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  • Time Factors  (17)
  • Nature Publishing Group (NPG)  (17)
  • National Academy of Sciences
  • American Geophysical Union (AGU)
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  • 1
    Publication Date: 2012-03-01
    Description: The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years. The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay. This evolutionary decay was driven by a series of five 'stratification' events. Each event suppressed X-Y crossing over within a chromosome segment or 'stratum', incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over. The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome, remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1-4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3292678/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3292678/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hughes, Jennifer F -- Skaletsky, Helen -- Brown, Laura G -- Pyntikova, Tatyana -- Graves, Tina -- Fulton, Robert S -- Dugan, Shannon -- Ding, Yan -- Buhay, Christian J -- Kremitzki, Colin -- Wang, Qiaoyan -- Shen, Hua -- Holder, Michael -- Villasana, Donna -- Nazareth, Lynne V -- Cree, Andrew -- Courtney, Laura -- Veizer, Joelle -- Kotkiewicz, Holland -- Cho, Ting-Jan -- Koutseva, Natalia -- Rozen, Steve -- Muzny, Donna M -- Warren, Wesley C -- Gibbs, Richard A -- Wilson, Richard K -- Page, David C -- R01 HG000257/HG/NHGRI NIH HHS/ -- R01 HG000257-17/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Feb 22;483(7387):82-6. doi: 10.1038/nature10843.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA. jhughes@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22367542" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromosomes, Human, Y/*genetics ; Conserved Sequence/*genetics ; Crossing Over, Genetic/genetics ; *Evolution, Molecular ; Gene Amplification/genetics ; *Gene Deletion ; Humans ; In Situ Hybridization, Fluorescence ; Macaca mulatta/*genetics ; Male ; Models, Genetic ; Molecular Sequence Data ; Pan troglodytes/genetics ; Radiation Hybrid Mapping ; Selection, Genetic/genetics ; Time Factors ; Y Chromosome/*genetics
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  • 2
    Publication Date: 2012-05-25
    Description: Warming experiments are increasingly relied on to estimate plant responses to global climate change. For experiments to provide meaningful predictions of future responses, they should reflect the empirical record of responses to temperature variability and recent warming, including advances in the timing of flowering and leafing. We compared phenology (the timing of recurring life history events) in observational studies and warming experiments spanning four continents and 1,634 plant species using a common measure of temperature sensitivity (change in days per degree Celsius). We show that warming experiments underpredict advances in the timing of flowering and leafing by 8.5-fold and 4.0-fold, respectively, compared with long-term observations. For species that were common to both study types, the experimental results did not match the observational data in sign or magnitude. The observational data also showed that species that flower earliest in the spring have the highest temperature sensitivities, but this trend was not reflected in the experimental data. These significant mismatches seem to be unrelated to the study length or to the degree of manipulated warming in experiments. The discrepancy between experiments and observations, however, could arise from complex interactions among multiple drivers in the observational data, or it could arise from remediable artefacts in the experiments that result in lower irradiance and drier soils, thus dampening the phenological responses to manipulated warming. Our results introduce uncertainty into ecosystem models that are informed solely by experiments and suggest that responses to climate change that are predicted using such models should be re-evaluated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolkovich, E M -- Cook, B I -- Allen, J M -- Crimmins, T M -- Betancourt, J L -- Travers, S E -- Pau, S -- Regetz, J -- Davies, T J -- Kraft, N J B -- Ault, T R -- Bolmgren, K -- Mazer, S J -- McCabe, G J -- McGill, B J -- Parmesan, C -- Salamin, N -- Schwartz, M D -- Cleland, E E -- England -- Nature. 2012 May 2;485(7399):494-7. doi: 10.1038/nature11014.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive 0116, La Jolla, California 92093, USA. wolkovich@biodiversity.ubc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22622576" target="_blank"〉PubMed〈/a〉
    Keywords: Artifacts ; Ecosystem ; Flowers/growth & development/physiology ; *Global Warming ; *Models, Biological ; *Periodicity ; Plant Development ; Plant Leaves/growth & development/physiology ; *Plant Physiological Phenomena ; Plants/classification ; Reproducibility of Results ; Soil/chemistry ; Temperature ; Time Factors ; *Uncertainty
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  • 3
    Publication Date: 2014-09-26
    Description: In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stasevich, Timothy J -- Hayashi-Takanaka, Yoko -- Sato, Yuko -- Maehara, Kazumitsu -- Ohkawa, Yasuyuki -- Sakata-Sogawa, Kumiko -- Tokunaga, Makio -- Nagase, Takahiro -- Nozaki, Naohito -- McNally, James G -- Kimura, Hiroshi -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Dec 11;516(7530):272-5. doi: 10.1038/nature13714. Epub 2014 Sep 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA [3] Transcription Imaging Consortium, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA. ; 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [3] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan. ; 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan. ; Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan. ; 1] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [2] Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan. ; 1] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan [2] RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan. ; Department of Biotechnology Research, Kazusa DNA Research Institute, Chiba, 292-0818, Japan. ; Mab Institute Inc., Sapporo, 001-0021, Japan. ; 1] Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Institute for Soft Matter and Functional Materials, Helmholtz Zentrum Berlin, Berlin, 14109, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25252976" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cell Line, Tumor ; Cell Survival ; Chromatin Immunoprecipitation ; Enzyme Activation ; Genome/genetics ; Histones/*chemistry/*metabolism ; Kinetics ; Lysine/metabolism ; Mice ; Microscopy, Fluorescence ; Phosphorylation ; RNA Polymerase II/*metabolism ; *Single-Cell Analysis ; Time Factors ; Transcription Elongation, Genetic ; Transcription Initiation, Genetic ; *Transcription, Genetic
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  • 4
    Publication Date: 2013-10-18
    Description: The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis methods to identify somatic variants across thousands of tumours. Here we present data and analytical results for point mutations and small insertions/deletions from 3,281 tumours across 12 tumour types as part of the TCGA Pan-Cancer effort. We illustrate the distributions of mutation frequencies, types and contexts across tumour types, and establish their links to tissues of origin, environmental/carcinogen influences, and DNA repair defects. Using the integrated data sets, we identified 127 significantly mutated genes from well-known (for example, mitogen-activated protein kinase, phosphatidylinositol-3-OH kinase, Wnt/beta-catenin and receptor tyrosine kinase signalling pathways, and cell cycle control) and emerging (for example, histone, histone modification, splicing, metabolism and proteolysis) cellular processes in cancer. The average number of mutations in these significantly mutated genes varies across tumour types; most tumours have two to six, indicating that the number of driver mutations required during oncogenesis is relatively small. Mutations in transcriptional factors/regulators show tissue specificity, whereas histone modifiers are often mutated across several cancer types. Clinical association analysis identifies genes having a significant effect on survival, and investigations of mutations with respect to clonal/subclonal architecture delineate their temporal orders during tumorigenesis. Taken together, these results lay the groundwork for developing new diagnostics and individualizing cancer treatment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927368/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927368/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kandoth, Cyriac -- McLellan, Michael D -- Vandin, Fabio -- Ye, Kai -- Niu, Beifang -- Lu, Charles -- Xie, Mingchao -- Zhang, Qunyuan -- McMichael, Joshua F -- Wyczalkowski, Matthew A -- Leiserson, Mark D M -- Miller, Christopher A -- Welch, John S -- Walter, Matthew J -- Wendl, Michael C -- Ley, Timothy J -- Wilson, Richard K -- Raphael, Benjamin J -- Ding, Li -- P01 CA101937/CA/NCI NIH HHS/ -- P01CA101937/CA/NCI NIH HHS/ -- R01 CA180006/CA/NCI NIH HHS/ -- R01 HG005690/HG/NHGRI NIH HHS/ -- R01CA180006/CA/NCI NIH HHS/ -- R01HG005690/HG/NHGRI NIH HHS/ -- U01 HG006517/HG/NHGRI NIH HHS/ -- U01HG006517/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54HG003079/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Oct 17;502(7471):333-9. doi: 10.1038/nature12634.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Genome Institute, Washington University in St Louis, Missouri 63108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24132290" target="_blank"〉PubMed〈/a〉
    Keywords: Carcinogenesis/*genetics ; Cell Cycle/genetics ; Clone Cells/metabolism/pathology ; Cohort Studies ; DNA Repair/genetics ; Humans ; INDEL Mutation/genetics ; Mitogen-Activated Protein Kinases/genetics ; Models, Genetic ; Mutation/*genetics ; Neoplasms/*classification/*genetics/metabolism/pathology ; Oncogenes/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Point Mutation/genetics ; Receptor Protein-Tyrosine Kinases/metabolism ; Survival Analysis ; Time Factors
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  • 5
    Publication Date: 2014-02-07
    Description: In line with global targets agreed under the Convention on Biological Diversity, the number of marine protected areas (MPAs) is increasing rapidly, yet socio-economic benefits generated by MPAs remain difficult to predict and under debate. MPAs often fail to reach their full potential as a consequence of factors such as illegal harvesting, regulations that legally allow detrimental harvesting, or emigration of animals outside boundaries because of continuous habitat or inadequate size of reserve. Here we show that the conservation benefits of 87 MPAs investigated worldwide increase exponentially with the accumulation of five key features: no take, well enforced, old (〉10 years), large (〉100 km(2)), and isolated by deep water or sand. Using effective MPAs with four or five key features as an unfished standard, comparisons of underwater survey data from effective MPAs with predictions based on survey data from fished coasts indicate that total fish biomass has declined about two-thirds from historical baselines as a result of fishing. Effective MPAs also had twice as many large (〉250 mm total length) fish species per transect, five times more large fish biomass, and fourteen times more shark biomass than fished areas. Most (59%) of the MPAs studied had only one or two key features and were not ecologically distinguishable from fished sites. Our results show that global conservation targets based on area alone will not optimize protection of marine biodiversity. More emphasis is needed on better MPA design, durable management and compliance to ensure that MPAs achieve their desired conservation value.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edgar, Graham J -- Stuart-Smith, Rick D -- Willis, Trevor J -- Kininmonth, Stuart -- Baker, Susan C -- Banks, Stuart -- Barrett, Neville S -- Becerro, Mikel A -- Bernard, Anthony T F -- Berkhout, Just -- Buxton, Colin D -- Campbell, Stuart J -- Cooper, Antonia T -- Davey, Marlene -- Edgar, Sophie C -- Forsterra, Gunter -- Galvan, David E -- Irigoyen, Alejo J -- Kushner, David J -- Moura, Rodrigo -- Parnell, P Ed -- Shears, Nick T -- Soler, German -- Strain, Elisabeth M A -- Thomson, Russell J -- England -- Nature. 2014 Feb 13;506(7487):216-20. doi: 10.1038/nature13022. Epub 2014 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Marine and Antarctic Studies, University of Tasmania, GPO Box 252-49, Hobart, Tasmania 7001, Australia. ; Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth PO4 9LY, UK. ; 1] Institute for Marine and Antarctic Studies, University of Tasmania, GPO Box 252-49, Hobart, Tasmania 7001, Australia [2] Stockholm Resilience Centre, Stockholm University, Kraftriket 2B, SE-106 91 Stockholm, Sweden. ; School of Plant Science, University of Tasmania, GPO Box 252, Hobart, Tasmania 7001, Australia. ; Charles Darwin Foundation, Puerto Ayora, Galapagos, Ecuador. ; The Bites Lab, Natural Products and Agrobiology Institute (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain. ; Elwandle Node, South African Environmental Observation network, Private Bag 1015, Grahamstown 6140, South Africa. ; Wildlife Conservation Society, Indonesia Marine Program, Jalan Atletik No. 8, Bogor Jawa Barat 16151, Indonesia. ; Department of Water, Perth, Western Australia 6000, Australia. ; Facultad de Recursos Naturales, Escuela de Ciencias del Mar, Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile. ; Centro Nacional Patagonico, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Bvd Brown 2915, 9120 Puerto Madryn, Argentina. ; Channel Islands National Park, United States National Park Service, 1901 Spinnaker Dr., Ventura, California 93001, USA. ; Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Rio de Janeiro 21941-902, Brazil. ; Scripps Institution of Oceanography, UC San Diego, Mail Code 0227, 9500 Gilman Dr., La Jolla, California 92093-0227, USA. ; Leigh Marine Laboratory, University of Auckland, 160 Goat Island Road, Leigh 0985, New Zealand. ; Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Universita di Bologna, Via San Alberto, Ravenna 163-48123, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24499817" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aquatic Organisms/physiology ; Biodiversity ; Biomass ; Conservation of Natural Resources/economics/legislation & ; jurisprudence/methods/*statistics & numerical data ; Coral Reefs ; Ecology/economics/legislation & jurisprudence/methods/*statistics & numerical ; data ; *Ecosystem ; Fisheries/legislation & jurisprudence/standards/*statistics & numerical data ; Fishes/*physiology ; Marine Biology/economics/legislation & jurisprudence/methods/statistics & ; numerical data ; Seawater ; Sharks ; Silicon Dioxide ; Time Factors
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  • 6
    Publication Date: 2015-12-18
    Description: Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance. However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size and the spread of agriculture in North America. Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyons, S Kathleen -- Amatangelo, Kathryn L -- Behrensmeyer, Anna K -- Bercovici, Antoine -- Blois, Jessica L -- Davis, Matt -- DiMichele, William A -- Du, Andrew -- Eronen, Jussi T -- Faith, J Tyler -- Graves, Gary R -- Jud, Nathan -- Labandeira, Conrad -- Looy, Cindy V -- McGill, Brian -- Miller, Joshua H -- Patterson, David -- Pineda-Munoz, Silvia -- Potts, Richard -- Riddle, Brett -- Terry, Rebecca -- Toth, Aniko -- Ulrich, Werner -- Villasenor, Amelia -- Wing, Scott -- Anderson, Heidi -- Anderson, John -- Waller, Donald -- Gotelli, Nicholas J -- England -- Nature. 2016 Jan 7;529(7584):80-3. doi: 10.1038/nature16447. Epub 2015 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA. ; Department of Environmental Science and Biology, The College at Brockport - SUNY, Brockport, New York 14420, USA. ; School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA. ; Department of Geology and Geophysics, Yale University, New Haven, Connecticut 06520, USA. ; Hominid Paleobiology Doctoral Program, Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology, George Washington University, Washington DC 20052, USA. ; Department of Geosciences and Geography, University of Helsinki, PO Box 64, 00014 University of Helsinki, Finland. ; School of Social Science, The University of Queensland, Brisbane, Queensland 4072, Australia. ; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA. ; Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen 2100, Denmark. ; Biological Sciences Graduate Program, University of Maryland, College Park, Maryland 20742, USA. ; Florida Museum of Natural History, University of Florida, Gainsville, Florida 32611, USA. ; Department of Entomology, University of Maryland College Park, College Park, Maryland 20742, USA. ; Key Lab of Insect Evolution and Environmental Changes, Capital Normal University, Beijing 100048, China. ; Department of Integrative Biology and Museum of Paleontology, University of California Berkeley, Berkeley, California 94720, USA. ; School Biology and Ecology &Sustainability Solutions Initiative, University of Maine, Orono, Maine 04469, USA. ; Department of Geology, University of Cincinnati, Cincinnati, Ohio 45221, USA. ; Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia. ; Department of Anthropology, Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA. ; School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, Nevada 89154, USA. ; Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331, USA. ; Chair of Ecology and Biogeography, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland. ; Evolutionary Studies Institute, University of the Witwatersrand, Jorissen Street, Braamfontein, Johannesburg 2001, South Africa. ; Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. ; Department of Biology, University of Vermont, Burlington, Vermont 05405, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26675730" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; Animals ; *Ecosystem ; History, Ancient ; Human Activities/*history ; Humans ; North America ; *Plant Physiological Phenomena ; Population Dynamics ; Time Factors
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  • 7
    Publication Date: 2009-11-20
    Description: Molecular regulation of embryonic stem cell (ESC) fate involves a coordinated interaction between epigenetic, transcriptional and translational mechanisms. It is unclear how these different molecular regulatory mechanisms interact to regulate changes in stem cell fate. Here we present a dynamic systems-level study of cell fate change in murine ESCs following a well-defined perturbation. Global changes in histone acetylation, chromatin-bound RNA polymerase II, messenger RNA (mRNA), and nuclear protein levels were measured over 5 days after downregulation of Nanog, a key pluripotency regulator. Our data demonstrate how a single genetic perturbation leads to progressive widespread changes in several molecular regulatory layers, and provide a dynamic view of information flow in the epigenome, transcriptome and proteome. We observe that a large proportion of changes in nuclear protein levels are not accompanied by concordant changes in the expression of corresponding mRNAs, indicating important roles for translational and post-translational regulation of ESC fate. Gene-ontology analysis across different molecular layers indicates that although chromatin reconfiguration is important for altering cell fate, it is preceded by transcription-factor-mediated regulatory events. The temporal order of gene expression alterations shows the order of the regulatory network reconfiguration and offers further insight into the gene regulatory network. Our studies extend the conventional systems biology approach to include many molecular species, regulatory layers and temporal series, and underscore the complexity of the multilayer regulatory mechanisms responsible for changes in protein expression that determine stem cell fate.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199216/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199216/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Rong -- Markowetz, Florian -- Unwin, Richard D -- Leek, Jeffrey T -- Airoldi, Edoardo M -- MacArthur, Ben D -- Lachmann, Alexander -- Rozov, Roye -- Ma'ayan, Avi -- Boyer, Laurie A -- Troyanskaya, Olga G -- Whetton, Anthony D -- Lemischka, Ihor R -- P50 GM071558/GM/NIGMS NIH HHS/ -- P50 GM071558-01A20007/GM/NIGMS NIH HHS/ -- P50 GM071558-020007/GM/NIGMS NIH HHS/ -- P50 GM071558-030007/GM/NIGMS NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2009 Nov 19;462(7271):358-62. doi: 10.1038/nature08575.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA. rlu@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924215" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cell Differentiation ; Embryonic Stem Cells/*cytology/*metabolism ; Epigenesis, Genetic ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Mice ; Proteome ; Time Factors
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  • 8
    Publication Date: 2009-01-30
    Description: The addition of iron to high-nutrient, low-chlorophyll regions induces phytoplankton blooms that take up carbon. Carbon export from the surface layer and, in particular, the ability of the ocean and sediments to sequester carbon for many years remains, however, poorly quantified. Here we report data from the CROZEX experiment in the Southern Ocean, which was conducted to test the hypothesis that the observed north-south gradient in phytoplankton concentrations in the vicinity of the Crozet Islands is induced by natural iron fertilization that results in enhanced organic carbon flux to the deep ocean. We report annual particulate carbon fluxes out of the surface layer, at three kilometres below the ocean surface and to the ocean floor. We find that carbon fluxes from a highly productive, naturally iron-fertilized region of the sub-Antarctic Southern Ocean are two to three times larger than the carbon fluxes from an adjacent high-nutrient, low-chlorophyll area not fertilized by iron. Our findings support the hypothesis that increased iron supply to the glacial sub-Antarctic may have directly enhanced carbon export to the deep ocean. The CROZEX sequestration efficiency (the amount of carbon sequestered below the depth of winter mixing for a given iron supply) of 8,600 mol mol(-1) was 18 times greater than that of a phytoplankton bloom induced artificially by adding iron, but 77 times smaller than that of another bloom initiated, like CROZEX, by a natural supply of iron. Large losses of purposefully added iron can explain the lower efficiency of the induced bloom(6). The discrepancy between the blooms naturally supplied with iron may result in part from an underestimate of horizontal iron supply.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pollard, Raymond T -- Salter, Ian -- Sanders, Richard J -- Lucas, Mike I -- Moore, C Mark -- Mills, Rachel A -- Statham, Peter J -- Allen, John T -- Baker, Alex R -- Bakker, Dorothee C E -- Charette, Matthew A -- Fielding, Sophie -- Fones, Gary R -- French, Megan -- Hickman, Anna E -- Holland, Ross J -- Hughes, J Alan -- Jickells, Timothy D -- Lampitt, Richard S -- Morris, Paul J -- Nedelec, Florence H -- Nielsdottir, Maria -- Planquette, Helene -- Popova, Ekaterina E -- Poulton, Alex J -- Read, Jane F -- Seeyave, Sophie -- Smith, Tania -- Stinchcombe, Mark -- Taylor, Sarah -- Thomalla, Sandy -- Venables, Hugh J -- Williamson, Robert -- Zubkov, Mike V -- England -- Nature. 2009 Jan 29;457(7229):577-80. doi: 10.1038/nature07716.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Oceanography Centre Southampton, Natural Environment Research Council and University of Southampton, European Way, Southampton SO14 3ZH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19177128" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; Carbon/*metabolism ; Chlorophyll/analysis/metabolism ; Eutrophication ; Geography ; Geologic Sediments/chemistry ; Iron/*metabolism ; Oceans and Seas ; Phytoplankton/metabolism ; Seasons ; Seawater/*chemistry ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2011-11-04
    Description: Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070744/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070744/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lorenzen, Eline D -- Nogues-Bravo, David -- Orlando, Ludovic -- Weinstock, Jaco -- Binladen, Jonas -- Marske, Katharine A -- Ugan, Andrew -- Borregaard, Michael K -- Gilbert, M Thomas P -- Nielsen, Rasmus -- Ho, Simon Y W -- Goebel, Ted -- Graf, Kelly E -- Byers, David -- Stenderup, Jesper T -- Rasmussen, Morten -- Campos, Paula F -- Leonard, Jennifer A -- Koepfli, Klaus-Peter -- Froese, Duane -- Zazula, Grant -- Stafford, Thomas W Jr -- Aaris-Sorensen, Kim -- Batra, Persaram -- Haywood, Alan M -- Singarayer, Joy S -- Valdes, Paul J -- Boeskorov, Gennady -- Burns, James A -- Davydov, Sergey P -- Haile, James -- Jenkins, Dennis L -- Kosintsev, Pavel -- Kuznetsova, Tatyana -- Lai, Xulong -- Martin, Larry D -- McDonald, H Gregory -- Mol, Dick -- Meldgaard, Morten -- Munch, Kasper -- Stephan, Elisabeth -- Sablin, Mikhail -- Sommer, Robert S -- Sipko, Taras -- Scott, Eric -- Suchard, Marc A -- Tikhonov, Alexei -- Willerslev, Rane -- Wayne, Robert K -- Cooper, Alan -- Hofreiter, Michael -- Sher, Andrei -- Shapiro, Beth -- Rahbek, Carsten -- Willerslev, Eske -- R01 HG003229/HG/NHGRI NIH HHS/ -- England -- Nature. 2011 Nov 2;479(7373):359-64. doi: 10.1038/nature10574.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for GeoGenetics, University of Copenhagen, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22048313" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bayes Theorem ; *Biota ; Bison ; Climate Change/*history ; DNA, Mitochondrial/analysis/genetics ; Europe ; *Extinction, Biological ; Fossils ; Genetic Variation ; Geography ; History, Ancient ; Horses ; Human Activities/*history ; Humans ; Mammals/genetics/*physiology ; Mammoths ; Molecular Sequence Data ; Population Dynamics ; Reindeer ; Siberia ; Species Specificity ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2012-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gray, George M -- Cohen, Joshua T -- England -- Nature. 2012 Sep 6;489(7414):27-8. doi: 10.1038/489027a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Risk Science and Public Health, George Washington University, Washington DC 20037, USA. gmgray@gwu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955594" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Formaldehyde/adverse effects ; High-Throughput Screening Assays ; Humans ; *Policy Making ; Public Health ; Risk Assessment/*methods/*standards ; Tetrachloroethylene/adverse effects ; Time Factors ; Uncertainty ; United States ; United States Environmental Protection Agency/*standards
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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