USAP-DC

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

[{"awards": "1142158 Cheng, Chi-Hing; 2224611 Schofield, Oscar; 1440435 Ducklow, Hugh; 1344502 Ducklow, Hugh; 1543383 Postlethwait, John; 2026045 Schofield, Oscar; 0636696 DeVries, Arthur", "bounds_geometry": "POLYGON((-180 -60,-144 -60,-108 -60,-72 -60,-36 -60,0 -60,36 -60,72 -60,108 -60,144 -60,180 -60,180 -63,180 -66,180 -69,180 -72,180 -75,180 -78,180 -81,180 -84,180 -87,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -87,-180 -84,-180 -81,-180 -78,-180 -75,-180 -72,-180 -69,-180 -66,-180 -63,-180 -60))", "dataset_titles": null, "datasets": null, "date_created": "Tue, 11 Mar 2025 00:00:00 GMT", "description": "Since 1990, Palmer LTER (PAL) research has been guided by the hypothesis that variability in the polar marine ecosystem is mechanistically coupled to changes in the annual advance, retreat and spatial extent of sea ice. Since that time, the hypothesis has been modified to incorporate climate migration, i.e. the displacement of a cold, dry polar climate by a warm, moist climate regime in the northern component of the PAL region, producing fundamental changes in food web structure and elemental cycling. The observed northern changes are affecting all trophic levels and elemental cycling, and the primary mechanism of change involves match-mismatch dynamics. The proposed research builds on previous findings, with a new emphasis on process studies and modeling to elucidate the mechanistic links between teleconnections, climate change, physical oceanographic forcing and ecosystem dynamics. The proposed research will examine the hypothesis that regional warming and sea ice decline associated with historical and on-going climate migration in the northern part of the study area have altered key phenological relationships, leading to changes in species distributions, increasing trophic mismatches and changes in habitat, food availability, ecosystem dynamics and biogeochemical cycling. Through targeted process studies linked to numerical model simulations, the research also will test the hypothesis that deep cross-shelf canyons characterizing the core study region are focal areas for ecosystem processes that result in predictable, elevated food resources for top-predators. The effort includes the addition of 3 new PIs: a zooplankton ecologist with expertise in biogeochemical fluxes, a phytoplankton ecologist focusing on bio-optics and autonomous observations using gliders, and a numerical simulation modeler specializing in coupled global models of ocean circulation, plankton ecology and biogeochemical cycles. The program will add trace metal sampling and analysis, moored physical oceanographic sensors, a moored sediment trap in the south, drifting sediment traps and stable carbon (del 13C) and nitrogen (del 15N) isotope analyses. Missions lasting up to 45 days using gliders deployed before, during and after summer cruises will, along with moorings and satellite remote sensing of sea ice, ocean color, sea surface temperatures and wind fields, greatly extend the observational program in space and time. Since its inception, PAL has been a leader in Information Management to enable knowledge-building within and beyond the Antarctic, oceanographic and LTER communities. PAL has designed and deployed a new information infrastructure with a relational database architecture to facilitate data distribution and sharing. The Education and Outreach program capitalizes on the public\u0027s fascination with Antarctica to promote scientific literacy from kindergarten students to adult citizens concerned with climate change and environmental sustainability. Through communicating results to the public and working with scientific assessment bodies (e.g., IPCC) and Antarctic Treaty parties to protect Earth\u0027s last frontier, PAL researchers contribute to the national scientific agenda and the greater public benefit.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "Antarctica; Cryonotothenioid; R/V LMG; Bellingshausen Sea; Southern Ocean; Notothenioid; FISHERIES", "locations": "Bellingshausen Sea; Southern Ocean; Antarctica", "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Integrated System Science; Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems; Antarctic Integrated System Science; Antarctic Organisms and Ecosystems; Antarctic Integrated System Science; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Corso, Andrew; Desvignes, Thomas; McDowell, Jan; Cheng, Chi-Hing; Biesack, Ellen; Steinberg, Deborah; Hilton, Eric", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e R/V LMG", "repositories": null, "science_programs": "LTER", "south": -90.0, "title": "LTER Palmer, Antarctica (PAL): Land-Shelf-Ocean Connectivity, Ecosystem Resilience and Transformation in a Sea-Ice Influenced Pelagic Ecosystem", "uid": "p0010494", "west": -180.0}, {"awards": "1955368 Daane, Jacob; 2324998 Daane, Jacob", "bounds_geometry": "POLYGON((-180 -60,-144 -60,-108 -60,-72 -60,-36 -60,0 -60,36 -60,72 -60,108 -60,144 -60,180 -60,180 -63,180 -66,180 -69,180 -72,180 -75,180 -78,180 -81,180 -84,180 -87,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -87,-180 -84,-180 -81,-180 -78,-180 -75,-180 -72,-180 -69,-180 -66,-180 -63,-180 -60))", "dataset_titles": null, "datasets": null, "date_created": "Thu, 01 Aug 2024 00:00:00 GMT", "description": "Part I: Nontechnical description The ecologically important notothenioid fish of the Southern Ocean surrounding Antarctica will be studied to address questions central to polar, evolutionary, and adaptational biology. The rapid diversification of the notothenioids into \u003e120 species following a period of Antarctic glaciation and cooling of the Southern Ocean is thought to have been facilitated by key evolutionary innovations, including antifreeze glycoproteins to prevent freezing and bone reduction to increase buoyancy. In this project, a large dataset of genomic sequences will be used to evaluate the genetic mechanisms that underly the broad pattern of novel trait evolution in these fish, including traits relevant to human diseases (e.g., bone density, renal function, and anemia). The team will develop new STEM-based research and teaching modules for undergraduate education at Northeastern University. The work will provide specific research training to scholars at all levels, including a post-doctoral researcher, a graduate student, undergraduate students, and high school students. The team will also contribute to public outreach, including, in part, the develop of teaching videos in molecular evolutionary biology and accompanying educational supplements. Part II: Technical description The researchers will leverage their comprehensive notothenioid phylogenomic dataset comprising \u003e250,000 protein-coding exons and conserved non-coding elements across 44 ingroup and 2 outgroup species to analyze the genetic origins of three iconic notothenioid traits: (1) loss of erythrocytes by the icefish clade in a cold, stable and highly-oxygenated marine environment; (2) reduction in bone mass and retention of juvenile skeletal characteristics as buoyancy mechanisms to facilitate foraging; and (3) loss of kidney glomeruli to retain energetically expensive antifreeze glycoproteins. The team will first track patterns of change in erythroid-related genes throughout the notothenioid phylogeny. They will then examine whether repetitive evolution of a pedomorphic skeleton in notothenioids is based on parallel or divergent evolution of genetic regulators of heterochrony. Third, they will determine whether there is mutational bias in the mechanisms of loss and re-emergence of kidney glomeruli. Finally, identified genetic mechanisms of evolutionary change will be validated by experimental testing using functional genomic strategies in the zebrafish model system. 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": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "United States Of America; FISH", "locations": "United States Of America", "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Daane, Jacob; Detrich, H. William", "platforms": null, "repositories": null, "science_programs": null, "south": -90.0, "title": "ANT LIA: Collaborative Research: Evolutionary Patterns and Mechanisms of Trait Diversification in the Antarctic Notothenioid Radiation", "uid": "p0010473", "west": -180.0}, {"awards": "2232891 Postlethwait, John", "bounds_geometry": "POLYGON((-180 -37,-144 -37,-108 -37,-72 -37,-36 -37,0 -37,36 -37,72 -37,108 -37,144 -37,180 -37,180 -42.3,180 -47.6,180 -52.9,180 -58.2,180 -63.5,180 -68.8,180 -74.1,180 -79.4,180 -84.69999999999999,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -84.7,-180 -79.4,-180 -74.1,-180 -68.8,-180 -63.5,-180 -58.2,-180 -52.9,-180 -47.6,-180 -42.300000000000004,-180 -37))", "dataset_titles": null, "datasets": null, "date_created": "Mon, 14 Aug 2023 00:00:00 GMT", "description": "Antarctic animals face tremendous threats as Antarctic ice sheets melt and temperatures rise. About 34 million years ago, when Antarctica began to cool, most species of fish became locally extinct. A group called the notothenioids, however, survived due to the evolution of antifreeze. The group eventually split into over 120 species. Why did this group of Antarctic fishes evolve into so many species? One possible reason why a single population splits into two species relates to sex genes and sex chromosomes. Diverging species often have either different sex determining genes (genes that specify whether an individual\u2019s gonads become ovaries or testes) or have different sex chromosomes (chromosomes that differ between males and females within a species, like the human X and Y chromosomes). We know the sex chromosomes of only a few notothenioid species and know the genetic basis for sex determination in none of them. The aims of this research are to: 1) identify sex chromosomes in species representing every major group of Antarctic notothenioid fish; 2) discover possible sex determining genes in every major group of Antarctic notothenioid fish; and 3) find sex chromosomes and possible sex determining genes in two groups of temperate, warmer water, notothenioid fish. These warmer water fish include groups that never experienced the frigid Southern Ocean and groups that had ancestors inhabiting Antarctic oceans that later adjusted to warmer waters. This project will help explain the mechanisms that led to the division of a group of species threatened by climate change. This information is critical to conserve declining populations of Antarctic notothenioids, which are major food sources for other Antarctic species such as bird and seals. The project will offer a diverse group of undergraduates the opportunity to develop a permanent exhibit at the Eugene Science Center Museum. The exhibit will describe the Antarctic environment and explain its rapid climate change. It will also introduce the continent\u2019s bizarre fishes that live below the freezing point of water. The project will collaborate with the university\u2019s Science and Comics Initiative and students in the English Department\u2019s Comics Studies Minor to prepare short graphic novels explaining Antarctic biogeography, icefish specialties, and the science of this project as it develops. As Antarctica cooled, most species disappeared from the continent\u2019s waters, but cryonotothenioid fish radiated into a species flock. What facilitated this radiation? Coyne\u2019s \u201ctwo rules of speciation\u201d offer explanations for why species diverge: 1) the dysgenic sex in an interspecies hybrid is the one with two different sex chromosomes (i.e., in humans, it would be XY males and not XX females); and 2) \u201csex chromosomes play an outsized role in speciation\u201d. These ideas propel the project\u2019s main hypothesis: new sex chromosomes and new sex determination genes associate with cryonotothenioid speciation events. The main objective of the research is to identify notothenioid sex chromosomes and candidate sex-determination genes in many notothenioid species. The project\u2019s first aim is to identify Antarctic fish sex chromosomes, asking the question: Did new sex chromosomes accompany speciation events? Knowledge gaps include: which species have cryptic sex chromosomes; which have newly evolved sex chromosomes; and which are chromosomally XX/XY or ZZ/ZW. Methods involve population genomics (RAD-seq and Pool-seq) for more than 20 Antarctic cryonotothenioids. The prediction is frequent turnover of sex chromosomes. The project\u2019s second aim is to Identify candidate Antarctic cryonotothenioid sex-determination genes, asking the question: Did new sex-determination genes accompany Antarctic cryonotothenioid speciation events? A knowledge gap is the identity of sex determination genes in any notothenioid. Preliminary data show that three sex-linked loci are in or adjacent to three different candidate sex determination genes: 1) a duplicate of bmpr1ba in blackfin icefish; 2) a tandem duplicate of gsdf in South Georgia icefish; and 3) a transposed duplicate of gsdf in striped notothen. Methods involve annotating the genomic neighborhoods of cryonotothenioid sex linked loci for anomalies in candidate sex genes, sequencing sex chromosomes, and testing sex gene variants by CRISPR mutagenesis in zebrafish. The prediction is frequent turnover of sex determination genes. The project\u2019s third aim is to identify sex chromosomes and sex-determination genes in temperate notothenioids. Basally diverging temperate notothenioids (\u2018basals\u2019) lack identifiable sex chromosomes, consistent with temperature-cued sex determination, and one \u2018basal\u2019 species is a hermaphrodite. The constantly cold Southern Ocean rules out temperature, a common sex determination cue in many temperate fish, favoring genetic sex determination. Some cryonotothenioids re-invaded temperate waters (\u2018returnees\u2019). Knowledge gaps include whether basals and returnees have strong sex determination genes. Methods employ pool-seq. The prediction is that genetic sex determination is weak in basals and that returnees have the same, but weaker, sex-linked loci as their Antarctic sister clade. A permanent exhibit will be established at the Eugene Science Center Museum tentatively entitled: The Antarctic: its fishes and climate change. Thousands of visitors, especially school children will be exposed, to the science of Antarctic ecosystems and the impacts of climate change. The research team will collaborate with the university\u2019s Science and Comics Initiative to produce short graphic novels explaining Antarctic biogeography, icefish specialties, and this project. 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": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "Speciation; Southern Ocean; Dragonfish; Antarctica; Plunderfish; Fish; Notothenioid; FISH; Eleginopsioidea; Icefish; MARINE ECOSYSTEMS; Cryonotothenioid; Sub-Antarctic", "locations": "Antarctica; Southern Ocean; Sub-Antarctic", "north": -37.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Postlethwait, John; Desvignes, Thomas", "platforms": null, "repositories": null, "science_programs": null, "south": -90.0, "title": "ANT LIA: The Role of Sex Determination in the Radiation of Antarctic Notothenioid Fish", "uid": "p0010431", "west": -180.0}, {"awards": "1543383 Postlethwait, John; 1947040 Postlethwait, John; 2232891 Postlethwait, John", "bounds_geometry": "POLYGON((-180 -37,-144 -37,-108 -37,-72 -37,-36 -37,0 -37,36 -37,72 -37,108 -37,144 -37,180 -37,180 -42.3,180 -47.6,180 -52.9,180 -58.2,180 -63.5,180 -68.8,180 -74.1,180 -79.4,180 -84.69999999999999,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -84.7,-180 -79.4,-180 -74.1,-180 -68.8,-180 -63.5,-180 -58.2,-180 -52.9,-180 -47.6,-180 -42.300000000000004,-180 -37))", "dataset_titles": "aBSREL tests for episodic diversifying selection on hemoglobin genes in notothenioids.; Genome-wide tRNA gene annotations in notothenioid fishes.; MEME tests of sites evolving under episodic diversifying selection in notothenioid hemoglobin genes.; Notothenioid hemoglobin protein 3D modeling.; Notothenioid species tree used in the study.; Phylogenetic analyses of MN hemoglobin genes.; Phylogenetic trees of hemoglobin proteins in notothenioids.; Rates of hemoglobin evolution among genes and across notothenioid species.; RELAX tests for pervasive changes in strength of natural selection on hemoglobin genes in notothenioids.; Transposable Elements and Repeat Analysis in notothenioid fishes.; tRNA gene annotations in the LA region of notothenioid fishes.", "datasets": [{"dataset_uid": "601969", "doi": "10.15784/601969", "keywords": "Antarctic; Cryosphere; Evolution; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Sub-Antarctic; Transfer RNA", "people": "Desvignes, Thomas; Postlethwait, John; Rivera-Col\u00f3n, Angel G.", "repository": "USAP-DC", "science_program": null, "title": "Genome-wide tRNA gene annotations in notothenioid fishes.", "url": "https://www.usap-dc.org/view/dataset/601969"}, {"dataset_uid": "601970", "doi": "10.15784/601970", "keywords": "Antarctic; Cryosphere; Evolution; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Sub-Antarctic; Transposable Elements", "people": "Desvignes, Thomas; Postlethwait, John; Rivera-Col\u00f3n, Angel G.", "repository": "USAP-DC", "science_program": null, "title": "Transposable Elements and Repeat Analysis in notothenioid fishes.", "url": "https://www.usap-dc.org/view/dataset/601970"}, {"dataset_uid": "601971", "doi": "10.15784/601971", "keywords": "Antarctic; Antarctica; Cryosphere; Evolution; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas; Rivera-Col\u00f3n, Angel G.", "repository": "USAP-DC", "science_program": null, "title": "Phylogenetic analyses of MN hemoglobin genes.", "url": "https://www.usap-dc.org/view/dataset/601971"}, {"dataset_uid": "601721", "doi": "10.15784/601721", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Plunderfish; Sub-Antarctic", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Notothenioid species tree used in the study.", "url": "https://www.usap-dc.org/view/dataset/601721"}, {"dataset_uid": "601722", "doi": "10.15784/601722", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Plunderfish; Sub-Antarctic", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Phylogenetic trees of hemoglobin proteins in notothenioids.", "url": "https://www.usap-dc.org/view/dataset/601722"}, {"dataset_uid": "601728", "doi": "10.15784/601728", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Gene; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "aBSREL tests for episodic diversifying selection on hemoglobin genes in notothenioids.", "url": "https://www.usap-dc.org/view/dataset/601728"}, {"dataset_uid": "601729", "doi": "10.15784/601729", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Rates of hemoglobin evolution among genes and across notothenioid species.", "url": "https://www.usap-dc.org/view/dataset/601729"}, {"dataset_uid": "601732", "doi": "10.15784/601732", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Notothenioid hemoglobin protein 3D modeling.", "url": "https://www.usap-dc.org/view/dataset/601732"}, {"dataset_uid": "601731", "doi": "10.15784/601731", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "RELAX tests for pervasive changes in strength of natural selection on hemoglobin genes in notothenioids.", "url": "https://www.usap-dc.org/view/dataset/601731"}, {"dataset_uid": "601968", "doi": "10.15784/601968", "keywords": "Antarctic; Cryosphere; Evolution; Fish; Gene; Hemoglobin; Icefish; Notothenioid; Sub-Antarctic; Transfer RNA", "people": "Rivera-Col\u00f3n, Angel G.; Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "tRNA gene annotations in the LA region of notothenioid fishes.", "url": "https://www.usap-dc.org/view/dataset/601968"}, {"dataset_uid": "601730", "doi": "10.15784/601730", "keywords": "Antarctica; Cold Adaptation; Cryonotothenioid; Dragonfish; Eleginopsioidea; Fish; Genetic Analysis; Hemoglobin; Icefish; Notothenioid; Notothenioid Fishes; Plunderfish; Sub-Antarctic", "people": "Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "MEME tests of sites evolving under episodic diversifying selection in notothenioid hemoglobin genes.", "url": "https://www.usap-dc.org/view/dataset/601730"}], "date_created": "Wed, 03 May 2023 00:00:00 GMT", "description": "Antarctic notothenioid fishes, also known as cryonotothenioids, inhabit the icy and highly oxygenated waters surrounding the Antarctic continent after diverging from notothenioids inhabiting more temperate waters. Notothenioid hemoglobin and blood parameters are known to have evolved along with the establishment of stable polar conditions, and among Antarctic notothenioids, icefishes are evolutionary oddities living without hemoglobin following the deletion of all functional hemoglobin genes from their genomes. In this project, we investigate the evolution of hemoglobin genes and gene clusters across the notothenioid radiation until their loss in the icefish ancestor after its divergence from the dragonfish lineage to understand the forces, mechanisms, and potential causes for hemoglobin gene loss in the icefish ancestor.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "FISH; Icefish; Cryonotothenioid; Gene; Plunderfish; Eleginopsioidea; Antarctica; AQUATIC ECOSYSTEMS; Dragonfish; Sub-Antarctic; Notothenioid; Blood; Hemoglobin", "locations": "Antarctica; Sub-Antarctic", "north": -37.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Desvignes, Thomas; Postlethwait, John; Rivera-Col\u00f3n, Angel G. ", "platforms": null, "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -90.0, "title": "Evolution of hemoglobin genes in notothenioid fishes", "uid": "p0010417", "west": -180.0}, {"awards": "1645087 Catchen, Julian", "bounds_geometry": null, "dataset_titles": "Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus\u2014The Closest Ancestral Proxy of Antarctic Cryonotothenioids; Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki; Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish", "datasets": [{"dataset_uid": "200331", "doi": "10.5061/dryad.ghx3ffbs3", "keywords": null, "people": null, "repository": "Dryad", "science_program": null, "title": "Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki", "url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.ghx3ffbs3"}, {"dataset_uid": "200330", "doi": "", "keywords": null, "people": null, "repository": "NCBI ", "science_program": null, "title": "Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA861284"}, {"dataset_uid": "200381", "doi": "", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus\u2014The Closest Ancestral Proxy of Antarctic Cryonotothenioids", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA917608"}, {"dataset_uid": "200380", "doi": "", "keywords": null, "people": null, "repository": "NCBI", "science_program": null, "title": "Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA857989"}], "date_created": "Mon, 10 Oct 2022 00:00:00 GMT", "description": "As plate tectonics pushed Antarctica into a polar position, by ~34 million years ago, the continent and its surrounding Southern Ocean (SO) became geographically and thermally isolated by the Antarctic Circumpolar Current. Terrestrial and marine glaciation followed, resulting in extinctions as well as the survival and radiation of unique flora and fauna. The notothenioid fish survived and arose from a common ancestral stock into tax with 120 species that dominates today?s SO fish fauna. The Notothenioids evolved adaptive traits including novel antifreeze proteins for survival in extreme cold, but also suffered seemingly adverse trait loss including red blood cells in the icefish family, and the ability to mount cellular responses to mitigate heat stress ? otherwise ubiquitous across all life. This project aims to understand how the notothenoid genomes have changed and contributed to their evolution in the cold. The project will sequence, analyze and compare the genomes of two strategic pairs of notothenioid fishes representing both red-blooded and white-blooded species. Each pair will consist of one Antarctic species and one that has readapted to the temperate waters of S. America or New Zealand. The project will also compare the Antarctic species genomes to a genome of the closet non-Antarctic relative representing the temperate notothenioid ancestor. The work aims to uncover the mechanisms that enabled the adaptive evolution of this ecologically vital group of fish in the freezing Southern Ocean, and shed light on their adaptability to a warming world. The finished genomes will be made available to promote and advance Antarctic research and the project will host a symposium of Polar researchers to discuss the cutting edge developments regarding of genomic adaptations in the polar region. Despite subzero, icy conditions that are perilous to teleost fish, the fish fauna of the isolated Southern Ocean (SO) surrounding Antarctica is remarkably bountiful. A single teleost group ? the notothenioid fishes ? dominate the fauna, comprising over 120 species that arose from a common ancestor. When Antarctica became isolated and SO temperatures began to plunge in early Oligocene, the prior temperate fishes became extinct. The ancestor of Antarctic notothenioids overcame forbidding polar conditions and, absent niche competition, it diversified and filled the SO. How did notothenioids adapt to freezing environmental selection pressures and achieve such extraordinary success? And having specialized to life in chronic cold for 30 myr, can they evolve in pace with today?s warming climate to stay viable? Past studies of Antarctic notothenioid evolutionary adaptation have discovered various remarkable traits including the key, life-saving antifreeze proteins. But life specialized to cold also led to paradoxical trait changes such as the loss of the otherwise universal heat shock response, and of the O2-transporting hemoglobin and red blood cells in the icefish family. A few species interestingly regained abilities to live in temperate waters following the escape of their ancestor out of the freezing SO. This proposed project is the first major effort to advance the field from single trait studies to understanding the full spectrum of genomic and genetic responses to climatic and environmental change during notothenioid evolution, and to evaluate their adaptability to continuing climate change. To this end, the project will sequence the genomes of four key species that embody genomic responses to different thermal selection regimes during notothenioids? evolutionary history, and by comparative analyses of genomic structure, architecture and content, deduce the responding changes. Specifically, the project will (i) obtain whole genome assemblies of the red-blooded T. borchgrevinki and the S. American icefish C. esox; (ii) using the finished genomes from (i) as template, obtain assemblies of the New Zealand notothenioid N. angustata, and the white-blooded icefish C. gunnari, representing a long (11 myr) and recent (1 myr) secondarily temperate evolutionary history respectively. Genes that are under selection in the temperate environment but not in the Antarctic environment can be inferred to be directly necessary for that environment ? and the reverse is also true for genes under selection in the Antarctic but not in the temperate environment. Further, genes important for survival in temperate waters will show parallel selection between N. angustata and C. esox despite the fact that the two fish left the Antarctic at far separated time points. Finally, gene families that expanded due to strong selection within the cold Antarctic should show a degradation of duplicates in the temperate environment. The project will test these hypotheses using a number of techniques to compare the content and form of genes, the structure of the chromosomes containing those genes, and through the identification of key characters, such as selfish genetic elements, introns, and structural variants.", "east": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Genome Assembly; FISH; McMurdo Sound; Icefish; SHIPS; Notothenioid; Puerto Natales, Chile", "locations": "McMurdo Sound; Puerto Natales, Chile", "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Catchen, Julian; Cheng, Chi-Hing", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e SHIPS", "repo": "Dryad", "repositories": "Dryad; NCBI; NCBI ", "science_programs": null, "south": null, "title": "Evolutionary Genomic Responses in Antarctic Notothenioid Fishes", "uid": "p0010384", "west": null}, {"awards": "1443637 Zakon, Harold", "bounds_geometry": null, "dataset_titles": "Evolutionary analysis of transient receptor potential (TRP) channels in notothenioid fishes; Functional characterization of temperature activated ion channels from Antarctic fishes; TagSeq tissue specific expression data for Antarctic Harpagifer antarcticus and tropical African cichlid Astatotilapia (Haplochromis) burtoni", "datasets": [{"dataset_uid": "200293", "doi": "", "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "TagSeq tissue specific expression data for Antarctic Harpagifer antarcticus and tropical African cichlid Astatotilapia (Haplochromis) burtoni", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA758918"}, {"dataset_uid": "601695", "doi": "10.15784/601695", "keywords": "Antarctica; Notothenioid; Southern Ocean", "people": "York, Julia", "repository": "USAP-DC", "science_program": null, "title": "Functional characterization of temperature activated ion channels from Antarctic fishes", "url": "https://www.usap-dc.org/view/dataset/601695"}, {"dataset_uid": "200292", "doi": "10.18738/T8/NXGNEI", "keywords": null, "people": null, "repository": "Texas Data Repository", "science_program": null, "title": "Evolutionary analysis of transient receptor potential (TRP) channels in notothenioid fishes", "url": "https://doi.org/10.18738/T8/NXGNEI"}], "date_created": "Fri, 03 Jun 2022 00:00:00 GMT", "description": "This project studies how the proteins of the nerves and muscles of fish that live in Antarctica function in the cold, which should provide information on the function of these same proteins in all animals, including humans. These proteins, called ion channels, open and close to allow ions (atoms or molecules with electrical charge) to flow into or out of cells which causes the electrical activity of nerves and muscles. Mutations that influence this process are the basis of numerous human disorders such as epilepsy, heart arrhythmias, and muscle paralysis. Thus, it is important to understand what parts of the proteins govern these transitions. The speed with which channels open and close depends on temperature. Human ion channels transition slowly when we are cold, which is why we become numb in the cold. Yet Antarctic fish, called icefish, are active at freezing temperatures that drastically limit the activity of human ion channels. The investigators have evidence that specific alterations in the icefishs\u0027 ion channels allow their channels to operate differently in the cold and they will use gene discovery and biophysical methods to test how these changes alter the transitions of icefish proteins at different temperatures. The project will also further the NSF goals of training new generations of scientists and of making scientific discoveries available to the general public. The gene discovery analysis will be done by undergraduate students including those from a minority-serving university and the investigators will develop a new course which will also serve students at that institution and elsewhere. In addition, the investigators will participate in educational outreach events with the general public as well as with groups with special needs. Notothenioid fishes are one of the most successful groups of vertebrates in Antarctica. Notothens have adaptations to the freezing water they inhabit and this project will study how their voltage-gated ion channels (VGICs) function in the cold. The molecular movements of ion channels are severely impaired by cold, yet notothens function at temperatures that would paralyze the nerves and muscles of \"cold-blooded\" temperate zone animals. Surprisingly, no biophysical or molecular investigations have been conducted on notothen VGICs. The investigators have preliminary data that amino acid substitutions occur at sites in VGICs that are evolutionarily conserved from fruit flies to humans. Some of these sites are known to impact channel function and the role of others in channel transitioning are unknown. The results from studying them will provide novel information also applicable to non-notothen, perhaps even human, VGICs as well as providing insights into how VGICs adapt to the cold. The project will biophysically characterize notothen VGICs using voltage-clamp techniques will and compare their properties over a range of temperatures to the same channel from two temperate zone fish. The role of unique notothen amino acid substitutions will be characterized by mutagenesis. One specific aim will be a project in which undergraduates mine notothen sequence databases to identify other potential amino acid substitutions in VGICs that might facilitate adaptation to the cold.", "east": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Amd/Us; USAP-DC; USA/NSF; FIELD INVESTIGATION; AMD; FISHERIES", "locations": null, "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Zakon, Harold", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD INVESTIGATION", "repo": "GenBank", "repositories": "GenBank; Texas Data Repository; USAP-DC", "science_programs": null, "south": null, "title": "Analysis of Voltage-gated Ion Channels in Antarctic Fish", "uid": "p0010331", "west": null}, {"awards": "1954241 O\u0027\u0027Brien, Kristin", "bounds_geometry": null, "dataset_titles": null, "datasets": null, "date_created": "Tue, 17 Aug 2021 00:00:00 GMT", "description": "Part 1: Non-technical description: Global climate warming is increasing the frequency and severity of low oxygen events in marine and freshwater environments worldwide, and these events threaten the health of aquatic ecosystems and the viability of fish populations. The Southern Ocean surrounding Antarctica has historically been a stable, icy-cold, and oxygen-rich environment, but is now warming at an unprecedented rate and faster than all other regions in the Southern hemisphere. Antarctic fishes have evolved in sub-zero temperatures that have been stable over long periods of time with traits allowing them to thrive in frigid waters, but with diminished resilience to warming temperatures. Presently little is known about the ability of Antarctic fishes to withstand hypoxic, or low-oxygen, conditions that often accompany warming. This research will investigate the hypoxia tolerance of four species of Antarctic fishes, including two species of icefishes that lack the oxygen-carrying protein, hemoglobin, which may compromise their ability to oxygenate tissues under hypoxic conditions. The hypoxia tolerance of four Antarctic fish species will be compared to that of a related fish species inhabiting warmer coastal regions of South America. Physiological and biochemical responses to hypoxia will be evaluated and compared amongst the five species to bolster our predictions of the capacity of Antarctic fishes to cope with a changing environment. This research will provide training opportunities for undergraduate and graduate students, and a postdoctoral research fellow. A year-long seminar series hosted by the Aquarium of the Pacific will feature female scientists who work in Antarctica to inspire youth in the greater Los Angeles area to pursue careers in science. Part 2: Technical description: The overarching hypothesis to be tested in this project is that the long evolution of Antarctic notothenioid fishes in a cold, oxygen-rich environment has reduced their capacity to mount a robust physiological, biochemical, and molecular response to hypoxia compared to related, cold-temperate fish species. Hypoxia tolerance will be compared among the red-blooded Antarctic notothenioids, Notothenia coriiceps and Notothenia rossii; the hemoglobinless Antarctic icefishes, Chaenocephalus aceratus and Chionodraco rastrospinosus; and the basal, cold-temperate notothenioid, Eleginops maclovinus, a species that has never inhabited waters south of the Polar Front. The minimum level of oxygen required to sustain maintenance metabolic requirements (O2crit) will be quantified. Animals will then be exposed to 65% of O2crit for 48 hours, and responses to hypoxia will be evaluated by measuring hematocrit and hemoglobin levels, as well as metabolites in brain, liver, glycolytic and cardiac muscles. Maximal activities of key enzymes of aerobic and anaerobic metabolism will be quantified to assess capacities for synthesizing ATP in hypoxic conditions. Gill remodeling will be analyzed using light and scanning electron microscopy. The molecular response to hypoxia will be characterized in liver and brains by quantifying levels of the master transcriptional regulator of oxygen homeostasis, hypoxia-inducible factor-1 (HIF-1), and hypoxic gene expression will be quantified using RNA-Seq. Cell cultures will be used to determine if a previously identified insertion mutation in notothenioid HIF-1 affects the ability of HIF-1 to drive gene expression and thus, hypoxia tolerance. The results of this project will provide the most comprehensive assessment of the hypoxia tolerance of Antarctic fishes to date. Broader impacts include research training opportunities for undergraduate and graduate students and a postdoctoral research associate, with a focus on involving Native Alaskan students in research. In partnership with the Aquarium of the Pacific, a year-long public seminar series will be held, showcasing the research and careers of 9 women who conduct research in Antarctica. The goal of the series is to cultivate and empower a community of middle and high school students in the greater Los Angeles area to pursue their interests in science and related fields, and to enhance the public engagement capacities of research scientists so that they may better inspire youth and early career scientists in STEM fields. 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": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Palmer Station; FIELD SURVEYS; USAP-DC; AMD; USA/NSF; Amd/Us; FISH", "locations": "Palmer Station", "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "O\u0027Brien, Kristin", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD SURVEYS", "repositories": null, "science_programs": null, "south": null, "title": "ANT LIA: Hypoxia Tolerance in Notothenioid Fishes", "uid": "p0010246", "west": null}, {"awards": "1744999 Todgham, Anne", "bounds_geometry": "POLYGON((162 -77,162.8 -77,163.6 -77,164.4 -77,165.2 -77,166 -77,166.8 -77,167.6 -77,168.4 -77,169.2 -77,170 -77,170 -77.1,170 -77.2,170 -77.3,170 -77.4,170 -77.5,170 -77.6,170 -77.7,170 -77.8,170 -77.9,170 -78,169.2 -78,168.4 -78,167.6 -78,166.8 -78,166 -78,165.2 -78,164.4 -78,163.6 -78,162.8 -78,162 -78,162 -77.9,162 -77.8,162 -77.7,162 -77.6,162 -77.5,162 -77.4,162 -77.3,162 -77.2,162 -77.1,162 -77))", "dataset_titles": "A comparative and ontogenetic examination of mitochondrial function in Antarctic notothenioid species; Differential temperature preferences exhibited in the juvenile Antarctic notothenioids Trematomus bernacchii and Trematomus pennellii", "datasets": [{"dataset_uid": "601765", "doi": null, "keywords": "Antarctica; McMurdo Sound; Ross Sea", "people": "Zillig, Ken; Frazier, Amanda; Todgham, Anne; Naslund, Andrew; Mandic, Milica", "repository": "USAP-DC", "science_program": null, "title": "Differential temperature preferences exhibited in the juvenile Antarctic notothenioids Trematomus bernacchii and Trematomus pennellii", "url": "https://www.usap-dc.org/view/dataset/601765"}, {"dataset_uid": "601766", "doi": null, "keywords": "Antarctica; McMurdo Sound", "people": "Mandic, Milica; Naslund, Andrew; Todgham, Anne; Frazier, Amanda", "repository": "USAP-DC", "science_program": null, "title": "A comparative and ontogenetic examination of mitochondrial function in Antarctic notothenioid species", "url": "https://www.usap-dc.org/view/dataset/601766"}], "date_created": "Thu, 12 Aug 2021 00:00:00 GMT", "description": "The Southern Ocean contains an extraordinary diversity of marine life. Many Antarctic marine organisms have evolved in stable, cold ocean conditions and possess limited ability to respond to environmental fluctuations. To date, research on the physiological limits of Antarctic fishes has focused largely on adult life stages. However, early life stages may be more sensitive to environmental change because they may need to prioritize energy to growth and development instead of maintenance of physiological balance and integrity- even under stress conditions. This project will examine the specific mechanisms that young (embryos, larvae and juveniles) Antarctic fishes use to respond to changes in ocean conditions at the molecular, cellular and physiological levels, so that they are able to survive. The aim is to provide a unifying framework for linking environmental change, gene expression, metabolism and organismal performance in different species that have various rates of growth and development. There is a diverse and robust education and outreach program linked with the research effort that will reach students, teachers, young scientists, community members and government officials at local and regions scales. Polar species have already been identified as highly vulnerable to global change. However as yet, there is no unifying framework for linking environmental change to organismal performance, in part because a mechanistic understanding of how stressors interact at the molecular, biochemical and physiological level is underdeveloped is lacking for most species. In the marine environment, this paucity of information limits our capacity to accurately predict the impacts of warming and CO2-acidification on polar species, and therefore prevents linking climate model projections to population health predictions. This research will evaluate whether metabolic capacity (i.e. the ability to match energy supply with energy demand) limits the capacity of Antarctic fishes to acclimate to the simultaneous stressors of ocean warming and CO2-acidification. If species are unable to reestablish metabolic homeostasis following exposure to stressors, increased energetic costs may lead to a decline in physiological performance, organismal fitness, and survival. This energy-mismatch hypothesis will be tested in a multi-species approach that focuses on the early life stages, as growing juveniles are likely more vulnerable to energetic constraints than adults, while different species are targeted in order to understand how differences in phenology and life history traits influence metabolic plasticity. The research will provide a mechanistic integration of gene expression and metabolite patterns, and metabolic responses at the cellular and whole organism levels to broadly understand metabolic plasticity of fishes. The research is aligned with the theme \"Decoding the genomic and transcriptomic bases of biological adaptation and response across Antarctic organisms and ecosystems\" which is one of three major themes identified by the National Academy of Sciences in their document \"A Strategic Vision for NSF Investments in Antarctic and Southern Ocean Research\". Additionally, this project builds environmental stewardship and awareness by increasing science literacy in the broader community in three main ways: First it will increase the diversity of students involved in environmental science research by supporting one PhD student, one postdoctoral scholar and two undergraduate students and promoting the training of young students from groups traditionally underrepresented in environmental biology. Second, the project will participate in UC Davis\u0027s OneClimate initiative, which leverages the community\u0027s expertise to develop broad perspectives regarding climate change, science and society, and engage K-12 students, government officials, and local and statewide communities on topics of Antarctic research, organismal adaptation as well as ongoing and potential future changes at the poles. Lastly, summer workshops will be conducted in collaborations with the NSF-funded education program APPLES (Arctic Plant Phenology: Learning through Engaged Science), to engage teachers and K-12 students in polar science. 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": 170.0, "geometry": "POINT(166 -77.5)", "instruments": null, "is_usap_dc": true, "keywords": "FIELD SURVEYS; AMD; McMurdo Sound; FISH; USA/NSF; Amd/Us; USAP-DC", "locations": "McMurdo Sound", "north": -77.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Todgham, Anne", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD SURVEYS", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -78.0, "title": "Interacting Stressors: Metabolic Capacity to Acclimate under Ocean Warming and CO2- Acidification in Early Developmental Stages of Antarctic Fishes", "uid": "p0010241", "west": 162.0}, {"awards": "1947040 Postlethwait, John", "bounds_geometry": "POLYGON((-65.3 -63.3,-65 -63.3,-64.7 -63.3,-64.4 -63.3,-64.1 -63.3,-63.8 -63.3,-63.5 -63.3,-63.2 -63.3,-62.9 -63.3,-62.6 -63.3,-62.3 -63.3,-62.3 -63.47,-62.3 -63.64,-62.3 -63.81,-62.3 -63.98,-62.3 -64.15,-62.3 -64.32,-62.3 -64.49,-62.3 -64.66,-62.3 -64.83,-62.3 -65,-62.6 -65,-62.9 -65,-63.2 -65,-63.5 -65,-63.8 -65,-64.1 -65,-64.4 -65,-64.7 -65,-65 -65,-65.3 -65,-65.3 -64.83,-65.3 -64.66,-65.3 -64.49,-65.3 -64.32,-65.3 -64.15,-65.3 -63.98,-65.3 -63.81,-65.3 -63.64,-65.3 -63.47,-65.3 -63.3))", "dataset_titles": "18 SSU rDNA type sequences for Notoxcellia coronata (nov. sp.); 18 SSU rDNA type sequences for Notoxcellia picta (nov. sp.); Expedition Data of LMG1805; Fish pictures and skin pathology of X-cell infection in Trematomus scotti.; Gonad and skin histology of Trematomus loennbergii infected by Notoxcellia sp.; Histopathology of X-cell xenomas in Trematomus scotti and Nototheniops larseni.; In situ hybridization of X-cell and host fish 18S SSU rRNA in alternate sections of tumor xenomas.; Metagenomic analysis of apparently healthy and tumor samples using Kaiju software ; microMRI analyses of Trematomus scotti Tsco_18_08 with X-cell xenomas; Morphological and pathological data of Trematomus scotti specimens captured on May 30th, 2018 in Andvord Bay.; Morphological, fecundity, and age data of Trematomus scotti from Andvord Bay and the Weddell Sea.; Nomenclatural Act for the genus Notoxcellia; Nomenclatural Act for the species Notoxcellia coronata; Nomenclatural Act for the species Notoxcellia picta; Phylogenetic Analysis of Notoxcellia species.; Phylogenetic Analysis of Notoxcellia species, including novel Ross Sea specimen; Raw Illumina sequencing reads from skin tumors and visually healthy skins from Trematomus scotti and Nototheniops larseni; Similarity matrices of Notoxcellia spp.; Temperature profiles at five fishing locations on the West Antarctic Peninsula during austral fall 2018.; Trematomus scotti mt-co1 sequence alignment.; Trematomus scotti with X-cell xenomas", "datasets": [{"dataset_uid": "601495", "doi": "10.15784/601495", "keywords": "Antarctica; Antarctic Peninsula", "people": "Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Temperature profiles at five fishing locations on the West Antarctic Peninsula during austral fall 2018.", "url": "https://www.usap-dc.org/view/dataset/601495"}, {"dataset_uid": "200443", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1805", "url": "https://doi.org/10.7284/907930"}, {"dataset_uid": "200384", "doi": "", "keywords": null, "people": null, "repository": "ZooBank", "science_program": null, "title": "Nomenclatural Act for the species Notoxcellia picta", "url": "https://zoobank.org/NomenclaturalActs/31062dd2-7202-47fa-86e0-7be5c55ac0e2"}, {"dataset_uid": "200383", "doi": "", "keywords": null, "people": null, "repository": "ZooBank", "science_program": null, "title": "Nomenclatural Act for the species Notoxcellia coronata", "url": "https://zoobank.org/NomenclaturalActs/194d91b2-e268-4238-89e2-385819f2c35b"}, {"dataset_uid": "200382", "doi": "", "keywords": null, "people": null, "repository": "ZooBank", "science_program": null, "title": "Nomenclatural Act for the genus Notoxcellia", "url": "https://zoobank.org/NomenclaturalActs/5cf9609e-0111-4386-8518-bd50b5bdde0e"}, {"dataset_uid": "200277", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "Raw Illumina sequencing reads from skin tumors and visually healthy skins from Trematomus scotti and Nototheniops larseni", "url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA789574"}, {"dataset_uid": "200276", "doi": "", "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "18 SSU rDNA type sequences for Notoxcellia picta (nov. sp.)", "url": "https://www.ncbi.nlm.nih.gov/nuccore/OL630145"}, {"dataset_uid": "200254", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1805", "url": "https://www.rvdata.us/search/cruise/LMG1805"}, {"dataset_uid": "200275", "doi": "", "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "18 SSU rDNA type sequences for Notoxcellia coronata (nov. sp.)", "url": "https://www.ncbi.nlm.nih.gov/nuccore/OL630144"}, {"dataset_uid": "601539", "doi": "10.15784/601539", "keywords": "Alveolata; Antarctica; Antarctic Peninsula; Notoxcellia Coronata; Notoxcellia Picta; Perkinsozoa; Xcellidae", "people": "Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "In situ hybridization of X-cell and host fish 18S SSU rRNA in alternate sections of tumor xenomas.", "url": "https://www.usap-dc.org/view/dataset/601539"}, {"dataset_uid": "601538", "doi": "10.15784/601538", "keywords": "Alveolata; Antarctica; Antarctic Peninsula; Notoxcellia Coronata; Notoxcellia Picta; Perkinsozoa; Xcellidae", "people": "Lauridsen, Henrik; Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "microMRI analyses of Trematomus scotti Tsco_18_08 with X-cell xenomas", "url": "https://www.usap-dc.org/view/dataset/601538"}, {"dataset_uid": "601537", "doi": "10.15784/601537", "keywords": "Alveolata; Antarctica; Antarctic Peninsula; Notoxcellia Coronata; Notoxcellia Picta; Perkinsozoa; Xcellidae", "people": "Fontenele, Rafaela S. ; Desvignes, Thomas; Postlethwait, John; Kraberger, Simona ; Varsani, Arvind", "repository": "USAP-DC", "science_program": null, "title": "Metagenomic analysis of apparently healthy and tumor samples using Kaiju software ", "url": "https://www.usap-dc.org/view/dataset/601537"}, {"dataset_uid": "601536", "doi": "10.15784/601536", "keywords": "Alveolata; Antarctica; Antarctic Peninsula; Notoxcellia Coronata; Notoxcellia Picta; Perkinsozoa; Xcellidae", "people": "Kent, Michael L. ; Desvignes, Thomas; Murray, Katrina N. ; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Histopathology of X-cell xenomas in Trematomus scotti and Nototheniops larseni.", "url": "https://www.usap-dc.org/view/dataset/601536"}, {"dataset_uid": "200262", "doi": "", "keywords": null, "people": null, "repository": "MorphoSource", "science_program": null, "title": "Trematomus scotti with X-cell xenomas", "url": "https://www.morphosource.org/projects/000405843?locale=en"}, {"dataset_uid": "601917", "doi": "10.15784/601917", "keywords": "Alveolata; Antarctic; Cryosphere; Notoxcellia Coronata; Notoxcellia Picta; Perkinsozoa; Xcellidae", "people": "P\u00e9ron, Clara; Devine, Jennifer; Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Similarity matrices of Notoxcellia spp.", "url": "https://www.usap-dc.org/view/dataset/601917"}, {"dataset_uid": "601916", "doi": "10.15784/601916", "keywords": "Alveolata; Antarctica; Cryosphere; Notoxcellia Coronata; Notoxcellia Picta; Perkinsozoa; Ross Sea; Xcellidae", "people": "Devine, Jennifer; Postlethwait, John; Desvignes, Thomas; P\u00e9ron, Clara", "repository": "USAP-DC", "science_program": null, "title": "Gonad and skin histology of Trematomus loennbergii infected by Notoxcellia sp.", "url": "https://www.usap-dc.org/view/dataset/601916"}, {"dataset_uid": "601892", "doi": "10.15784/601892", "keywords": "Antarctica; Biota; CO1; COX1; Cryonotothenioid; Cryosphere; Genetic Sequences; LMG1805; MT-CO1; Nototheniidae; Notothenioid; Population Genetics", "people": "Papetti, Chiara; Postlethwait, John; Schiavon, Luca ; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Trematomus scotti mt-co1 sequence alignment.", "url": "https://www.usap-dc.org/view/dataset/601892"}, {"dataset_uid": "601893", "doi": "10.15784/601893", "keywords": "Age; Antarctica; Biota; Cryonotothenioid; Cryosphere; Fecundity; Growth; Length; Nototheniidae; Oceans; Otolith; Reproduction; Weight", "people": "Streeter, Margaret; Le Francois, Nathalie; Lucassen, Magnus; Mark, Felix C; Detrich, H. William; Papetti, Chiara; Postlethwait, John; La Mesa, Mario; Cal\u00ec, Federico; Riginella, Emilio; Desvignes, Thomas; Grondin, Jacob; Sguotti, Camilla; Valdivieso, Alejandro", "repository": "USAP-DC", "science_program": null, "title": "Morphological, fecundity, and age data of Trematomus scotti from Andvord Bay and the Weddell Sea.", "url": "https://www.usap-dc.org/view/dataset/601893"}, {"dataset_uid": "601915", "doi": "10.15784/601915", "keywords": "Alveolata; Antarctic; Cryosphere; Notoxcellia Coronata; Notoxcellia Picta; Perkinsozoa; Xcellidae", "people": "Devine, Jennifer; P\u00e9ron, Clara; Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Phylogenetic Analysis of Notoxcellia species, including novel Ross Sea specimen", "url": "https://www.usap-dc.org/view/dataset/601915"}, {"dataset_uid": "601494", "doi": "10.15784/601494", "keywords": "Andvord Bay; Antarctica; Fish", "people": "Lauridsen, Henrik; Desvignes, Thomas; Postlethwait, John; Le Francois, Nathalie", "repository": "USAP-DC", "science_program": null, "title": "Morphological and pathological data of Trematomus scotti specimens captured on May 30th, 2018 in Andvord Bay.", "url": "https://www.usap-dc.org/view/dataset/601494"}, {"dataset_uid": "601501", "doi": "10.15784/601501", "keywords": "Alveolata; Antarctica; Antarctic Peninsula; Biota; Notoxcellia Coronata; Notoxcellia Picta; Oceans; Perkinsozoa; Xcellidae", "people": "Varsani, Arvind; Postlethwait, John; Desvignes, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Phylogenetic Analysis of Notoxcellia species.", "url": "https://www.usap-dc.org/view/dataset/601501"}, {"dataset_uid": "601496", "doi": "10.15784/601496", "keywords": "Andvord Bay; Antarctica; Fish", "people": "Lauridsen, Henrik; Desvignes, Thomas; Postlethwait, John", "repository": "USAP-DC", "science_program": null, "title": "Fish pictures and skin pathology of X-cell infection in Trematomus scotti.", "url": "https://www.usap-dc.org/view/dataset/601496"}], "date_created": "Thu, 01 Jul 2021 00:00:00 GMT", "description": "Antarctica\u2019s native animals face increasing stressors from warming oceans. A key unanswered question is how Antarctic life will respond. If warmer waters contribute to fish disease susceptibility, then iconic Antarctic predators they support, including penguins, seals, and killer whales, will suffer. A recent scientific cruise on the Antarctic peninsula encountered a population of crowned notothen fish that were plagued by pink, wart-like tumors that covered 10% to 30% of the body surface on about a third of the animals. Similar tumors had not previously been reported, suggesting that this might be a new disease that threatens Antarctic fish. The goal of proposed work is to identify the biological origins of the tumor and how it affects cell function and organismal physiology. The work is potentially transformative because it studies what might be a harbinger of Antarctic fish responses to global climate change. The project has several Broader Impacts. First, it will publicize the tumors. Because Antarctic researchers have never reported a tumor epidemic, the community must become aware of the outbreak and the tumor\u2019s distinct diagnostic features. Second, dissemination of project results will stir further research to determine if this is an isolated event or is becoming a general phenomenon, and thus a broad concern for Antarctic ecosystems. Third, assays the project develops to detect the disease will enhance research infrastructure. Finally, work will broaden the nation\u2019s scientific workforce by providing authentic research experiences for high school students and undergraduates from groups underrepresented in scientific research. The overall goal of proposed work is to identify the biological origins of the neoplasia and how it affects cell function and physiology. Aim 1 is to identify the pathogenic agent. Aim 1a is to test the hypothesis that a virus causes the neoplasia by isolating and sequencing viral nucleic acids from neoplasias and from animals that are not visibly affected. Aim 1b is to test neoplasias for bacteria, fungi, protozoa, or invertebrate parasites not present in healthy skin. Aim 2 is to learn how the disease alters the biology of affected cells. Aim 2a is to examine histological sections of affected and control tissues to see if the neoplasias are similar to previously reported skin diseases in temperate water fishes. Aim 2b is to examine the function of neoplastic cells by RNA-seq transcriptomics to identify genes that are differentially expressed in neoplasias and normal skin. Achieving these Aims will advance knowledge by identifying the causes and consequences of an outbreak of neoplasias in Antarctic fish. Proposed work is significant because it is the first to investigate a neoplasia cluster in Antarctic fish. 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": -62.3, "geometry": "POINT(-63.8 -64.15)", "instruments": null, "is_usap_dc": true, "keywords": "FIELD SURVEYS; Andvord Bay; Amd/Us; PROTISTS; BENTHIC; FISH; Dallmann Bay; USAP-DC; NSF/USA; AMD", "locations": "Andvord Bay; Dallmann Bay", "north": -63.3, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Postlethwait, John; Varsani, Arvind; Desvignes, Thomas", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD SURVEYS", "repo": "USAP-DC", "repositories": "GenBank; MorphoSource; NCBI SRA; R2R; USAP-DC; ZooBank", "science_programs": null, "south": -65.0, "title": "EAGER: Origin and Physiological Consequences of a Neoplasm Outbreak in Antarctic Fish ", "uid": "p0010221", "west": -65.3}, {"awards": "1644196 Cziko, Paul", "bounds_geometry": "POLYGON((163.47 -77.14,163.803 -77.14,164.136 -77.14,164.469 -77.14,164.802 -77.14,165.135 -77.14,165.468 -77.14,165.801 -77.14,166.134 -77.14,166.467 -77.14,166.8 -77.14,166.8 -77.216,166.8 -77.292,166.8 -77.368,166.8 -77.444,166.8 -77.52,166.8 -77.596,166.8 -77.672,166.8 -77.748,166.8 -77.824,166.8 -77.9,166.467 -77.9,166.134 -77.9,165.801 -77.9,165.468 -77.9,165.135 -77.9,164.802 -77.9,164.469 -77.9,164.136 -77.9,163.803 -77.9,163.47 -77.9,163.47 -77.824,163.47 -77.748,163.47 -77.672,163.47 -77.596,163.47 -77.52,163.47 -77.444,163.47 -77.368,163.47 -77.292,163.47 -77.216,163.47 -77.14))", "dataset_titles": "High-resolution nearshore benthic seawater temperature from around McMurdo Sound, Antarctica (2017-2019); Long-Term broadband underwater acoustic recordings from McMurdo Sound, Antarctica (2017-2019); Long-term underwater images from around a single mooring site in McMurdo Sound, Antarctica (2017-2019)", "datasets": [{"dataset_uid": "601416", "doi": "10.15784/601416", "keywords": "Antarctica; Bioacoustics; Biota; Hydroacoustics; Killer Whales; Leptonychotes Weddellii; McMurdo Sound; Oceans; Orcinus Orca; Sea Ice; Weddell Seal; Whales", "people": "Cziko, Paul", "repository": "USAP-DC", "science_program": null, "title": "Long-Term broadband underwater acoustic recordings from McMurdo Sound, Antarctica (2017-2019)", "url": "https://www.usap-dc.org/view/dataset/601416"}, {"dataset_uid": "601417", "doi": "10.15784/601417", "keywords": "Antarctica; Benthic Ecology; Benthic Invertebrates; Biota; McMurdo Sound; Notothenioid; Notothenioid Fishes; Photo/video; Photo/Video; Rocky Reef Community; Soft-Bottom Community; Timelaps Images", "people": "Cziko, Paul", "repository": "USAP-DC", "science_program": null, "title": "Long-term underwater images from around a single mooring site in McMurdo Sound, Antarctica (2017-2019)", "url": "https://www.usap-dc.org/view/dataset/601417"}, {"dataset_uid": "601420", "doi": "10.15784/601420", "keywords": "Antarctica; Benthic Ecology; CTD; Depth; McMurdo Sound; Oceanography; Oceans; Physical Oceanography; Pressure; Salinity; Seawater Measurements; Seawater Temperature; Supercooling; Tides", "people": "Cziko, Paul", "repository": "USAP-DC", "science_program": null, "title": "High-resolution nearshore benthic seawater temperature from around McMurdo Sound, Antarctica (2017-2019)", "url": "https://www.usap-dc.org/view/dataset/601420"}], "date_created": "Tue, 15 Dec 2020 00:00:00 GMT", "description": "Notothenioid fishes live in the world\u0027s coldest marine waters surrounding Antarctica and have evolved strategies to avoid freezing. Past studies have shown that most Antarctic notothenioids produce special antifreeze proteins that prevent the growth of ice crystals that enter the body. While these proteins help prevent individuals from being killed by growing ice crystals, it is unclear how these fish avoid the accumulation of these small ice crystals inside their tissues over time. This project will observe how ice crystal accumulation relates to the harshness of the fish\u0027s habitat and the fish\u0027s behavior within different habitats of McMurdo Sound, Antarctica. The researchers will collect fishes and ocean observations at different field sites that cover a range of habitat severity in terms of temperature and iciness. Researchers will install an underwater ocean observatory near McMurdo Station which will include a HD video camera and hydrophone. The observatory will allow continuous monitoring of ocean conditions and fish behavior that will help explain the conditions and behaviors that contribute to the acquisition and accrual of ice inside the body. Acoustic and video data from the observatory will be available to other scientists and to the public. The project will advance understanding of the many challenges life faces in extreme cold environments. This work continues a line of inquiry that has resulted in the discovery of potential medical and food preservation applications. Hundreds of antifreeze protein (AFP) structure-function studies have been conducted in the laboratory, providing a basic physical understanding of the AFP-ice interaction. How AFPs function within fishes and their range of environments, however, is far from clear. This project will provide an understanding of notothenioid\u0027s freezing avoidance mechanisms, and strategies by quantifying the acquisition, accumulation, and loss of internal ice crystals. Specifically, the goal is to determine if and how habitat severity (as defined by iciness, seawater temperature, and prevalence of supercooled water) and fish behavior influence the abundance of ice crystals in their tissues. Four locations in the McMurdo Sound with different levels of habitat severity will be sampled for oceanographic conditions and ice crystal count within fish tissues. Researchers will use a new technique to count the number of splenic ice crystals, expanding on and simplifying previous methods. Environmental data loggers will be deployed for the duration of the project at the four sites to provide context and real-time assessment of environmental conditions. An oceanographic observatory near McMurdo Station will provide year-round, real-time and archival records of oceanographic conditions, in situ video observations of anchor ice growth and ice-organism interactions, hydroacoustic recordings, and serve as proof-of concept for expanding scientific infrastructure in McMurdo Sound related to monitoring of supercooled waters and oceanographic information.", "east": 166.8, "geometry": "POINT(165.135 -77.52)", "instruments": null, "is_usap_dc": true, "keywords": "Benthic Ecology; ANIMALS/VERTEBRATES; USA/NSF; OCEAN TEMPERATURE; USAP-DC; MAMMALS; FIELD INVESTIGATION; Amd/Us; McMurdo Sound; FISH; AMD", "locations": "McMurdo Sound", "north": -77.14, "nsf_funding_programs": "Antarctic Instrumentation and Support; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Cziko, Paul; DeVries, Arthur", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD INVESTIGATION", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -77.9, "title": "Habitat Severity and Internal Ice in Antarctic Notothenioid Fishes", "uid": "p0010147", "west": 163.47}, {"awards": "0231006 DeVries, Arthur; 1142158 Cheng, Chi-Hing", "bounds_geometry": "POLYGON((163 -76.5,163.5 -76.5,164 -76.5,164.5 -76.5,165 -76.5,165.5 -76.5,166 -76.5,166.5 -76.5,167 -76.5,167.5 -76.5,168 -76.5,168 -76.63,168 -76.76,168 -76.89,168 -77.02,168 -77.15,168 -77.28,168 -77.41,168 -77.54,168 -77.67,168 -77.8,167.5 -77.8,167 -77.8,166.5 -77.8,166 -77.8,165.5 -77.8,165 -77.8,164.5 -77.8,164 -77.8,163.5 -77.8,163 -77.8,163 -77.67,163 -77.54,163 -77.41,163 -77.28,163 -77.15,163 -77.02,163 -76.89,163 -76.76,163 -76.63,163 -76.5))", "dataset_titles": "High-resolution benthic seawater temperature record 1999-2012 (25-40m depth) from near intake jetty at McMurdo Station, Antarctica; Metadata associated with the description of Akarotaxis gouldae n. sp. (Bathydraconidae)", "datasets": [{"dataset_uid": "601275", "doi": null, "keywords": "Antarctica; Benthic; McMurdo Sound; Mcmurdo Station; Oceans; Physical Oceanography; Temperature Probe; Water Temperature", "people": "Devries, Arthur; Cziko, Paul; Cheng, Chi-Hing", "repository": "USAP-DC", "science_program": null, "title": "High-resolution benthic seawater temperature record 1999-2012 (25-40m depth) from near intake jetty at McMurdo Station, Antarctica", "url": "https://www.usap-dc.org/view/dataset/601275"}, {"dataset_uid": "601811", "doi": null, "keywords": "Antarctica; Bellingshausen Sea; Cryosphere; Southern Ocean", "people": "Corso, Andrew; Cheng, Chi-Hing; McDowell, Jan; Biesack, Ellen; Steinberg, Deborah; Hilton, Eric; Desvignes, Thomas", "repository": "USAP-DC", "science_program": "LTER", "title": "Metadata associated with the description of Akarotaxis gouldae n. sp. (Bathydraconidae)", "url": "https://www.usap-dc.org/view/dataset/601811"}], "date_created": "Wed, 08 Apr 2020 00:00:00 GMT", "description": "Antarctic notothenioid fishes exhibit two adaptive traits to survive in frigid temperatures. The first of these is the production of anti-freeze proteins in their blood and tissues. The second is a system-wide ability to perform cellular and physiological functions at extremely cold temperatures.The proposal goals are to show how Antarctic fishes use these characteristics to avoid freezing, and which additional genes are turned on, or suppressed in order for these fishes to maintain normal physiological function in extreme cold temperatures. Progressively colder habitats are encountered in the high latitude McMurdo Sound and Ross Shelf region, along with somewhat milder near?shore water environments in the Western Antarctic Peninsula (WAP). By quantifying the extent of ice crystals invading and lodging in the spleen, the percentage of McMurdo Sound fish during austral summer (Oct-Feb) will be compared to the WAP intertidal fish during austral winter (Jul-Sep) to demonstrate their capability and extent of freeze avoidance. Resistance to ice entry in surface epithelia (e.g. skin, gill and intestinal lining) is another expression of the adaptation of these fish to otherwise lethally freezing conditions. The adaptive nature of a uniquely characteristic polar genome will be explored by the study of the transcriptome (the set of expressed RNA transcripts that constitutes the precursor to set of proteins expressed by an entire genome). Three notothenioid species (E.maclovinus, D. Mawsoni and C. aceratus) will be analysed to document evolutionary genetic changes (both gain and loss) shaped by life under extreme chronic cold. A differential gene expression (DGE) study will be carried out on these different species to evaluate evolutionary modification of tissue-wide response to heat challenges. The transcriptomes and other sequencing libraries will contribute to de novo ice-fish genome sequencing efforts.", "east": 168.0, "geometry": "POINT(165.5 -77.15)", "instruments": "IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e CTD", "is_usap_dc": true, "keywords": "McMurdo Sound; MARINE ECOSYSTEMS; Water Temperature; AQUATIC SCIENCES; OCEAN TEMPERATURE; FIELD INVESTIGATION; USAP-DC", "locations": "McMurdo Sound", "north": -76.5, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Cheng, Chi-Hing; Devries, Arthur", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD INVESTIGATION", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -77.8, "title": "Antarctic Notothenioid Fish Freeze Avoidance and Genome-wide Evolution for Life in the Cold", "uid": "p0010091", "west": 163.0}, {"awards": "1341661 Near, Thomas", "bounds_geometry": "POLYGON((-180 -60,-144 -60,-108 -60,-72 -60,-36 -60,0 -60,36 -60,72 -60,108 -60,144 -60,180 -60,180 -63,180 -66,180 -69,180 -72,180 -75,180 -78,180 -81,180 -84,180 -87,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -87,-180 -84,-180 -81,-180 -78,-180 -75,-180 -72,-180 -69,-180 -66,-180 -63,-180 -60))", "dataset_titles": "Phylogenomics of Antarctic notothenioid fishes", "datasets": [{"dataset_uid": "601264", "doi": null, "keywords": "Adaptive Radiation; Antarctica; Fish; Notothenioidei; Phylogeny; Southern Ocean; Speciation", "people": "Dornburg, Alex; Near, Thomas", "repository": "USAP-DC", "science_program": null, "title": "Phylogenomics of Antarctic notothenioid fishes", "url": "https://www.usap-dc.org/view/dataset/601264"}, {"dataset_uid": "601262", "doi": "10.15784/601262", "keywords": "Adaptive Radiation; Antarctica; Fish; Notothenioidei; Phylogeny; Southern Ocean; Speciation", "people": "Near, Thomas; Dornburg, Alex", "repository": "USAP-DC", "science_program": null, "title": "Phylogenomics of Antarctic notothenioid fishes", "url": "https://www.usap-dc.org/view/dataset/601262"}], "date_created": "Sat, 29 Feb 2020 00:00:00 GMT", "description": "Understanding how groups of organisms respond to climate change is fundamentally important to assessing the impacts of human activities as well as understanding how past climatic shifts have shaped biological diversity over deep stretches of time. The fishes occupying the near-shore marine habitats around Antarctica are dominated by one group of closely related species called notothenioids. It appears dramatic changes in Antarctic climate were important in the origin and evolutionary diversification of this economically important lineage of fishes. Deposits of fossil fishes in Antarctica that were formed when the continent was experiencing milder temperatures show that the area was home to a much more diverse array of fish lineages. Today the waters of the Southern Ocean are very cold, and often below freezing, but notothenioids fishes exhibit a number of adaptions to live in this harsh set of marine habitats, including the presence of anti-freeze proteins. This research project will collect DNA sequences from hundreds of genes to infer the genealogical relationships of nearly all 124 notothenioid species, and use mathematical techniques to estimate the ages of species and lineages. Knowledge on the timing of evolutionary divergence in notothenioids will allow investigators to assess if timing of previous major climatic shifts in Antarctica are correlated with key events in the formation of the modern Southern Ocean fish fauna. The project will also further the NSF goals of making scientific discoveries available to the general public and of training new generations of scientists. The project will support educational outreach activities to teenager groups and to the general public through a natural history museum exhibit and other public lectures. It will provide professional training opportunities for graduate students and a postdoctoral research scholar. Adaptive radiation, where lineages experience high rates of evolutionary diversification coincident with ecological divergence, is mostly studied in island ecosystems. Notothenioids dominate the fish fauna of the Southern Ocean and exhibit antifreeze glycoproteins that allow occupation of the subzero waters. Notothenioids are noted as one of the only examples of adaptive radiation among marine fishes, but the evolutionary history of diversification and radiation into different ecological habitats is poorly understood. This research will generate a species phylogeny (evolutionary history) for nearly all of the 124 recognized notothenioid species to investigate the mechanisms of adaptive radiation in this lineage. The phylogeny is inferred from approximately 350 genes sampled using next generation DNA sequencing and related techniques. Morphometric data are taken for museum specimens to investigate the tempo of morphological diversification and to determine if there are correlations between rates of lineage diversification and the origin of morphological disparity. The patterns of lineage, morphological, and ecological diversification in the notothenioid radiation will be compared to the paleoclimatic record to determine if past instances of global climate change have shaped the evolutionary diversification of this lineage of polar-adapted fishes.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": "NOT APPLICABLE \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "is_usap_dc": true, "keywords": "FISH; Fish; AMD; USA/NSF; Southern Ocean; Amd/Us; NOT APPLICABLE; USAP-DC; MARINE ECOSYSTEMS; Notothenioidei; Phylogeny", "locations": "Southern Ocean", "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Near, Thomas", "platforms": "OTHER \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -90.0, "title": "Phylogenomic Study of Adaptive Radiation in Antarctic Fishes", "uid": "p0010087", "west": -180.0}, {"awards": "1341663 O\u0027Brien, Kristin; 1341602 Crockett, Elizabeth", "bounds_geometry": null, "dataset_titles": "Acclimation of cardiovascular function in Notothenia coriiceps; Adrenergic and adenosinergic regulation of the cardiovascular system in the Antarctic icefish Chaenocephalus aceratus; Cardiac metabolism in Antarctic fishes in response to an acute increase in temperature; Chaenocephalus aceratus HIF-1A mRNA, complete cds; Chionodraco rastrospinosus HIF-1A mRNA, partial cds; Effects of acute warming on cardiovascular performance of Antarctic fishes; Eleginops maclovinus HIF-1A mRNA, partial cds; Gymnodraco acuticeps HIF-1A mRNA, partial cds; Hypoxia response of hearts of Antarctic fishes; Maximum cardiac performance of Antarctic fishes that lack haemoglobin and myoglobin: exploring the effect of warming on nature\u2019s natural knockouts; Measurements of splenic contraction in Antarctic fishes; Mitochondrial membranes in cardiac muscle from Antarctic notothenioid fishes vary in phospholipid composition and membrane fluidity; Notothenia coriiceps HIF-1A mRNA, complete cds; Parachaenichthys charcoti HIF-1A mRNA, partial cds; Physical, chemical, and functional properties of neuronal membranes vary between species of Antarctic notothenioids differing in thermal tolerance; Thermal sensitivity of membrane fluidity and integrity in hearts of Antarctic fishes that vary in expression of hemoglobin and myoglobin", "datasets": [{"dataset_uid": "200184", "doi": "10.5061/dryad.83vc5", "keywords": null, "people": null, "repository": "Dryad", "science_program": null, "title": "Maximum cardiac performance of Antarctic fishes that lack haemoglobin and myoglobin: exploring the effect of warming on nature\u2019s natural knockouts", "url": "https://doi.org/10.5061/dryad.83vc5"}, {"dataset_uid": "601405", "doi": "10.15784/601405", "keywords": "Antarctica; Antarctic Peninsula", "people": "O\u0027Brien, Kristin", "repository": "USAP-DC", "science_program": null, "title": "Cardiac metabolism in Antarctic fishes in response to an acute increase in temperature", "url": "https://www.usap-dc.org/view/dataset/601405"}, {"dataset_uid": "601406", "doi": "10.15784/601406", "keywords": "Antarctica; Antarctic Peninsula", "people": "O\u0027Brien, Kristin", "repository": "USAP-DC", "science_program": null, "title": "Hypoxia response of hearts of Antarctic fishes", "url": "https://www.usap-dc.org/view/dataset/601406"}, {"dataset_uid": "601407", "doi": "10.15784/601407", "keywords": "Antarctica; Antarctic Peninsula", "people": "Joyce, William; Axelsson, Michael; O\u0027Brien, Kristin", "repository": "USAP-DC", "science_program": null, "title": "Measurements of splenic contraction in Antarctic fishes", "url": "https://www.usap-dc.org/view/dataset/601407"}, {"dataset_uid": "601408", "doi": "10.15784/601408", "keywords": "Antarctica; Antarctic Peninsula", "people": "Crockett, Elizabeth; Axelsson, Michael; Joyce, William; Egginton, Stuart; Farrell, Anthony; O\u0027Brien, Kristin", "repository": "USAP-DC", "science_program": null, "title": "Acclimation of cardiovascular function in Notothenia coriiceps", "url": "https://www.usap-dc.org/view/dataset/601408"}, {"dataset_uid": "601409", "doi": "10.15784/601409", "keywords": "Antarctica; Antarctic Peninsula", "people": "O\u0027Brien, Kristin; Egginton, Stuart; Farrell, Anthony; Axelsson, Michael; Joyce, Michael", "repository": "USAP-DC", "science_program": null, "title": "Adrenergic and adenosinergic regulation of the cardiovascular system in the Antarctic icefish Chaenocephalus aceratus", "url": "https://www.usap-dc.org/view/dataset/601409"}, {"dataset_uid": "601410", "doi": "10.15784/601410", "keywords": "Antarctica; Antarctic Peninsula; Biota; Fish", "people": "Axelsson, Michael; Egginton, Stuart; O\u0027Brien, Kristin; Crockett, Elizabeth; Farrell, Anthony; Joyce, William", "repository": "USAP-DC", "science_program": null, "title": "Effects of acute warming on cardiovascular performance of Antarctic fishes", "url": "https://www.usap-dc.org/view/dataset/601410"}, {"dataset_uid": "601414", "doi": "10.15784/601414", "keywords": "Antarctica; Antarctic Peninsula", "people": "Crockett, Elizabeth; O\u0027Brien, Kristin; Farnoud, Amir; Evans, Elizabeth", "repository": "USAP-DC", "science_program": null, "title": "Thermal sensitivity of membrane fluidity and integrity in hearts of Antarctic fishes that vary in expression of hemoglobin and myoglobin", "url": "https://www.usap-dc.org/view/dataset/601414"}, {"dataset_uid": "200192", "doi": null, "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "Chionodraco rastrospinosus HIF-1A mRNA, partial cds", "url": "https://www.ncbi.nlm.nih.gov/nuccore/kx950831"}, {"dataset_uid": "200191", "doi": null, "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "Gymnodraco acuticeps HIF-1A mRNA, partial cds", "url": "https://www.ncbi.nlm.nih.gov/nuccore/kx950832"}, {"dataset_uid": "200190", "doi": null, "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "Parachaenichthys charcoti HIF-1A mRNA, partial cds", "url": "https://www.ncbi.nlm.nih.gov/nuccore/KX950833"}, {"dataset_uid": "200189", "doi": null, "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "Eleginops maclovinus HIF-1A mRNA, partial cds", "url": "https://www.ncbi.nlm.nih.gov/nuccore/KX950830"}, {"dataset_uid": "200188", "doi": null, "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "Notothenia coriiceps HIF-1A mRNA, complete cds", "url": "https://www.ncbi.nlm.nih.gov/nuccore/KX950829"}, {"dataset_uid": "200187", "doi": null, "keywords": null, "people": null, "repository": "GenBank", "science_program": null, "title": "Chaenocephalus aceratus HIF-1A mRNA, complete cds", "url": "https://www.ncbi.nlm.nih.gov/nuccore/KX950828"}, {"dataset_uid": "200186", "doi": "10.5061/dryad.qm0b25h", "keywords": null, "people": null, "repository": "Dryad", "science_program": null, "title": "Physical, chemical, and functional properties of neuronal membranes vary between species of Antarctic notothenioids differing in thermal tolerance", "url": "https://doi.org/10.5061/dryad.qm0b25h"}, {"dataset_uid": "200185", "doi": "10.5061/dryad.k90h35k", "keywords": null, "people": null, "repository": "Dryad", "science_program": null, "title": "Mitochondrial membranes in cardiac muscle from Antarctic notothenioid fishes vary in phospholipid composition and membrane fluidity", "url": "https://doi.org/10.5061/dryad.k90h35k"}], "date_created": "Wed, 26 Feb 2020 00:00:00 GMT", "description": "The ocean surrounding Antarctica is home to an extraordinary assemblage of fishes, dominated by a single group that are extremely well-suited to life in icy waters and which are of significant ecological importance there. Of great concern is the capacity of these fishes to withstand increases in temperature as the region of the Western Antarctic Peninsula warms at a rate faster than any other area in the Southern hemisphere. One particular group of Antarctic fishes, known as the icefishes, are particularly vulnerable to increases in temperature because unlike all other vertebrates on earth, icefishes are white-blooded due to their lack of the oxygen-binding protein hemoglobin. This greatly reduces their capacity to transport and deliver oxygen to tissues compared to red-blooded Antarctic fishes. Previous studies have shown that icefishes are indeed less tolerant to elevations in temperature but the underlying factors are completely unknown. Additionally, it is not understood if red- or white-blooded Antarctic fishes can adjust, or acclimate, to modest increases in temperature, similar to those changes in temperature the animals might experience as the earth warms. The investigators will determine if heart function and/or nervous system function limits thermal tolerance of Antarctic fishes, and will determine their capacity to acclimate to warmer temperatures. The project will further the NSF goal of training new generations of scientists by training graduate and undergraduate students. In addition, the project will collaborate with a high school biology teacher from a school which serves a largely minority student body. The students will learn about the marine environment, and will construct a camera to be used in the field to learn more about Antarctic fishes. Two students and the teacher will also attend a summer marine biology internship program. Antarctic fishes within the suborder Notothenioidei (called \"notothenioids\") are among the organisms on earth least able to deal with changes in temperature. The hemoglobinless icefish are even less able to withstand temperature changes than are red-blooded notothenioids. While this is well documented, the underlying physiological and biochemical mechanisms responsible are unknown. The investigators will test the hypotheses that cardiac work is significantly greater in icefishes compared to red-blooded species, and that as temperature increases, the greater cardiac work of icefishes, coupled with reduced blood oxygen-carrying capacity, results in cardiac failure at a lower temperature compared to red-blooded species. They also hypothesize that neuronal function limits thermal tolerance of red-blooded notothenioids. These hypotheses will be tested using a wide variety of experiments. For example, the investigators will measure heart rate concurrently with critical thermal maximum. They will also characterize metabolic and gene-expression responses to elevated temperature and determine if mitochondrial function contributes to thermal tolerance using a variety of techniques. To determine if neuronal function limits thermal tolerance they will quantify behavioral responses to warming of whole animals and to warming of only the brain area. They will also determine if acclimation to warmer temperatures impacts heart function and they will measure activities of a variety of enzymes from central metabolic pathways.", "east": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Antarctica; Amd/Us; FISH; USA/NSF; FIELD INVESTIGATION; AMD; Antarctic Peninsula; LABORATORY; USAP-DC", "locations": "Antarctica; Antarctic Peninsula", "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Crockett, Elizabeth; O\u0027Brien, Kristin", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD INVESTIGATION; OTHER \u003e PHYSICAL MODELS \u003e LABORATORY", "repo": "Dryad", "repositories": "Dryad; GenBank; USAP-DC", "science_programs": null, "south": null, "title": "Collaborative Research: The Physiological and Biochemical Underpinnings of Thermal Tolerance in Antarctic Notothenioid Fishes", "uid": "p0010084", "west": null}, {"awards": "1543383 Postlethwait, John", "bounds_geometry": "POLYGON((-66 -62,-65.2 -62,-64.4 -62,-63.6 -62,-62.8 -62,-62 -62,-61.2 -62,-60.4 -62,-59.6 -62,-58.8 -62,-58 -62,-58 -62.4,-58 -62.8,-58 -63.2,-58 -63.6,-58 -64,-58 -64.4,-58 -64.8,-58 -65.2,-58 -65.6,-58 -66,-58.8 -66,-59.6 -66,-60.4 -66,-61.2 -66,-62 -66,-62.8 -66,-63.6 -66,-64.4 -66,-65.2 -66,-66 -66,-66 -65.6,-66 -65.2,-66 -64.8,-66 -64.4,-66 -64,-66 -63.6,-66 -63.2,-66 -62.8,-66 -62.4,-66 -62))", "dataset_titles": "C. aceratus pronephric kidney (head kidney) miRNA; mirtop\r\ncommand lines tool to annotate miRNAs with a standard mirna/isomir naming; Patagonotothen cornucola isolate Pcor_18_01 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial; Patagonotothen sima isolate Psim_18_11 cardiac muscle myosin heavy chain 6 (myh6) gene, partial cds; Patagonotothen sima isolate Psim_18_11 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial; Patagonotothen sima isolate Psim_18_12 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial; Prost!, a tool for miRNA annotation and next generation smallRNA sequencing experiment analysis; Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.; Quantifying expression levels of smallRNAs between tissues in three-spined stickleback", "datasets": [{"dataset_uid": "200132", "doi": "", "keywords": null, "people": null, "repository": "GitHub", "science_program": null, "title": "mirtop\r\ncommand lines tool to annotate miRNAs with a standard mirna/isomir naming", "url": "https://github.com/miRTop"}, {"dataset_uid": "200131", "doi": "", "keywords": null, "people": null, "repository": "GitHub", "science_program": null, "title": "Prost!, a tool for miRNA annotation and next generation smallRNA sequencing experiment analysis", "url": "https://github.com/uoregon-postlethwait/prost"}, {"dataset_uid": "200134", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Patagonotothen sima isolate Psim_18_11 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial", "url": "https://www.ncbi.nlm.nih.gov/search/all/?term=MN136232"}, {"dataset_uid": "200135", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Patagonotothen sima isolate Psim_18_12 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial", "url": "https://www.ncbi.nlm.nih.gov/search/all/?term=MN136233+"}, {"dataset_uid": "200133", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Patagonotothen cornucola isolate Pcor_18_01 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial", "url": "https://www.ncbi.nlm.nih.gov/search/all/?term=MN136231"}, {"dataset_uid": "200136", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Patagonotothen sima isolate Psim_18_11 cardiac muscle myosin heavy chain 6 (myh6) gene, partial cds", "url": "https://www.ncbi.nlm.nih.gov/search/all/?term=MN136234+"}, {"dataset_uid": "200128", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "Quantifying expression levels of smallRNAs between tissues in three-spined stickleback", "url": "https://www.ncbi.nlm.nih.gov/search/all/?term=SRP157992"}, {"dataset_uid": "200129", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", "url": "https://www.ncbi.nlm.nih.gov/search/all/?term=SRP039502"}, {"dataset_uid": "200130", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "C. aceratus pronephric kidney (head kidney) miRNA", "url": "https://www.ncbi.nlm.nih.gov/search/all/?term=SRP069031"}], "date_created": "Wed, 26 Feb 2020 00:00:00 GMT", "description": "Icefish live in frigid Antarctic seas, and have unique traits such as the absence of red blood cells, enlarged hearts, large diameter blood vessels, low bone mineral densities, and fat droplets that disrupt their muscles. These features would be harmful in other animals. In mammals and fish inhabiting warm waters, development of organs involved in these traits is modulated by genes that encode specific proteins, but the rate of protein production is often regulated by short RNA molecules called microRNAs (miRNAs). Genes that code for proteins must first make an RNA copy, and the actual protein is made from this RNA copy intermediate. MiRNAs regulate the amount of protein that is made by binding to the RNA intermediate and interrupting its production of protein. Binding of miRNAs to RNA depends strongly on temperature. Regulation of genes by miRNAs has not been studied in Antarctic fish, which live in seas with temperatures below the freezing point of fresh water. This project will compare miRNA regulation 1) in Antarctic fish vs. warm-water fish to learn how miRNAs regulate gene expression in constant cold; and 2) in Antarctic icefish with no red blood cells, enlarged hearts, and reduced bone density vs. closely related Antarctic fish containing red blood cells, normal hearts, and dense bones. The project will have broad impacts to science and society nationally and globally. First, this will be the first study of important factors in gene regulation (miRNAs) in Antarctic fish, which are an essential component of the entire ecology of the Southern Ocean, and will shed light on how these fish might respond to the warming of Antarctic waters. Second, it will bring Antarctic science to under-represented high school students at a local alternative downtown high school by conducting video conferences during the Antarctic field seasons and hosting student investigations of Antarctic fish in the research laboratory. microRNAs (miRNAs) are key post-transcriptional regulators of gene expression that modulate development and physiology in temperate animals. Although miRNAs act by binding to messenger RNAs (mRNAs), a process that is strongly sensitive to temperature, miRNAs have yet not been studied in Antarctic animals, including Notothenioid fish, which dominate the Southern Ocean. This project will compare miRNA regulation in 1) Antarctic vs. temperate fish to learn the roles of miRNA regulation in adaptation to constant cold; and in 2) bottom-dwelling, dense-boned, red-blooded Nototheniods vs. high buoyancy, osteopenic, white-blooded icefish to understand miRNA regulation in specialized organs after the evolution of the loss of hemoglobin genes and red blood cells, the origin of enlarged heart and vasculature, and the evolution of increased buoyancy, which arose by decreased bone mineralization and increased lipid deposition. Aim 1 is to test the hypothesis that Antarctic fish evolved miRNA-related genome specializations in response to constant cold. The project will compare four Antarctic Notothenioid species to two temperate Notothenioids and two temperate laboratory species to test the hypotheses that (a) Antarctic fish evolved miRNA genome repertoires by loss of ancestral genes and/or gain of new genes, (b) express miRNAs that are involved in cold tolerance, and (c) respond to temperature change by changing miRNA gene expression. Aim 2 is to test the hypothesis that the evolution of icefish from red-blooded bottom-dwelling ancestors was accompanied by an altered miRNA genomic repertoire, sequence, and/or expression. The project will test the hypotheses that (a) miRNAs in icefish evolved in sequence and/or in expression in icefish specializations, including head kidney (origin of red blood cells); heart (changes in vascular system), cranium and pectoral girdle (reduced bone mineral density); and skeletal muscle (lipid deposition), and (b) miRNAs that evolved in icefish specializations had ancestral functions related to their derived roles in icefish, as determined by functional tests of zebrafish orthologs of icefish miRNAs in developing zebrafish. The program will isolate, sequence, and determine the expression of miRNAs and mRNAs using high-throughput transcriptomics and novel software. Results will show how the microRNA system evolves in vertebrate animals pushed to physiological extremes and provide insights into the prospects of key species in the most rapidly warming part of the globe.", "east": -58.0, "geometry": "POINT(-62 -64)", "instruments": null, "is_usap_dc": true, "keywords": "USAP-DC; Palmer Station; NOT APPLICABLE; FISH", "locations": "Palmer Station", "north": -62.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Postlethwait, John; Desvignes, Thomas", "platforms": "OTHER \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "repo": "GitHub", "repositories": "GitHub; NCBI GenBank; NCBI SRA", "science_programs": null, "south": -66.0, "title": "Antarctic Fish and MicroRNA Control of Development and Physiology", "uid": "p0010085", "west": -66.0}, {"awards": "1444167 Detrich, H. William", "bounds_geometry": "POLYGON((-70 -58,-68.5 -58,-67 -58,-65.5 -58,-64 -58,-62.5 -58,-61 -58,-59.5 -58,-58 -58,-56.5 -58,-55 -58,-55 -59.8,-55 -61.6,-55 -63.4,-55 -65.2,-55 -67,-55 -68.8,-55 -70.6,-55 -72.4,-55 -74.2,-55 -76,-56.5 -76,-58 -76,-59.5 -76,-61 -76,-62.5 -76,-64 -76,-65.5 -76,-67 -76,-68.5 -76,-70 -76,-70 -74.2,-70 -72.4,-70 -70.6,-70 -68.8,-70 -67,-70 -65.2,-70 -63.4,-70 -61.6,-70 -59.8,-70 -58))", "dataset_titles": "Assembled Contig Dat for Daane et al. (2019); E-MTAB-6759: RNA-seq across tissues in four Notothenioid species (Antarctic icefish); Expedition Data of LMG1603; Expedition Data of LMG1604; Expedition Data of LMG1605; Expedition Data of LMG1803; Expedition Data of LMG1804; Expedition Data of LMG1805; Full raw data set, computer code, and evolutionary trajectories for all species in Damsgaard et al. (2019); Histology-, CT-, ultrasound-, and MRI-scans (~2 TB) for Damsgaard et al. (2019); PRJNA420419: Genome and Transcriptome Data for Kim et al. (2019) Blackfin Icefish Genome; PRJNA531677: Sequencing Data for Daane et al. (2019); S-BSST132: Assembled Transcriptomes for Berthelot et al. (2018); SRP047484 RAD-tag Sequences of Genetically Mapped Notothenia coriiceps embryos; SRP118539: RAD-tag Sequences of Genetically Mapped Chaenocephalus aceratus Embryos; Transposable element sequences and genome sizes, refs 142597 to MF142757", "datasets": [{"dataset_uid": "200098", "doi": "", "keywords": null, "people": null, "repository": "NCBI BioProject", "science_program": null, "title": "PRJNA531677: Sequencing Data for Daane et al. (2019)", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA531677"}, {"dataset_uid": "200254", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1805", "url": "https://www.rvdata.us/search/cruise/LMG1805"}, {"dataset_uid": "200253", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1605", "url": "https://www.rvdata.us/search/cruise/LMG1605"}, {"dataset_uid": "200252", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1604", "url": "https://www.rvdata.us/search/cruise/LMG1604"}, {"dataset_uid": "200251", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1804", "url": "https://www.rvdata.us/search/cruise/LMG1804"}, {"dataset_uid": "200250", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1603", "url": "https://www.rvdata.us/search/cruise/LMG1603"}, {"dataset_uid": "200249", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data of LMG1803", "url": "https://www.rvdata.us/search/cruise/LMG1803"}, {"dataset_uid": "200092", "doi": "", "keywords": null, "people": null, "repository": "NCBI BioProject", "science_program": null, "title": "PRJNA420419: Genome and Transcriptome Data for Kim et al. (2019) Blackfin Icefish Genome", "url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=prjna420419"}, {"dataset_uid": "200093", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "SRP118539: RAD-tag Sequences of Genetically Mapped Chaenocephalus aceratus Embryos", "url": "https://www.ncbi.nlm.nih.gov/sra/SRP118539 "}, {"dataset_uid": "200094", "doi": "", "keywords": null, "people": null, "repository": "Array Express", "science_program": null, "title": "E-MTAB-6759: RNA-seq across tissues in four Notothenioid species (Antarctic icefish)", "url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6759/"}, {"dataset_uid": "200095", "doi": "", "keywords": null, "people": null, "repository": "BioStudies", "science_program": null, "title": "S-BSST132: Assembled Transcriptomes for Berthelot et al. (2018)", "url": "https://www.ebi.ac.uk/biostudies/studies/S-BSST132"}, {"dataset_uid": "200096", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "SRP047484 RAD-tag Sequences of Genetically Mapped Notothenia coriiceps embryos", "url": "https://www.ncbi.nlm.nih.gov/sra/?term=SRP047484"}, {"dataset_uid": "200099", "doi": "10.5281/zenodo.2628936", "keywords": null, "people": null, "repository": "Zenodo", "science_program": null, "title": "Assembled Contig Dat for Daane et al. (2019)", "url": "https://zenodo.org/record/2628936#.Xegqj3dFw2w"}, {"dataset_uid": "200102", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Transposable element sequences and genome sizes, refs 142597 to MF142757", "url": "https://www.ncbi.nlm.nih.gov/nuccore?LinkName=pubmed_nuccore\u0026from_uid=29739320"}, {"dataset_uid": "200103", "doi": "", "keywords": null, "people": null, "repository": "GitHub", "science_program": null, "title": "Full raw data set, computer code, and evolutionary trajectories for all species in Damsgaard et al. (2019)", "url": "https://github.com/elifesciences-publications/Retinaevolution"}, {"dataset_uid": "200104", "doi": "", "keywords": null, "people": null, "repository": "eLife", "science_program": null, "title": "Histology-, CT-, ultrasound-, and MRI-scans (~2 TB) for Damsgaard et al. (2019)", "url": "https://retinaevolution.bios.au.dk/eLife%20documentation/README.txt"}], "date_created": "Wed, 04 Dec 2019 00:00:00 GMT", "description": "Antarctic fish and their early developmental stages are an important component of the food web that sustains life in the cold Southern Ocean (SO) that surrounds Antarctica. They feed on smaller organisms and in turn are eaten by larger animals, including seals and killer whales. Little is known about how rising ocean temperatures will impact the development of Antarctic fish embryos and their growth after hatching. This project will address this gap by assessing the effects of elevated temperatures on embryo viability, on the rate of embryo development, and on the gene \"toolkits\" that respond to temperature stress. One of the two species to be studied does not produce red blood cells, a defect that may make its embryos particularly vulnerable to heat. The outcomes of this research will provide the public and policymakers with \"real world\" data that are necessary to inform decisions and design strategies to cope with changes in the Earth\u0027s climate, particularly with respect to protecting life in the SO. The project will also further the NSF goals of training new generations of scientists, including providing scientific training for undergraduate and graduate students, and of making scientific discoveries available to the general public. This includes the unique educational opportunity for undergraduates to participate in research in Antarctica and engaging the public in several ways, including the development of professionally-produced educational videos with bi-lingual closed captioning. Since the onset of cooling of the SO about 40 million years ago, evolution of Antarctic marine organisms has been driven by the development of cold temperatures. Because body temperatures of Antarctic fishes fall in a narrow range determined by their habitat (-1.9 to +2.0 C) they are particularly attractive models for understanding how organismal physiology and biochemistry have been shaped to maintain life in a cooling environment. The long-term objective of this project is to understand the capacities of Antarctic fishes to acclimatize and/or adapt to rapid oceanic warming through analysis of their underlying genetic \"toolkits.\" This objective will be accomplished through three Specific Aims: 1) assessing the effects of elevated temperatures on gene expression during development of embryos; 2) examining the effects of elevated temperatures on embryonic morphology and on the temporal and spatial patterns of gene expression; and 3) evaluating the evolutionary mechanisms that have led to the loss of the red blood cell genetic program by the white-blooded fishes. Aims 1 and 2 will be investigated by acclimating experimental embryos of both red-blooded and white-blooded fish to elevated temperatures. Differential gene expression will be examined through the use of high throughput RNA sequencing. The temporal and spatial patterns of gene expression in the context of embryonic morphology (Aim 2) will be determined by microscopic analysis of embryos \"stained\" with (hybridized to) differentially expressed gene probes revealed by Aim 1; other developmental marker genes will also be used. The genetic lesions resulting from loss of red blood cells by the white-blooded fishes (Aim 3) will be examined by comparing genes and genomes in the two fish groups.", "east": -55.0, "geometry": "POINT(-62.5 -67)", "instruments": "NOT APPLICABLE \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "is_usap_dc": true, "keywords": "NOT APPLICABLE; Polar; South Shetland Islands; USAP-DC; COASTAL", "locations": "Polar; South Shetland Islands", "north": -58.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Detrich, H. William", "platforms": "OTHER \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "repo": "NCBI BioProject", "repositories": "Array Express; BioStudies; eLife; GitHub; NCBI BioProject; NCBI GenBank; NCBI SRA; R2R; Zenodo", "science_programs": null, "south": -76.0, "title": "Antarctic Notothenioid Fishes: Sentinel Taxa for Southern Ocean Warming", "uid": "p0010073", "west": -70.0}, {"awards": "1543419 Place, Sean", "bounds_geometry": "POLYGON((163 -76,163.5 -76,164 -76,164.5 -76,165 -76,165.5 -76,166 -76,166.5 -76,167 -76,167.5 -76,168 -76,168 -76.2,168 -76.4,168 -76.6,168 -76.8,168 -77,168 -77.2,168 -77.4,168 -77.6,168 -77.8,168 -78,167.5 -78,167 -78,166.5 -78,166 -78,165.5 -78,165 -78,164.5 -78,164 -78,163.5 -78,163 -78,163 -77.8,163 -77.6,163 -77.4,163 -77.2,163 -77,163 -76.8,163 -76.6,163 -76.4,163 -76.2,163 -76))", "dataset_titles": "Hspa4 MK948004; miRNA Characterization in Antarctic fish", "datasets": [{"dataset_uid": "200057", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "miRNA Characterization in Antarctic fish", "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128132"}, {"dataset_uid": "200495", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Hspa4 MK948004", "url": "https://www.ncbi.nlm.nih.gov/nuccore/MK948004"}], "date_created": "Thu, 19 Sep 2019 00:00:00 GMT", "description": "The project will integrate analyses of fish physiology, protein production and genetics to determine if regulation of molecular chaperones (a class of proteins that facilitate the proper folding of proteins in a cell) has been permanently lost in a key fish species (Trematomus bernacchii) inhabiting the Southern Ocean. To do so, efforts will be undertaken to analyze chaperones in these fishes and how elevated temperatures impact protein turnover and protein damage. These studies should more definitively determine if the interruption of chaperone function is environmentally controlled (which could suggest these fish could benefit in some form by increasing sea surface temperatures) or if there is complete loss of chaperone function due to a change in its structure through evolutionary processes (which would suggest these fish are less likely to be able to adapt to warming). In addition to filling key gaps in our knowledge about the diversity and evolution of fishes in the southern ocean and the potential impacts changing temperatures might have on fish populations, the project will support the training of undergraduate and graduate students at an RUI institution. Specifically, activities and content directly related to this project\u0027s aims will be incorporated into the undergraduate curriculum at Sonoma State University in an effort to increase undergraduate participation in research, especially with respect to underrepresented groups. The project has specific aims to perform a comparative analysis of nucleotide divergence resulting in non-synonymous amino acid changes in the trans-regulatory elements, namely members of the heat shock factor (HSF) family of transcription factors, in T. bernacchii and N. angustata. The project will also utilize metabolic labeling of newly synthesized proteins from isolated hepatocytes to monitor protein turnover rates in fish acclimated to both -1.5 and +4 \u00b0C for an extended period. Changes in chaperoning capacity and levels of damaged proteins will be quantified in multiple tissues to gain a better understanding of the cellular requirements for maintaining protein homeostasis under long-term acclimations to +4 \u00b0C. In combination, the work will help answer questions regarding divergence in these fishes as well a fundamental information regarding protein structure and function that may also have bio-medical implications.", "east": 168.0, "geometry": "POINT(165.5 -77)", "instruments": null, "is_usap_dc": true, "keywords": "USAP-DC; FISH; NOT APPLICABLE; Southern Ocean", "locations": "Southern Ocean", "north": -76.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Place, Sean", "platforms": "OTHER \u003e NOT APPLICABLE \u003e NOT APPLICABLE", "repo": "NCBI GenBank", "repositories": "NCBI GenBank", "science_programs": null, "south": -78.0, "title": "RUI: Characterizing Protein Homeostasis and the Regulatory Mechanisms Controlling Molecular Chaperone Expression in the Highly Stenothermal Notothenioid Fish, Trematomus Bernacchii", "uid": "p0010055", "west": 163.0}, {"awards": "1247510 Detrich, H. William", "bounds_geometry": null, "dataset_titles": "E-MTAB-6759: RNA-seq across tissues in four Notothenioid species (Antarctic icefish); Expedition Data; Expedition data of LMG1003; Expedition data of LMG1004; PRJNA420419: Chaenocephalus aceratus Genome sequencing; PRJNA66471: Notothenia coriiceps Genome Sequencing Notothenia coriiceps isolate:Sejong01 (black rockcod); S-BSST 132: Assembled Transcriptomes for Berthelot et al. (2018); SRA091269: Notothenia coriiceps RNA Raw Sequence Reads; SRP047484: RAD-tag Sequences of Genetically Mapped Notothenia coriiceps Embryos ; SRP118539: RAD-tag Sequences of Genetically Mapped Chaenocephalus aceratus Embryos", "datasets": [{"dataset_uid": "002685", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG1004", "url": "https://www.rvdata.us/search/cruise/LMG1004"}, {"dataset_uid": "200146", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "SRP047484: RAD-tag Sequences of Genetically Mapped Notothenia coriiceps Embryos ", "url": "https://www.ncbi.nlm.nih.gov/sra/?term=SRP047484"}, {"dataset_uid": "200145", "doi": "", "keywords": null, "people": null, "repository": "BioStudies", "science_program": null, "title": "S-BSST 132: Assembled Transcriptomes for Berthelot et al. (2018)", "url": "https://www.ebi.ac.uk/biostudies/studies/S-BSST132"}, {"dataset_uid": "200144", "doi": "", "keywords": null, "people": null, "repository": "Array Express", "science_program": null, "title": "E-MTAB-6759: RNA-seq across tissues in four Notothenioid species (Antarctic icefish)", "url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6759/"}, {"dataset_uid": "200143", "doi": "", "keywords": null, "people": null, "repository": "NCBI BioProject", "science_program": null, "title": "PRJNA420419: Chaenocephalus aceratus Genome sequencing", "url": "https://www.ncbi.nlm.nih.gov/bioproject/420419"}, {"dataset_uid": "200142", "doi": "", "keywords": null, "people": null, "repository": "NCBI BioProject", "science_program": null, "title": "PRJNA66471: Notothenia coriiceps Genome Sequencing Notothenia coriiceps isolate:Sejong01 (black rockcod)", "url": "https://www.ncbi.nlm.nih.gov/bioproject/66471"}, {"dataset_uid": "200093", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "SRP118539: RAD-tag Sequences of Genetically Mapped Chaenocephalus aceratus Embryos", "url": "https://www.ncbi.nlm.nih.gov/sra/SRP118539 "}, {"dataset_uid": "001508", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0807"}, {"dataset_uid": "001509", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0806"}, {"dataset_uid": "200026", "doi": "", "keywords": null, "people": null, "repository": "NCBI SRA", "science_program": null, "title": "SRA091269: Notothenia coriiceps RNA Raw Sequence Reads", "url": "https://www.ncbi.nlm.nih.gov/sra/?term=SRA091269"}, {"dataset_uid": "002684", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG1003", "url": "https://www.rvdata.us/search/cruise/LMG1003"}], "date_created": "Mon, 08 Apr 2019 00:00:00 GMT", "description": "Since the advent of Antarctic continental glaciation, the opening of the Drake Passage between South America and the Antarctic Peninsula, and the onset of cooling of the Southern Ocean ~40-25 million years ago, evolution of the Antarctic marine biota has been driven by the development of extreme cold temperatures. As circum-Antarctic coastal temperatures declined during this period from ~20\u00b0C to the modern ?1.9 to +2.0\u00b0C (reached ~8-10 million years ago), the psychrophilic (cold-loving) ectotherms of the Southern Ocean evolved compensatory molecular, cellular, and physiological traits that enabled them to maintain normal metabolic function at cold temperatures. Today, these organisms are threatened by rapid warming of the Southern Ocean over periods measured in centuries (as much as 5\u00b0C/100 yr), a timeframe so short that re-adaptation and/or acclimatization to the ?new warm? may not be possible. Thus, the long-term goals of this research project are: 1) to understand the biochemical and physiological capacities of the embryos of Antarctic notothenioid fish to resist or compensate for rapid oceanic warming; and 2) to assess the genetic toolkit available to support the acclimatization and adaptation of Antarctic notothenioid embryos to their warming habitat. The specific aims of this work are: 1) to determine the capacity of the chaperonin complex of notothenioid fishes to assist protein folding at temperatures between ?4 and +20\u00b0C; and 2) to evaluate the genetic responses of notothenioid embryos, measured as global differential gene transcription, to temperature challenge, with ?1.9\u00b0C as the ?normal? control and +4 and +10\u00b0C as high temperature insults. The physiology of embryonic development of marine stenotherms under future climate change scenarios is an important but understudied problem. This project will provide valuable insights into the capacity of Antarctic fish embryos to acclimatize and adapt to plausible climate change scenarios by examining multiple levels of biological organization, from the biochemical to the organismal. The results should also be broadly applicable to understanding the impact of global warming on marine biota worldwide. The research will also introduce graduate and REU undergraduate students to state-of-the-art biochemical, cellular, and molecular-biological research relevant to ecological and environmental issues of the Antarctic marine ecosystem.", "east": null, "geometry": null, "instruments": "IN SITU/LABORATORY INSTRUMENTS \u003e SAMPLERS \u003e TRAWLS/NETS \u003e BOTTOM TRAWL", "is_usap_dc": false, "keywords": "AQUATIC SCIENCES; R/V LMG; USAP-DC; Southern Ocean", "locations": "Southern Ocean", "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Detrich, H. William", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e R/V LMG", "repo": "R2R", "repositories": "Array Express; BioStudies; NCBI BioProject; NCBI SRA; R2R", "science_programs": null, "south": null, "title": "Protein Folding and Embryogenesis in Antarctic Fishes: A Comparative Approach to Environmental Stress", "uid": "p0010024", "west": null}, {"awards": "1043781 O\u0027Brien, Kristin; 1043576 Crockett, Elizabeth", "bounds_geometry": "POLYGON((-64.45 -63.467,-64.2633 -63.467,-64.0766 -63.467,-63.8899 -63.467,-63.7032 -63.467,-63.5165 -63.467,-63.3298 -63.467,-63.1431 -63.467,-62.9564 -63.467,-62.7697 -63.467,-62.583 -63.467,-62.583 -63.5653,-62.583 -63.6636,-62.583 -63.7619,-62.583 -63.8602,-62.583 -63.9585,-62.583 -64.0568,-62.583 -64.1551,-62.583 -64.2534,-62.583 -64.3517,-62.583 -64.45,-62.7697 -64.45,-62.9564 -64.45,-63.1431 -64.45,-63.3298 -64.45,-63.5165 -64.45,-63.7032 -64.45,-63.8899 -64.45,-64.0766 -64.45,-64.2633 -64.45,-64.45 -64.45,-64.45 -64.3517,-64.45 -64.2534,-64.45 -64.1551,-64.45 -64.0568,-64.45 -63.9585,-64.45 -63.8602,-64.45 -63.7619,-64.45 -63.6636,-64.45 -63.5653,-64.45 -63.467))", "dataset_titles": "Electronic fishing logs; Expedition data of LMG1104; Redox Balance in Antarctic Notothenioid Fishes", "datasets": [{"dataset_uid": "600390", "doi": "10.15784/600390", "keywords": "Antarctica; Biota; Southern Ocean", "people": "Crockett, Elizabeth", "repository": "USAP-DC", "science_program": null, "title": "Electronic fishing logs", "url": "https://www.usap-dc.org/view/dataset/600390"}, {"dataset_uid": "002687", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG1104", "url": "https://www.rvdata.us/search/cruise/LMG1104"}, {"dataset_uid": "600382", "doi": "10.15784/600382", "keywords": "Antarctica; Antarctic Peninsula; Biota; Fish; Sample/collection Description; Sample/Collection Description; Southern Ocean", "people": "O\u0027Brien, Kristin", "repository": "USAP-DC", "science_program": null, "title": "Redox Balance in Antarctic Notothenioid Fishes", "url": "https://www.usap-dc.org/view/dataset/600382"}], "date_created": "Tue, 06 Dec 2016 00:00:00 GMT", "description": "Antarctic channichthyid icefishes are stunning examples of the unique physiological traits that can arise during evolution in a constantly cold environment. Icefishes are the only vertebrates that as adults, lack the circulating oxygen-binding protein hemoglobin (Hb); several species within this family also lack the intracellular oxygen-binding protein myoglobin (Mb) in their heart ventricle. The loss of Hb and Mb has resulted in striking modifications in the cardiovascular system to ensure adequate tissue oxygenation, some of which are energetically costly. Recent indicate there may be at least one benefit to not expressing these heme-centered proteins - oxidized proteins and lipids are higher in red-blooded notothenioids compared to icefishes. The research will address the hypothesis that the loss of Hb and Mb reduces oxidative stress in icefishes compared to red-blooded notothenioid fishes, resulting in a lower rate of protein turnover and energetic cost savings. Specifically, the project will (1) Characterize levels of oxidative stress in red- and white-blooded notothenioid fishes, (2) Determine if red- and white-blooded notothenioids differ in their regulation of iron, (3) Determine if lower levels of oxidized proteins in icefishes result in lower rates of protein turnover and energetic cost savings, and (4) Determine if oxygen-binding proteins promote oxidative stress in-vivo and in-vitro. The results will contribute to the understanding of iron-catalyzed oxidative stress, which is associated with the progression of Alzheimer\u0027s, Parkinson\u0027s and cardiovascular diseases. Moreover, the research will increase understanding of factors related to iron metabolism and oxidative stress in notothenioid fishes that may have played key roles in the success of channichthyid icefishes. The broader impacts include development of a website will enable teachers and students to learn more about the fascinating biology of Antarctic icefishes, as well as the impacts of global climate change and commercial fishing activities on Antarctic fishes. Additionally, Alaska Native high school and undergraduate students will be involved in research at the University of Alaska, Fairbanks.", "east": -62.583, "geometry": "POINT(-63.5165 -63.9585)", "instruments": "EARTH REMOTE SENSING INSTRUMENTS \u003e PASSIVE REMOTE SENSING \u003e POSITIONING/NAVIGATION \u003e GPS \u003e GPS", "is_usap_dc": true, "keywords": "Not provided; R/V LMG", "locations": null, "north": -63.467, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Crockett, Elizabeth; O\u0027Brien, Kristin", "platforms": "Not provided; WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e R/V LMG", "repo": "USAP-DC", "repositories": "R2R; USAP-DC", "science_programs": null, "south": -64.45, "title": "Collaborative research: Redox Balance in Antarctic Notothenioid fishes: Do Icefishes have an Advantage?", "uid": "p0000320", "west": -64.45}, {"awards": "1447291 Place, Sean; 1040945 Place, Sean; 1040957 Sarmiento, Jorge", "bounds_geometry": "POLYGON((-180 90,-144 90,-108 90,-72 90,-36 90,0 90,36 90,72 90,108 90,144 90,180 90,180 72,180 54,180 36,180 18,180 0,180 -18,180 -36,180 -54,180 -72,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -72,-180 -54,-180 -36,-180 -18,-180 0,-180 18,-180 36,-180 54,-180 72,-180 90))", "dataset_titles": "Does the strength of the carbonate pump change with ocean stratification and acidification and how? Project data; NCBI GenBank RNA sequences, Pagothenia borchgrevinki; NCBI GenBank RNA sequences, Trematomus bernacchii; NCBI GenBank RNA sequences, Trematomus newnesi; NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015", "datasets": [{"dataset_uid": "000163", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus bernacchii", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA289753"}, {"dataset_uid": "000219", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "Does the strength of the carbonate pump change with ocean stratification and acidification and how? Project data", "url": "http://www.bco-dmo.org/project/521216"}, {"dataset_uid": "000186", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus newnesi", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294787"}, {"dataset_uid": "000185", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Pagothenia borchgrevinki", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294774"}, {"dataset_uid": "000184", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus bernacchii", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA289753"}, {"dataset_uid": "000166", "doi": "", "keywords": null, "people": null, "repository": "BCO-DMO", "science_program": null, "title": "NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015", "url": "http://www.bco-dmo.org/dataset/665853"}, {"dataset_uid": "000165", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Trematomus newnesi", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294787"}, {"dataset_uid": "000164", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "NCBI GenBank RNA sequences, Pagothenia borchgrevinki", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294774"}], "date_created": "Mon, 12 Jan 2015 00:00:00 GMT", "description": "The proposed research will investigate the interacting and potentially synergistic influence of two oceanographic features - ocean acidification and the projected rise in mean sea surface temperature - on the performance of Notothenioids, the dominant fish of the Antarctic marine ecosystem. Understanding the joint effects of acidification and temperature rise on these fish is a vital component of predicting the resilience of coastal marine ecosystems. Notothenioids have repeatedly displayed a narrow window of physiological tolerances when subjected to abiotic stresses. Given that evolutionary adaptation may have led to finely-tuned traits with narrow physiological limits in these organisms, this system provides a unique opportunity to examine physiological trade-offs associated with acclimation to the multi-stressor environment expected from future atmospheric CO2 projections. Understanding these trade-offs will provide valuable insight into the capacity species have for responses to climate change via phenotypic plasticity. As an extension to functional measurements, this study will use evolutionary approaches to map variation in physiological responses onto the phylogeny of these fishes and the genetic diversity within species. These approaches offer insight into the historical constraints and future potential for evolutionary optimization. The research will significantly expand the genomic resources available to polar researchers and will support the training of graduate students and a post doc at an EPSCoR institution. Research outcomes will be incorporated into classroom curriculum.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": 90.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems; Antarctic Integrated System Science", "paleo_time": null, "persons": "Place, Sean; Sarmiento, Jorge; Dudycha, Jeffry; Kwon, Eun-Young", "platforms": "Not provided", "repo": "NCBI GenBank", "repositories": "BCO-DMO; NCBI GenBank", "science_programs": null, "south": -90.0, "title": "Ocean Acidification Category 1: Identifying Adaptive Responses of Polar Fishes in a Vulnerable Ecosystem", "uid": "p0000006", "west": -180.0}, {"awards": "1019305 Grim, Jeffrey", "bounds_geometry": null, "dataset_titles": "Impact of Rising Oceanic Temperatures on the Embryonic Development of Antarctic Notothenioid Fishes", "datasets": [{"dataset_uid": "600119", "doi": "10.15784/600119", "keywords": "Biota; Fish Logs; LMG1203; LMG1204; LMG1205; Oceans; Pot; Southern Ocean; Trawl", "people": "Grim, Jeffrey", "repository": "USAP-DC", "science_program": null, "title": "Impact of Rising Oceanic Temperatures on the Embryonic Development of Antarctic Notothenioid Fishes", "url": "https://www.usap-dc.org/view/dataset/600119"}], "date_created": "Mon, 10 Feb 2014 00:00:00 GMT", "description": "Survival of Antarctic notothenioid fishes in the context of global climate change will depend upon the impact of rising oceanic temperatures on their embryonic development, yet little is known regarding the molecular mechanisms underlying this complex suite of processes. Many notothenioids are characterized by secondary pelagicism, which enables them to exploit food sources in the water column and is supported in part by skeletal pedomorphism. Here the PI proposes to examine the hypothesis that reactive oxygen species (ROS) regulate notothenioid skeletal pedomorphism. The PI proposes to examine the hypothesis that reactive oxygen species (ROS) regulate notothenioid skeletal pedomorphism. The research objectives are : 1) To quantify and localize ROS production and identify the point(s) of origin of ROS production in embryonic Antarctic fishes that differ in skeletal phenotypes 2) To determine whether the time course of embryogenesis and the extent of osteological development in embryonic Antarctic fishes can be altered by changing the oxidative status of the animal during embryogenesis 3) To evaluate whether transgenic alteration of oxidative status can induce skeletal pedomorphism in a fish model. Broader Impacts will include teaching undergraduate lectures, recruiting undergraduate students to help with lab analyses (and possibly field work), lectures and demonstrations to high school students, and allowing secondary educators access to personal photos and videos of research animals for curriculum development.", "east": null, "geometry": null, "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Grim, Jeffrey", "platforms": "Not provided", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": null, "title": "PostDoctoral Research Fellowship", "uid": "p0000482", "west": null}, {"awards": "0741301 O\u0027Brien, Kristin; 1142720 Crockett, Elizabeth", "bounds_geometry": "POLYGON((-64.45 -63.29,-64.249 -63.29,-64.048 -63.29,-63.847 -63.29,-63.646 -63.29,-63.445 -63.29,-63.244 -63.29,-63.043 -63.29,-62.842 -63.29,-62.641 -63.29,-62.44 -63.29,-62.44 -63.370999999999995,-62.44 -63.452,-62.44 -63.533,-62.44 -63.614,-62.44 -63.69499999999999,-62.44 -63.775999999999996,-62.44 -63.857,-62.44 -63.937999999999995,-62.44 -64.01899999999999,-62.44 -64.1,-62.641 -64.1,-62.842 -64.1,-63.043 -64.1,-63.244 -64.1,-63.445 -64.1,-63.646 -64.1,-63.847 -64.1,-64.048 -64.1,-64.249 -64.1,-64.45 -64.1,-64.45 -64.01899999999999,-64.45 -63.937999999999995,-64.45 -63.857,-64.45 -63.775999999999996,-64.45 -63.69499999999999,-64.45 -63.614,-64.45 -63.533,-64.45 -63.452,-64.45 -63.370999999999995,-64.45 -63.29))", "dataset_titles": "Linkages among Mitochondrial Form, Function and Thermal Tolerance of Antarctic Notothenioid Fishes", "datasets": [{"dataset_uid": "600084", "doi": "10.15784/600084", "keywords": "Biota; Oceans; Pot; Southern Ocean; Trawl", "people": "O\u0027Brien, Kristin", "repository": "USAP-DC", "science_program": null, "title": "Linkages among Mitochondrial Form, Function and Thermal Tolerance of Antarctic Notothenioid Fishes", "url": "https://www.usap-dc.org/view/dataset/600084"}], "date_created": "Sat, 30 Nov 2013 00:00:00 GMT", "description": "Abstract Antarctic notothenioid fishes have evolved in the Southern Ocean for 10-14 MY under an unusual set of circumstances. Their characteristics include the complete absence of the circulating oxygen-binding protein, hemoglobin (Hb) within the Channichthyid (Icefish) family of notothenioids. Moreover, some species within the 16 members of this family have also lost the ability to express the oxygen-binding and storage protein, myoglobin (Mb) in cardiac muscle. Our previous work has determined that the loss of Hb and/or Mb is correlated with significant increases in densities of mitochondria within oxidative tissues, and extensive remodeling of these vital organelles. To date, nothing is known about how modifications in mitochondrial architecture of icefishes affect organelle function, or more importantly, how they affect organismal-level physiology. Most critical for Antarctic fishes is that mitochondrial characteristics have been linked to how well ectotherms can withstand increases in temperature. This collaborative research project will address the hypothesis that the unusual mitochondrial architecture of Antarctic Channichthyids has led to changes in function that impact their ability to withstand elevations in temperature. Specifically, the research will (1) determine if the unusual mitochondrial architecture of icefishes affects function and contributes to organismal thermal sensitivity, (2) identify differences in organismal thermal tolerance between red- and white- blooded notothenioids, (3) identify molecular mechanisms regulating changes in mitochondrial structure in icefishes. The results may establish channichthyid icefishes as a sentinel taxon for signaling the impact of global warming on the Southern Ocean. Broad impacts of this project will be realized by participation of high school biology teachers in field work through cooperation with the ARMADA project at the University of Rhode Island, as well as graduate education.", "east": -62.44, "geometry": "POINT(-63.445 -63.695)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": -63.29, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Crockett, Elizabeth; O\u0027Brien, Kristin", "platforms": "Not provided", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -64.1, "title": "Collaborative Research: Linkages among Mitochondrial Form, Function and Thermal Tolerance of Antarctic Notothenioid Fishes", "uid": "p0000483", "west": -64.45}, {"awards": "0839007 Near, Thomas", "bounds_geometry": "POLYGON((-180 -60,-144 -60,-108 -60,-72 -60,-36 -60,0 -60,36 -60,72 -60,108 -60,144 -60,180 -60,180 -63,180 -66,180 -69,180 -72,180 -75,180 -78,180 -81,180 -84,180 -87,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -87,-180 -84,-180 -81,-180 -78,-180 -75,-180 -72,-180 -69,-180 -66,-180 -63,-180 -60))", "dataset_titles": "Genetic Sequence Data", "datasets": [{"dataset_uid": "000151", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Genetic Sequence Data", "url": "http://www.ncbi.nlm.nih.gov/genbank/"}], "date_created": "Fri, 22 Nov 2013 00:00:00 GMT", "description": "This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).\u003cbr/\u003e\u003cbr/\u003eThe teleost fish fauna in the waters surrounding Antarctica are completely dominated by a single clade of closely related species, the Notothenioidei. This clade offers an unprecedented opportunity to investigate the effects of deep time paleogeographic transformations and periods of global climate change on lineage diversification and facilitation of adaptive radiation. With over 100 species, the Antarctic notothenioid radiation has been the subject of intensive investigation of biochemical, physiological, and morphological adaptations associated with freezing avoidance in the subzero Southern Ocean marine habitats. However, broadly sampled time-calibrated phylogenetic hypotheses of notothenioids have not been used to examine patterns of adaptive radiation in this clade. The goals of this project are to develop an intensive phylogenomic scale dataset for 90 of the 124 recognized notothenioid species, and use this genomic resource to generate time-calibrated molecular phylogenetic trees. The results of pilot phylogenetic studies indicate a very exciting correlation of the initial diversification of notothenioids with the fragmentation of East Gondwana approximately 80 million years ago, and the origin of the Antarctic Clade adaptive radiation at a time of global cooling and formation of polar conditions in the Southern Ocean, approximately 35 million years ago. This project will provide research experiences for undergraduates, training for a graduate student, and support a post doctoral researcher. In addition the project will include three high school students from New Haven Public Schools for summer research internships.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Near, Thomas", "platforms": "Not provided", "repo": "NCBI GenBank", "repositories": "NCBI GenBank", "science_programs": null, "south": -90.0, "title": "Genomic Approaches to Resolving Phylogenies of Antarctic Notothenioid Fishes", "uid": "p0000497", "west": -180.0}, {"awards": "0125890 Sidell, Bruce", "bounds_geometry": "POLYGON((-68.1413 -52.6755,-67.47503 -52.6755,-66.80876 -52.6755,-66.14249 -52.6755,-65.47622 -52.6755,-64.80995 -52.6755,-64.14368 -52.6755,-63.47741 -52.6755,-62.81114 -52.6755,-62.14487 -52.6755,-61.4786 -52.6755,-61.4786 -53.8957,-61.4786 -55.1159,-61.4786 -56.3361,-61.4786 -57.5563,-61.4786 -58.7765,-61.4786 -59.9967,-61.4786 -61.2169,-61.4786 -62.4371,-61.4786 -63.6573,-61.4786 -64.8775,-62.14487 -64.8775,-62.81114 -64.8775,-63.47741 -64.8775,-64.14368 -64.8775,-64.80995 -64.8775,-65.47622 -64.8775,-66.14249 -64.8775,-66.80876 -64.8775,-67.47503 -64.8775,-68.1413 -64.8775,-68.1413 -63.6573,-68.1413 -62.4371,-68.1413 -61.2169,-68.1413 -59.9967,-68.1413 -58.7765,-68.1413 -57.5563,-68.1413 -56.3361,-68.1413 -55.1159,-68.1413 -53.8957,-68.1413 -52.6755))", "dataset_titles": "Expedition Data; Expedition data of LMG0304; Expedition data of LMG0304A", "datasets": [{"dataset_uid": "001596", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0506"}, {"dataset_uid": "002706", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG0304", "url": "https://www.rvdata.us/search/cruise/LMG0304"}, {"dataset_uid": "002707", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG0304A", "url": "https://www.rvdata.us/search/cruise/LMG0304A"}, {"dataset_uid": "002708", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG0304A", "url": "https://www.rvdata.us/search/cruise/LMG0304A"}, {"dataset_uid": "001704", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0304"}, {"dataset_uid": "001597", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0505"}], "date_created": "Tue, 04 May 2010 00:00:00 GMT", "description": "Notothenioid fishes that dominate the fish fauna surrounding Antarctica have been evolving for 10-14 million years at a nearly constant body temperature of ~0C throughout their life histories. As a result, this group of animals is uniquely suited to studies aimed at understanding and identifying features of physiology and biochemistry that result from the process of evolution at cold body temperature. This project has three major objectives aimed at examining adaptations for life in cold environments: \u003cbr/\u003e\u003cbr/\u003e1. Identify the amino acid substitutions in the fatty acid-binding pocket of fatty acyl CoA synthetase (FACS) that explain its substrate specificity. Fatty acids are a major fuel of energy metabolism in Antarctic fishes. FACS catalyzes the condensation of CoASH and fatty acids to fatty acyl CoA esters, a step required for subsequent metabolism of these important compounds. This research may permit us to resolve the specific amino acid substitutions that explain both substrate specificity and preservation of catalytic rate of notothenioid FACS at cold physiological temperatures.\u003cbr/\u003e\u003cbr/\u003e2. Produce a rigorous biochemical and biophysical characterization of the intracellular calcium-binding protein, parvalbumin, from white axial musculature of Antarctic fishes. Parvalbumin plays a pivotal role in facilitating the relaxation phase of fast-contracting muscles and is a likely site of strong selective pressure. Preliminary data strongly indicate that the protein from Antarctic fishes has been modified to ensure function at cold temperature. A suite of physical techniques will be used to determine dissociation constants of Antarctic fish parvalbumins for calcium and magnesium and unidirectional rate constants of ion-dissociation from the protein. Full-length cDNA clones for Antarctic fish parvalbumin(s) will permit deduction of primary amino acid sequence These data will yield insight into structural elements that permit the protein from notothenioid fishes to function at very cold body temperature.\u003cbr/\u003e\u003cbr/\u003e3. Conduct a broad survey of the pattern of cardiac myoglobin expression in the Suborder Notothenoidei. Previous work has indicated a variable pattern of presence or absence of the intracellular oxygen-binding protein, myoglobin (Mb), in hearts of one family of Antarctic notothenioid fishes (Channichthyidae; icefishes). Because Mb is of physiological value in species that express the protein, the observed pattern of interspecific expression has been attributed to unusually low niche competition in the Southern Ocean. This leads to the prediction that similar loss of cardiac Mb should be observed in other notothenioid taxa. This part of the project will survey for the presence and absence of cardiac Mb in as many notothenioid species as possible and, if Mb-lacking species are detected, will extend analyses to determine the mechanism(s) responsible for loss of its expression using molecular biological techniques.", "east": -61.4786, "geometry": "POINT(-64.80995 -58.7765)", "instruments": "IN SITU/LABORATORY INSTRUMENTS \u003e PRESSURE/HEIGHT METERS \u003e PRESSURE SENSORS; IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e CTD; EARTH REMOTE SENSING INSTRUMENTS \u003e PASSIVE REMOTE SENSING \u003e POSITIONING/NAVIGATION \u003e GPS \u003e GPS; IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e ACOUSTIC SOUNDERS \u003e ADCP", "is_usap_dc": false, "keywords": "R/V LMG", "locations": null, "north": -52.6755, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Sidell, Bruce; Detrich, H. William", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e R/V LMG", "repo": "R2R", "repositories": "R2R", "science_programs": null, "south": -64.8775, "title": "Cold Body Temperature as an Evolutionary Shaping force in the Physiology of Antarctic Fishes", "uid": "p0000241", "west": -68.1413}, {"awards": "9909055 Sidell, Bruce", "bounds_geometry": null, "dataset_titles": "Expedition Data; Expedition data of LMG0105", "datasets": [{"dataset_uid": "002693", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG0105", "url": "https://www.rvdata.us/search/cruise/LMG0105"}, {"dataset_uid": "001869", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0105"}], "date_created": "Tue, 04 May 2010 00:00:00 GMT", "description": "The suborder Notothenoidei is the dominant fish group of the Southern Ocean surrounding Antarctica, both in terms of number of species and biomass. For about fourteen million years, these highly successful fish evolved under stable thermal conditions that result in body temperatures of about zero degrees centigrade throughout their life histories. Evolution this cold environment has led to unusual physiological and biochemical characteristics. In some cases, the characteristics contribute to overcoming constraints of cold temperature on biological processes. In other instances, mutations that probably would have been lethal in warmer, less oxygen-rich environments than the Southern Ocean have been retained in Antarctic fishes. This research project focuses on three major objectives that exploit these unusual conditions to identify mechanisms compatible with normal cellular function at cold temperature and to gain unique insights into the physiological roles of key intracellular proteins. The three lines of study proposed are the molecular basis for the failure of the myoglobin encoding gene to be expressed in certain Antarctic notothenioid fishes, the basis of the substrate specificity of the enzyme fatty acyl-CoA synthetase that is involved in the catabolism of fatty acids, and the functional roles played by different isoforms of creatine phosphokinase in locomotory muscle of Antarctic fish. Results from this study will not only provide insight into the evolutionary biology of the Antarctic notothenioid fishes, but will elucidate important general principles that are applicable to widely different taxa beyond the Antarctic.", "east": null, "geometry": null, "instruments": null, "is_usap_dc": false, "keywords": "R/V LMG", "locations": null, "north": null, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Sidell, Bruce", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e R/V LMG", "repo": "R2R", "repositories": "R2R", "science_programs": null, "south": null, "title": "Proteins of Oxygen-Binding and Energy Metabolism in Muscles of Antarctic Fishes: Evolutionary Adjustments to Life at Cold Temperature", "uid": "p0000863", "west": null}, {"awards": "0132032 Detrich, H. William", "bounds_geometry": "POLYGON((-68.84315 -42.87167,-61.576321 -42.87167,-54.309492 -42.87167,-47.042663 -42.87167,-39.775834 -42.87167,-32.509005 -42.87167,-25.242176 -42.87167,-17.975347 -42.87167,-10.708518 -42.87167,-3.441689 -42.87167,3.82514 -42.87167,3.82514 -44.482708,3.82514 -46.093746,3.82514 -47.704784,3.82514 -49.315822,3.82514 -50.92686,3.82514 -52.537898,3.82514 -54.148936,3.82514 -55.759974,3.82514 -57.371012,3.82514 -58.98205,-3.441689 -58.98205,-10.708518 -58.98205,-17.975347 -58.98205,-25.242176 -58.98205,-32.509005 -58.98205,-39.775834 -58.98205,-47.042663 -58.98205,-54.309492 -58.98205,-61.576321 -58.98205,-68.84315 -58.98205,-68.84315 -57.371012,-68.84315 -55.759974,-68.84315 -54.148936,-68.84315 -52.537898,-68.84315 -50.92686,-68.84315 -49.315822,-68.84315 -47.704784,-68.84315 -46.093746,-68.84315 -44.482708,-68.84315 -42.87167))", "dataset_titles": "Expedition Data", "datasets": [{"dataset_uid": "001655", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/NBP0404"}], "date_created": "Tue, 04 May 2010 00:00:00 GMT", "description": "Notothenioid fish are a major group of fish in the Southern Ocean. The ancestral notothenioid fish stock of Antarctica probably arose as a sluggish, bottom-dwelling perciform species that evolved some 40-60 million years ago in the then temperate shelf waters of the Antarctic continent. The grounding of the ice sheet on the continental shelf and changing trophic conditions may have eliminated the taxonomically diverse late Eocene fauna and initiated the original diversification of notothenioids. On the High Antarctic shelf, notothenioids today dominate the ichthyofauna in terms of species diversity, abundance and biomass, the latter two at levels of 90-95%. Since the International Geophysical Year of 1957-58, fish biologists from the Antarctic Treaty nations have made impressive progress in understanding the notothenioid ichthyofauna of the cold Antarctic marine ecosystem. However, integration of this work into the broader marine context has been limited, largely due to lack of access to, and analysis of, specimens of Sub-Antarctic notothenioid fishes. Sub-Antarctic fishes of the notothenioid suborder are critical for a complete understanding of the evolution, population dynamics, eco-physiology, and eco-biochemistry of their Antarctic relatives. This project will support an international, collaborative research cruise to collect and study fish indigenous to sub-antarctic habitats. The topics included in the research plans of the international team of researchers includes Systematics and Evolutionary Studies; Life History Strategies and Population Dynamics; Physiological, Biochemical, and Molecular Biological Investigations of Major Organ and Tissue Systems; Genomic Resources for the Sub-Antarctic Notothenioids; and Ecological Studies of Transitional Benthic Invertebrates. In a world that is experiencing changes in global climate, the loss of biological diversity, and the depletion of marine fisheries, the Antarctic, Sub-Antarctic, and their biota offer compelling natural laboratories for understanding the evolutionary impacts of these processes. The proposed work will contribute to development of a baseline understanding of these sensitive ecosystems, one against which future changes in species distribution and survival may be evaluated judiciously.", "east": 3.82514, "geometry": "POINT(-32.509005 -50.92686)", "instruments": "IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e CTD; IN SITU/LABORATORY INSTRUMENTS \u003e MAGNETIC/MOTION SENSORS \u003e GRAVIMETERS \u003e GRAVIMETERS; EARTH REMOTE SENSING INSTRUMENTS \u003e PASSIVE REMOTE SENSING \u003e POSITIONING/NAVIGATION \u003e GPS \u003e GPS; IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e ACOUSTIC SOUNDERS \u003e ADCP", "is_usap_dc": false, "keywords": "R/V NBP", "locations": null, "north": -42.87167, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Detrich, H. 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(Bathydraconidae)", "datasets": [{"dataset_uid": "001493", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0810"}, {"dataset_uid": "001504", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0809"}, {"dataset_uid": "002728", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG0809", "url": "https://www.rvdata.us/search/cruise/LMG0809"}, {"dataset_uid": "601811", "doi": null, "keywords": "Antarctica; Bellingshausen Sea; Cryosphere; Southern Ocean", "people": "Corso, Andrew; Cheng, Chi-Hing; McDowell, Jan; Biesack, Ellen; Steinberg, Deborah; Hilton, Eric; Desvignes, Thomas", "repository": "USAP-DC", "science_program": "LTER", "title": "Metadata associated with the description of Akarotaxis gouldae n. sp. (Bathydraconidae)", "url": "https://www.usap-dc.org/view/dataset/601811"}], "date_created": "Tue, 04 May 2010 00:00:00 GMT", "description": "Antarctic notothenioid fish evolved antifreeze (AF) proteins that prevent ice crystals that enter their body fluids from growing, and thereby avoid freezing in their icy habitats. However, even in the extreme cold Antarctic marine environment, regional gradations of severity are found. The biological correlate for environmental severity in fish is the endogenous ice load, which likely determines the tolerable limit of environmental severity for notothenioid habitation. The endogenous ice load develops from environmental ice crystals entering through body surfaces and somehow localizing to the spleen. How prone the surface tissues are to ice entry, how ice reaches the spleen, and what the fate of splenic ice is, requires elucidation. Spleen sequestration of ice raises the hypothesis that macrophages may play a role in the translocation and perhaps elimination of AF-bound ice crystals. Antifreeze glycoproteins (AFGP) act in concert with a second, recently discovered antifreeze called antifreeze potentiating protein (AFPP), necessitating an assessment of the contribution of AFPP to freezing avoidance. Recent research suggests that the exocrine pancreas and the anterior stomach, not the liver, synthesize AFGPs and secrete them into the intestine, from where they may be returned to the blood. A GI-to-blood transport is a highly unconventional path for a major plasma protein and also begs the questions, What is the source of blood AFPP?. Why are two distinct AF proteins needed and what is the chronology of their evolution? What genomic changes in the DNA are associated with the development or loss of the antifreeze trait? Experiments described in this proposal address these interrelated questions of environmental, organismal, and evolutionary physiology, and will further our understanding of novel vertebrate physiologies, the limits of environmental adaptation, and climatically driven changes in the genome. The proposed research will (1) determine the temporal and spatial heterogeneity of environmental temperature and iciness in progressively more severe fish habitats in the greater McMurdo Sound area, and in the milder Arthur Harbor at Palmer Station. The splenic ice load in fishes inhabiting these sites will be determined to correlate to environmental severity and habitability. (2) Assess the surface tissue site of ice entry and their relative barrier properties in intact fish and isolated tissues preparations (3) Assess the role of immune cells in the fate of endogenous ice, (4) determine whether the blood AFGPs are from intestinal/rectal uptake, (5) examine the contribution of AFPP to the total blood AF activity (6) evaluate the progression of genomic changes in the AFGP locus across Notothenioidei as modulated by disparate thermal environments, in four selected species through the analyses of large insert DNA BAC clones. The origin and evolution of AFPP will be examined also by analyzing BAC clones encompassing the AFPP genomic locus. The broader impacts of the proposed research include training of graduate and undergraduate students in research approaches ranging from physical field measurements to cutting edge genomics. Undergraduate research projects have lead to co-authored publications and will continue to do so. Outreach includes establishing Wiki websites on topics of Antarctic fish biology and freeze avoidance, providing advisory services to the San Francisco Science Exploratorium, and making BAC libraries available to interested polar biologists. This research theme has repeatedly received national and international science news coverage and will continue to be disseminated to the public in that manner.", "east": -58.7029, "geometry": "POINT(-63.3527 -58.8725)", "instruments": "IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e CTD; EARTH REMOTE SENSING INSTRUMENTS \u003e PASSIVE REMOTE SENSING \u003e POSITIONING/NAVIGATION \u003e GPS \u003e GPS; IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e ACOUSTIC SOUNDERS \u003e ADCP", "is_usap_dc": false, "keywords": "R/V LMG", "locations": null, "north": -52.7599, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Devries, Arthur", "platforms": "WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e R/V LMG", "repo": "R2R", "repositories": "R2R; USAP-DC", "science_programs": null, "south": -64.9851, "title": "Environmental, Organismal and Evolutionary Physiology of Freeze Avoidance in Antarctic Notothenioid Fishes", "uid": "p0000560", "west": -68.0025}, {"awards": "0437887 Sidell, Bruce", "bounds_geometry": "POLYGON((-180 -60,-144 -60,-108 -60,-72 -60,-36 -60,0 -60,36 -60,72 -60,108 -60,144 -60,180 -60,180 -63,180 -66,180 -69,180 -72,180 -75,180 -78,180 -81,180 -84,180 -87,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -87,-180 -84,-180 -81,-180 -78,-180 -75,-180 -72,-180 -69,-180 -66,-180 -63,-180 -60))", "dataset_titles": "Differential Expression of Oxygen-binding Proteins in Antarctic Fishes Affects Nitric Oxide-mediated Pathways of Angiogenesis and Mitochondrial Biogenesis; Expedition Data; Expedition data of LMG0705; Expedition data of LMG0706", "datasets": [{"dataset_uid": "600039", "doi": "10.15784/600039", "keywords": "Biota; Oceans; Pot; Sample/collection Description; Sample/Collection Description; Southern Ocean; Trawl", "people": "Sidell, Bruce", "repository": "USAP-DC", "science_program": null, "title": "Differential Expression of Oxygen-binding Proteins in Antarctic Fishes Affects Nitric Oxide-mediated Pathways of Angiogenesis and Mitochondrial Biogenesis", "url": "https://www.usap-dc.org/view/dataset/600039"}, {"dataset_uid": "002712", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG0705", "url": "https://www.rvdata.us/search/cruise/LMG0705"}, {"dataset_uid": "002713", "doi": null, "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition data of LMG0706", "url": "https://www.rvdata.us/search/cruise/LMG0706"}, {"dataset_uid": "001534", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0705"}], "date_created": "Sun, 06 Dec 2009 00:00:00 GMT", "description": "The polar ocean presently surrounding Antarctica is the coldest, most thermally stable marine environment on earth. Because oxygen solubility in seawater is inversely proportional to temperature, the cold Antarctic seas are an exceptionally oxygen-rich aquatic habitat. Eight families of a single perciform suborder, the Notothenioidei, dominate the present fish fauna surrounding Antarctica. Notothenioids account for approximately 35% of fish species and 90% of fish biomass south of the Antarctic Polar Front. Radiation of closely related notothenioid species thus has occurred rapidly and under a very unusual set of conditions: relative oceanographic isolation from other faunas due to circumpolar currents and deep ocean trenches surrounding the continent, chronically, severely cold water temperatures, very high oxygen availability, very low levels of niche competition in a Southern Ocean depauperate of species subsequent to a dramatic crash in species diversity of fishes that occurred sometime between the mid-Tertiary and present. These features make Antarctic notothenioid fishes an uniquely attractive group for the study of physiological and biochemical adaptations to cold body temperature. \u003cbr/\u003eFew distinctive features of Antarctic fishes are as unique as the pattern of expression of oxygen-binding proteins in one notothenioid family, the Channichthyidae (Antarctic icefishes). All channichthyid icefishes lack the circulating oxygen-binding protein, hemoglobin (Hb); the intracellular oxygen-binding protein, myoglobin (Mb) is not uniformly expressed in species of this family. Both proteins are normally considered essential for adequate delivery of oxygen to aerobically poised tissues of animals. To compensate for the absence of Hb, icefishes have developed large hearts, rapidly circulate a large blood volume and possess elaborate vasculature of larger lumenal diameter than is seen in red-blooded fishes. Loss of Mb expression in oxidative muscles correlates with dramatic elevation in density of mitochondria within the cell, although each individual organelle is less densely packed with respiratory proteins. \u003cbr/\u003eWithin the framework of oxygen movement, the adaptive significance of greater vascular density and mitochondrial populations is understandable but mechanisms underlying development of these characteristics remain unknown. The answer may lie in another major function of both Hb and Mb, degradation of the ubiquitous bioactive compound, nitric oxide (NO). The research will test the hypothesis that loss of hemoprotein expression in icefishes has resulted in an increase in levels of NO that mediate modification of vascular systems and expansion of mitochondrial populations in oxidative tissues. The objectives of the proposal are to quantify the vascular density of retinas in +Hb and -Hb notothenioid species, to characterize NOS isoforms and catalytic activity in retina and cardiac muscle of Antarctic notothenioid fishes, to evaluate level of expression of downstream factors implicated in angiogenesis (in retinal tissue) and mitochondrial biogenesis (in cardiac muscle), and to determine whether inhibition of NOS in vivo results in regression of angiogenic and mitochondrial biogenic responses in icefishes. Broader impacts range from basic biology, through training of young scientists, to enhanced understanding of clinically relevant biomedical processes.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": "IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e CTD; EARTH REMOTE SENSING INSTRUMENTS \u003e PASSIVE REMOTE SENSING \u003e POSITIONING/NAVIGATION \u003e GPS \u003e GPS; IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e ACOUSTIC SOUNDERS \u003e ADCP; IN SITU/LABORATORY INSTRUMENTS \u003e PRESSURE/HEIGHT METERS \u003e PRESSURE SENSORS; IN SITU/LABORATORY INSTRUMENTS \u003e PHOTON/OPTICAL DETECTORS \u003e TURBIDITY METERS", "is_usap_dc": true, "keywords": "R/V LMG; Not provided", "locations": null, "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Sidell, Bruce", "platforms": "Not provided; WATER-BASED PLATFORMS \u003e VESSELS \u003e SURFACE \u003e R/V LMG", "repo": "USAP-DC", "repositories": "R2R; USAP-DC", "science_programs": null, "south": -90.0, "title": "Collaborative Research: Differential Expression of Oxygen-binding Proteins in Antarctic Fishes Affects Nitric Oxide-mediated Pathways of Angiogenesis and Mitochondrial Biogenesis.", "uid": "p0000527", "west": -180.0}, {"awards": "0436190 Eastman, Joseph", "bounds_geometry": "POLYGON((-180 -60,-144 -60,-108 -60,-72 -60,-36 -60,0 -60,36 -60,72 -60,108 -60,144 -60,180 -60,180 -63,180 -66,180 -69,180 -72,180 -75,180 -78,180 -81,180 -84,180 -87,180 -90,144 -90,108 -90,72 -90,36 -90,0 -90,-36 -90,-72 -90,-108 -90,-144 -90,-180 -90,-180 -87,-180 -84,-180 -81,-180 -78,-180 -75,-180 -72,-180 -69,-180 -66,-180 -63,-180 -60))", "dataset_titles": "Biodiversity, Buoyancy and Morphological Studies of Non-Antarctic Notothenioid Fishes", "datasets": [{"dataset_uid": "600038", "doi": "10.15784/600038", "keywords": "Biota; NBP0404; Oceans; R/v Nathaniel B. Palmer; Southern Ocean", "people": "Eastman, Joseph", "repository": "USAP-DC", "science_program": null, "title": "Biodiversity, Buoyancy and Morphological Studies of Non-Antarctic Notothenioid Fishes", "url": "https://www.usap-dc.org/view/dataset/600038"}], "date_created": "Mon, 30 Mar 2009 00:00:00 GMT", "description": "Patterns of biodiversity, as revealed by basic research in organismal biology, may be derived from ecological and evolutionary processes expressed in unique settings, such as Antarctica. The polar regions and their faunas are commanding increased attention as declining species diversity, environmental change, commercial fisheries, and resource management are now being viewed in a global context. Commercial fishing is known to have a direct and pervasive effect on marine biodiversity, and occurs in the Southern Ocean as far south as the Ross Sea. \u003cbr/\u003eThe nature of fish biodiversity in the Antarctic is different than in all other ocean shelf areas. Waters of the Antarctic continental shelf are ice covered for most of the year and water temperatures are nearly constant at -1.5 C. In these waters components of the phyletically derived Antarctic clade of Notothenioids dominate fish diversity. In some regions, including the southwestern Ross Sea, Notothenioids are overwhelmingly dominant in terms of number of species, abundance, and biomass. Such dominance by a single taxonomic group is unique among shelf faunas of the world. In the absence of competition from a taxonomically diverse fauna, Notothenioids underwent a habitat or depth related diversification keyed to the utilization of unfilled niches in the water column, especially pelagic or partially pelagic zooplanktivory and piscivory. This has been accomplished in the absence of a swim bladder for buoyancy control. They also may form a special type of adaptive radiation known as a species flock, which is an assemblage of a disproportionately high number of related species that have evolved rapidly within a defined area where most species are endemic. Diversification in buoyancy is the hallmark of the notothenioid radiation. Buoyancy is the feature of notothenioid biology that determines whether a species lives on the substrate, in the water column or both. Buoyancy also influences other key aspects of life history including swimming, feeding and reproduction and thus has implications for the role of the species in the ecosystem. \u003cbr/\u003eWith similarities to classic evolutionary hot spots, the Antarctic shelf and its Notothenioid radiation merit further exploration. The 2004 \"International Collaborative Expedition to collect and study Fish Indigenous to Sub-Antarctic Habitats,\" or, \"ICEFISH,\" provided a platform for collection of notothenioid fishes from sub-Antarctic waters between South America and Africa, which will be examined in this project. This study will determine buoyancy for samples of all notothenioid species captured during the ICEFISH cruise. This essential aspect of the biology is known for only 19% of the notothenioid fauna. Also, the gross and microscopic anatomy of brains and sense organs of the phyletically basal families Bovichtidae, Eleginopidae, and of the non-Antarctic species of the primarily Antarctic family Nototheniidae will be examined. The fish biodiversity and endemicity in poorly known localities along the ICEFISH cruise track, seamounts and deep trenches will be quantified. Broader impacts include improved information for comprehending and conserving biodiversity, a scientific and societal priority.", "east": 180.0, "geometry": "POINT(0 -89.999)", "instruments": null, "is_usap_dc": true, "keywords": "Not provided", "locations": null, "north": -60.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Eastman, Joseph", "platforms": "Not provided", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -90.0, "title": "Biodiversity, Buoyancy and Morphological Studies of Non-Antarctic Notothenioid Fishes", "uid": "p0000106", "west": -180.0}]

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