bty338}, abstract = {RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential.We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses.The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk. The source code is available at: https://github.com/sRNAworkbenchuea/UEA\_sRNA\_WorkbenchSupplementary data are available at Bioinformatics online.}, number = {19}, urldate = {2023-12-18}, journal = {Bioinformatics}, author = {Stocks, Matthew B and Mohorianu, Irina and Beckers, Matthew and Paicu, Claudia and Moxon, Simon and Thody, Joshua and Dalmay, Tamas and Moulton, Vincent}, month = oct, year = {2018}, pages = {3382--3384}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\5U2HX24I\\Stocks et al. - 2018 - The UEA sRNA Workbench (version 4.4) a comprehens.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\EDKDRZWQ\\4990822.html:text/html}, } @article{stocks_uea_2012, title = {The {UEA} {sRNA} workbench: a suite of tools for analysing and visualizing next generation sequencing {microRNA} and small {RNA} datasets}, volume = {28}, issn = {1367-4803}, shorttitle = {The {UEA} {sRNA} workbench}, url = {https://doi.org/10.1093/bioinformatics/bts311}, doi = {10.1093/bioinformatics/bts311}, abstract = {Summary: RNA silencing is a complex, highly conserved mechanism mediated by small RNAs (sRNAs), such as microRNAs (miRNAs), that is known to be involved in a diverse set of biological functions including development, pathogen control, genome maintenance and response to environmental change. Advances in next generation sequencing technologies are producing increasingly large numbers of sRNA reads per sample at a fraction of the cost of previous methods. However, many bioinformatics tools do not scale accordingly, are cumbersome, or require extensive support from bioinformatics experts. Therefore, researchers need user-friendly, robust tools, capable of not only processing large sRNA datasets in a reasonable time frame but also presenting the results in an intuitive fashion and visualizing sRNA genomic features. Herein, we present the UEA sRNA workbench, a suite of tools that is a successor to the web-based UEA sRNA Toolkit, but in downloadable format and with several enhanced and additional features.Availability: The program and help pages are available at http://srna-workbench.cmp.uea.ac.uk.Contact:  vincent.moulton@cmp.uea.ac.uk}, number = {15}, urldate = {2023-12-18}, journal = {Bioinformatics}, author = {Stocks, Matthew B. and Moxon, Simon and Mapleson, Daniel and Woolfenden, Hugh C. and Mohorianu, Irina and Folkes, Leighton and Schwach, Frank and Dalmay, Tamas and Moulton, Vincent}, month = aug, year = {2012}, pages = {2059--2061}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\75G927FL\\Stocks et al. - 2012 - The UEA sRNA workbench a suite of tools for analy.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\N6CTYF2V\\236705.html:text/html}, } @article{studholme_deep_2012, title = {Deep sequencing of small {RNAs} in plants: applied bioinformatics}, volume = {11}, issn = {2041-2649}, shorttitle = {Deep sequencing of small {RNAs} in plants}, url = {https://doi.org/10.1093/bfgp/elr039}, doi = {10.1093/bfgp/elr039}, abstract = {Small RNAs, including microRNA and short-interfering RNAs, play important roles in plants. In recent years, developments in sequencing technology have enabled the large-scale discovery of sRNAs in various cells, tissues and developmental stages and in response to various stresses. This review describes the bioinformatics challenges to analysing these large datasets of short-RNA sequences and some of the solutions to those challenges.}, number = {1}, urldate = {2023-12-18}, journal = {Briefings in Functional Genomics}, author = {Studholme, David J.}, month = jan, year = {2012}, keywords = {read}, pages = {71--85}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\E5XZD92N\\Studholme - 2012 - Deep sequencing of small RNAs in plants applied b.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\ZUZB4PEC\\191646.html:text/html}, } @article{di_bella_benchmarking_2020, title = {A benchmarking of pipelines for detecting {ncRNAs} from {RNA}-{Seq} data}, volume = {21}, issn = {1477-4054}, url = {https://doi.org/10.1093/bib/bbz110}, doi = {10.1093/bib/bbz110}, abstract = {Next-Generation Sequencing (NGS) is a high-throughput technology widely applied to genome sequencing and transcriptome profiling. RNA-Seq uses NGS to reveal RNA identities and quantities in a given sample. However, it produces a huge amount of raw data that need to be preprocessed with fast and effective computational methods. RNA-Seq can look at different populations of RNAs, including ncRNAs. Indeed, in the last few years, several ncRNAs pipelines have been developed for ncRNAs analysis from RNA-Seq experiments. In this paper, we analyze eight recent pipelines (iSmaRT, iSRAP, miARma-Seq, Oasis 2, SPORTS1.0, sRNAnalyzer, sRNApipe, sRNA workbench) which allows the analysis not only of single specific classes of ncRNAs but also of more than one ncRNA classes. Our systematic performance evaluation aims at guiding users to select the appropriate pipeline for processing each ncRNA class, focusing on three key points: (i) accuracy in ncRNAs identification, (ii) accuracy in read count estimation and (iii) deployment and ease of use.}, number = {6}, urldate = {2023-12-20}, journal = {Briefings in Bioinformatics}, author = {Di Bella, Sebastiano and La Ferlita, Alessandro and Carapezza, Giovanni and Alaimo, Salvatore and Isacchi, Antonella and Ferro, Alfredo and Pulvirenti, Alfredo and Bosotti, Roberta}, month = dec, year = {2020}, keywords = {unread}, pages = {1987--1998}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\8ZMZAQCE\\Di Bella et al. - 2020 - A benchmarking of pipelines for detecting ncRNAs f.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\Z5A4IW2H\\5618829.html:text/html}, } @article{bortolomeazzi_survey_2019, title = {A survey of software tools for {microRNA} discovery and characterization using {RNA}-seq}, volume = {20}, issn = {1467-5463}, url = {https://dx.doi.org/10.1093/bib/bbx148}, doi = {10.1093/bib/bbx148}, abstract = {Abstract. Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed the discovery of thousands new microRNAs (miRNAs) in humans and many}, language = {en}, number = {3}, urldate = {2023-12-20}, journal = {Briefings in Bioinformatics}, author = {Bortolomeazzi, Michele and Gaffo, Enrico and Bortoluzzi, Stefania}, month = may, year = {2019}, note = {Publisher: Oxford Academic}, keywords = {unread}, pages = {918--930}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\MXBYM9J7\\Bortolomeazzi et al. - 2019 - A survey of software tools for microRNA discovery .pdf:application/pdf}, } @article{veneziano_noncoding_2016, title = {Noncoding {RNA}: {Current} {Deep} {Sequencing} {Data} {Analysis} {Approaches} and {Challenges}}, volume = {37}, copyright = {© 2016 WILEY PERIODICALS, INC.}, issn = {1098-1004}, shorttitle = {Noncoding {RNA}}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23066}, doi = {10.1002/humu.23066}, abstract = {One of the most significant biological discoveries of the last decade is represented by the reality that the vast majority of the transcribed genomic output comprises diverse classes of noncoding RNAs (ncRNAs) that may play key roles and/or be affected by many biochemical cellular processes (i.e., RNA editing), with implications in human health and disease. With 90\% of the human genome being transcribed and novel classes of ncRNA emerging (tRNA-derived small RNAs and circular RNAs among others), the great majority of the human transcriptome suggests that many important ncRNA functions/processes are yet to be discovered. An approach to filling such vast void of knowledge has been recently provided by the increasing application of next-generation sequencing (NGS), offering the unprecedented opportunity to obtain a more accurate profiling with higher resolution, increased throughput, sequencing depth, and low experimental complexity, concurrently posing an increasing challenge in terms of efficiency, accuracy, and usability of data analysis software. This review provides an overview of ncRNAs, NGS technology, and the most recent/popular computational approaches and the challenges they attempt to solve, which are essential to a more sensitive and comprehensive ncRNA annotation capable of furthering our understanding of this still vastly uncharted genomic territory.}, number = {12}, urldate = {2023-12-20}, journal = {Human Mutation}, author = {Veneziano, Dario and Di Bella, Sebastiano and Nigita, Giovanni and Laganà, Alessandro and Ferro, Afredo and Croce, Carlo M.}, year = {2016}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/humu.23066}, keywords = {unread, circRNA, computational approaches, lncRNA, ncRNA, NGS, RNA editing, small ncRNA, tRF}, pages = {1283--1298}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\NTNVQEWB\\Veneziano et al. - 2016 - Noncoding RNA Current Deep Sequencing Data Analys.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\A24T6D8D\\humu.html:text/html}, } @article{vivek_computational_2021, title = {Computational methods for annotation of plant regulatory non-coding {RNAs} using {RNA}-seq}, volume = {22}, issn = {1477-4054}, url = {https://doi.org/10.1093/bib/bbaa322}, doi = {10.1093/bib/bbaa322}, abstract = {Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.}, number = {4}, urldate = {2023-12-20}, journal = {Briefings in Bioinformatics}, author = {Vivek, A T and Kumar, Shailesh}, month = jul, year = {2021}, keywords = {unread}, pages = {bbaa322}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\NEE3T5LH\\Vivek and Kumar - 2021 - Computational methods for annotation of plant regu.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\5SWTMF7B\\6041165.html:text/html}, } @article{connelly_antibiotics_2023, title = {Antibiotics reduce \textit{{Pocillopora}} coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression}, issn = {0962-1083, 1365-294X}, url = {https://www.webofscience.com/api/gateway?GWVersion=2&SrcAuth=DynamicDOIArticle&SrcApp=WOS&KeyAID=10.1111%2Fmec.17049&DestApp=DOI&SrcAppSID=USW2EC0EBA7sleLTN6a2Nu47ML62u&SrcJTitle=MOLECULAR+ECOLOGY&DestDOIRegistrantName=Wiley+%28Blackwell+Publishing%29}, doi = {10.1111/mec.17049}, abstract = {Corals are important models for understanding invertebrate host-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral-bacteria associations are needed. Coral-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-building corals Pocillopora meandrina and P. verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-associated bacteria.}, language = {English}, urldate = {2024-01-08}, journal = {MOLECULAR ECOLOGY}, author = {Connelly, Michael T. and Snyder, Grace and Palacio-Castro, Ana M. and Gillette, Phillip R. and Baker, Andrew C. and Traylor-Knowles, Nikki}, month = jun, year = {2023}, note = {Num Pages: 18 Place: Hoboken Publisher: Wiley Web of Science ID: WOS:001010563900001}, keywords = {transcriptome, coral, unread, antibiotics, bacteria, CONTRIBUTE, DAMICORNIS, holobiont, HOST, microbiome, MICROBIOME, MULTIPLE SEQUENCE ALIGNMENT, R PACKAGE, REEF}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\KNASLXKU\\Connelly et al. - 2023 - Antibiotics reduce Pocillopora coral-associ.pdf:application/pdf}, } @article{roff_evolutionary_2021, title = {Evolutionary {History} {Drives} {Biogeographic} {Patterns} of {Coral} {Reef} {Resilience}}, volume = {71}, issn = {0006-3568}, url = {https://doi.org/10.1093/biosci/biaa145}, doi = {10.1093/biosci/biaa145}, abstract = {Modern-day Indo-Pacific coral reefs are characterized by rapid recovery driven by pulses of coral recruitment, but Caribbean reefs exhibit low rates of recruitment and poor recovery following a wide range of disturbance events. The contrasting evolutionary history of coral taxa offers key insight into biogeographic patterns of coral resilience. Following the closure of the Isthmus of Panama approximately 2.8 million years ago, widespread extinction of Caribbean corals led to an evolutionary bottleneck that favored large and long-lived species with a relatively high reliance on asexual versus sexual reproduction. In contrast, adaptive radiation led to the evolution of superrecruiting tabular, digitate, and corymbose corals that drive the rapid recovery of modern-day Indo-Pacific reefs following disturbance. The dominance of branching growth forms and evolutionary absence of superrecruiting growth forms throughout the entire evolutionary history of the Caribbean (approximately 38 million years ago to present) may explain the exceptionally high recruitment rates on modern-day Indo-Pacific reefs and low historical recruitment on Caribbean reefs. The evolutionary history of the Caribbean coral reef-building taxa implies that, even with a reversal of ecosystem state, widespread recovery of Caribbean reefs may be limited.}, number = {1}, urldate = {2024-01-08}, journal = {BioScience}, author = {Roff, George}, month = jan, year = {2021}, keywords = {coral, read}, pages = {26--39}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\JWVBJLIU\\Roff - 2021 - Evolutionary History Drives Biogeographic Patterns.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\M566FKG2\\6030118.html:text/html}, } @article{humanes_effects_2017, title = {Effects of suspended sediments and nutrient enrichment on juvenile corals}, volume = {125}, issn = {0025-326X}, url = {https://www.sciencedirect.com/science/article/pii/S0025326X17306732}, doi = {10.1016/j.marpolbul.2017.08.003}, abstract = {Three to six-month-old juveniles of Acropora tenuis, A. millepora and Pocillopora acuta were experimentally co-exposed to nutrient enrichment and suspended sediments (without light attenuation or sediment deposition) for 40days. Suspended sediments reduced survivorship of A. millepora strongly, proportional to the sediment concentration, but not in A. tenuis or P. acuta juveniles. However, juvenile growth of the latter two species was reduced to less than half or to zero, respectively. Additionally, suspended sediments increased effective quantum yields of symbionts associated with A. millepora and A. tenuis, but not those associated with P. acuta. Nutrient enrichment did not significantly affect juvenile survivorship, growth or photophysiology for any of the three species, either as a sole stressor or in combination with suspended sediments. Our results indicate that exposure to suspended sediments can be energetically costly for juveniles of some coral species, implying detrimental longer-term but species-specific repercussions for populations and coral cover.}, number = {1}, urldate = {2024-01-09}, journal = {Marine Pollution Bulletin}, author = {Humanes, Adriana and Fink, Artur and Willis, Bette L. and Fabricius, Katharina E. and de Beer, Dirk and Negri, Andrew P.}, month = dec, year = {2017}, keywords = {unread, Coral, Juvenile, Nutrient, Physiology, Recruitment, Sediment}, pages = {166--175}, file = {Humanes et al. - 2017 - Effects of suspended sediments and nutrient enrich.pdf:C\:\\Users\\Owner\\Zotero\\storage\\9BYTKN6D\\Humanes et al. - 2017 - Effects of suspended sediments and nutrient enrich.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\WM3G55D3\\S0025326X17306732.html:text/html}, } @article{tamiru_regulation_2018, title = {Regulation of genome-wide {DNA} methylation by mobile small {RNAs}}, volume = {217}, copyright = {© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust}, issn = {1469-8137}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.14874}, doi = {10.1111/nph.14874}, abstract = {Contents Summary 540 I. Introduction 540 II. There are different types of sRNA mobility 541 III. Mechanisms of sRNA movement 541 IV. Long-distance, shoot–root, mobile siRNAs influence DNA methylation in recipient tissues 541 V. Classes of interactions between shoot–root mobile siRNAs and DNA methylation 542 VI. Loci targeted directly and indirectly by shoot–root mobile siRNAs are associated with different histone modifications 543 VII. Is mobile siRNA-regulated DNA methylation important in specific tissues or under specific conditions? 543 VIII. Mobile sRNAs can be used to modify plant traits 544 IX. Conclusions 544 Acknowledgements 544 References 544 Summary RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA–DNA methylation interactions and the limits of current knowledge. Finally, we discuss potential applications of mobile sRNAs in modifying plant traits.}, language = {en}, number = {2}, urldate = {2024-01-10}, journal = {New Phytologist}, author = {Tamiru, Muluneh and Hardcastle, Thomas J. and Lewsey, Mathew G.}, year = {2018}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14874}, keywords = {unread, grafting, plant epigenetics, RNA silencing, RNA-directed DNA methylation, small RNA}, pages = {540--546}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YCQMQTVG\\Tamiru et al. - 2018 - Regulation of genome-wide DNA methylation by mobil.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\GLBNV287\\nph.html:text/html}, } @article{su_characterizing_2011, title = {Characterizing the role of {miRNAs} within gene regulatory networks using integrative genomics techniques}, volume = {7}, issn = {1744-4292}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130556/}, doi = {10.1038/msb.2011.23}, abstract = {Integrative genomics and genetics approaches have proven to be a useful tool in elucidating the complex relationships often found in gene regulatory networks. More importantly, a number of studies have provided the necessary experimental evidence confirming the validity of the causal relationships inferred using such an approach. By integrating messenger RNA (mRNA) expression data with microRNA (miRNA) (i.e. small non-coding RNA with well-established regulatory roles in a myriad of biological processes) expression data, we show how integrative genomics approaches can be used to characterize the role played by approximately a third of registered mouse miRNAs within the context of a liver gene regulatory network. Our analysis reveals that the transcript abundances of miRNAs are subject to regulatory control by many more loci than previously observed for mRNA expression. Moreover, our results indicate that miRNAs exist as highly connected hub-nodes and function as key sensors within the transcriptional network. We also provide evidence supporting the hypothesis that miRNAs can act cooperatively or redundantly to regulate a given pathway and that miRNAs play a subtle role by dampening expression of their target gene through the use of feedback loops.}, urldate = {2024-01-10}, journal = {Molecular Systems Biology}, author = {Su, Wan-Lin and Kleinhanz, Robert R and Schadt, Eric E}, month = may, year = {2011}, pmid = {21613979}, pmcid = {PMC3130556}, keywords = {unread}, pages = {490}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YHPFGB9H\\Su et al. - 2011 - Characterizing the role of miRNAs within gene regu.pdf:application/pdf}, } @article{liu_small_2021, title = {Small noncoding {RNA} discovery and profiling with {sRNAtools} based on high-throughput sequencing}, volume = {22}, issn = {1477-4054}, url = {https://doi.org/10.1093/bib/bbz151}, doi = {10.1093/bib/bbz151}, abstract = {Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https://bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.}, number = {1}, urldate = {2024-01-10}, journal = {Briefings in Bioinformatics}, author = {Liu, Qi and Ding, Changjun and Lang, Xiaoqiang and Guo, Ganggang and Chen, Jiafei and Su, Xiaohua}, month = jan, year = {2021}, keywords = {unread}, pages = {463--473}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\G3QJUD99\\Liu et al. - 2021 - Small noncoding RNA discovery and profiling with s.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\2YU6E3X4\\5686255.html:text/html}, } @article{george_triploid_2023, title = {Triploid {Pacific} oysters exhibit stress response dysregulation and elevated mortality following heatwaves}, volume = {29}, copyright = {© 2023 John Wiley \& Sons Ltd.}, issn = {1365-2486}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.16880}, doi = {10.1111/gcb.16880}, abstract = {Polyploidy has been suggested to negatively impact environmental stress tolerance, resulting in increased susceptibility to extreme climate events. In this study, we compared the genomic and physiological response of diploid (2n) and triploid (3n) Pacific oysters (Crassostrea gigas) to conditions present during an atmospheric heatwave that impacted the Pacific Northwestern region of the United States in the summer of 2021. Climate stressors were applied either singly (single stressor; elevated seawater temperature, 30°C) or in succession (multiple stressor; elevated seawater temperature followed by aerial emersion at 44°C), replicating conditions present within the intertidal over a tidal cycle during the event. Oyster mortality rate was elevated within stress treatments with respect to the control and was significantly higher in triploids than diploids following multiple stress exposure (36.4\% vs. 14.8\%). Triploids within the multiple stressor treatment exhibited signs of energetic limitation, including metabolic depression, a significant reduction in ctenidium Na+/K+ ATPase activity, and the dysregulated expression of genes associated with stress response, innate immunity, glucose metabolism, and mitochondrial function. Functional enrichment analysis of ploidy-specific gene sets identified that biological processes associated with metabolism, stress tolerance, and immune function were overrepresented within triploids across stress treatments. Our results suggest that triploidy impacts the transcriptional regulation of key processes that underly the stress response of Pacific oysters, resulting in downstream shifts in physiological tolerance limits that may increase susceptibility to extreme climate events that present multiple environmental stressors. The impact of chromosome set manipulation on the climate resilience of marine organisms has important implications for domestic food security within future climate scenarios, especially as triploidy induction becomes an increasingly popular tool to elicit reproductive control across a wide range of species used within marine aquaculture.}, language = {en}, number = {24}, urldate = {2024-01-11}, journal = {Global Change Biology}, author = {George, Matthew N. and Cattau, Olivia and Middleton, Mollie A. and Lawson, Delaney and Vadopalas, Brent and Gavery, Mackenzie and Roberts, Steven B.}, year = {2023}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.16880}, keywords = {Pacific oyster, unread, climate change, Crassostrea gigas, functional genomics, multiple stressors, physiological tolerance, triploid mortality}, pages = {6969--6987}, file = {George et al. - 2023 - Triploid Pacific oysters exhibit stress response d.pdf:C\:\\Users\\Owner\\Zotero\\storage\\4JN4STFW\\George et al. - 2023 - Triploid Pacific oysters exhibit stress response d.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\IKUPB5PM\\gcb.html:text/html}, } @article{silliman_epigenetic_2023, title = {Epigenetic and {Genetic} {Population} {Structure} is {Coupled} in a {Marine} {Invertebrate}}, volume = {15}, issn = {1759-6653}, url = {https://doi.org/10.1093/gbe/evad013}, doi = {10.1093/gbe/evad013}, abstract = {Delineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27\% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.}, number = {2}, urldate = {2024-01-11}, journal = {Genome Biology and Evolution}, author = {Silliman, Katherine and Spencer, Laura H and White, Samuel J and Roberts, Steven B}, month = feb, year = {2023}, keywords = {unread}, pages = {evad013}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\2S4DPM6Y\\Silliman et al. - 2023 - Epigenetic and Genetic Population Structure is Cou.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\A4B3UCMF\\7026322.html:text/html}, } @article{nelson_microrna_2003, title = {The {microRNA} world: small is mighty}, volume = {28}, issn = {0968-0004}, shorttitle = {The {microRNA} world}, url = {https://www.sciencedirect.com/science/article/pii/S0968000403002147}, doi = {10.1016/j.tibs.2003.08.005}, abstract = {A new paradigm of RNA-directed gene expression regulation has emerged recently, profound in scope but arresting in the apparent simplicity of its core mechanism. Cells express numerous small (∼22 nucleotide) RNAs that act as specificity determinants to direct destruction or translational repression of their mRNA targets. These small RNAs arise from processing of double-stranded RNA by the Dicer nuclease and incorporate with proteins that belong to the Argonaute family. Small RNAs might also target and silence homologous DNA sequences. The immense potential of small RNAs as controllers of gene networks is just beginning to unfold.}, number = {10}, urldate = {2024-01-12}, journal = {Trends in Biochemical Sciences}, author = {Nelson, Peter and Kiriakidou, Marianthi and Sharma, Anup and Maniataki, Elsa and Mourelatos, Zissimos}, month = oct, year = {2003}, keywords = {unread, FISH521}, pages = {534--540}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\IPX4GWLR\\S0968000403002147.html:text/html;Submitted Version:C\:\\Users\\Owner\\Zotero\\storage\\UZV3T5KU\\Nelson et al. - 2003 - The microRNA world small is mighty.pdf:application/pdf}, } @article{hiley_detection_2005, title = {Detection and discovery of {RNA} modifications using microarrays}, volume = {33}, issn = {0305-1048}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546174/}, doi = {10.1093/nar/gni002}, abstract = {Using a microarray that tiles all known yeast non-coding RNAs, we compared RNA from wild-type cells with RNA from mutants encoding known and putative RNA modifying enzymes. We show that at least five types of RNA modification (dihydrouridine, m1G, m22G, m1A and m26A) catalyzed by 10 different enzymes (Trm1p, Trm5, Trm10p, Dus1p-Dus4p, Dim1p, Gcd10p and Gcd14p) can be detected by virtue of differential hybridization to oligonucleotides on the array that are complementary to the modified sites. Using this approach, we identified a previously undetected m1A modification in GlnCTG tRNA, the formation of which is catalyzed by the Gcd10/Gcd14 complex.}, number = {1}, urldate = {2024-01-12}, journal = {Nucleic Acids Research}, author = {Hiley, Shawna L. and Jackman, Jane and Babak, Tomas and Trochesset, Miles and Morris, Quaid D. and Phizicky, Eric and Hughes, Timothy R.}, year = {2005}, pmid = {15640439}, pmcid = {PMC546174}, keywords = {unread, FISH521}, pages = {e2}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\M88DCPLH\\Hiley et al. - 2005 - Detection and discovery of RNA modifications using.pdf:application/pdf}, } @article{huttenhofer_experimental_2004, title = {Experimental {RNomics}: a global approach to identifying small nuclear {RNAs} and their targets in different model organisms}, volume = {265}, issn = {1064-3745}, shorttitle = {Experimental {RNomics}}, doi = {10.1385/1-59259-775-0:409}, abstract = {Non-messenger RNAs (nmRNAs) play a wide and essential role in cellular functions. Computational identification of novel nmRNAs in genomes of model organisms is severely restricted owing to their lack of an open reading frame. Hence, we describe experimental approaches for their identification by generating cDNA libraries derived from nmRNAs for which we coined the term experimental RNomics. Two different procedures are introduced for cDNA library construction. First, we describe the construction of a general purpose cDNA library from sized RNA fractions. Second, we introduce a more specialized RNomics strategy employing this approach to generate a cDNA library from a specific abundant class of nmRNAs. This is illustrated using as a paradigm the two families of small nucleolar RNAs that guide modification of nucleotides in rRNAs or spliceosomal RNAs small nuclear RNAs (snRNAs) by short antisense elements complementary to the modification site. Following the identification of novel members from the class of small nuclear RNAs by experimental RNomics, we demonstrate how their target sequences in rRNAs or snRNAs can be identified.}, language = {eng}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, author = {Hüttenhofer, Alexander and Cavaillé, Jérome and Bachellerie, Jean-Pierre}, year = {2004}, pmid = {15103086}, keywords = {unread, FISH521, Base Sequence, Cloning, Molecular, DNA Primers, DNA, Complementary, Electrophoresis, Polyacrylamide Gel, Gene Library, Models, Molecular, Nucleic Acid Conformation, Reverse Transcriptase Polymerase Chain Reaction, RNA, RNA, Messenger, RNA, Small Nucleolar, Sequence Analysis, RNA}, pages = {409--428}, file = {Hüttenhofer et al. - 2004 - Experimental RNomics a global approach to identif.pdf:C\:\\Users\\Owner\\Zotero\\storage\\GKIHXGTW\\Hüttenhofer et al. - 2004 - Experimental RNomics a global approach to identif.pdf:application/pdf}, } @article{mattick_challenging_2003, title = {Challenging the dogma: the hidden layer of non-protein-coding {RNAs} in complex organisms}, volume = {25}, copyright = {Copyright © 2003 Wiley Periodicals, Inc.}, issn = {1521-1878}, shorttitle = {Challenging the dogma}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.10332}, doi = {10.1002/bies.10332}, abstract = {The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher eukaryotes and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoietic development and phenotypic variation. BioEssays 25:930–939, 2003. © 2003 Wiley Periodicals, Inc.}, language = {en}, number = {10}, urldate = {2024-01-12}, journal = {BioEssays}, author = {Mattick, John S.}, year = {2003}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.10332}, keywords = {unread, FISH521}, pages = {930--939}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\38ZBIHDG\\Mattick - 2003 - Challenging the dogma the hidden layer of non-pro.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\2E6XW9UQ\\bies.html:text/html}, } @article{mattick_rna_2004, title = {{RNA} regulation: a new genetics?}, volume = {5}, copyright = {2004 Springer Nature Limited}, issn = {1471-0064}, shorttitle = {{RNA} regulation}, url = {https://www.nature.com/articles/nrg1321}, doi = {10.1038/nrg1321}, abstract = {Do non-coding RNAs that are derived from the introns and exons of protein-coding and non-protein-coding genes represent a fundamental advance in the genetic operating system of higher organisms? Recent evidence from comparative genomics and molecular genetics indicates that this might be the case. If so, there will be profound consequences for our understanding of the genetics of these organisms, and in particular how the trajectories of differentiation and development and the differences among individuals and species are genomically programmed. But how might this hypothesis be tested?}, language = {en}, number = {4}, urldate = {2024-01-12}, journal = {Nature Reviews Genetics}, author = {Mattick, John S.}, month = apr, year = {2004}, note = {Number: 4 Publisher: Nature Publishing Group}, keywords = {unread, FISH521, Agriculture, Animal Genetics and Genomics, Biomedicine, Cancer Research, Gene Function, general, Human Genetics}, pages = {316--323}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\BWN3MVIQ\\Mattick - 2004 - RNA regulation a new genetics.pdf:application/pdf}, } @article{chen_long_2020, title = {Long non-coding {RNAs} in plants: emerging modulators of gene activity in development and stress responses}, volume = {252}, issn = {1432-2048}, shorttitle = {Long non-coding {RNAs} in plants}, url = {https://doi.org/10.1007/s00425-020-03480-5}, doi = {10.1007/s00425-020-03480-5}, abstract = {Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms.}, language = {en}, number = {5}, urldate = {2024-01-12}, journal = {Planta}, author = {Chen, Li and Zhu, Qian-Hao and Kaufmann, Kerstin}, month = oct, year = {2020}, keywords = {unread, FISH521, Arabidopsis, Development, Long non-coding RNAs (LncRNAs), Rice, Stress response}, pages = {92}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\HVN9ZBZW\\Chen et al. - 2020 - Long non-coding RNAs in plants emerging modulator.pdf:application/pdf}, } @article{wu_bidirectional_2022, title = {Bidirectional {lncRNA} {Transfer} between {Cuscuta} {Parasites} and {Their} {Host} {Plant}}, volume = {23}, issn = {1422-0067}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8745499/}, doi = {10.3390/ijms23010561}, abstract = {Dodder species (Cuscuta spp.) are holoparasites that have extensive material exchange with their host plants through vascular connections. Recent studies on cross-species transfer have provided breakthrough insights, but little is known about the interaction mechanisms of the inter-plant mobile substances in parasitic systems. We sequenced the transcriptomes of dodder growing on soybean hosts to characterize the long non-coding RNA (lncRNA) transfer between the two species, and found that lncRNAs can move in high numbers (365 dodder lncRNAs and 14 soybean lncRNAs) in a bidirectional manner. Reverse transcription-polymerase chain reaction further confirmed that individual lncRNAs were trafficked in the dodder–soybean parasitic system. To reveal the potential functions of mobile transcripts, the Gene Ontology terms of mobile lncRNA target genes were predicted, and mobile dodder target genes were found to be mainly enriched in “metabolic process”, “catalytic activity”, “signaling”, and “response to stimulus” categories, whereas mobile soybean target genes were enriched in organelle-related categories, indicating that specific mobile lncRNAs may be important in regulating dodder parasitism. Our findings reveal that lncRNAs are transferred between dodder and its host soybean plants, which may act as critical regulators to coordinate the host–dodder interaction at the whole parasitic level.}, number = {1}, urldate = {2024-01-12}, journal = {International Journal of Molecular Sciences}, author = {Wu, Yuguo and Luo, Dong and Fang, Longfa and Zhou, Qiang and Liu, Wenxian and Liu, Zhipeng}, month = jan, year = {2022}, pmid = {35008986}, pmcid = {PMC8745499}, keywords = {unread, FISH521}, pages = {561}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\PTNRCHBD\\Wu et al. - 2022 - Bidirectional lncRNA Transfer between Cuscuta Para.pdf:application/pdf}, } @article{dhanasekaran_noncoding_2013, title = {Noncoding {RNAs} in {Chromatin} {Organization} and {Transcription} {Regulation}: {An} {Epigenetic} {View}}, volume = {61}, issn = {978-94-007-4524-7}, shorttitle = {Noncoding {RNAs} in {Chromatin} {Organization} and {Transcription} {Regulation}}, doi = {10.1007/978-94-007-4525-4_15}, abstract = {The Genome of a eukaryotic cell harbors genetic material in the form of DNA which carries the hereditary information encoded in their bases. Nucleotide bases of DNA are transcribed into complimentary RNA bases which are further translated into protein, performing defined set of functions. The central dogma of life ensures sequential flow of genetic information among these biopolymers. Noncoding RNAs (ncRNAs) serve as exceptions for this principle as they do not code for any protein. Nevertheless, a major portion of the human transcriptome comprises noncoding RNAs. These RNAs vary in size, as well as they vary in the spatio-temporal distribution. These ncRnAs are functional and are shown to be involved in diverse cellular activities. Precise location and expression of ncRNA is essential for the cellular homeostasis. Failures of these events ultimately results in numerous disease conditions including cancer. The present review lists out the various classes of ncRNAs with a special emphasis on their role in chromatin organization and transcription regulation.}, journal = {Sub-cellular biochemistry}, author = {Dhanasekaran, Karthigeyan and Kumari, Sujata and Kanduri, Chandrasekhar}, month = jun, year = {2013}, keywords = {unread, FISH521}, pages = {343--372}, file = {Dhanasekaran et al. - 2013 - Noncoding RNAs in Chromatin Organization and Trans.pdf:C\:\\Users\\Owner\\Zotero\\storage\\GFJ9DVXS\\Dhanasekaran et al. - 2013 - Noncoding RNAs in Chromatin Organization and Trans.pdf:application/pdf}, } @article{kung_long_2013, title = {Long {Noncoding} {RNAs}: {Past}, {Present}, and {Future}}, volume = {193}, issn = {0016-6731}, shorttitle = {Long {Noncoding} {RNAs}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583990/}, doi = {10.1534/genetics.112.146704}, abstract = {Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology’s longstanding concern with the evolution and function of genomes.}, number = {3}, urldate = {2024-01-12}, journal = {Genetics}, author = {Kung, Johnny T. Y. and Colognori, David and Lee, Jeannie T.}, month = mar, year = {2013}, pmid = {23463798}, pmcid = {PMC3583990}, keywords = {unread, FISH521}, pages = {651--669}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\9UKFWURU\\Kung et al. - 2013 - Long Noncoding RNAs Past, Present, and Future.pdf:application/pdf}, } @article{dogini_new_2014, title = {The new world of {RNAs}}, volume = {37}, issn = {1415-4757}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983583/}, abstract = {One of the major developments that resulted from the human genome sequencing projects was a better understanding of the role of non-coding RNAs (ncRNAs). NcRNAs are divided into several different categories according to size and function; however, one shared feature is that they are not translated into proteins. In this review, we will discuss relevant aspects of ncRNAs, focusing on two main types: i) microRNAs, which negatively regulate gene expression either by translational repression or target mRNA degradation, and ii) small interfering RNAs (siRNAs), which are involved in the biological process of RNA interference (RNAi). Our knowledge regarding these two types of ncRNAs has increased dramatically over the past decade, and they have a great potential to become therapeutic alternatives for a variety of human conditions.}, number = {1 Suppl}, urldate = {2024-01-12}, journal = {Genetics and Molecular Biology}, author = {Dogini, Danyella Barbosa and Pascoal, Vinícius D’Avila Bittencourt and Avansini, Simoni Helena and Vieira, André Schwambach and Pereira, Tiago Campos and Lopes-Cendes, Iscia}, month = mar, year = {2014}, pmid = {24764762}, pmcid = {PMC3983583}, keywords = {unread, FISH521}, pages = {285--293}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\ITRLI422\\Dogini et al. - 2014 - The new world of RNAs.pdf:application/pdf}, } @misc{noauthor_mirmachine_nodate, title = {{mirMachine}: {A} {One}-{Stop} {Shop} for {Plant} {miRNA} {Annotation}}, shorttitle = {{mirMachine}}, url = {https://app.jove.com/t/62430/mirmachine-a-one-stop-shop-for-plant-mirna-annotation}, abstract = {Of different types of noncoding RNAs, microRNAs (miRNAs) have arguably been in the spotlight over the last decade. As post-transcriptional regulators of ...}, language = {en}, urldate = {2024-01-17}, keywords = {unread}, file = {mirMachine A One-Stop Shop for Plant miRNA Annota.pdf:C\:\\Users\\Owner\\Zotero\\storage\\SCL647XH\\mirMachine A One-Stop Shop for Plant miRNA Annota.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\8ZAE8GXU\\mirmachine-a-one-stop-shop-for-plant-mirna-annotation.html:text/html}, } @misc{noauthor_proposal_recipejpg_nodate, title = {proposal\_recipe.jpg (2438×3413)}, url = {https://uw-fish521.github.io/website/references/proposal_recipe.jpg}, urldate = {2024-01-19}, file = {proposal_recipe.jpg (2438×3413):C\:\\Users\\Owner\\Zotero\\storage\\V7LFL8B2\\proposal_recipe.html:text/html}, } @article{lamka_epigenetics_2022, title = {Epigenetics in {Ecology}, {Evolution}, and {Conservation}}, volume = {10}, issn = {2296-701X}, url = {https://www.frontiersin.org/articles/10.3389/fevo.2022.871791}, abstract = {Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.}, urldate = {2024-01-23}, journal = {Frontiers in Ecology and Evolution}, author = {Lamka, Gina F. and Harder, Avril M. and Sundaram, Mekala and Schwartz, Tonia S. and Christie, Mark R. and DeWoody, J. Andrew and Willoughby, Janna R.}, year = {2022}, keywords = {unread}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\Z2NEHLUY\\Lamka et al. - 2022 - Epigenetics in Ecology, Evolution, and Conservatio.pdf:application/pdf}, } @article{yevenes_epigenetic_2023, title = {Epigenetic variation mediated by {lncRNAs} accounts for adaptive genomic differentiation of the endemic blue mussel {Mytiluschilensis}}, volume = {10}, issn = {2405-8440}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10776947/}, doi = {10.1016/j.heliyon.2023.e23695}, abstract = {Epigenetic variation affects gene expression without altering the underlying DNA sequence of genes controlling ecologically relevant phenotypes through different mechanisms, one of which is long non-coding RNAs (lncRNAs). This study identified and evaluated the gene expression of lncRNAs in the gill and mantle tissues of Mytilus chilensis individuals from two ecologically different sites: Cochamó (41°S) and Yaldad (43°S), southern Chile, both impacted by climatic-related conditions and by mussel farming given their use as seedbeds. Sequences identified as lncRNAs exhibited tissue-specific differences, mapping to 3.54 \% of the gill transcriptome and 1.96 \% of the mantle transcriptome, representing an average of 2.76 \% of the whole transcriptome. Using a high fold change value (≥{\textbar}100{\textbar}), we identified 43 and 47 differentially expressed lncRNAs (DE-lncRNAs) in the gill and mantle tissue of individuals sampled from Cochamó and 21 and 17 in the gill and mantle tissue of individuals sampled from Yaldad. Location-specific DE-lncRNAs were also detected in Cochamó (65) and Yaldad (94) samples. Via analysis of the differential expression of neighboring protein-coding genes, we identified enriched GO terms related to metabolic, genetic, and environmental information processing and immune system functions, reflecting how the impact of local ecological conditions may influence the M. chilensis (epi)genome expression. These DE-lncRNAs represent complementary biomarkers to DNA sequence variation for maintaining adaptive differences and phenotypic plasticity to cope with natural and human-driven perturbations., •Differentially expressed (DE) lncRNAs in the M. chilensisgenome represent approximately 2.76\% of its transcriptome.•Expression patterns of these DE-lncRNAs differentiate mussels from two ecologically distinct natural seedbeds.•DE-lncRNAs linked with neighboring genes impact diverse biological processes and potentially influence fitness traits..•Monitoring and conserving M. chilensis seedbeds can be facilitated by integrating variation in epigenetic factor expression.}, number = {1}, urldate = {2024-01-24}, journal = {Heliyon}, author = {Yévenes, Marco and Gallardo-Escárate, Cristian and Gajardo, Gonzalo}, month = dec, year = {2023}, pmid = {38205306}, pmcid = {PMC10776947}, keywords = {unread}, pages = {e23695}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\FA9Y2R6D\\Yévenes et al. - 2023 - Epigenetic variation mediated by lncRNAs accounts .pdf:application/pdf}, } @article{rodriguez-casariego_multi-omic_2023, title = {Multi-omic characterization of mechanisms contributing to rapid phenotypic plasticity in the coral {Acropora} cervicornis under divergent environments}, issn = {1432-0975}, url = {https://doi.org/10.1007/s00338-023-02446-9}, doi = {10.1007/s00338-023-02446-9}, abstract = {Phenotypic plasticity is defined as a property of individual genotypes to produce different phenotypes when exposed to different environmental conditions. This ability may be expressed at behavioral, biochemical, physiological, and/or developmental levels, exerting direct influence over species' demographic performance. In reef-building corals, a group critically threatened by global change in the Anthropocene, non-genetic mechanisms (i.e., epigenetic and microbiome variation) have been shown to participate in plastic physiological responses to environmental change. Yet, the precise way in which these mechanisms interact, contribute to such responses, and their adaptive potential is still obscure. The present work aims to fill this gap by using a multi-omics approach to elucidate the contribution and interconnection of the mechanisms modulating phenotypic plasticity in staghorn coral (Acropora cervicornis) clones subject to different depth conditions. Results show changes in lipidome, epigenome and transcriptome, but not in symbiotic and microbial communities. In addition, a potential shift toward a more heterotrophic feeding behavior was evidenced in corals at the deeper site. These observations are consistent with a multi-mechanism modulation of rapid acclimation in corals, underscoring the complexity of this process and the importance of a multifactorial approach to inform potential intervention to enhance coral adaptive capacity.}, language = {en}, urldate = {2024-01-24}, journal = {Coral Reefs}, author = {Rodriguez-Casariego, Javier A. and Mercado-Molina, Alex and Lemos, Leila Soledade and Quinete, Natalia Soares and Bellantuono, Anthony and Rodriguez-Lanetty, Mauricio and Sabat, Alberto and Eirin-Lopez, Jose M.}, month = dec, year = {2023}, keywords = {Symbiodiniaceae, Transcriptome, unread, Epigenetics, Lipidome, Microbiome, Phenotypic plasticity, Staghorn coral, WGBS}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\XMSF46BP\\Rodriguez-Casariego et al. - 2023 - Multi-omic characterization of mechanisms contribu.pdf:application/pdf}, } @article{liew_intergenerational_2020, title = {Intergenerational epigenetic inheritance in reef-building corals}, volume = {10}, copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited}, issn = {1758-6798}, url = {https://www.nature.com/articles/s41558-019-0687-2}, doi = {10.1038/s41558-019-0687-2}, abstract = {The perception that the inheritance of phenotypic traits operates solely through genetic means is slowly being eroded: epigenetic mechanisms have been shown to induce heritable changes in gene activity in plants1,2 and metazoans1,3. Inheritance of DNA methylation patterns provides a potential pathway for environmentally induced phenotypes to contribute to evolution of species and populations1–5. However, in basal metazoans, it is unknown whether inheritance of CpG methylation patterns occurs across the genome (as in plants) or as rare exceptions (as in mammals)4. Here, we show that DNA methylation patterns in a reef-building coral are determined by genotype and developmental stage, as well as by parental environment. Transmission of CpG methylation from adults to their sperm and larvae demonstrates genome-wide inheritance. Variation in the hypermethylation of genes in adults and their sperm from distinct environments suggests intergenerational acclimatization to local temperature and salinity. Furthermore, genotype-independent adjustments of methylation levels in stress-related genes were strongly correlated with offspring survival rates under heat stress. These findings support a role of DNA methylation in the intergenerational inheritance of traits in corals, which could extend to enhancing their capacity to adapt to climate change.}, language = {en}, number = {3}, urldate = {2024-01-24}, journal = {Nature Climate Change}, author = {Liew, Yi Jin and Howells, Emily J. and Wang, Xin and Michell, Craig T. and Burt, John A. and Idaghdour, Youssef and Aranda, Manuel}, month = mar, year = {2020}, note = {Number: 3 Publisher: Nature Publishing Group}, keywords = {unread, Ecological genetics, Marine biology, Climate-change ecology, Evolutionary ecology, Molecular ecology}, pages = {254--259}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\MMRI6AAF\\Liew et al. - 2020 - Intergenerational epigenetic inheritance in reef-b.pdf:application/pdf}, } @article{laurel_loss_2020, title = {Loss of spawning habitat and prerecruits of {Pacific} cod during a {Gulf} of {Alaska} heatwave}, volume = {77}, issn = {0706-652X}, url = {https://cdnsciencepub.com/doi/full/10.1139/cjfas-2019-0238}, doi = {10.1139/cjfas-2019-0238}, abstract = {Pacific cod (Gadus macrocephalus) stocks in the Gulf of Alaska experienced steep, unexpected declines following an unprecedented 3-year marine heatwave (i.e., “warm blob”) from 2014 to 2016. We contend that stock reproductive potential was reduced during this period, evidenced by a combination of new laboratory data demonstrating narrow thermal hatch success (3–6 °C), mechanistic-based models of spawning habitat, and correlations with prerecruit time series. With the exception of single-year El Niño events (1998, 2003), the recent 3-year heatwave (2014–2016) and return to similar conditions in 2019 were potentially the most negative impacts on spawning habitat for Pacific cod in the available time series (1994–2019). Continued warming will likely reduce the duration and spatial extent of Pacific cod spawning in the Gulf of Alaska.}, number = {4}, urldate = {2024-02-03}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, author = {Laurel, Benjamin J. and Rogers, Lauren A.}, month = apr, year = {2020}, note = {Publisher: NRC Research Press}, keywords = {unread, Gadus macrocephalus, Pacific cod}, pages = {644--650}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\SHJ59P8D\\Laurel and Rogers - 2020 - Loss of spawning habitat and prerecruits of Pacifi.pdf:application/pdf}, } @article{alderdice_effects_1971, title = {Effects of {Salinity}, {Temperature}, and {Dissolved} {Oxygen} on {Early} {Development} of the {Pacific} {Cod} ({Gadus} macrocephalus)}, volume = {28}, issn = {0015-296X}, url = {https://cdnsciencepub.com/doi/abs/10.1139/f71-130}, doi = {10.1139/f71-130}, abstract = {Effects of various combinations of levels of salinity, temperature, and dissolved oxygen on incubation of Pacific cod (Gadus macrocephalus) eggs were investigated in the laboratory. Quantitative relations were determined, by response surface analysis, between the environmental variables and four criteria used to estimate success of egg development. Larval size at mean hatching time, and percentages of total hatch, viable hatch, and postmature eggs that failed to hatch were optimized at intermediate salinities (about 15‰), low temperatures (3–5 C), and over a wide range of dissolved oxygen concentrations. Pacific cod eggs are judged to be euryhaline, euryoxic, and stenothermal. As long as temperatures are within the range of about 3–5 C, the developing egg is tolerant of a wide range of salinities, and of dissolved oxygen levels to a minimum of about 2 or 3 ppm. Below 3 C developmental success decreases precipitously; above 5 C it attenuates more slowly.Distribution and abundance of Pacific cod are reviewed in light of the experimental results. Temperature is suggested to be of major importance to successful egg development in the natural environment; the temperature range associated with reasonable egg viability and incubation success is estimated to extend from about 2.5 to 8.5 C.The distribution of cod in the spawning season appears associated with water temperatures between 2.5 and 8.5 C in Asian waters. Near the southern limit of cod distribution on the North American coast the following associations are suggested in relation to temperatures of the upper mixed layer of coastal waters in the spawning period: limit of commercial abundance, 9 C; extent of limited commercial landings, 10 C; limit of occurrence, 13.5 C.}, number = {6}, urldate = {2024-02-03}, journal = {Journal of the Fisheries Research Board of Canada}, author = {Alderdice, D. F. and Forrester, C. R.}, month = jun, year = {1971}, note = {Publisher: NRC Research Press}, keywords = {unread, Gadus macrocephalus, Pacific cod}, pages = {883--902}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\JPLVMX72\\Alderdice and Forrester - 1971 - Effects of Salinity, Temperature, and Dissolved Ox.pdf:application/pdf}, } @article{bond_causes_2015, title = {Causes and impacts of the 2014 warm anomaly in the {NE} {Pacific}}, volume = {42}, copyright = {©2015. The Authors.}, issn = {1944-8007}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/2015GL063306}, doi = {10.1002/2015GL063306}, abstract = {Strongly positive temperature anomalies developed in the NE Pacific Ocean during the boreal winter of 2013–2014. Based on a mixed layer temperature budget, these anomalies were caused by lower than normal rates of the loss of heat from the ocean to the atmosphere and of relatively weak cold advection in the upper ocean. Both of these mechanisms can be attributed to an unusually strong and persistent weather pattern featuring much higher than normal sea level pressure over the waters of interest. This anomaly was the greatest observed in this region since at least the 1980s. The region of warm sea surface temperature anomalies subsequently expanded and reached coastal waters in spring and summer 2014. Impacts on fisheries and regional weather are discussed. It is found that sea surface temperature anomalies in this region affect air temperatures downwind in Washington state.}, language = {en}, number = {9}, urldate = {2024-02-03}, journal = {Geophysical Research Letters}, author = {Bond, Nicholas A. and Cronin, Meghan F. and Freeland, Howard and Mantua, Nathan}, year = {2015}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/2015GL063306}, keywords = {northeast Pacific Ocean, regional and downwind impacts, seasonal heating mechanisms, SLP anomalies, warm SST, Pacific, warm blob, read}, pages = {3414--3420}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\JK2CE72R\\Bond et al. - 2015 - Causes and impacts of the 2014 warm anomaly in the.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\WRI65HE5\\2015GL063306.html:text/html}, } @article{hurst_ontogenetic_2010, title = {Ontogenetic patterns and temperature-dependent growth rates in early life stages of {Pacific} cod ({Gadus} macrocephalus)}, volume = {108}, issn = {0090-0656}, url = {http://hdl.handle.net/1834/25384}, abstract = {Pacific cod (Gadus macrocephalus) is an important componentof fisheries and food webs in the North Pacific Ocean and Bering Sea. However, vital rates of early life stages ofthis species have yet to be described in detail. We determined the thermal sensitivity of growth rates ofembryos, preflexion and postflexion larvae, and postsettlement juveniles. Growth rates (length and mass) ateach ontogenetic stage were measured in three replicate tanks at four to five temperatures. Nonlinear regressionwas used to obtain parameters for independent stage-specific growth functions and a unified size- and temperature-dependent growth function. Specific growth rates increased with temperature at all stages and generallydecreased with increases in body size. However, these analyses revealed a departure from a strict size-basedallometry in growth patterns, as reduced growth rates were observed among preflexion larvae: the reduction in specific growth rate between embryos and free-swimming larvaewas greater than expected based on body size differences. Growth reductions in the preflexion larvae appear to be associated with increased metabolic rates and the transition from endogenous to exogenous feeding. Infuture studies, experiments should be integrated across life transitions to more clearly define intrinsic ontogenetic and size-dependent growth patterns because these are critical for evaluations of spatial and temporalvariation in habitat quality.}, language = {en}, number = {4}, urldate = {2024-02-03}, journal = {Fishery Bulletin}, author = {Hurst, Thomas P. and Laurel, Benjamin J. and Ciannelli, Lorenzo}, year = {2010}, keywords = {unread, Gadus macrocephalus, Pacific cod, Biology, Ecology, Fisheries}, pages = {382--392}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\8MKMX3VM\\Hurst et al. - 2010 - Ontogenetic patterns and temperature-dependent gro.pdf:application/pdf}, } @article{kelsch_temperature_1990, title = {Temperature {Preference} versus {Acclimation} in {Fishes}: {Selection} for {Changing} {Metabolic} {Optima}}, volume = {119}, copyright = {© 1990 American Fisheries Society}, issn = {1548-8659}, shorttitle = {Temperature {Preference} versus {Acclimation} in {Fishes}}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1577/1548-8659%281990%29119%3C0601%3ATPVAIF%3E2.3.CO%3B2}, doi = {10.1577/1548-8659(1990)119<0601:TPVAIF>2.3.CO;2}, abstract = {We present a model that accounts for the variety in observed relationships between temperature preference and acclimation in fishes. The preferred temperature is that temperature at which Fryˈs scope for metabolism is maximized. Thermal acclimation shifts the temperature for maximum scope in such a way that Zahnˈs types of temperature-preference acclimation correspond with Prechtˈs types of metabolic compensation. The model predicts that fishes exhibiting Prechtˈs “partial,” “no,” and “inverse” compensation prefer temperatures that are increasing, independent, and decreasing functions of acclimation temperature, respectively. Experiments with bluegill Lepomis macrochirus and blue tilapia Tilapia aurea, together with information from the literature, provide support for the model.}, language = {en}, number = {4}, urldate = {2024-02-03}, journal = {Transactions of the American Fisheries Society}, author = {Kelsch, Steven W. and Neill, William H.}, year = {1990}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1577/1548-8659\%281990\%29119\%3C0601\%3ATPVAIF\%3E2.3.CO\%3B2}, keywords = {unread}, pages = {601--610}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\UPNS42F9\\Kelsch and Neill - 1990 - Temperature Preference versus Acclimation in Fishe.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\ENYF73V4\\1548-8659(1990)1190601TPVAIF2.3.html:text/html}, } @article{laurel_role_2008, title = {The role of temperature on the growth and survival of early and late hatching {Pacific} cod larvae ({Gadus} macrocephalus)}, volume = {30}, issn = {0142-7873}, url = {https://doi.org/10.1093/plankt/fbn057}, doi = {10.1093/plankt/fbn057}, abstract = {Fish larvae hatch asynchronously from egg batches despite experiencing a common environment during their development. The consequences for growth and survival of early and late hatching larvae were examined in pre-feeding Pacific cod larvae under varying temperatures (i.e. 0–8°C) in the laboratory. As expected, time-to-first hatch and variation in time-to-hatch were negatively correlated with temperature. Larvae successfully hatched in the 0°C treatment, but hatch rates were poorer at this temperature relative to other temperature treatments. Size-at-hatch and the maximum size achieved during the pre-feeding larval stage were highest in the 0–4°C treatments, indicating that these temperatures are likely optimal for the conversion of endogenous resources to growth. At all temperatures, early hatching larvae were smaller but had more lipid reserves and survived longer after hatch in the absence of food than late hatching larvae. Together these data suggest that temperature fluctuations in the North Pacific have direct potential to impact the size, growth and endogenous reserves of Pacific cod larvae, which in turn, will likely influence survival through interactions with the prey and predator field.}, number = {9}, urldate = {2024-02-03}, journal = {Journal of Plankton Research}, author = {Laurel, Benjamin J. and Hurst, Thomas P. and Copeman, Louise A. and Davis, Michael W.}, month = sep, year = {2008}, keywords = {unread, Gadus macrocephalus, Pacific cod}, pages = {1051--1060}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\PHC8MKN3\\Laurel et al. - 2008 - The role of temperature on the growth and survival.pdf:application/pdf}, } @article{laurel_regional_2021, title = {Regional warming exacerbates match/mismatch vulnerability for cod larvae in {Alaska}}, volume = {193}, issn = {0079-6611}, url = {https://www.sciencedirect.com/science/article/pii/S0079661121000434}, doi = {10.1016/j.pocean.2021.102555}, abstract = {The match-mismatch hypothesis predicts that variability in spring primary production will increase starvation risk for marine fish populations. However, it is often unclear whether the synergic effects of temperature, phytoplankton phenology and metabolic demands of fish support these prediction within and across regions. In this study, we combine experimentally-derived rates of larval survival in relation to water temperature with satellite remote-sensing estimates of chlorophyll a and sea surface temperature to predict habitat quality of first feeding Pacific cod (Gadus macrocephalus) larvae in two adjacent large marine ecosystems; southeast Bering Sea (BS) and Gulf of Alaska (GOA). Predictions are made from 1998 to 2019, a period comprised of both warm and cool springs, followed by a series of extreme warming events (heatwaves) beginning in 2014. Model results indicate that the drivers of a mismatch between cod larvae and their food is fundamentally different between the two systems. In the GOA, larval habitat suitability is highly dependent on interannual fluctuations in sea surface temperature that regulate yolk reserves in embryos. In contrast, larval habitat suitability in the BS was more sensitive to the onset of the surface expression of Chl a production. The combined effects of changes in timing of Chl a and increased metabolic demands of larvae were captured by the model during the GOA marine heatwave (2014–16, 2019), which predicted significant loss of larval habitat across the entire region. These habitat models integrate important spatial, temporal and physiological components of match-mismatch theory that can be used to examine marine fish populations experiencing different rates of climate stress across regions.}, urldate = {2024-02-03}, journal = {Progress in Oceanography}, author = {Laurel, Benjamin J. and Hunsicker, Mary E. and Ciannelli, Lorenzo and Hurst, Thomas P. and Duffy-Anderson, Janet and O'Malley, Robert and Behrenfeld, Michael}, month = apr, year = {2021}, keywords = {Gadus macrocephalus, Pacific cod, read}, pages = {102555}, file = {Laurel et al. - 2021 - Regional warming exacerbates matchmismatch vulner.pdf:C\:\\Users\\Owner\\Zotero\\storage\\PWKEKGG9\\Laurel et al. - 2021 - Regional warming exacerbates matchmismatch vulner.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\9LBX5CC6\\S0079661121000434.html:text/html}, } @article{laurel_experimental_2011, title = {An experimental examination of temperature interactions in the match–mismatch hypothesis for {Pacific} cod larvae}, copyright = {2011}, url = {https://cdnsciencepub.com/doi/10.1139/F10-130}, doi = {10.1139/F10-130}, abstract = {The match–mismatch hypothesis (MMH) predicts that marine fish larvae will have their highest rate of growth and survival when they overlap with their prey. However, Pacific cod (Gadus macrocephalus) and other gadids continue to thrive in the Bering Sea despite delayed prey production resulting from warming and loss of sea ice. In this study, we examined how temperature mediates growth and survival of Pacific cod larvae under varying match–mismatch conditions. Cod larvae were reared at two temperatures (3 °C and 8 °C) and exposed to one of five different food treatments over a 6-week period: (i) high food (HF) (match); (ii) low food (LF); (iii) HF then LF (HF–LF); and (iv) LF then HF (LF–HF) (2–4 mismatch); and (v) no food (NF) (complete mismatch). Results showed that cold environments allow Pacific cod larvae to bridge gaps in prey availability (i.e., timing and magnitude), but negatively impact survival over longer periods. Under warmer conditions, mismatches in prey significantly impacted growth and survival. However, both yolk reserves and compensatory growth mechanisms reduced the severity of mismatches occurring in the first 3 weeks of development. Our results demonstrate a clear need to incorporate the direct effects of temperature on fish larvae in food limitation models.}, language = {en}, urldate = {2024-02-03}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, author = {Laurel, Benjamin J. LaurelB J. and Hurst, Thomas P. HurstT P. and Ciannelli, Lorenzo CiannelliL}, month = jan, year = {2011}, keywords = {Gadus macrocephalus, Pacific cod, read}, file = {Laurel et al. - 2011 - An experimental examination of temperature interac.pdf:C\:\\Users\\Owner\\Zotero\\storage\\VWSVX395\\Laurel et al. - 2011 - An experimental examination of temperature interac.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\6KS9K42Q\\F10-130.html:text/html}, } @article{behrenfeld_revaluating_2016, title = {Revaluating ocean warming impacts on global phytoplankton}, volume = {6}, copyright = {2015 Springer Nature Limited}, issn = {1758-6798}, url = {https://www.nature.com/articles/nclimate2838}, doi = {10.1038/nclimate2838}, abstract = {Global satellite observations document expansions of the low-chlorophyll central ocean gyres and an overall inverse relationship between anomalies in sea surface temperature and phytoplankton chlorophyll concentrations. These findings can provide an invaluable glimpse into potential future ocean changes, but only if the story they tell is accurately interpreted. Chlorophyll is not simply a measure of phytoplankton biomass, but also registers changes in intracellular pigmentation arising from light-driven (photoacclimation) and nutrient-driven physiological responses. Here, we show that the photoacclimation response is an important component of temporal chlorophyll variability across the global ocean. This attribution implies that contemporary relationships between chlorophyll changes and ocean warming are not indicative of proportional changes in productivity, as light-driven decreases in chlorophyll can be associated with constant or even increased photosynthesis. Extension of these results to future change, however, requires further evaluation of how the multifaceted stressors of a warmer, higher-CO2 world will impact plankton communities.}, language = {en}, number = {3}, urldate = {2024-02-05}, journal = {Nature Climate Change}, author = {Behrenfeld, Michael J. and O’Malley, Robert T. and Boss, Emmanuel S. and Westberry, Toby K. and Graff, Jason R. and Halsey, Kimberly H. and Milligan, Allen J. and Siegel, David A. and Brown, Matthew B.}, month = mar, year = {2016}, note = {Number: 3 Publisher: Nature Publishing Group}, keywords = {unread, Marine biology, Microbial biooceanography, Phenology}, pages = {323--330}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\IFAXV389\\Behrenfeld et al. - 2016 - Revaluating ocean warming impacts on global phytop.pdf:application/pdf}, } @article{behrenfeld_climate-driven_2006, title = {Climate-driven trends in contemporary ocean productivity}, volume = {444}, copyright = {2006 Springer Nature Limited}, issn = {1476-4687}, url = {https://www.nature.com/articles/nature05317}, doi = {10.1038/nature05317}, abstract = {The SeaWiFS instrument on board the OrbView-2 satellite has accumulated a unique series of high-resolution colour measurements of the world's oceans during the past decade. Ocean colour reflects the abundance of photosynthetic phytoplankton in surface waters, which in turn is a measure of ocean productivity on a global scale. Comparison with environmental factors reveals a close link between ocean productivity and global climate trends during this period, with a notable reduction in ocean productivity during the post-1999 period of warming. This dataset will provide important background on how future climate change can alter marine food webs.}, language = {en}, number = {7120}, urldate = {2024-02-05}, journal = {Nature}, author = {Behrenfeld, Michael J. and O’Malley, Robert T. and Siegel, David A. and McClain, Charles R. and Sarmiento, Jorge L. and Feldman, Gene C. and Milligan, Allen J. and Falkowski, Paul G. and Letelier, Ricardo M. and Boss, Emmanuel S.}, month = dec, year = {2006}, note = {Number: 7120 Publisher: Nature Publishing Group}, keywords = {unread, Humanities and Social Sciences, multidisciplinary, Science}, pages = {752--755}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\3I5SMAF6\\Behrenfeld et al. - 2006 - Climate-driven trends in contemporary ocean produc.pdf:application/pdf}, } @article{abookire_post-settlement_2022, title = {Post-settlement abundance, condition, and survival in a climate-stressed population of {Pacific} cod}, volume = {79}, issn = {0706-652X}, url = {https://cdnsciencepub.com/doi/full/10.1139/cjfas-2021-0224}, doi = {10.1139/cjfas-2021-0224}, abstract = {The Pacific cod (Gadus macrocephalus) fishery recently collapsed in the Gulf of Alaska after a series of marine heatwaves that began in 2014. To gauge the likelihood of population recovery following these extreme warming events, we investigate potential thermal stress on age-0 cohorts through a comprehensive analysis of juvenile cod abundance, condition, growth, and survival data collected from 15 years of beach seine surveys. Abundance was strongly negatively related to ocean temperature during the egg and larval phase (winter–spring), but age-0 cod were larger in the early summer following warm winter–spring temperatures. Body condition indices suggest that warm summers may improve energetic reserves prior to the first winter; however, there was no summer temperature effect on post-settlement growth or survival. Spatial differences in abundance, condition, or growth were not detected, and density-dependent effects were either weak or positive. While the positive effects of increased summer temperatures on juvenile condition may benefit overwintering survival, they cannot compensate for high pre-settlement mortality from warming winter–spring temperatures. We conclude the critical thermal bottleneck for juvenile abundance occurs pre-settlement.}, number = {6}, urldate = {2024-02-05}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, author = {Abookire, Alisa A. and Litzow, Michael A. and Malick, Michael J. and Laurel, Benjamin J.}, month = jun, year = {2022}, note = {Publisher: NRC Research Press}, keywords = {Gadus macrocephalus, Pacific cod, read}, pages = {958--968}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YRS6727E\\Abookire et al. - 2022 - Post-settlement abundance, condition, and survival.pdf:application/pdf}, } @article{laurel_pacific_2023, title = {Pacific cod in the {Anthropocene}: {An} early life history perspective under changing thermal habitats}, volume = {24}, copyright = {© 2023 The Authors. Fish and Fisheries published by John Wiley \& Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.}, issn = {1467-2979}, shorttitle = {Pacific cod in the {Anthropocene}}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12779}, doi = {10.1111/faf.12779}, abstract = {The rapid decline in Pacific cod (Gadus macrocephalus, Gadidae) biomass following multiple Gulf of Alaska marine heatwaves (2014–2016 and 2019) may be one of the most dramatic documented changes in a sustainably managed marine fishery. As such, fisheries managers are exploring new recruitment paradigms for Pacific cod under novel environmental conditions. In this review, we address the challenges of managing and forecasting Pacific cod populations in the Eastern Pacific where thermal habitats for early life stages are undergoing varying rates of change across space and time. We use observational data to examine changes in distribution, abundance and demographics of the population from 1993 to 2020, and model contemporary and future changes of thermal habitat for both spawning success and age-0 juvenile growth potential. Results indicate that reduced spawning habitat and early life stage abundance may be a precursor to regional population decline, but the recent apparent increases in size-at-age of pre-recruits will have unknown impacts on future recruitment in these regions. We contend that continued monitoring of early life stages will be necessary to track changes in phenology and growth that likely determine size-at-age and the survival trajectories of year classes into the adult population. These include complex size- and temperature-dependent energetics spanning seasonal habitats through the first winter. Climate-ready management of Pacific cod will, therefore, require new process investigations beyond single-season surveys focused on one-life stage.}, language = {en}, number = {6}, urldate = {2024-02-05}, journal = {Fish and Fisheries}, author = {Laurel, Benjamin J. and Abookire, Alisa and Barbeaux, Steve J. and Almeida, L. Zoe and Copeman, Louise A. and Duffy-Anderson, Janet and Hurst, Thomas P. and Litzow, Michael A. and Kristiansen, Trond and Miller, Jessica A. and Palsson, Wayne and Rooney, Sean and Thalmann, Hillary L. and Rogers, Lauren A.}, year = {2023}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12779}, keywords = {unread, Gadus macrocephalus, Pacific cod, eggs, juvenile fish, larvae, size-at-age, spawning}, pages = {959--978}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\IALUD3JD\\Laurel et al. - 2023 - Pacific cod in the Anthropocene An early life his.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\ITTEF9UE\\faf.html:text/html}, } @article{hulson_assessment_2022, title = {Assessment of the {Pacific} cod stock}, language = {en}, author = {Hulson, Pete and Barbeaux, Steve J. and Ferriss, Bridget and McDermott, Susanne and Spies, Ingrid}, year = {2022}, keywords = {unread, Gadus macrocephalus, Pacific cod}, file = {Hulson - 2022 - Assessment of the Pacific cod stock.pdf:C\:\\Users\\Owner\\Zotero\\storage\\KPBI2U9S\\Hulson - 2022 - Assessment of the Pacific cod stock.pdf:application/pdf}, } @article{langfelder_wgcna_2008, title = {{WGCNA}: an {R} package for weighted correlation network analysis}, volume = {9}, issn = {1471-2105}, shorttitle = {{WGCNA}}, url = {https://doi.org/10.1186/1471-2105-9-559}, doi = {10.1186/1471-2105-9-559}, abstract = {Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial.}, number = {1}, urldate = {2024-02-06}, journal = {BMC Bioinformatics}, author = {Langfelder, Peter and Horvath, Steve}, month = dec, year = {2008}, keywords = {Brown Module, Correlation Network, Hierarchical Cluster Dendrogram, Module Eigengene, Module Membership}, pages = {559}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\X9M67QF7\\Langfelder and Horvath - 2008 - WGCNA an R package for weighted correlation netwo.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\D78KYXCP\\1471-2105-9-559.html:text/html}, } @article{sheybani_integrated_2021, title = {An integrated analysis of {mRNAs}, {lncRNAs}, and {miRNAs} based on weighted gene co-expression network analysis involved in bovine endometritis}, volume = {11}, copyright = {2021 The Author(s)}, issn = {2045-2322}, url = {https://www.nature.com/articles/s41598-021-97319-y}, doi = {10.1038/s41598-021-97319-y}, abstract = {In dairy cattle, endometritis is a severe infectious disease that occurs following parturition. It is clear that genetic factors are involved in the etiology of endometritis, however, the molecular pathogenesis of endometritis is not entirely understood. In this study, a system biology approach was used to better understand the molecular mechanisms underlying the development of endometritis. Forty transcriptomic datasets comprising of 20 RNA-Seq (GSE66825) and 20 miRNA-Seq (GSE66826) were obtained from the GEO database. Next, the co-expressed modules were constructed based on RNA-Seq (Rb-modules) and miRNA-Seq (mb-modules) data, separately, using a weighted gene co-expression network analysis (WGCNA) approach. Preservation analysis was used to find the non-preserved Rb-modules in endometritis samples. Afterward, the non-preserved Rb-modules were assigned to the mb-modules to construct the integrated regulatory networks. Just highly connected genes (hubs) in the networks were considered and functional enrichment analysis was used to identify the biological pathways associated with the development of the disease. Furthermore, additional bioinformatic analysis including protein–protein interactions network and miRNA target prediction were applied to enhance the reliability of the results. Thirty-five Rb-modules and 10 mb-modules were identified and 19 and 10 modules were non-preserved, respectively, which were enriched in biological pathways related to endometritis like inflammation and ciliogenesis. Two non-preserved Rb-modules were significantly assigned to three mb-modules and three and two important sub-networks in the Rb-modules were identified, respectively, including important mRNAs, lncRNAs and miRNAs genes like IRAK1, CASP3, CCDC40, CCDC39, ZMYND10, FOXJ1, TLR4, IL10, STAT3, FN1, AKT1, CD68, ENSBTAG00000049936, ENSBTAG00000050527, ENSBTAG00000051242, ENSBTAG00000049287, bta-miR-449, bta-miR-484, bta-miR-149, bta-miR-30b and bta-miR-423. The potential roles of these genes have been previously demonstrated in endometritis or related pathways, which reinforced putative functions of the suggested integrated regulatory networks in the endometritis pathogenesis. These findings may help further elucidate the underlying mechanisms of bovine endometritis.}, language = {en}, number = {1}, urldate = {2024-02-08}, journal = {Scientific Reports}, author = {Sheybani, Negin and Bakhtiarizadeh, Mohammad Reza and Salehi, Abdolreza}, month = sep, year = {2021}, note = {Number: 1 Publisher: Nature Publishing Group}, keywords = {unread, Non-coding RNAs, Transcriptomics, multi-omics, ncRNAs, WGCNA, E5}, pages = {18050}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\TRADBX3B\\Sheybani et al. - 2021 - An integrated analysis of mRNAs, lncRNAs, and miRN.pdf:application/pdf}, } @article{sun_differential_2018, title = {Differential {lncRNA} expression profiles reveal the potential roles of {lncRNAs} in antiviral immune response of \textit{{Crassostrea} gigas}}, volume = {81}, issn = {1050-4648}, url = {https://www.sciencedirect.com/science/article/pii/S1050464818304303}, doi = {10.1016/j.fsi.2018.07.032}, abstract = {Long noncoding RNAs (lncRNAs) may play widespread roles in various biological processes. However, systematic profiles of lncRNAs in the biological responses of Pacific Oyster (Crassostrea gigas) to pathogen infection have not yet been demonstrated. Here, we have conducted an exhaustive comparative transcriptome analysis using a bioinformatics approach to exam the functions of lncRNAs response to Ostreid herpesvirus 1μVar (OsHV-1μVar) challenge. In total, 101 differentially expressed lncRNAs (DE-lncRNA) during OsHV-1μVar infections were identified. Compared with differentially expressed mRNAs (DE-mRNA), DE-lncRNAs are shorter in terms of overall length but longer in terms of exon length. These lncRNAs shared similar characteristics with previously reported invertebrate lncRNAs, such as relatively low GC content, low exon number and low sequence conservation, but low expression level were not observed. 20 DE-lncRNAs are typically co-expressed with their neighboring genes annotated as GO terms (GO: 0044237), indicating that these lncRNAs are involved in binding and cellular process functions in cis mode. The weighted gene co-expression network (WGCNA) analysis resulted in 15 modules. The highlighted blue module was specifically demonstrated a co-expression relationship between 14 DE-lncRNAs and 17 immune-related DE-mRNAs (IR-DE-mRNA). Three hub lncRNAs within this module were co-expressed with one hub IR-DE-mRNA involved in fibrinogen-related protein. It was speculated that lncRNAs is extensively involved in oyster antiviral innate immune system. The present study will facilitate subsequently experimental studies to unravel the function of lncRNAs in marine invertebrate response to pathogen infection.}, urldate = {2024-02-08}, journal = {Fish \& Shellfish Immunology}, author = {Sun, Weiming and Feng, Jixing}, month = oct, year = {2018}, keywords = {Transcriptome analysis, unread, ncRNA, WGCNA, Innate immune, Long noncoding RNA, Ostreid herpesvirus, Differential expression, E5}, pages = {233--241}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\S7ZEIMNM\\S1050464818304303.html:text/html}, } @article{umu_accurate_2023, title = {Accurate {microRNA} annotation of animal genomes using trained covariance models of curated {microRNA} complements in {MirMachine}}, volume = {3}, issn = {2666-979X}, url = {https://www.sciencedirect.com/science/article/pii/S2666979X23001234}, doi = {10.1016/j.xgen.2023.100348}, abstract = {The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using {\textgreater}16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.}, number = {8}, urldate = {2024-02-09}, journal = {Cell Genomics}, author = {Umu, Sinan Uğur and Paynter, Vanessa M. and Trondsen, Håvard and Buschmann, Tilo and Rounge, Trine B. and Peterson, Kevin J. and Fromm, Bastian}, month = aug, year = {2023}, keywords = {unread, ncRNA, evolution, genome annotation, genomics, machine learning, microRNAs, E5, MirMachine, miRNA}, pages = {100348}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\7Z9MBI7W\\Umu et al. - 2023 - Accurate microRNA annotation of animal genomes usi.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\RD7WHF5K\\S2666979X23001234.html:text/html}, } @article{liu_priming_2022, title = {Priming crops for the future: rewiring stress memory}, volume = {27}, issn = {1360-1385}, shorttitle = {Priming crops for the future}, url = {https://www.cell.com/trends/plant-science/abstract/S1360-1385(21)00321-6}, doi = {10.1016/j.tplants.2021.11.015}, language = {English}, number = {7}, urldate = {2024-02-09}, journal = {Trends in Plant Science}, author = {Liu, Haipei and Able, Amanda J. and Able, Jason A.}, month = jul, year = {2022}, pmid = {34906381}, note = {Publisher: Elsevier}, keywords = {unread, cross-stress tolerance, epigenetic modification, molecular breeding, stress memory, stress priming, transgenerational inheritance, epigenetics, E5 meeting}, pages = {699--716}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\LJI8F372\\Liu et al. - 2022 - Priming crops for the future rewiring stress memo.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\CA827GMD\\S1360138521003216.html:text/html}, } @article{gallusci_epigenetics_2017, title = {Epigenetics for {Plant} {Improvement}: {Current} {Knowledge} and {Modeling} {Avenues}}, volume = {22}, issn = {1360-1385}, shorttitle = {Epigenetics for {Plant} {Improvement}}, url = {https://www.sciencedirect.com/science/article/pii/S1360138517300894}, doi = {10.1016/j.tplants.2017.04.009}, abstract = {Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits.}, number = {7}, urldate = {2024-02-09}, journal = {Trends in Plant Science}, author = {Gallusci, Philippe and Dai, Zhanwu and Génard, Michel and Gauffretau, Arnaud and Leblanc-Fournier, Nathalie and Richard-Molard, Céline and Vile, Denis and Brunel-Muguet, Sophie}, month = jul, year = {2017}, keywords = {unread, ncRNA, adaptation, epigenetics, development, environment, modeling, plant breeding}, pages = {610--623}, file = {Gallusci et al. - 2017 - Epigenetics for Plant Improvement Current Knowled.pdf:C\:\\Users\\Owner\\Zotero\\storage\\4FQMLI74\\Gallusci et al. - 2017 - Epigenetics for Plant Improvement Current Knowled.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\IVNU3NL8\\S1360138517300894.html:text/html}, } @article{yamamoto_induced_1988, title = {Induced triploidy in {Pacific} oyster {Crassostrea} gigas, and performance of triploid larvae}, journal = {Tohuko Journal of Agricultural Research}, author = {Yamamoto, Satoshi and Sugawara, Yoshio and Nomura, Tadashi and Oshino, Akio}, year = {1988}, keywords = {Pacific oyster, unread, Crassostrea gigas, triploidy}, file = {KJ00000714940.pdf:C\:\\Users\\Owner\\Zotero\\storage\\4RNYQQ7J\\KJ00000714940.pdf:application/pdf}, } @article{j_brianik_need_2023, title = {The need for more information on the resistance to biological and environmental stressors in triploid oysters}, volume = {577}, issn = {0044-8486}, url = {https://www.sciencedirect.com/science/article/pii/S0044848623006877}, doi = {10.1016/j.aquaculture.2023.739913}, abstract = {Triploid bivalves, specifically oysters, have become an increasingly popular aquaculture product over the last 3 decades due to their superior growth and meat quality. Despite a significant growth advantage, there remain surprisingly few consistent physiological or metabolic differences between diploid and triploid bivalves. This review summarizes the technical approaches used for triploid production before focusing on how triploidy affects key physiological performances, including growth and survivorship, tolerance to environmental stressors, resistance to disease, and immune performances. Survival trends appear to be similar between diploid and triploid oysters, though some immunological features appear to be enhanced in the larger cells present in triploid animals. Broad disease trends also appear to be similar between diploid and triploid oysters, although this topic remains relatively under-investigated and infrequently considers the genetic background of evaluated stocks, hence large knowledge gaps concerning how ploidy may influence host-parasite dynamics remain. Triploid oysters also seem to be equally capable of tolerating common environmental stressors, but coinciding stress appears to impact them more severely than diploids. The vast majority of work concerning triploid bivalves derive from field-based studies and as such considerable knowledge gaps exist outside of growth and survival prompting the need for more controlled approaches. Specifically, the impact of larger triploid cells that contain 50\% more DNA on basic molecular and cellular functioning remains largely unexplored and may represent a fertile ground for fundamental and applied research.}, urldate = {2024-02-13}, journal = {Aquaculture}, author = {J. Brianik, Christopher and Allam, Bassem}, month = dec, year = {2023}, keywords = {oysters, triploidy, Disease, Immunity, Polyploid, Resistance, Stress, read}, pages = {739913}, file = {J. Brianik and Allam - 2023 - The need for more information on the resistance to.pdf:C\:\\Users\\Owner\\Zotero\\storage\\JXBCKGN3\\J. Brianik and Allam - 2023 - The need for more information on the resistance to.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\3RXWKLCJ\\S0044848623006877.html:text/html}, } @article{bodenstein_survival_2023, title = {Survival and growth of triploid eastern oysters, \textit{{Crassostrea} virginica}, produced from wild diploids collected from low-salinity areas}, volume = {564}, issn = {0044-8486}, url = {https://www.sciencedirect.com/science/article/pii/S0044848622011498}, doi = {10.1016/j.aquaculture.2022.739032}, abstract = {Triploid Eastern oysters have been reported to suffer greater mortalities than diploids when exposed to low-salinity ({\textless}5) conditions in the U.S. Gulf of Mexico and Atlantic estuaries. As such, the effect of broodstock parentage was investigated on the low-salinity tolerance of triploid progeny produced by mating diploid females (collected from three Louisiana estuaries differing in salinity regimes) with male tetraploids at two hatcheries. Diploid crosses were also produced using the wild broodstocks to verify expected differences in low-salinity tolerance among diploid progeny and between ploidy levels. All progeny were deployed at low and moderate-salinity (averages of 9.3 and 19.4) field sites to monitor monthly growth and mortality. Sex ratio, gametogenic stage, gonad-to-body ratio, condition index, and Perkinsus marinus infection were also measured periodically at both field sites Although high triploid mortality at the low-salinity site prevented complete analysis, results indicated that diploid parentage had little effect on triploid survival at low salinity. Broodstock parentage affected diploid mortality and growth, although results did not match with predictions made based on historical salinity at broodstock collection sites. Ploidy level had the largest effect on triploid survival and growth followed by the hatchery site where the oysters were produced.}, urldate = {2024-02-13}, journal = {Aquaculture}, author = {Bodenstein, Sarah and Callam, Brian R. and Walton, William C. and Rikard, F. Scott and Tiersch, Terrence R. and La Peyre, Jerome F.}, month = feb, year = {2023}, keywords = {unread, triploidy, Gametogenesis, Mortality, Ploidy, Salinity, Temperature, Crassostrea virginica, oyster, polyploidy}, pages = {739032}, file = {Accepted Version:C\:\\Users\\Owner\\Zotero\\storage\\VEIQ4839\\Bodenstein et al. - 2023 - Survival and growth of triploid eastern oysters, .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\PAXM3725\\S0044848622011498.html:text/html}, } @misc{coxe_hypoxia_2023, title = {Hypoxia and {Anoxia} {Tolerance} in {Diploid} and {Triploid} {Eastern} {Oysters} at {High} {Temperature}}, url = {https://bioone.org/journals/journal-of-shellfish-research/volume-42/issue-1/035.042.0104/Hypoxia-and-Anoxia-Tolerance-in-Diploid-and-Triploid-Eastern-Oysters/10.2983/035.042.0104.full}, urldate = {2024-02-15}, author = {Coxe, Nicholas and Mize, Genesis and Casas, Sandra and La Peyre, Megan K. and Lavaud, Romain and Callam, Brian R. and Rikard, F. Scott and La Peyre, Jerome F.}, year = {2023}, file = {Hypoxia and Anoxia Tolerance in Diploid and Triplo.pdf:C\:\\Users\\Owner\\Zotero\\storage\\H2WPJCKV\\Hypoxia and Anoxia Tolerance in Diploid and Triplo.pdf:application/pdf;Hypoxia and Anoxia Tolerance in Diploid and Triploid Eastern Oysters at High Temperature:C\:\\Users\\Owner\\Zotero\\storage\\HJD92SPM\\035.042.0104.html:text/html}, } @article{li_comparative_2022, title = {Comparative transcriptomic analyses reveal differences in the responses of diploid and triploid {Pacific} oysters (\textit{{Crassostrea} gigas}) to thermal stress}, volume = {555}, issn = {0044-8486}, url = {https://www.sciencedirect.com/science/article/pii/S0044848622003350}, doi = {10.1016/j.aquaculture.2022.738219}, abstract = {Triploid oysters often have higher growth rates and survival rates than diploid oysters. However, some studies have observed the opposite patterns. Triploid oysters have also been observed to show reduced resistance to stress and disease compared with diploid oysters. We compared the transcriptional patterns of diploid and triploid Pacific Oysters (Crassostrea gigas) in response to acute and prolonged thermal stress. The survival rate of triploid C. gigas was lower than that of diploid oysters after prolonged heat stress at 28 °C. A total of 779 and 396 differentially expressed genes (DEGs) were detected in diploid and triploid oysters exposed to acute heat stress, respectively, and the number of DEGs was 418 in diploids and 483 in triploids after prolonged heat stress. Functional enrichment analysis revealed that the DEGs were significantly enriched in protein processing in the endoplasmic reticulum pathway, NF-kappa B signaling pathway, NOD-like receptor signaling pathway, and TNF signaling pathway in both diploid and triploid C. gigas under heat stress. Genes encoding translation initiation factors, including MKNK1, eIF4G3, eIF2a kinase 1, and eIF2a kinase 3, were differentially expressed under acute heat stress in diploid oysters. The number of differentially expressed HSP and IAP genes was greater in diploids than in triploids under acute heat stress, and the expression levels of most of these HSP and IAP genes were higher in diploid oysters than in triploid oysters. Overall, our findings revealed differences in the response of diploid and triploid C. gigas to thermal stress. Triploid C. gigas might be less capable of rapidly modifying the inflammatory response and apoptosis in response to heat stress compared with diploid C. gigas. Different genetic lines of diploid and tetraploid oysters should be used to produce triploid oysters with increased stress resistance.}, urldate = {2024-02-15}, journal = {Aquaculture}, author = {Li, Yongguo and Jiang, Kunyin and Li, Qi}, month = jun, year = {2022}, keywords = {Pacific oyster, unread, Crassostrea gigas, triploidy, Diploid, triploid, Heat stress, Survival rate, Transcriptomic analyses}, pages = {738219}, file = {Li et al. - 2022 - Comparative transcriptomic analyses reveal differe.pdf:C\:\\Users\\Owner\\Zotero\\storage\\628ZJBBM\\Li et al. - 2022 - Comparative transcriptomic analyses reveal differe.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\MKINKDZ9\\S0044848622003350.html:text/html}, } @article{shpigel_effects_1992, title = {Effects of elevated temperature on growth, gametogenesis, physiology, and biochemical composition in diploid and triploid {Pacific} oysters, \textit{{Crassostrea} gigas} {Thunberg}}, volume = {161}, issn = {0022-0981}, url = {https://www.sciencedirect.com/science/article/pii/002209819290186E}, doi = {10.1016/0022-0981(92)90186-E}, abstract = {Growth, gametogenesis, physiology, and biochemical composition of 1-yr-old diploid and triploid Pacific oysters, Crassostrea gigas Thunberg, were simultaneously examined at ambient (8–15°C) and at elevated (30°C) temperatures. Triploid oysters grew significantly faster (P ≤ 0.01) and exhibited a significantly higher (P {\textless} 0.0001) condition index than diploid oysters at the elevated temperature. No significant differences were found between diploid and triploid oysters in rates of oxygen consumption and ammonia excretion at either temperature. Biochemical composition (total protein, carbohydrate, lipid and ash) was similar for both groups at ambient temperature. At elevated temperature, however, triploid oysters had significantly higher levels of carbohydrate (P ≤ 0.016) and protein (P≤0.003) than diploid oysters. Both diploid and triploid oysters developed gametes at ambient temperature, but gonadal development in triploid individuals was 60–80\% lower than in diploid individuals. At elevated temperature, 92\% of the diploids were found to be ripe, compared to 0\% of the triploids. The greater dry tissue weight, condition index, and protein and carbohydrate levels of triploid oyster at 30°C may be attributable to their decreased reproductive effort compared to diploids, thereby giving triploid oysters an energetic advantage at stressful temperatures.}, number = {1}, urldate = {2024-02-15}, journal = {Journal of Experimental Marine Biology and Ecology}, author = {Shpigel, Muki and Barber, Bruce J. and Mann, Roger}, month = oct, year = {1992}, keywords = {Pacific oyster, unread, Physiology, Crassostrea gigas, triploidy, Gametogenesis, Temperature, Biochemical composition, Triploidy, stress}, pages = {15--25}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\ABGX9PMA\\002209819290186E.html:text/html;Shpigel et al. - 1992 - Effects of elevated temperature on growth, gametog.pdf:C\:\\Users\\Owner\\Zotero\\storage\\DQJVF6S7\\Shpigel et al. - 1992 - Effects of elevated temperature on growth, gametog.pdf:application/pdf}, } @article{tan_effects_2021, title = {Effects of stocking density on the aquaculture performance of diploid and triploid, {Pacific} oyster {Crassostrea} gigas and {Portuguese} oyster {C}. angulata in warm water aquaculture}, volume = {52}, copyright = {© 2021 John Wiley \& Sons Ltd}, issn = {1365-2109}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/are.15489}, doi = {10.1111/are.15489}, abstract = {The Pacific oyster (Crassostrea gigas) and the Portuguese oyster (C. angulata) are important oyster species for commercial aquaculture. In this study, three stocking density regimes, including 20, 30 and 40 oysters/basket, were used to study the effects of stocking density on growth performance, survival rate and lipid nutritional quality of diploid and triploid C. gigas and C. angulata. The experiment lasted 163 days, from to 22 November 2011 to 3 April 2012. The main findings of this study are as follows: (1) C. gigas has growth advantage over C. angulata in Shantou waters; (2) geographic origin of the oysters has an impact on the overall performance of diploid and triploid oysters; (3) triploids are generally no growth and survival advantage over diploids in spring and summer; (4) oysters at low stocking density were generally outperformed those at high stocking density; (5) lipid composition of oysters is not affected by ploidy and stocking density; (6) in Shantou waters, C. angulata is more nutritious than C. gigas. This study compares the performance of C. gigas and C. angulata triploidy for the first time. The findings of this study can provide useful information to be applied in oysters aquaculture.}, language = {en}, number = {12}, urldate = {2024-02-15}, journal = {Aquaculture Research}, author = {Tan, Karsoon and Deng, Longhui and Zheng, Huaiping}, year = {2021}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/are.15489}, keywords = {Pacific oyster, unread, Crassostrea gigas, triploidy, Crassostrea spp., fatty acids, growth performance, ploidy, survival rate}, pages = {6268--6279}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\IU3D8SWM\\Tan et al. - 2021 - Effects of stocking density on the aquaculture per.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\VK4QENL7\\are.html:text/html}, } @article{jang_response_2011, title = {Response of the ocean mixed layer depth to global warming and its impact on primary production: a case for the {North} {Pacific} {Ocean}}, volume = {68}, issn = {1054-3139}, shorttitle = {Response of the ocean mixed layer depth to global warming and its impact on primary production}, url = {https://doi.org/10.1093/icesjms/fsr064}, doi = {10.1093/icesjms/fsr064}, abstract = {Jang, C. J., Park, J., Park, T., and Yoo, S. 2011. Response of the ocean mixed layer depth to global warming and its impact on primary production: a case for the North Pacific Ocean. – ICES Journal of Marine Science, 68: 996–1007.This study investigates changes in the mixed layer depth (MLD) in the North Pacific Ocean in response to global warming and their impact on primary production by comparing outputs from 11 models of the coupled model intercomparison projects phase 3. The MLD in the 21st century decreases in most regions of the North Pacific, whereas the spatial pattern of the MLD is nearly unchanged. The overall shoaling results in part from intensified upper-ocean stratification caused by both surface warming and freshening. A significant MLD decrease (\>30 m) is found in the Kuroshio extension (KE), which is predominantly driven by reduced surface cooling, caused by weakening of wind. Associated with the mixed layer shoaling in the KE, the primary production component resulting from seasonal vertical mixing will be reduced by 10.7–40.3\% (ranges of medians from 11 models) via decreased nitrate fluxes from below it. Spring blooms in most models are projected to initiate earlier in the KE by 0–13 d (ranges of medians from 11 models). Despite the overall trends, the magnitude of changes in primary production and timing of spring blooms are quite different depending on models and latitudes.}, number = {6}, urldate = {2024-02-16}, journal = {ICES Journal of Marine Science}, author = {Jang, Chan Joo and Park, Jisoo and Park, Taewook and Yoo, Sinjae}, month = jul, year = {2011}, keywords = {unread, Pacific, primary production}, pages = {996--1007}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\EJJR99Y9\\Jang et al. - 2011 - Response of the ocean mixed layer depth to global .pdf:application/pdf}, } @misc{noauthor_e5_nodate, title = {E5 {Proposal}}, file = {E5 Proposal.pdf:C\:\\Users\\Owner\\Zotero\\storage\\ZTU9ANU7\\E5 Proposal.pdf:application/pdf}, } @article{knauer_review_1999, title = {A {Review} of the {Nutritional} {Requirements} of {Bivalves} and the {Development} of {Alternative} and {Artificial} {Diets} for {Bivalve} {Aquaculture}}, volume = {7}, issn = {1064-1262}, url = {https://doi.org/10.1080/10641269908951362}, doi = {10.1080/10641269908951362}, abstract = {The culture of live microalgae to feed larvae and spat is one of the major bottlenecks in bivalve culture. Consequently, there is a strong need for alternative diets to replace live microalgae as food for bivalves in commercial and research hatcheries. This article initially reviews the literature on the nutritional requirements of bivalves and continues with a review of the development of alternative and artificial diets for bivalves. Although a limited number of such diets have been assessed experimentally, their nutritional value is currently limited by a general lack of knowledge of the nutritional requirements of bivalves. The importance of the development of artificial diets, whose nutritional composition can be precisely manipulated, in order to study bivalve nutrition is emphasized. In the absence of clearly defined artificial diets, dietary vehicles such as microcapsules and spray-dried microalgae are currently the most promising tools to study the nutritional requirements of bivalves.}, number = {3-4}, urldate = {2024-02-21}, journal = {Reviews in Fisheries Science}, author = {Knauer, Jens and Southgate, Paul C.}, month = jan, year = {1999}, note = {Publisher: Taylor \& Francis \_eprint: https://doi.org/10.1080/10641269908951362}, keywords = {experimental design, oysters, read, aquaculture, artificial diets, bivalves, nutritional requirements, feeding stress, diet}, pages = {241--280}, file = {A Review of the Nutritional Requirements of Bivalves and the Development of Alternative and Artificial Diets for Bivalve Aquaculture.pdf:C\:\\Users\\Owner\\Zotero\\storage\\HM3US9RH\\A Review of the Nutritional Requirements of Bivalves and the Development of Alternative and Artificial Diets for Bivalve Aquaculture.pdf:application/pdf;Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\DIQ4UJKF\\Knauer and Southgate - 1999 - A Review of the Nutritional Requirements of Bivalv.pdf:application/pdf}, } @inproceedings{bodoy_mass_1990, title = {Mass mortalities of oysters ({Crassostrea} gigas) during spring 1988 in the {Bay} of {Marennes}-{Oleron}, related to environmental conditions}, url = {https://archimer.ifremer.fr/doc/00000/3030/}, abstract = {Mass mortalities of oysters were recorded in the South of the Bay of Marennes-Oleron, during spring 1988. The percentages of mortality averaged 50 \% and reached up to 90 \% in some areas of bottom culture. The losses were estimated to 7 800 tonnes. This paper present the results of the investigations carried out in several fields. Among them, pathological examination revealed that no pathogenic agent or parasitic infestation could be evoked to explain these mortalities. Analyses of pollutants were either negatives, or the concentrations were far below the toxicity levels. Climatological and hydrological observations showed that rainfalls were twice more abundant then the average, for a period of 6 months preceding the mortalities. The salinity was low and fluctuating in the area, and the temperature was warmer, then the average during the same period. Phytoplanktonic blooms were recorded only by the end of May, latter then usual. These ecological changes resulted in a poor physiological condition of the oysters, which became critical for the grounds located at the South of the bay. Both their high tidal position and low quantities of phytoplankton are characteristic of this area. The high densities of oysters in the parks were also evoked as contributing to the establishment of such critical conditions.}, language = {en}, urldate = {2024-02-21}, author = {Bodoy, Alain and Garnier, Jacqueline and Razet, Daniel and Geairon, Philippe}, month = oct, year = {1990}, keywords = {experimental design, Pacific oyster, unread, Crassostrea gigas, feeding stress}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\EHMLK5QY\\Bodoy et al. - 1990 - Mass mortalities of oysters (Crassostrea gigas) du.pdf:application/pdf}, } @article{pernet_spatial_2014, title = {Spatial and {Temporal} {Dynamics} of {Mass} {Mortalities} in {Oysters} {Is} {Influenced} by {Energetic} {Reserves} and {Food} {Quality}}, volume = {9}, issn = {1932-6203}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088469}, doi = {10.1371/journal.pone.0088469}, abstract = {Although spatial studies of diseases on land have a long history, far fewer have been made on aquatic diseases. Here, we present the first large-scale, high-resolution spatial and temporal representation of a mass mortality phenomenon cause by the Ostreid herpesvirus (OsHV-1) that has affected oysters (Crassostrea gigas) every year since 2008, in relation to their energetic reserves and the quality of their food. Disease mortality was investigated in healthy oysters deployed at 106 locations in the Thau Mediterranean lagoon before the start of the epizootic in spring 2011. We found that disease mortality of oysters showed strong spatial dependence clearly reflecting the epizootic process of local transmission. Disease initiated inside oyster farms spread rapidly beyond these areas. Local differences in energetic condition of oysters, partly driven by variation in food quality, played a significant role in the spatial and temporal dynamics of disease mortality. In particular, the relative contribution of diatoms to the diet of oysters was positively correlated with their energetic reserves, which in turn decreased the risk of disease mortality.}, language = {en}, number = {2}, urldate = {2024-02-21}, journal = {PLOS ONE}, author = {Pernet, Fabrice and Lagarde, Franck and Jeannée, Nicolas and Daigle, Gaetan and Barret, Jean and Gall, Patrik Le and Quere, Claudie and D’orbcastel, Emmanuelle Roque}, month = feb, year = {2014}, note = {Publisher: Public Library of Science}, keywords = {experimental design, Pacific oyster, unread, Crassostrea gigas, Oysters, feeding stress, Bivalves, Carbohydrates, Death rates, Food, Lagoons, Ocean temperature, Oyster farming}, pages = {e88469}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\V6K5M8HW\\Pernet et al. - 2014 - Spatial and Temporal Dynamics of Mass Mortalities .pdf:application/pdf}, } @article{vaquer_feeding_2000, title = {Feeding rate of the oyster {Crassostrea} gigas in a natural planktonic community of the {Mediterranean} {Thau} {Lagoon}}, volume = {205}, issn = {0171-8630, 1616-1599}, url = {https://www.int-res.com/abstracts/meps/v205/p171-184/}, doi = {10.3354/meps205171}, abstract = {The Mediterranean Thau Lagoon is an important oyster farming area in Europe. Oyster growth rates are among the highest in France, although chlorophyll a concentration is low. Previous studies have demonstrated that picophytoplankton, nano-microphytoplankton, dinoflagellates and loricate ciliates such as tintinnids are abundant. However, heterotrophic flagellates and aloricate ciliates have not been investigated. The aim of this study was to assess picophytoplankton, protist and zooplankton abundances in the Lagoon and to investigate the particular structure of the microbial food web, which may explain such paradoxical oyster growth. In oligotrophic waters in the Thau Lagoon, the picoeukaryote Ostreococcus tauri is the dominant autotrophic picoplankter, with an abundance maximum in summer. On 17 August 1998, following a rainfall event, pico- and nanophytoplankton abundances were not as high as expected and we observed a high abundance of large diatoms. At this time, the available carbon resources were produced by microphytoplankton (84.5{\textbackslash}\#000), and picoplanktonic cells represented only 1.27{\textbackslash}\#000 in terms of carbon. Heterotrophic cells were low in abundance and constituted {\textless}14{\textbackslash}\#000 of carbon resources. In order to evaluate the importance of the Œprotozoan trophic link¹ for energy transfer from the microbial food web to large benthic suspension feeders, the oyster Crassostrea gigas was offered a planktonic community as potential prey. In the grazing experiment, all {\textgreater}5 µm flagellates, microphytoplankton, dinoflagellates, ciliates and large zooplankton were retained by the oyster gills. Only flagellates {\textless}5 µm and O. tauri were not very well retained (45 and 2{\textbackslash}\#000 respectively). The high clearance rates of C. gigas found in this experiment can be explained by a low concentration of suspended particulate matter (0.65 mg l-1). The oysters adapted their retention mechanism when they lived in oligotrophic waters. These results indicate that, under the given experimental conditions, picophytoplankton did not represent a valuable trophic resource for farmed oysters because (1) C. gigas cannot retain picoparticles and (2) the picoplankton represented a poor carbon resource capable of being transferred via a weak heterotrophic protist community. In the oyster pens of the Thau Lagoon during this study, microphytoplanktonic primary producers, in particular diatoms, were the main food sources for bivalve suspension feeders.}, language = {en}, urldate = {2024-02-21}, journal = {Marine Ecology Progress Series}, author = {Vaquer, Christine Dupuy André and Lam-Höai, Thong and Rougier, Claude and Mazouni, Nabila and Lautier, Jacques and Collos, Yves and Gall, Solange Le}, month = oct, year = {2000}, keywords = {experimental design, Bivalve, unread, Crassostrea gigas, Food source, Heterotrophic protist, Microbial food web, Oyster, Picophytoplankton, Thau Lagoon, Trophic link, Pacific oysters}, pages = {171--184}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\28ZCRCBD\\Vaquer et al. - 2000 - Feeding rate of the oyster Crassostrea gigas in a .pdf:application/pdf}, } @article{rico-villa_influence_2006, title = {Influence of phytoplankton diet mixtures on microalgae consumption, larval development and settlement of the {Pacific} oyster \textit{{Crassostrea} gigas} ({Thunberg})}, volume = {256}, issn = {0044-8486}, url = {https://www.sciencedirect.com/science/article/pii/S0044848606001165}, doi = {10.1016/j.aquaculture.2006.02.015}, abstract = {Microalgae commonly used as feed for bivalves, Pavlova lutheri (P), Isochrysis affinis galbana (T) and Chaetoceros calcitrans forma pumilum (Cp), were fed to Pacific oyster Crassostrea gigas to assess their nutritional value for larval development and metamorphosis during two experiments. Monospecific, bispecific and trispecific diets were firstly evaluated during 3weeks from D larvae to young postlarvae. Then bispecific diets, based on different T and Cp proportions, were assessed during a similar period. Concurrently, ingestion was studied through the whole larval and postlarval development for each diet and/or diet mixture. Because lipids are assumed to be a key nutrient for bivalves, biochemical analysis was undertaken on the second set of trials focused on fatty acids and sterols. Compared to the other diet mixtures (mono and plurispecific diet) TCp induced the best larval growth performance (13.2μm day−1), a high larval survival (98\%) but did not result in higher metamorphosis (72\%). In contrast, monospecific diet P was the poorest for larvae with low growth and low survival. When varying T and Cp proportions, best larval developments were induced with 25T/75Cp and 50T/50Cp diets, though quite similar to that obtained with 75T/25Cp. In contrast, unbalanced diets (95T/5Cp and 95Cp/5T) led to low larval performances. In addition, grazing experiences showed preferential uptake of microalgae with P{\textless}PT≪T≪Cp≪TCp=PCp=PTCp. For mixed diets a low daily consumption ({\textless}10000 microalgae per larvae) was noted during the first week followed by a second phase (next 8–10days) with a sharp increase and regular intake, reaching 90000 microalgae per larvae per day. Finally, a marked drop (40000 microalgae per larvae) was observed at the beginning of metamorphosis from days 20 to 21. Principal component analysis between main fatty acids (19) and sterols (7) detected in larvae and postlarvae was used to discriminate profiles according to diets and/or metamorphosis competence. The correlation circle representation showed that the 26 variables are well explained by these combined variables (78\%) with a repartition along the first principal component according to diets with a gradient from 5T/95Cp to 95T/5Cp. In contrast, postlarvae and larvae were discriminated on the second principal component while no relationships were found between competent and incompetent larvae.}, number = {1}, urldate = {2024-02-21}, journal = {Aquaculture}, author = {Rico-Villa, B. and Le Coz, J. R. and Mingant, C. and Robert, R.}, month = jun, year = {2006}, keywords = {experimental design, Pacific oyster, unread, Crassostrea gigas, Grazing, Growth, Larvae, Lipids, Metamorphosis, diet}, pages = {377--388}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\5LJ8U4TW\\Rico-Villa et al. - 2006 - Influence of phytoplankton diet mixtures on microa.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\SWABX6VB\\S0044848606001165.html:text/html}, } @article{azra_contributions_2021, title = {The {Contributions} of {Shellfish} {Aquaculture} to {Global} {Food} {Security}: {Assessing} {Its} {Characteristics} {From} a {Future} {Food} {Perspective}}, volume = {8}, issn = {2296-7745}, shorttitle = {The {Contributions} of {Shellfish} {Aquaculture} to {Global} {Food} {Security}}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2021.654897}, abstract = {The United Nation’s 2030 development agenda adopted in 2015 outlines 17 Sustainable Development Goals (SDGs), and the organization has continued to put food security in the center of its vocalization. Aquaculture is currently the fastest-growing food production sector globally and a sustainable option for attaining food security. Food as a basic necessity for man’s survival is always a timely issue. Hence, owing to aquaculture’s unique role, it is expected that the demand for aquatic products (especially seafood) will continue to increase due to geometric population growth. Many seafood products are among the critical protein sources in the world. This is partly because they have micronutrients and essential fatty acids that are not present in land-based protein sources. According to the Food and Agriculture Organization, shellfish is one of the main cultured aquaculture groups in the world. Hence, the development of shellfish aquaculture has an important role in sustainable food supply and food security. In this article, an overview of the current and projected contributions of shellfish aquaculture to global food security is presented. Apparently, shellfish aquaculture in the next few decades will have to be intensified to bridge the gap between demand and supply in a cost-effective manner. Also, food waste would have to be reduced and natural resources should be used more efficiently to minimize the negative impacts on aquaculture on the environment.}, urldate = {2024-02-29}, journal = {Frontiers in Marine Science}, author = {Azra, Mohamad Nor and Okomoda, Victor Tosin and Tabatabaei, Meisam and Hassan, Marina and Ikhwanuddin, Mhd}, year = {2021}, keywords = {oysters, food security}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\MI4AY376\\Azra et al. - 2021 - The Contributions of Shellfish Aquaculture to Glob.pdf:application/pdf}, } @article{botta_review_2020, title = {A review of global oyster aquaculture production and consumption}, volume = {117}, issn = {0308-597X}, url = {https://www.sciencedirect.com/science/article/pii/S0308597X19305433}, doi = {10.1016/j.marpol.2020.103952}, abstract = {Oyster farming is one of the oldest forms of aquaculture and oysters are farmed around the globe. As with aquaculture in general, oyster aquaculture production has increased rapidly in recent decades. Despite this, global trends in this production and its markets have received limited attention. This paper presents an overview of global oyster aquaculture production at a country-scale, as well as factors influencing the observed trends. Currently, global oyster aquaculture production is dominated by China, who accounted for 86\% of global production by weight in 2016. Beyond China, production is stagnant, and is limited by disease, parasites, and regulatory issues, depending on the country. There appears to be increasing demand for farmed oysters that producers are not able to exploit due to the supply side issues that have limited total production. Additionally, a test for market integration found that there is no global market. Hence, while the increasing prices in some markets provides an opportunity, this is exploited only to a limited extent with Canadian exports to the United States as the best example.}, urldate = {2024-03-01}, journal = {Marine Policy}, author = {Botta, Robert and Asche, Frank and Borsum, J. Scott and Camp, Edward V.}, month = jul, year = {2020}, keywords = {oysters, unread, review, Aquaculture, aquaculture, Oyster, Market, Production}, pages = {103952}, file = {Botta et al. - 2020 - A review of global oyster aquaculture production a.pdf:C\:\\Users\\Owner\\Zotero\\storage\\V28KLGJM\\Botta et al. - 2020 - A review of global oyster aquaculture production a.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\KE5EY5BL\\S0308597X19305433.html:text/html}, } @article{petton_pacific_2021, title = {The {Pacific} {Oyster} {Mortality} {Syndrome}, a {Polymicrobial} and {Multifactorial} {Disease}: {State} of {Knowledge} and {Future} {Directions}}, volume = {12}, issn = {1664-3224}, shorttitle = {The {Pacific} {Oyster} {Mortality} {Syndrome}, a {Polymicrobial} and {Multifactorial} {Disease}}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.630343}, abstract = {The Pacific oyster (Crassostreae gigas) has been introduced from Asia to numerous countries around the world during the 20th century. C. gigas is the main oyster species farmed worldwide and represents more than 98\% of oyster production. The severity of disease outbreaks that affect C. gigas, which primarily impact juvenile oysters, has increased dramatically since 2008. The most prevalent disease, Pacific oyster mortality syndrome (POMS), has become panzootic and represents a threat to the oyster industry. Recently, major steps towards understanding POMS have been achieved through integrative molecular approaches. These studies demonstrated that infection by Ostreid herpesvirus type 1 µVar (OsHV-1 µvar) is the first critical step in the infectious process and leads to an immunocompromised state by altering hemocyte physiology. This is followed by dysbiosis of the microbiota, which leads to a secondary colonization by opportunistic bacterial pathogens, which in turn results in oyster death. Host and environmental factors (e.g. oyster genetics and age, temperature, food availability, and microbiota) have been shown to influence POMS permissiveness. However, we still do not understand the mechanisms by which these different factors control disease expression. The present review discusses current knowledge of this polymicrobial and multifactorial disease process and explores the research avenues that must be investigated to fully elucidate the complexity of POMS. These discoveries will help in decision-making and will facilitate the development of tools and applied innovations for the sustainable and integrated management of oyster aquaculture.}, urldate = {2024-03-01}, journal = {Frontiers in Immunology}, author = {Petton, Bruno and Destoumieux-Garzón, Delphine and Pernet, Fabrice and Toulza, Eve and de Lorgeril, Julien and Degremont, Lionel and Mitta, Guillaume}, year = {2021}, keywords = {Pacific oyster, unread, Crassostrea gigas, review, summer mortality}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\5UJBAZIK\\Petton et al. - 2021 - The Pacific Oyster Mortality Syndrome, a Polymicro.pdf:application/pdf}, } @incollection{de_voogt_climate_2019, address = {Cham}, title = {Climate {Change} and {Bivalve} {Mass} {Mortality} in {Temperate} {Regions}}, volume = {251}, isbn = {978-3-030-27148-0 978-3-030-27149-7}, url = {http://link.springer.com/10.1007/398_2019_31}, language = {en}, urldate = {2024-03-01}, booktitle = {Reviews of {Environmental} {Contamination} and {Toxicology} {Volume} 251}, publisher = {Springer International Publishing}, author = {Soon, Tan Kar and Zheng, Huaiping}, editor = {De Voogt, Pim}, year = {2019}, doi = {10.1007/398_2019_31}, note = {Series Title: Reviews of Environmental Contamination and Toxicology}, keywords = {oysters, unread, review, summer mortslity}, pages = {109--129}, file = {Soon and Zheng - 2019 - Climate Change and Bivalve Mass Mortality in Tempe.pdf:C\:\\Users\\Owner\\Zotero\\storage\\SLDBDJSW\\Soon and Zheng - 2019 - Climate Change and Bivalve Mass Mortality in Tempe.pdf:application/pdf}, } @article{zhang_metabolomic_2023, title = {Metabolomic analysis provides new insights into the heat-hardening response of {Manila} clam (\textit{{Ruditapes} philippinarum}) to high temperature stress}, volume = {857}, issn = {0048-9697}, url = {https://www.sciencedirect.com/science/article/pii/S0048969722065299}, doi = {10.1016/j.scitotenv.2022.159430}, abstract = {The temperature has always been a key environmental factor in Manila clam (Ruditapes philippinarum) culture. In this study, the Manila clam was treated to different temperature pre-heat (28 °C, 30 °C) and gained heat tolerance after recover of 12 h, and a survival rate (14.7 \%–49.1 \%) advantage after high temperature challenge (30 and 32 °C). To further investigate the physiological and metabolism changes in Manila clam that had experienced a heat stress, non-targeted metabolomics (LC-MS/MS) was used to analyze the metabolic responses of gills in three group Manila clams during the heat challenge. Metabolic profiles revealed that high temperature caused changes in fatty acid composition, energy metabolism, antioxidant metabolites, hydroxyl compounds, and amino acids in heat-hardened clams compared to non-hardened clams. We found a number of significantly enriched pathways, including cAMP signaling pathway, serotonergic synapse, and biosynthesis of unsaturated fatty acids in heat-hardened Manila clam compared with non-hardened and untreated Manila clam. After a brief high temperature treatment, the physiological maintenance ability of Manila clam was improved. Combined with metabolomics analysis, heat hardening treatment may improve the energy metabolism and antioxidant ability of Manila clam. These results provide new insights into the cellular and metabolic responses of Manila clams following high temperature stress.}, urldate = {2024-03-04}, journal = {Science of The Total Environment}, author = {Zhang, Yanming and Nie, Hongtao and Yan, Xiwu}, month = jan, year = {2023}, keywords = {Heat stress, Heat-hardening, KEGG, Manila clam, Metabolomic analysis, bivalve, clams, hardening, priming}, pages = {159430}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\9G4NJPKV\\S0048969722065299.html:text/html;Zhang et al. - 2023 - Metabolomic analysis provides new insights into th.pdf:C\:\\Users\\Owner\\Zotero\\storage\\68U4KI6S\\Zhang et al. - 2023 - Metabolomic analysis provides new insights into th.pdf:application/pdf}, } @phdthesis{shukla_resisting_2023, address = {United States -- California}, type = {Ph.{D}.}, title = {Resisting {Global} {Change}: {Oyster} {Aquaculture} and {Disease} in an {Era} of {Marine} {Heatwaves}}, copyright = {Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.}, shorttitle = {Resisting {Global} {Change}}, url = {https://www.proquest.com/docview/2866287372/abstract/EBD70E28DEFC40CDPQ/1}, abstract = {Climate change is expected to increase heatwaves (MHWs) and disease transmission, potentially incurring losses of aquaculture stocks. Ostreid herpesvirus (OsHV-1) is a temperature-associated pathogen that predominantly affects the commercially important Pacific Oyster (Magallana gigas) and other species around the world, with some µVars causing {\textgreater} 95\% mortality of oyster stocks. Over the course of three studies, we explored the utility of stress hardening (SH) in ameliorating the effects of MHWs (Chapter 1) and disease outbreaks (Chapter 2) by exposing multiple oyster species to a stressor before the onset of an event as well as a comprehensive overview of OsHV-1 detections in different locations and hosts (Chapter 3). In Chapter 1, we exposed juvenile Olympia oysters (Ostrea lurida), Kumamoto oysters (Crassostrea sikamea), and M. gigas to a two-week-long SH phase that involved exposure to a combination of temperature (15˚C v. 21˚C) and tide (immersion v. 6-hour tidal cycle) prior to a 72-hour simulated MHW at one of four temperatures (15˚C, 18˚C, 21˚C, 24˚C). Once the MHWs ended, a portion of O. lurida seed were grouped by their SH treatments, outplanted in Tomales Bay, CA, USA, and then assessed for mortality after nine months. Outplanted O. lurida that experienced tidal SH had perished by the time they were retrieved 279 days later. In contrast, 53.4\% of O. lurida fully immersed during SH at 21˚C survived outplanting, while only 13.3\% of those in the 15˚C SH treatment remained. Less than 10\% of oysters across all species perished during the SH and MHW phases of the experiment, with C. sikamea experiencing the greatest losses. For Chapter 2, we investigated the effects of laboratory-based stress hardening (SH) via temperature (15˚C/16˚C v. 21˚C) and tide (tidal cycle vs. full submersion) on M. gigas and C. sikamea with the expectation that short-term exposure to warmer conditions and a simulated tidal regime would improve the performance of outplanted oysters. In 2021 and 2022, we exposed oysters to SH mechanisms before outplanting oysters at three sites spanning a thermal gradient in Tomales Bay, where they were exposed to OsHV-1 outbreaks in the field. We compared these outcomes to a baseline study completed in 2020, where M. gigas that had not been conditioned were exposed to OsHV-1 at two sites. M. gigas submerged in the warmer SH treatment had lower mortality in 2021, and those that experienced tidal fluctuations during SH had higher growth rates in 2022. In 2021, we saw no effect of SH on C. sikamea growth or mortality, but oysters were infected with OsHV-1. To our knowledge, this is the first study to provide OsHV-1 copy numbers (mg tissue-1) for C. sikamea. In Chapter 3, we used peer-reviewed literature, government reports, and unpublished data to describe the timeline of OsHV-1 variant detections, countries where M. gigas has tested positive, and other known hosts. We also summarized mean prevalence and peak infection intensity when that information was provided in the studies we assessed. Overall, SH has the potential to improve the resilience of aquaculture impacted by MHWs and disease, but it, along with the database of OsHV-1 detections we collated here, will likely be best used as part of an array of solutions addressing the multifaceted effects of climate change.}, language = {English}, urldate = {2024-03-06}, school = {University of California, Davis}, author = {Shukla, Priya}, year = {2023}, note = {ISBN: 9798380364881}, keywords = {unread, Crassostrea gigas, Ostreid herpesvirus, Aquaculture, Oysters, priming, Marine heatwaves, Stress Hardening}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\EX5K2GQS\\Shukla - 2023 - Resisting Global Change Oyster Aquaculture and Di.pdf:application/pdf}, } @misc{noauthor_26-year_nodate, title = {A 26-year time series of mortality and growth of the {Pacific} oyster {C}. gigas recorded along {French} coasts {\textbar} {Scientific} {Data}}, url = {https://www.nature.com/articles/s41597-022-01511-2}, urldate = {2024-03-07}, file = {A 26-year time series of mortality and growth of the Pacific oyster C. gigas recorded along French coasts | Scientific Data:C\:\\Users\\Owner\\Zotero\\storage\\KTPM7NTB\\s41597-022-01511-2.html:text/html}, } @article{hackerott_coral_2021, title = {Coral environmental memory: causes, mechanisms, and consequences for future reefs}, volume = {36}, issn = {0169-5347}, shorttitle = {Coral environmental memory}, url = {https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(21)00187-7}, doi = {10.1016/j.tree.2021.06.014}, language = {English}, number = {11}, urldate = {2024-03-13}, journal = {Trends in Ecology \& Evolution}, author = {Hackerott, Serena and Martell, Harmony A. and Eirin-Lopez, Jose M.}, month = nov, year = {2021}, pmid = {34366170}, note = {Publisher: Elsevier}, keywords = {coral resilience, phenotypic plasticity, coral, hardening, priming, environmental epigenetics, reef conservation, stress hardening, transcriptional memory, memory}, pages = {1011--1023}, file = {Hackerott et al. - 2021 - Coral environmental memory causes, mechanisms, an.pdf:C\:\\Users\\Owner\\Zotero\\storage\\73IZ55CR\\Hackerott et al. - 2021 - Coral environmental memory causes, mechanisms, an.pdf:application/pdf}, } @incollection{wijsman_global_2019, address = {Cham}, title = {Global {Production} of {Marine} {Bivalves}. {Trends} and {Challenges}}, isbn = {978-3-319-96776-9}, url = {https://doi.org/10.1007/978-3-319-96776-9_2}, abstract = {The global production of marine bivalves for human consumption is more than 15 million tonnes per year (average period 2010–2015), which is about 14\% of the total marine production in the world. Most of the marine bivalve production (89\%) comes from aquaculture and only 11\% comes from the wild fishery. Asia, especially China, is by far the largest producer of marine bivalves, accounting for 85\% of the world production and responsible for the production growth. In other continents, the production is stabilizing or decreasing (Europe) the last decades. In order to stimulate growth, sustainability (Planet, Profit, People) of the aquaculture activities is a key issue. Environmental (Planet) aspects for sustainable aquaculture include the fishery on seed resources, carrying capacity, invasive species and organic loading. Food safety issues due to environmental contaminants and biotoxines should be minimized to increase the reliability of marine bivalves as a healthy food source and to stimulate market demands. Properly designed monitoring programs are important tools to accomplish sustainable growth of marine bivalve production.}, language = {en}, urldate = {2024-03-13}, booktitle = {Goods and {Services} of {Marine} {Bivalves}}, publisher = {Springer International Publishing}, author = {Wijsman, J. W. M. and Troost, K. and Fang, J. and Roncarati, A.}, editor = {Smaal, Aad C. and Ferreira, Joao G. and Grant, Jon and Petersen, Jens K. and Strand, Øivind}, year = {2019}, doi = {10.1007/978-3-319-96776-9_2}, keywords = {Mussels, oysters, unread, review, Oysters, bivalves, Bivalves, China, Europe, Stock assessment, Sustainability, 双壳贝类 · 牡蛎 · 贻贝 · 中国 · 欧洲 · 资源评估 ·可持续性}, pages = {7--26}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\CS2YBUKW\\Wijsman et al. - 2019 - Global Production of Marine Bivalves. Trends and C.pdf:application/pdf}, } @article{kimmerer_braiding_nodate, title = {Braiding {Sweetgrass}}, language = {en}, author = {Kimmerer, Robin}, keywords = {DEI}, file = {Kimmerer - Braiding Sweetgrass.pdf:C\:\\Users\\Owner\\Zotero\\storage\\G88BXRKB\\Kimmerer - Braiding Sweetgrass.pdf:application/pdf}, } @misc{venkataraman_dna_2024, title = {{DNA} methylation modulates transcriptional noise in response to elevated {pCO} $_{\textrm{2}}$ in the eastern oyster ( \textit{{Crassostrea} virginica} )}, url = {http://biorxiv.org/lookup/doi/10.1101/2024.04.04.588108}, doi = {10.1101/2024.04.04.588108}, abstract = {Ocean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms that contribute to adaptive plasticity in response to environmental change like DNA methylation. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. To this end, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica. After a 30-day exposure to control (572 ppm) or elevated pCO2 (2,827 ppm), whole genome bisulfite sequencing (WGBS) and RNA-Seq data were generated from adult female gonad and male sperm samples. Although differentially methylated loci (DML) were identified in female (89) and male (2,916) gonad tissues, there were no differentially expressed genes, and only one differentially expressed transcript in females. However, gene body methylation impacted other transcript-level processes in sperm, such as the maximum number of transcripts expressed per gene and shifts in the predominant transcript. Elevated pCO2 exposure increased gene expression variability (transcriptional noise) in males but decreased noise in females, suggesting a sex-specific role of methylation in gene expression regulation. Functional annotation of genes with changes in transcript-level expression or containing DML revealed several enriched biological processes potentially involved in elevated pCO2 response, including apoptotic pathways and signal transduction, as well as reproductive functions. Taken together, these results suggest that DNA methylation may regulate gene expression variability to maintain homeostasis in elevated pCO2 conditions and could play a key role in environmental resilience in marine invertebrates.}, language = {en}, urldate = {2024-05-23}, author = {Venkataraman, Yaamini R. and Huffmyer, Ariana S. and White, Samuel J. and Downey-Wall, Alan and Ashey, Jill and Becker, Danielle M. and Bengtsson, Zachary and Putnam, Hollie M. and Strand, Emma and Rodríguez-Casariego, Javier A. and Wanamaker, Shelly A. and Lotterhos, Kathleen E. and Roberts, Steven B.}, month = apr, year = {2024}, keywords = {unread}, file = {Venkataraman et al. - 2024 - DNA methylation modulates transcriptional noise in.pdf:C\:\\Users\\Owner\\Zotero\\storage\\PM9Z5TUB\\Venkataraman et al. - 2024 - DNA methylation modulates transcriptional noise in.pdf:application/pdf}, } @article{obrien_overview_2018, title = {Overview of {MicroRNA} {Biogenesis}, {Mechanisms} of {Actions}, and {Circulation}}, volume = {9}, issn = {1664-2392}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085463/}, doi = {10.3389/fendo.2018.00402}, abstract = {MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in regulating gene expression. The majority of miRNAs are transcribed from DNA sequences into primary miRNAs and processed into precursor miRNAs, and finally mature miRNAs. In most cases, miRNAs interact with the 3′ untranslated region (3′ UTR) of target mRNAs to induce mRNA degradation and translational repression. However, interaction of miRNAs with other regions, including the 5′ UTR, coding sequence, and gene promoters, have also been reported. Under certain conditions, miRNAs can also activate translation or regulate transcription. The interaction of miRNAs with their target genes is dynamic and dependent on many factors, such as subcellular location of miRNAs, the abundancy of miRNAs and target mRNAs, and the affinity of miRNA-mRNA interactions. miRNAs can be secreted into extracellular fluids and transported to target cells via vesicles, such as exosomes, or by binding to proteins, including Argonautes. Extracellular miRNAs function as chemical messengers to mediate cell-cell communication. In this review, we provide an update on canonical and non-canonical miRNA biogenesis pathways and various mechanisms underlying miRNA-mediated gene regulations. We also summarize the current knowledge of the dynamics of miRNA action and of the secretion, transfer, and uptake of extracellular miRNAs.}, urldate = {2024-06-04}, journal = {Frontiers in Endocrinology}, author = {O'Brien, Jacob and Hayder, Heyam and Zayed, Yara and Peng, Chun}, month = aug, year = {2018}, pmid = {30123182}, pmcid = {PMC6085463}, keywords = {ncRNA, miRNA}, pages = {402}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\3X2Z7G7V\\O'Brien et al. - 2018 - Overview of MicroRNA Biogenesis, Mechanisms of Act.pdf:application/pdf}, } @article{tomari_microrna_2005, title = {{MicroRNA} {Biogenesis}: {Drosha} {Can}'t {Cut} {It} without a {Partner}}, volume = {15}, issn = {0960-9822}, shorttitle = {{MicroRNA} {Biogenesis}}, url = {https://www.sciencedirect.com/science/article/pii/S0960982204010401}, doi = {10.1016/j.cub.2004.12.057}, abstract = {The ribonuclease Drosha requires a dedicated double-stranded RNA binding protein to convert long, nuclear primary microRNA transcripts into shorter pre-microRNA stem–loops, the cytoplasmic precursors from which mature microRNAs are ultimately excised.}, number = {2}, urldate = {2024-06-04}, journal = {Current Biology}, author = {Tomari, Yukihide and Zamore, Phillip D.}, month = jan, year = {2005}, keywords = {unread, ncRNA, miRNA}, pages = {R61--R64}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\I5R8PTWA\\Tomari and Zamore - 2005 - MicroRNA Biogenesis Drosha Can't Cut It without a.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\MNJYT7SL\\S0960982204010401.html:text/html}, } @article{jagadeeswaran_deep_2010, title = {Deep sequencing of small {RNA} libraries reveals dynamic regulation of conserved and novel {microRNAs} and {microRNA}-stars during silkworm development}, volume = {11}, issn = {1471-2164}, url = {https://doi.org/10.1186/1471-2164-11-52}, doi = {10.1186/1471-2164-11-52}, abstract = {In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm (Bombyx mori L.) is one of the most suitable lepidopteran insects for studying the molecular aspects of metamorphosis because of its large size, availability of mutants and genome sequence. Besides, this insect also has been amply studied from a physiological and biochemical perspective. Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs.}, language = {en}, number = {1}, urldate = {2024-06-12}, journal = {BMC Genomics}, author = {Jagadeeswaran, Guru and Zheng, Yun and Sumathipala, Niranji and Jiang, Haobo and Arrese, Estela L. and Soulages, Jose L. and Zhang, Weixiong and Sunkar, Ramanjulu}, month = jan, year = {2010}, keywords = {miRNA, Juvenile Hormone, miRNA Family, Pupal Stage, Silk Gland, Small RNAs, mature miRNA, miRNA*}, pages = {52}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\5B55ZFXT\\Jagadeeswaran et al. - 2010 - Deep sequencing of small RNA libraries reveals dyn.pdf:application/pdf}, } @article{mattick_long_2023, title = {Long non-coding {RNAs}: definitions, functions, challenges and recommendations}, volume = {24}, copyright = {2023 Springer Nature Limited}, issn = {1471-0080}, shorttitle = {Long non-coding {RNAs}}, url = {https://www.nature.com/articles/s41580-022-00566-8}, doi = {10.1038/s41580-022-00566-8}, abstract = {Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term ‘lncRNAs’ encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.}, language = {en}, number = {6}, urldate = {2024-06-14}, journal = {Nature Reviews Molecular Cell Biology}, author = {Mattick, John S. and Amaral, Paulo P. and Carninci, Piero and Carpenter, Susan and Chang, Howard Y. and Chen, Ling-Ling and Chen, Runsheng and Dean, Caroline and Dinger, Marcel E. and Fitzgerald, Katherine A. and Gingeras, Thomas R. and Guttman, Mitchell and Hirose, Tetsuro and Huarte, Maite and Johnson, Rory and Kanduri, Chandrasekhar and Kapranov, Philipp and Lawrence, Jeanne B. and Lee, Jeannie T. and Mendell, Joshua T. and Mercer, Timothy R. and Moore, Kathryn J. and Nakagawa, Shinichi and Rinn, John L. and Spector, David L. and Ulitsky, Igor and Wan, Yue and Wilusz, Jeremy E. and Wu, Mian}, month = jun, year = {2023}, note = {Publisher: Nature Publishing Group}, keywords = {lncRNA, Transcriptomics, Long non-coding RNAs}, pages = {430--447}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\3ALYWV9M\\Mattick et al. - 2023 - Long non-coding RNAs definitions, functions, chal.pdf:application/pdf}, } @article{chillon_molecular_2020, title = {The molecular structure of long non-coding {RNAs}: emerging patterns and functional implications}, volume = {55}, issn = {1040-9238}, shorttitle = {The molecular structure of long non-coding {RNAs}}, url = {https://www.tandfonline.com/doi/full/10.1080/10409238.2020.1828259}, doi = {10.1080/10409238.2020.1828259}, number = {6}, urldate = {2024-06-14}, journal = {Critical Reviews in Biochemistry and Molecular Biology}, author = {Chillón, Isabel and Marcia, Marco}, month = nov, year = {2020}, note = {Publisher: Taylor \& Francis}, keywords = {lncRNA, kissing loops, pseudoknots, right-turns, RNA chemical probing, RNA evolution, RNA protein interactions, RNA secondary and tertiary structure, RNA triple helix, structural biology}, pages = {662--690}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\Z9GVJPGX\\Chillón and Marcia - 2020 - The molecular structure of long non-coding RNAs e.pdf:application/pdf}, } @article{li_small_2022, title = {Small {RNAs} in {Cnidaria}: {A} review}, volume = {16}, issn = {1752-4571}, shorttitle = {Small {RNAs} in {Cnidaria}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9923473/}, doi = {10.1111/eva.13445}, abstract = {As fundamental components of RNA silencing, small RNA (sRNA) molecules ranging from 20 to 32 nucleotides in length have been found as potent regulators of gene expression and genome stability in many biological processes of eukaryotes. Three major small RNAs are active in animals, including the microRNA (miRNA), short interfering RNA (siRNA), and PIWI‐interacting RNA (piRNA). Cnidarians, the sister group to bilaterians, are at a critical phylogenetic node to better model eukaryotic small RNA pathway evolution. To date, most of our understanding of sRNA regulation and its potential contribution to evolution has been limited to a few triploblastic bilaterian and plant models. The diploblastic nonbilaterians, including the cnidarians, are understudied in this regard. Therefore, this review will present the current‐known small RNA information in cnidarians to enhance our understanding of the development of the small RNA pathways in early branch animals.}, number = {2}, urldate = {2024-06-14}, journal = {Evolutionary Applications}, author = {Li, Yiqian and Hui, Jerome H. L.}, month = jul, year = {2022}, pmid = {36793685}, pmcid = {PMC9923473}, keywords = {Cnidaria, miRNA, corals, sncRNA}, pages = {354--364}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\D6FBHGRZ\\Li and Hui - 2022 - Small RNAs in Cnidaria A review.pdf:application/pdf}, } @article{moran_cnidarian_2014-1, title = {Cnidarian {microRNAs} frequently regulate targets by cleavage}, volume = {24}, issn = {1088-9051}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975064/}, doi = {10.1101/gr.162503.113}, abstract = {In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA “seed”) to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.}, number = {4}, urldate = {2024-06-14}, journal = {Genome Research}, author = {Moran, Yehu and Fredman, David and Praher, Daniela and Li, Xin Z. and Wee, Liang Meng and Rentzsch, Fabian and Zamore, Phillip D. and Technau, Ulrich and Seitz, Hervé}, month = apr, year = {2014}, pmid = {24642861}, pmcid = {PMC3975064}, keywords = {Cnidaria, miRNA, corals}, pages = {651--663}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\4R2KVIMR\\Moran et al. - 2014 - Cnidarian microRNAs frequently regulate targets by.pdf:application/pdf}, } @article{houssin_abnormal_2019, title = {Abnormal mortality of triploid adult {Pacific} oysters: {Is} there a correlation with high gametogenesis in {Normandy}, {France}?}, volume = {505}, issn = {0044-8486}, shorttitle = {Abnormal mortality of triploid adult {Pacific} oysters}, url = {https://www.sciencedirect.com/science/article/pii/S0044848618320015}, doi = {10.1016/j.aquaculture.2019.02.043}, abstract = {Summer mortalities of the adult Pacific oysters Crassostrea gigas are an important economic concern. In 2015 and 2016, the mortality of hatchery origin spat comprising 4 diploid batches and 9 triploid batches as well as 12 batches of wild caught diploids was followed at 3 sites in Normandy. Abnormal mortalities ({\textgreater}20\%) were observed at one site only and were significantly higher in triploid animals (P {\textless} .05). Triploid oysters are believed to be partially sterile but a high level of gametogenesis was observed in all monitored triploid batches. In 2015, preliminary results revealed that triploid oysters underwent strong gametogenesis with mature gametes (stage 3) and 50\% of them were non-perturbed (i.e. named alpha). In 2016, 42\% of triploid oysters were alpha. This study revealed that triploid oyster maturation occurred in September, which corresponded to the time of high mortalities in Normandy.}, urldate = {2024-06-14}, journal = {Aquaculture}, author = {Houssin, Maryline and Trancart, Suzanne and Denechere, Lucie and Oden, Elise and Adeline, Beatrice and Lepoitevin, Mélanie and Pitel, Pierre-Hugues}, month = apr, year = {2019}, keywords = {Crassostrea gigas, triploid mortality, Gametogenesis, Mortality, ploidy, Pacific oysters, Triploid, gametogenisis}, pages = {63--71}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\7ULUUBU3\\Houssin et al. - 2019 - Abnormal mortality of triploid adult Pacific oyste.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\DM5ZBZMT\\S0044848618320015.html:text/html}, } @article{bodenstein_energetic_2023, title = {Energetic budget of diploid and triploid eastern oysters during a summer die-off}, volume = {10}, issn = {2296-7745}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2023.1194296}, doi = {10.3389/fmars.2023.1194296}, abstract = {Triploid oysters are widely used in off-bottom aquaculture of eastern oysters, Crassostrea virginica. However, farmers of the Gulf of Mexico (GoM) and Atlantic coast estuaries have observed unresolved, late-spring die-offs of triploid oysters, threatening the sustainability of triploid aquaculture. To investigate this, the physiological processes underlying oyster growth (e.g., feeding, respiration) and mortality of one-year-old diploid and triploid oysters were compared in early summer following an uptick in mortality. It was predicted that higher triploid mortality was the result of energetic imbalances (increased metabolic demands and decreased feeding behavior). Oyster clearance rates, percentage of time valves were open, absorption efficiency, oxygen consumption rates (basal and routine), ammonia excretion rate were measured in the laboratory and scope for growth was calculated. In addition, their condition index, gametogenic stage, Perkinsus marinus infection intensity, and mortality were measured. Mortality of triploids in the laboratory was greater than for diploids, mirroring mortality observed in a related field study. The physiological parameters measured, however, could not explain triploid mortality. Scope for growth, condition index, and clearance rates of triploids were greater than for diploids, suggesting sufficient energy reserves, while all other measurements where similar between the ploidies. It remains to be determined whether mortality could be caused from disruption of energy homeostasis at the cellular level.}, language = {English}, urldate = {2024-06-14}, journal = {Frontiers in Marine Science}, author = {Bodenstein, Sarah and Casas, Sandra M. and Tiersch, Terrence R. and La Peyre, Jerome F.}, month = may, year = {2023}, note = {Publisher: Frontiers}, keywords = {oysters, Physiology, triploid mortality, Crassostrea virginica, ploidy, Cohorts, Dermo, Scope for Growth, Summer mortality, Eastern oysters, energetics}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YKLHN856\\Bodenstein et al. - 2023 - Energetic budget of diploid and triploid eastern o.pdf:application/pdf}, } @mastersthesis{ritter_fecundity_2019, address = {United States -- Virginia}, title = {Fecundity of {Triploid} {Eastern} {Oyster} ({Crassostrea} virginica) as a {Function} of {Tetraploid} {Lineage}}, copyright = {Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.}, url = {https://www.proquest.com/docview/2315224070/abstract/7F98BEECF54C4CC3PQ/1}, abstract = {Rapid growth rate and partial sterility have made triploid eastern oysters (Crassostrea virginica) the most popular crop variety for the Virginia oyster aquaculture industry, typically comprising greater than 90\% of larvae and juvenile sales. Triploid advantages, however, sometimes come with the disadvantage of higher mortality in late spring and early summer, dubbed “triploid mortality.” In recent years, farms up and down the East Coast, especially Maryland and south into the Gulf of Mexico have experienced triploid mortality. Some of the reports include observations of elevated triploid fecundity. Triploid oysters are created by crossing tetraploids to diploids, and much of the commercial broodstock is acquired through the Virginia Institute of Marine Science Aquaculture Genetics and Breeding Technology Center (ABC). Tetraploid oysters are created from fecund triploid females and propagated favoring the most fertile tetraploids. We hypothesized that heritable fertility may be transferred to the commercial product, possibly yielding fertile triploid oysters. To investigate this possibility, twelve half-sibling families were produced by crossing individual tetraploid males with aliquots from a pooled source of eggs from diploid females. Tetraploid males came from tetraploid lines bred for one, two, five, or eight generations. Two replicates of each family were deployed to two sites: a site known for episodes of triploid mortality on the Eastern Shore of Chesapeake Bay, and at a control site in the Rappahannock River. Temperature and salinity exhibited typical patterns at both sites while oysters were raised to market size. When compared to the control site, cumulative mortality of triploid oysters at the Eastern Shore location was significantly higher, with significantly lower growth rate and fecundity; the latter measured by direct egg counts at peak ripeness. Diploid oysters performed similarly at both sites and exhibited significantly greater fecundity than triploids. Fecundity differed significantly among several triploid families based upon paternal lineage, but fecundity did not vary as a function of tetraploid lineage.}, language = {English}, urldate = {2024-06-14}, school = {The College of William and Mary}, author = {Ritter, Kate M.}, year = {2019}, note = {ISBN: 9781088396308}, keywords = {oysters, triploid mortality, triploidy, Gametogenesis, Crassostrea virginica, Aquaculture, Oyster, Eastern oysters, Fecundity, Triploid mortality, fecundity, reproduction}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\GGAX4DVZ\\Ritter - 2019 - Fecundity of Triploid Eastern Oyster (Crassostrea .pdf:application/pdf}, } @article{sokolova_energy-limited_2013, title = {Energy-{Limited} {Tolerance} to {Stress} as a {Conceptual} {Framework} to {Integrate} the {Effects} of {Multiple} {Stressors}}, volume = {53}, issn = {1540-7063}, url = {https://doi.org/10.1093/icb/ict028}, doi = {10.1093/icb/ict028}, abstract = {Integrating the effects of multiple stressors and predicting their consequences for the species’ survival and distribution is an important problem in ecological physiology. This review applies the concept of energy-limited tolerance to stress to develop bioenergetic markers that can assist in integrating the effects of multiple stressors and distinguishing between the moderate stress compatible with long-term survival of populations and bioenergetically unsustainable extreme stress. These markers reflect the progressive decline of the aerobic scope of an organism (defined as the fraction of the energy flux and metabolic power supporting this flux available after the basal maintenance costs of an organism are met) with increasing levels of the environmental stress. During the exposure to moderate stress (i.e., in the pejus range of the environmental conditions), the aerobic scope is positive but reduced compared with the optimum conditions. The reduction of the metabolic scope can be due to the (1) elevated costs of basal metabolism, (2) activation of the mechanisms for protection and damage repair, (3) reduced assimilation of food, and/or (4) stress-induced impacts on the aerobic pathways producing ATP. This leads to suboptimal growth and reproductive rates in the pejus range of environmental conditions and is commonly observed in food-limited and energy-limited wild populations. The tolerance windows of the organisms are delimited by the pessimum range(s) of environmental conditions in which the aerobic scope of the organism disappears (so that all available energy and metabolic capacity are used in support of basal metabolism), energy resources are depleted, and partial anaerobiosis and/or metabolic rate depression set in. The habitats where environmental conditions remain in the pessimum zone long enough to prevent consistent growth and reproduction often coincide with the species’ distributional limits. Thus, focus on the bioenergetic effects of environmental stressors and their immediate consequences for fitness provides a suitable framework for integrating physiology and functional ecology and can assist in understanding the driving forces and limitations of environmental adaptation and improving assessment of ecological risk as well as environmental management in field populations facing multiple stressors.}, number = {4}, urldate = {2024-06-18}, journal = {Integrative and Comparative Biology}, author = {Sokolova, Inna M.}, month = oct, year = {2013}, keywords = {energetics}, pages = {597--608}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\HKSQHH8I\\Sokolova - 2013 - Energy-Limited Tolerance to Stress as a Conceptual.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\TTDFWTPZ\\632460.html:text/html}, } @article{sokolova_energy_2012, title = {Energy homeostasis as an integrative tool for assessing limits of environmental stress tolerance in aquatic invertebrates}, volume = {79}, issn = {0141-1136}, url = {https://www.sciencedirect.com/science/article/pii/S0141113612000712}, doi = {10.1016/j.marenvres.2012.04.003}, abstract = {Energy balance is a fundamental requirement of stress adaptation and tolerance. We explore the links between metabolism, energy balance and stress tolerance using aquatic invertebrates as an example and demonstrate that using key parameters of energy balance (aerobic scope for growth, reproduction and activity; tissue energy status; metabolic rate depression; and compensatory onset of anaerobiosis) can assist in integrating the effects of multiple stressors and their interactions and in predicting the whole-organism and population-level consequences of environmental stress. We argue that limitations of both the amount of available energy and the rates of its acquisition and metabolic conversions result in trade-offs between basal maintenance of a stressed organism and energy costs of fitness-related functions such as reproduction, development and growth and can set limit to the tolerance of a broad range of environmental stressors. The degree of stress-induced disturbance of energy balance delineates transition from moderate stress compatible with population persistence (pejus range) to extreme stress where only time-limited existence is possible (pessimum range). It also determines the predominant adaptive strategy of metabolic responses (energy compensation vs. conservation) that allows an organism to survive the disturbance. We propose that energy-related biomarkers can be used to determine the conditions when these metabolic transitions occur and thus predict ecological consequences of stress exposures. Bioenergetic considerations can also provide common denominator for integrating stress responses and predicting tolerance limits under the environmentally realistic scenarios when multiple and often variable stressors act simultaneously on an organism. Determination of bioenergetic sustainability at the organism's level (or lack thereof) has practical implications. It can help identify the habitats and/or conditions where a population can survive (even if at the cost of reduced reproduction and growth) and those that are incapable of supporting viable populations. Such an approach will assist in explaining and predicting the species' distribution limits in the face of the environmental change and informing the conservation efforts and resource management practices.}, urldate = {2024-06-18}, journal = {Marine Environmental Research}, author = {Sokolova, Inna M. and Frederich, Markus and Bagwe, Rita and Lannig, Gisela and Sukhotin, Alexey A.}, month = aug, year = {2012}, keywords = {Aerobic scope, Bioenergetics, energetics, Energy metabolism, Marine invertebrates, Metabolic markers, Multiple stressors, Stress tolerance}, pages = {1--15}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\2C7UVYEZ\\S0141113612000712.html:text/html;Sokolova et al. - 2012 - Energy homeostasis as an integrative tool for asse.pdf:C\:\\Users\\Owner\\Zotero\\storage\\3J6B3YT5\\Sokolova et al. - 2012 - Energy homeostasis as an integrative tool for asse.pdf:application/pdf}, } @article{marshall_developmental_2020, title = {Developmental cost theory predicts thermal environment and vulnerability to global warming}, volume = {4}, copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited}, issn = {2397-334X}, url = {https://www.nature.com/articles/s41559-020-1114-9}, doi = {10.1038/s41559-020-1114-9}, abstract = {Metazoans must develop from zygotes to feeding organisms. In doing so, developing offspring consume up to 60\% of the energy provided by their parent. The cost of development depends on two rates: metabolic rate, which determines the rate that energy is used; and developmental rate, which determines the length of the developmental period. Both development and metabolism are highly temperature-dependent such that developmental costs should be sensitive to the local thermal environment. Here, we develop, parameterize and test developmental cost theory, a physiologically explicit theory that reveals that ectotherms have narrow thermal windows in which developmental costs are minimized (Topt). Our developmental cost theory-derived estimates of Topt predict the natural thermal environment of 71 species across seven phyla remarkably well (R2 {\textasciitilde}0.83). Developmental cost theory predicts that costs of development are much more sensitive to small changes in temperature than classic measures such as survival. Warming-driven changes to developmental costs are predicted to strongly affect population replenishment and developmental cost theory provides a mechanistic foundation for determining which species are most at risk. Developmental cost theory predicts that tropical aquatic species and most non-nesting terrestrial species are likely to incur the greatest increase in developmental costs from future warming.}, language = {en}, number = {3}, urldate = {2024-06-18}, journal = {Nature Ecology \& Evolution}, author = {Marshall, Dustin J. and Pettersen, Amanda K. and Bode, Michael and White, Craig R.}, month = mar, year = {2020}, note = {Publisher: Nature Publishing Group}, keywords = {Biogeography, energetics, Evolutionary developmental biology, Evolutionary theory, Population dynamics, Theoretical ecology}, pages = {406--411}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\Q6C8XTL5\\Marshall et al. - 2020 - Developmental cost theory predicts thermal environ.pdf:application/pdf}, } @article{breese_hatchery_1975, title = {Hatchery {Manual} for the {Pacific} {Oyster}}, volume = {Agricultural Experiment Station}, url = {https://ir.library.oregonstate.edu/downloads/db78td066}, language = {en}, number = {443}, journal = {Oregon State University Sea Grant College Program}, author = {Breese, Wilbur P and Malouf, Robert E}, month = dec, year = {1975}, file = {Breese and Malouf - Hatchery Manual for the Pacific Oyster.pdf:C\:\\Users\\Owner\\Zotero\\storage\\N5HXUQFS\\Breese and Malouf - Hatchery Manual for the Pacific Oyster.pdf:application/pdf}, } @article{breese1975, title = {Hatchery Manual for the Pacific Oyster}, author = {Breese, Wilbur P and Malouf, Robert E}, year = {1975}, month = {12}, date = {1975-12}, journal = {Oregon State University Sea Grant College Program}, volume = {Agricultural Experiment Station}, number = {443}, url = {https://ir.library.oregonstate.edu/downloads/db78td066}, langid = {en} } @article{ubertini_gametogenesis_2017, title = {Gametogenesis, spawning behavior and larval abundance of the {Pacific} oyster \textit{{Crassostrea} gigas} in the {Thau} lagoon: {Evidence} of an environment-dependent strategy}, volume = {473}, issn = {0044-8486}, shorttitle = {Gametogenesis, spawning behavior and larval abundance of the {Pacific} oyster \textit{{Crassostrea} gigas} in the {Thau} lagoon}, url = {https://www.sciencedirect.com/science/article/pii/S0044848617301618}, doi = {10.1016/j.aquaculture.2017.01.025}, abstract = {The Thau lagoon, located at the South of France, provides 10\% of the French pacific oyster Crassostrea gigas production. Despite this intensive shellfish production, the larval recruitment of this species within the Thau lagoon is still misunderstood and spat collection remains highly variable; as a consequence, shellfish farmers rely mostly on hatchery”s spat. The present study aimed to describe reproduction features of C. gigas within the Mediterranean, as well as to explore spawning triggers of this species. To achieve this goal, the reproduction cycle from gametogenesis to spawning was followed during two years in several locations within the Mediterranean Thau lagoon. The spawning behavior of C. gigas within the Thau lagoon appeared to be slightly different from the one of the Atlantic Coast, showing several spawning events from June to October. The minimal temperature for massive spawning was 23°C, which is much higher than temperatures mentioned in the literature for this species. A strong relationship was found between phytoplankton communities and gametogenesis, the latter being improved by a higher diatom/dinoflagellate ratio. Temperature was insufficient alone to explain spawning, highlighting other potential triggers such as the moon or lightning strikes. We made the hypothesis of a hierarchy of events triggering spawning, encompassing locking, synchrony and intensifying triggers. Statement of relevance This paper is filling in a gap in the literature regarding to reproduction of C. gigas in the Thau lagoon, which is always associated to temperature. However, temperature may not be the only factor involved in oyster reproduction, that is what we tried to show in this paper.}, urldate = {2024-06-21}, journal = {Aquaculture}, author = {Ubertini, Martin and Lagarde, Franck and Mortreux, Serge and Le Gall, Patrik and Chiantella, Claude and Fiandrino, Annie and Bernard, Ismaël and Pouvreau, Stéphane and Roque d'Orbcastel, Emmanuelle}, month = apr, year = {2017}, keywords = {Crassostrea gigas, gametogenisis, Mollusc physiology, Oysters, Pacific oyster, reproduction, spawning, Spawning triggers}, pages = {51--61}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\7EJKQGAZ\\Ubertini et al. - 2017 - Gametogenesis, spawning behavior and larval abunda.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\DJGX3VPL\\S0044848617301618.html:text/html}, } @article{setiyawan_current_2020, title = {Current {Topics} in {Molluscan} {Aquaculture} {Proceedings} of {AFS} 581: {Current} {Topics} in {Molluscan} {Aquaculture}}, shorttitle = {Current {Topics} in {Molluscan} {Aquaculture} {Proceedings} of {AFS} 581}, abstract = {The Pacific oyster, Crassostrea gigas (Thunberg, 1975) a native to East Asia, has been introduced to many locations all around the world. Recently, the production of aquaculture oysters is the most massive if compared with other bivalves. High demand for the oyster brings researcher interest to develop the research about supply chain topic because that is an essential issue for food security among producer and consumer. The high survival rate for oysters is one consideration for the farmer to straight-line keep the mollusk to harvest in any condition, which is growing well in the warm temperature. The shell length market of the oyster is about 80 shell length mm with a high-quality product. Aquaculture is more reliable to develop the oyster than wild capture because easier to treat, control, and produce reliably to meet market demand. Pacific oyster is profitable and marketable for seafood consumption. Lastly, traceability research should develop in the future for the oyster to reduce the risk of seafood security, waste, and boost the market value of the high-quality product.}, author = {Setiyawan, Agus and Pleskun, Taras and Suganda, Diky}, month = may, year = {2020}, file = {Setiyawan et al. - 2020 - Current Topics in Molluscan Aquaculture Proceeding.pdf:C\:\\Users\\Owner\\Zotero\\storage\\6L88FHVA\\Setiyawan et al. - 2020 - Current Topics in Molluscan Aquaculture Proceeding.pdf:application/pdf}, } @article{muranaka_broodstock_1984, series = {Recent {Innovations} in {Cultivation} of {Pacific} {Molluscs}}, title = {Broodstock management of \textit{{Crassostrea} gigas}: {Environmental} influences on broodstock conditioning}, volume = {39}, issn = {0044-8486}, shorttitle = {Broodstock management of \textit{{Crassostrea} gigas}}, url = {https://www.sciencedirect.com/science/article/pii/0044848684902679}, doi = {10.1016/0044-8486(84)90267-9}, abstract = {Maximum larval survival is realized when broodstock are in an optimum stage of gonadal development and the efficiency of larval culture may be substantially improved by using only optimally conditioned broodstock. The conditioning requirement to bring broodstock into this optimum stage is dependent upon the stage of gonadal development at the commencement of conditioning and upon the rate of conditioning. The stage of gonadal development at the commencement of conditioning may be determined directly or inferred by understanding the annual cycle of gonadal development occurring in the broodstock. The rate of conditioning, on the other hand, is regulated by the conditioning environment. In the present study, we have observed the influence of three components of the conditioning environment: temperature, salinity, and supplemental feeding on the rate of gonadal development during hatchery conditioning of broodstock. The rate of gonadal development is a function of temperature intensity and time rather than accumulated thermal exposure. Salinity exerted a negative influence on the rate of development in oysters conditioned at salinity levels below 30 parts per thousand (ppt). Furthermore, when oysters conditioned at 20 ppt relative to 30 ppt were spawned and the larvae were reared under standardized hatchery conditions, larval survival was markedly reduced in the former. Fecundity of broodstock was 60\% greater when fed an algal food supplement of the diatom Thalassiosira pseudonana relative to starved controls, although the rate of gonadal development and gamete viability was not significantly different. Using these empirically determined functions, a simplistic quatitative model may be employed to predict broodstock conditioning requirements in order to increase the proportion of optimally conditioned brood oysters.}, number = {1}, urldate = {2024-06-21}, journal = {Aquaculture}, author = {Muranaka, Michael Shigeo and Lannan, James E.}, month = jun, year = {1984}, keywords = {Crassostrea gigas, gametogenisis, hatchery, Pacific oyster, spawning}, pages = {217--228}, file = {Muranaka and Lannan - 1984 - Broodstock management of Crassostrea gigas.pdf:C\:\\Users\\Owner\\Zotero\\storage\\CFUGNGFU\\Muranaka and Lannan - 1984 - Broodstock management of Crassostrea gigas.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\HT2ZMPNK\\0044848684902679.html:text/html}, } @article{chavez-villalba_broodstock_2002, title = {Broodstock conditioning of the oyster \textit{{Crassostrea} gigas}: origin and temperature effect}, volume = {214}, issn = {0044-8486}, shorttitle = {Broodstock conditioning of the oyster \textit{{Crassostrea} gigas}}, url = {https://www.sciencedirect.com/science/article/pii/S0044848601008985}, doi = {10.1016/S0044-8486(01)00898-5}, abstract = {Broodstock conditioning of the pacific oyster Crassostrea gigas (Thunberg) was examined in the laboratory under controlled conditions. Three experiments were undertaken to determine (i) the effect of the origin on gametogenesis, (ii) the time necessary to obtain the first mature oocytes in standard conditioning procedures, and (iii) the impact of different conditioning temperatures (16, 19, 22 and 25 °C) on gametogenesis. Oocyte size was used to identify mature oocytes. Significant differences among populations were observed in the number of mature oocytes produced. Only the oysters from northern locations (Normandy and Brittany) reached the mature stage by the end of the standard conditioning. Concerning the effect of different temperatures during conditioning, the first mature oocytes were detected (absolute days) by the 27th day at 16 °C, 23rd day at 19 °C, 19th day at 22 °C and 22nd day at 25 °C. This information was applied to fit a logistic model to predict oocyte growth using temperature and time as main affecting parameters; D=Dmax/(1+ae−kt) with D—oocyte diameter at time t (μm), Dmax—the asymptotic oocyte diameter (μm), a—adjustment parameter, k—slope of the curve during growing stage and t—time (days). The model fit consistently with values achieved at 16, 19 and 22 °C. The results obtained during this study could be used to improve conditioning procedures for C. gigas.}, number = {1}, urldate = {2024-06-21}, journal = {Aquaculture}, author = {Chávez-Villalba, Jorge and Pommier, Julien and Andriamiseza, Jimmy and Pouvreau, Stéphane and Barret, Jean and Cochard, Jean-Claude and Le Pennec, Marcel}, month = nov, year = {2002}, keywords = {Conditioning, Crassostrea gigas, Gametogenesis, gametogenisis, Pacific oyster, spawning, Temperature}, pages = {115--130}, file = {Chávez-Villalba et al. - 2002 - Broodstock conditioning of the oyster Crassostr.pdf:C\:\\Users\\Owner\\Zotero\\storage\\9BRN9LC5\\Chávez-Villalba et al. - 2002 - Broodstock conditioning of the oyster Crassostr.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\MW469JUD\\S0044848601008985.html:text/html}, } @phdthesis{shukla2023, title = {Resisting Global Change: Oyster Aquaculture and Disease in an Era of Marine Heatwaves}, author = {Shukla, Priya}, year = {2023}, date = {2023}, url = {https://www.proquest.com/docview/2866287372/abstract/EBD70E28DEFC40CDPQ/1}, note = {ISBN: 9798380364881}, address = {United States -- California}, langid = {English} } @article{moyen_single_2020, title = {A single heat-stress bout induces rapid and prolonged heat acclimation in the {California} mussel, {Mytilus} californianus}, volume = {287}, issn = {0962-8452}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7739924/}, doi = {10.1098/rspb.2020.2561}, abstract = {Climate change is not only causing steady increases in average global temperatures but also increasing the frequency with which extreme heating events occur. These extreme events may be pivotal in determining the ability of organisms to persist in their current habitats. Thus, it is important to understand how quickly an organism's heat tolerance can be gained and lost relative to the frequency with which extreme heating events occur in the field. We show that the California mussel, Mytilus californianus—a sessile intertidal species that experiences extreme temperature fluctuations and cannot behaviourally thermoregulate—can quickly (in 24–48 h) acquire improved heat tolerance after exposure to a single sublethal heat-stress bout (2 h at 30 or 35°C) and then maintain this improved tolerance for up to three weeks without further exposure to elevated temperatures. This adaptive response improved survival rates by approximately 75\% under extreme heat-stress bouts (2 h at 40°C). To interpret these laboratory findings in an ecological context, we evaluated 4 years of mussel body temperatures recorded in the field. The majority (approx. 64\%) of consecutive heat-stress bouts were separated by 24–48 h, but several consecutive heat bouts were separated by as much as 22 days. Thus, the ability of M. californianus to maintain improved heat tolerance for up to three weeks after a single sublethal heat-stress bout significantly improves their probability of survival, as approximately 33\% of consecutive heat events are separated by 3–22 days. As a sessile animal, mussels likely evolved the capability to rapidly gain and slowly lose heat tolerance to survive the intermittent, and often unpredictable, heat events in the intertidal zone. This adaptive strategy will likely prove beneficial under the extreme heat events predicted with climate change.}, number = {1940}, urldate = {2024-06-21}, journal = {Proceedings of the Royal Society B: Biological Sciences}, author = {Moyen, Nicole E. and Crane, Rachel L. and Somero, George N. and Denny, Mark W.}, month = dec, year = {2020}, pmid = {33290677}, pmcid = {PMC7739924}, pages = {20202561}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\5N8TQZJV\\Moyen et al. - 2020 - A single heat-stress bout induces rapid and prolon.pdf:application/pdf}, } @article{scanes_acclimation_2023, title = {Acclimation in intertidal animals reduces potential pathogen load and increases survival following a heatwave}, volume = {26}, issn = {2589-0042}, url = {https://www.sciencedirect.com/science/article/pii/S2589004223008908}, doi = {10.1016/j.isci.2023.106813}, abstract = {Intertidal animals can experience intense heat during a heatwave, leading to mortality. The causes of death for intertidal animals following heatwaves have often been attributed to a breakdown in physiological processes. This, however, contrasts with research in other animals where heatwave mortality is attributed to existing or opportunistic diseases. We acclimated intertidal oysters to four treatment levels, including an antibiotic treatment, and then exposed all treatments to a 50°C heatwave for 2 h, replicating what can be experienced on Australian shorelines. We found that both acclimation and antibiotics increased survival and reduced the presence of potential pathogens. Non-acclimated oysters had a significant shift in their microbiome, with increasing abundances of bacteria from the Vibrio genera, including known potential pathogens. Our results demonstrate that bacterial infection plays a pivotal role in post-heatwave mortality. We anticipate these findings to inform the management of aquaculture and intertidal habitats as climate change intensifies.}, number = {6}, urldate = {2024-06-21}, journal = {iScience}, author = {Scanes, Elliot and Siboni, Nachshon and Rees, Brendon and Seymour, Justin R.}, month = jun, year = {2023}, keywords = {Biological sciences, Global change, Marine organism}, pages = {106813}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\FDQ4M99K\\Scanes et al. - 2023 - Acclimation in intertidal animals reduces potentia.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\DH9LQA4R\\S2589004223008908.html:text/html}, } @article{he_repeated_2021, title = {Repeated exposure to simulated marine heatwaves enhances the thermal tolerance in pearl oysters}, volume = {239}, issn = {0166-445X}, url = {https://www.sciencedirect.com/science/article/pii/S0166445X21002186}, doi = {10.1016/j.aquatox.2021.105959}, abstract = {In an era of unprecedented climate change, marine heatwaves (MHWs) are projected to increase in frequency, intensity, and duration, severely affecting marine organisms and fisheries and causing profound ecological and socioeconomic impacts. However, very little is known about effects of MHWs on ecologically and economically important bivalve species. Here, we investigate how pearl oysters, Pinctada maxima (Jameson), respond to MHWs under various simulated scenarios. Acute 3-day exposure to MHWs, mimicked by increasing the ambient seawater temperature from 24°C to 28°C, 32°C, and 36°C, respectively, induced significant changes (initially sustained increase and late decrease) in activities of antioxidant enzymes (GSH-Px, SOD, CAT, MDA, and T-AOC) and biomineralizaiton-related enzymes (AKP and ACP). Likewise, energy-metabolizing enzymes (NKA, CMA, and T-ATP) showed remarkable acute responses, with significant increases occurring at the beginning and end of thermal exposure. Following repeated exposure to MHWs, without exception, acute responses of assayed enzymes to MHWs were significantly alleviated, implying that pearl oysters have the ability to implement more efficient and less costly energy-utilizing strategies to compensate for thermal stress induced physiological interferences. These findings indicate that marine bivalves can respond plastically and acclimate rapidly to MHWs and pave the way for predicting the fate of this important taxonomic groups in rapidly changing oceans.}, urldate = {2024-06-21}, journal = {Aquatic Toxicology}, author = {He, Guixiang and Liu, Xiaolong and Xu, Yang and Liang, Jian and Deng, Yuewen and Zhang, Yuehuan and Zhao, Liqiang}, month = oct, year = {2021}, keywords = {Acclimation, Bioenergetics, Biomineralizaiton, Marine heatwaves, Physiology}, pages = {105959}, file = {He et al. - 2021 - Repeated exposure to simulated marine heatwaves en.pdf:C\:\\Users\\Owner\\Zotero\\storage\\BBVCY78A\\He et al. - 2021 - Repeated exposure to simulated marine heatwaves en.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\ERGQ7AZX\\S0166445X21002186.html:text/html}, } @article{giomi_importance_2016, title = {The importance of thermal history: costs and benefits of heat exposure in a tropical, rocky shore oyster}, volume = {219}, issn = {0022-0949}, shorttitle = {The importance of thermal history}, url = {https://doi.org/10.1242/jeb.128892}, doi = {10.1242/jeb.128892}, abstract = {Although thermal performance is widely recognised to be pivotal in determining species’ distributions, assessment of this performance is often based on laboratory-acclimated individuals, neglecting their proximate thermal history. The thermal history of a species sums the evolutionary history and, importantly, the thermal events recently experienced by individuals, including short-term acclimation to environmental variations. Thermal history is perhaps of greatest importance for species inhabiting thermally challenging environments and therefore assumed to be living close to their thermal limits, such as in the tropics. To test the importance of thermal history, the responses of the tropical oyster Isognomon nucleus to short-term differences in thermal environments were investigated. Critical and lethal temperatures and oxygen consumption were improved in oysters that previously experienced elevated air temperatures, and were associated with an enhanced heat shock response, indicating that recent thermal history affects physiological performance as well as inducing short-term acclimation to acute conditions. These responses were, however, associated with trade-offs in feeding activity, with oysters that experienced elevated temperatures showing reduced energy gain. Recent thermal history, therefore, seems to rapidly invoke physiological mechanisms that enhance survival of short-term thermal challenge but also longer term climatic changes and consequently needs to be incorporated into assessments of species’ thermal performances.}, number = {5}, urldate = {2024-06-21}, journal = {Journal of Experimental Biology}, author = {Giomi, Folco and Mandaglio, Concetta and Ganmanee, Monthon and Han, Guo-Dong and Dong, Yun-Wei and Williams, Gray A. and Sarà, Gianluca}, month = mar, year = {2016}, pages = {686--694}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\K6LHWPR9\\Giomi et al. - 2016 - The importance of thermal history costs and benef.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\3VRU2JGY\\The-importance-of-thermal-history-costs-and.html:text/html}, } @article{pereira_can_2020, title = {Can prior exposure to stress enhance resilience to ocean warming in two oyster species?}, volume = {15}, issn = {1932-6203}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228527}, doi = {10.1371/journal.pone.0228527}, abstract = {Securing economically and ecologically significant molluscs, as our oceans warm due to climate change, is a global priority. South eastern Australia receives warm water in a strengthening East Australia Current and so resident species are vulnerable to elevated temperature and marine heat waves. This study tested whether prior exposure to elevated temperature can enhance resilience of oysters to ocean warming. Two Australian species, the flat oyster, Ostrea angasi, and the Sydney rock oyster, Saccostrea glomerata, were obtained as adults and “heat shocked” by exposure to a dose of warm water in the laboratory. Oysters were then transferred to elevated seawater temperature conditions where the thermal outfall from power generation was used as a proxy to investigate the impacts of ocean warming. Shell growth, condition index, lipid content and survival of flat oysters and condition of Sydney rock oysters were all significantly reduced by elevated seawater temperature in the field. Flat oysters grew faster than Sydney rock oysters at ambient temperature, but their growth and survival was more sensitive to elevated temperature. “Stress inoculation” by heat shock did little to ameliorate the negative effects of increased temperature, although the survival of heat-shocked flat oysters was greater than non-heat shocked oysters. Further investigations are required to determine if early exposure to heat stress can enhance resilience of oysters to ocean warming.}, language = {en}, number = {4}, urldate = {2024-06-21}, journal = {PLOS ONE}, author = {Pereira, Roberta R. C. and Scanes, Elliot and Gibbs, Mitchell and Byrne, Maria and Ross, Pauline M.}, month = apr, year = {2020}, note = {Publisher: Public Library of Science}, keywords = {Heat shock response, Lipid profiles, Lipids, Ocean temperature, Oysters, Power stations, Sea water, Thermal stresses}, pages = {e0228527}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\TJNYUZJ7\\Pereira et al. - 2020 - Can prior exposure to stress enhance resilience to.pdf:application/pdf}, } @article{nancollas_influence_2022, title = {The influence of stochastic temperature fluctuations in shaping the physiological performance of the {California} mussel, {Mytilus} californianus}, volume = {225}, issn = {0022-0949}, url = {https://doi.org/10.1242/jeb.243729}, doi = {10.1242/jeb.243729}, abstract = {Climate change is forecasted to increase temperature variability and stochasticity. Most of our understanding of thermal physiology of intertidal organisms has come from laboratory experiments that acclimate organisms to submerged conditions and steady-state increases in temperatures. For organisms experiencing the ebb and flow of tides with unpredictable low tide aerial temperatures, the reliability of reported tolerances and thus predicted responses to climate change requires incorporation of environmental complexity into empirical studies. Using the mussel Mytilus californianus, our study examined how stochasticity of the thermal regime influences physiological performance. Mussels were acclimated to either submerged conditions or a tidal cycle that included either predictable, unpredictable or no thermal stress during daytime low tide. Physiological performance was measured through anaerobic metabolism, energy stores and cellular stress mechanisms just before low tide, and cardiac responses during a thermal ramp. Both air exposure and stochasticity of temperature change were important in determining thermal performance. Glycogen content was highest in the mussels from the unpredictable treatment, but there was no difference in the expression of heat shock proteins between thermal treatments, suggesting that mussels prioritise energy reserves to deal with unpredictable low tide conditions. Mussels exposed to fluctuating thermal regimes had lower gill anaerobic metabolism, which could reflect increased metabolic capacity. Our results suggest that although thermal magnitude plays an important role in shaping physiological performance, other key elements of the intertidal environment complexity such as stochasticity, thermal variability and thermal history are also important considerations for determining how species will respond to climate warming.}, number = {14}, urldate = {2024-06-21}, journal = {Journal of Experimental Biology}, author = {Nancollas, Sarah J. and Todgham, Anne E.}, month = jul, year = {2022}, pages = {jeb243729}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\27WT6XIU\\Nancollas and Todgham - 2022 - The influence of stochastic temperature fluctuatio.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\DN7P5CVV\\The-influence-of-stochastic-temperature.html:text/html}, } @article{oliver_marine_2021, title = {Marine {Heatwaves}}, volume = {13}, issn = {1941-1405, 1941-0611}, url = {https://www.annualreviews.org/content/journals/10.1146/annurev-marine-032720-095144}, doi = {10.1146/annurev-marine-032720-095144}, abstract = {Ocean temperature variability is a fundamental component of the Earth\'s climate system, and extremes in this variability affect the health of marine ecosystems around the world. The study of marine heatwaves has emerged as a rapidly growing field of research, given notable extreme warm-water events that have occurred against a background trend of global ocean warming. This review summarizes the latest physical and statistical understanding of marine heatwaves based on how they are identified, defined, characterized, and monitored through remotely sensed and in situ data sets. We describe the physical mechanisms that cause marine heatwaves, along with their global distribution, variability, and trends. Finally, we discuss current issues in this developing research area, including considerations related to thechoice of climatological baseline periods in defining extremes and how to communicate findings in the context of societal needs.}, language = {en}, number = {Volume 13, 2021}, urldate = {2024-06-21}, journal = {Annual Review of Marine Science}, author = {Oliver, Eric C. J. and Benthuysen, Jessica A. and Darmaraki, Sofia and Donat, Markus G. and Hobday, Alistair J. and Holbrook, Neil J. and Schlegel, Robert W. and Gupta, Alex Sen}, month = jan, year = {2021}, note = {Publisher: Annual Reviews}, pages = {313--342}, file = {Oliver et al. - 2021 - Marine Heatwaves.pdf:C\:\\Users\\Owner\\Zotero\\storage\\ZK6YTS2A\\Oliver et al. - 2021 - Marine Heatwaves.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\GRL2AGPP\\annurev-marine-032720-095144.html:text/html}, } @article{white_unprecedented_2023, title = {The unprecedented {Pacific} {Northwest} heatwave of {June} 2021}, volume = {14}, copyright = {2023 The Author(s)}, issn = {2041-1723}, url = {https://www.nature.com/articles/s41467-023-36289-3}, doi = {10.1038/s41467-023-36289-3}, abstract = {In late June 2021 a heatwave of unprecedented magnitude impacted the Pacific Northwest region of Canada and the United States. Many locations broke all-time maximum temperature records by more than 5 °C, and the Canadian national temperature record was broken by 4.6 °C, with a new record temperature of 49.6 °C. Here, we provide a comprehensive summary of this event and its impacts. Upstream diabatic heating played a key role in the magnitude of this anomaly. Weather forecasts provided advanced notice of the event, while sub-seasonal forecasts showed an increased likelihood of a heat extreme with lead times of 10-20 days. The impacts of this event were catastrophic, including hundreds of attributable deaths across the Pacific Northwest, mass-mortalities of marine life, reduced crop and fruit yields, river flooding from rapid snow and glacier melt, and a substantial increase in wildfires—the latter contributing to landslides in the months following. These impacts provide examples we can learn from and a vivid depiction of how climate change can be so devastating.}, language = {en}, number = {1}, urldate = {2024-06-21}, journal = {Nature Communications}, author = {White, Rachel H. and Anderson, Sam and Booth, James F. and Braich, Ginni and Draeger, Christina and Fei, Cuiyi and Harley, Christopher D. G. and Henderson, Sarah B. and Jakob, Matthias and Lau, Carie-Ann and Mareshet Admasu, Lualawi and Narinesingh, Veeshan and Rodell, Christopher and Roocroft, Eliott and Weinberger, Kate R. and West, Greg}, month = feb, year = {2023}, note = {Publisher: Nature Publishing Group}, keywords = {Climate sciences, Climate-change impacts, Natural hazards}, pages = {727}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\6U86BCVD\\White et al. - 2023 - The unprecedented Pacific Northwest heatwave of Ju.pdf:application/pdf}, } @article{chen_persistent_2021, title = {A {Persistent} and {Intense} {Marine} {Heatwave} in the {Northeast} {Pacific} {During} 2019–2020}, volume = {48}, copyright = {© 2021. American Geophysical Union. All Rights Reserved.}, issn = {1944-8007}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2021GL093239}, doi = {10.1029/2021GL093239}, abstract = {Motivated by increasing marine heatwaves (MHWs) and their dramatic climate effects, we analyze the persistent 2019–2020 MHW, which showed significant positive sea surface temperature (SST) anomalies in the Northeast Pacific. Four SST peaks were identified during its evolution, which appeared in November 2019, April, July, and November 2020. Positive temperature anomalies were mostly located within the mixed layer for the first-year winter peak. However, the warm core was centered around 50 m below (at the bottom of) the mixed layer for the summer (second-year winter) peak. The dominant factor for the two wintertime peaks was a surface heat flux anomaly, with reduction in evaporative cooling due to the easterly anomaly. The heat flux and potentially the vertical entrainment combined to induce the peak in spring. In the tropical Pacific, a La Niña event occurred following this MHW, while other recorded double-peak events were associated with El Niño or neutral conditions.}, language = {en}, number = {13}, urldate = {2024-06-21}, journal = {Geophysical Research Letters}, author = {Chen, Ziyan and Shi, Jian and Liu, Qinyu and Chen, Hui and Li, Chun}, year = {2021}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021GL093239}, keywords = {heat budget, heat flux, La Niña, mixed layer, surface winds, warm blob}, pages = {e2021GL093239}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\87PLGDEY\\Chen et al. - 2021 - A Persistent and Intense Marine Heatwave in the No.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\D5PMVGA6\\2021GL093239.html:text/html}, } @article{li_physiological_2022, title = {Physiological and gene expression responses of diploid and triploid {Pacific} oyster ( \textit{{Crassostrea} gigas} ) to heat acclimation}, volume = {53}, issn = {1355-557X, 1365-2109}, url = {https://onlinelibrary.wiley.com/doi/10.1111/are.16133}, doi = {10.1111/are.16133}, abstract = {High temperature is considered to be one of the important causes of mass mortality of diploid and triploid oysters in summer. In order to compare the tolerance adaptability of diploid and triploid oysters to heat stress, the activities of superoxide dismutase activity (SOD), catalase activity (CAT) and contents of malondialdehyde (MDA) and the expression of Hsp70 and metallothionein (MT) genes in diploid and triploid oysters under acute and chronic heat stress were studied. The results showed that the survival rate of diploid oysters was significantly higher than that of triploid oysters under acute and chronic heat stress (p {\textless} 0.05). Under acute heat stress, the SOD levels in gills of both diploid and triploid oysters increased significantly from hour 3 (p {\textless} 0.05), but there was no significant difference in SOD levels between diploid and triploid oysters at all time points. The SOD level in hepatopancreas of triploid oysters was significantly higher than that of diploid oysters at all time points except 48 h (p {\textless} 0.05). The CAT level of diploid and triploid oysters decreased sharply at 48 h and that of diploid oysters was significantly higher than that of triploid oysters (p {\textless} 0.05). Under acute heat stress, the increase in MDA content in triploid oysters was significantly higher than that in diploid oysters (p {\textless} 0.05). Under acute heat stress, the expression levels of Hsp70 in the gills and hepatopancreas were significantly increased in diploid and triploid oysters (p {\textless} 0.05), but increased varies between gills and hepatopancreas. The expression levels of MT in the gills and hepatopancreas were significantly decreased in diploid and triploid oysters (p {\textless} 0.05). The results obtained in this study provide physiological and immunological evidence to explain differences in high-­temperature tolerance between diploid and triploid oysters and help us better understand the mass mortality of oysters that occurs during high temperatures in summer.}, language = {en}, number = {18}, urldate = {2024-06-24}, journal = {Aquaculture Research}, author = {Li, Yongguo and Xu, Chengxun and Li, Qi}, month = dec, year = {2022}, keywords = {Crassostrea gigas, Pacific oyster, ploidy}, pages = {6641--6650}, file = {Li et al. - 2022 - Physiological and gene expression responses of dip.pdf:C\:\\Users\\Owner\\Zotero\\storage\\6GHIFCCK\\Li et al. - 2022 - Physiological and gene expression responses of dip.pdf:application/pdf}, } @article{haberkorn_effects_2010, title = {Effects of \textit{{Alexandrium} minutum} exposure upon physiological and hematological variables of diploid and triploid oysters, \textit{{Crassostrea} gigas}}, volume = {97}, issn = {0166-445X}, url = {https://www.sciencedirect.com/science/article/pii/S0166445X09004172}, doi = {10.1016/j.aquatox.2009.12.006}, abstract = {The effects of an artificial bloom of the toxin-producing dinoflagellate, Alexandrium minutum, upon physiological parameters of the Pacific oyster, Crassostrea gigas, were assessed. Diploid and triploid oysters were exposed to cultured A. minutum and compared to control diploid and triploid oysters fed T. Isochrysis. Experiments were repeated twice, in April and mid-May 2007, to investigate effects of maturation stage on oyster responses to A. minutum exposure. Oyster maturation stage, Paralytic Shellfish Toxin (PST) accumulation, as well as several digestive gland and hematological variables, were assessed at the ends of the exposures. In both experiments, triploid oysters accumulated more PSTs (approximately twice) than diploid oysters. Significant differences, in terms of phenoloxidase activity (PO) and reactive oxygen species (ROS) production of hemocytes, were observed between A. minutum-exposed and non-exposed oysters. PO in hemocytes was lower in oysters exposed to A. minutum than in control oysters in an early maturation stage (diploids and triploids in April experiment and triploids in May experiment), but this contrast was reversed in ripe oysters (diploids in May experiment). In the April experiment, granulocytes of oysters exposed to A. minutum produced more ROS than those of control oysters; however, in the May experiment, ROS production of granulocytes was lower in A. minutum-exposed oysters. Moreover, significant decreases in free fatty acid, monoacylglycerol, and diacylglycerol contents in digestive glands of oysters exposed to A. minutum were observed. Concurrently, the ratio of reserve lipids (triacylglycerol, ether glycerides and sterol esters) to structural lipids (sterols) decreased upon A. minutum exposure in both experiments. Also, several physiological responses to A. minutum exposure appeared to be modulated by maturation stage as well as ploidy of the oysters.}, number = {2}, urldate = {2024-06-24}, journal = {Aquatic Toxicology}, author = {Haberkorn, Hansy and Lambert, Christophe and Le Goïc, Nelly and Guéguen, Marielle and Moal, Jeanne and Palacios, Elena and Lassus, Patrick and Soudant, Philippe}, month = apr, year = {2010}, keywords = {Crassostrea gigas, Harmful-algal bloom, Oysters, Pacific oysters, Physiology, ploidy, Ploidy, PST accumulation, toxin}, pages = {96--108}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\GTMW8HCD\\Haberkorn et al. - 2010 - Effects of Alexandrium minutum exposure upo.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\K48J7ARU\\S0166445X09004172.html:text/html}, } @article{jouaux_impact_2013, title = {Impact of energy storage strategies on gametogenesis and reproductive effort in diploid and triploid {Pacific} oysters \textit{{Crassostrea} gigas —} {Involvement} of insulin signaling}, volume = {388-391}, issn = {0044-8486}, url = {https://www.sciencedirect.com/science/article/pii/S0044848613000136}, doi = {10.1016/j.aquaculture.2013.01.009}, abstract = {Gametogenesis of the Pacific oyster Crassostrea gigas follows an annual cycle. In this work, we used contrasting dietary conditions (fed and unfed) for a preconditioning treatment in order to impact glycogen storage supporting reproductive pathways in diploid and triploid animals before a broodstock conditioning treatment. In diploid oysters, food deprivation during preconditioning led to reduced gonia proliferation as demonstrated by lower PCNA (Proliferating Cell Nuclear Antigen) expression and subsequently, the reproductive effort was significantly reduced. For triploid animals exhibiting arrested gametogenesis, dietary conditions impacted the ratio of α (animals with unlocked gametogenesis) and β (animals with locked gametogenesis). Thermal stress applied to these conditioned animals confirmed the weakness of diploid animals with high stored reserves and intense reproductive effort, versus low reproductive effort. Moreover, only low mortalities were observed for triploid animals whatever the reproductive status. The involvement of the insulin pathway in the regulation of gametogenesis and storage rebuilding was assessed by measuring an increased expression of CIR (C. gigas insulin related receptor) in unfed oysters.}, urldate = {2024-06-24}, journal = {Aquaculture}, author = {Jouaux, A. and Blin, J. L. and Adeline, B. and Heude-Berthelin, C. and Sourdaine, P. and Mathieu, M. and Kellner, K.}, month = apr, year = {2013}, keywords = {Crassostrea gigas, diet, Diploid, Gametogenesis, gametogenisis, glycogen, Insulin-like, Pacific oyster, Storage metabolism, Triploid}, pages = {173--181}, file = {Jouaux et al. - 2013 - Impact of energy storage strategies on gametogenes.pdf:C\:\\Users\\Owner\\Zotero\\storage\\EDA6N3YB\\Jouaux et al. - 2013 - Impact of energy storage strategies on gametogenes.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\WSBBSQN4\\S0044848613000136.html:text/html}, } @article{goulletquer_peformances_1995, title = {Peformances de croissance d'huîtres cresuses triploïdes {Crassostrea} gigas ({Thunberg}) élevées dans un système à capacité trophique élevée : taux de survie, croissance et composition biochimique}, volume = {25}, shorttitle = {Peformances de croissance d'huîtres cresuses triploïdes {Crassostrea} gigas ({Thunberg}) élevées dans un système à capacité trophique élevée}, url = {https://archimer.ifremer.fr/doc/00000/3088/}, abstract = {triploid oysters crassllstrea gigas were: produced in 1990 by treating fertilized eggs with cytochalasin b (cs). triploids, treated diploids, and controls were deployed early 1991 in a high carrying capacity ecosystem on the eastern coast of normandy (france). a monthly monitoring in 1992 showed that triploids yielded significantly higher growth rate and biochemical composition. however, growth was more heterogeneous. no evidence was found for a length or weight bimodal frequency distribution within triploid groups after a 26 months rearing cycle. triploids showed retardation of gametogenesis. carbohydrates content in triploids remained almost constant (40\%) from june to september. their survival rates were significantly lower than controls. moreover treated diploids were found more sensitive to environmental conditions than controls, demonstrating long term cs effect on oysters. therefore, the method of induction should be improved to maximize triploidy and long term survival rates. we recommend further field testings to assess triploid response to stressfui environmental conditions, particularly 10 low carrying capacity ecosystems.}, language = {en}, urldate = {2024-06-24}, journal = {Haliotis}, author = {Goulletquer, Philippe and Joly, Jean-Pierre and Gerard, Andre and Le Gagneur, Eric and Moriceau, Jacques and Peignon, Jean-Marie and Heurtebise, Serge and Phelipot, Pascal and Gerard, Andre and Le Gagneur, Eric and Moriceau, Jacques and Peignon, Jean-Marie and Heurtebise, Serge and Phelipot, Pascal}, month = dec, year = {1995}, note = {Publisher: Société Française de Malacololgie}, keywords = {Crassostrea gigas, Pacific oyster, ploidy}, pages = {1--12}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\H6789S5L\\Goulletquer et al. - 1995 - Peformances de croissance d'huîtres cresuses tripl.pdf:application/pdf}, } @article{allen_performance_1986, title = {Performance of triploid {Pacific} oysters, \textit{{Crassostrea} gigas} ({Thunberg}). {I}. {Survival}, growth, glycogen content, and sexual maturation in yearlings}, volume = {102}, issn = {0022-0981}, url = {https://www.sciencedirect.com/science/article/pii/0022098186901760}, doi = {10.1016/0022-0981(86)90176-0}, abstract = {Triploid Pacific oysters (Crassostrea gigas Thunberg) were produced by treating newly fertilized eggs with cytochalasin B. Triploid and diploid spat were planted in the field and, 1 yr later, sampled during the reproductive period. As measured by cross-sectional area, triploid males produced half as much and triploid females a quarter as much gonad as diploids. Reduced gonadogenesis affected growth and glycogen utilization. Triploids grew linearly through the period of reproduction, whereas diploids grew little until spawning when weight decreased by 64\%; growth of diploids and triploids was parallel subsequently. Diploids showed a typical pattern of glycogen utilization, reaching a low of 4.8\% glycogen as dry weight prior to spawning and increasing thereafter. Glycogen levels in triploids also declined, but at a slower rate; glycogen in triploids continued to decline for 2 months after the diploid nadir. Triploids had higher survival rates than diploids, but this is probably not a consequence of reduced sexual maturation. Partial reproductive sterility observed in triploid oysters greatly affects reproductive physiology. Triploidy may be a valuable tool in studies of physiological energetics to partition somatic and reproductive effort.}, number = {2}, urldate = {2024-06-24}, journal = {Journal of Experimental Marine Biology and Ecology}, author = {Allen, Standish K. and Downing, Sandra L.}, month = nov, year = {1986}, keywords = {Crassostrea gigas, Gametogenesis, Genetics, glycogen, Glycogen, Growth, Pacific oyster, Pacific oysters, Physiological energetics, physiology, triploid, Triploidy}, pages = {197--208}, file = {Allen and Downing - 1986 - Performance of triploid Pacific oysters, Crasso.pdf:C\:\\Users\\Owner\\Zotero\\storage\\4E68USYY\\Allen and Downing - 1986 - Performance of triploid Pacific oysters, Crasso.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\J24WSQN4\\0022098186901760.html:text/html}, } @article{wadsworth_meta-analysis_2019, title = {A meta-analysis of growth rate in diploid and triploid oysters}, volume = {499}, issn = {0044-8486}, url = {https://www.sciencedirect.com/science/article/pii/S0044848618300978}, doi = {10.1016/j.aquaculture.2018.09.018}, abstract = {Around 34 years ago, the first reports on the performance of triploid oysters were published. Since then, triploid oysters have offered many benefits to the oyster industry, such as faster growth, improved meat quality, partial sterility, and increased survival due to disease resistance. However, the extent of a triploid growth advantage, in particular, can vary across studies, measurement parameters, environmental conditions and husbandry practices. To quantitatively compare diploid and triploid oyster growth rates, a meta-analysis was performed with 29 published studies using triploid oysters produced by chemical induction or by crossing diploid and tetraploid oysters (i.e., “mated triploids”). The difference in growth rate between ploidy was evaluated using natural log transformed response ratios (ln[3n/2n]) in a random-effects model weighted by sample size. The positive response ratios in 126 of the 148 independent experiments showed a significant growth advantage of the triploid over the diploid. On average, mated triploids grew 20\% faster than diploids in shell height and 49\% faster in whole wet weight. While chemically induced triploids had marginally less growth advantage than mated triploids, growing on average 8\% faster than diploids in shell height and 31\% faster in whole wet weight. Response ratios for experiments using mated triploids and measuring whole wet weight was significantly affected by species and length of study, while response ratios for experiments using chemically induced triploids and measuring whole wet weight was significantly affected by initial size at deployment. Conversely, response ratios for experiments using mated triploids or chemically induced triploids and measuring shell height were not affected by any tested moderator. The lack of a triploid growth advantage in 15\% of the experiments (22/148) could have been influenced by a variety of factors including intraspecific variation, differences in sampling, husbandry practices, and environmental conditions.}, urldate = {2024-06-24}, journal = {Aquaculture}, author = {Wadsworth, Pandora and Wilson, Alan E. and Walton, William C.}, month = jan, year = {2019}, keywords = {Crassostrea gigas, Pacific oyster, ploidy}, pages = {9--16}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\8IFC4MI4\\S0044848618300978.html:text/html;Wadsworth et al. - 2019 - A meta-analysis of growth rate in diploid and trip.pdf:C\:\\Users\\Owner\\Zotero\\storage\\F2NVHH3G\\Wadsworth et al. - 2019 - A meta-analysis of growth rate in diploid and trip.pdf:application/pdf}, } @article{hawkins_genetic_1994, title = {A genetic and metabolic basis for faster growth among triploids induced by blocking meiosis {I} but not meiosis {II} in the larviparous {European} flat oyster, \textit{{Ostrea} edulis} {L}.}, volume = {184}, issn = {0022-0981}, url = {https://www.sciencedirect.com/science/article/pii/0022098194901643}, doi = {10.1016/0022-0981(94)90164-3}, abstract = {This study establishes a genetic and metabolic basis to faster triploid growth in the oyster Ostrea edulis. Triploidy was induced using cytochalasin B, and image analysis of biopsied tissue employed to ensure similar ploidy of all animals within each class. Results indicate that lifetime growth in total dry tissue weight over 15 months was more than 60\% faster (p{\textless}0.001) in meiosis I triploids than in diploid siblings or meiosis II triploids, with no difference between meiosis II triploids and their diploid siblings. For six polymorphic enzyme loci, single-locus heterozygosity was consistently greatest in meiosis I triploids (p{\textless}0.001), so that average multiple-locus heterozygosity in meiosis I triploids was 49\% higher than in normal diploids, and 55\% higher than in meiosis II triploids (p{\textless}0.001). This suggests that faster growth resulted from increased allelic diversity, rather than the increased allelic quantity that results from the addition of one entire set of chromosomes among triploids generally. Results also confirm that the faster growth of meiosis I triploids resulted from reduced energy expenditure, associated with lower concentrations of RNA per unit total tissue protein, which infer reduced rates of whole-body protein turnover. Statistical analyses confirmed that differences in oxygen consumption and growth were associated with both ploidy class and average multiple-locus heterozygosity, indicating that performance in meiosis I triploids is not only improved as a result of reduced reproductive output, but also through the metabolic consequences associated with increased heterozygosity.}, number = {1}, urldate = {2024-06-24}, journal = {Journal of Experimental Marine Biology and Ecology}, author = {Hawkins, A. J. S. and Day, A. J. and Gérard, A. and Naciri, Y. and Ledu, C. and Bayne, B. L. and Héral, M.}, month = nov, year = {1994}, keywords = {Growth, Heterozygosity, Meiosis I triploid, Meiosis II triploid, RNA/ protein ratio}, pages = {21--40}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\MF5U4QGB\\0022098194901643.html:text/html}, } @article{yang_transcriptional_2017, title = {The transcriptional response of the {Pacific} oyster \textit{{Crassostrea} gigas} against acute heat stress}, volume = {68}, issn = {1050-4648}, url = {https://www.sciencedirect.com/science/article/pii/S1050464817304096}, doi = {10.1016/j.fsi.2017.07.016}, abstract = {The Pacific oyster, Crassostrea gigas, has evolved sophisticated mechanisms to adapt the changing ambient conditions, and protect themselves from stress-induced injuries. In the present study, the expression profiles of mRNA transcripts in the haemocytes of oysters under heat stress were examined to reveal the possible mechanism of heat stress response. There were 23,315, 23,904, 23,123 and 23,672 transcripts identified in the haemocytes of oysters cultured at 25 °C for 0, 6, 12, and 24 h (designed as B, H6, H12, H24), respectively. And 22,330 differentially expressed transcripts (DTs) were yielded in the pairwise comparisons between the above four samples, which corresponded to 8074 genes. There were 9, 12 and 22 Gene Ontology (GO) terms identified in the DT pairwise comparison groups of H6\_B, H12\_H6 and H24\_H12, respectively, and the richest GO terms in biological process category were cellular catabolic process, translational initiation and apoptotic process, respectively. There were 108, 102 and 102 KEGG pathways successfully retrieved from DTs comparison groups DTH6\_B, DTH12\_H6 and DTH24\_H12, respectively, among which 93 pathways were shared by all three comparison groups, and most of them were related to metabolism of protein, carbohydrate and fat. The expression patterns of 12 representative heat stress response-relevant genes detected by quantitative real-time PCR (qRT-PCR) were similar to those obtained from transcriptome analysis. By flow cytometric analysis, the apoptosis rate of haemocytes increased significantly after oysters were treated at 25 °C for 24 h and recovered at 4 °C for 12 h (p {\textless} 0.05) and 36 h (p {\textless} 0.01), and it also increased significantly when the heat treatment lasted to 60 h (p {\textless} 0.01). The present results indicated that, when oysters encountered short term heat stress, the expression of genes related to energy metabolism, as well as unfolded protein response (UPR) and anti-apoptotic system, were firstly regulated to maintain basic life activities, and then a large number of genes involved in stabilizing protein conformation and facilitating further protein refolding were activated to repair the stress injury. However, the stress injury gradually became irreparable with the stress persisting, and apoptosis was activated when the heat treatment prolonged to 24 h. The information was useful to better understand the molecular mechanism of heat stress response and develop strategies for the improvement of oyster survival rate during summer high-temperature period.}, urldate = {2024-06-25}, journal = {Fish \& Shellfish Immunology}, author = {Yang, Chuanyan and Gao, Qiang and Liu, Chang and Wang, Lingling and Zhou, Zhi and Gong, Changhao and Zhang, Anguo and Zhang, Huan and Qiu, Limei and Song, Linsheng}, month = sep, year = {2017}, keywords = {Pacific oyster, Crassostrea gigas, Heat stress, Apoptosis, Haemocytes, Transcriptional response, heat shock, hsp70}, pages = {132--143}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\9E5LZPRW\\S1050464817304096.html:text/html;Yang et al. - 2017 - The transcriptional response of the Pacific oyster.pdf:C\:\\Users\\Owner\\Zotero\\storage\\LE8CF2B3\\Yang et al. - 2017 - The transcriptional response of the Pacific oyster.pdf:application/pdf}, } @article{lim_thermal_2016, title = {Thermal stress induces a distinct transcriptome profile in the {Pacific} oyster \textit{{Crassostrea} gigas}}, volume = {19}, issn = {1744-117X}, url = {https://www.sciencedirect.com/science/article/pii/S1744117X16300454}, doi = {10.1016/j.cbd.2016.06.006}, abstract = {Oysters are frequently subjected to heat stress during tidal emersion/immersion cycles in their habitats due to attachment on the rocky shore. To understand the effect of temperature elevation on the whole transcriptome over time, the Pacific oyster Crassostrea gigas was exposed to seawater temperature 32°C for 72h from the control 20°C. RNA-seq identified differentially expressed stress responsive transcripts upon thermal stress in the gill tissues of C. gigas. The primary effect of heat stress appears to be significantly induced transcription of molecular chaperones, including members of the heat shock protein (hsp) families, while genes typically associated with protein metabolism, such as those involved in protein degradation (e.g. ATP-dependent proteolysis pathway) and biosynthesis (e.g. ribosomal protein genes), were repressed. In particular, several hsp70 isoforms and a small hsp20 maintained prolonged mRNA expressions for 72h. This study provides preliminary insights into the molecular response of C. gigas to heat stress and suggests a basis for future studies examining molecular adaptation or thermotolerance metabolism in the Pacific oyster.}, urldate = {2024-06-25}, journal = {Comparative Biochemistry and Physiology Part D: Genomics and Proteomics}, author = {Lim, Hyun-Jeong and Kim, Bo-Mi and Hwang, In Joon and Lee, Jeong-Soo and Choi, Ik-Young and Kim, Youn-Jung and Rhee, Jae-Sung}, month = sep, year = {2016}, keywords = {Transcriptome, Pacific oyster, Crassostrea gigas, Temperature, Oyster, hsp70, Thermal stress}, pages = {62--70}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\WCVDRI7N\\S1744117X16300454.html:text/html}, } @article{li_synergistic_2007, title = {Synergistic impacts of heat shock and spawning on the physiology and immune health of {Crassostrea} gigas: an explanation for summer mortality in {Pacific} oysters}, volume = {293}, issn = {0363-6119}, shorttitle = {Synergistic impacts of heat shock and spawning on the physiology and immune health of {Crassostrea} gigas}, url = {https://journals.physiology.org/doi/full/10.1152/ajpregu.00463.2007}, doi = {10.1152/ajpregu.00463.2007}, abstract = {Mass mortality is often observed in cultured oysters during the period following spawning in the summer season. To examine the underlying causes leading to this phenomenon, thermotolerance of the Pacific oyster Crassostrea gigas was assessed using pre- and postspawning oysters that were sequentially treated with sublethal (37°C) and lethal heat shocks (44°C). The effects were examined on a range of immune and metabolic parameters in addition to mortality rate. A preventative 37°C significantly reduced oyster mortality after exposure to a second heat shock of 44°C, but in postspawning oysters mortality remained at 80\%, compared with {\textless} 10\% in prespawning oysters. Levels of the 72 kDa and 69 kDa heat shock proteins were low in the gill tissue from postspawning oysters stimulated by heat shock, indicating spawning reduced heat shock protein synthesis. The postspawning oysters had depleted glycogen stores in the mantle tissue and reduced adenylate energy charge after heat shock, indicative of lower energy for metabolic activity. A cumulative effect of spawning and heat shock was observed on the immunocompetence of oysters, demonstrated by reduced hemocyte phagocytosis and hemolymph antimicrobial activity. These results support the hypothesis that the energy expended during reproduction compromises the thermotolerance and immune status of oysters, leaving them easily subject to mortality if heat stress occurs in postspawning stage. This study improves our understanding of oyster summer mortality and has implications for the long-term persistence of mollusks under the influence of global warming.}, number = {6}, urldate = {2024-06-25}, journal = {American Journal of Physiology-Regulatory, Integrative and Comparative Physiology}, author = {Li, Yan and Qin, Jian G. and Abbott, Catherine A. and Li, Xiaoxu and Benkendorff, Kirsten}, month = dec, year = {2007}, note = {Publisher: American Physiological Society}, keywords = {Pacific oyster, Crassostrea gigas, hsp70, energy trade-offs, heat shock proteins, immunocompetence, induced thermotolerance, metabolic activity}, pages = {R2353--R2362}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\3FSQXVWC\\Li et al. - 2007 - Synergistic impacts of heat shock and spawning on .pdf:application/pdf}, } @article{jackson_duration_2011, title = {Duration of induced thermal tolerance and tissue-specific expression of hsp/hsc70 in the eastern oyster, \textit{{Crassostrea} virginica} and the pacific oyster, \textit{{Crassostrea} gigas}}, volume = {317}, issn = {0044-8486}, url = {https://www.sciencedirect.com/science/article/pii/S004484861100281X}, doi = {10.1016/j.aquaculture.2011.04.004}, abstract = {We compared thermotolerance and the heat shock response of Pacific oysters (Crassostrea gigas) and Eastern oysters (Crassostrea virginica), both are very valuable commercial species. The former were much more resistant to high temperature, reaching maximum induced thermotolerance (IT) by 2days after a sublethal heat shock (SHS) and lasting for at least 3weeks, a possible record for the duration of IT in any animal. Two constitutive isoforms of 77 and 72kD, and an inducible 69kD protein were detected in both oysters, their amounts and time course after SHS varied, depending on the tissue examined. Synthesis of these three proteins in gills (ctenidia) of C. gigas was reduced to control levels within 2days after SHS as judged by 14C-amino acid incorporation. However, western blotting showed that the levels of these stress proteins in tissues from heat shocked C. gigas remained higher than those in controls, suggesting a reduction in protein degradation after SHS. Variable patterns of these three isoforms were detected in gills, mantle, adductor muscle and digestive gland before and after SHS. The general features described for C. gigas tissues were also observed in adductor muscle, gill and mantle of C. virginica, although some differences were also noted. We discuss the difficulties and importance associated with the use of commercially-available antibodies in the study of these stress proteins in oysters.}, number = {1}, urldate = {2024-06-25}, journal = {Aquaculture}, author = {Jackson, Susan A. and Uhlinger, Kevin R. and Clegg, James S.}, month = jul, year = {2011}, keywords = {Pacific oyster, Crassostrea gigas, Stress response, Oysters, hsp70, 70kD hsp family, Stress proteins, Thermal tolerance}, pages = {168--174}, file = {Jackson et al. - 2011 - Duration of induced thermal tolerance and tissue-s.pdf:C\:\\Users\\Owner\\Zotero\\storage\\AR6ZVX6R\\Jackson et al. - 2011 - Duration of induced thermal tolerance and tissue-s.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\8SEL42Y2\\S004484861100281X.html:text/html}, } @article{hamdoun_phenotypic_2003, title = {Phenotypic {Plasticity} of {HSP70} and {HSP70} {Gene} {Expression} in the {Pacific} {Oyster} ({Crassostrea} gigas): {Implications} for {Thermal} {Limits} and {Induction} of {Thermal} {Tolerance}}, volume = {205}, issn = {0006-3185}, shorttitle = {Phenotypic {Plasticity} of {HSP70} and {HSP70} {Gene} {Expression} in the {Pacific} {Oyster} ({Crassostrea} gigas)}, url = {https://www.journals.uchicago.edu/doi/full/10.2307/1543236}, doi = {10.2307/1543236}, abstract = {Pacific oysters, Crassostrea gigas, living at a range of tidal heights, routinely encounter large seasonal fluctuations in temperature. We demonstrate that the thermal limits of oysters are relatively plastic, and that these limits are correlated with changes in the expression of one family of heat-shock proteins (HSP70). Oysters were cultured in the intertidal zone, at two tidal heights, and monitored for changes in expression of cognate (HSC) and inducible (HSP) heat-shock proteins during the progression from spring through winter. We found that the “control” levels (i.e., prior to laboratory heat shock) of HSC77 and HSC72 are positively correlated with increases in ambient temperature and were significantly higher in August than in January. The elevated level of HSCs during the summer was associated with moderate, 2–3 °C, increases in the upper thermal limits for survival. We measured concomitant increases in the threshold temperatures (Ton) required for induction of HSP70. Total hsp70 mRNA expression reflected the seasonal changes in the expression of inducible but not cognate members of the HSP70 family of proteins. A potential cost of increased Ton in the summer is that there was no extension of the upper thermal limits for survival (i.e., induction of thermotolerance) after sublethal heat shock at temperatures that were sufficient to induce thermotolerance during the winter months.}, number = {2}, urldate = {2024-06-25}, journal = {The Biological Bulletin}, author = {Hamdoun, Amro M. and Cheney, Daniel P. and Cherr, Gary N.}, month = oct, year = {2003}, note = {Publisher: The University of Chicago Press}, keywords = {Pacific oyster, Crassostrea gigas, hsp70}, pages = {160--169}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\VNSSM62Q\\Hamdoun et al. - 2003 - Phenotypic Plasticity of HSP70 and HSP70 Gene Expr.pdf:application/pdf}, } @article{li_integrated_2017, title = {Integrated application of transcriptomics and metabolomics provides insights into glycogen content regulation in the {Pacific} oyster {Crassostrea} gigas}, volume = {18}, issn = {1471-2164}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5594505/}, doi = {10.1186/s12864-017-4069-8}, abstract = {Background The Pacific oyster Crassostrea gigas is an important marine fishery resource, which contains high levels of glycogen that contributes to the flavor and the quality of the oyster. However, little is known about the molecular and chemical mechanisms underlying glycogen content differences in Pacific oysters. Using a homogeneous cultured Pacific oyster family, we explored these regulatory networks at the level of the metabolome and the transcriptome. Results Oysters with the highest and lowest natural glycogen content were selected for differential transcriptome and metabolome analysis. We identified 1888 differentially-expressed genes, seventy-five differentially-abundant metabolites, which are part of twenty-seven signaling pathways that were enriched using an integrated analysis of the interaction between the differentially-expressed genes and the differentially-abundant metabolites. Based on these results, we found that a high expression of carnitine O-palmitoyltransferase 2 (CPT2), indicative of increased fatty acid degradation, is associated with a lower glycogen content. Together, a high level of expression of phosphoenolpyruvate carboxykinase (PEPCK), and high levels of glucogenic amino acids likely underlie the increased glycogen production in high-glycogen oysters. In addition, the higher levels of the glycolytic enzymes hexokinase (HK) and pyruvate kinase (PK), as well as of the TCA cycle enzymes malate dehydrogenase (MDH) and pyruvate carboxylase (PYC), imply that there is a concomitant up-regulation of energy metabolism in high-glycogen oysters. High-glycogen oysters also appeared to have an increased ability to cope with stress, since the levels of the antioxidant glutathione peroxidase enzyme 5 (GPX5) gene were also increased. Conclusion Our results suggest that amino acids and free fatty acids are closely related to glycogen content in oysters. In addition, oysters with a high glycogen content have a greater energy production capacity and a greater ability to cope with stress. These findings will not only provide insights into the molecular mechanisms underlying oyster quality, but also promote research into the molecular breeding of oysters. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4069-8) contains supplementary material, which is available to authorized users.}, urldate = {2024-07-11}, journal = {BMC Genomics}, author = {Li, Busu and Song, Kai and Meng, Jie and Li, Li and Zhang, Guofan}, month = sep, year = {2017}, pmid = {28893177}, pmcid = {PMC5594505}, pages = {713}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\IYS3FQTW\\Li et al. - 2017 - Integrated application of transcriptomics and meta.pdf:application/pdf}, } @article{ghaffari_thermotolerance_2019, title = {Thermotolerance {Divergence} {Revealed} by the {Physiological} and {Molecular} {Responses} in {Two} {Oyster} {Subspecies} of {Crassostrea} gigas in {China}}, volume = {10}, issn = {1664-042X}, url = {https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2019.01137/full}, doi = {10.3389/fphys.2019.01137}, abstract = {{\textless}p{\textgreater}Investigating the physiological mechanisms of closely related species that exhibit distinct geographic distributions and thermal niches is essential for understanding their thermal tolerance capacities and local adaptations in view of climate warming. The variations in upper thermal limits (LT$_{\textrm{50}}$) under acute heat shock and cardiac activity, standard metabolic rate (SMR), anaerobic metabolite production and molecular responses (expression of molecular chaperones and glycolysis metabolism genes) under increasing temperatures in two oyster subspecies were studied. The populations of two oyster subspecies, {\textless}italic{\textgreater}Crassostrea gigas gigas{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}C. gigas angulata{\textless}/italic{\textgreater}, exhibit different latitudinal distributions along the northern and southern coastlines of China, respectively, which experience different environmental conditions. The LT$_{\textrm{50}}$ was significantly higher, by ∼1°C, in the southern than in the northern oysters. In both subspecies, temperature increases had powerful effects on heart rate, SMR and gene expression. The southern oysters had the highest Arrhenius breakpoint temperatures for heart rate (31.4 ± 0.17°C) and SMR (33.09°C), whereas the heart rate (28.86 ± 0.3°C) and SMR (29.22°C) of the northern oysters were lower. The same patterns were observed for the {\textless}italic{\textgreater}Q{\textless}/italic{\textgreater}$_{\textrm{10}}$ coefficients. More thermal sensitivity was observed in the northern oysters than in their southern counterparts, as the heat-shock proteins (HSPs) in the northern oysters were expressed first and had a higher induction at a lower temperature than those of southern oysters. Furthermore, different expression patterns of energetic metabolism genes ({\textless}italic{\textgreater}HK, PK{\textless}/italic{\textgreater}, and {\textless}italic{\textgreater}PEPCK{\textless}/italic{\textgreater}) were observed. In the northern oysters, increasing anaerobic glycolysis genes ({\textless}italic{\textgreater}PEPCK{\textless}/italic{\textgreater}) and end products (succinate) were found at 36–43°C, indicating a transition from aerobic to anaerobic metabolism and a lower aerobic scope compared with the southern oysters. These two subspecies experience different environmental conditions, and their physiological performances suggested species-specific thermal tolerance windows in which the southern oysters, with mild physiological flexibility, had a higher potential capability to withstand heat stress. Overall, our results indicate that comparing and unifying physiological and molecular mechanisms can provide a framework for understanding the likely effects of global warming on marine ectotherms in intertidal regions.{\textless}/p{\textgreater}}, language = {English}, urldate = {2024-07-11}, journal = {Frontiers in Physiology}, author = {Ghaffari, Hamze and Wang, Wei and Li, Ao and Zhang, Guofan and Li, Li}, month = sep, year = {2019}, note = {Publisher: Frontiers}, keywords = {adaptive variation, Heart Rate, Metabolism, Physiological performance, thermal tolerance}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\9D7SGR3J\\Ghaffari et al. - 2019 - Thermotolerance Divergence Revealed by the Physiol.pdf:application/pdf}, } @article{rajagopal_thermal_2005, title = {Thermal tolerance of the invasive oyster \textit{{Crassostrea} gigas}: {Feasibility} of heat treatment as an antifouling option}, volume = {39}, issn = {0043-1354}, shorttitle = {Thermal tolerance of the invasive oyster \textit{{Crassostrea} gigas}}, url = {https://www.sciencedirect.com/science/article/pii/S0043135405004744}, doi = {10.1016/j.watres.2005.08.021}, abstract = {Pacific oysters, Crassostrea gigas are traditionally considered shellfish of great fishery and aquaculture value. For these reasons they are introduced worldwide. Recently there has been increasing reports about the prevalence of C. gigas as biofouling organism in cooling water systems. In the absence of relevant data on the susceptibility of oysters to commonly employed antifouling techniques such as heat treatment, it was presumed that oysters would be controlled by treatment programmes directed against other major fouling organisms. The present study was carried out to test the above hypothesis, and results showed that C. gigas has an upper temperature tolerance that is much higher than other major marine fouling animals including blue mussel Mytilus edulis. Apparently, temperature regimes presently used in heat treatment of cooling water systems fouled by mussels need to be increased, if C. gigas are to be controlled effectively. Our results also indicate that previous exposure of C. gigas to sublethal high temperatures could make them more resistant to subsequent thermal treatment, an aspect that should be taken into account when heat treatment is used as a fouling control option against oyster fouling.}, number = {18}, urldate = {2024-07-11}, journal = {Water Research}, author = {Rajagopal, Sanjeevi and van der Velde, Gerard and Jansen, Jeroen and van der Gaag, Marinus and Atsma, Guido and Janssen-Mommen, Joke P. M. and Polman, Harry and Jenner, Henk A.}, month = nov, year = {2005}, keywords = {Biofouling, Heat treatment, Induced thermotolerance, Mortality, Oxygen consumption, Oysters}, pages = {4335--4342}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\K7DZP6JT\\S0043135405004744.html:text/html}, } @article{riffo-campos_tools_2016, title = {Tools for {Sequence}-{Based} {miRNA} {Target} {Prediction}: {What} to {Choose}?}, volume = {17}, issn = {1422-0067}, shorttitle = {Tools for {Sequence}-{Based} {miRNA} {Target} {Prediction}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187787/}, doi = {10.3390/ijms17121987}, abstract = {MicroRNAs (miRNAs) are defined as small non-coding RNAs {\textasciitilde}22 nt in length. They regulate gene expression at a post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and therefore blocking translation. In the last decade, the dysfunction of miRNAs has been related to the development and progression of many diseases. Currently, researchers need a method to identify precisely the miRNA targets, prior to applying experimental approaches that allow a better functional characterization of miRNAs in biological processes and can thus predict their effects. Computational prediction tools provide a rapid method to identify putative miRNA targets. However, since a large number of tools for the prediction of miRNA:mRNA interactions have been developed, all with different algorithms, the biological researcher sometimes does not know which is the best choice for his study and many times does not understand the bioinformatic basis of these tools. This review describes the biological fundamentals of these prediction tools, characterizes the main sequence-based algorithms, and offers some insights into their uses by biologists.}, number = {12}, urldate = {2024-07-17}, journal = {International Journal of Molecular Sciences}, author = {Riffo-Campos, Ángela L. and Riquelme, Ismael and Brebi-Mieville, Priscilla}, month = dec, year = {2016}, pmid = {27941681}, pmcid = {PMC5187787}, pages = {1987}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\7DGVPJWL\\Riffo-Campos et al. - 2016 - Tools for Sequence-Based miRNA Target Prediction .pdf:application/pdf}, } @article{peterson_common_2014, title = {Common features of {microRNA} target prediction tools}, volume = {5}, issn = {1664-8021}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927079/}, doi = {10.3389/fgene.2014.00023}, abstract = {The human genome encodes for over 1800 microRNAs (miRNAs), which are short non-coding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one miRNA to target multiple gene transcripts, miRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of miRNA targets is a critical initial step in identifying miRNA:mRNA target interactions for experimental validation. The available tools for miRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to miRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all miRNA target prediction tools, four main aspects of the miRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MiRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.}, urldate = {2024-07-18}, journal = {Frontiers in Genetics}, author = {Peterson, Sarah M. and Thompson, Jeffrey A. and Ufkin, Melanie L. and Sathyanarayana, Pradeep and Liaw, Lucy and Congdon, Clare Bates}, month = feb, year = {2014}, pmid = {24600468}, pmcid = {PMC3927079}, pages = {23}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\NTPEIIDA\\Peterson et al. - 2014 - Common features of microRNA target prediction tool.pdf:application/pdf}, } @article{witkos_practical_2011, title = {Practical {Aspects} of {microRNA} {Target} {Prediction}}, volume = {11}, issn = {1566-5240}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182075/}, doi = {10.2174/156652411794859250}, abstract = {microRNAs (miRNAs) are endogenous non-coding RNAs that control gene expression at the posttranscriptional level. These small regulatory molecules play a key role in the majority of biological processes and their expression is also tightly regulated. Both the deregulation of genes controlled by miRNAs and the altered miRNA expression have been linked to many disorders, including cancer, cardiovascular, metabolic and neurodegenerative diseases. Therefore, it is of particular interest to reliably predict potential miRNA targets which might be involved in these diseases. However, interactions between miRNAs and their targets are complex and very often there are numerous putative miRNA recognition sites in mRNAs. Many miRNA targets have been computationally predicted but only a limited number of these were experimentally validated. Although a variety of miRNA target prediction algorithms are available, results of their application are often inconsistent. Hence, finding a functional miRNA target is still a challenging task. In this review, currently available and frequently used computational tools for miRNA target prediction, i.e., PicTar, TargetScan, DIANA-microT, miRanda, rna22 and PITA are outlined and various practical aspects of miRNA target analysis are extensively discussed. Moreover, the performance of three algorithms (PicTar, TargetScan and DIANA-microT) is both demonstrated and evaluated by performing an in-depth analysis of miRNA interactions with mRNAs derived from genes triggering hereditary neurological disorders known as trinucleotide repeat expansion diseases (TREDs), such as Huntington’s disease (HD), a number of spinocerebellar ataxias (SCAs), and myotonic dystrophy type 1 (DM1).}, number = {2}, urldate = {2024-07-18}, journal = {Current Molecular Medicine}, author = {Witkos, T.M and Koscianska, E and Krzyzosiak, W.J}, month = mar, year = {2011}, pmid = {21342132}, pmcid = {PMC3182075}, pages = {93--109}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\GB7TLQJW\\Witkos et al. - 2011 - Practical Aspects of microRNA Target Prediction.pdf:application/pdf}, } @article{yue_survey_2009, title = {Survey of {Computational} {Algorithms} for {MicroRNA} {Target} {Prediction}}, volume = {10}, issn = {1389-2029}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808675/}, doi = {10.2174/138920209789208219}, abstract = {MicroRNAs (miRNAs) are 19 to 25 nucleotides non-coding RNAs known to possess important post-transcriptional regulatory functions. Identifying targeting genes that miRNAs regulate are important for understanding their specific biological functions. Usually, miRNAs down-regulate target genes through binding to the complementary sites in the 3' untranslated region (UTR) of the targets. In part, due to the large number of miRNAs and potential targets, an experimental based prediction design would be extremely laborious and economically unfavorable. However, since the bindings of the animal miRNAs are not a perfect one-to-one match with the complementary sites of their targets, it is difficult to predict targets of animal miRNAs by accessing their alignment to the 3' UTRs of potential targets. Consequently, sophisticated computational approaches for miRNA target prediction are being considered as essential methods in miRNA research., We surveyed most of the current computational miRNA target prediction algorithms in this paper. Particularly, we provided a mathematical definition and formulated the problem of target prediction under the framework of statistical classification. Moreover, we summarized the features of miRNA-target pairs in target prediction approaches and discussed these approaches according to two categories, which are the rule-based and the data-driven approaches. The rule-based approach derives the classifier mainly on biological prior knowledge and important observations from biological experiments, whereas the data driven approach builds statistic models using the training data and makes predictions based on the models. Finally, we tested a few different algorithms on a set of experimentally validated true miRNA-target pairs [] and a set of false miRNA-target pairs, derived from miRNA overexpression experiment []. Receiver Operating Characteristic (ROC) curves were drawn to show the performances of these algorithms.}, number = {7}, urldate = {2024-07-18}, journal = {Current Genomics}, author = {Yue, Dong and Liu, Hui and Huang, Yufei}, month = nov, year = {2009}, pmid = {20436875}, pmcid = {PMC2808675}, pages = {478--492}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\HE6MPFRS\\Yue et al. - 2009 - Survey of Computational Algorithms for MicroRNA Ta.pdf:application/pdf}, } @misc{timmins-schiffman_reproductive_2024, title = {Reproductive {Resilience}: {Pathways} to {Gametogenic} {Success} in {Montipora} capitata after {Bleaching}}, shorttitle = {Reproductive {Resilience}}, url = {https://www.researchsquare.com/article/rs-4559943/v1}, doi = {10.21203/rs.3.rs-4559943/v1}, abstract = {Thermal bleaching, or the loss of symbiotic algae that provide most energetic resources for the coral host, is an increasing threat to reefs worldwide and is projected to worsen with climate change. While bleaching is a well-recognized threat, the impact on the process of reproduction in bleaching survivors is not well resolved, despite being central to coral resilience. Montipora capitata can survive bleaching while completing a full gametogenic cycle, offering an ideal system to study gametogenic resilience and physiological tradeoffs. We experimentally bleached fragments of M. capitata colonies and followed their gametogenesis and physiological responses for 10 months (six time points). All bleached colonies produced gametes at the same time as controls, suggesting that reproductive processes were energetically prioritized. However, proteomic analysis revealed tradeoffs and delays in activating key physiological processes earlier in gametogenesis in areas such as skeletal growth and reproductive hormone synthesis. Tradeoffs during the gametogenic cycle, likely a direct response to thermal bleaching, resulted in smaller oocytes from bleached colonies, potentially indicating decreased transfer of parental resources to gametes. While gametogenesis is likely to continue in this species, it is unknown how the viability and success of future offspring may be impacted by future bleaching events.}, urldate = {2024-07-18}, author = {Timmins-Schiffman, E. and Duselis, E. and Brown, T. and Axworthy, J. B. and Backstrom, C. H. and Riffle, M. and Dilworth, J. and Kenkel, C. D. and Rodrigues, L. F. and Nunn, B. L. and Padilla-Gamiño, J. L.}, month = jul, year = {2024}, note = {ISSN: 2693-5015}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\UKB53X3Z\\Timmins-Schiffman et al. - 2024 - Reproductive Resilience Pathways to Gametogenic S.pdf:application/pdf}, } @article{shamseldin_induced_1997, title = {Induced thermotolerance in the {Pacific} oyster, {Crassostrea} gigas}, volume = {16}, url = {http://www.biodiversitylibrary.org/item/23128}, number = {2}, journal = {Journal of Shellfish Research}, author = {Shamseldin, Ally A. and Clegg, James S. and Friedman, Carolyn S. and Cherr, Gary N. and Pillai, Murali C.}, year = {1997}, pages = {487--491}, file = {pillai_induced.pdf:C\:\\Users\\Owner\\Zotero\\storage\\C8BLM4CD\\pillai_induced.pdf:application/pdf}, } @article{he_metabolic_2024, title = {Metabolic dysfunctions in pearl oysters following recurrent marine heatwaves}, volume = {200}, issn = {0141-1136}, url = {https://www.sciencedirect.com/science/article/pii/S0141113624003027}, doi = {10.1016/j.marenvres.2024.106641}, abstract = {Marine heatwaves (MHWs) have become more frequent, intense and extreme in oceanic systems in the past decade, resulting in mass mortality events of marine invertebrates and devastating coastal marine ecosystems. While metabolic homeostasis is a fundamental requirement in stress tolerance, little is known about its role under intensifying MHWs conditions. Here, we investigated impacts of MHWs on the metabolism in pearl oysters (Pinctada maxima) – an ecologically and economically significant bivalve species in tropical ecosystems. Activities of digestive enzymes (gastric proteases, lipases, and amylases) did not significantly respond to various scenario of recurrent MHWs varying from 24 °C to 28 °C (moderate) and 32 °C (severe). The metabolomics analysis revealed nine and five key metabolism pathways under both MHWs scenarios. Specifically, pathways associated with energy metabolism were impaired by moderate MHWs, manifesting in downregulation of differential metabolite (The nicotinic acid and N-acetyl-glutamic acid). The content of CDP-ethanolamine was significantly decrease, and the perturbations of oxidative stress caused by the decreased of content of D-glutamine. Metabolites related to a suite of body functions (e.g., the lipid metabolism, biomineralization, and antioxidant defenses) showed significantly negative responses by severe MHWs. These findings reveal the metabolic impairments of marine bivalves when subjected to MHWs varying in intensity and frequency, implying cascading consequences which deserve further investigation.}, urldate = {2024-07-22}, journal = {Marine Environmental Research}, author = {He, Guixiang and Liu, Xiaolong and Xu, Yang and Liu, Yong and Masanja, Fortunatus and Deng, Yuewen and Zhao, Liqiang}, month = sep, year = {2024}, keywords = {Climate change, Marine heatwaves, Metabolism}, pages = {106641}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\PRXK579U\\S0141113624003027.html:text/html}, } @article{movassagh_mirtarrnaseq_2022, title = {{mirTarRnaSeq}: {An} {R}/{Bioconductor} {Statistical} {Package} for {miRNA}-{mRNA} {Target} {Identification} and {Interaction} {Analysis}}, volume = {23}, issn = {1471-2164}, shorttitle = {{mirTarRnaSeq}}, url = {https://doi.org/10.1186/s12864-022-08558-w}, doi = {10.1186/s12864-022-08558-w}, abstract = {We introduce mirTarRnaSeq, an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a statistical package to explore predicted or pre-hypothesized miRNA-mRNA relationships following target prediction.}, number = {1}, urldate = {2024-07-22}, journal = {BMC Genomics}, author = {Movassagh, Mercedeh and Morton, Sarah U. and Hehnly, Christine and Smith, Jasmine and Doan, Trang T. and Irizarry, Rafael and Broach, James R. and Schiff, Steven J. and Bailey, Jeffrey A. and Paulson, Joseph N.}, month = jun, year = {2022}, pages = {439}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\7KRAS8CG\\Movassagh et al. - 2022 - mirTarRnaSeq An RBioconductor Statistical Packag.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\XFLK96TV\\s12864-022-08558-w.html:text/html}, } @article{hwang_involvement_2023, title = {The involvement of {GSK3β} for glycogen synthesis throughout the annual cycle of {Pacific} oyster, {Crassostrea} gigas ({Magallana} gigas)}, volume = {75}, copyright = {https://creativecommons.org/licenses/by-nc-nd/4.0}, issn = {0792-156X}, url = {https://ija.scholasticahq.com/article/67818-the-involvement-of-gsk3-for-glycogen-synthesis-throughout-the-annual-cycle-of-pacific-oyster-crassostrea-gigas-magallana-gigas}, doi = {10.46989/001c.67818}, abstract = {Crassostrea gigas is a frequently studied species in understanding physiological processes in bivalves. Similar to other animals, oysters store glucose in the body as glycogen. Glycogen is known to supply energy for germ cell development and maintenance. Glycogen is synthesized by glycogen synthase. GSK3β regulates glycogen synthase activity and plays an important role in glycogen synthesis. Therefore, this study aims to examine the effect of GSK3β on the annual cycle of oysters and the glycogen synthesis pathway and to investigate the energy pathway in comparison with seasonal variation. Oysters were sampled monthly for one year and were subjected to glycogen content, RT-PCR, FISH, and western blot analysis. The year-round glycogen content significantly differs only in the mantle edge during spring and summer of both sexes but not in labial palp, digestive gland, gonad, and adductor muscle. The expression of GSK3β mRNA level was highest in October for females and April for males. Both sexes had the lowest expression in July. In the adductor muscle, females and males showed the highest expression in April and the lowest in July and October. The pattern of GSK3β expression in gonads and adductor muscle was similarly confirmed through FISH. As a result of examining the signaling system, p-GSK3β (serine 9) increased. At the same time, glycogen synthase decreased in May when the condition index was the highest, pGSK3β decreased in October and July when spawning occurred, and glycogen synthase increased. Overall, it is thought that p-GSK3β expression is high in C. gigas at ripe, which inhibits glycogen synthesis and is used as energy for growth and maturation. Glycogen synthesis occurs for energy storage during degeneration.}, language = {en}, number = {1}, urldate = {2024-07-22}, journal = {Israeli Journal of Aquaculture - Bamidgeh}, author = {Hwang, Soyeon and Park, Su-Jin and Cadangin, Josel and Seo, Bong-Seung and Lee, Yein and Choi, Youn H.}, month = jan, year = {2023}, file = {Hwang et al. - 2023 - The involvement of GSK3β for glycogen synthesis th.pdf:C\:\\Users\\Owner\\Zotero\\storage\\WIETNVGA\\Hwang et al. - 2023 - The involvement of GSK3β for glycogen synthesis th.pdf:application/pdf}, } @article{lethi_monthly_2023, title = {Monthly variation in the lipid composition and content of {Pacific} oysters, {\textbackslash}({\textbackslash}textit\{{Crassostrea} gigas\}{\textbackslash}), cultured in {Van} {Don}, {Quang} {Ninh}}, volume = {23}, doi = {10.15625/1859-3097/18275}, abstract = {We conduct a study to investigate the year-round fluctuation of lipid composition and content in Pacific oysters (Crassostrea gigas) cultured in Van Don, Quang Ninh, for the first time. Our results showed that the total lipid content of oysters ranged from 1\% to 1.6\%, with the highest levels observed during their pre-reproductive period (July and December). Polyunsaturated fatty acids were the most abundant type of lipids in oysters, ranging from 41.66\% to 53.36\%. We identified six lipid classes in Pacific oysters, with the three dominant classes being PoL, ST, and TG, which exhibited significant variation, with the highest variability observed in May and June and the lowest in July. The primary fatty acids in oyster lipids were 14:0, 16:0, 18:0, 18:1n-7, 20:4n-6, 20:5n-3, and 22:6n-3. In summary, our study provides novel insights into the lipid composition and content of Pacific oysters cultured in Van Don, Quang Ninh.The results demonstrate the temporal variability in lipid classes and fatty acid composition throughout the year, with the highest lipid content observed during the pre-reproductive period. These findings could contribute to better understanding the nutritional value of Pacific oysters and inform future aquaculture practices.}, journal = {Vietnam Journal of Marine Science and Technology}, author = {LeThi, Thanh and Quoc, Long and Quang, Dai and Thảo, Lại and Hong, Nhung and Thi, Phuong and Thi, Bich and Quoc, Toan}, month = mar, year = {2023}, pages = {73--80}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\I7Z6Q8VR\\LeThi et al. - 2023 - Monthly variation in the lipid composition and con.pdf:application/pdf}, } @article{stefansson_correlation_2024, title = {The correlation between {CpG} methylation and gene expression is driven by sequence variants}, copyright = {2024 The Author(s)}, issn = {1546-1718}, url = {https://www.nature.com/articles/s41588-024-01851-2}, doi = {10.1038/s41588-024-01851-2}, abstract = {Gene promoter and enhancer sequences are bound by transcription factors and are depleted of methylated CpG sites (cytosines preceding guanines in DNA). The absence of methylated CpGs in these sequences typically correlates with increased gene expression, indicating a regulatory role for methylation. We used nanopore sequencing to determine haplotype-specific methylation rates of 15.3 million CpG units in 7,179 whole-blood genomes. We identified 189,178 methylation depleted sequences where three or more proximal CpGs were unmethylated on at least one haplotype. A total of 77,789 methylation depleted sequences ({\textasciitilde}41\%) associated with 80,503 cis-acting sequence variants, which we termed allele-specific methylation quantitative trait loci (ASM-QTLs). RNA sequencing of 896 samples from the same blood draws used to perform nanopore sequencing showed that the ASM-QTL, that is, DNA sequence variability, drives most of the correlation found between gene expression and CpG methylation. ASM-QTLs were enriched 40.2-fold (95\% confidence interval 32.2, 49.9) among sequence variants associating with hematological traits, demonstrating that ASM-QTLs are important functional units in the noncoding genome.}, language = {en}, urldate = {2024-07-24}, journal = {Nature Genetics}, author = {Stefansson, Olafur Andri and Sigurpalsdottir, Brynja Dogg and Rognvaldsson, Solvi and Halldorsson, Gisli Hreinn and Juliusson, Kristinn and Sveinbjornsson, Gardar and Gunnarsson, Bjarni and Beyter, Doruk and Jonsson, Hakon and Gudjonsson, Sigurjon Axel and Olafsdottir, Thorunn Asta and Saevarsdottir, Saedis and Magnusson, Magnus Karl and Lund, Sigrun Helga and Tragante, Vinicius and Oddsson, Asmundur and Hardarson, Marteinn Thor and Eggertsson, Hannes Petur and Gudmundsson, Reynir L. and Sverrisson, Sverrir and Frigge, Michael L. and Zink, Florian and Holm, Hilma and Stefansson, Hreinn and Rafnar, Thorunn and Jonsdottir, Ingileif and Sulem, Patrick and Helgason, Agnar and Gudbjartsson, Daniel F. and Halldorsson, Bjarni V. and Thorsteinsdottir, Unnur and Stefansson, Kari}, month = jul, year = {2024}, note = {Publisher: Nature Publishing Group}, keywords = {Epigenetics, Genomics, DNA sequencing, Gene expression, Genome-wide association studies}, pages = {1--8}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\QVDJK68U\\Stefansson et al. - 2024 - The correlation between CpG methylation and gene e.pdf:application/pdf}, } @article{praher_conservation_2021, title = {Conservation and turnover of {miRNAs} and their highly complementary targets in early branching animals}, volume = {288}, url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.3169}, doi = {10.1098/rspb.2020.3169}, abstract = {MicroRNAs (miRNAs) are crucial post-transcriptional regulators that have been extensively studied in Bilateria, a group comprising the majority of extant animals, where more than 30 conserved miRNA families have been identified. By contrast, bilaterian miRNA targets are largely not conserved. Cnidaria is the sister group to Bilateria and thus provides a unique opportunity for comparative studies. Strikingly, like their plant counterparts, cnidarian miRNAs have been shown to predominantly have highly complementary targets leading to transcript cleavage by Argonaute proteins. Here, we assess the conservation of miRNAs and their targets by small RNA sequencing followed by miRNA target prediction in eight species of Anthozoa (sea anemones and corals), the earliest-branching cnidarian class. We uncover dozens of novel miRNAs but only a few conserved ones. Further, given their high complementarity, we were able to computationally identify miRNA targets in each species. Besides evidence for conservation of specific miRNA target sites, which are maintained between sea anemones and stony corals across 500 Myr of evolution, we also find indications for convergent evolution of target regulation by different miRNAs. Our data indicate that cnidarians have only few conserved miRNAs and corresponding targets, despite their high complementarity, suggesting a high evolutionary turnover.}, number = {1945}, urldate = {2024-08-16}, journal = {Proceedings of the Royal Society B: Biological Sciences}, author = {Praher, Daniela and Zimmermann, Bob and Dnyansagar, Rohit and Miller, David J. and Moya, Aurelie and Modepalli, Vengamanaidu and Fridrich, Arie and Sher, Daniel and Friis-Møller, Lene and Sundberg, Per and Fôret, Sylvain and Ashby, Regan and Moran, Yehu and Technau, Ulrich}, month = feb, year = {2021}, note = {Publisher: Royal Society}, keywords = {Cnidaria, miRNAs, ncRNA, microRNAs, miRNA, corals, cnidaria, conservation, microRNA targets, turnover}, pages = {20203169}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\K6Z42UPL\\Praher et al. - 2021 - Conservation and turnover of miRNAs and their high.pdf:application/pdf}, } @article{wani_modular_2021, title = {Modular network inference between {miRNA}–{mRNA} expression profiles using weighted co-expression network analysis}, volume = {18}, issn = {1613-4516}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709739/}, doi = {10.1515/jib-2021-0029}, abstract = {Connecting transcriptional and post-transcriptional regulatory networks solves an important puzzle in the elucidation of gene regulatory mechanisms. To decipher the complexity of these connections, we build co-expression network modules for mRNA as well as miRNA expression profiles of breast cancer data. We construct gene and miRNA co-expression modules using the weighted gene co-expression network analysis (WGCNA) method and establish the significance of these modules (Genes/miRNAs) for cancer phenotype. This work also infers an interaction network between the genes of the turquoise module from mRNA expression data and hubs of the turquoise module from miRNA expression data. A pathway enrichment analysis using a miRsystem web tool for miRNA hubs and some of their targets, reveal their enrichment in several important pathways associated with the progression of cancer.}, number = {4}, urldate = {2024-08-27}, journal = {Journal of Integrative Bioinformatics}, author = {Wani, Nisar and Barh, Debmalya and Raza, Khalid}, month = nov, year = {2021}, pmid = {34800012}, pmcid = {PMC8709739}, keywords = {WGCNA, miRNA, mRNA}, pages = {20210029}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\RFA8DY8B\\Wani et al. - 2021 - Modular network inference between miRNA–mRNA expre.pdf:application/pdf}, } @article{ricci_deep_2024, title = {Deep sea treasures - {Insights} from museum archives shed light on coral microbial diversity within deepest ocean ecosystems}, volume = {10}, issn = {2405-8440}, url = {https://www.cell.com/heliyon/abstract/S2405-8440(24)03544-8}, doi = {10.1016/j.heliyon.2024.e27513}, language = {English}, number = {5}, urldate = {2024-08-29}, journal = {Heliyon}, author = {Ricci, Francesco and Leggat, William and Pasella, Marisa M. and Bridge, Tom and Horowitz, Jeremy and Girguis, Peter R. and Ainsworth, Tracy}, month = mar, year = {2024}, pmid = {38333877}, note = {Publisher: Elsevier}, keywords = {Cyanobacteria, Deep sea, Deep water corals}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\NGAIYZCI\\Ricci et al. - 2024 - Deep sea treasures - Insights from museum archives.pdf:application/pdf}, } @incollection{schubert_symbiotic_2017, title = {Symbiotic {Versus} {Non}-symbiotic {Octocorals}: {Physiological} and {Ecological} {Implications}}, isbn = {978-3-319-17001-5}, shorttitle = {Symbiotic {Versus} {Non}-symbiotic {Octocorals}}, abstract = {Octocorals are a major component of the sessile benthic fauna worldwide, especially important in tropical regions, such as the Indo-Pacific and Caribbean, where together with hard corals they represent the most common group of macrobenthic animals of coral reefs. Despite their importance, little is known about their physiology, specifically the importance of their symbiotic relationship with the algal endosymbiont from the genus Symbiodinium, and the advantages/disadvantages associated with this symbiosis. In symbiotic species, the energetic contribution from Symbiodinium to the host might increase their resistance and/or recovery from stressful conditions, but the presence of these algal endosymbionts also limits octocoral distribution to the photic zone, where light is available. During the past few decades, octocorals have gained dominance in some tropical areas where scleractinian corals have declined due to climate change and local perturbations, increasing the need for research related to this understudied group. This chapter summarizes the current knowledge available about the ecology and physiology of octocorals, focusing on differences that are the result of the presence or absence of endosymbionts, and discusses the implications of having endosymbionts in the context of how octocorals may respond to global climate change. http://link.springer.com/referenceworkentry/10.1007/978-3-319-17001-5\_54-1}, author = {Schubert, Nadine and Brown, Darren and Rossi, Sergio}, month = feb, year = {2017}, doi = {10.1007/978-3-319-17001-5_54-1}, pages = {1--32}, } @article{van_de_water_host-microbe_2018, title = {Host-microbe interactions in octocoral holobionts - recent advances and perspectives}, volume = {6}, issn = {2049-2618}, url = {https://doi.org/10.1186/s40168-018-0431-6}, doi = {10.1186/s40168-018-0431-6}, abstract = {Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses.}, language = {en}, number = {1}, urldate = {2024-08-29}, journal = {Microbiome}, author = {van de Water, Jeroen A. J. M. and Allemand, Denis and Ferrier-Pagès, Christine}, month = apr, year = {2018}, keywords = {Microbiome, Immunity, Bacteria, Fungi, Gorgonians, Holobiont, Octocoral, Soft coral, Symbiodinium}, pages = {64}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\UDWC6XJQ\\van de Water et al. - 2018 - Host-microbe interactions in octocoral holobionts .pdf:application/pdf}, } @misc{noauthor_coral_nodate, title = {The coral microbiome in sickness, in health and in a changing world {\textbar} {Nature} {Reviews} {Microbiology}}, url = {https://www.nature.com/articles/s41579-024-01015-3}, urldate = {2024-09-10}, file = {The coral microbiome in sickness, in health and in a changing world | Nature Reviews Microbiology:C\:\\Users\\Owner\\Zotero\\storage\\GK9KRPSN\\s41579-024-01015-3.html:text/html}, } @article{baker_ancient_2013, title = {Ancient {DNA} from {Coral}-{Hosted} {Symbiodinium} {Reveal} a {Static} {Mutualism} over the {Last} 172 {Years}}, volume = {8}, issn = {1932-6203}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055057}, doi = {10.1371/journal.pone.0055057}, abstract = {Ancient DNA (aDNA) provides powerful evidence for detecting the genetic basis for adaptation to environmental change in many taxa. Among the greatest of changes in our biosphere within the last century is rapid anthropogenic ocean warming. This phenomenon threatens corals with extinction, evidenced by the increasing observation of widespread mortality following mass bleaching events. There is some evidence and conjecture that coral-dinoflagellate symbioses change partnerships in response to changing external conditions over ecological and evolutionary timescales. Until now, we have been unable to ascertain the genetic identity of Symbiodinium hosted by corals prior to the rapid global change of the last century. Here, we show that Symbiodinium cells recovered from dry, century old specimens of 6 host species of octocorals contain sufficient DNA for amplification of the ITS2 subregion of the nuclear ribosomal DNA, commonly used for genotyping within this genus. Through comparisons with modern specimens sampled from similar locales we show that symbiotic associations among several species have been static over the last century, thereby suggesting that adaptive shifts to novel symbiont types is not common among these gorgonians, and perhaps, symbiotic corals in general.}, language = {en}, number = {2}, urldate = {2024-09-10}, journal = {PLOS ONE}, author = {Baker, David M. and Weigt, Lee and Fogel, Marilyn and Knowlton, Nancy}, month = feb, year = {2013}, note = {Publisher: Public Library of Science}, keywords = {Corals, Symbiosis, Bleaching, DNA extraction, Florida, Islands, Museum collections, Polymerase chain reaction}, pages = {e55057}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\FTVEBQSG\\Baker et al. - 2013 - Ancient DNA from Coral-Hosted Symbiodinium Reveal .pdf:application/pdf}, } @article{connelly_unlocking_2024, title = {Unlocking the treasure trove: leveraging dry coral specimens for museum genomics}, volume = {43}, issn = {1432-0975}, shorttitle = {Unlocking the treasure trove}, url = {https://doi.org/10.1007/s00338-024-02525-5}, doi = {10.1007/s00338-024-02525-5}, abstract = {Natural history museums house the largest biodiversity collections in the world and represent an enormous repository of genetic information. Much of this information, however, has remained inaccessible until recently. Emerging technologies, such as techniques for isolation of historical DNA (hDNA) and target enrichment sequencing of ultraconserved elements (UCEs) that can utilize degraded DNA as input material, have the potential to unlock museum collections for genomics research. Here, we demonstrate that hDNA extracted from dried Pocillopora coral specimens, collected up to 90 yrs ago, can be used as input for UCE target enrichment sequencing. The resulting sequence data can be used in phylogenetic studies to resolve questions about taxonomic species identities, biogeographic distributions, and evolutionary histories. Our results provide a blueprint for research groups seeking to take advantage of untapped genetic information stored in natural history museum collections.}, language = {en}, number = {4}, urldate = {2024-09-10}, journal = {Coral Reefs}, author = {Connelly, Michael T. and Catapang, Mary Grace and Quattrini, Andrea M.}, month = aug, year = {2024}, keywords = {Biodiversity, Museum collections, Historical DNA, Museomics, UCEs}, pages = {1153--1159}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\8VPG5B34\\Connelly et al. - 2024 - Unlocking the treasure trove leveraging dry coral.pdf:application/pdf}, } @article{niiranen_epigenomic_2022, title = {Epigenomic {Modifications} in {Modern} and {Ancient} {Genomes}}, volume = {13}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2073-4425}, url = {https://www.mdpi.com/2073-4425/13/2/178}, doi = {10.3390/genes13020178}, abstract = {Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.}, language = {en}, number = {2}, urldate = {2024-09-16}, journal = {Genes}, author = {Niiranen, Laura and Leciej, Dawid and Edlund, Hanna and Bernhardsson, Carolina and Fraser, Magdalena and Quinto, Federico Sánchez and Herzig, Karl-Heinz and Jakobsson, Mattias and Walkowiak, Jarosław and Thalmann, Olaf}, month = feb, year = {2022}, note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {DNA methylation, epigenetics, diet, ancient DNA, lifestyle diseases, paleoepigenomics}, pages = {178}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\L3TU3URB\\Niiranen et al. - 2022 - Epigenomic Modifications in Modern and Ancient Gen.pdf:application/pdf}, } @article{raxworthy_mining_2021, title = {Mining museums for historical {DNA}: advances and challenges in museomics}, volume = {36}, issn = {0169-5347}, shorttitle = {Mining museums for historical {DNA}}, url = {https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(21)00214-7}, doi = {10.1016/j.tree.2021.07.009}, language = {English}, number = {11}, urldate = {2024-09-16}, journal = {Trends in Ecology \& Evolution}, author = {Raxworthy, Christopher J. and Smith, Brian Tilston}, month = nov, year = {2021}, pmid = {34456066}, note = {Publisher: Elsevier}, keywords = {ancient DNA, bioinformatics, collections, DNA degradation, historical DNA, museomics}, pages = {1049--1060}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\7FNC7XF5\\Raxworthy and Smith - 2021 - Mining museums for historical DNA advances and ch.pdf:application/pdf}, } @article{hahn_museum_2020, title = {Museum {Epigenomics}: {Charting} the {Future} by {Unlocking} the {Past}}, volume = {35}, issn = {0169-5347}, shorttitle = {Museum {Epigenomics}}, url = {https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(19)30347-7}, doi = {10.1016/j.tree.2019.12.005}, language = {English}, number = {4}, urldate = {2024-09-16}, journal = {Trends in Ecology \& Evolution}, author = {Hahn, Erin E. and Grealy, Alicia and Alexander, Marina and Holleley, Clare E.}, month = apr, year = {2020}, pmid = {31955919}, note = {Publisher: Elsevier}, keywords = {collections, epigenomics, gene regulation, genome, museum, temporal trends}, pages = {295--300}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\G6GC2GZI\\Hahn et al. - 2020 - Museum Epigenomics Charting the Future by Unlocki.pdf:application/pdf}, } @article{rubi_museum_2020, title = {Museum epigenomics: {Characterizing} cytosine methylation in historic museum specimens}, volume = {20}, copyright = {© 2019 John Wiley \& Sons Ltd}, issn = {1755-0998}, shorttitle = {Museum epigenomics}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13115}, doi = {10.1111/1755-0998.13115}, abstract = {Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we developed and tested methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulphite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013–2016. We successfully estimated methylation in specimens of all age groups, although older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1–3 years old), which may reflect post-mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.}, language = {en}, number = {5}, urldate = {2024-09-16}, journal = {Molecular Ecology Resources}, author = {Rubi, Tricia L. and Knowles, L. Lacey and Dantzer, Ben}, year = {2020}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13115}, keywords = {epigenetics, epigenomics, historic DNA, methylation, natural history collections, Peromyscus}, pages = {1161--1170}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\XBNMVY4G\\Rubi et al. - 2020 - Museum epigenomics Characterizing cytosine methyl.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\X8YIJFJM\\1755-0998.html:text/html}, } @article{rubi_patterns_2023, title = {Patterns of {Genetic} {And} {Epigenetic} {Diversity} {Across} {A} {Range} {Expansion} in {The} {White}-{Footed} {Mouse} ({Peromyscus} {Leucopus})}, volume = {5}, issn = {2517-4843}, doi = {10.1093/iob/obad038}, abstract = {Populations at the leading front of a range expansion must rapidly adapt to novel conditions. Increased epigenetic diversity has been hypothesized to facilitate adaptation and population persistence via non-genetic phenotypic variation, especially if there is reduced genetic diversity when populations expand (i.e., epigenetic diversity compensates for low genetic diversity). In this study, we use the spatial distribution of genetic and epigenetic diversity to test this hypothesis in populations of the white-footed mouse (Peromyscus leucopus) sampled across a purported recent range expansion gradient. We found mixed support for the epigenetic compensation hypothesis and a lack of support for expectations for expansion populations of mice at the range edge, which likely reflects a complex history of expansion in white-footed mice in the Upper Peninsula of Michigan. Specifically, epigenetic diversity was not increased in the population at the purported edge of the range expansion in comparison to the other expansion populations. However, input from an additional ancestral source populations may have increased genetic diversity at this range edge population, counteracting the expected genetic consequences of expansion, as well as reducing the benefit of increased epigenetic diversity at the range edge. Future work will expand the focal populations to include expansion areas with a single founding lineage to test for the robustness of a general trend that supports the hypothesized compensation of reduced genetic diversity by epigenetic variation observed in the expansion population that was founded from a single historical source.}, language = {eng}, number = {1}, journal = {Integrative Organismal Biology (Oxford, England)}, author = {Rubi, T. L. and do Prado, J. R. and Knowles, L. L. and Dantzer, B.}, year = {2023}, pmid = {37942286}, pmcid = {PMC10628966}, pages = {obad038}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\FCAZ2ICA\\Rubi et al. - 2023 - Patterns of Genetic And Epigenetic Diversity Acros.pdf:application/pdf}, } @article{rubenstein_target-enriched_2023, title = {Target-enriched enzymatic methyl sequencing: {Flexible}, scalable and inexpensive hybridization capture for quantifying {DNA} methylation}, volume = {18}, issn = {1932-6203}, shorttitle = {Target-enriched enzymatic methyl sequencing}, doi = {10.1371/journal.pone.0282672}, abstract = {The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling (Lamprotornis superbus), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.}, language = {eng}, number = {3}, journal = {PloS One}, author = {Rubenstein, Dustin R. and Solomon, Joseph}, year = {2023}, pmid = {36893162}, pmcid = {PMC9997987}, keywords = {Computational Biology, High-Throughput Nucleotide Sequencing, CpG Islands, DNA Methylation, Nucleic Acid Hybridization, Reproducibility of Results, Sequence Analysis, DNA}, pages = {e0282672}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\YX45TNUU\\Rubenstein and Solomon - 2023 - Target-enriched enzymatic methyl sequencing Flexi.pdf:application/pdf}, } @article{dixon_benchmarking_2021, title = {Benchmarking {DNA} methylation assays in a reef-building coral}, volume = {21}, copyright = {© 2020 John Wiley \& Sons Ltd}, issn = {1755-0998}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13282}, doi = {10.1111/1755-0998.13282}, abstract = {Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is currently too costly to apply at the scales required for ecological research. Here, we evaluate different methods for measuring DNA methylation for ecological epigenetics. We compare whole genome bisulphite sequencing (WGBS) with methylated CpG binding domain sequencing (MBD-seq), and a modified version of MethylRAD we term methylation-dependent restriction site-associated DNA sequencing (mdRAD). We evaluate these three assays in measuring variation in methylation across the genome, between genotypes, and between polyp types in the reef-building coral Acropora millepora. We find that all three assays measure absolute methylation levels similarly for gene bodies (gbM), as well as exons and 1 Kb windows with a minimum Pearson correlation 0.66. Differential gbM estimates were less correlated, but still concurrent across assays. We conclude that MBD-seq and mdRAD are reliable and cost-effective alternatives to WGBS. The considerably lower sequencing effort required for mdRAD to produce comparable methylation estimates makes it particularly useful for ecological epigenetics.}, language = {en}, number = {2}, urldate = {2024-09-17}, journal = {Molecular Ecology Resources}, author = {Dixon, Groves and Matz, Mikhail}, year = {2021}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13282}, keywords = {DNA methylation, coral, ecological epigenetics, gene body methylation, marine}, pages = {464--477}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\3W3GF75E\\Dixon and Matz - 2021 - Benchmarking DNA methylation assays in a reef-buil.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\5NDZKVQ9\\1755-0998.html:text/html}, } @article{putnam_avenues_2021, title = {Avenues of reef-building coral acclimatization in response to rapid environmental change}, volume = {224}, issn = {0022-0949}, url = {https://doi.org/10.1242/jeb.239319}, doi = {10.1242/jeb.239319}, abstract = {The swiftly changing climate presents a challenge to organismal fitness by creating a mismatch between the current environment and phenotypes adapted to historic conditions. Acclimatory mechanisms may be especially crucial for sessile benthic marine taxa, such as reef-building corals, where climate change factors including ocean acidification and increasing temperature elicit strong negative physiological responses such as bleaching, disease and mortality. Here, within the context of multiple stressors threatening marine organisms, I describe the wealth of metaorganism response mechanisms to rapid ocean change and the ontogenetic shifts in organism interactions with the environment that can generate plasticity. I then highlight the need to consider the interactions of rapid and evolutionary responses in an adaptive (epi)genetic continuum. Building on the definitions of these mechanisms and continuum, I also present how the interplay of the microbiome, epigenetics and parental effects creates additional avenues for rapid acclimatization. To consider under what conditions epigenetic inheritance has a more substantial role, I propose investigation into the offset of timing of gametogenesis leading to different environmental integration times between eggs and sperm and the consequences of this for gamete epigenetic compatibility. Collectively, non-genetic, yet heritable phenotypic plasticity will have significant ecological and evolutionary implications for sessile marine organism persistence under rapid climate change. As such, reef-building corals present ideal and time-sensitive models for further development of our understanding of adaptive feedback loops in a multi-player (epi)genetic continuum.}, number = {Suppl\_1}, urldate = {2024-09-17}, journal = {Journal of Experimental Biology}, author = {Putnam, Hollie M.}, month = feb, year = {2021}, pages = {jeb239319}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\ZZIYW6W4\\Putnam - 2021 - Avenues of reef-building coral acclimatization in .pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\NPSAHABI\\Avenues-of-reef-building-coral-acclimatization-in.html:text/html}, } @article{gavery_dna_2010, title = {{DNA} methylation patterns provide insight into epigenetic regulation in the {Pacific} oyster ({Crassostrea} gigas)}, volume = {11}, issn = {1471-2164}, url = {https://doi.org/10.1186/1471-2164-11-483}, doi = {10.1186/1471-2164-11-483}, abstract = {DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (Crassostrea gigas).}, number = {1}, urldate = {2024-09-17}, journal = {BMC Genomics}, author = {Gavery, Mackenzie R. and Roberts, Steven B.}, month = aug, year = {2010}, keywords = {Amino Terminal Fragment, Contig Database, Intragenic Methylation, Pacific Oyster, Slim Term}, pages = {483}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\4WLMLFBK\\Gavery and Roberts - 2010 - DNA methylation patterns provide insight into epig.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\EZLW26WD\\1471-2164-11-483.html:text/html}, } @article{gavery_predominant_2013, title = {Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc}, volume = {1}, issn = {2167-8359}, doi = {10.7717/peerj.215}, abstract = {Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.}, language = {eng}, journal = {PeerJ}, author = {Gavery, Mackenzie R. and Roberts, Steven B.}, year = {2013}, pmid = {24282674}, pmcid = {PMC3840415}, keywords = {Gene regulation, DNA methylation, Bivalve, Epigenetics, Methylome, Mollusc}, pages = {e215}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\MYJ3X95X\\Gavery and Roberts - 2013 - Predominant intragenic methylation is associated w.pdf:application/pdf}, } @article{dixon_bimodal_2014, title = {Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral {Acropora} millepora}, volume = {15}, issn = {1471-2164}, url = {https://doi.org/10.1186/1471-2164-15-1109}, doi = {10.1186/1471-2164-15-1109}, abstract = {In invertebrates, genes belonging to dynamically regulated functional categories appear to be less methylated than “housekeeping” genes, suggesting that DNA methylation may modulate gene expression plasticity. To date, however, experimental evidence to support this hypothesis across different natural habitats has been lacking.}, number = {1}, urldate = {2024-09-17}, journal = {BMC Genomics}, author = {Dixon, Groves B. and Bay, Line K. and Matz, Mikhail V.}, month = dec, year = {2014}, keywords = {DNA methylation, Coral, Gene expression, Acropora millepora, Flexibility, Gene body methylation, Plasticity}, pages = {1109}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\DYR5L7T2\\Dixon et al. - 2014 - Bimodal signatures of germline methylation are lin.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\UNXNFQLT\\1471-2164-15-1109.html:text/html}, } @article{dixon_evolutionary_2016, title = {Evolutionary {Consequences} of {DNA} {Methylation} in a {Basal} {Metazoan}}, volume = {33}, issn = {0737-4038}, url = {https://doi.org/10.1093/molbev/msw100}, doi = {10.1093/molbev/msw100}, abstract = {Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons.}, number = {9}, urldate = {2024-09-17}, journal = {Molecular Biology and Evolution}, author = {Dixon, Groves B. and Bay, Line K. and Matz, Mikhail V.}, month = sep, year = {2016}, pages = {2285--2293}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\DTNMGVB5\\Dixon et al. - 2016 - Evolutionary Consequences of DNA Methylation in a .pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\HMMLK3JM\\2579041.html:text/html}, } @article{dimond_germline_2016, title = {Germline {DNA} methylation in reef corals: patterns and potential roles in response to environmental change}, volume = {25}, copyright = {© 2015 John Wiley \& Sons Ltd}, issn = {1365-294X}, shorttitle = {Germline {DNA} methylation in reef corals}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13414}, doi = {10.1111/mec.13414}, abstract = {DNA methylation is an epigenetic mark that plays an inadequately understood role in gene regulation, particularly in nonmodel species. Because it can be influenced by the environment, DNA methylation may contribute to the ability of organisms to acclimatize and adapt to environmental change. We evaluated the distribution of gene body methylation in reef-building corals, a group of organisms facing significant environmental threats. Gene body methylation in six species of corals was inferred from in silico transcriptome analysis of CpG O/E, an estimate of germline DNA methylation that is highly correlated with patterns of methylation enrichment. Consistent with what has been documented in most other invertebrates, all corals exhibited bimodal distributions of germline methylation suggestive of distinct fractions of genes with high and low levels of methylation. The hypermethylated fractions were enriched with genes with housekeeping functions, while genes with inducible functions were highly represented in the hypomethylated fractions. High transcript abundance was associated with intermediate levels of methylation. In three of the coral species, we found that genes differentially expressed in response to thermal stress and ocean acidification exhibited significantly lower levels of methylation. These results support a link between gene body hypomethylation and transcriptional plasticity that may point to a role of DNA methylation in the response of corals to environmental change.}, language = {en}, number = {8}, urldate = {2024-09-17}, journal = {Molecular Ecology}, author = {Dimond, James L. and Roberts, Steven B.}, year = {2016}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13414}, keywords = {DNA methylation, coral, climate change, epigenetics}, pages = {1895--1904}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\WW6WKY6F\\Dimond and Roberts - 2016 - Germline DNA methylation in reef corals patterns .pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\BWNJ2HNU\\mec.html:text/html}, } @article{peterson_mixed_2024, title = {Mixed {Patterns} of {Intergenerational} {DNA} {Methylation} {Inheritance} in {Acropora}}, volume = {41}, issn = {1537-1719}, url = {https://doi.org/10.1093/molbev/msae008}, doi = {10.1093/molbev/msae008}, abstract = {For sessile organisms at high risk from climate change, phenotypic plasticity can be critical to rapid acclimation. Epigenetic markers like DNA methylation are hypothesized as mediators of plasticity; methylation is associated with the regulation of gene expression, can change in response to ecological cues, and is a proposed basis for the inheritance of acquired traits. Within reef-building corals, gene-body methylation (gbM) can change in response to ecological stressors. If coral DNA methylation is transmissible across generations, this could potentially facilitate rapid acclimation to environmental change. We investigated methylation heritability in Acropora, a stony reef-building coral. Two Acropora millepora and two Acropora selago adults were crossed, producing eight offspring crosses (four hybrid, two of each species). We used whole-genome bisulfite sequencing to identify methylated loci and allele-specific alignments to quantify per-locus inheritance. If methylation is heritable, differential methylation (DM) between the parents should equal DM between paired offspring alleles at a given locus. We found a mixture of heritable and nonheritable loci, with heritable portions ranging from 44\% to 90\% among crosses. gBM was more heritable than intergenic methylation, and most loci had a consistent degree of heritability between crosses (i.e. the deviation between parental and offspring DM were of similar magnitude and direction). Our results provide evidence that coral methylation can be inherited but that heritability is heterogenous throughout the genome. Future investigations into this heterogeneity and its phenotypic implications will be important to understanding the potential capability of intergenerational environmental acclimation in reef building corals.}, number = {2}, urldate = {2024-09-17}, journal = {Molecular Biology and Evolution}, author = {Peterson, Christopher R and Scott, Carly B and Ghaffari, Rashin and Dixon, Groves and Matz, Mikhail V}, month = feb, year = {2024}, pages = {msae008}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\MMX9BYUK\\Peterson et al. - 2024 - Mixed Patterns of Intergenerational DNA Methylatio.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\LS66MYDB\\7577635.html:text/html}, } @article{delaunay_rna_2024, title = {{RNA} modifications in physiology and disease: towards clinical applications}, volume = {25}, copyright = {2023 Springer Nature Limited}, issn = {1471-0064}, shorttitle = {{RNA} modifications in physiology and disease}, url = {https://www.nature.com/articles/s41576-023-00645-2}, doi = {10.1038/s41576-023-00645-2}, abstract = {The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules — to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.}, language = {en}, number = {2}, urldate = {2024-09-23}, journal = {Nature Reviews Genetics}, author = {Delaunay, Sylvain and Helm, Mark and Frye, Michaela}, month = feb, year = {2024}, note = {Publisher: Nature Publishing Group}, keywords = {Gene regulation, Gene expression}, pages = {104--122}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\JD2SGZ2K\\Delaunay et al. - 2024 - RNA modifications in physiology and disease towar.pdf:application/pdf}, } @article{li_pivotal_2014, title = {The {Pivotal} {Regulatory} {Landscape} of {RNA} {Modifications}}, volume = {15}, issn = {1527-8204, 1545-293X}, url = {https://www.annualreviews.org/content/journals/10.1146/annurev-genom-090413-025405}, doi = {10.1146/annurev-genom-090413-025405}, abstract = {Posttranscriptionally modified nucleosides in RNA play integral roles in the cellular control of biological information that is encoded in DNA. The modifications of RNA span all three phylogenetic domains (Archaea, Bacteria, and Eukarya) and are pervasive across RNA types, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and (less frequently) small nuclear RNA (snRNA) and microRNA (miRNA). Nucleotide modifications are also one of the most evolutionarily conserved properties of RNAs, and the sites of modification are under strong selective pressure. However, many of these modifications, as well as their prevalence and impact, have only recently been discovered. Here, we examine both labile and permanent modifications, from simple methylation to complex transcript alteration (RNA editing and intron retention); detail the models for their processing; and highlight remaining questions in the field of the epitranscriptome.}, language = {en}, number = {Volume 15, 2014}, urldate = {2024-09-23}, journal = {Annual Review of Genomics and Human Genetics}, author = {Li, Sheng and Mason, Christopher E.}, month = aug, year = {2014}, note = {Publisher: Annual Reviews}, pages = {127--150}, file = {Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\VMJL237I\\annurev-genom-090413-025405.html:text/html}, } @article{roundtree_dynamic_2017, title = {Dynamic {RNA} {Modifications} in {Gene} {Expression} {Regulation}}, volume = {169}, issn = {0092-8674, 1097-4172}, url = {https://www.cell.com/cell/abstract/S0092-8674(17)30638-4}, doi = {10.1016/j.cell.2017.05.045}, language = {English}, number = {7}, urldate = {2024-09-23}, journal = {Cell}, author = {Roundtree, Ian A. and Evans, Molly E. and Pan, Tao and He, Chuan}, month = jun, year = {2017}, pmid = {28622506}, note = {Publisher: Elsevier}, pages = {1187--1200}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\7DGAP97N\\Roundtree et al. - 2017 - Dynamic RNA Modifications in Gene Expression Regul.pdf:application/pdf}, } @article{li_transcriptome-wide_2016, title = {Transcriptome-wide mapping reveals reversible and dynamic {N}(1)-methyladenosine methylome}, volume = {12}, issn = {1552-4469}, doi = {10.1038/nchembio.2040}, abstract = {N(1)-Methyladenosine (m(1)A) is a prevalent post-transcriptional RNA modification, yet little is known about its abundance, topology and dynamics in mRNA. Here, we show that m(1)A is prevalent in Homo sapiens mRNA, which shows an m(1)A/A ratio of ∼0.02\%. We develop the m(1)A-ID-seq technique, based on m(1)A immunoprecipitation and the inherent ability of m(1)A to stall reverse transcription, as a means for transcriptome-wide m(1)A profiling. m(1)A-ID-seq identifies 901 m(1)A peaks (from 600 genes) in mRNA and noncoding RNA and reveals a prominent feature, enrichment in the 5' untranslated region of mRNA transcripts, that is distinct from the pattern for N(6)-methyladenosine, the most abundant internal mammalian mRNA modification. Moreover, m(1)A in mRNA is reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, we show that m(1)A methylation responds dynamically to stimuli, and we identify hundreds of stress-induced m(1)A sites. Collectively, our approaches allow comprehensive analysis of m(1)A modification and provide tools for functional studies of potential epigenetic regulation via the reversible and dynamic m(1)A methylation.}, language = {eng}, number = {5}, journal = {Nature Chemical Biology}, author = {Li, Xiaoyu and Xiong, Xushen and Wang, Kun and Wang, Lixia and Shu, Xiaoting and Ma, Shiqing and Yi, Chengqi}, month = may, year = {2016}, pmid = {26863410}, keywords = {Transcriptome, Humans, Methylation, Base Sequence, RNA, Messenger, Adenosine, AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase, Antibodies, Cell Line, Dioxygenases, DNA Repair Enzymes, Gene Expression Regulation, RNA Processing, Post-Transcriptional}, pages = {311--316}, } @article{leger_rna_2021, title = {{RNA} modifications detection by comparative {Nanopore} direct {RNA} sequencing}, volume = {12}, copyright = {2021 The Author(s)}, issn = {2041-1723}, url = {https://www.nature.com/articles/s41467-021-27393-3}, doi = {10.1038/s41467-021-27393-3}, abstract = {RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. In recent years, a growing number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework that identifies modifications from these data. Our strategy compares an RNA sample of interest against a non-modified control sample, not requiring a training set and allowing the use of replicates. We show that Nanocompore can detect different RNA modifications with position accuracy in vitro, and we apply it to profile m6A in vivo in yeast and human RNAs, as well as in targeted non-coding RNAs. We confirm our results with orthogonal methods and provide novel insights on the co-occurrence of multiple modified residues on individual RNA molecules.}, language = {en}, number = {1}, urldate = {2024-09-23}, journal = {Nature Communications}, author = {Leger, Adrien and Amaral, Paulo P. and Pandolfini, Luca and Capitanchik, Charlotte and Capraro, Federica and Miano, Valentina and Migliori, Valentina and Toolan-Kerr, Patrick and Sideri, Theodora and Enright, Anton J. and Tzelepis, Konstantinos and van Werven, Folkert J. and Luscombe, Nicholas M. and Barbieri, Isaia and Ule, Jernej and Fitzgerald, Tomas and Birney, Ewan and Leonardi, Tommaso and Kouzarides, Tony}, month = dec, year = {2021}, note = {Publisher: Nature Publishing Group}, keywords = {RNA sequencing, Transcriptomics, Software, Bioinformatics}, pages = {7198}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\FZN2DVXQ\\Leger et al. - 2021 - RNA modifications detection by comparative Nanopor.pdf:application/pdf}, } @article{engel_role_2018, title = {The {Role} of {m6A}/m-{RNA} {Methylation} in {Stress} {Response} {Regulation}}, volume = {99}, issn = {0896-6273}, url = {https://www.cell.com/neuron/abstract/S0896-6273(18)30583-X}, doi = {10.1016/j.neuron.2018.07.009}, language = {English}, number = {2}, urldate = {2024-09-23}, journal = {Neuron}, author = {Engel, Mareen and Eggert, Carola and Kaplick, Paul M. and Eder, Matthias and Röh, Simone and Tietze, Lisa and Namendorf, Christian and Arloth, Janine and Weber, Peter and Rex-Haffner, Monika and Geula, Shay and Jakovcevski, Mira and Hanna, Jacob H. and Leshkowitz, Dena and Uhr, Manfred and Wotjak, Carsten T. and Schmidt, Mathias V. and Deussing, Jan M. and Binder, Elisabeth B. and Chen, Alon}, month = jul, year = {2018}, pmid = {30048615}, note = {Publisher: Elsevier}, keywords = {stress, Fto, m6A, m6Am, major depressive disorder, Mettl3, post-transcriptional regulation, RNA modification}, pages = {389--403.e9}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\P6KHCDSH\\Engel et al. - 2018 - The Role of m6Am-RNA Methylation in Stress Respon.pdf:application/pdf}, } @article{wilkinson_context-dependent_2021, title = {Context-{Dependent} {Roles} of {RNA} {Modifications} in {Stress} {Responses} and {Diseases}}, volume = {22}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/22/4/1949}, doi = {10.3390/ijms22041949}, abstract = {RNA modifications are diverse post-transcriptional modifications that regulate RNA metabolism and gene expression. RNA modifications, and the writers, erasers, and readers that catalyze these modifications, serve as important signaling machineries in cellular stress responses and disease pathogenesis. In response to stress, RNA modifications are mobilized to activate or inhibit the signaling pathways that combat stresses, including oxidative stress, hypoxia, therapeutic stress, metabolic stress, heat shock, DNA damage, and ER stress. The role of RNA modifications in response to these cellular stressors is context- and cell-type-dependent. Due to their pervasive roles in cell biology, RNA modifications have been implicated in the pathogenesis of different diseases, including cancer, neurologic and developmental disorders and diseases, and metabolic diseases. In this review, we aim to summarize the roles of RNA modifications in molecular and cellular stress responses and diseases.}, language = {en}, number = {4}, urldate = {2024-09-23}, journal = {International Journal of Molecular Sciences}, author = {Wilkinson, Emma and Cui, Yan-Hong and He, Yu-Ying}, month = jan, year = {2021}, note = {Number: 4 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {cellular stress, disease, m$^{\textrm{6}}$A, RNA modifications}, pages = {1949}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\UBNPBXST\\Wilkinson et al. - 2021 - Context-Dependent Roles of RNA Modifications in St.pdf:application/pdf}, } @article{moser_targeted_2020, title = {Targeted bisulfite sequencing: {A} novel tool for the assessment of {DNA} methylation with high sensitivity and increased coverage}, volume = {120}, issn = {0306-4530}, shorttitle = {Targeted bisulfite sequencing}, url = {https://www.sciencedirect.com/science/article/pii/S0306453020302055}, doi = {10.1016/j.psyneuen.2020.104784}, abstract = {DNA methylation analysis is increasingly used in stress research. Available methods are expensive, laborious and often limited by either the analysis of short CpG stretches or low assay sensitivity. Here, we present a cost-efficient next generation sequencing-based strategy for the simultaneous investigation of multiple candidate genes in large cohorts. To illustrate the method, we present analysis of four candidate genes commonly assessed in psychoneuroendocrine research: Glucocorticoid receptor (NR3C1), Serotonin transporter (SLC6A4), FKBP Prolyl isomerase 5 (FKBP5), and the Oxytocin receptor (OXTR). DNA methylation standards (100 \%; 75 \%; 50 \%; 25 \% and 0 \%) and DNA of a female and male donor were bisulfite treated in three independent trials and were used to generate sequencing libraries for 42 CpGs from the NR3C1 1 F promoter region, 84 CpGs of the SLC6A4 5′ regulatory region, 5 CpGs located in FKBP5 intron 7, and additional 12 CpGs located in a potential enhancer element in intron 3 of the OXTR. In addition, DNA of 45 patients with borderline personality disorder (BPD) and 45 healthy controls was assayed. Multiplex libraries of all samples were sequenced on a MiSeq system and analyzed for mean methylation values of all CpG sites using amplikyzer2 software. Results indicated excellent accuracy of the assays when investigating replicates generated from the same bisulfite converted DNA, and very high linearity (R2 {\textgreater} 0.9) of the assays shown by the analysis of differentially methylated DNA standards. Comparing DNA methylation between BPD and healthy controls revealed no biologically relevant differences. The technical approach as described here facilitates targeted DNA methylation analysis and represents a highly sensitive, cost-efficient and high throughput tool to close the gap between coverage and precision in epigenetic research of stress-associated phenotypes.}, urldate = {2024-09-23}, journal = {Psychoneuroendocrinology}, author = {Moser, D. A. and Müller, S. and Hummel, E. M. and Limberg, A. S. and Dieckmann, L. and Frach, L. and Pakusch, J. and Flasbeck, V and Brüne, M. and Beygo, J. and Klein-Hitpass, L. and Kumsta, R.}, month = oct, year = {2020}, keywords = {DNA methylation, Epigenetics, Borderline personality disorder (BPD), Targeted bisulfite sequencing}, pages = {104784}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\NGEN9IUW\\S0306453020302055.html:text/html;Submitted Version:C\:\\Users\\Owner\\Zotero\\storage\\MZDJNQFX\\Moser et al. - 2020 - Targeted bisulfite sequencing A novel tool for th.pdf:application/pdf}, } @article{kloc_invertebrate_2024, title = {Invertebrate {Immunity}, {Natural} {Transplantation} {Immunity}, {Somatic} and {Germ} {Cell} {Parasitism}, and {Transposon} {Defense}}, volume = {25}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/25/2/1072}, doi = {10.3390/ijms25021072}, abstract = {While the vertebrate immune system consists of innate and adaptive branches, invertebrates only have innate immunity. This feature makes them an ideal model system for studying the cellular and molecular mechanisms of innate immunity sensu stricto without reciprocal interferences from adaptive immunity. Although invertebrate immunity is evolutionarily older and a precursor of vertebrate immunity, it is far from simple. Despite lacking lymphocytes and functional immunoglobulin, the invertebrate immune system has many sophisticated mechanisms and features, such as long-term immune memory, which, for decades, have been exclusively attributed to adaptive immunity. In this review, we describe the cellular and molecular aspects of invertebrate immunity, including the epigenetic foundation of innate memory, the transgenerational inheritance of immunity, genetic immunity against invading transposons, the mechanisms of self-recognition, natural transplantation, and germ/somatic cell parasitism.}, language = {en}, number = {2}, urldate = {2024-09-23}, journal = {International Journal of Molecular Sciences}, author = {Kloc, Malgorzata and Halasa, Marta and Kubiak, Jacek Z. and Ghobrial, Rafik M.}, month = jan, year = {2024}, note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {transgenerational inheritance, epigenetics, hemocyte, innate immunity, innate memory, invertebrate, transposons}, pages = {1072}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\NTL7UJQL\\Kloc et al. - 2024 - Invertebrate Immunity, Natural Transplantation Imm.pdf:application/pdf}, } @article{alon_majority_2015, title = {The majority of transcripts in the squid nervous system are extensively recoded by {A}-to-{I} {RNA} editing}, volume = {4}, issn = {2050-084X}, url = {https://doi.org/10.7554/eLife.05198}, doi = {10.7554/eLife.05198}, abstract = {RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.}, urldate = {2024-09-23}, journal = {eLife}, author = {Alon, Shahar and Garrett, Sandra C and Levanon, Erez Y and Olson, Sara and Graveley, Brenton R and Rosenthal, Joshua J C and Eisenberg, Eli}, editor = {Guigó, Roderic}, month = jan, year = {2015}, note = {Publisher: eLife Sciences Publications, Ltd}, keywords = {RNA editing, Doryteuthis pealeii, recoding}, pages = {e05198}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\6H9XLALK\\Alon et al. - 2015 - The majority of transcripts in the squid nervous s.pdf:application/pdf}, } @article{ivanisevic_rna_2023, title = {{RNA} {Editing}-{Dependent} and -{Independent} {Roles} of {Adenosine} {Deaminases} {Acting} on {RNA} {Proteins} in {Herpesvirus} {Infection}—{Hints} on {Another} {Layer} of {Complexity}}, volume = {15}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {1999-4915}, url = {https://www.mdpi.com/1999-4915/15/10/2007}, doi = {10.3390/v15102007}, abstract = {The Adenosine Deaminases Acting on RNA (ADAR) catalyze the posttranscriptional deamination of adenosine residues to inosine in double-stranded RNAs (dsRNAs, A-to-I editing), preventing the overactivation of dsRNA sensor molecules and interferons. RNA editing is the cornerstone of innate immunity that distinguishes between self and non-self (virus), and it is essential for normal regulation of cellular homeostasis. Although much is already known about the role of ADAR proteins in RNA virus infection, the role of ADAR proteins in herpesvirus infection remains largely unexplored. In this review, we provide several lines of evidence from studies of different herpesviruses for another level of complexity in regulating the already intricate biphasic life cycle of herpesviruses.}, language = {en}, number = {10}, urldate = {2024-09-23}, journal = {Viruses}, author = {Ivanišević, Vlatka and Žilić, Lidia and Čunko, Marina and Fadiga, Hana and Munitić, Ivana and Jurak, Igor}, month = oct, year = {2023}, note = {Number: 10 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {RNA editing, miRNA, innate immunity, ADAR, dsRNA, herpesvirus, latency}, pages = {2007}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\AMAP8MQX\\Ivanišević et al. - 2023 - RNA Editing-Dependent and -Independent Roles of Ad.pdf:application/pdf}, } @book{noauthor_read_nodate, title = {Read "{Ecosystem} {Concepts} for {Sustainable} {Bivalve} {Mariculture}" at {NAP}.edu}, url = {https://nap.nationalacademies.org/read/12802/chapter/9}, abstract = {Read chapter 7 Ecosystem Services of Bivalves: Implications for Restoration: U.S. mariculture production of bivalve molluscs-those cultivated in the marin...}, language = {en}, urldate = {2024-09-23}, doi = {10.17226/12802}, file = {Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\7LQA6CL8\\9.html:text/html}, } @article{mazaleyrat_26-year_2022, title = {A 26-year time series of mortality and growth of the {Pacific} oyster {C}. gigas recorded along {French} coasts}, volume = {9}, copyright = {2022 The Author(s)}, issn = {2052-4463}, url = {https://www.nature.com/articles/s41597-022-01511-2}, doi = {10.1038/s41597-022-01511-2}, abstract = {We used a compiled data set from a monitoring network of oyster production coordinated by IFREMER (the French Research Institute for the Exploitation of the Sea). This network monitors the growth and mortality of the Pacific oyster Crassostrea gigas along French coasts since 1993. The archive, although publicly available, has been challenging to use due to changes in protocols and little information on metadata. Here, we describe data collection for almost 30 years, cleaning and processing. For 13 locations, we modeled growth and mortality of spat (less than one-year-old individuals) and half-grown oysters (between one and two-year-old individuals) as a function of time to cope with changes in data acquisition frequency, and produced standardized annual growth and cumulative mortality indicators to improve data usability. This improved database is expected to be used by ecologists interested in the evolution of life-cycle indicators of a marine species under the influence of climate change. It can also be valuable for epidemiologists because mortality data traces the emergence and spread of a massive epizootic.}, language = {en}, number = {1}, urldate = {2024-09-23}, journal = {Scientific Data}, author = {Mazaleyrat, Anna and Normand, Julien and Dubroca, Laurent and Fleury, Elodie}, month = jul, year = {2022}, note = {Publisher: Nature Publishing Group}, keywords = {Ecological modelling, Marine biology, Biooceanography, Standardization, Time series}, pages = {392}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\PSSS52FD\\Mazaleyrat et al. - 2022 - A 26-year time series of mortality and growth of t.pdf:application/pdf}, } @article{radchuk_adaptive_2019, title = {Adaptive responses of animals to climate change are most likely insufficient}, volume = {10}, copyright = {2019 The Author(s)}, issn = {2041-1723}, url = {https://www.nature.com/articles/s41467-019-10924-4}, doi = {10.1038/s41467-019-10924-4}, abstract = {Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.}, language = {en}, number = {1}, urldate = {2024-09-23}, journal = {Nature Communications}, author = {Radchuk, Viktoriia and Reed, Thomas and Teplitsky, Céline and van de Pol, Martijn and Charmantier, Anne and Hassall, Christopher and Adamík, Peter and Adriaensen, Frank and Ahola, Markus P. and Arcese, Peter and Miguel Avilés, Jesús and Balbontin, Javier and Berg, Karl S. and Borras, Antoni and Burthe, Sarah and Clobert, Jean and Dehnhard, Nina and de Lope, Florentino and Dhondt, André A. and Dingemanse, Niels J. and Doi, Hideyuki and Eeva, Tapio and Fickel, Joerns and Filella, Iolanda and Fossøy, Frode and Goodenough, Anne E. and Hall, Stephen J. G. and Hansson, Bengt and Harris, Michael and Hasselquist, Dennis and Hickler, Thomas and Joshi, Jasmin and Kharouba, Heather and Martínez, Juan Gabriel and Mihoub, Jean-Baptiste and Mills, James A. and Molina-Morales, Mercedes and Moksnes, Arne and Ozgul, Arpat and Parejo, Deseada and Pilard, Philippe and Poisbleau, Maud and Rousset, Francois and Rödel, Mark-Oliver and Scott, David and Senar, Juan Carlos and Stefanescu, Constanti and Stokke, Bård G. and Kusano, Tamotsu and Tarka, Maja and Tarwater, Corey E. and Thonicke, Kirsten and Thorley, Jack and Wilting, Andreas and Tryjanowski, Piotr and Merilä, Juha and Sheldon, Ben C. and Pape Møller, Anders and Matthysen, Erik and Janzen, Fredric and Dobson, F. Stephen and Visser, Marcel E. and Beissinger, Steven R. and Courtiol, Alexandre and Kramer-Schadt, Stephanie}, month = jul, year = {2019}, note = {Publisher: Nature Publishing Group}, keywords = {Climate-change ecology, Evolutionary ecology, Conservation biology}, pages = {3109}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\K93W8B4P\\Radchuk et al. - 2019 - Adaptive responses of animals to climate change ar.pdf:application/pdf}, } @book{samain_summer_2008, title = {Summer {Mortality} of {Pacific} {Oyster} {Crassostrea} {Gigas}: {The} {Morest} {Project}}, isbn = {978-2-7592-0054-2}, shorttitle = {Summer {Mortality} of {Pacific} {Oyster} {Crassostrea} {Gigas}}, abstract = {Mass oyster mortalities have been known for many years throughout the world, but no strictly pathological explication has been found. This book describes how environmental influences, reproduction, stress, genetics, pathogens and temperature contribute to oyster summer mortality in France. An interaction model is derived from the results and recommendations are made for forecasting and managing risk factors.}, language = {en}, publisher = {Editions Quae}, author = {Samain, Jean-François and McCombie, Helen}, month = feb, year = {2008}, note = {Google-Books-ID: QiajU0f3j8gC}, keywords = {Technology \& Engineering / Fisheries \& Aquaculture}, } @article{ahsan_signal_2024, title = {A signal processing and deep learning framework for methylation detection using {Oxford} {Nanopore} sequencing}, volume = {15}, copyright = {2024 The Author(s)}, issn = {2041-1723}, url = {https://www.nature.com/articles/s41467-024-45778-y}, doi = {10.1038/s41467-024-45778-y}, abstract = {Oxford Nanopore sequencing can detect DNA methylations from ionic current signal of single molecules, offering a unique advantage over conventional methods. Additionally, adaptive sampling, a software-controlled enrichment method for targeted sequencing, allows reduced representation methylation sequencing that can be applied to CpG islands or imprinted regions. Here we present DeepMod2, a comprehensive deep-learning framework for methylation detection using ionic current signal from Nanopore sequencing. DeepMod2 implements both a bidirectional long short-term memory (BiLSTM) model and a Transformer model and can analyze POD5 and FAST5 signal files generated on R9 and R10 flowcells. Additionally, DeepMod2 can run efficiently on central processing unit (CPU) through model pruning and can infer epihaplotypes or haplotype-specific methylation calls from phased reads. We use multiple publicly available and newly generated datasets to evaluate the performance of DeepMod2 under varying scenarios. DeepMod2 has comparable performance to Guppy and Dorado, which are the current state-of-the-art methods from Oxford Nanopore Technologies that remain closed-source. Moreover, we show a high correlation (r = 0.96) between reduced representation and whole-genome Nanopore sequencing. In summary, DeepMod2 is an open-source tool that enables fast and accurate DNA methylation detection from whole-genome or adaptive sequencing data on a diverse range of flowcell types.}, language = {en}, number = {1}, urldate = {2024-09-25}, journal = {Nature Communications}, author = {Ahsan, Mian Umair and Gouru, Anagha and Chan, Joe and Zhou, Wanding and Wang, Kai}, month = feb, year = {2024}, note = {Publisher: Nature Publishing Group}, keywords = {Computational models, Machine learning}, pages = {1448}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\SMBN7ZRV\\Ahsan et al. - 2024 - A signal processing and deep learning framework fo.pdf:application/pdf}, } @article{bekesi_detection_2021, title = {Detection of {Genomic} {Uracil} {Patterns}}, volume = {22}, issn = {1422-0067}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070346/}, doi = {10.3390/ijms22083902}, abstract = {The appearance of uracil in the deoxyuridine moiety of DNA is among the most frequently occurring genomic modifications. Three different routes can result in genomic uracil, two of which do not require specific enzymes: spontaneous cytosine deamination due to the inherent chemical reactivity of living cells, and thymine-replacing incorporation upon nucleotide pool imbalances. There is also an enzymatic pathway of cytosine deamination with multiple DNA (cytosine) deaminases involved in this process. In order to describe potential roles of genomic uracil, it is of key importance to utilize efficient uracil-DNA detection methods. In this review, we provide a comprehensive and critical assessment of currently available uracil detection methods with special focus on genome-wide mapping solutions. Recent developments in PCR-based and in situ detection as well as the quantitation of genomic uracil are also discussed.}, number = {8}, urldate = {2024-09-25}, journal = {International Journal of Molecular Sciences}, author = {Békési, Angéla and Holub, Eszter and Pálinkás, Hajnalka Laura and Vértessy, Beáta G.}, month = apr, year = {2021}, pmid = {33918885}, pmcid = {PMC8070346}, pages = {3902}, file = {PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\7KQD23AP\\Békési et al. - 2021 - Detection of Genomic Uracil Patterns.pdf:application/pdf}, } @article{li_small_2022, title = {Small {RNAs} in {Cnidaria}: {A} review}, volume = {16}, issn = {1752-4571}, shorttitle = {Small {RNAs} in {Cnidaria}}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9923473/}, doi = {10.1111/eva.13445}, abstract = {As fundamental components of RNA silencing, small RNA (sRNA) molecules ranging from 20 to 32 nucleotides in length have been found as potent regulators of gene expression and genome stability in many biological processes of eukaryotes. Three major small RNAs are active in animals, including the microRNA (miRNA), short interfering RNA (siRNA), and PIWI‐interacting RNA (piRNA). Cnidarians, the sister group to bilaterians, are at a critical phylogenetic node to better model eukaryotic small RNA pathway evolution. To date, most of our understanding of sRNA regulation and its potential contribution to evolution has been limited to a few triploblastic bilaterian and plant models. The diploblastic nonbilaterians, including the cnidarians, are understudied in this regard. Therefore, this review will present the current‐known small RNA information in cnidarians to enhance our understanding of the development of the small RNA pathways in early branch animals.}, number = {2}, urldate = {2024-06-14}, journal = {Evolutionary Applications}, author = {Li, Yiqian and Hui, Jerome H. L.}, month = jul, year = {2022}, pmid = {36793685}, pmcid = {PMC9923473}, keywords = {Cnidaria, cnidarians, corals, evolution, miRNA, small RNAs, sncRNA}, pages = {354--364}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\ZKJ7Y3BZ\\Li and Hui - 2023 - Small RNAs in Cnidaria A review.pdf:application/pdf;Praveen Guleria (editor), Vineet Kumar (editor) - Guleria, P_ Plant Small RNA-Academic Press Inc (2020).pdf:C\:\\Users\\Owner\\Zotero\\storage\\H9KXENAG\\Praveen Guleria (editor), Vineet Kumar (editor) - Guleria, P_ Plant Small RNA-Academic Press Inc (2020).pdf:application/pdf;PubMed Central Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\D6FBHGRZ\\Li and Hui - 2022 - Small RNAs in Cnidaria A review.pdf:application/pdf}, } @article{huang_lncrna-mediated_2022, title = {{LncRNA}-mediated {DNA} methylation: an emerging mechanism in cancer and beyond}, volume = {41}, issn = {1756-9966}, shorttitle = {{LncRNA}-mediated {DNA} methylation}, url = {https://doi.org/10.1186/s13046-022-02319-z}, doi = {10.1186/s13046-022-02319-z}, abstract = {DNA methylation is one of the most important epigenetic mechanisms to regulate gene expression, which is highly dynamic during development and specifically maintained in somatic cells. Aberrant DNA methylation patterns are strongly associated with human diseases including cancer. How are the cell-specific DNA methylation patterns established or disturbed is a pivotal question in developmental biology and cancer epigenetics. Currently, compelling evidence has emerged that long non-coding RNA (lncRNA) mediates DNA methylation in both physiological and pathological conditions. In this review, we provide an overview of the current understanding of lncRNA-mediated DNA methylation, with emphasis on the roles of this mechanism in cancer, which to the best of our knowledge, has not been systematically summarized. In addition, we also discuss the potential clinical applications of this mechanism in RNA-targeting drug development.}, language = {en}, number = {1}, urldate = {2024-10-01}, journal = {Journal of Experimental \& Clinical Cancer Research}, author = {Huang, Wanxu and Li, Hua and Yu, Qingsong and Xiao, Wei and Wang, Dan Ohtan}, month = mar, year = {2022}, keywords = {Cancer, DNA methylation, DNMT, lncRNA, Non-coding RNA, TET}, pages = {100}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\6FB6BEYP\\Huang et al. - 2022 - LncRNA-mediated DNA methylation an emerging mecha.pdf:application/pdf}, } @article{zhao_long_2016, title = {Long noncoding {RNAs} in {DNA} methylation: new players stepping into the old game}, volume = {6}, issn = {2045-3701}, shorttitle = {Long noncoding {RNAs} in {DNA} methylation}, url = {https://doi.org/10.1186/s13578-016-0109-3}, doi = {10.1186/s13578-016-0109-3}, abstract = {Long non-coding RNAs (lncRNAs) are being discovered as a novel family of regulators of gene expression at the epigenetic level. Emerging lines of evidence demonstrate that interplays between lncRNAs and DNA methylation machinery are an important layer of epigenetic regulation. Here in this mini-review we summarize the current findings in the field and focus particularly on the interactions mediated through direct physical association between lncRNAs and DNA methyltransferases (DNMTs).}, language = {en}, number = {1}, urldate = {2024-10-01}, journal = {Cell \& Bioscience}, author = {Zhao, Yu and Sun, Hao and Wang, Huating}, month = jul, year = {2016}, keywords = {Dnmt, Epigenetics, lncRNAs, Methylation}, pages = {45}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\IG8IR4AL\\Zhao et al. - 2016 - Long noncoding RNAs in DNA methylation new player.pdf:application/pdf}, } @article{yu_dna_2020, title = {{DNA} methylation of noncoding {RNAs}: new insights into osteogenesis and common bone diseases}, volume = {11}, issn = {1757-6512}, shorttitle = {{DNA} methylation of noncoding {RNAs}}, url = {https://doi.org/10.1186/s13287-020-01625-7}, doi = {10.1186/s13287-020-01625-7}, abstract = {Bone diseases such as osteoarthritis, osteoporosis, and bone tumor present a severe public health problem. Osteogenic differentiation is a complex process associated with the differentiation of different cells, which could regulate transcription factors, cytokines, many signaling pathways, noncoding RNAs (ncRNAs), and epigenetic modulation. DNA methylation is a kind of stable epigenetic alterations in CpG islands without DNA sequence changes and is involved in cancer and other diseases, including bone development and homeostasis. ncRNAs can perform their crucial biological functions at the RNA level, and many findings have demonstrated essential functions of ncRNAs in osteogenic differentiation. In this review, we highlight current researches in DNA methylation of two relevant ncRNAs, including microRNAs and long noncoding RNAs, in the initiation and progression of osteogenesis and bone diseases.}, language = {en}, number = {1}, urldate = {2024-10-01}, journal = {Stem Cell Research \& Therapy}, author = {Yu, Liyuan and Xia, Kai and Cen, Xiao and Huang, Xinqi and Sun, Wentian and Zhao, Zhihe and Liu, Jun}, month = mar, year = {2020}, keywords = {Bone, DNA methylation, Noncoding RNAs, Osteogenesis}, pages = {109}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\AMWSEETC\\Yu et al. - 2020 - DNA methylation of noncoding RNAs new insights in.pdf:application/pdf}, } @article{he_non-coding_2014, title = {Non-{Coding} {RNA} {Transcription} and {RNA}-{Directed} {DNA} {Methylation} in {Arabidopsis}}, volume = {7}, issn = {1674-2052}, url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(14)60944-8}, doi = {10.1093/mp/ssu075}, language = {English}, number = {9}, urldate = {2024-10-01}, journal = {Molecular Plant}, author = {He, Xin-Jian and Ma, Ze-Yang and Liu, Zhang-Wei}, month = sep, year = {2014}, pmid = {24966349}, note = {Publisher: Elsevier}, keywords = {DNA methylation, Pol IV, Pol V, RdDM, siRNA, transcriptional gene silencing}, pages = {1406--1414}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\HKNWL5AK\\He et al. - 2014 - Non-Coding RNA Transcription and RNA-Directed DNA .pdf:application/pdf}, } @article{strmsek_microrna_2015, title = {{MicroRNA} {Silencing} by {DNA} {Methylation} in {Human} {Cancer}: a {Literature} {Analysis}}, volume = {1}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2311-553X}, shorttitle = {{MicroRNA} {Silencing} by {DNA} {Methylation} in {Human} {Cancer}}, url = {https://www.mdpi.com/2311-553X/1/1/44}, doi = {10.3390/ncrna1010044}, abstract = {MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate the expression of target mRNAs. MicroRNA genes themselves are regulated through epigenetic mechanisms, such as histone modifications and/or DNA methylation of CpG islands. Aberrant CpG island methylation patterns are frequently associated with cancer and thus researching DNA methylation of miRNA genes is a topic of increased research interest. Large quantities of available data from various studies are fragmented and incomplete; therefore, integration was performed. Data from 150 articles revealed 180 miRNA genes shown to be regulated via DNA methylation in 36 cancer types. From the total of 2588 known mature miRNA 6.9\% (180/2588) miRNAs have been shown to be epigenetically regulated by DNA methylation. 45.5\% (82/180) of miRNA genes were shown to be methylated in at least two cancer types among them hsa-miR-34b, hsa-miR-34c and hsa-miR-34a were found to be silenced in 24, 21 and 17 cancer types, respectively. The other 54.4\% (98/180) miRNA genes regulated by DNA methylation were found to be specific for a certain type of cancer and therefore represent specific biomarker potential. Because specific miRNAs have diagnostic, prognostic and therapeutic potential, the systematically review of the field offers an overview of the field and facilitates experiment planning, generation of more targeted hypotheses and more efficient biomarker and target development.}, language = {en}, number = {1}, urldate = {2024-10-01}, journal = {Non-Coding RNA}, author = {Strmsek, Ziga and Kunej, Tanja}, month = jun, year = {2015}, note = {Number: 1 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {cancer, DNA methylation, epigenetics, microRNA (miRNA), oncomiRs}, pages = {44--52}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\AP7Z9IMM\\Strmsek and Kunej - 2015 - MicroRNA Silencing by DNA Methylation in Human Can.pdf:application/pdf}, } @article{cuerda-gil_non-canonical_2016, title = {Non-canonical {RNA}-directed {DNA} methylation}, volume = {2}, copyright = {2016 Macmillan Publishers Limited}, issn = {2055-0278}, url = {https://www.nature.com/articles/nplants2016163}, doi = {10.1038/nplants.2016.163}, abstract = {Small RNA-directed DNA methylation (RdDM) has been extensively studied in plants, resulting in a deep understanding of a major ‘canonical RdDM’ mechanism. However, current models of canonical RdDM cannot explain how this self-perpetuating mechanism is initiated. Recent investigations into the initiation of epigenetic silencing have determined that there are several alternative ‘non-canonical RdDM’ pathways that function through distinct mechanisms to modify chromatin. This Review aims to illustrate the diversity of non-canonical RdDM mechanisms described to date, recognize common themes within this dizzying array of interconnected pathways, and identify the key unanswered questions remaining in this field.}, language = {en}, number = {11}, urldate = {2024-10-01}, journal = {Nature Plants}, author = {Cuerda-Gil, Diego and Slotkin, R. Keith}, month = nov, year = {2016}, note = {Publisher: Nature Publishing Group}, keywords = {DNA methylation, RNAi}, pages = {1--8}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\39EYLJUD\\Cuerda-Gil and Slotkin - 2016 - Non-canonical RNA-directed DNA methylation.pdf:application/pdf}, } @article{yang_insights_2022, title = {Insights into the role of long non-coding {RNAs} in {DNA} methylation mediated transcriptional regulation}, volume = {9}, issn = {2296-889X}, url = {https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2022.1067406/full}, doi = {10.3389/fmolb.2022.1067406}, abstract = {{\textless}p{\textgreater}DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.{\textless}/p{\textgreater}}, language = {English}, urldate = {2024-10-01}, journal = {Frontiers in Molecular Biosciences}, author = {Yang, Zhen and Xu, Feng and Teschendorff, Andrew E. and Zhao, Yi and Yao, Lei and Li, Jian and He, Yungang}, month = dec, year = {2022}, note = {Publisher: Frontiers}, keywords = {circRNA, DNA Methylation, histone modification, lncRNA, regulatory network, Transcriptional regulation}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\FJTYKY4H\\Yang et al. - 2022 - Insights into the role of long non-coding RNAs in .pdf:application/pdf}, } @article{fuso_complex_2020, series = {B vitamins and one carbon metabolism in health and disease}, title = {The complex interplay between {DNA} methylation and {miRNAs} in gene expression regulation}, volume = {173}, issn = {0300-9084}, url = {https://www.sciencedirect.com/science/article/pii/S0300908420300341}, doi = {10.1016/j.biochi.2020.02.006}, abstract = {The short, non-coding RNAs, also called microRNAs (miRNAs) can bind complementary sequences on cellular mRNAs. The consequence of this binding is generally the degradation of mRNA and the inhibition of its translation. For this reason, miRNAs are included among the epigenetic factors acting as a modulator of gene expression. How miRNAs expression is, in turn, regulated is still the object of active investigation, but DNA methylation, another epigenetic modification, seems to play a central role in this sense. The “one-carbon” metabolism is responsible for the metabolic regulation of trans-methylation reactions and, therefore, DNA methylation. For this reason, to investigate the possible correlations between alterations of the one-carbon metabolism and differential DNA methylation sounds interesting. Moreover, recent evidence indicates that, vice-versa, miRNAs are associated with DNA methylation modulation, in a mutual cross-talk. The present review will discuss the interplay between miRNAs and DNA methylation and its fall-out on gene expression regulation.}, urldate = {2024-10-01}, journal = {Biochimie}, author = {Fuso, Andrea and Raia, Tiziana and Orticello, Michela and Lucarelli, Marco}, month = jun, year = {2020}, keywords = {B vitamins, DNA methylation, microRNAs, One-carbon metabolism, Transcriptional modulation}, pages = {12--16}, file = {Fuso et al. - 2020 - The complex interplay between DNA methylation and .pdf:C\:\\Users\\Owner\\Zotero\\storage\\2BB6IVIT\\Fuso et al. - 2020 - The complex interplay between DNA methylation and .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\SMDQ66ER\\S0300908420300341.html:text/html}, } @article{ma_mechanism_2023, title = {The {Mechanism} of {DNA} {Methylation} and {miRNA} in {Breast} {Cancer}}, volume = {24}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/24/11/9360}, doi = {10.3390/ijms24119360}, abstract = {Breast cancer is the most prevalent cancer in the world. Currently, the main treatments for breast cancer are radiotherapy, chemotherapy, targeted therapy and surgery. The treatment measures for breast cancer depend on the molecular subtype. Thus, the exploration of the underlying molecular mechanisms and therapeutic targets for breast cancer remains a hotspot in research. In breast cancer, a high level of expression of DNMTs is highly correlated with poor prognosis, that is, the abnormal methylation of tumor suppressor genes usually promotes tumorigenesis and progression. MiRNAs, as non-coding RNAs, have been identified to play key roles in breast cancer. The aberrant methylation of miRNAs could lead to drug resistance during the aforementioned treatment. Therefore, the regulation of miRNA methylation might serve as a therapeutic target in breast cancer. In this paper, we reviewed studies on the regulatory mechanisms of miRNA and DNA methylation in breast cancer from the last decade, focusing on the promoter region of tumor suppressor miRNAs methylated by DNMTs and the highly expressed oncogenic miRNAs inhibited by DNMTs or activating TETs.}, language = {en}, number = {11}, urldate = {2024-10-01}, journal = {International Journal of Molecular Sciences}, author = {Ma, Lingyuan and Li, Chenyu and Yin, Hanlin and Huang, Jiashu and Yu, Shenghao and Zhao, Jin and Tang, Yongxu and Yu, Min and Lin, Jie and Ding, Lei and Cui, Qinghua}, month = jan, year = {2023}, note = {Number: 11 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {breast cancer, DNA methylation, drug resistance, miRNA}, pages = {9360}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\93Q6KWT2\\Ma et al. - 2023 - The Mechanism of DNA Methylation and miRNA in Brea.pdf:application/pdf}, } @article{saviana_crosstalk_2023, title = {Crosstalk between {miRNAs} and {DNA} {Methylation} in {Cancer}}, volume = {14}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2073-4425}, url = {https://www.mdpi.com/2073-4425/14/5/1075}, doi = {10.3390/genes14051075}, abstract = {miRNAs are some of the most well-characterized regulators of gene expression. Integral to several physiological processes, their aberrant expression often drives the pathogenesis of both benign and malignant diseases. Similarly, DNA methylation represents an epigenetic modification influencing transcription and playing a critical role in silencing numerous genes. The silencing of tumor suppressor genes through DNA methylation has been reported in many types of cancer and is associated with tumor development and progression. A growing body of literature has described the crosstalk between DNA methylation and miRNAs as an additional layer in the regulation of gene expression. Methylation in miRNA promoter regions inhibits its transcription, while miRNAs can target transcripts and subsequently regulate the proteins responsible for DNA methylation. Such relationships between miRNA and DNA methylation serve an important regulatory role in several tumor types and highlight a novel avenue for potential therapeutic targets. In this review, we discuss the crosstalk between DNA methylation and miRNA expression in the pathogenesis of cancer and describe how miRNAs influence DNA methylation and, conversely, how methylation impacts the expression of miRNAs. Finally, we address how these epigenetic modifications may be leveraged as biomarkers in cancer.}, language = {en}, number = {5}, urldate = {2024-10-01}, journal = {Genes}, author = {Saviana, Michela and Le, Patricia and Micalo, Lavender and Del Valle-Morales, Daniel and Romano, Giulia and Acunzo, Mario and Li, Howard and Nana-Sinkam, Patrick}, month = may, year = {2023}, note = {Number: 5 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {cancer, DNA methylation, miRNA}, pages = {1075}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\CB7NXVK2\\Saviana et al. - 2023 - Crosstalk between miRNAs and DNA Methylation in Ca.pdf:application/pdf}, } @article{ali_noncoding_2024, title = {Noncoding {RNA}-{Mediated} {Regulation} of {DNA} {Methylation}: {Insights} into {Plant} {Epigenetic} {Mechanisms}}, issn = {1435-8107}, shorttitle = {Noncoding {RNA}-{Mediated} {Regulation} of {DNA} {Methylation}}, url = {https://doi.org/10.1007/s00344-024-11462-0}, doi = {10.1007/s00344-024-11462-0}, abstract = {Cytosine methylation (5mC) of DNA is a conserved epigenetic mark important for plant growth and development. Extensive studies have been conducted to elucidate the regulatory processes governing DNA methylation and demethylation in both plants and animals under normal and stress conditions. Plants possess specific DNA methyltransferase enzymes that establish and maintain DNA methylation in all sequence contexts (CG, CHH, CHG) within targeted regions of both euchromatin and heterochromatin on the chromosomes. Various epigenetic marks rely on each other and are interconnected for their establishment and maintenance. Long noncoding RNAs regulate genomic organization, chromatin structure, compaction, and genome stability. These noncoding RNAs are categorized by their functions and formations, which display considerable diversity in DNA methylation among different plant species. Transcriptionally, the abundance of noncoding RNA is controlled by various epigenetic modifications, especially DNA methylation. Due to their participation in several epigenetic and genetic regulatory mechanisms, small interfering RNAs (siRNAs), microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) may influence developmental processes, stress responses, and adaptability. This review offers a comprehensive summary of the latest advancements in understanding the intricate relationship between DNA methylation and noncoding RNAs. It delves into the processes involved in their interdependence, particularly in the establishment and maintenance of DNA methylation within targeted regions.}, language = {en}, urldate = {2024-10-01}, journal = {Journal of Plant Growth Regulation}, author = {Ali, Shahid and Tang, Yulin}, month = sep, year = {2024}, keywords = {DNA demethylation, DNA methylation, Noncoding RNAs, Plant development, RdDM}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\P8VRGZ2R\\Ali and Tang - 2024 - Noncoding RNA-Mediated Regulation of DNA Methylati.pdf:application/pdf}, } @article{liu_small_2020, title = {Small {DNA} {Methylation}, {Big} {Player} in {Plant} {Abiotic} {Stress} {Responses} and {Memory}}, volume = {11}, issn = {1664-462X}, url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.595603/full}, doi = {10.3389/fpls.2020.595603}, abstract = {{\textless}p{\textgreater}DNA methylation is a conserved epigenetic mark that plays important roles in maintaining genome stability and regulating gene expression. As sessile organisms, plants have evolved sophisticated regulatory systems to endure or respond to diverse adverse abiotic environmental challenges, i.e., abiotic stresses, such as extreme temperatures (cold and heat), drought and salinity. Plant stress responses are often accompanied by changes in chromatin modifications at diverse responsive loci, such as 5-methylcytosine (5mC) and {\textless}italic{\textgreater}N{\textless}/italic{\textgreater}$^{\textrm{6}}$-methyladenine (6mA) DNA methylation. Some abiotic stress responses are memorized for several hours or days through mitotic cell divisions and quickly reset to baseline levels after normal conditions are restored, which is referred to as somatic memory. In some cases, stress-induced chromatin marks are meiotically heritable and can impart the memory of stress exposure from parent plants to at least the next stress-free offspring generation through the mechanisms of transgenerational epigenetic inheritance, which may offer the descendants the potential to be adaptive for better fitness. In this review, we briefly summarize recent achievements regarding the establishment, maintenance and reset of DNA methylation, and highlight the diverse roles of DNA methylation in plant responses to abiotic stresses. Further, we discuss the potential role of DNA methylation in abiotic stress-induced somatic memory and transgenerational inheritance. Future research directions are proposed to develop stress-tolerant engineered crops to reduce the negative effects of abiotic stresses.{\textless}/p{\textgreater}}, language = {English}, urldate = {2024-10-01}, journal = {Frontiers in Plant Science}, author = {Liu, Junzhong and He, Zuhua}, month = dec, year = {2020}, note = {Publisher: Frontiers}, keywords = {Abiotic stress responses, cytosine methylation, N6-methyladenine DNA methylation, Somatic memory, Transgenerational inheritance}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\AQI8BLU2\\Liu and He - 2020 - Small DNA Methylation, Big Player in Plant Abiotic.pdf:application/pdf}, } @article{fan_plant_2022, title = {Plant {DNA} {Methylation} {Responds} to {Nutrient} {Stress}}, volume = {13}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2073-4425}, url = {https://www.mdpi.com/2073-4425/13/6/992}, doi = {10.3390/genes13060992}, abstract = {Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.}, language = {en}, number = {6}, urldate = {2024-10-01}, journal = {Genes}, author = {Fan, Xiaoru and Peng, Lirun and Zhang, Yong}, month = jun, year = {2022}, note = {Number: 6 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {abiotic stress, DNA methylation, epigenetic, nutrient stress, plants}, pages = {992}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\SD2SW9UZ\\Fan et al. - 2022 - Plant DNA Methylation Responds to Nutrient Stress.pdf:application/pdf}, } @article{akhter_response_2021, title = {In {Response} to {Abiotic} {Stress}, {DNA} {Methylation} {Confers} {EpiGenetic} {Changes} in {Plants}}, volume = {10}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/10/6/1096}, doi = {10.3390/plants10061096}, abstract = {Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their growth and development. We emphasize the molecular process underlying changes in DNA methylation, differential variation for different species, the roles of non-coding RNAs in epigenetic modification, techniques for studying DNA methylation, and its role in crop improvement in tolerance to abiotic stress (drought, salinity, and heat). We summarize DNA methylation as a significant future research priority for tailoring crops according to various challenging environmental issues.}, language = {en}, number = {6}, urldate = {2024-10-01}, journal = {Plants}, author = {Akhter, Zahida and Bi, Zhenzhen and Ali, Kazim and Sun, Chao and Fiaz, Sajid and Haider, Fasih Ullah and Bai, Jiangping}, month = jun, year = {2021}, note = {Number: 6 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {abiotic stresses, DNA methylation, epigenetics alterations, plant improvements}, pages = {1096}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\ECWYSN24\\Akhter et al. - 2021 - In Response to Abiotic Stress, DNA Methylation Con.pdf:application/pdf}, } @article{chow_small_2023, title = {Small {RNA}-mediated {DNA} methylation during plant reproduction}, volume = {35}, issn = {1040-4651}, url = {https://doi.org/10.1093/plcell/koad010}, doi = {10.1093/plcell/koad010}, abstract = {Reproductive tissues are a rich source of small RNAs, including several classes of short interfering (si)RNAs that are restricted to this stage of development. In addition to RNA polymerase IV-dependent 24-nt siRNAs that trigger canonical RNA-directed DNA methylation, abundant reproductive-specific siRNAs are produced from companion cells adjacent to the developing germ line or zygote and may move intercellularly before inducing methylation. In some cases, these siRNAs are produced via non-canonical biosynthesis mechanisms or from sequences with little similarity to transposons. While the precise role of these siRNAs and the methylation they trigger is unclear, they have been implicated in specifying a single megaspore mother cell, silencing transposons in the male germ line, mediating parental dosage conflict to ensure proper endosperm development, hypermethylation of mature embryos, and trans-chromosomal methylation in hybrids. In this review, we summarize the current knowledge of reproductive siRNAs, including their biosynthesis, transport, and function.}, number = {6}, urldate = {2024-10-01}, journal = {The Plant Cell}, author = {Chow, Hiu Tung and Mosher, Rebecca A}, month = jun, year = {2023}, pages = {1787--1800}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\XQGWCTWD\\Chow and Mosher - 2023 - Small RNA-mediated DNA methylation during plant re.pdf:application/pdf}, } @article{singh_deciphering_2023, title = {Deciphering the role of {miRNA} in reprogramming plant responses to drought stress}, volume = {43}, issn = {0738-8551}, url = {https://doi.org/10.1080/07388551.2022.2047880}, doi = {10.1080/07388551.2022.2047880}, abstract = {Drought is the most prevalent environmental stress that affects plants’ growth, development, and crop productivity. However, plants have evolved adaptive mechanisms to respond to the harmful effects of drought. They reprogram their: transcriptome, proteome, and metabolome that alter their cellular and physiological processes and establish cellular homeostasis. One of the crucial regulatory processes that govern this reprogramming is post-transcriptional regulation by microRNAs (miRNAs). miRNAs are small non-coding RNAs, involved in the downregulation of the target mRNA via translation inhibition/mRNA degradation/miRNA-mediated mRNA decay/ribosome drop off/DNA methylation. Many drought-inducible miRNAs have been identified and characterized in plants. Their main targets are regulatory genes that influence growth, development, osmotic stress tolerance, antioxidant defense, phytohormone-mediated signaling, and delayed senescence during drought stress. Overexpression of drought-responsive miRNAs (Osa-miR535, miR160, miR408, Osa-miR393, Osa-miR319, and Gma-miR394) in certain plants has led to tolerance against drought stress indicating their vital role in stress mitigation. Similarly, knock down (miR166/miR398c) or deletion (miR169 and miR827) of miRNAs has also resulted in tolerance to drought stress. Likewise, engineered Arabidopsis plants with miR165, miR166 using short tandem target mimic strategy, exhibited drought tolerance. Since miRNAs regulate the expression of an array of drought-responsive genes, they can act as prospective targets for genetic manipulations to enhance drought tolerance in crops and achieve sustainable agriculture. Further investigations toward functional characterization of diverse miRNAs, and understanding stress-responses regulated by these miRNAs and their utilization in biotechnological applications is highly recommended.}, number = {4}, urldate = {2024-10-01}, journal = {Critical Reviews in Biotechnology}, author = {Singh, Archana and Jain, Deepti and Pandey, Jyotsna and Yadav, Manisha and Bansal, Kailash C. and Singh, Indrakant K.}, month = may, year = {2023}, pmid = {35469523}, note = {Publisher: Taylor \& Francis \_eprint: https://doi.org/10.1080/07388551.2022.2047880}, keywords = {biotechnological applications, drought-tolerance, gene silencing, miRNA, miRNA targets, translation inhibition}, pages = {613--627}, file = {Singh et al. - 2023 - Deciphering the role of miRNA in reprogramming pla.pdf:C\:\\Users\\Owner\\Zotero\\storage\\FH93VCWG\\Singh et al. - 2023 - Deciphering the role of miRNA in reprogramming pla.pdf:application/pdf}, } @article{singh_regulation_2022, title = {Regulation of small {RNA}-mediated high temperature stress responses in crop plants}, volume = {41}, issn = {1432-203X}, url = {https://doi.org/10.1007/s00299-021-02745-x}, doi = {10.1007/s00299-021-02745-x}, abstract = {Small RNAs have emerged as key players of gene expression regulation. Several lines of evidences highlight their role in modulating high temperature stress responsiveness in plants.}, language = {en}, number = {3}, urldate = {2024-10-01}, journal = {Plant Cell Reports}, author = {Singh, Roshan Kumar and Prasad, Ashish and Maurya, Jyoti and Prasad, Manoj}, month = mar, year = {2022}, keywords = {DNA methylation, Gene regulation, High temperature stress, Micropeptides, Small RNA}, pages = {765--773}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\NXJ6QMVJ\\Singh et al. - 2022 - Regulation of small RNA-mediated high temperature .pdf:application/pdf}, } @article{gallego-bartolome_dna_2020, title = {{DNA} methylation in plants: mechanisms and tools for targeted manipulation}, volume = {227}, copyright = {© 2020 The Author. New Phytologist © 2020 New Phytologist Trust}, issn = {1469-8137}, shorttitle = {{DNA} methylation in plants}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16529}, doi = {10.1111/nph.16529}, abstract = {DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been instrumental in the study of this mark in plants, although their genome-wide effect complicates the direct association between changes in methylation and a particular phenotype. A variety of tools that allow locus-specific manipulation of DNA methylation can be used to assess its direct role in specific processes, as well as to create novel epialleles. Recently, new tools that recruit the methylation machinery directly to target loci through programmable DNA-binding proteins have expanded the tool kit available to researchers. This review provides an overview of DNA methylation in plants and discusses the tools that have recently been developed for its manipulation.}, language = {en}, number = {1}, urldate = {2024-10-01}, journal = {New Phytologist}, author = {Gallego-Bartolomé, Javier}, year = {2020}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16529}, keywords = {artificial zinc finger proteins, CRISPR SunTag, DNA methylation, RNA-directed DNA methylation, transcriptional gene silencing}, pages = {38--44}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\YEWXNMTW\\Gallego-Bartolomé - 2020 - DNA methylation in plants mechanisms and tools fo.pdf:application/pdf}, } @article{huang_review_2021, title = {A {Review} of {Discovery} {Profiling} of {PIWI}-{Interacting} {RNAs} and {Their} {Diverse} {Functions} in {Metazoans}}, volume = {22}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/22/20/11166}, doi = {10.3390/ijms222011166}, abstract = {PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.}, language = {en}, number = {20}, urldate = {2024-10-01}, journal = {International Journal of Molecular Sciences}, author = {Huang, Songqian and Yoshitake, Kazutoshi and Asakawa, Shuichi}, month = jan, year = {2021}, note = {Number: 20 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {metazoans, piRNA discovery, piRNA function, PIWI-interacting RNA, sRNA-seq, transposable elements}, pages = {11166}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\R8LI8N9Q\\Huang et al. - 2021 - A Review of Discovery Profiling of PIWI-Interactin.pdf:application/pdf}, } @article{ow_inheritance_2024, title = {Inheritance of {Stress} {Responses} via {Small} {Non}-{Coding} {RNAs} in {Invertebrates} and {Mammals}}, volume = {8}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2075-4655}, url = {https://www.mdpi.com/2075-4655/8/1/1}, doi = {10.3390/epigenomes8010001}, abstract = {While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.}, language = {en}, number = {1}, urldate = {2024-10-01}, journal = {Epigenomes}, author = {Ow, Maria C. and Hall, Sarah E.}, month = mar, year = {2024}, note = {Number: 1 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {epigenetic, intergenerational inheritance, miRNA, piRNA, siRNA, small non-coding RNA, transgenerational inheritance, tRF}, pages = {1}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\7N5KKMNR\\Ow and Hall - 2024 - Inheritance of Stress Responses via Small Non-Codi.pdf:application/pdf}, } @article{xie_molecular_2024, title = {Molecular mechanisms of the {RNA} polymerases in plant {RNA}-directed {DNA} methylation}, volume = {49}, issn = {0968-0004}, url = {https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(23)00294-3}, doi = {10.1016/j.tibs.2023.11.005}, language = {English}, number = {3}, urldate = {2024-10-01}, journal = {Trends in Biochemical Sciences}, author = {Xie, Guohui and Du, Xuan and Hu, Hongmiao and Du, Jiamu}, month = mar, year = {2024}, pmid = {38072749}, note = {Publisher: Elsevier}, keywords = {epigenetics, plants, Pol IV, Pol V, RDR2, RNA-directed DNA methylation}, pages = {247--256}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\I9CTDAMX\\Xie et al. - 2024 - Molecular mechanisms of the RNA polymerases in pla.pdf:application/pdf}, } @article{pillai_epigenetic_2021, title = {Epigenetic {Regulation} in {Hydra}: {Conserved} and {Divergent} {Roles}}, volume = {9}, issn = {2296-634X}, shorttitle = {Epigenetic {Regulation} in {Hydra}}, url = {https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2021.663208/full}, doi = {10.3389/fcell.2021.663208}, abstract = {{\textless}p{\textgreater}Transitions in gene regulatory processes responsible for the emergence of specialized cell types and spatiotemporal regulation of developmental signaling prior to the divergence of Cnidaria and Bilateria are poorly understood. As a sister group of Bilateria, the phylum Cnidaria can provide significant insights into these processes. Among the cnidarians, hydrae have been studied for \>250 years to comprehend the mechanisms underlying their unique immortality and robust regenerative capacity. Studies on {\textless}italic{\textgreater}Hydra{\textless}/italic{\textgreater} spp. and other pre-bilaterians alike have advanced our understanding of the evolutionary underpinnings governing eumetazoan tissue development, homeostasis, and regeneration. In addition to its regenerative potential, {\textless}italic{\textgreater}Hydra{\textless}/italic{\textgreater} exhibits continuously active axial patterning due to its peculiar tissue dynamics. These distinctive physiological processes necessitate large scale gene expression changes that are governed by the multitude of epigenetic mechanisms operating in cells. This review highlights the contemporary knowledge of epigenetic regulation in {\textless}italic{\textgreater}Hydra{\textless}/italic{\textgreater} with contemporary studies from other members of Cnidaria, as well as the interplay between regulatory mechanisms wherever demonstrated. The studies covered in the scope of this review reveal both ancestral and divergent roles played by conserved epigenetic mechanisms with emphasis on transcriptional regulation. Additionally, single-cell transcriptomics data was mined to predict the physiological relevance of putative gene regulatory components, which is in agreement with published findings and yielded insights into the possible functions of the gene regulatory mechanisms that are yet to be deciphered in {\textless}italic{\textgreater}Hydra{\textless}/italic{\textgreater}, such as DNA methylation. Finally, we delineate potentially rewarding epigenetics research avenues that can further leverage the unique biology of {\textless}italic{\textgreater}Hydra{\textless}/italic{\textgreater}.{\textless}/p{\textgreater}}, language = {English}, urldate = {2024-10-01}, journal = {Frontiers in Cell and Developmental Biology}, author = {Pillai, Anirudh and Gungi, Akhila and Reddy, Puli Chandramouli and Galande, Sanjeev}, month = may, year = {2021}, note = {Publisher: Frontiers}, keywords = {Chromatin, Cis regulatory elements, Cnidaria, Enhancer, Head organizer, Histone Modifications, Hydra, RNAi}, file = {Full Text:C\:\\Users\\Owner\\Zotero\\storage\\4Q87SGEZ\\Pillai et al. - 2021 - Epigenetic Regulation in Hydra Conserved and Dive.pdf:application/pdf}, } @article{kim_review_2024, title = {A review of environmental epigenetics in aquatic invertebrates}, volume = {208}, issn = {0025-326X}, url = {https://www.sciencedirect.com/science/article/pii/S0025326X24009883}, doi = {10.1016/j.marpolbul.2024.117011}, abstract = {Aquatic ecosystems face significant challenges due to increasing human-induced environmental stressors. Recent studies emphasize the role of epigenetic mechanisms in the stress responses and adaptations of organisms to those stressors. Epigenetics influences gene expression, enabling phenotypic plasticity and transgenerational effects. Therefore, understanding the epigenetic responses of aquatic invertebrates to environmental stressors is imperative for aquatic ecosystem research. In this study, we organize the mechanisms of epigenetics in aquatic invertebrates and explore their roles in the responses of aquatic invertebrates to environmental stressors. Furthermore, we discuss the inheritance of epigenetic changes and their influence across generations in aquatic invertebrates. A comprehensive understanding of epigenetic responses is crucial for long-term ecosystem management and conservation strategies in the face of irreversible climate change in aquatic environments. In this review, we synthesize existing knowledge about environmental epigenetics in aquatic invertebrates to provide insights and suggest directions for future research.}, urldate = {2024-10-01}, journal = {Marine Pollution Bulletin}, author = {Kim, Min-Sub and Kim, Duck-Hyun and Lee, Jae-Seong}, month = nov, year = {2024}, keywords = {Aquatic invertebrates, Environmental stressors, Epigenetics, Global climate change}, pages = {117011}, file = {Kim et al. - 2024 - A review of environmental epigenetics in aquatic i.pdf:C\:\\Users\\Owner\\Zotero\\storage\\47CWSPSJ\\Kim et al. - 2024 - A review of environmental epigenetics in aquatic i.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\CAV9VJBQ\\S0025326X24009883.html:text/html}, } @article{axtell2013, title = {ShortStack: Comprehensive annotation and quantification of small RNA genes}, author = {Axtell, Michael J.}, year = {2013}, month = {06}, date = {2013-06}, journal = {RNA}, pages = {740--751}, volume = {19}, number = {6}, doi = {10.1261/rna.035279.112}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683909/}, note = {PMID: 23610128 PMCID: PMC3683909} } @article{rubi_museum_2020, title = {Museum epigenomics: {Characterizing} cytosine methylation in historic museum specimens}, volume = {20}, copyright = {© 2019 John Wiley \& Sons Ltd}, issn = {1755-0998}, shorttitle = {Museum epigenomics}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13115}, doi = {10.1111/1755-0998.13115}, abstract = {Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we developed and tested methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulphite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013–2016. We successfully estimated methylation in specimens of all age groups, although older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1–3 years old), which may reflect post-mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.}, language = {en}, number = {5}, urldate = {2024-09-16}, journal = {Molecular Ecology Resources}, author = {Rubi, Tricia L. and Knowles, L. Lacey and Dantzer, Ben}, year = {2020}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13115}, keywords = {epigenetics, epigenomics, historic DNA, methylation, natural history collections, Peromyscus}, pages = {1161--1170}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\XBNMVY4G\\Rubi et al. - 2020 - Museum epigenomics Characterizing cytosine methyl.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\X8YIJFJM\\1755-0998.html:text/html}, } @article{deng_p646_2024, title = {P646: {Development} of an affordable rapid human genome sequencing assay using long read {PromethiON} 2}, volume = {2}, issn = {29497744}, shorttitle = {P646}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2949774424006988}, doi = {10.1016/j.gimo.2024.101552}, abstract = {Introduction: Long-read Oxford nanopore sequencing offers advantages in identifying transcript isoforms and structural variants in human genomes. However, its widespread clinical use is limited by high costs and low throughput, with an entire \$800 flow cell required for adequate genome coverage. Our recent experiments with the PromethION 2 (P2) yielded an average of 80 Gb sequence data per flow cell but faced challenges like rapid pore deterioration after 48 hours and up to 30\% unassigned reads when using custom barcodes for multiplexing samples. Here we describe an approach that improves multiplexing and sequencing efficiency to support a sub-\$300 NGS assay with less than 5-day turnaround time for confirmation of difficult variants. Methods: To address the high percentage of unassigned reads, we tested i) longer transposon-based (Tn5) barcodes (24mer and 36mer) and ii) native barcodes (24mer). We designed 3 unique Tn-5 based barcodes of each length and tested 10 native barcodes. We used gDNA from benchmark sample NA12878 and Lambda control to test barcode assignment efficiency. We multiplexed 3 samples per flow cell (R10.4.1) and ran samples on the P2 Solo. To improve the total yield of each flow cell, we i) extended run time to 4 days an ii) monitored pore health and performed a wash/reload cycle when the available pore count dropped below 30\% of the starting value. Real-time base calling and sample demultiplexing were performed in MinKNOW. Performance was measured by genome coverage, SNP detection, methylation profiling and variant detection using well characterized Genome-in-a-Bottle (GIAB) samples. Results: When compared with the 16mer barcodes (30\% unclassified reads), the Tn5-attached indexes of 24mer and 36mer had fewer unclassified reads (15\% and 18\%, respectively), suggesting improved performance of longer barcodes. In comparison, native barcodes performed best, with a mean 9\% unclassified reads and better uniformity among classified barcodes. Tn5 sheared NA12878 library (average 14kb) loading on a single P2 flow cell yielded a total output of 151 Gb after washing and re-loading at 54 hours with an extended run of 4 days, which gave a 39X overall depth across the human genome. We then multiplexed g-tube sheared DNA of NA12878, NA24385 and NA06905 using native barcodes and performed sequencing on a single flow cell that generated a total output of 154 Gb in 96 hours. After barcode demultiplexing, each GIAB sample obtained a mean 12X depth and N50 of 6.5kb with SNP detection sensitivity greater than 98\% for both NA12878 and NA24385. In NA06905, a female FMR1 premutation carrier, we were able to detect the premutation allele with 75 CGG repeats and also observed DNA methylation in associated reads, matching what is reported in the literature. In addition, we evaluated variant detection in NA24385 with 100\% sensitivity (30/30) for deletions {\textgreater}10kb. Conclusion: Nuclease wash and sample reloading increased the output of a PromethiON flow cell by over 80\%, and sample multiplexing in this study reduced whole genome sequencing cost to below \$300 per sample. With the help of GPU base call, real-time demultiplexing and genome alignment, the sample-toresult turnaround time was shortened to 5 days. Our study shows that a clinically viable, cost-effective, and rapid long-read sequencing method is feasible. This method may have broad applications for variant orthogonal confirmation or discovery.}, language = {en}, urldate = {2025-04-09}, journal = {Genetics in Medicine Open}, author = {Deng, Wayne Xianding and Sun, Monika and Ng, Pauline and Shah, Premal and Im, Kate and Kumar, Akash}, year = {2024}, pages = {101552}, file = {Deng et al. - 2024 - P646 Development of an affordable rapid human gen.pdf:C\:\\Users\\Owner\\Zotero\\storage\\95MUDJKH\\Deng et al. - 2024 - P646 Development of an affordable rapid human gen.pdf:application/pdf}, } @article{krishna_deep_2013, title = {Deep sequencing reveals unique small {RNA} repertoire that is regulated during head regeneration in {Hydra} magnipapillata}, volume = {41}, issn = {0305-1048}, url = {https://doi.org/10.1093/nar/gks1020}, doi = {10.1093/nar/gks1020}, abstract = {Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50\% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem–loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping–pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration.}, number = {1}, urldate = {2025-04-10}, journal = {Nucleic Acids Research}, author = {Krishna, Srikar and Nair, Aparna and Cheedipudi, Sirisha and Poduval, Deepak and Dhawan, Jyotsna and Palakodeti, Dasaradhi and Ghanekar, Yashoda}, month = jan, year = {2013}, pages = {599--616}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\PI4FFCJI\\Krishna et al. - 2013 - Deep sequencing reveals unique small RNA repertoir.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\T6G2DRA2\\1146895.html:text/html}, } @phdthesis{grinblat_biogeography_2021, type = {phd}, title = {Biogeography, reproductive biology and early development in scleractinian corals}, copyright = {open}, url = {https://doi.org/10.25903/5v26-zb37}, abstract = {Mila Grinblat studied micro RNA expression in different life stages of hard corals. She found micro RNAs that were involved in spawning, sex determination and early development. Understanding the biology of reproduction, development and recruitment of corals is increasingly important in enabling reef management and conservation planning}, language = {en}, urldate = {2025-04-11}, school = {James Cook University}, author = {Grinblat, Mila}, year = {2021}, doi = {10.25903/5v26-zb37}, file = {Full Text PDF:C\:\\Users\\Owner\\Zotero\\storage\\8ZIN4QN3\\Grinblat - 2021 - Biogeography, reproductive biology and early devel.pdf:application/pdf;Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\FZDT6WYB\\75562.html:text/html}, } @article{fridrich_ancient_2023, title = {An ancient pan-cnidarian {microRNA} regulates stinging capsule biogenesis in \textit{{Nematostella} vectensis}}, volume = {42}, issn = {2211-1247}, url = {https://www.sciencedirect.com/science/article/pii/S2211124723010835}, doi = {10.1016/j.celrep.2023.113072}, abstract = {An ancient evolutionary innovation of a novel cell type, the stinging cell (cnidocyte), appeared {\textgreater}600 million years ago in the phylum Cnidaria (sea anemones, corals, hydroids, and jellyfish). A complex bursting nano-injector of venom, the cnidocyst, is embedded in cnidocytes and enables cnidarians to paralyze their prey and predators, contributing to this phylum’s evolutionary success. In this work, we show that post-transcriptional regulation by a pan-cnidarian microRNA, miR-2022, is essential for biogenesis of these cells in the sea anemone Nematostella vectensis. By manipulation of miR-2022 levels in a transgenic reporter line of cnidocytes, followed by transcriptomics, single-cell data analysis, prey paralysis assays, and cell sorting of transgenic cnidocytes, we reveal that miR-2022 enables cnidocyte biogenesis in Nematostella, while exhibiting a conserved expression domain with its targets in cnidocytes of other cnidarian species. Thus, here we revealed a functional basis to the conservation of one of nature’s most ancient microRNAs.}, number = {9}, urldate = {2025-04-11}, journal = {Cell Reports}, author = {Fridrich, Arie and Salinas-Saaverda, Miguel and Kozlolvski, Itamar and Surm, Joachim M. and Chrysostomou, Eleni and Tripathi, Abhinandan M. and Frank, Uri and Moran, Yehu}, month = sep, year = {2023}, keywords = {Cnidaria, cnidocyte, Hydractinia, microRNA, nematocyte Nematostella, post-transcriptional regulation}, pages = {113072}, file = {ScienceDirect Snapshot:C\:\\Users\\Owner\\Zotero\\storage\\MNGQVITL\\S2211124723010835.html:text/html;Submitted Version:C\:\\Users\\Owner\\Zotero\\storage\\69F4V8T9\\Fridrich et al. - 2023 - An ancient pan-cnidarian microRNA regulates stingi.pdf:application/pdf}, } @phdthesis{teefy2020, title = {The Function of Small RNA Pathways in Cnidarians}, author = {Teefy, Bryan Barrett}, year = {2020}, date = {2020}, url = {https://www.proquest.com/docview/2503663922/abstract/885C0525BC204266PQ/1}, note = {ISBN: 9798582535119}, address = {United States -- California}, langid = {English} } @Article{d17030173, AUTHOR = {Sarmiento, Adriana and Calixto-Botía, Iván and Julio-Rodríguez, Tatiana and Quattrini, Andrea M. and Sánchez, Juan A.}, TITLE = {Uncovering the Evolutionary History in Lineage of Caribbean Octocorals: Phylogenomics Reveals Unrecognized Diversity in Eunicea}, JOURNAL = {Diversity}, VOLUME = {17}, YEAR = {2025}, NUMBER = {3}, ARTICLE-NUMBER = {173}, URL = {https://www.mdpi.com/1424-2818/17/3/173}, ISSN = {1424-2818}, ABSTRACT = {The evolutionary history of the Caribbean candelabrum octocorals from the genus Eunicea (Plexauridae: Octocorallia) remains unknown despite their high diversity and abundance in reef environments. Understanding the evolutionary relationships between and within the Eunicea species is critical to accurately measuring the group diversity. Furthermore, this group has a high potential for cryptic diversity and new species, particularly given the rich morphological variability. Conventional molecular markers, however, have not provided a precise positioning for the species inside the genus. Here, we provide the first phylogenomic reconstruction of these candelabrum octocorals employing NextRAD, a reduced-representation sequencing technique, to generate thousands of SNPs. We include 15 morphospecies sampled between valid and new species throughout the Caribbean. At large, the phylogeny is well supported and resolved. In total, 13 species-level clades are discernible, including two lineages with demonstrated genetic and morphological variation that are considered and described as two new species, Eunicea criptica sp. nov. and E. colombiensis sp. nov., both previously assigned as E. clavigera and the second as the “thick morphotype”, thereby increasing the diversity of the group. Understanding the magnitude of species diversity within Eunicea is essential for directing conservation initiatives and clarifying the biological processes in reef ecosystems.}, DOI = {10.3390/d17030173} }