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  • Proceedings of the National Academy of Sciences  (8)
  • Biology  (8)
  • 1
    Online Resource
    Online Resource
    De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Abstract: De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains 〈 1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability ( h 2 ), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1902766117
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 2
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    Demographic history and rare allele sharing among human populations
    Proceedings of the National Academy of Sciences ; 2011
    In:  Proceedings of the National Academy of Sciences Vol. 108, No. 29 ( 2011-07-19), p. 11983-11988
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 108, No. 29 ( 2011-07-19), p. 11983-11988
    Abstract: High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1019276108
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2011
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 3
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    Disruption of the acyl-CoA:cholesterol acyltransferase gene in mice: Evidence suggesting multiple cholesterol esterification enzymes in mammals
    Proceedings of the National Academy of Sciences ; 1996
    In:  Proceedings of the National Academy of Sciences Vol. 93, No. 24 ( 1996-11-26), p. 14041-14046
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 93, No. 24 ( 1996-11-26), p. 14041-14046
    Abstract: The microsomal enzyme acyl-CoA:cholesterol acyltransferase (ACAT; EC 2.3.1.26 ) catalyzes the esterification of cellular cholesterol with fatty acids to form cholesterol esters. ACAT activity is found in many tissues, including macrophages, the adrenal glands, and the liver. In macrophages, ACAT is thought to participate in foam cell formation and thereby to contribute to atherosclerotic lesion development. Disruption of the gene for ACAT ( Acact ) in mice resulted in decreased cholesterol esterification in ACAT-deficient fibroblasts and adrenal membranes, and markedly reduced cholesterol ester levels in adrenal glands and peritoneal macrophages; the latter finding will be useful in testing the role of ACAT and macrophage foam cell formation in atherosclerosis. In contrast, the livers of ACAT-deficient mice contained substantial amounts of cholesterol esters and exhibited no reduction in cholesterol esterification activity. These tissue-specific reductions in cholesterol esterification provide evidence that in mammals this process involves more than one form of esterification enzyme.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.93.24.14041
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 1996
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    detail.hit.zdb_id: 1461794-8
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  • 4
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    Online Resource
    Groundwater depletion and sustainability of irrigation in the US High Plains and Central Valley
    Proceedings of the National Academy of Sciences ; 2012
    In:  Proceedings of the National Academy of Sciences Vol. 109, No. 24 ( 2012-06-12), p. 9320-9325
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 24 ( 2012-06-12), p. 9320-9325
    Abstract: Aquifer overexploitation could significantly impact crop production in the United States because 60% of irrigation relies on groundwater. Groundwater depletion in the irrigated High Plains and California Central Valley accounts for ∼50% of groundwater depletion in the United States since 1900. A newly developed High Plains recharge map shows that high recharge in the northern High Plains results in sustainable pumpage, whereas lower recharge in the central and southern High Plains has resulted in focused depletion of 330 km 3 of fossil groundwater, mostly recharged during the past 13,000 y. Depletion is highly localized with about a third of depletion occurring in 4% of the High Plains land area. Extrapolation of the current depletion rate suggests that 35% of the southern High Plains will be unable to support irrigation within the next 30 y. Reducing irrigation withdrawals could extend the lifespan of the aquifer but would not result in sustainable management of this fossil groundwater. The Central Valley is a more dynamic, engineered system, with north/south diversions of surface water since the 1950s contributing to ∼7× higher recharge. However, these diversions are regulated because of impacts on endangered species. A newly developed Central Valley Hydrologic Model shows that groundwater depletion since the 1960s, totaling 80 km 3 , occurs mostly in the south (Tulare Basin) and primarily during droughts. Increasing water storage through artificial recharge of excess surface water in aquifers by up to 3 km 3 shows promise for coping with droughts and improving sustainability of groundwater resources in the Central Valley.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1200311109
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 5
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    Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 51 ( 2013-12-17), p. 20669-20674
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 51 ( 2013-12-17), p. 20669-20674
    Abstract: Animals that sustain high levels of aerobic activity under hypoxic conditions (e.g., birds that fly at high altitude) face the physiological challenge of jointly optimizing blood-O 2 affinity for O 2 loading in the pulmonary circulation and O 2 unloading in the systemic circulation. At high altitude, this challenge is especially acute for small endotherms like hummingbirds that have exceedingly high mass-specific metabolic rates. Here we report an experimental analysis of hemoglobin (Hb) function in South American hummingbirds that revealed a positive correlation between Hb-O 2 affinity and native elevation. Protein engineering experiments and ancestral-state reconstructions revealed that this correlation is attributable to derived increases in Hb-O 2 affinity in highland lineages, as well as derived reductions in Hb-O 2 affinity in lowland lineages. Site-directed mutagenesis experiments demonstrated that repeated evolutionary transitions in biochemical phenotype are mainly attributable to repeated amino acid replacements at two epistatically interacting sites that alter the allosteric regulation of Hb-O 2 affinity. These results demonstrate that repeated changes in biochemical phenotype involve parallelism at the molecular level, and that mutations with indirect, second-order effects on Hb allostery play key roles in biochemical adaptation.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1315456110
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 6
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    Online Resource
    Genome scan of human systemic lupus erythematosus: Evidence for linkage on chromosome 1q in African-American pedigrees
    Proceedings of the National Academy of Sciences ; 1998
    In:  Proceedings of the National Academy of Sciences Vol. 95, No. 25 ( 1998-12-08), p. 14869-14874
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 95, No. 25 ( 1998-12-08), p. 14869-14874
    Abstract: Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by production of autoantibodies against intracellular antigens including DNA, ribosomal P, Ro (SS-A), La (SS-B), and the spliceosome. Etiology is suspected to involve genetic and environmental factors. Evidence of genetic involvement includes: associations with HLA-DR3, HLA-DR2, Fcγ receptors (FcγR) IIA and IIIA, and hereditary complement component deficiencies, as well as familial aggregation, monozygotic twin concordance 〉 20%, λ s 〉 10, purported linkage at 1q41â42, and inbred mouse strains that consistently develop lupus. We have completed a genome scan in 94 extended multiplex pedigrees by using model-based linkage analysis. Potential [log 10 of the odds for linkage (lod) 〉 2.0] SLE loci have been identified at chromosomes 1q41, 1q23, and 11q14â23 in African-Americans; 14q11, 4p15, 11q25, 2q32, 19q13, 6q26â27, and 12p12â11 in European-Americans; and 1q23, 13q32, 20q13, and 1q31 in all pedigrees combined. An effect for the FcγRIIA candidate polymorphism) at 1q23 (lod = 3.37 in African-Americans) is syntenic with linkage in a murine model of lupus. Sib-pair and multipoint nonparametric analyses also support linkage ( P 〈 0.05) at nine loci detected by using two-point lod score analysis (lod 〉 2.0). Our results are consistent with the presumed complexity of genetic susceptibility to SLE and illustrate racial origin is likely to influence the specific nature of these genetic effects.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.95.25.14869
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 1998
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    detail.hit.zdb_id: 1461794-8
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  • 7
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    Resolution of a paradox: Hummingbird flight at high elevation does not come without a cost
    Proceedings of the National Academy of Sciences ; 2004
    In:  Proceedings of the National Academy of Sciences Vol. 101, No. 51 ( 2004-12-21), p. 17731-17736
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 101, No. 51 ( 2004-12-21), p. 17731-17736
    Abstract: Flight at high elevation is energetically demanding because of parallel reductions in air density and oxygen availability. The hovering flight of hummingbirds is one of the most energetically expensive forms of animal locomotion, but hummingbirds are nonetheless abundant at high elevations throughout the Americas. Two mechanisms enhance aerodynamic performance in high-elevation hummingbirds: increase in wing size and wing stroke amplitude during hovering. How do these changes in morphology, kinematics, and physical properties of air combine to influence the aerodynamic power requirements of flight across elevations? Here, we present data on the flight performance of 43 Andean hummingbird species as well as a 76-taxon multilocus molecular phylogeny that served as the historical framework for comparative analyses. Along a 4,000-m elevational transect, hummingbird body mass increased systematically, placing further aerodynamic demands on high-elevation taxa. However, we found that the minimum power requirements for hovering flight remain constant with respect to elevation because hummingbirds compensate sufficiently through increases in wing size and stroke amplitude. Thus, high-elevation hummingbirds are not limited in their capacity for hovering flight despite the challenges imposed by hypobaric environments. Other flight modes including vertical ascent and fast forward flight are more mechanically and energetically demanding, and we accordingly also tested for the maximum power available to hummingbirds by using a load-lifting assay. In contrast to hovering, excess power availability decreased substantially across elevations, thereby reducing the biomechanical potential for more complex flight such as competitive and escape maneuvers.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0405260101
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2004
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  • 8
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    Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex ( Phrynosoma )
    Proceedings of the National Academy of Sciences ; 2009
    In:  Proceedings of the National Academy of Sciences Vol. 106, No. 30 ( 2009-07-28), p. 12418-12423
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 106, No. 30 ( 2009-07-28), p. 12418-12423
    Abstract: Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard ( Phrynosoma coronatum ) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci ( RAG − 1 , 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0906380106
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2009
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    detail.hit.zdb_id: 1461794-8
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