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Sökning: WFRF:(Fujita Matthew)

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1.
  • Forskningsöversikt (refereegranskat)
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2.
  • Alfoeldi, Jessica, et al. (författare)
  • The genome of the green anole lizard and a comparative analysis with birds and mammals
  • 2011
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 477:7366, s. 587-591
  • Tidskriftsartikel (refereegranskat)abstract
    • The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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3.
  • Green, Richard E., et al. (författare)
  • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
  • 2014
  • Ingår i: Science. - 0036-8075 .- 1095-9203. ; 346:6215, s. 1335-
  • Tidskriftsartikel (refereegranskat)abstract
    • To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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4.
  • Li, Cai, et al. (författare)
  • Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
  • 2014
  • Ingår i: GigaScience. - 2047-217X .- 2047-217X. ; 3
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adelie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Results: Phylogenetic dating suggests that early penguins arose similar to 60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from similar to 1 million years ago to similar to 100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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5.
  • Rands, Chris M., et al. (författare)
  • Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence
  • 2013
  • Ingår i: BMC Genomics. - 1471-2164 .- 1471-2164. ; 14, s. 95-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin's (Galapagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galapagos archipelago took place in the last 2-3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. Results: 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin's finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. Conclusions: These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin's finches.
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6.
  • Campbell, PJ, et al. (författare)
  • Pan-cancer analysis of whole genomes
  • 2020
  • Ingår i: Nature. - : Nature Publishing Group. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
  • Tidskriftsartikel (refereegranskat)
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7.
  • Larson, Greger, et al. (författare)
  • Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in island southeast Asia and Oceania
  • 2007
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 104:12, s. 4834-4839
  • Tidskriftsartikel (refereegranskat)abstract
    • Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called "wild" pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region.
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8.
  • Mitchell, Paul J., et al. (författare)
  • Quality Improvement Initiatives in Fragility Fracture Care and Prevention
  • Ingår i: Current Osteoporosis Reports. - : Current Science, Inc.. - 1544-1873. ; 17:6, s. 510-520
  • Forskningsöversikt (refereegranskat)abstract
    • Purpose of Review: This review sought to describe quality improvement initiatives in fragility fracture care and prevention. Recent Findings: A major care gap persists throughout the world in the secondary prevention of fragility fractures. Systematic reviews have confirmed that the Fracture Liaison Service (FLS) model of care is associated with significant improvements in rates of bone mineral density testing, initiation of osteoporosis treatment and adherence with treatment for individuals who sustain fragility fractures. Further, these improvements in the processes of care resulted in significant reductions in refracture risk and lower post-fracture mortality. The primary challenge facing health systems now is to ensure that best practice is delivered effectively in the local healthcare setting. Publication of clinical standards for FLS at the organisational and patient level in combination with the establishment of national registries has provided a mechanism for FLS to benchmark and improve their performance. Summary: Major efforts are ongoing at the global, regional and national level to improve the acute care, rehabilitation and secondary prevention for individuals who sustain fragility fractures. Active participation in these initiatives has the potential to eliminate current care gaps in the coming decade.
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9.
  • O'Connell, Kyle A. (författare)
  • A Tale of Two Skates : Comparative Phylogeography of North American Skate Species with Implications for Conservation
  • 2019
  • Ingår i: Copeia. - 0045-8511 .- 1938-5110. ; 107:2, s. 297-304
  • Tidskriftsartikel (refereegranskat)abstract
    • Genomic data can provide novel insights into the natural history of oceanic species. These data can inform the management of vulnerable and slow-maturing species by estimating population structure, rates of migration, and the distribution of genetic diversity. In this study we focus on two protected elasmobranch species, the Winter Skate, Leucoraja ocellata, and the Little Skate, L. erinacea. We use genome-wide SNPs to estimate population structure, and quantify migration and genetic diversity among both species from four sampling localities across the Atlantic coast of North America. We find that species of Leucoraja are generally isolated by distance, although we infer some fine-scale population structure. Specifically, estimates of effective migration infer fine-scale population structure in L. ocellata between the northern sites of Georges Bank and the Mid-Atlantic sampling sites, whereas L. erinacea shows no evidence of population genetic structure in any analyses. We also found that genetic diversity is concentrated in the central sites of Georges Bank and the Mid-Atlantic Bight for L. ocellata, but is reduced at these two sites in L. erinacea, suggesting opposite distributions of genetic diversity between species. Thus, genomic data suggest that while species of Leucoraja lack discrete population structure, they likely employ only mid-range dispersal. These findings correspond to ecological studies that have found eco physiological differences between embryonic and juvenile Leucoraja from different localities. Taken together, small-bodied skate research emphasizes the importance of local adaptive plasticity for marine species, even without population genetic structure. Conservation strategies should focus on managing the portions of the Atlantic coast considered most vital to reproduction of Leucoraja, but should not recognize multiple populations across their range.
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10.
  • Tiemeyer, Michael, et al. (författare)
  • GlyTouCan: an accessible glycan structure repository.
  • 2017
  • Ingår i: Glycobiology. - 1460-2423. ; 27:10, s. 915-919
  • Tidskriftsartikel (refereegranskat)abstract
    • Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.
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