USAP-DC

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

[{"awards": "2324998 Daane, Jacob; 1955368 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.; 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 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.", "datasets": [{"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": "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": "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"}, {"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": "Postlethwait, John; Desvignes, Thomas", "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": "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": "Postlethwait, John; Desvignes, Thomas", "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": "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": "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"}], "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; AQUATIC ECOSYSTEMS; Dragonfish; Sub-Antarctic; Notothenioid; Blood; Hemoglobin", "locations": "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", "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": "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": "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": "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"}, {"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"}], "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": "NCBI ", "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": "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"}, {"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": "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"}], "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": "Texas Data Repository", "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": "1341602 Crockett, Elizabeth; 1341663 O\u0027Brien, Kristin", "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": "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"}, {"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": "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": "601407", "doi": "10.15784/601407", "keywords": "Antarctica; Antarctic Peninsula", "people": "O\u0027Brien, Kristin; Joyce, William; Axelsson, Michael", "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": "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": "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": "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": "601410", "doi": "10.15784/601410", "keywords": "Antarctica; Antarctic Peninsula; Biota; Fish", "people": "Farrell, Anthony; O\u0027Brien, Kristin; Crockett, Elizabeth; Egginton, Stuart; Axelsson, Michael; 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": "601409", "doi": "10.15784/601409", "keywords": "Antarctica; Antarctic Peninsula", "people": "O\u0027Brien, Kristin; Farrell, Anthony; Joyce, Michael; Egginton, Stuart; Axelsson, 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": "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": "601408", "doi": "10.15784/601408", "keywords": "Antarctica; Antarctic Peninsula", "people": "Axelsson, Michael; Farrell, Anthony; Egginton, Stuart; O\u0027Brien, Kristin; Crockett, Elizabeth; Joyce, William", "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": "601414", "doi": "10.15784/601414", "keywords": "Antarctica; Antarctic Peninsula", "people": "Farnoud, Amir; Crockett, Elizabeth; O\u0027Brien, Kristin; 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": "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"}], "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": "GenBank", "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": "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": "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": "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": "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": "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": "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"}, {"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": "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"}], "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": "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": "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": "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"}, {"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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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"}], "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": "R2R", "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": "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": "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"}, {"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": "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": "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": "001508", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0807"}, {"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": "001509", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0806"}, {"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": "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 "}], "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": "NCBI SRA", "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": "1341701 Bilyk, Kevin", "bounds_geometry": null, "dataset_titles": "Antarctic Ice fish; submission ID #SRP113562", "datasets": [{"dataset_uid": "000206", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "Antarctic Ice fish; submission ID #SRP113562", "url": "https://www.ncbi.nlm.nih.gov/genbank/"}], "date_created": "Mon, 31 Jul 2017 00:00:00 GMT", "description": "This work will broaden our knowledge and insights into genetic trait loss or change accompanying species evolution in general as well as within the uniquely isolated and frigid Southern Ocean. The system of oxygen-carrying and related proteins being studied is very important to human health and the two proteins being specifically studied in this work (haptoglobin and hemopexin) have crucial roles in preventing excess iron loading in the kidneys. As such, the project has the potential to contribute novel insights that could be valuable to medical science. 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 lead principal investigator on the project is an early career scientist whose career development will be enhanced by this project. It will also support the training of several undergraduate students in molecular biology, protein biochemistry, and appreciation of the unique Antarctic fish fauna and environment. The project will contribute to a content-rich web site that will bring to the public the history of biological discoveries and sciences on fishes of the Southern Ocean and through this project the investigators will contribute to an annual polar event at a children\u0027s science museum. The Antarctic icefishes have thrived despite the striking evolutionary loss of the normally indispensable respiratory protein hemoglobin in all species and myoglobin in some. Studies over the past decades have predominately focused on the mechanisms behind hemoprotein losses and the resulting compensatory adaptations in these fish, while evolutionary impact of such losses on the supporting protein genes and functions has remained unaddressed. This project investigates the evolutionary fate of two important partner proteins, the hemoglobin scavenger haptoglobin and the heme scavenger hemopexin (heme groups are the iron-containing functional group of proteins such as hemoglobin and myoglobin). With the permanent hemoglobin-null state in Antarctic icefishes, and particularly in dual hemoglobin- and myoglobin-null species, the preservation of a functional haptoglobin would seem unessential and the role of hemopexin likely diminished. This project seeks to resolve whether co-evolutionary loss or reduction of these supporting proteins occurred with the extinction of the hemoglobin trait in the icefishes, and the molecular mechanisms underlying such changes. The investigators envisage the cold and oxygen rich marine environment as the start of a cascade of relaxation of selection pressures. Initially this would have obviated the need for maintaining functional oxygen carrying proteins, ultimately leading to their permanent loss. These events in turn would have relaxed the maintenance of the network of supporting systems, leading to additional trait loss or change.", "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": "Bilyk, Kevin", "platforms": "Not provided", "repo": "NCBI GenBank", "repositories": "NCBI GenBank", "science_programs": null, "south": null, "title": "Evolutionary Fates of Hemoglobin and Heme Scavengers in White-blooded Antarctic Icefishes", "uid": "p0000396", "west": null}, {"awards": "1043576 Crockett, Elizabeth; 1043781 O\u0027Brien, Kristin", "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": "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"}, {"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"}], "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": "1142720 Crockett, Elizabeth; 0741301 O\u0027Brien, Kristin", "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": "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": "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": "001596", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0506"}, {"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"}, {"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": "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"}], "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": "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": "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": "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": "001534", "doi": "", "keywords": null, "people": null, "repository": "R2R", "science_program": null, "title": "Expedition Data", "url": "https://www.rvdata.us/search/cruise/LMG0705"}, {"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"}], "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": "R2R", "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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