USAP-DC

{"dp_type": "Project", "free_text": "Methylation"}

[{"awards": "2317995 Herman, Rachael", "bounds_geometry": "POLYGON((-65 -61,-64 -61,-63 -61,-62 -61,-61 -61,-60 -61,-59 -61,-58 -61,-57 -61,-56 -61,-55 -61,-55 -61.5,-55 -62,-55 -62.5,-55 -63,-55 -63.5,-55 -64,-55 -64.5,-55 -65,-55 -65.5,-55 -66,-56 -66,-57 -66,-58 -66,-59 -66,-60 -66,-61 -66,-62 -66,-63 -66,-64 -66,-65 -66,-65 -65.5,-65 -65,-65 -64.5,-65 -64,-65 -63.5,-65 -63,-65 -62.5,-65 -62,-65 -61.5,-65 -61))", "dataset_titles": null, "datasets": null, "date_created": "Fri, 04 Oct 2024 00:00:00 GMT", "description": "Gentoo penguins (Pygoscelis papua) inhabit one of the fastest warming regions on Earth, the Western Antarctic Peninsula (WAP), where environmental shifts are measured in years, not decades. Despite this, the species is flourishing, growing in numbers and colonizing new habitats while sister species, such as Ad\u00e9lie penguins (P. adeliae), are declining in the region. This project will investigate to what extent epigenetics contributes to the success of gentoo penguins. Epigenetic variation is controlled by modifications to DNA or chromatin structure that affect the expression of genes, rather than changes to the underlying DNA sequence. This project will improve the understanding of gentoo penguin adaptation to climate change, and whether it is a result of increased flexibility in behavior and physiology driven by a greater capacity for epigenetic changes (i.e., epigenetic potential). The most studied form of epigenetic variation is the profiling of DNA methylation patterns. Environmental effects can trigger changes in DNA methylation that target specific tissues, allowing for localized gene expression shifts that result in modifications to the phenotype of an organism without any alteration to the underlying genotype. Given that epigenetic variation between populations often exceeds genetic variation, fine-scale genetic differentiation observed amongst gentoo penguin colonies suggests the possibility for local adaptation via even more divergent epigenetic changes and provides a framework for examining epigenetic variation across the gentoo penguin breeding range along multiple ecological axes. The researchers will test this by comprehensively characterizing the epigenomic profiles via patterns of DNA methylation in wild gentoo and Ad\u00e9lie penguins using cutting-edge high-resolution genomics techniques. Specifically, they will investigate whether gentoo penguins exhibit a greater degree of differences in DNA-methylation than underlying genetic differences, suggesting such epigenetic variation is driven by external environmental variables, potentially leading to improved capacity for local adaptation. This project will explore whether epigenetic potential may be selected for in individuals who disperse to new colony locations by comparing older, established colonies to new colonies at the range-edge. By implementing cutting-edge epigenetic methods in wild populations of gentoo penguins, this project will help address ecological questions on environmental plasticity that will impact conservation efforts and decisions on Marine Protected Areas (MPAs) on the Antarctic Peninsula. This award reflects NSF\u0027s statutory mission and has been deemed worthy of support through evaluation using the Foundation\u0027s intellectual merit and broader impacts review criteria.", "east": -55.0, "geometry": "POINT(-60 -63.5)", "instruments": null, "is_usap_dc": true, "keywords": "Gentoo Penguin; ECOLOGICAL DYNAMICS; Adaptation; Methylation; Antarctic Peninsula; Climate Change; Epigenetic Variation; PENGUINS", "locations": "Antarctic Peninsula", "north": -61.0, "nsf_funding_programs": "Post Doc/Travel; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Herman, Rachael", "platforms": null, "repositories": null, "science_programs": null, "south": -66.0, "title": "Postdoctoral Fellowship: OPP-PRF: Epigenetic Potential as a Driver of Local Adaptation in Gentoo Penguins (Pygoscelis Papua) along the Western Antarctic Peninsula", "uid": "p0010477", "west": -65.0}, {"awards": "2053726 Hofmann, Gretchen", "bounds_geometry": "POLYGON((163 -77,163.4 -77,163.8 -77,164.2 -77,164.6 -77,165 -77,165.4 -77,165.8 -77,166.2 -77,166.6 -77,167 -77,167 -77.1,167 -77.2,167 -77.3,167 -77.4,167 -77.5,167 -77.6,167 -77.7,167 -77.8,167 -77.9,167 -78,166.6 -78,166.2 -78,165.8 -78,165.4 -78,165 -78,164.6 -78,164.2 -78,163.8 -78,163.4 -78,163 -78,163 -77.9,163 -77.8,163 -77.7,163 -77.6,163 -77.5,163 -77.4,163 -77.3,163 -77.2,163 -77.1,163 -77))", "dataset_titles": "Analyses combining ATAC-seq, RRBS, and RNA-seq data for purple urchins", "datasets": [{"dataset_uid": "200288", "doi": "", "keywords": null, "people": null, "repository": "GitHub", "science_program": null, "title": "Analyses combining ATAC-seq, RRBS, and RNA-seq data for purple urchins", "url": "https://github.com/snbogan/Sp_RRBS_ATAC"}], "date_created": "Thu, 14 Apr 2022 00:00:00 GMT", "description": "Part 1: Non-technical description: With support from the Office of Polar Programs, this project will evaluate how an important part of the food web in the coastal ocean of Antarctica will respond to climate change. The focal study organism in the plankton is a shelled mollusk, the Antarctic pteropod, Limacina helicina antarctica, an Southern Ocean organism that this known to respond to climate driven changes in ocean acidification and ocean warming. Ocean acidification, the lowering of ocean pH via the absorption of atmospheric carbon dioxide in the surface of the ocean, is a change in the ocean that is expected to cross deleterious thresholds of pH within decades. This study will improve understanding of how pteropods will respond, which will provide insight into predicting the resilience of the Antarctic marine ecosystem during future changes, one of the planet\u2019s last marine wildernesses. The project will use tools of molecular biology to examine specifically how gene expression is modulated in the pteropods, and further, how the changes and regulation of genes act to resist the stress of low pH and high temperature. In addition, this project supports the training of Ph.D. graduate students and advances the goal of inclusive excellence in STEM and in marine sciences, in particular. The students involved in this project are from groups traditionally under-represented in marine science including first-generation college students. Overall, the project contributes to the development of the U.S. work force and contributes to diversity and inclusive excellence in the geosciences. Part 2: Technical description: The overarching goal of this project is to investigate the molecular response of the Antarctic thecosome pteropod, Limacina helicina antarctica to ocean acidification (OA) and ocean warming. The project will investigate changes in the epigenome of juvenile L. h. antarctica, by assessing the dynamics of DNA methylation in response to three scenarios of environmental conditions that were simulated in laboratory mesocosm CO2 experiments: (1) present-day pCO2 conditions for summer and winter, (2) future ocean acidification expected within 10-15 years, and (3) a multiple stressor experiment to investigate synergistic interaction of OA and high temperature stress. Recent lab-based mesocosm experiment research showed significant changes in the dynamics of global DNA methylation in the pteropod genome, along with variation in gene expression in response to abiotic changes. Thus, it is clear that juvenile L. h. antarctica are capable of mounting a substantial epigenetic response to ocean acidification. However, it is not known how DNA methylation, as an epigenetic process, is modulating changes in the transcriptome. In order to address this gap in the epigenetic knowledge regarding pteropods, the project will use next-generation sequencing approaches (e.g., RNA sequencing and reduced representation bisulfite sequencing) to integrate changes in methylation status with changes in gene expression in juvenile pteropods. Overall, this investigation is an important step in exploring environmental transcriptomics and phenotypic plasticity of an ecologically important member of Southern Ocean macrozoooplankton in response to anthropogenic climate change. This award reflects NSF\u0027s statutory mission and has been deemed worthy of support through evaluation using the Foundation\u0027s intellectual merit and broader impacts review criteria.", "east": 167.0, "geometry": "POINT(165 -77.5)", "instruments": null, "is_usap_dc": true, "keywords": "USAP-DC; McMurdo Sound; Amd/Us; FIELD INVESTIGATION; USA/NSF; AMD; MARINE ECOSYSTEMS; ANIMALS/INVERTEBRATES", "locations": "McMurdo Sound", "north": -77.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Hofmann, Gretchen", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD INVESTIGATION", "repo": "GitHub", "repositories": "GitHub", "science_programs": null, "south": -78.0, "title": "The Role of the Epigenetic Mechanism, DNA Methylation, in the Tolerance and Resistance of Antarctic Pteropods to Ocean Acidification and Warming", "uid": "p0010313", "west": 163.0}, {"awards": "1543412 Reinfelder, John", "bounds_geometry": null, "dataset_titles": "16S rRNA gene libraries of krill gut microbial communities; Microbial gene libraries of krill gut microbial communities", "datasets": [{"dataset_uid": "601171", "doi": "10.15784/601171", "keywords": "Antarctica; Biota; Krill; LTER Palmer Station; Microbiome; Oceans; Southern Ocean", "people": "Reinfelder, John", "repository": "USAP-DC", "science_program": "LTER", "title": "16S rRNA gene libraries of krill gut microbial communities", "url": "https://www.usap-dc.org/view/dataset/601171"}, {"dataset_uid": "200024", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Microbial gene libraries of krill gut microbial communities", "url": "https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fbioproject%2F531145\u0026amp;data=02%7C01%7Creinfeld%40envsci.rutgers.edu%7C7e30a0192dc748ab271408d6b9d57d08%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636900723909188941\u0026amp;sdata=G6cNg4bBHzeikrWSCYITcT6XS3NLWwjQ1yNdwtrALPc%3D\u0026amp;reserved=0"}], "date_created": "Sun, 31 Mar 2019 00:00:00 GMT", "description": "Marine food webs can concentrate monomethylmercury (MMHg), a neurotoxin in mammals, in upper trophic level consumers. Despite their remoteness, coastal Antarctic marine ecosystems accumulate and biomagnify MMHg to levels observed at lower latitudes and in the Arctic. Marine sediments and other anoxic habitats in the oceans are typical areas where methylation of mercury occurs and these are likely places where MMHg is being produced. Krill, and more specifically their digestive tracts, may be a previously unaccounted for site where the production of MMHg may be occurring in the Antarctic. If monomethylmercury production is occurring in krill, current views regarding bioaccumulation in the food web and processes leading to the production and accumulation of mercury in the Antarctic Ocean could be better informed, if not transformed. This project will conduct a preliminary assessment of the krill gut microbiomes, the microbiome\u0027s genomic content and potential for production of monomethyl mercury by detecting the genes involved in mercury transformations. By analyzing the krill gut microbiome, the project will provide insights regarding animal-microbe interactions and their potential role in globally important biogeochemical cycles. This project will conduct a preliminary assessment of the krill gut microbiomes, the microbiomes genomic content and potential for production of monomethylmercury. The diversity and metabolic profiles of microorganisms in krill digestive tracts will be evaluated using massively parallel Illumina DNA sequencing technology to produce 16S rRNA gene libraries and assembled whole metagenomes. The project will also quantify the abundance and expression of Hg methylation genes, hgcAB, and identify their taxonomic affiliations in the microbiome communities. Environmental metagenomes, 16S rRNA gene inventories produced from this project will provide the polar science community with valuable databases and experimental tools with which to examine coastal Antarctic microbial ecology and biogeochemistry. The project will seek to provide a wider window into the diversity of extremophile microbial communities and the identification of potentially unique and useful bioactive compounds. In addition to public education and outreach. This project will train graduate students and provide educational and outreach opportunities at the participating institutions", "east": -68.2816, "geometry": "POINT(-69.09295 -66.8017)", "instruments": "NOT APPLICABLE \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "is_usap_dc": true, "keywords": "USAP-DC; Antarctica; NOT APPLICABLE; BACTERIA/ARCHAEA", "locations": "Antarctica", "north": -65.8708, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Schaefer, Jeffra; Reinfelder, John; Barkar, T.", "platforms": "OTHER \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "repo": "USAP-DC", "repositories": "NCBI GenBank; USAP-DC", "science_programs": "LTER", "south": -67.7326, "title": "Methylmercury in Antarctic Krill Microbiomes", "uid": "p0010023", "west": -69.9043}, {"awards": "0944557 Marsh, Adam", "bounds_geometry": "POINT(166 78)", "dataset_titles": "Environmental Genomics of an Antarctic Polychaete #SRP040946", "datasets": [{"dataset_uid": "000223", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Environmental Genomics of an Antarctic Polychaete #SRP040946", "url": "https://www.ncbi.nlm.nih.gov/sra/?term=SRP040946"}], "date_created": "Tue, 13 Jan 2015 00:00:00 GMT", "description": "Genome-enabled biology provides a foundation for understanding the genetic basis of organism-environment interactions. . The research project links gene expression, genome methylation, and metabolic rates to assess the mechanisms of environmental adaptation (temperature) across multiple generations in a polar, and closely related temperate, polychaete. By comparing these two species, the research will assess how a polar environment shapes responses to environmental stress. This work will produce: 1) a database of full transcriptome (gene specific) profiling data for the polar polychaete cultured at two temperatures; 2) the contribution of genome methylation to the suppression of gene transcription activities; 3) the linkage between shifts in mRNA pools and total cellular activities (as ATP consumption via respiration); 4) an assessment of the inheritance of patterns of gene expression and metabolic activities across three generations; and 5) a simple demographic model of the polar polychaete population dynamics under normal and \u0027global-warming\u0027 temperature scenarios. Broader impacts include two outreach activities. The first is a mentoring program, where African-American undergraduate students spend 1.5 years working on a research project with a UD faculty member (2 summers plus their senior academic year). The second is a children\u0027s display activity at UD?s School of Marine Science \"Coast Day\".", "east": 166.0, "geometry": "POINT(166 -78)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": -78.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Marsh, Adam G.", "platforms": "Not provided", "repo": "NCBI GenBank", "repositories": "NCBI GenBank", "science_programs": null, "south": -78.0, "title": "Environmental Genomics in an Antarctic polychaete", "uid": "p0000355", "west": 166.0}]

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