@article{ball2002,
  title = {Coral Development: From Classical Embryology to Molecular Control},
  shorttitle = {Coral Development},
  author = {Ball, Eldon E. and Hayward, David C. and Reece-Hoyes, John S. and Hislop, Nikki R. and Samuel, Gabrielle and Saint, Robert and Harrison, Peter L. and Miller, David J.},
  date = {2002},
  journaltitle = {The International Journal of Developmental Biology},
  shortjournal = {Int J Dev Biol},
  volume = {46},
  number = {4},
  eprint = {12141456},
  eprinttype = {pmid},
  pages = {671--678},
  issn = {0214-6282},
  abstract = {The phylum Cnidaria is the closest outgroup to the triploblastic metazoans and as such offers unique insights into evolutionary questions at several levels. In the post-genomic era, a knowledge of the gene complement of representative cnidarians will be important for understanding the relationship between the expansion of gene families and the evolution of morphological complexity among more highly evolved metazoans. Studies of cnidarian development and its molecular control will provide information about the origins of the major bilaterian body axes, the origin of the third tissue layer, the mesoderm, and the evolution of nervous system patterning. We are studying the cnidarian Acropora millepora, a reef building scleractinian coral, and a member of the basal cnidarian class, the Anthozoa. We review ourwork on descriptive embryology and studies of selected transcription factor gene families, where our knowledge from Acropora is particularly advanced relative to other cnidarians. We also describe a recent preliminary whole genome initiative, a coral EST database.},
  langid = {english},
  keywords = {Animals,Anthozoa,Cell Nucleus,DNA-Binding Proteins,Expressed Sequence Tags,Gene Expression Regulation Developmental,Likelihood Functions,Models Biological,Phylogeny,Transcription Factors}
}

@article{chen2023,
  title = {Ultrafast One-Pass {{FASTQ}} Data Preprocessing, Quality Control, and Deduplication Using Fastp},
  author = {Chen, Shifu},
  date = {2023},
  journaltitle = {iMeta},
  volume = {2},
  number = {2},
  pages = {e107},
  issn = {2770-596X},
  doi = {10.1002/imt2.107},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/imt2.107},
  urldate = {2024-10-18},
  abstract = {A large amount of sequencing data is generated and processed every day with the continuous evolution of sequencing technology and the expansion of sequencing applications. One consequence of such sequencing data explosion is the increasing cost and complexity of data processing. The preprocessing of FASTQ data, which means removing adapter contamination, filtering low-quality reads, and correcting wrongly represented bases, is an indispensable but resource intensive part of sequencing data analysis. Therefore, although a lot of software applications have been developed to solve this problem, bioinformatics scientists and engineers are still pursuing faster, simpler, and more energy-efficient software. Several years ago, the author developed fastp, which is an ultrafast all-in-one FASTQ data preprocessor with many modern features. This software has been approved by many bioinformatics users and has been continuously maintained and updated. Since the first publication on fastp, it has been greatly improved, making it even faster and more powerful. For instance, the duplication evaluation module has been improved, and a new deduplication module has been added. This study aimed to introduce the new features of fastp and demonstrate how it was designed and implemented.},
  langid = {english},
  keywords = {adapter,duplication,FASTQ,filtering,preprocessing,quality control},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\Q9LEI958\\Chen - 2023 - Ultrafast one-pass FASTQ data preprocessing, quali.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\L6R5BKH6\\imt2.html}
}

@article{chille2021,
  title = {Developmental Series of Gene Expression Clarifies Maternal {{mRNA}} Provisioning and Maternal-to-Zygotic Transition in a Reef-Building Coral},
  author = {Chille, Erin and Strand, Emma and Neder, Mayaan and Schmidt, Valeria and Sherman, Madeleine and Mass, Tali and Putnam, Hollie},
  date = {2021-11-11},
  journaltitle = {BMC Genomics},
  shortjournal = {BMC Genomics},
  volume = {22},
  number = {1},
  pages = {815},
  issn = {1471-2164},
  doi = {10.1186/s12864-021-08114-y},
  url = {https://doi.org/10.1186/s12864-021-08114-y},
  urldate = {2024-10-04},
  abstract = {Maternal mRNA provisioning of oocytes regulates early embryogenesis. Maternal transcripts are degraded as zygotic genome activation (ZGA) intensifies, a phenomenon known as the maternal-to-zygotic transition (MZT). Here, we examine gene expression over nine developmental stages in the Pacific rice coral, Montipora capitata, from eggs and embryos at 1, 4, 9, 14, 22, and 36~h-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies.},
  keywords = {Embryo,Epigenetics,Oocyte,Resilience,Time course,WGCNA},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\Z7TTNXRJ\\Chille et al. - 2021 - Developmental series of gene expression clarifies .pdf;C\:\\Users\\ssdon\\Zotero\\storage\\FUNQ48VA\\s12864-021-08114-y.html}
}

@article{chille2021a,
  title = {Developmental Series of Gene Expression Clarifies Maternal {{mRNA}} Provisioning and Maternal-to-Zygotic Transition in a Reef-Building Coral},
  author = {Chille, Erin and Strand, Emma and Neder, Mayaan and Schmidt, Valeria and Sherman, Madeleine and Mass, Tali and Putnam, Hollie},
  date = {2021-12},
  journaltitle = {BMC Genomics},
  shortjournal = {BMC Genomics},
  volume = {22},
  number = {1},
  pages = {815},
  issn = {1471-2164},
  doi = {10.1186/s12864-021-08114-y},
  url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-08114-y},
  urldate = {2022-06-28},
  abstract = {Background: Maternal mRNA provisioning of oocytes regulates early embryogenesis. Maternal transcripts are degraded as zygotic genome activation (ZGA) intensifies, a phenomenon known as the maternal-to-zygotic transition (MZT). Here, we examine gene expression over nine developmental stages in the Pacific rice coral, Montipora capitata, from eggs and embryos at 1, 4, 9, 14, 22, and 36 h-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies. Results: Weighted Gene Coexpression Network Analysis revealed four expression peaks, identifying the maternal complement, two waves of the MZT, and adult expression. Gene ontology enrichment revealed maternal mRNAs are dominated by cell division, methylation, biosynthesis, metabolism, and protein/RNA processing and transport functions. The first MZT wave occurs from \textasciitilde 4-14 hpf and is enriched in terms related to biosynthesis, methylation, cell division, and transcription. In contrast, functional enrichment in the second MZT wave, or ZGA, from 22 hpf9dpf, includes ion/peptide transport and cell signaling. Finally, adult expression is enriched for functions related to signaling, metabolism, and ion/peptide transport. Our proposed MZT timing is further supported by expression of enzymes involved in zygotic transcriptional repression (Kaiso) and activation (Sox2), which peak at 14 hpf and 22 hpf, respectively. Further, DNA methylation writing (DNMT3a) and removing (TET1) enzymes peak and remain stable past \textasciitilde 4 hpf, suggesting that methylome programming occurs before 4 hpf. Conclusions: Our high-resolution insight into the coral maternal mRNA and MZT provides essential baseline information to understand parental carryover effects and the sensitivity of developmental success under increasing environmental stress.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\PHIQEIAB\Chille et al. - 2021 - Developmental series of gene expression clarifies .pdf}
}

@article{chille2022a,
  title = {Energetics, but Not Development, Is Impacted in Coral Embryos Exposed to Ocean Acidification},
  author = {Chille, E. E. and Strand, E. L. and Scucchia, F. and Neder, M. and Schmidt, V. and Sherman, M. O. and Mass, T. and Putnam, H. M.},
  date = {2022-10-10},
  journaltitle = {Journal of Experimental Biology},
  shortjournal = {Journal of Experimental Biology},
  volume = {225},
  number = {19},
  pages = {jeb243187},
  issn = {0022-0949},
  doi = {10.1242/jeb.243187},
  url = {https://doi.org/10.1242/jeb.243187},
  urldate = {2024-09-10},
  abstract = {In light of the chronic stress and mass mortality reef-building corals face under climate change, it is critical to understand the processes driving reef persistence and replenishment, including coral reproduction and development. Here, we quantified gene expression and sensitivity to ocean acidification across a set of developmental stages in the rice coral, Montipora capitata. Embryos and swimming larvae were exposed to pH treatments of 7.8 (ambient), 7.6 (low) and 7.3 (extreme low) from fertilization to 9\>days post-fertilization. Embryo and larval volume, and stage-specific gene expression were compared between treatments to determine the effects of acidified seawater on early development. Although there was no measurable size differentiation between pH treatments at the fertilized egg and prawn chip (9\>h post-fertilization) stages, early gastrulae and larvae raised in reduced pH treatments were significantly smaller than those raised in ambient seawater, suggesting an energetic cost to developing under low pH. However, no differentially expressed genes were found until the swimming larval stage. Notably, gene expression patterns of larvae developing at pH~7.8 and pH~7.3 were more similar than those of larvae developing at pH~7.6. Larvae from pH~7.6 showed upregulation of genes involved in cell division, regulation of transcription, lipid metabolism and response to oxidative stress in comparison to the other two treatments. Although low pH appears to increase energetic demands and trigger oxidative stress in larvae, the developmental process is robust to this at a molecular level, with the swimming larval stage reached in all pH treatments.},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\G82VD8YY\\Chille et al. - 2022 - Energetics, but not development, is impacted in co.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\2R4YK8C7\\Energetics-but-not-development-is-impacted-in.html}
}

@article{coleman2020,
  title = {Restore or {{Redefine}}: {{Future Trajectories}} for {{Restoration}}},
  shorttitle = {Restore or {{Redefine}}},
  author = {Coleman, Melinda Ann and Wood, Georgina and Filbee-Dexter, Karen and Minne, Antoine J. P. and Goold, Hugh Douglas and Vergés, Adriana and Marzinelli, Ezequiel Miguel and Steinberg, Peter David and Wernberg, Thomas},
  date = {2020},
  journaltitle = {Frontiers in Marine Science},
  volume = {7},
  issn = {2296-7745},
  url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00237},
  urldate = {2022-01-31},
  abstract = {Global habitat deterioration of marine ecosystems has led to a need for active interventions to halt or reverse the loss of ecological function. Restoration has historically been a key tool to reverse habitat loss and restore functions, but the extent to which this will be sufficient under future climates is uncertain. Emerging genetic technologies now provide the ability for restoration to proactively match adaptability of target species to predicted future environmental conditions, which opens up the possibility of boosting resistance to future stress in degraded and threatened habitats. As such, the choice of whether to restore to historical baselines or anticipate the future remains a key decision that will influence restoration success in the face of environmental and climate change. Here, we present an overview of the different motives for restoration – to recover or revive lost or degraded habitats to extant or historical states, or to reinforce or redefine for future conditions. We focus on the genetic and adaptive choices that underpin each option and subsequent consequences for restoration success. These options span a range of possible trajectories, technological advances and societal acceptability, and represent a framework for progressing restoration of marine habitat forming species into the future.},
  file = {C:\Users\ssdon\Zotero\storage\C549JULA\Coleman et al. - 2020 - Restore or Redefine Future Trajectories for Resto.pdf}
}

@article{cribari-neto2010,
  title = {Beta {{Regression}} in {{{\emph{R}}}}},
  author = {Cribari-Neto, Francisco and Zeileis, Achim},
  date = {2010},
  journaltitle = {Journal of Statistical Software},
  shortjournal = {J. Stat. Soft.},
  volume = {34},
  number = {2},
  issn = {1548-7660},
  doi = {10.18637/jss.v034.i02},
  url = {http://www.jstatsoft.org/v34/i02/},
  urldate = {2024-10-18},
  abstract = {The class of beta regression models is commonly used by practitioners to model variables that assume values in the standard unit interval (0, 1). It is based on the assumption that the dependent variable is beta-distributed and that its mean is related to a set of regressors through a linear predictor with unknown coefficients and a link function. The model also includes a precision parameter which may be constant or depend on a (potentially different) set of regressors through a link function as well. This approach naturally incorporates features such as heteroskedasticity or skewness which are commonly observed in data taking values in the standard unit interval, such as rates or proportions. This paper describes the betareg package which provides the class of beta regressions in the R system for statistical computing. The underlying theory is briefly outlined, the implementation discussed and illustrated in various replication exercises.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\UXASWC7L\Cribari-Neto and Zeileis - 2010 - Beta Regression in R.pdf}
}

@article{eddy2018,
  title = {Historical Baselines of Coral Cover on Tropical Reefs as Estimated by Expert Opinion},
  author = {Eddy, Tyler D. and Cheung, William W.L. and Bruno, John F.},
  date = {2018-01-24},
  journaltitle = {PeerJ},
  shortjournal = {PeerJ},
  volume = {6},
  eprint = {29379692},
  eprinttype = {pmid},
  pages = {e4308},
  issn = {2167-8359},
  doi = {10.7717/peerj.4308},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786882/},
  urldate = {2022-03-16},
  abstract = {Coral reefs are important habitats that represent global marine biodiversity hotspots and provide important benefits to people in many tropical regions. However, coral reefs are becoming increasingly threatened by climate change, overfishing, habitat destruction, and pollution. Historical baselines of coral cover are important to understand how much coral cover has been lost, e.g., to avoid the ‘shifting baseline syndrome’. There are few quantitative observations of coral reef cover prior to the industrial revolution, and therefore baselines of coral reef cover are difficult to estimate. Here, we use expert and ocean-user opinion surveys to estimate baselines of global coral reef cover. The overall mean estimated baseline coral cover was 59\% (±19\% standard deviation), compared to an average of 58\% (±18\% standard deviation) estimated by professional scientists. We did not find evidence of the shifting baseline syndrome, whereby respondents who first observed coral reefs more recently report lower estimates of baseline coral cover. These estimates of historical coral reef baseline cover are important for scientists, policy makers, and managers to understand the extent to which coral reefs have become depleted and to set appropriate recovery targets.},
  pmcid = {PMC5786882},
  file = {C:\Users\ssdon\Zotero\storage\46IM9PLS\Eddy et al. - 2018 - Historical baselines of coral cover on tropical re.pdf}
}

@article{ewels2016,
  title = {{{MultiQC}}: Summarize Analysis Results for Multiple Tools and Samples in a Single Report},
  shorttitle = {{{MultiQC}}},
  author = {Ewels, Philip and Magnusson, Måns and Lundin, Sverker and Käller, Max},
  date = {2016-10-01},
  journaltitle = {Bioinformatics (Oxford, England)},
  shortjournal = {Bioinformatics},
  volume = {32},
  number = {19},
  eprint = {27312411},
  eprinttype = {pmid},
  pages = {3047--3048},
  issn = {1367-4811},
  doi = {10.1093/bioinformatics/btw354},
  abstract = {MOTIVATION: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis. RESULTS: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization. AVAILABILITY AND IMPLEMENTATION: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info CONTACT: phil.ewels@scilifelab.se.},
  langid = {english},
  pmcid = {PMC5039924},
  keywords = {Computational Biology,High-Throughput Nucleotide Sequencing,Quality Control,Software},
  file = {C:\Users\ssdon\Zotero\storage\46PLLRKA\Ewels et al. - 2016 - MultiQC summarize analysis results for multiple t.pdf}
}

@article{gambardella2024,
  title = {High Concentrations of Phthalates Affect the Early Development of the Sea Urchin {{{\emph{Paracentrotus}}}}{\emph{ Lividus}}},
  author = {Gambardella, Chiara and Miroglio, Roberta and Prieto Amador, Marina and Castelli, Filippo and Castellano, Laura and Piazza, Veronica and Faimali, Marco and Garaventa, Francesca},
  date = {2024-07-01},
  journaltitle = {Ecotoxicology and Environmental Safety},
  shortjournal = {Ecotoxicology and Environmental Safety},
  volume = {279},
  pages = {116473},
  issn = {0147-6513},
  doi = {10.1016/j.ecoenv.2024.116473},
  url = {https://www.sciencedirect.com/science/article/pii/S0147651324005499},
  urldate = {2024-05-28},
  abstract = {The toxicity of three phthalates (PAEs) - butylbenzyl phthalate (BBP), diethyl phthalate (DEP), and di-(2-ethylhexyl) phthalate (DEHP) - was tested on the Mediterranean sea urchin Paracentrotus lividus. Fertilized eggs were exposed to environmental and high PAE concentrations for 72\,h. The potential toxic effects on larval development and any morphological anomalies were then assessed to estimate PAEs impact. Environmental concentrations never affected development, while high concentrations induced toxic effects in larvae exposed to BBP (EC50: 2.9 ×103 µg/L) and DEHP (EC50: 3.72 ×103 µg/L). High concentrations caused skeletal anomalies, with a slight to moderate impact for DEP/DEHP and BBP, respectively. PAE toxicity was: BBP{$>$}DEHP{$>$}DEP. In conclusion, the three PAEs at environmental concentrations do not pose a risk to sea urchins. However, PAE concentrations should be further monitored in order not to constitute a concern to marine species, especially at their early developmental stages.},
  keywords = {Bis(2-ethylhexyl) phthalate,Butyl benzyl phthalate,Contaminant impact,Diethyl phthalate,Larvae,Toxicity},
  file = {C:\Users\ssdon\Zotero\storage\MZ6JKFRE\S0147651324005499.html}
}

@article{gandaraesilva2016,
  title = {Leachate from Microplastics Impairs Larval Development in Brown Mussels},
  author = {Gandara e Silva, Pablo Pena and Nobre, Caio Rodrigues and Resaffe, Pryscila and Pereira, Camilo Dias Seabra and Gusmão, Felipe},
  date = {2016-12-01},
  journaltitle = {Water Research},
  shortjournal = {Water Research},
  volume = {106},
  pages = {364--370},
  issn = {0043-1354},
  doi = {10.1016/j.watres.2016.10.016},
  url = {https://www.sciencedirect.com/science/article/pii/S0043135416307667},
  urldate = {2021-12-05},
  abstract = {Microplastic debris is a pervasive type of contaminant in marine ecosystems, being considered a major threat to marine biota. One of the problems of microplastics is that they can adsorb contaminants in extremely high concentrations. When released from the particle, these contaminants have the potential to cause toxic effects in the biota. So far, reports of toxic effects are mostly linked with the direct exposure of organisms through ingestion of contaminated microplastics. There is little information on the toxicity of leachates from microplastics to marine organisms. In this study, we conducted experiments to evaluate the toxicity of leachates from virgin and beached plastic pellets to embryo development of the brown mussel (Perna perna). We compared the efficiency of two test procedures, and evaluated the toxicity of beached pellets collected in a coastal marine protected area. We observed that mussel embryo is sensitive to leachate from both virgin and beached pellets. However, the toxicity of the leachate from beached pellets was much higher than that of virgin pellets. We suggest contaminants adsorbed onto the surface of beached pellets were responsible for the high toxicity of leachate from beached pellets, while the toxicity of leachate from virgin pellets was mainly due to plastic additives. Our results suggest microplastic debris may be harmful even if ingestion is not the only or main pathway of interaction of marine organisms with contaminated plastic debris.},
  langid = {english},
  keywords = {Beach,Ecotoxicology,Embryo development,Mollusc,Persistent organic pollutants,Plastic pellets},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\LI9MTA9J\\Gandara e Silva et al. - 2016 - Leachate from microplastics impairs larval develop.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\NFG2NNT9\\S0043135416307667.html}
}

@article{grasso2008,
  title = {Microarray Analysis Identifies Candidate Genes for Key Roles in Coral Development},
  author = {Grasso, Lauretta C. and Maindonald, John and Rudd, Stephen and Hayward, David C. and Saint, Robert and Miller, David J. and Ball, Eldon E.},
  date = {2008-11-14},
  journaltitle = {BMC genomics},
  shortjournal = {BMC Genomics},
  volume = {9},
  eprint = {19014561},
  eprinttype = {pmid},
  pages = {540},
  issn = {1471-2164},
  doi = {10.1186/1471-2164-9-540},
  abstract = {BACKGROUND: Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef ecosystems, the stony corals are anthozoans of particular ecological significance. To better understand the molecular bases of both cnidarian development in general and coral-specific processes such as skeletogenesis and symbiont acquisition, microarray analysis was carried out through the period of early development - when skeletogenesis is initiated, and symbionts are first acquired. RESULTS: Of 5081 unique peptide coding genes, 1084 were differentially expressed (P},
  langid = {english},
  pmcid = {PMC2629781},
  keywords = {Amino Acid Sequence,Animals,Anthozoa,Calcification Physiologic,Cluster Analysis,DNA Complementary,Expressed Sequence Tags,Gene Expression Profiling,Metamorphosis Biological,Molecular Sequence Data,Oligonucleotide Array Sequence Analysis,Symbiosis},
  file = {C:\Users\ssdon\Zotero\storage\Z45U5JV6\Grasso et al. - 2008 - Microarray analysis identifies candidate genes for.pdf}
}

@article{hagedorn2015,
  title = {Effects of {{Toxic Compounds}} in {{Montipora}} Capitata on {{Exogenous}} and {{Endogenous Zooxanthellae Performance}} and {{Fertilization Success}}},
  author = {Hagedorn, Mary and Farrell, Ann and Carter, Virginia and Zuchowicz, Nikolas and Johnston, Erika and Padilla-Gamiño, Jacqueline and Gunasekera, Sarath and Paul, Valerie},
  date = {2015-02-25},
  journaltitle = {PLOS ONE},
  shortjournal = {PLOS ONE},
  volume = {10},
  number = {2},
  pages = {e0118364},
  publisher = {Public Library of Science},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0118364},
  url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118364},
  urldate = {2024-09-09},
  abstract = {Studies have identified chemicals within the stony coral genus Montipora that have significant biological activities. For example, Montiporic acids A and B and other compounds have been isolated from the adult tissue and eggs of Montipora spp. and have displayed antimicrobial activity and cytotoxicity in cultured cells. The ecological role of these toxic compounds is currently unclear. This study examines the role these toxins play in reproduction. Toxins were found in the eggs and larvae of the coral Montipora capitata. Releasing these toxins by crushing both the eggs and larvae resulted in irreversible inhibition of photosynthesis in endogenous and exogenous zooxanthellae within minutes. Moreover, these toxins were stable, as frozen storage of eggs and larvae did not affect toxicity. Photosynthetic competency of Porites compressa zooxanthellae treated with either frozen or fresh, crushed eggs was inhibited similarly (P {$>$} 0.05, ANCOVA). Addition of toxic eggs plugs to live P. compressa fragments caused complete tissue necrosis under the exposed area on the fragments within 1 week. Small volumes of M. capitata crushed eggs added to sperm suspensions reduced in vitro fertilization success by killing the sperm. After 30 min, untreated sperm maintained 90 ± 1.9\% SEM motility while those treated with crushed eggs were rendered immotile, 4 ± 1.4\% SEM. Flow cytometry indicated membrane disruption of the immotile sperm. Fertilization success using untreated sperm was 79 ± 4\% SEM, whereas the success rate dropped significantly after exposure to the crushed eggs, 1.3 ± 0\% SEM. Unlike the eggs and the larvae, M. capitata sperm did not reduce the photosynthetic competency of P. compressa zooxanthellae, suggesting the sperm was nontoxic. The identity of the toxins, cellular mechanism of action, advantage of the toxins for M. capitata and their role on the reef are still unknown.},
  langid = {english},
  keywords = {Coral reefs,Corals,Eggs,Fertilization,Larvae,Ova,Sperm,Toxins},
  file = {C:\Users\ssdon\Zotero\storage\YWVGDZJH\Hagedorn et al. - 2015 - Effects of Toxic Compounds in Montipora capitata o.pdf}
}

@article{hancock2021,
  title = {Coral Husbandry for Ocean Futures: Leveraging Abiotic Factors to Increase Survivorship, Growth, and Resilience in Juvenile {{Montipora}} Capitata},
  shorttitle = {Coral Husbandry for Ocean Futures},
  author = {Hancock, Jr and Barrows, Ar and Roome, Tc and Huffmyer, As and Matsuda, Sb and Munk, Nj and Rahnke, Sa and Drury, C},
  date = {2021-01-07},
  journaltitle = {Marine Ecology Progress Series},
  shortjournal = {Mar. Ecol. Prog. Ser.},
  volume = {657},
  pages = {123--133},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps13534},
  url = {https://www.int-res.com/abstracts/meps/v657/p123-133/},
  urldate = {2022-04-02},
  abstract = {Reef restoration via direct outplanting of sexually propagated juvenile corals is a key strategy in preserving coral reef ecosystem function in the face of global and local stressors (e.g. ocean warming). To advance our capacity to scale and maximize the efficiency of restoration initiatives, we examined how abiotic conditions (i.e. larval rearing temperature, substrate condition, light intensity, and flow rate) interact to enhance post-settlement survival and growth of sexually propagated juvenile Montipora capitata. Larvae were reared at 3 temperatures (high: 28.9°C, ambient: 27.2°C, low: 24.5°C) for 72 h during larval development, and were subsequently settled on aragonite plugs conditioned in seawater (1 or 10 wk) and raised in different light and flow regimes. These juvenile corals underwent a natural bleaching event in Kāne‘ohe Bay, O‘ahu, Hawai‘i (USA), in summer 2019, allowing us to opportunistically measure bleaching response in addition to survivorship and growth. This study demonstrates how leveraging light and flow can increase the survivorship and growth of juvenile M. capitata. In contrast, larval preconditioning and substrate conditioning had little overall effect on survivorship, growth, or bleaching response. Importantly, there was no optimal combination of abiotic conditions that maximized survival and growth in addition to bleaching tolerances. This study highlights the ability to tailor sexual reproduction for specific restoration goals by addressing knowledge gaps and incorporating practices that could improve resilience in propagated stocks.},
  langid = {english},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\2LRSNM3M\\Hancock et al. - 2021 - Coral husbandry for ocean futures leveraging abio.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\5WLZNMPK\\Hancock et al. - 2021 - Coral husbandry for ocean futures leveraging abio.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\ACTXP5BI\\Hancock et al. - 2021 - Coral husbandry for ocean futures leveraging abio.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\WYGP7ANL\\Hancock et al. - 2021 - Coral husbandry for ocean futures leveraging abio.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\5TCI56RG\\p123-133.html}
}

@article{hedouin2013,
  title = {Assessing Fertilization Success of the Coral {{{\emph{Montipora}}}}{\emph{ Capitata}} under Copper Exposure: {{Does}} the Night of Spawning Matter?},
  shorttitle = {Assessing Fertilization Success of the Coral {{{\emph{Montipora}}}}{\emph{ Capitata}} under Copper Exposure},
  author = {Hédouin, Laetitia and Gates, Ruth D.},
  date = {2013-01-15},
  journaltitle = {Marine Pollution Bulletin},
  shortjournal = {Marine Pollution Bulletin},
  volume = {66},
  number = {1},
  pages = {221--224},
  issn = {0025-326X},
  doi = {10.1016/j.marpolbul.2012.11.020},
  url = {https://www.sciencedirect.com/science/article/pii/S0025326X12005589},
  urldate = {2024-09-09},
  abstract = {Metal pollution is a major threat in tropical areas due to increasing pressure from anthropogenic activities along coastlines. Unfortunately there are very few toxicological studies that assess the effects of metals on marine organisms in tropical areas. To help fill this gap, this study investigated how Cu alters the fertilization success of the coral Montipora capitata over several nights of spawning. Results indicate that gametes of M. capitata are sensitive to Cu pollution, with EC50 after 3h ranging from 16.6 to 31.7μgl−1. Moreover, the sensitivity of the gametes to Cu toxicity was influenced by the night of spawning during which fertilization experiments were performed. This result likely reflected changes in the quality of gamete over the spawning period.},
  keywords = {Copper,Fertilization,Gametes,Spawning,Toxicity},
  file = {C:\Users\ssdon\Zotero\storage\XARAGUXR\S0025326X12005589.html}
}

@article{hirose2000,
  title = {Early Development of Zooxanthella-Containing Eggs of the Corals {{Pocillopora}} Verrucosa and {{P}}. Eydouxi with Special Reference to the Distribution of Zooxanthellae},
  author = {Hirose, M. and Kinzie, R. A. and Hidaka, M.},
  date = {2000-08},
  journaltitle = {The Biological Bulletin},
  shortjournal = {Biol Bull},
  volume = {199},
  number = {1},
  eprint = {10975644},
  eprinttype = {pmid},
  pages = {68--75},
  issn = {0006-3185},
  doi = {10.2307/1542708},
  abstract = {Some hermatypic corals spawn eggs that contain zooxanthellae. We followed development of zooxanthella-containing eggs of two such species, Pocillopora verrucosa and P. eydouxi. We also documented changes in the distribution pattern of zooxanthellae during development. Oocytes of both species took up zooxanthellae 3 to 4 days before spawning. At first, zooxanthellae were evenly distributed in oocytes, but they later moved to the hemisphere that contained the germinal vesicle. After fertilization, early cleavage events were holoblastic, progressing by furrow formation. The first cleavage furrow started at the hemisphere that contained zooxanthellae, dividing the zooxanthellate complement of the zygote about equally into the two blastomeres. The second division divided each blastomere into one zooxanthellae-rich cell and one with few zooxanthellae. With continued cell division, blastomeres containing zooxanthellae moved into the blastocoel. The blastocoel disappeared at about 5 h after the first cleavage, and the central region of the embryo was filled with cells containing either zooxanthellae or lipid droplets, forming a stereogastrula. Our results suggest that only blastomeres that had been determined to develop into gastrodermal cells receive zooxanthellae during cleavage. This determination appears to take place, at the latest, by the second cell division at the four-cell stage.},
  langid = {english},
  keywords = {Animals,Cleavage Stage Ovum,Cnidaria,Dinoflagellida,Oocytes,Ovum},
  file = {C:\Users\ssdon\Zotero\storage\Y3JZIVKX\Hirose et al. - 2000 - Early development of zooxanthella-containing eggs .pdf}
}

@article{hirose2006,
  title = {Early {{Development}} of {{Zooxanthella-containing Eggs}} of the {{Corals Porites}} Cylindrica and {{Montipora}} Digitata: {{The Endodermal Localization}} of {{Zooxanthellae}}},
  shorttitle = {Early {{Development}} of {{Zooxanthella-containing Eggs}} of the {{Corals Porites}} Cylindrica and {{Montipora}} Digitata},
  author = {Hirose, Mamiko and Hidaka, Michio},
  date = {2006-10},
  journaltitle = {Zoological Science},
  shortjournal = {jzoo},
  volume = {23},
  number = {10},
  pages = {873--881},
  publisher = {Zoological Society of Japan},
  issn = {0289-0003},
  doi = {10.2108/zsj.23.873},
  url = {https://bioone.org/journals/zoological-science/volume-23/issue-10/zsj.23.873/Early-Development-of-Zooxanthella-containing-Eggs-of-the-Corals-Porites/10.2108/zsj.23.873.full},
  urldate = {2024-09-10},
  abstract = {We studied the early development of zooxanthellae-containing eggs of the scleractinian corals Porites cylindrica and Montipora digitata to elucidate how zooxanthellae become localized to the endoderm of planulae during the course of development. In both species, zooxanthellae were distributed evenly in the oocytes and delivered almost equally to the blastomeres during cleavage. In P. cylindrica, gastrulation occurred via delamination or ingression, and blastomeres containing zooxanthellae dropped into the blastocoel during gastrulation. Thus, zooxanthellae were restricted to the endodermal cells at the gastrula or early planula stage in P. cylindrica. In M. digitata, gastrulation occurred by a combination of invagination and epiboly to form a somewhat concave gastrula. Zooxanthellae were present in both endodermal and ectodermal cells of early planulae, but they disappeared from the ectoderm as the planulae matured. In our previous study on two species of Pocillopora, we found that zooxanthellae were localized in eggs as well as in embryos, and that blastomeres containing zooxanthellae later dropped into the blastocoel to become restricted to the endoderm (Hirose et al., 2000). The timing and mechanism of zooxanthella localization and types of gastrulation differed among species belonging to the three genera. These results suggest that zooxanthella localization in the embryos reflects the timing of the determination of presumptive endoderm cells and/or specificity of zooxanthellae toward presumptive endoderm cells.},
  keywords = {Animals,Anthozoa,Eukaryota,Ovum,Symbiosis},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\43VRW3QZ\\Hirose and Hidaka - 2006 - Early development of zooxanthella-containing eggs .pdf;C\:\\Users\\ssdon\\Zotero\\storage\\UTMTB5CK\\Hirose and Hidaka - 2006 - Early Development of Zooxanthella-containing Eggs .pdf}
}

@article{isa2022,
  title = {Phthalates Bioconcentration in the Soft Corals: {{Inter-}} and Intra- Species Differences and Ecological Aspects},
  shorttitle = {Phthalates Bioconcentration in the Soft Corals},
  author = {Isa, Valerio and Saliu, Francesco and Bises, Chiara and Vencato, Sara and Raguso, Clarissa and Montano, Simone and Lasagni, Marina and Lavorano, Silvia and Clemenza, Massimiliano and Galli, Paolo},
  date = {2022-06},
  journaltitle = {Chemosphere},
  shortjournal = {Chemosphere},
  volume = {297},
  pages = {134247},
  issn = {00456535},
  doi = {10.1016/j.chemosphere.2022.134247},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0045653522007408},
  urldate = {2022-03-14},
  abstract = {The bioconcentration of dimethyl phthalate (DMP) diethyl phthalate (DEP) dibutyl phthalate (DBP) butyl benzyl phthalate (BBzP), di-(2-ethy hexyl) phthalates (DEHP), mono-butyl phthalate (MBP), mono-benzyl phthalate (MBzP), mono-(2-ethy hexyl) phthalate (MEHP) in the soft corals Coelogorgia palmosa, Sinularia sp., Sarcophyton glaucum, and Lobophytum sp. was investigated. Specimens were cultured in a microcosm environment built-up at the Genova Aquarium and analyses were carried out by in vivo SPME-LC-MS/MS. The distributions of the phthalates among the four surveyed species resulted significantly different. Calculated bioconcentration factors (BCFs) showed values spanning over two orders of magnitude, from a minimum of log10 BCFDEP = 1.0 in Sar­ cophyton glaucum to a maximum of log10 BCFDBP = 3,9 calculated for Coelogorgia palmosa. Moreover, the calculated BCFs of the long chain phthalates resulted up to three orders of magnitude lower than theoretically predicted (from logKow), whereas BCF of short chain phthalates resulted higher. This, together with the detection of phthalic acid monoesters, suggests the presence of species-specific different metabolic transformation among the surveyed soft coral species that involve DEHP.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\53GSFT7D\Isa et al. - 2022 - Phthalates bioconcentration in the soft corals In.pdf}
}

@article{isa2024b,
  title = {Physical and Cellular Impact of Environmentally Relevant Microplastic Exposure on Thermally Challenged {{Pocillopora}} Damicornis ({{Cnidaria}}, {{Scleractinia}})},
  author = {Isa, Valerio and Seveso, Davide and Diamante, Luca and Montalbetti, Enrico and Montano, Simone and Gobbato, Jacopo and Lavorano, Silvia and Galli, Paolo and Louis, Yohan Didier},
  date = {2024-03},
  journaltitle = {Science of The Total Environment},
  shortjournal = {Science of The Total Environment},
  volume = {918},
  pages = {170651},
  issn = {00489697},
  doi = {10.1016/j.scitotenv.2024.170651},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969724007903},
  urldate = {2024-10-03},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\5V3K2GMU\Isa et al. - 2024 - Physical and cellular impact of environmentally re.pdf}
}

@article{jimenez-guri2023,
  title = {{{PVC}} Pellet Leachates Affect Adult Immune System and Embryonic Development but Not Reproductive Capacity in the Sea Urchin {{Paracentrotus}} Lividus},
  author = {Jimenez-Guri, Eva and Murano, Carola and Paganos, Periklis and Arnone, Maria Ina},
  date = {2023-11-01},
  journaltitle = {Marine Pollution Bulletin},
  shortjournal = {Marine Pollution Bulletin},
  volume = {196},
  pages = {115604},
  issn = {0025-326X},
  doi = {10.1016/j.marpolbul.2023.115604},
  url = {https://www.sciencedirect.com/science/article/pii/S0025326X23010391},
  urldate = {2023-10-16},
  abstract = {Microplastic pollution is a major concern of our age, eliciting a range of effects on organisms including during embryonic development. Plastic preproduction pellets stunt the development of sea urchins through the leaching of teratogenic compounds. However, the effect of these leachates on adult sea urchins and their fertility is unknown. Here we investigate the effect of PVC leachates on the capacity to produce normal embryos, and demonstrate that adults kept in contaminated water still produce viable offspring. However, we observe a cumulative negative effect by continued exposure to highly polluted water: adult animals had lower counts and disturbed morphological profiles of immune cells, were under increased oxidative stress, and produced embryos less tolerant of contaminated environments. Our findings suggest that even in highly polluted areas, sea urchins are fertile, but that sublethal effects seen in the adults may lead to transgenerational effects that reduce developmental robustness of the embryos.},
  keywords = {Immune cells,Leachates,Oxidative stress,PVC nurdles,Reproduction,Sea urchin},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\DPEMH2NA\\Jimenez-Guri et al. - 2023 - PVC pellet leachates affect adult immune system an.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\44RBHIPX\\S0025326X23010391.html}
}

@article{kim2019,
  title = {Graph-Based Genome Alignment and Genotyping with {{HISAT2}} and {{HISAT-genotype}}},
  author = {Kim, Daehwan and Paggi, Joseph M. and Park, Chanhee and Bennett, Christopher and Salzberg, Steven L.},
  date = {2019-08},
  journaltitle = {Nature Biotechnology},
  shortjournal = {Nat Biotechnol},
  volume = {37},
  number = {8},
  pages = {907--915},
  publisher = {Nature Publishing Group},
  issn = {1546-1696},
  doi = {10.1038/s41587-019-0201-4},
  url = {https://www.nature.com/articles/s41587-019-0201-4},
  urldate = {2024-10-21},
  abstract = {The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index. We use HISAT2 to represent and search an expanded model of the human reference genome in which over 14.5 million genomic variants in combination with haplotypes are incorporated into the data structure used for searching and alignment. We benchmark HISAT2 using simulated and real datasets to demonstrate that our strategy of representing a population of genomes, together with a fast, memory-efficient search algorithm, provides more detailed and accurate variant analyses than other methods. We apply HISAT2 for HLA typing and DNA fingerprinting; both applications form part of the HISAT-genotype software that enables analysis of haplotype-resolved genes or genomic regions. HISAT-genotype outperforms other computational methods and matches or exceeds the performance of laboratory-based assays.},
  langid = {english},
  keywords = {Genetics research,Genome informatics,Population genetics},
  file = {C:\Users\ssdon\Zotero\storage\KWN9P7NQ\Kim et al. - 2019 - Graph-based genome alignment and genotyping with H.pdf}
}

@article{mincarelli2021,
  title = {Consequences of Combined Exposure to Thermal Stress and the Plasticiser {{DEHP}} in {{Mytilus}} Spp. Differ by Sex},
  author = {Mincarelli, Luana Fiorella and Rotchell, Jeanette M. and Chapman, Emma C. and Turner, Alexander P. and Wollenberg Valero, Katharina C.},
  date = {2021-09},
  journaltitle = {Marine Pollution Bulletin},
  shortjournal = {Marine Pollution Bulletin},
  volume = {170},
  pages = {112624},
  issn = {0025326X},
  doi = {10.1016/j.marpolbul.2021.112624},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0025326X21006585},
  urldate = {2022-03-16},
  abstract = {Little is known about the combined effect of environmental factors and contaminants on commercially important marine species, and whether this effect differs by sex. In this study, blue mussels were exposed for seven days to both single and combined stressors (i.e., +3 ◦C elevated temperature and two environmentally relevant con­ centrations of the plastic softener DEHP, 0.5 and 50 μg/l) in a factorial design. Males were observed to be more sensitive to high temperature, demonstrated by the significant increase in out-of-season spawning gonads and higher gene expression of the antioxidant catalase and the estrogen receptor genes. On the other hand, while the gametogenesis cycle in females was more resilient than in males, DEHP exposure altered the estrogen-related receptor gene expression.},
  langid = {english},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\9SVSIY5T\\Mincarelli et al. - 2021 - Consequences of combined exposure to thermal stres.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\XACF2SAP\\Mincarelli et al. - 2021 - Consequences of combined exposure to thermal stres.pdf}
}

@article{montano2020,
  title = {Spatial Variability of Phthalates Contamination in the Reef-Building Corals {{Porites}} Lutea, {{Pocillopora}} Verrucosa and {{Pavona}} Varians},
  author = {Montano, Simone and Seveso, Davide and Maggioni, Davide and Galli, Paolo and Corsarini, Stefano and Saliu, Francesco},
  date = {2020-06},
  journaltitle = {Marine Pollution Bulletin},
  shortjournal = {Marine Pollution Bulletin},
  volume = {155},
  pages = {111117},
  issn = {0025326X},
  doi = {10.1016/j.marpolbul.2020.111117},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0025326X20302356},
  urldate = {2022-01-20},
  abstract = {Microplastic pollution represents a serious hazard for the marine environment, including coral reefs. Scleractinian corals can easily mistake microplastics with their natural preys, and ingest them and all the annexed plasticizer additives. Here we selectively searched on field for five phthalates esters (PAEs) namely dibutyl-phthalate (DBP), benzylbutyl-phthalate (BBzP), diethyl-phthalate (DEP), Bis(2-ethylhexyl)-phthalate (DEHP), and dimethyl-phthalate (DMP) in the coral species Pocillopora verrucosa, Porites lutea and Pavona varians. Our data reveal that {$>$} 95\% of corals sampled were contaminated, with a maximum of 172.4 ng/g, a value 7 time-fold higher than those found in a previous study. The Σ5 PAEs showed an average of about 30 ng/g per coral, but no differences in PAEs contamination was detected between species, depth or reef exposure. Despite their effects on coral physiology are not yet known, PAEs should be now considered as a novel, and ubiquitous, form of contamination in corals.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\N3Y2UUIC\Montano et al. - 2020 - Spatial variability of phthalates contamination in.pdf}
}

@article{net2015a,
  title = {Reliable Quantification of Phthalates in Environmental Matrices (Air, Water, Sludge, Sediment and Soil): A Review},
  shorttitle = {Reliable Quantification of Phthalates in Environmental Matrices (Air, Water, Sludge, Sediment and Soil)},
  author = {Net, Sopheak and Delmont, Anne and Sempéré, Richard and Paluselli, Andrea and Ouddane, Baghdad},
  date = {2015-05-15},
  journaltitle = {The Science of the Total Environment},
  shortjournal = {Sci Total Environ},
  volume = {515--516},
  eprint = {25723871},
  eprinttype = {pmid},
  pages = {162--180},
  issn = {1879-1026},
  doi = {10.1016/j.scitotenv.2015.02.013},
  abstract = {Because of their widespread application, phthalates or phthalic acid esters (PAEs) are ubiquitous in the environment. Their presence has attracted considerable attention due to their potential impacts on ecosystem functioning and on public health, so their quantification has become a necessity. Various extraction procedures as well as gas/liquid chromatography and mass spectrometry detection techniques are found as suitable for reliable detection of such compounds. However, PAEs are ubiquitous in the laboratory environment including ambient air, reagents, sampling equipment, and various analytical devices, that induces difficult analysis of real samples with a low PAE background. Therefore, accurate PAE analysis in environmental matrices is a challenging task. This paper reviews the extensive literature data on the techniques for PAE quantification in natural media. Sampling, sample extraction/pretreatment and detection for quantifying PAEs in different environmental matrices (air, water, sludge, sediment and soil) have been reviewed and compared. The concept of "green analytical chemistry" for PAE determination is also discussed. Moreover useful information about the material preparation and the procedures of quality control and quality assurance are presented to overcome the problem of sample contamination and these encountered due to matrix effects in order to avoid overestimating PAE concentrations in the environment.},
  langid = {english},
  keywords = {Atmosphere,DEHP,Derivatization,Environment,Environmental matrices,Environmental Monitoring,Environmental Pollutants,Extraction,GC–MS,Green chemistry,LC–MS,Phthalates,Phthalic Acids,Quantification,Sewage,Soil,Water},
  file = {C:\Users\ssdon\Zotero\storage\KIYIZ59W\Net et al. - 2015 - Reliable quantification of phthalates in environme.pdf}
}

@article{okubo2013,
  title = {Comparative {{Embryology}} of {{Eleven Species}} of {{Stony Corals}} ({{Scleractinia}})},
  author = {Okubo, Nami and Mezaki, Takuma and Nozawa, Yoko and Nakano, Yoshikatsu and Lien, Yi-Ting and Fukami, Hironobu and Hayward, David C. and Ball, Eldon E.},
  editor = {Medina, Mónica},
  date = {2013-12-18},
  journaltitle = {PLoS ONE},
  shortjournal = {PLoS ONE},
  volume = {8},
  number = {12},
  pages = {e84115},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0084115},
  url = {https://dx.plos.org/10.1371/journal.pone.0084115},
  urldate = {2024-09-03},
  langid = {english},
  keywords = {Blastomeres,Corals,Ectoderm,Eggs,Embryos,Endoderm,Lipids,Swimming},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\35CGKFDE\\Okubo et al. - 2013 - Comparative Embryology of Eleven Species of Stony .pdf;C\:\\Users\\ssdon\\Zotero\\storage\\BDCHB7LU\\Okubo et al. - 2013 - Comparative Embryology of Eleven Species of Stony .pdf}
}

@article{okubo2016,
  title = {A Comparative View of Early Development in the Corals {{Favia}} Lizardensis, {{Ctenactis}} Echinata, and {{Acropora}} Millepora - Morphology, Transcriptome, and Developmental Gene Expression},
  author = {Okubo, Nami and Hayward, David C. and Forêt, Sylvain and Ball, Eldon E.},
  date = {2016-02-29},
  journaltitle = {BMC Evolutionary Biology},
  shortjournal = {BMC Evolutionary Biology},
  volume = {16},
  number = {1},
  pages = {48},
  issn = {1471-2148},
  doi = {10.1186/s12862-016-0615-2},
  url = {https://doi.org/10.1186/s12862-016-0615-2},
  urldate = {2024-09-27},
  abstract = {Research into various aspects of coral biology has greatly increased in recent years due to anthropogenic threats to coral health including pollution, ocean warming and acidification. However, knowledge of coral early development has lagged. The present paper describes the embryonic development of two previously uncharacterized robust corals, Favia lizardensis (a massive brain coral) and Ctenactis echinata (a solitary coral) and compares it to that of the previously characterized complex coral, Acropora millepora, both morphologically and in terms of the expression of a set of key developmental genes.},
  keywords = {Acropora,brachyury,chordin,Coral development,Ctenactis,Favia,forkhead,In situ hybridization,Transcriptome},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\74S9XYC3\\Okubo et al. - 2016 - A comparative view of early development in the cor.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\4QQ2W3JJ\\s12862-016-0615-2.html}
}

@article{padilla-gamino2011,
  title = {Formation and Structural Organization of the Egg–Sperm Bundle of the Scleractinian Coral {{Montipora}} Capitata},
  author = {Padilla-Gamiño, J. L. and Weatherby, T. M. and Waller, R. G. and Gates, R. D.},
  date = {2011-06-01},
  journaltitle = {Coral Reefs},
  shortjournal = {Coral Reefs},
  volume = {30},
  number = {2},
  pages = {371--380},
  issn = {1432-0975},
  doi = {10.1007/s00338-010-0700-8},
  url = {https://doi.org/10.1007/s00338-010-0700-8},
  urldate = {2024-09-09},
  abstract = {The majority of scleractinian corals are hermaphrodites that broadcast spawn their gametes separately or packaged as egg–sperm bundles during spawning events that are timed to the lunar cycle. The egg–sperm bundle is an efficient way of transporting gametes to the ocean surface where fertilization takes place, while minimizing sperm dilution and maximizing the opportunity for gamete encounters during a spawning event. To date, there are few studies that focus on the formation and structure of egg–sperm bundle. This study explores formation, ultrastructure, and longevity of the egg–sperm bundle in Montipora capitata, a major reef building coral in Hawai‘i. Our results show that the egg–sperm bundle is formed by a mucus layer secreted by the oocytes. The sperm package is located at the center of each bundle, possibly reflecting the development of male and female gametes in different mesenteries. Once the egg–sperm bundle has reached the ocean surface, it breaks open within 10–35~min, depending on the environmental conditions (i.e., wind, water turbulence). Although the bundle has an ephemeral life span, the formation of an egg–sperm bundle is a fundamental part of the reproductive process that could be strongly influenced by climate change and deterioration of water quality (due to anthropogenic effects) and thus requires further investigation.},
  langid = {english},
  keywords = {Dispersal,Gamete packaging,Gametes,Hermaphrodite,Spawning,Ultrastructure},
  file = {C:\Users\ssdon\Zotero\storage\NMGRBCXM\Padilla-Gamiño et al. - 2011 - Formation and structural organization of the egg–s.pdf}
}

@article{padilla-gamino2013,
  title = {Are All Eggs Created Equal? {{A}} Case Study from the {{Hawaiian}} Reef-Building Coral {{Montipora}} Capitata},
  shorttitle = {Are All Eggs Created Equal?},
  author = {Padilla-Gamiño, Jacqueline L. and Bidigare, Robert R. and Barshis, Daniel J. and Alamaru, Ada and Hédouin, Laetitia and Hernández-Pech, Xavier and Kandel, Frederique and Leon Soon, Sherril and Roth, Melissa S. and Rodrigues, Lisa J. and Grottoli, Andrea G. and Portocarrero, Claudia and Wagenhauser, Stephanie A. and Buttler, Fenina and Gates, Ruth D.},
  date = {2013-03-01},
  journaltitle = {Coral Reefs},
  shortjournal = {Coral Reefs},
  volume = {32},
  number = {1},
  pages = {137--152},
  issn = {1432-0975},
  doi = {10.1007/s00338-012-0957-1},
  url = {https://doi.org/10.1007/s00338-012-0957-1},
  urldate = {2024-09-03},
  abstract = {Parental effects have been largely unexplored in marine organisms and may play a significant role in dictating the phenotypic range of traits in coral offspring, influencing their ability to survive environmental challenges. This study explored parental effects and life-stage differences in the Hawaiian reef-building coral Montipora capitata from different environments by examining the biochemical composition of mature coral colonies and their eggs. Our results indicate that there are large biochemical differences between adults and eggs, with the latter containing higher concentration of lipids (mostly wax esters), ubiquitinated proteins (which may indicate high turnover rate of proteins) and antioxidants (e.g., manganese superoxide dismutase). Adults displayed high phenotypic plasticity, with corals from a high-light environment having more wax esters, lighter tissue δ13C signatures and higher Symbiodinium densities than adults from the low-light environment who had higher content of accessory pigments. A green-algal pigment (α-carotene) and powerful antioxidant was present in eggs; it is unclear whether this pigment is acquired from heterotrophic food sources or from endolithic green algae living in the adult coral skeletons. Despite the broad phenotypic plasticity displayed by adults, parental investment in the context of provisioning of energy reserves and antioxidant defense was the same in eggs from the different sites. Such equality in investment maximizes the capacity of all embryos and larvae to cope with challenging conditions associated with floating at the surface and to disperse successfully until an appropriate habitat for settlement is found.},
  langid = {english},
  keywords = {Biochemical phenotype,Coral eggs,Coral reproduction,Egg provisioning,Environmental Chemistry,Gamete variation,Maternal effects,Spawner},
  file = {C:\Users\ssdon\Zotero\storage\B6E7D69W\Padilla-Gamiño et al. - 2013 - Are all eggs created equal A case study from the .pdf}
}

@article{padilla-gaminoParentGameteVertical2012,
  title = {From {{Parent}} to {{Gamete}}: {{Vertical Transmission}} of {{Symbiodinium}} ({{Dinophyceae}}) {{ITS2 Sequence Assemblages}} in the {{Reef Building Coral Montipora}} Capitata},
  shorttitle = {From {{Parent}} to {{Gamete}}},
  author = {Padilla-Gamiño, Jacqueline L. and Pochon, Xavier and Bird, Christopher and Concepcion, Gregory T. and Gates, Ruth D.},
  editor = {Ferse, Sebastian C. A.},
  date = {2012-06-06},
  journaltitle = {PLoS ONE},
  shortjournal = {PLoS ONE},
  volume = {7},
  number = {6},
  pages = {e38440},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0038440},
  url = {https://dx.plos.org/10.1371/journal.pone.0038440},
  urldate = {2022-04-02},
  abstract = {Parental effects are ubiquitous in nature and in many organisms play a particularly critical role in the transfer of symbionts across generations; however, their influence and relative importance in the marine environment has rarely been considered. Coral reefs are biologically diverse and productive marine ecosystems, whose success is framed by symbiosis between reefbuilding corals and unicellular dinoflagellates in the genus Symbiodinium. Many corals produce aposymbiotic larvae that are infected by Symbiodinium from the environment (horizontal transmission), which allows for the acquisition of new endosymbionts (different from their parents) each generation. In the remaining species, Symbiodinium are transmitted directly from parent to offspring via eggs (vertical transmission), a mechanism that perpetuates the relationship between some or all of the Symbiodinium diversity found in the parent through multiple generations. Here we examine vertical transmission in the Hawaiian coral Montipora capitata by comparing the Symbiodinium ITS2 sequence assemblages in parent colonies and the eggs they produce. Parental effects on sequence assemblages in eggs are explored in the context of the coral genotype, colony morphology, and the environment of parent colonies. Our results indicate that ITS2 sequence assemblages in eggs are generally similar to their parents, and patterns in parental assemblages are different, and reflect environmental conditions, but not colony morphology or coral genotype. We conclude that eggs released by parent colonies during mass spawning events are seeded with different ITS2 sequence assemblages, which encompass phylogenetic variability that may have profound implications for the development, settlement and survival of coral offspring.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\REAZG3TN\Padilla-Gamiño et al. - 2012 - From Parent to Gamete Vertical Transmission of Sy.pdf}
}

@article{padilla-gaminoSpawningDynamicsHawaiian2012,
  title = {Spawning Dynamics in the {{Hawaiian}} Reef-Building Coral {{Montipora}} Capitata},
  author = {Padilla-Gamiño, Jl and Gates, Rd},
  date = {2012-03-08},
  journaltitle = {Marine Ecology Progress Series},
  shortjournal = {Mar. Ecol. Prog. Ser.},
  volume = {449},
  pages = {145--160},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps09530},
  url = {http://www.int-res.com/abstracts/meps/v449/p145-160/},
  urldate = {2022-04-02},
  abstract = {The release of gametes into the water column by broadcast-spawning marine invertebrates represents the culmination of several physiological events in the parents and the first step in the supply of new recruits to marine ecosystem. The input of new propagules to coral reefs relies on spawning events that display remarkable synchronicity during limited periods each year. Although the timing of spawning is known for most species, other aspects of coral reproduction (polyp fecundity or spawning synchronicity) are less understood. This largely reflects the sporadic nature of reproductive activities and logistical problems of studying the ephemeral coral spawning events in situ on the reef at night. Here, we address this gap by exploring the spatial and temporal spawning dynamics of Montipora capitata, a broadcast-spawning, reef-building coral from the central Pacific Ocean, by using the systematic sampling of gametes in the field. Our results indicate that spawning in this species varies among years, months and lunar days, and that the proportion of colonies spawning and synchrony of spawning do not reflect coral colony morphology, colony size or the differences in environments between sites within a year. Major differences in reproductive outputs (spawned material) were observed between the 2 yr studied, which most probably reflects variability in temperature between years or shifts in the timing of spawning (phenology). This study highlights the complexity of spawning dynamics in corals and suggests that a more comprehensive understanding of interplay between reproduction and environment is fundamentally important to accurately predict the effects of climate change in these important ecosystems.},
  langid = {english},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\C64KA3JV\\Padilla-Gamiño and Gates - 2012 - Spawning dynamics in the Hawaiian reef-building co.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\F34QBQJG\\Padilla-Gamiño and Gates - 2012 - Spawning dynamics in the Hawaiian reef-building co.pdf}
}

@article{rendell-bhatti2021,
  title = {Developmental Toxicity of Plastic Leachates on the Sea Urchin {{Paracentrotus}} Lividus},
  author = {Rendell-Bhatti, Flora and Paganos, Periklis and Pouch, Anna and Mitchell, Christopher and D’Aniello, Salvatore and Godley, Brendan J. and Pazdro, Ksenia and Arnone, Maria Ina and Jimenez-Guri, Eva},
  date = {2021-01},
  journaltitle = {Environmental Pollution},
  shortjournal = {Environmental Pollution},
  volume = {269},
  pages = {115744},
  issn = {02697491},
  doi = {10.1016/j.envpol.2020.115744},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749120364332},
  urldate = {2023-08-11},
  abstract = {Microplastic pollution has become ubiquitous, affecting a wide variety of biota. Although microplastics are known to alter the development of a range of marine invertebrates, no studies provide a detailed morphological characterisation of the developmental defects. Likewise, the developmental toxicity of chemicals leached from plastic particles is understudied. The consequences of these developmental effects are likely underestimated, and the effects on ecosystems are unknown. Using the sea urchin Paracentrotus lividus as a model, we studied the effects of leachates of three forms of plastic pellet: new industrial pre-production plastic nurdles, beached pre-production nurdles, and floating filters, known as biobeads, also retrieved from the environment. Our chemical analyses show that leachates from beached pellets (biobead and nurdle pellets) and highly plasticised industrial pellets (PVC) contain polycyclic aromatic hydrocarbons and polychlorinated biphenyls, which are known to be detrimental to development and other life stages of animals. We also demonstrate that these microplastic leachates elicit severe, consistent and treatment-specific developmental abnormalities in P. lividus at embryonic and larval stages. Those embryos exposed to virgin polyethylene leachates with no additives nor environmental contaminants developed normally, suggesting that the abnormalities observed are the result of exposure to either environmentally adsorbed contaminants or pre-existing industrial additives within the polymer matrix. In the light of the chemical contents of the leachates and other characteristics of the plastic particles used, we discuss the phenotypes observed during our study, which include abnormal gastrulation, impaired skeletogenesis, abnormal neurogenesis, redistribution of pigmented cells and embryo radialisation.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\779TFPHV\Rendell-Bhatti et al. - 2021 - Developmental toxicity of plastic leachates on the.pdf}
}

@article{sanchez-avila2012,
  title = {Organic Micropollutants in Coastal Waters from {{NW Mediterranean Sea}}: {{Sources}} Distribution and Potential Risk},
  shorttitle = {Organic Micropollutants in Coastal Waters from {{NW Mediterranean Sea}}},
  author = {Sánchez-Avila, Juan and Tauler, Romà and Lacorte, Silvia},
  date = {2012-10},
  journaltitle = {Environment International},
  shortjournal = {Environment International},
  volume = {46},
  pages = {50--62},
  issn = {01604120},
  doi = {10.1016/j.envint.2012.04.013},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S016041201200102X},
  urldate = {2022-06-23},
  abstract = {This study provides a first estimation on the sources, distribution and risk of organic micropollutants (OMPs) in coastal waters from NW Mediterranean Sea. Polycyclic aromatic hydrocarbons, polychlorinated biphenyls, organochlorinated pesticides, polybrominated diphenyl ethers, phthalates and alkylphenols were analyzed by solid phase extraction and gas chromatography coupled to tandem mass spectrometry (SPE–GC–EI-MS/MS). River waters and wastewater treatment plant effluents discharging to the sea were identified as the main sources of OMPs to coastal waters, with an estimated input amount of around of 25,800 g d−1. The concentration of ΣOMPs in coastal areas ranged from 17.4 to 8442 ng L−1, and was the highest in port waters, followed by coastal and river mouth seawaters. A summarized overview of the patterns and sources of OMP contamination on the investigated coastal sea waters of NW Mediterranean Sea, as well as of their geographical distribution was obtained by Principal Component Analysis of the complete data set after its adequate pretreatment. Alkylphenols, bisphenol A and phthalates were the main contributors to ΣOMPs and produced an estimated significant pollution risk for fish, algae and the sensitive mysid shrimp organisms in seawater samples. The combination of GC-MS/MS, chemometrics and risk analysis is proven to be useful for a better control and management of OMP discharges.},
  langid = {english},
  keywords = {Animals,Benzhydryl Compounds,Decapoda,Environmental Monitoring,Fishes,Fresh Water,Gas Chromatography-Mass Spectrometry,Halogenated Diphenyl Ethers,Mediterranean Sea,Microalgae,Pesticides,Phenols,Phthalic Acids,Polychlorinated Biphenyls,Principal Component Analysis,Rivers,Seawater,Solid Phase Extraction,Tandem Mass Spectrometry,Waste Water,Water Pollutants Chemical,Zooplankton},
  file = {C:\Users\ssdon\Zotero\storage\5IWD3A2A\Sánchez-Avila et al. - 2012 - Organic micropollutants in coastal waters from NW .pdf}
}

@article{shumaker2019,
  title = {Genome Analysis of the Rice Coral {{Montipora}} Capitata},
  author = {Shumaker, Alexander and Putnam, Hollie M. and Qiu, Huan and Price, Dana C. and Zelzion, Ehud and Harel, Arye and Wagner, Nicole E. and Gates, Ruth D. and Yoon, Hwan Su and Bhattacharya, Debashish},
  date = {2019-02-22},
  journaltitle = {Scientific Reports},
  shortjournal = {Sci Rep},
  volume = {9},
  number = {1},
  pages = {2571},
  publisher = {Nature Publishing Group},
  issn = {2045-2322},
  doi = {10.1038/s41598-019-39274-3},
  url = {http://www.nature.com/articles/s41598-019-39274-3},
  urldate = {2022-04-06},
  abstract = {Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based \textasciitilde 886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai’i. Our work provides insights into the architecture of coral genomes and shows how they differ in size and gene inventory, putatively due to population size variation. We describe a recent example of foreign gene acquisition via a bacterial gene transfer agent and illustrate the major pathways of stress response that can be used to predict regulatory components of the transcriptional networks in M. capitata. These genomic resources provide insights into the adaptive potential of these sessile, long-lived species in both natural and human influenced environments and facilitate functional and population genomic studies aimed at Hawaiian reef restoration and conservation.},
  issue = {1},
  langid = {english},
  keywords = {Animals,Anthozoa,Genome,Genome evolution,Molecular evolution,Stress Physiological,Transcription Genetic},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\KM6CISMC\\Shumaker et al. - 2019 - Genome analysis of the rice coral Montipora capita.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\R4YRHB8S\\Shumaker et al. - 2019 - Genome analysis of the rice coral Montipora capita.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\JN6MA8N5\\s41598-019-39274-3.html}
}

@article{sokolowski2024,
  title = {Environmental and {{Food Contamination}} by {{Phthalic Acid Esters}} ({{PAEs}}): {{Overview}}},
  shorttitle = {Environmental and {{Food Contamination}} by {{Phthalic Acid Esters}} ({{PAEs}})},
  author = {Sokołowski, Artur and Kończak, Magdalena and Oleszczuk, Patryk and Gao, Yanzheng and Czech, Bożena},
  date = {2024-05-06},
  journaltitle = {Water, Air, \& Soil Pollution},
  shortjournal = {Water Air Soil Pollut},
  volume = {235},
  number = {5},
  pages = {313},
  issn = {1573-2932},
  doi = {10.1007/s11270-024-07121-5},
  url = {https://doi.org/10.1007/s11270-024-07121-5},
  urldate = {2024-10-10},
  abstract = {Phthalic acid esters (PAEs) are dialkyl or alkyl/aryl ester derivatives of phthalic acid. PAEs are colorless, odorless, and flavorless oily liquids. PAEs are the main plasticizers used in industry and households. DEHP (di-(2-ethyl hexyl) phthalate) is the main plasticizer used in the polymer industry, whereas DMP (dimethyl phthalate) and DEP (diethyl phthalate) are used mainly as solvents or fixatives in cosmetics and personal care products. PAEs are synthetic organic compounds poorly soluble in water but soluble in organic solvents. Into the environment, they are introduced during the production, use and degradation, packaging, and transportation of plastic products. In the environment, PAEs are degraded in three ways: by hydrolysis, photodegradation, and microbial degradation, whereas the biodegradation and hydrolysis of PAEs in the environment are very slow. PAEs are pollutants of soil, water, groundwater, river water, marine water, air, sediments, vegetables, and biota. Due to the great interest in the subject of environmental pollution by PAEs and the emergence of new information in this area, it is extremely important to systematically review the current knowledge. In the presented paper, the occurrence of PAEs in different environmental matrices was reviewed. The toxicity to plants, animals, and humans was also described.},
  langid = {english},
  keywords = {Bioavailability,DEHP,DMP,Environmental Chemistry,Phthalic acid esters (PAEs),Toxicity},
  file = {C:\Users\ssdon\Zotero\storage\3MFBZTDS\Sokołowski et al. - 2024 - Environmental and Food Contamination by Phthalic A.pdf}
}

@article{stephens2022,
  title = {High-Quality Genome Assemblies from Key {{Hawaiian}} Coral Species},
  author = {Stephens, Timothy G and Lee, JunMo and Jeong, YuJin and Yoon, Hwan Su and Putnam, Hollie M and Majerová, Eva and Bhattacharya, Debashish},
  date = {2022-01-01},
  journaltitle = {GigaScience},
  shortjournal = {GigaScience},
  volume = {11},
  pages = {giac098},
  issn = {2047-217X},
  doi = {10.1093/gigascience/giac098},
  url = {https://doi.org/10.1093/gigascience/giac098},
  urldate = {2024-10-03},
  abstract = {Coral reefs house about 25\% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies.We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal.These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawaiʻi but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\HJ4827TB\\Stephens et al. - 2022 - High-quality genome assemblies from key Hawaiian c.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\7CIFVYW7\\6815755.html}
}

@article{teuten2009,
  title = {Transport and Release of Chemicals from Plastics to the Environment and to Wildlife},
  author = {Teuten, Emma L. and Saquing, Jovita M. and Knappe, Detlef R. U. and Barlaz, Morton A. and Jonsson, Susanne and Björn, Annika and Rowland, Steven J. and Thompson, Richard C. and Galloway, Tamara S. and Yamashita, Rei and Ochi, Daisuke and Watanuki, Yutaka and Moore, Charles and Viet, Pham Hung and Tana, Touch Seang and Prudente, Maricar and Boonyatumanond, Ruchaya and Zakaria, Mohamad P. and Akkhavong, Kongsap and Ogata, Yuko and Hirai, Hisashi and Iwasa, Satoru and Mizukawa, Kaoruko and Hagino, Yuki and Imamura, Ayako and Saha, Mahua and Takada, Hideshige},
  date = {2009-07-27},
  journaltitle = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  shortjournal = {Philos Trans R Soc Lond B Biol Sci},
  volume = {364},
  number = {1526},
  eprint = {19528054},
  eprinttype = {pmid},
  pages = {2027--2045},
  issn = {0962-8436},
  doi = {10.1098/rstb.2008.0284},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873017/},
  urldate = {2022-07-26},
  abstract = {Plastics debris in the marine environment, including resin pellets, fragments and microscopic plastic fragments, contain organic contaminants, including polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons, petroleum hydrocarbons, organochlorine pesticides (2,2′-bis(p-chlorophenyl)-1,1,1-trichloroethane, hexachlorinated hexanes), polybrominated diphenylethers, alkylphenols and bisphenol A, at concentrations from sub ng g–1 to µg g–1. Some of these compounds are added during plastics manufacture, while others adsorb from the surrounding seawater. Concentrations of hydrophobic contaminants adsorbed on plastics showed distinct spatial variations reflecting global pollution patterns. Model calculations and experimental observations consistently show that polyethylene accumulates more organic contaminants than other plastics such as polypropylene and polyvinyl chloride. Both a mathematical model using equilibrium partitioning and experimental data have demonstrated the transfer of contaminants from plastic to organisms. A feeding experiment indicated that PCBs could transfer from contaminated plastics to streaked shearwater chicks. Plasticizers, other plastics additives and constitutional monomers also present potential threats in terrestrial environments because they can leach from waste disposal sites into groundwater and/or surface waters. Leaching and degradation of plasticizers and polymers are complex phenomena dependent on environmental conditions in the landfill and the chemical properties of each additive. Bisphenol A concentrations in leachates from municipal waste disposal sites in tropical Asia ranged from sub µg l–1 to mg l–1 and were correlated with the level of economic development.},
  pmcid = {PMC2873017},
  file = {C:\Users\ssdon\Zotero\storage\M54BMX8B\Teuten et al. - 2009 - Transport and release of chemicals from plastics t.pdf}
}

@article{vandenberg2012,
  title = {Hormones and Endocrine-Disrupting Chemicals: Low-Dose Effects and Nonmonotonic Dose Responses},
  shorttitle = {Hormones and Endocrine-Disrupting Chemicals},
  author = {Vandenberg, Laura N and Colborn, Theo and Hayes, Tyrone B and Heindel, Jerrold J and Jacobs, David R and Lee, Duk-Hee and Shioda, Toshi and Soto, Ana M and family=Saal, given=Frederick S, prefix=vom, useprefix=true and Welshons, Wade V and Zoeller, R Thomas and Myers, John Peterson},
  date = {2012-06-01},
  journaltitle = {Endocrine reviews},
  shortjournal = {Endocr Rev},
  volume = {33},
  number = {3},
  eprint = {22419778},
  eprinttype = {pmid},
  pages = {378--455},
  issn = {1945-7189},
  doi = {10.1210/er.2011-1050},
  url = {https://europepmc.org/articles/PMC3365860},
  urldate = {2022-11-17},
  abstract = {For decades, studies of endocrine-disrupting chemicals (EDCs) have challenged traditional concepts in toxicology, in particular the dogma of "the dose makes the poison," because EDCs can have effects at low doses that are not predicted by effects at higher doses. Here, we review two major concepts in EDC studies: low dose and nonmonotonicity. Low-dose effects were defined by the National Toxicology Program as those that occur in the range of human exposures or effects observed at doses below those used for traditional toxicological studies. We review the mechanistic data for low-dose effects and use a weight-of-evidence approach to analyze five examples from the EDC literature. Additionally, we explore nonmonotonic dose-response curves, defined as a nonlinear relationship between dose and effect where the slope of the curve changes sign somewhere within the range of doses examined. We provide a detailed discussion of the mechanisms responsible for generating these phenomena, plus hundreds of examples from the cell culture, animal, and epidemiology literature. We illustrate that nonmonotonic responses and low-dose effects are remarkably common in studies of natural hormones and EDCs. Whether low doses of EDCs influence certain human disorders is no longer conjecture, because epidemiological studies show that environmental exposures to EDCs are associated with human diseases and disabilities. We conclude that when nonmonotonic dose-response curves occur, the effects of low doses cannot be predicted by the effects observed at high doses. Thus, fundamental changes in chemical testing and safety determination are needed to protect human health.},
  langid = {english},
  pmcid = {PMC3365860},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\64TH3477\\Vandenberg et al. - 2012 - Hormones and Endocrine-Disrupting Chemicals Low-D.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\F4E7S8RH\\Vandenberg et al. - 2012 - Hormones and endocrine-disrupting chemicals low-d.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\JUP9AA7Z\\Vandenberg et al. - 2012 - Hormones and Endocrine-Disrupting Chemicals Low-D.pdf}
}

@article{vanoppen2017,
  title = {Shifting Paradigms in Restoration of the World's Coral Reefs},
  author = {family=Oppen, given=Madeleine J. H., prefix=van, useprefix=true and Gates, Ruth D. and Blackall, Linda L. and Cantin, Neal and Chakravarti, Leela J. and Chan, Wing Y. and Cormick, Craig and Crean, Angela and Damjanovic, Katarina and Epstein, Hannah and Harrison, Peter L. and Jones, Thomas A. and Miller, Margaret and Pears, Rachel J. and Peplow, Lesa M. and Raftos, David A. and Schaffelke, Britta and Stewart, Kristen and Torda, Gergely and Wachenfeld, David and Weeks, Andrew R. and Putnam, Hollie M.},
  date = {2017},
  journaltitle = {Global Change Biology},
  volume = {23},
  number = {9},
  pages = {3437--3448},
  issn = {1365-2486},
  doi = {10.1111/gcb.13647},
  url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.13647},
  urldate = {2022-01-31},
  abstract = {Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine-protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required. We have recently discussed options for using assisted evolution (i.e., selective breeding, assisted gene flow, conditioning or epigenetic programming, and the manipulation of the coral microbiome) as a means to enhance environmental stress tolerance of corals and the success of coral reef restoration efforts. The 2014–2016 global coral bleaching event has sharpened the focus on such interventionist approaches. We highlight the necessity for consideration of alternative (e.g., hybrid) ecosystem states, discuss traits of resilient corals and coral reef ecosystems, and propose a decision tree for incorporating assisted evolution into restoration initiatives to enhance climate resilience of coral reefs.},
  langid = {english},
  keywords = {assisted evolution,climate change,coral reefs,global warming,hybrid ecosystems,rehabilitation,restoration,scleractinia},
  file = {C\:\\Users\\ssdon\\Zotero\\storage\\2WZ5BHNL\\van Oppen et al. - 2017 - Shifting paradigms in restoration of the world's c.pdf;C\:\\Users\\ssdon\\Zotero\\storage\\WN5SRAKS\\gcb.html}
}

@article{veron1989,
  title = {Annotated {{Checklist}} of the {{Hermatypic Corals}} of the {{Philippines}}!},
  author = {Veron, J E N and Hodgson, Gregor},
  date = {1989},
  journaltitle = {PACIFIC SCIENCE},
  volume = {43},
  abstract = {All known reef-building corals of the Philippines are listed in systematic order. Records are from original field studies combined with reevaluations of major taxonomic collections in Philippines universities. Field studies were conducted in 1986 and 1988 on reefs near Bolinao (Luzon), Puerto Galera (Mindoro), Mactan (Cebu), Apo Island (Negros), and EI Nido (Palawan), an area of over half the east-west and north-south extent of the country. Detailed studies were made of collections at the University of the Philippines (Marine Science Institute, Zoology Department, and Bolinao Marine Laboratory), the University of San Carlos, and Silliman University. Synonomies are proposed, based on reevaluations of all available type specimens that have the Philippines as type locality. All taxa are indexed.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\NEAGFMCU\Veron and Hodgson - 1989 - Annotated Checklist of the Hermatypic Corals of th.pdf}
}

@article{zhang2021,
  title = {Hazards of Phthalates ({{PAEs}}) Exposure: {{A}} Review of Aquatic Animal Toxicology Studies},
  shorttitle = {Hazards of Phthalates ({{PAEs}}) Exposure},
  author = {Zhang, Ying and Jiao, Yaqi and Li, Zixu and Tao, Yue and Yang, Yang},
  date = {2021-06-01},
  journaltitle = {Science of The Total Environment},
  shortjournal = {Science of The Total Environment},
  volume = {771},
  pages = {145418},
  issn = {0048-9697},
  doi = {10.1016/j.scitotenv.2021.145418},
  url = {https://www.sciencedirect.com/science/article/pii/S0048969721004861},
  urldate = {2022-07-31},
  abstract = {Phthalates (PAEs) are of wide concern because they are commonly used in various plastic products as plasticizers, and can found their way into the environment. However, their interaction with the environment and their toxicity in aquatic animals is still a matter of intense debate. In this review on PAEs in aquatic environments (lakes, rivers and seas), it is found that there is a large variety and abundance of PAEs in developing countries, and the total concentration of PAEs even exceeds 200~μg / L. The interaction between metabolic processes involved in the toxicity induced by various PAEs is summarized for the first time in the article. Exposure of PAEs can lead to activation of the detoxification system CYP450 and endocrine system receptors of aquatic animals, which in turn causes oxidative stress, metabolic disorders, endocrine disorders, and immunosuppression. Meanwhile, each system can activate / inhibit each other, causing genotoxicity and cell apoptosis, resulting in the growth and development of organisms being blocked. The mixed PAEs shows no cumulative toxicity changes to aquatic animals. For the combined pollution of other chemicals and PAEs, PAE can act as an agonist or antagonist, leading to combined toxicity in different directions. Phthalate monoesters (MPEs), the metabolites of PAEs, are also toxic to aquatic animals, however, the toxicity is weaker than the corresponding parent compounds. This review summarizes and analyzes the current ecotoxicological effects of PAEs on aquatic animals, and provides guidance for future research.},
  langid = {english},
  keywords = {Aquatic toxicity,Combined pollution,Endocrine toxicity,Oxidative stress,Phthalate monoesters,Phthalates},
  file = {C:\Users\ssdon\Zotero\storage\DW2REE3B\S0048969721004861.html}
}

@article{zhang2021a,
  title = {Rapid and Accurate Alignment of Nucleotide Conversion Sequencing Reads with {{HISAT-3N}}},
  author = {Zhang, Yun and Park, Chanhee and Bennett, Christopher and Thornton, Micah and Kim, Daehwan},
  date = {2021-07-01},
  journaltitle = {Genome Research},
  shortjournal = {Genome Res.},
  volume = {31},
  number = {7},
  eprint = {34103331},
  eprinttype = {pmid},
  pages = {1290--1295},
  publisher = {Cold Spring Harbor Lab},
  issn = {1088-9051, 1549-5469},
  doi = {10.1101/gr.275193.120},
  url = {https://genome.cshlp.org/content/31/7/1290},
  urldate = {2024-10-07},
  abstract = {Sequencing technologies using nucleotide conversion techniques such as cytosine to thymine in bisulfite-seq and thymine to cytosine in SLAM seq are powerful tools to explore the chemical intricacies of cellular processes. To date, no one has developed a unified methodology for aligning converted sequences and consolidating alignment of these technologies in one package. In this paper, we describe hierarchical indexing for spliced alignment of transcripts–3 nucleotides (HISAT-3N), which can rapidly and accurately align sequences consisting of any nucleotide conversion by leveraging the powerful hierarchical index and repeat index algorithms originally developed for the HISAT software. Tests on real and simulated data sets show that HISAT-3N is faster than other modern systems, with greater alignment accuracy, higher scalability, and smaller memory requirements. HISAT-3N therefore becomes an ideal aligner when used with converted sequence technologies.},
  langid = {english},
  file = {C:\Users\ssdon\Zotero\storage\Y887INFG\Zhang et al. - 2021 - Rapid and accurate alignment of nucleotide convers.pdf}
}

@online{zotero-3994,
  title = {{{ASTM D1141-98 Technical Bulletin}}.Pdf},
  url = {https://drive.google.com/file/u/1/d/1QmkJYhUODVJLhCBcDb24XovCmirgV4Fc/view?usp=embed_facebook},
  urldate = {2024-10-10},
  organization = {Google Docs},
  keywords = {ASTM},
  file = {C:\Users\ssdon\Zotero\storage\4FFXNGI3\view.html}
}