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  • 1
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    Using temperature to analyse temporal dynamics in the songbird motor pathway (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-11-14
    Description: Many complex behaviours, like speech or music, have a hierarchical organization with structure on many timescales, but it is not known how the brain controls the timing of behavioural sequences, or whether different circuits control different timescales of the behaviour. Here we address these issues by using temperature to manipulate the biophysical dynamics in different regions of the songbird forebrain involved in song production. We find that cooling the premotor nucleus HVC (formerly known as the high vocal centre) slows song speed across all timescales by up to 45 per cent but only slightly alters the acoustic structure, whereas cooling the downstream motor nucleus RA (robust nucleus of the arcopallium) has no observable effect on song timing. Our observations suggest that dynamics within HVC are involved in the control of song timing, perhaps through a chain-like organization. Local manipulation of brain temperature should be broadly applicable to the identification of neural circuitry that controls the timing of behavioural sequences and, more generally, to the study of the origin and role of oscillatory and other forms of brain dynamics in neural systems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723166/" 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/PMC2723166/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, Michael A -- Fee, Michale S -- DC009280/DC/NIDCD NIH HHS/ -- K99 DC009280/DC/NIDCD NIH HHS/ -- K99 DC009280-02/DC/NIDCD NIH HHS/ -- MH067105/MH/NIMH NIH HHS/ -- R01 MH067105/MH/NIMH NIH HHS/ -- R01 MH067105-04/MH/NIMH NIH HHS/ -- England -- Nature. 2008 Nov 13;456(7219):189-94. doi: 10.1038/nature07448.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19005546" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cold Temperature ; Efferent Pathways/physiology ; Finches/*physiology ; High Vocal Center/*physiology ; Neurons/physiology ; Prosencephalon/*physiology/radiography ; Time Factors ; Vocalization, Animal/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    James Watson's genome sequenced at high speed (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadman, Meredith -- England -- Nature. 2008 Apr 17;452(7189):788. doi: 10.1038/452788b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18431822" target="_blank"〉PubMed〈/a〉
    Keywords: Genetic Counseling/trends ; *Genome, Human ; Genomics/economics/*trends ; History, 21st Century ; Humans ; Individuality ; Male ; Reference Standards ; Sequence Analysis, DNA/economics/*trends ; Time Factors
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Orbital and millennial-scale features of atmospheric CH4 over the past 800,000 years (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-16
    Description: Atmospheric methane is an important greenhouse gas and a sensitive indicator of climate change and millennial-scale temperature variability. Its concentrations over the past 650,000 years have varied between approximately 350 and approximately 800 parts per 10(9) by volume (p.p.b.v.) during glacial and interglacial periods, respectively. In comparison, present-day methane levels of approximately 1,770 p.p.b.v. have been reported. Insights into the external forcing factors and internal feedbacks controlling atmospheric methane are essential for predicting the methane budget in a warmer world. Here we present a detailed atmospheric methane record from the EPICA Dome C ice core that extends the history of this greenhouse gas to 800,000 yr before present. The average time resolution of the new data is approximately 380 yr and permits the identification of orbital and millennial-scale features. Spectral analyses indicate that the long-term variability in atmospheric methane levels is dominated by approximately 100,000 yr glacial-interglacial cycles up to approximately 400,000 yr ago with an increasing contribution of the precessional component during the four more recent climatic cycles. We suggest that changes in the strength of tropical methane sources and sinks (wetlands, atmospheric oxidation), possibly influenced by changes in monsoon systems and the position of the intertropical convergence zone, controlled the atmospheric methane budget, with an additional source input during major terminations as the retreat of the northern ice sheet allowed higher methane emissions from extending periglacial wetlands. Millennial-scale changes in methane levels identified in our record as being associated with Antarctic isotope maxima events are indicative of ubiquitous millennial-scale temperature variability during the past eight glacial cycles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loulergue, Laetitia -- Schilt, Adrian -- Spahni, Renato -- Masson-Delmotte, Valerie -- Blunier, Thomas -- Lemieux, Benedicte -- Barnola, Jean-Marc -- Raynaud, Dominique -- Stocker, Thomas F -- Chappellaz, Jerome -- England -- Nature. 2008 May 15;453(7193):383-6. doi: 10.1038/nature06950.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Glaciologie et Geophysique de l'Environnement, CNRS-Universite Joseph Fourier Grenoble, 54 Rue Moliere, 38402 St Martin d'Heres, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480822" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; Greenhouse Effect ; History, Ancient ; Ice Cover ; Methane/*analysis ; Temperature ; Time Factors ; Tropical Climate ; Wetlands
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Microbiology: metagenomics (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hugenholtz, Philip -- Tyson, Gene W -- England -- Nature. 2008 Sep 25;455(7212):481-3. doi: 10.1038/455481a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818648" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; Computational Biology/trends ; *Ecosystem ; *Environmental Microbiology ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; *Genetics, Microbial/methods ; Genome/genetics ; *Genomics/economics/methods/trends ; Humans ; Marine Biology ; Prokaryotic Cells/metabolism ; Sequence Analysis, DNA/economics ; Time Factors ; Viruses/genetics
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Loss of plant species after chronic low-level nitrogen deposition to prairie grasslands (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-02-08
    Description: Rates of atmospheric deposition of biologically active nitrogen (N) are two to seven times the pre-industrial rates in many developed nations because of combustion of fossil fuels and agricultural fertilization. They are expected to increase similarly over the next 50 years in industrializing nations of Asia and South America. Although the environmental impacts of high rates of nitrogen addition have been well studied, this is not so for the lower, chronic rates that characterize much of the globe. Here we present results of the first multi-decadal experiment to examine the impacts of chronic, experimental nitrogen addition as low as 10 kg N ha(-1) yr(-1) above ambient atmospheric nitrogen deposition (6 kg N ha(-1) yr(-1) at our site). This total input rate is comparable to terrestrial nitrogen deposition in many industrialized nations. We found that this chronic low-level nitrogen addition rate reduced plant species numbers by 17% relative to controls receiving ambient N deposition. Moreover, species numbers were reduced more per unit of added nitrogen at lower addition rates, suggesting that chronic but low-level nitrogen deposition may have a greater impact on diversity than previously thought. A second experiment showed that a decade after cessation of nitrogen addition, relative plant species number, although not species abundances, had recovered, demonstrating that some effects of nitrogen addition are reversible.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clark, Christopher M -- Tilman, David -- England -- Nature. 2008 Feb 7;451(7179):712-5. doi: 10.1038/nature06503.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Evolution and Behavior, 100 Ecology, 1987 Upper Buford Circle, University of Minnesota, St. Paul, Minnesota 55108, USA. clark134@umn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256670" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Biomass ; *Ecosystem ; Nitrogen/*metabolism ; Plants/classification/*metabolism ; *Poaceae/metabolism ; Random Allocation ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Palaeotemperature trend for Precambrian life inferred from resurrected proteins (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-02-08
    Description: Biosignatures and structures in the geological record indicate that microbial life has inhabited Earth for the past 3.5 billion years or so. Research in the physical sciences has been able to generate statements about the ancient environment that hosted this life. These include the chemical compositions and temperatures of the early ocean and atmosphere. Only recently have the natural sciences been able to provide experimental results describing the environments of ancient life. Our previous work with resurrected proteins indicated that ancient life lived in a hot environment. Here we expand the timescale of resurrected proteins to provide a palaeotemperature trend of the environments that hosted life from 3.5 to 0.5 billion years ago. The thermostability of more than 25 phylogenetically dispersed ancestral elongation factors suggest that the environment supporting ancient life cooled progressively by 30 degrees C during that period. Here we show that our results are robust to potential statistical bias associated with the posterior distribution of inferred character states, phylogenetic ambiguity, and uncertainties in the amino-acid equilibrium frequencies used by evolutionary models. Our results are further supported by a nearly identical cooling trend for the ancient ocean as inferred from the deposition of oxygen isotopes. The convergence of results from natural and physical sciences suggest that ancient life has continually adapted to changes in environmental temperatures throughout its evolutionary history.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gaucher, Eric A -- Govindarajan, Sridhar -- Ganesh, Omjoy K -- England -- Nature. 2008 Feb 7;451(7179):704-7. doi: 10.1038/nature06510.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256669" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Bacteria/classification/*metabolism ; Bacterial Proteins/analysis/*chemistry ; *Biological Evolution ; Enzyme Stability ; History, Ancient ; Hot Temperature ; Peptide Elongation Factor Tu/analysis/chemistry ; Phylogeny ; Seawater/*microbiology ; *Temperature ; Time Factors ; Uncertainty
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  • 7
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    Complex speciation of humans and chimpanzees (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-14
    Description: Genetic data from two or more species provide information about the process of speciation. In their analysis of DNA from humans, chimpanzees, gorillas, orangutans and macaques (HCGOM), Patterson et al. suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and--even if the null model could be rejected--they do not consider other explanations of a short divergence time on the X chromosome. These include natural selection on the X chromosome in the common ancestor of humans and chimpanzees, changes in the ratio of male-to-female mutation rates over time, and less extreme versions of divergence with gene flow (see ref. 2, for example). I therefore believe that their claim of hybridization is unwarranted.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wakeley, John -- England -- Nature. 2008 Mar 13;452(7184):E3-4; discussion E4. doi: 10.1038/nature06805.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. wakeley@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337768" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromosomes, Mammalian/genetics ; Female ; *Genetic Speciation ; Humans ; Male ; *Models, Genetic ; Mutagenesis/genetics ; Pan troglodytes/*genetics ; Phylogeny ; Reproducibility of Results ; Selection, Genetic ; Sex Characteristics ; Time Factors ; X Chromosome/genetics
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  • 8
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    Late Pliocene Greenland glaciation controlled by a decline in atmospheric CO2 levels (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-30
    Description: It is thought that the Northern Hemisphere experienced only ephemeral glaciations from the Late Eocene to the Early Pliocene epochs (about 38 to 4 million years ago), and that the onset of extensive glaciations did not occur until about 3 million years ago. Several hypotheses have been proposed to explain this increase in Northern Hemisphere glaciation during the Late Pliocene. Here we use a fully coupled atmosphere-ocean general circulation model and an ice-sheet model to assess the impact of the proposed driving mechanisms for glaciation and the influence of orbital variations on the development of the Greenland ice sheet in particular. We find that Greenland glaciation is mainly controlled by a decrease in atmospheric carbon dioxide during the Late Pliocene. By contrast, our model results suggest that climatic shifts associated with the tectonically driven closure of the Panama seaway, with the termination of a permanent El Nino state or with tectonic uplift are not large enough to contribute significantly to the growth of the Greenland ice sheet; moreover, we find that none of these processes acted as a priming mechanism for glacial inception triggered by variations in the Earth's orbit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lunt, Daniel J -- Foster, Gavin L -- Haywood, Alan M -- Stone, Emma J -- England -- Nature. 2008 Aug 28;454(7208):1102-5. doi: 10.1038/nature07223.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BRIDGE, School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK. d.j.lunt@bristol.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18756254" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; Carbon Dioxide/analysis/*metabolism ; Climate ; Greenland ; History, Ancient ; *Ice Cover ; North America ; Rain ; Time Factors
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  • 9
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    Temporal identity in axonal target layer recognition (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-11-04
    Description: The segregation of axon and dendrite projections into distinct synaptic layers is a fundamental principle of nervous system organization and the structural basis for information processing in the brain. Layer-specific recognition molecules that allow projecting neurons to stabilize transient contacts and initiate synaptogenesis have been identified. However, most of the neuronal cell-surface molecules critical for layer organization are expressed broadly in the developing nervous system, raising the question of how these so-called permissive adhesion molecules support synaptic specificity. Here we show that the temporal expression dynamics of the zinc-finger protein sequoia is the major determinant of Drosophila photoreceptor connectivity into distinct synaptic layers. Neighbouring R8 and R7 photoreceptors show consecutive peaks of elevated sequoia expression, which correspond to their sequential target-layer innervation. Loss of sequoia in R7 leads to a projection switch into the R8 recipient layer, whereas a prolonged expression in R8 induces a redirection of their axons into the R7 layer. The sequoia-induced axon targeting is mediated through the ubiquitously expressed Cadherin-N cell adhesion molecule. Our data support a model in which recognition specificity during synaptic layer formation is generated through a temporally restricted axonal competence to respond to broadly expressed adhesion molecules. Because developing neurons innervating the same target area often project in a distinct, birth-order-dependent sequence, temporal identity seems to contain crucial information in generating not only cell type diversity during neuronal division but also connection diversity of projecting neurons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petrovic, Milan -- Hummel, Thomas -- England -- Nature. 2008 Dec 11;456(7223):800-3. doi: 10.1038/nature07407. Epub 2008 Nov 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Neurobiologie, Universitat Munster, Badestrasse 9, D-48149 Munster, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18978776" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/metabolism/physiology ; Cadherins/metabolism ; Compound Eye, Arthropod/growth & development ; DNA-Binding Proteins/genetics/metabolism ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/genetics/*growth & development/*metabolism ; Gene Expression Regulation, Developmental ; Nerve Tissue Proteins/genetics/metabolism ; Photoreceptor Cells, Invertebrate/metabolism/physiology ; Protein Transport ; Time Factors
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  • 10
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    The coming acceleration of global population ageing (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-01-22
    Description: The future paths of population ageing result from specific combinations of declining fertility and increasing life expectancies in different parts of the world. Here we measure the speed of population ageing by using conventional measures and new ones that take changes in longevity into account for the world as a whole and for 13 major regions. We report on future levels of indicators of ageing and the speed at which they change. We show how these depend on whether changes in life expectancy are taken into account. We also show that the speed of ageing is likely to increase over the coming decades and to decelerate in most regions by mid-century. All our measures indicate a continuous ageing of the world's population throughout the century. The median age of the world's population increases from 26.6 years in 2000 to 37.3 years in 2050 and then to 45.6 years in 2100, when it is not adjusted for longevity increase. When increases in life expectancy are taken into account, the adjusted median age rises from 26.6 in 2000 to 31.1 in 2050 and only to 32.9 in 2100, slightly less than what it was in the China region in 2005. There are large differences in the regional patterns of ageing. In North America, the median age adjusted for life expectancy change falls throughout almost the entire century, whereas the conventional median age increases significantly. Our assessment of trends in ageing is based on new probabilistic population forecasts. The probability that growth in the world's population will end during this century is 88%, somewhat higher than previously assessed. After mid-century, lower rates of population growth are likely to coincide with slower rates of ageing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lutz, Wolfgang -- Sanderson, Warren -- Scherbov, Sergei -- England -- Nature. 2008 Feb 7;451(7179):716-9. doi: 10.1038/nature06516. Epub 2008 Jan 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉World Population Program, International Institute for Applied Systems Analysis, Schlossplatz 1, A-2361 Laxenburg, Austria. lutz@iiasa.ac.at〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18204438" target="_blank"〉PubMed〈/a〉
    Keywords: Age Distribution ; Aged ; Aged, 80 and over ; Aging/physiology ; Emigration and Immigration ; *Geography ; Humans ; *Internationality ; Life Expectancy/ethnology/*trends ; Longevity ; Middle Aged ; Mortality/trends ; Population Density ; Time Factors
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  • 11
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    Formation of accumbens GluR2-lacking AMPA receptors mediates incubation of cocaine craving (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-27
    Description: Relapse to cocaine use after prolonged abstinence is an important clinical problem. This relapse is often induced by exposure to cues associated with cocaine use. To account for the persistent propensity for relapse, it has been suggested that cue-induced cocaine craving increases over the first several weeks of abstinence and remains high for extended periods. We and others identified an analogous phenomenon in rats that was termed 'incubation of cocaine craving': time-dependent increases in cue-induced cocaine-seeking over the first months after withdrawal from self-administered cocaine. Cocaine-seeking requires the activation of glutamate projections that excite receptors for alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) in the nucleus accumbens. Here we show that the number of synaptic AMPA receptors in the accumbens is increased after prolonged withdrawal from cocaine self-administration by the addition of new AMPA receptors lacking glutamate receptor 2 (GluR2). Furthermore, we show that these new receptors mediate the incubation of cocaine craving. Our results indicate that GluR2-lacking AMPA receptors could be a new target for drug development for the treatment of cocaine addiction. We propose that after prolonged withdrawal from cocaine, increased numbers of synaptic AMPA receptors combined with the higher conductance of GluR2-lacking AMPA receptors causes increased reactivity of accumbens neurons to cocaine-related cues, leading to an intensification of drug craving and relapse.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574981/" 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/PMC2574981/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conrad, Kelly L -- Tseng, Kuei Y -- Uejima, Jamie L -- Reimers, Jeremy M -- Heng, Li-Jun -- Shaham, Yavin -- Marinelli, Michela -- Wolf, Marina E -- DA00453/DA/NIDA NIH HHS/ -- DA015835/DA/NIDA NIH HHS/ -- DA020654/DA/NIDA NIH HHS/ -- DA09621/DA/NIDA NIH HHS/ -- Z01 DA000434-08/Intramural NIH HHS/ -- England -- Nature. 2008 Jul 3;454(7200):118-21. doi: 10.1038/nature06995. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, Illinois 60064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500330" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cocaine ; Cocaine-Related Disorders/genetics/metabolism/*physiopathology ; Cues ; Gene Expression Regulation ; Male ; Nucleus Accumbens/*metabolism/physiopathology ; Rats ; Rats, Long-Evans ; Rats, Sprague-Dawley ; Receptors, AMPA/deficiency/genetics/*metabolism ; Self Administration ; Time Factors
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    Big data: How do your data grow? (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lynch, Clifford -- England -- Nature. 2008 Sep 4;455(7209):28-9. doi: 10.1038/455028a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Coalition for Networked Information, 21 Dupont Circle, Washington DC 20036, USA. cliff@cni.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18769419" target="_blank"〉PubMed〈/a〉
    Keywords: Archives ; Databases, Factual/economics/standards ; Humans ; Information Management/economics/*methods/organization & ; administration/*standards ; Information Storage and Retrieval/economics/methods/standards ; Research/economics/organization & administration/standards ; *Research Design ; Time Factors
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    Spatio-temporal correlations and visual signalling in a complete neuronal population (2008)
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    Publication Date: 2008-07-25
    Description: Statistical dependencies in the responses of sensory neurons govern both the amount of stimulus information conveyed and the means by which downstream neurons can extract it. Although a variety of measurements indicate the existence of such dependencies, their origin and importance for neural coding are poorly understood. Here we analyse the functional significance of correlated firing in a complete population of macaque parasol retinal ganglion cells using a model of multi-neuron spike responses. The model, with parameters fit directly to physiological data, simultaneously captures both the stimulus dependence and detailed spatio-temporal correlations in population responses, and provides two insights into the structure of the neural code. First, neural encoding at the population level is less noisy than one would expect from the variability of individual neurons: spike times are more precise, and can be predicted more accurately when the spiking of neighbouring neurons is taken into account. Second, correlations provide additional sensory information: optimal, model-based decoding that exploits the response correlation structure extracts 20% more information about the visual scene than decoding under the assumption of independence, and preserves 40% more visual information than optimal linear decoding. This model-based approach reveals the role of correlated activity in the retinal coding of visual stimuli, and provides a general framework for understanding the importance of correlated activity in populations of neurons.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684455/" 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/PMC2684455/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pillow, Jonathan W -- Shlens, Jonathon -- Paninski, Liam -- Sher, Alexander -- Litke, Alan M -- Chichilnisky, E J -- Simoncelli, Eero P -- EY018003/EY/NEI NIH HHS/ -- R01 EY018003/EY/NEI NIH HHS/ -- R01 EY018003-01/EY/NEI NIH HHS/ -- R01 EY018003-02/EY/NEI NIH HHS/ -- R01 EY018003-03/EY/NEI NIH HHS/ -- England -- Nature. 2008 Aug 21;454(7207):995-9. doi: 10.1038/nature07140. Epub 2008 Jul 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gatsby Computational Neuroscience Unit, UCL, 17 Queen Square, London WC1N 3AR, UK. pillow@gatsby.ucl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18650810" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Macaca mulatta/*physiology ; *Models, Neurological ; Photic Stimulation ; Retinal Ganglion Cells/*physiology ; Time Factors ; Vision, Ocular/*physiology
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    Old-growth forests as global carbon sinks (2008)
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    Publication Date: 2008-09-12
    Description: Old-growth forests remove carbon dioxide from the atmosphere at rates that vary with climate and nitrogen deposition. The sequestered carbon dioxide is stored in live woody tissues and slowly decomposing organic matter in litter and soil. Old-growth forests therefore serve as a global carbon dioxide sink, but they are not protected by international treaties, because it is generally thought that ageing forests cease to accumulate carbon. Here we report a search of literature and databases for forest carbon-flux estimates. We find that in forests between 15 and 800 years of age, net ecosystem productivity (the net carbon balance of the forest including soils) is usually positive. Our results demonstrate that old-growth forests can continue to accumulate carbon, contrary to the long-standing view that they are carbon neutral. Over 30 per cent of the global forest area is unmanaged primary forest, and this area contains the remaining old-growth forests. Half of the primary forests (6 x 10(8) hectares) are located in the boreal and temperate regions of the Northern Hemisphere. On the basis of our analysis, these forests alone sequester about 1.3 +/- 0.5 gigatonnes of carbon per year. Thus, our findings suggest that 15 per cent of the global forest area, which is currently not considered when offsetting increasing atmospheric carbon dioxide concentrations, provides at least 10 per cent of the global net ecosystem productivity. Old-growth forests accumulate carbon for centuries and contain large quantities of it. We expect, however, that much of this carbon, even soil carbon, will move back to the atmosphere if these forests are disturbed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luyssaert, Sebastiaan -- Schulze, E-Detlef -- Borner, Annett -- Knohl, Alexander -- Hessenmoller, Dominik -- Law, Beverly E -- Ciais, Philippe -- Grace, John -- England -- Nature. 2008 Sep 11;455(7210):213-5. doi: 10.1038/nature07276.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium. sebastiaan.luyssaert@ua.ac.be〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18784722" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atmosphere/chemistry ; Biomass ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Databases, Factual ; Disasters ; *Ecosystem ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Human Activities ; Time Factors ; Trees/*metabolism
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    Open debate could slow flu vaccine production (2008)
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    Publication Date: 2008-08-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Inglis, Stephen -- Wood, John -- Minor, Philip -- England -- Nature. 2008 Aug 21;454(7207):939. doi: 10.1038/454939c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719565" target="_blank"〉PubMed〈/a〉
    Keywords: Drug Industry/organization & administration/standards ; Humans ; Influenza Vaccines/classification/standards/*supply & distribution ; Orthomyxoviridae/physiology ; Orthomyxoviridae Infections/prevention & control ; Time Factors ; Virus Cultivation ; World Health Organization
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    Beyond the notes (2008)
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    Publication Date: 2008-06-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cook, Nicholas -- England -- Nature. 2008 Jun 26;453(7199):1186-7. doi: 10.1038/4531186a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉AHRC Research Centre for the History and Analysis of Recorded Music, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18580933" target="_blank"〉PubMed〈/a〉
    Keywords: Acoustic Stimulation ; Humans ; Music/*psychology ; Time Factors
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    Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery (2008)
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    Publication Date: 2008-07-11
    Description: Polo-like kinase-1 (PLK1) is an essential mitotic kinase regulating multiple aspects of the cell division process. Activation of PLK1 requires phosphorylation of a conserved threonine residue (Thr 210) in the T-loop of the PLK1 kinase domain, but the kinase responsible for this has not yet been affirmatively identified. Here we show that in human cells PLK1 activation occurs several hours before entry into mitosis, and requires aurora A (AURKA, also known as STK6)-dependent phosphorylation of Thr 210. We find that aurora A can directly phosphorylate PLK1 on Thr 210, and that activity of aurora A towards PLK1 is greatly enhanced by Bora (also known as C13orf34 and FLJ22624), a known cofactor for aurora A (ref. 7). We show that Bora/aurora-A-dependent phosphorylation is a prerequisite for PLK1 to promote mitotic entry after a checkpoint-dependent arrest. Importantly, expression of a PLK1-T210D phospho-mimicking mutant partially overcomes the requirement for aurora A in checkpoint recovery. Taken together, these data demonstrate that the initial activation of PLK1 is a primary function of aurora A.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macurek, Libor -- Lindqvist, Arne -- Lim, Dan -- Lampson, Michael A -- Klompmaker, Rob -- Freire, Raimundo -- Clouin, Christophe -- Taylor, Stephen S -- Yaffe, Michael B -- Medema, Rene H -- CA112967/CA/NCI NIH HHS/ -- GM-60594/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Sep 4;455(7209):119-23. doi: 10.1038/nature07185. Epub 2008 Jul 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Oncology, University Medical Center Utrecht, Utrecht 3584CG, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18615013" target="_blank"〉PubMed〈/a〉
    Keywords: Aurora Kinase A ; Aurora Kinases ; Cell Cycle/*physiology ; Cell Cycle Proteins/genetics/*metabolism ; Cell Line ; DNA Damage ; Enzyme Activation ; Humans ; Mitosis ; Molecular Sequence Data ; Phosphorylation ; Phosphothreonine/metabolism ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Proto-Oncogene Proteins/genetics/*metabolism ; Time Factors
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    Costa Rica's biotech project still on track for end of year (2008)
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    Publication Date: 2008-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corrales, Antonieta -- England -- Nature. 2008 May 29;453(7195):586. doi: 10.1038/453586b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18509417" target="_blank"〉PubMed〈/a〉
    Keywords: Biotechnology/economics/organization & administration/standards/*trends ; Costa Rica ; European Union/economics ; Time Factors
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    Replication fork movement sets chromatin loop size and origin choice in mammalian cells (2008)
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    Publication Date: 2008-08-22
    Description: Genome stability requires one, and only one, DNA duplication at each S phase. The mechanisms preventing origin firing on newly replicated DNA are well documented, but much less is known about the mechanisms controlling the spacing of initiation events(2,3), namely the completion of DNA replication. Here we show that origin use in Chinese hamster cells depends on both the movement of the replication forks and the organization of chromatin loops. We found that slowing the replication speed triggers the recruitment of latent origins within minutes, allowing the completion of S phase in a timely fashion. When slowly replicating cells are shifted to conditions of fast fork progression, although the decrease in the overall number of active origins occurs within 2 h, the cells still have to go through a complete cell cycle before the efficiency specific to each origin is restored. We observed a strict correlation between replication speed during a given S phase and the size of chromatin loops in the next G1 phase. Furthermore, we found that origins located at or near sites of anchorage of chromatin loops in G1 are activated preferentially in the following S phase. These data suggest a mechanism of origin programming in which replication speed determines the spacing of anchorage regions of chromatin loops, that, in turn, controls the choice of initiation sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Courbet, Sylvain -- Gay, Sophie -- Arnoult, Nausica -- Wronka, Gerd -- Anglana, Mauro -- Brison, Olivier -- Debatisse, Michelle -- England -- Nature. 2008 Sep 25;455(7212):557-60. doi: 10.1038/nature07233. Epub 2008 Aug 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Curie, 26 rue d'Ulm, 75248 Paris, France; UPMC Univ. Paris 06, F-75005 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18716622" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Chromatin/genetics/*metabolism ; Cricetinae ; Cricetulus ; DNA/biosynthesis/genetics ; DNA Replication/*physiology ; G1 Phase ; *Movement ; Nuclear Matrix/metabolism ; Replication Origin/*genetics ; S Phase ; Time Factors
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    Polar bear numbers set to fall (2008)
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    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Courtland, Rachel -- England -- Nature. 2008 May 22;453(7194):432-3. doi: 10.1038/453432a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497777" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arctic Regions ; Conservation of Natural Resources/*legislation & jurisprudence/trends ; *Greenhouse Effect ; *Ice Cover ; Internationality ; Population Density ; Time Factors ; United States ; Ursidae/*physiology
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    Neuroscience: Cool songs (2008)
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    Publication Date: 2008-11-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Glaze, Chris M -- Troyer, Todd -- England -- Nature. 2008 Nov 13;456(7219):187-8. doi: 10.1038/456187a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19005545" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cold Temperature ; Finches/*physiology ; High Vocal Center/physiology ; Time Factors ; Vocalization, Animal/*physiology
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    Chaos in a long-term experiment with a plankton community (2008)
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    Publication Date: 2008-02-15
    Description: Mathematical models predict that species interactions such as competition and predation can generate chaos. However, experimental demonstrations of chaos in ecology are scarce, and have been limited to simple laboratory systems with a short duration and artificial species combinations. Here, we present the first experimental demonstration of chaos in a long-term experiment with a complex food web. Our food web was isolated from the Baltic Sea, and consisted of bacteria, several phytoplankton species, herbivorous and predatory zooplankton species, and detritivores. The food web was cultured in a laboratory mesocosm, and sampled twice a week for more than 2,300 days. Despite constant external conditions, the species abundances showed striking fluctuations over several orders of magnitude. These fluctuations displayed a variety of different periodicities, which could be attributed to different species interactions in the food web. The population dynamics were characterized by positive Lyapunov exponents of similar magnitude for each species. Predictability was limited to a time horizon of 15-30 days, only slightly longer than the local weather forecast. Hence, our results demonstrate that species interactions in food webs can generate chaos. This implies that stability is not required for the persistence of complex food webs, and that the long-term prediction of species abundances can be fundamentally impossible.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beninca, Elisa -- Huisman, Jef -- Heerkloss, Reinhard -- Johnk, Klaus D -- Branco, Pedro -- Van Nes, Egbert H -- Scheffer, Marten -- Ellner, Stephen P -- England -- Nature. 2008 Feb 14;451(7180):822-5. doi: 10.1038/nature06512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Nieuwe Achtergracht 127, 1018 WS Amsterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18273017" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/metabolism ; *Food Chain ; Models, Biological ; *Nonlinear Dynamics ; Oceans and Seas ; Plankton/*metabolism ; Population Dynamics ; Species Specificity ; Time Factors
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    New York to police air monitoring (2008)
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    Publication Date: 2008-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Courtland, Rachel -- England -- Nature. 2008 Jan 31;451(7178):508. doi: 10.1038/451508a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235463" target="_blank"〉PubMed〈/a〉
    Keywords: Environmental Monitoring/instrumentation/*legislation & jurisprudence ; *Law Enforcement ; New York City ; Police/*legislation & jurisprudence ; Security Measures/legislation & jurisprudence ; Terrorism/prevention & control ; Time Factors ; United States ; United States Department of Homeland Security/legislation & jurisprudence
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    Transient FTY720 treatment promotes immune-mediated clearance of a chronic viral infection (2008)
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    Publication Date: 2008-08-16
    Description: For a wide variety of microbial pathogens, the outcome of the infection is indeterminate. In some individuals the microbe is cleared, but in others it establishes a chronic infection, and the factors that tip this balance are often unknown. In a widely used model of chronic viral infection, C57BL/6 mice clear the Armstrong strain of lymphocytic choriomeningitis virus (LCMV), but the clone 13 strain persists. Here we show that the Armstrong strain induces a profound lymphopenia at days 1-3 after infection, but the clone 13 strain does not. If we transiently augment lymphopenia by treating the clone-13-infected mice with the drug FTY720 at days 0-2 after infection, the mice successfully clear the infection by day 30. Clearance does not occur when CD4 T cells are absent at the time of treatment, indicating that the drug is not exerting direct antiviral effects. Notably, FTY720 treatment of an already established persistent infection also leads to viral clearance. In both models, FTY720 treatment preserves or augments LCMV-specific CD4 and CD8 T-cell responses, a result that is counter-intuitive because FTY720 is generally regarded as a new immunosuppressive agent. Because FTY720 targets host pathways that are completely evolutionarily conserved, our results may be translatable into new immunotherapies for the treatment of chronic microbial infections in humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Premenko-Lanier, Mary -- Moseley, Nelson B -- Pruett, Sarah T -- Romagnoli, Pablo A -- Altman, John D -- 5F32AI062002/AI/NIAID NIH HHS/ -- AI042373/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Aug 14;454(7206):894-8. doi: 10.1038/nature07199.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Emory Vaccine Center and Department of Microbiology and Immunology, Yerkes National Primate Research Center and Emory University School of Medicine, 954 Gatewood Road, Atlanta, Georgia 30329, USA. mflanie@emory.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18704087" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chronic Disease ; Fingolimod Hydrochloride ; Lymphocytic Choriomeningitis/complications/*drug therapy/*immunology/prevention & ; control ; Lymphocytic choriomeningitis virus/*immunology/physiology ; Lymphopenia/etiology ; Mice ; Mice, Inbred C57BL ; Propylene Glycols/administration & dosage/*pharmacology/*therapeutic use ; Sphingosine/administration & dosage/*analogs & ; derivatives/pharmacology/therapeutic use ; T-Lymphocytes/drug effects/immunology ; Time Factors
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    Template-directed synthesis of a genetic polymer in a model protocell (2008)
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    Publication Date: 2008-06-06
    Description: Contemporary phospholipid-based cell membranes are formidable barriers to the uptake of polar and charged molecules ranging from metal ions to complex nutrients. Modern cells therefore require sophisticated protein channels and pumps to mediate the exchange of molecules with their environment. The strong barrier function of membranes has made it difficult to understand the origin of cellular life and has been thought to preclude a heterotrophic lifestyle for primitive cells. Although nucleotides can cross dimyristoyl phosphatidylcholine membranes through defects formed at the gel-to-liquid transition temperature, phospholipid membranes lack the dynamic properties required for membrane growth. Fatty acids and their corresponding alcohols and glycerol monoesters are attractive candidates for the components of protocell membranes because they are simple amphiphiles that form bilayer membrane vesicles that retain encapsulated oligonucleotides and are capable of growth and division. Here we show that such membranes allow the passage of charged molecules such as nucleotides, so that activated nucleotides added to the outside of a model protocell spontaneously cross the membrane and take part in efficient template copying in the protocell interior. The permeability properties of prebiotically plausible membranes suggest that primitive protocells could have acquired complex nutrients from their environment in the absence of any macromolecular transport machinery; that is, they could have been obligate heterotrophs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743009/" 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/PMC2743009/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mansy, Sheref S -- Schrum, Jason P -- Krishnamurthy, Mathangi -- Tobe, Sylvia -- Treco, Douglas A -- Szostak, Jack W -- F32 GM074506-01/GM/NIGMS NIH HHS/ -- F32 GM07450601/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Jul 3;454(7200):122-5. doi: 10.1038/nature07018. Epub 2008 Jun 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Biology and the Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528332" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Cell Membrane/chemistry/*metabolism ; Cell Membrane Permeability/physiology ; *Cell Physiological Phenomena ; Fatty Acids/metabolism ; Heterotrophic Processes ; *Models, Biological ; Nucleotides/metabolism ; Oligonucleotides/*metabolism ; Ribose/metabolism ; Templates, Genetic ; Time Factors
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    Financial planning (2008)
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    Publication Date: 2008-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldston, David -- England -- Nature. 2008 Aug 7;454(7205):680. doi: 10.1038/454680a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉House Committee on Science. partyofonecolumn@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18685673" target="_blank"〉PubMed〈/a〉
    Keywords: Budgets/*legislation & jurisprudence/*trends ; *Federal Government ; *Politics ; Research Support as Topic/economics/*legislation & jurisprudence ; Science/*economics/legislation & jurisprudence ; Time Factors ; United States
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    Evolutionary biology: a first for bats (2008)
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    Details
    Publication Date: 2008-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Speakman, John -- England -- Nature. 2008 Feb 14;451(7180):774-5. doi: 10.1038/451774a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18270540" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Chiroptera/anatomy & histology/*physiology ; Cochlea/anatomy & histology/physiology ; Darkness ; Echolocation/*physiology ; Extremities/anatomy & histology/physiology ; Flight, Animal/*physiology ; Fossils ; Models, Biological ; Time Factors ; Wyoming
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Following translation by single ribosomes one codon at a time (2008)
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    Publication Date: 2008-03-11
    Description: We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation--and-pause cycles. The distribution of pause lengths, with a median of 2.8 s, indicates that at least two rate-determining processes control each pause. Each translocation step measures three bases--one codon-and occurs in less than 0.1 s. Analysis of the times required for translocation reveals, surprisingly, that there are three substeps in each step. Pause lengths, and thus the overall rate of translation, depend on the secondary structure of the mRNA; the applied force destabilizes secondary structure and decreases pause durations, but does not affect translocation times. Translocation and RNA unwinding are strictly coupled ribosomal functions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556548/" 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/PMC2556548/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wen, Jin-Der -- Lancaster, Laura -- Hodges, Courtney -- Zeri, Ana-Carolina -- Yoshimura, Shige H -- Noller, Harry F -- Bustamante, Carlos -- Tinoco, Ignacio -- R01 GM010840/GM/NIGMS NIH HHS/ -- R01 GM010840-49/GM/NIGMS NIH HHS/ -- R01 GM010840-50/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 3;452(7187):598-603. doi: 10.1038/nature06716. Epub 2008 Mar 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18327250" target="_blank"〉PubMed〈/a〉
    Keywords: Aminoacylation ; Base Pairing ; Codon/*genetics ; Kinetics ; *Optical Tweezers ; Protein Biosynthesis/*physiology ; RNA, Messenger/chemistry/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Ribosomes/*metabolism ; Time Factors
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    Innate immunity and intestinal microbiota in the development of Type 1 diabetes (2008)
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    Publication Date: 2008-09-23
    Description: Type 1 diabetes (T1D) is a debilitating autoimmune disease that results from T-cell-mediated destruction of insulin-producing beta-cells. Its incidence has increased during the past several decades in developed countries, suggesting that changes in the environment (including the human microbial environment) may influence disease pathogenesis. The incidence of spontaneous T1D in non-obese diabetic (NOD) mice can be affected by the microbial environment in the animal housing facility or by exposure to microbial stimuli, such as injection with mycobacteria or various microbial products. Here we show that specific pathogen-free NOD mice lacking MyD88 protein (an adaptor for multiple innate immune receptors that recognize microbial stimuli) do not develop T1D. The effect is dependent on commensal microbes because germ-free MyD88-negative NOD mice develop robust diabetes, whereas colonization of these germ-free MyD88-negative NOD mice with a defined microbial consortium (representing bacterial phyla normally present in human gut) attenuates T1D. We also find that MyD88 deficiency changes the composition of the distal gut microbiota, and that exposure to the microbiota of specific pathogen-free MyD88-negative NOD donors attenuates T1D in germ-free NOD recipients. Together, these findings indicate that interaction of the intestinal microbes with the innate immune system is a critical epigenetic factor modifying T1D predisposition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574766/" 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/PMC2574766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wen, Li -- Ley, Ruth E -- Volchkov, Pavel Yu -- Stranges, Peter B -- Avanesyan, Lia -- Stonebraker, Austin C -- Hu, Changyun -- Wong, F Susan -- Szot, Gregory L -- Bluestone, Jeffrey A -- Gordon, Jeffrey I -- Chervonsky, Alexander V -- DK063452/DK/NIDDK NIH HHS/ -- DK30292/DK/NIDDK NIH HHS/ -- DK42086/DK/NIDDK NIH HHS/ -- DK45735/DK/NIDDK NIH HHS/ -- DK70977/DK/NIDDK NIH HHS/ -- P30 DK042086/DK/NIDDK NIH HHS/ -- P30 DK042086-16/DK/NIDDK NIH HHS/ -- P30 DK045735/DK/NIDDK NIH HHS/ -- P30 DK045735-10/DK/NIDDK NIH HHS/ -- P30 DK045735-119006/DK/NIDDK NIH HHS/ -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-07/DK/NIDDK NIH HHS/ -- P30 DK056341-08/DK/NIDDK NIH HHS/ -- P30 DK063720/DK/NIDDK NIH HHS/ -- P30 DK063720-01/DK/NIDDK NIH HHS/ -- P30 DK63720/DK/NIDDK NIH HHS/ -- R01 DK030292/DK/NIDDK NIH HHS/ -- R01 DK030292-24/DK/NIDDK NIH HHS/ -- R01 DK070977/DK/NIDDK NIH HHS/ -- R01 DK070977-04/DK/NIDDK NIH HHS/ -- R21 DK063452/DK/NIDDK NIH HHS/ -- R21 DK063452-02/DK/NIDDK NIH HHS/ -- R37 AI046643/AI/NIAID NIH HHS/ -- R37 AI046643-10/AI/NIAID NIH HHS/ -- R37 AI46643/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Oct 23;455(7216):1109-13. doi: 10.1038/nature07336. Epub 2008 Sep 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Endocrinology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18806780" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/classification/genetics/*immunology/isolation & purification ; CD8-Positive T-Lymphocytes/immunology ; Diabetes Mellitus, Type 1/genetics/*immunology/*microbiology ; Female ; Immunity, Innate/genetics/*immunology ; Interferon-gamma/immunology ; Intestines/*microbiology ; Islets of Langerhans/pathology ; Male ; Mice ; Mice, Inbred NOD ; Mice, Knockout ; Mice, SCID ; Molecular Sequence Data ; Myeloid Differentiation Factor 88/genetics ; Phylogeny ; Specific Pathogen-Free Organisms ; Time Factors
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    Hazy reasoning behind clean air (2008)
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    Publication Date: 2008-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldston, David -- England -- Nature. 2008 Apr 3;452(7187):519. doi: 10.1038/452519a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard University's Center for the Environment. partyofonecolumn@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18385707" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/analysis/*legislation & jurisprudence/prevention & control ; *Federal Government ; Humans ; Ozone/analysis/toxicity ; Plants/drug effects ; Smog/analysis/prevention & control ; Time Factors ; Uncertainty ; United States ; United States Environmental Protection Agency/*legislation & jurisprudence
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    The amphioxus genome and the evolution of the chordate karyotype (2008)
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    Publication Date: 2008-06-20
    Description: Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Putnam, Nicholas H -- Butts, Thomas -- Ferrier, David E K -- Furlong, Rebecca F -- Hellsten, Uffe -- Kawashima, Takeshi -- Robinson-Rechavi, Marc -- Shoguchi, Eiichi -- Terry, Astrid -- Yu, Jr-Kai -- Benito-Gutierrez, E Lia -- Dubchak, Inna -- Garcia-Fernandez, Jordi -- Gibson-Brown, Jeremy J -- Grigoriev, Igor V -- Horton, Amy C -- de Jong, Pieter J -- Jurka, Jerzy -- Kapitonov, Vladimir V -- Kohara, Yuji -- Kuroki, Yoko -- Lindquist, Erika -- Lucas, Susan -- Osoegawa, Kazutoyo -- Pennacchio, Len A -- Salamov, Asaf A -- Satou, Yutaka -- Sauka-Spengler, Tatjana -- Schmutz, Jeremy -- Shin-I, Tadasu -- Toyoda, Atsushi -- Bronner-Fraser, Marianne -- Fujiyama, Asao -- Holland, Linda Z -- Holland, Peter W H -- Satoh, Nori -- Rokhsar, Daniel S -- BBS/B/12067/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/12067/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Jun 19;453(7198):1064-71. doi: 10.1038/nature06967.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563158" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chordata/classification/*genetics ; Conserved Sequence ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Duplication ; Genes/genetics ; Genetic Linkage ; Genome/*genetics ; Humans ; Introns/genetics ; Karyotyping ; Multigene Family ; Phylogeny ; Polymorphism, Genetic/genetics ; Proteins/genetics ; Synteny ; Time Factors ; Vertebrates/classification/genetics
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    Ecology: The heart of the wood (2008)
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    Publication Date: 2008-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marris, Emma -- England -- Nature. 2008 Sep 18;455(7211):277-80. doi: 10.1038/455277a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800107" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/methods ; *Ecosystem ; Human Activities ; Models, Biological ; Nature ; Poland ; Time Factors ; *Trees/physiology
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    Control of segment number in vertebrate embryos (2008)
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    Publication Date: 2008-06-20
    Description: The vertebrate body axis is subdivided into repeated segments, best exemplified by the vertebrae that derive from embryonic somites. The number of somites is precisely defined for any given species but varies widely from one species to another. To determine the mechanism controlling somite number, we have compared somitogenesis in zebrafish, chicken, mouse and corn snake embryos. Here we present evidence that in all of these species a similar 'clock-and-wavefront' mechanism operates to control somitogenesis; in all of them, somitogenesis is brought to an end through a process in which the presomitic mesoderm, having first increased in size, gradually shrinks until it is exhausted, terminating somite formation. In snake embryos, however, the segmentation clock rate is much faster relative to developmental rate than in other amniotes, leading to a greatly increased number of smaller-sized somites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gomez, Celine -- Ozbudak, Ertugrul M -- Wunderlich, Joshua -- Baumann, Diana -- Lewis, Julian -- Pourquie, Olivier -- Cancer Research UK/United Kingdom -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Jul 17;454(7202):335-9. doi: 10.1038/nature07020. Epub 2008 Jun 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563087" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Body Patterning/genetics ; Chick Embryo/*embryology ; Gene Expression Regulation, Developmental ; Mice/*embryology ; Molecular Sequence Data ; Snakes/*embryology ; Somites/*embryology ; Time Factors ; Zebrafish/*embryology
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    Slow shipping hobbles Chinese science (2008)
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    Publication Date: 2008-12-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2008 Dec 4;456(7222):550-1. doi: 10.1038/456550a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19052587" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; China ; Commerce/economics ; Indicators and Reagents/*supply & distribution ; Mice ; *Postal Service/economics ; Science/economics/*instrumentation ; Time Factors
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    Imaging the biogenesis of individual HIV-1 virions in live cells (2008)
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    Publication Date: 2008-05-27
    Description: Observations of individual virions in live cells have led to the characterization of their attachment, entry and intracellular transport. However, the assembly of individual virions has never been observed in real time. Insights into this process have come primarily from biochemical analyses of populations of virions or from microscopic studies of fixed infected cells. Thus, some assembly properties, such as kinetics and location, are either unknown or controversial. Here we describe quantitatively the genesis of individual virions in real time, from initiation of assembly to budding and release. We studied fluorescently tagged derivatives of Gag, the major structural component of HIV-1-which is sufficient to drive the assembly of virus-like particles-with the use of fluorescence resonance energy transfer, fluorescence recovery after photobleaching and total-internal-reflection fluorescent microscopy in living cells. Virions appeared individually at the plasma membrane, their assembly rate accelerated as Gag protein accumulated in cells, and typically 5-6 min was required to complete the assembly of a single virion. These approaches allow a previously unobserved view of the genesis of individual virions and the determination of parameters of viral assembly that are inaccessible with conventional techniques.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708942/" 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/PMC2708942/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jouvenet, Nolwenn -- Bieniasz, Paul D -- Simon, Sanford M -- P20 GM072015/GM/NIGMS NIH HHS/ -- P20 GM072015-01/GM/NIGMS NIH HHS/ -- P20 GM072015-02/GM/NIGMS NIH HHS/ -- P20 GM072015-02S1/GM/NIGMS NIH HHS/ -- P20 GM072015-03/GM/NIGMS NIH HHS/ -- P20 GM072015-04/GM/NIGMS NIH HHS/ -- P20 GM072015-04S1/GM/NIGMS NIH HHS/ -- R01 AI089844/AI/NIAID NIH HHS/ -- R01 GM087977/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jul 10;454(7201):236-40. doi: 10.1038/nature06998. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500329" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism ; Cell Survival ; Fluorescence Recovery After Photobleaching ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/*analysis ; HIV-1/genetics/*growth & development/metabolism ; HeLa Cells ; Humans ; Kinetics ; Microscopy, Fluorescence ; Time Factors ; Virion/*growth & development/metabolism ; *Virus Replication ; gag Gene Products, Human Immunodeficiency Virus/genetics/metabolism
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    Japan fast-tracks stem-cell patent (2008)
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    Publication Date: 2008-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2008 Sep 18;455(7211):269. doi: 10.1038/455269b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800093" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/physiology ; Animals ; Humans ; Internationality ; Japan ; Mice ; Patents as Topic/*legislation & jurisprudence ; *Pluripotent Stem Cells/cytology ; Time Factors ; United States ; Universities
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    Ancient asexuals: darwinulids not exposed (2008)
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    Publication Date: 2008-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martens, Koen -- Schon, Isa -- England -- Nature. 2008 May 29;453(7195):587. doi: 10.1038/453587b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18509420" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crustacea/anatomy & histology/*physiology ; Female ; History, 19th Century ; History, Ancient ; Male ; Reproduction, Asexual/*physiology ; Rotifera/*physiology ; Time Factors
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    Neuropathology: Alzheimer's in real time (2008)
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    Publication Date: 2008-02-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Masliah, Eliezer -- England -- Nature. 2008 Feb 7;451(7179):638-9. doi: 10.1038/451638a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256653" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/*metabolism/*pathology ; Amyloid beta-Peptides/*metabolism/toxicity ; Animals ; Axons/metabolism ; Dendrites/metabolism ; Disease Models, Animal ; Disease Progression ; Humans ; Mice ; Microglia/metabolism ; Plaque, Amyloid/*metabolism/*pathology ; Time Factors
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    Transient cyclical methylation of promoter DNA (2008)
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    Publication Date: 2008-03-07
    Description: Methylation of CpG dinucleotides is generally associated with epigenetic silencing of transcription and is maintained through cellular division. Multiple CpG sequences are rare in mammalian genomes, but frequently occur at the transcriptional start site of active genes, with most clusters of CpGs being hypomethylated. We reported previously that the proximal region of the trefoil factor 1 (TFF1, also known as pS2) and oestrogen receptor alpha (ERalpha) promoters could be partially methylated by treatment with deacetylase inhibitors, suggesting the possibility of dynamic changes in DNA methylation. Here we show that cyclical methylation and demethylation of CpG dinucleotides, with a periodicity of around 100 min, is characteristic for five selected promoters, including the oestrogen (E2)-responsive pS2 gene, in human cells. When the pS2 gene is actively transcribed, DNA methylation occurs after the cyclical occupancy of ERalpha and RNA polymerase II (polII). Moreover, we report conditions that provoke methylation cycling of the pS2 promoter in cell lines in which pS2 expression is quiescent and the proximal promoter is methylated. This coincides with a low-level re-expression of ERalpha and of pS2 transcripts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kangaspeska, Sara -- Stride, Brenda -- Metivier, Raphael -- Polycarpou-Schwarz, Maria -- Ibberson, David -- Carmouche, Richard Paul -- Benes, Vladimir -- Gannon, Frank -- Reid, George -- England -- Nature. 2008 Mar 6;452(7183):112-5. doi: 10.1038/nature06640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322535" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; CpG Islands/genetics ; DNA/genetics/*metabolism ; *DNA Methylation/drug effects ; Doxorubicin/pharmacology ; Estrogen Receptor alpha/genetics/metabolism ; *Gene Expression Regulation/drug effects ; Humans ; Promoter Regions, Genetic/*genetics ; RNA Polymerase II/metabolism ; RNA, Messenger/genetics/metabolism ; Time Factors ; Transcription, Genetic/drug effects ; Tumor Suppressor Proteins/genetics
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    Love: you have 4 minutes to choose your perfect mate (2008)
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    Publication Date: 2008-02-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaplan, Matt -- England -- Nature. 2008 Feb 14;451(7180):760-2. doi: 10.1038/451760a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18272991" target="_blank"〉PubMed〈/a〉
    Keywords: Courtship/*psychology ; Decision Making ; Female ; Humans ; *Love ; Male ; Social Sciences/*methods ; Surveys and Questionnaires ; Time Factors
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    Stem-cell claim gets cold reception (2008)
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    Publication Date: 2008-03-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- Baker, Monya -- England -- Nature. 2008 Mar 13;452(7184):132. doi: 10.1038/452132a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337778" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Adult Stem Cells/*cytology ; Embryonic Stem Cells/*cytology ; Endocytosis ; Genetic Vectors ; Humans ; Male ; *Nanotubes, Carbon/adverse effects ; Peer Review, Research/standards ; Pluripotent Stem Cells/*cytology ; Reproducibility of Results ; Spermatozoa/cytology ; Time Factors ; Transfection/instrumentation/*methods ; Uncertainty
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    Coherent ecological dynamics induced by large-scale disturbance (2008)
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    Publication Date: 2008-07-18
    Description: Aggregate community-level response to disturbance is a principle concern in ecology because post-disturbance dynamics are integral to the ability of ecosystems to maintain function in an uncertain world. Community-level responses to disturbance can be arrayed along a spectrum ranging from synchronous oscillations where all species rise and fall together, to compensatory dynamics where total biomass remains relatively constant despite fluctuations in the densities of individual species. An important recent insight is that patterns of synchrony and compensation can vary with the timescale of analysis and that spectral time series methods can enable detection of coherent dynamics that would otherwise be obscured by opposing patterns occurring at different scales. Here I show that application of wavelet analysis to experimentally manipulated plankton communities reveals strong synchrony after disturbance. The result is paradoxical because it is well established that these communities contain both disturbance-sensitive and disturbance-tolerant species leading to compensation within functional groups. Theory predicts that compensatory substitution of functionally equivalent species should stabilize ecological communities, yet I found at the whole-community level a large increase in seasonal biomass variation. Resolution of the paradox hinges on patterns of seasonality among species. The compensatory shift in community composition after disturbance resulted in a loss of cold-season dominants, which before disturbance had served to stabilize biomass throughout the year. Species dominating the disturbed community peaked coherently during the warm season, explaining the observed synchrony and increase in seasonal biomass variation. These results suggest that theory relating compensatory dynamics to ecological stability needs to consider not only complementarity in species responses to environmental change, but also seasonal complementarity among disturbance-tolerant and disturbance-sensitive species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keitt, Timothy H -- England -- Nature. 2008 Jul 17;454(7202):331-4. doi: 10.1038/nature06935.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Integrative Biology, University of Texas, Austin, Texas 78712, USA. tkeitt@mail.utexas.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18633416" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomass ; Crustacea/physiology ; *Ecosystem ; Fresh Water ; Hot Temperature ; Hydrogen-Ion Concentration ; Plankton/*physiology ; Population Dynamics ; Seasons ; Time Factors
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    Guarding the gateway to cortex with attention in visual thalamus (2008)
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    Publication Date: 2008-10-14
    Description: The massive visual input from the eye to the brain requires selective processing of some visual information at the expense of other information, a process referred to as visual attention. Increases in the responses of visual neurons with attention have been extensively studied along the visual processing streams in monkey cerebral cortex, from primary visual areas to parietal and frontal cortex. Here we show, by recording neurons in attending macaque monkeys (Macaca mulatta), that attention modulates visual signals before they even reach cortex by increasing responses of both magnocellular and parvocellular neurons in the first relay between retina and cortex, the lateral geniculate nucleus (LGN). At the same time, attention decreases neuronal responses in the adjacent thalamic reticular nucleus (TRN). Crick argued for such modulation of the LGN by observing that it is inhibited by the TRN, and suggested that "if the thalamus is the gateway to the cortex, the reticular complex might be described as the guardian of the gateway", a reciprocal relationship we now show to be more than just hypothesis. The reciprocal modulation in LGN and TRN appears only during the initial visual response, but the modulation of LGN reappears later in the response, suggesting separate early and late sources of attentional modulation in LGN.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713033/" 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/PMC2713033/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McAlonan, Kerry -- Cavanaugh, James -- Wurtz, Robert H -- Z01 EY000109-27/Intramural NIH HHS/ -- England -- Nature. 2008 Nov 20;456(7220):391-4. doi: 10.1038/nature07382. Epub 2008 Oct 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. km@nei.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849967" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Attention/*physiology ; Cues ; Fixation, Ocular/physiology ; Macaca mulatta/*physiology ; Photic Stimulation ; Retina/physiology ; Thalamic Nuclei/cytology/*physiology ; Time Factors ; Visual Cortex/*physiology ; Visual Perception/*physiology
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    Mechanism of shape determination in motile cells (2008)
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    Publication Date: 2008-05-24
    Description: The shape of motile cells is determined by many dynamic processes spanning several orders of magnitude in space and time, from local polymerization of actin monomers at subsecond timescales to global, cell-scale geometry that may persist for hours. Understanding the mechanism of shape determination in cells has proved to be extremely challenging due to the numerous components involved and the complexity of their interactions. Here we harness the natural phenotypic variability in a large population of motile epithelial keratocytes from fish (Hypsophrys nicaraguensis) to reveal mechanisms of shape determination. We find that the cells inhabit a low-dimensional, highly correlated spectrum of possible functional states. We further show that a model of actin network treadmilling in an inextensible membrane bag can quantitatively recapitulate this spectrum and predict both cell shape and speed. Our model provides a simple biochemical and biophysical basis for the observed morphology and behaviour of motile cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877812/" 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/PMC2877812/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keren, Kinneret -- Pincus, Zachary -- Allen, Greg M -- Barnhart, Erin L -- Marriott, Gerard -- Mogilner, Alex -- Theriot, Julie A -- U54 GM064346/GM/NIGMS NIH HHS/ -- U54 GM064346-099040/GM/NIGMS NIH HHS/ -- U54 GM64346/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 May 22;453(7194):475-80. doi: 10.1038/nature06952.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Technion- Israel Institute of Technology, Haifa 32000, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497816" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/chemistry/metabolism ; Actins/chemistry/metabolism ; Animals ; Biophysical Phenomena ; Biophysics ; Cell Membrane/chemistry/metabolism ; Cell Movement/*physiology ; Cell Shape/*physiology ; Cells, Cultured ; *Cichlids ; Epithelial Cells/*cytology ; Models, Biological ; Pseudopodia/metabolism ; Time Factors
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    Unlocking the mysteries of the ice ages (2008)
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    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raymo, Maureen E -- Huybers, Peter -- England -- Nature. 2008 Jan 17;451(7176):284-5. doi: 10.1038/nature06589.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Boston University, 685 Commonwealth Avenue, Boston, Massachusetts 02215, USA. raymo@bu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202644" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate ; Fossils ; History, 19th Century ; History, 20th Century ; History, Ancient ; *Ice Cover ; *Models, Theoretical ; Solar Activity ; Time Factors
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    Anthropogenically enhanced fluxes of water and carbon from the Mississippi River (2008)
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    Publication Date: 2008-01-25
    Description: The water and dissolved inorganic carbon exported by rivers are important net fluxes that connect terrestrial and oceanic water and carbon reservoirs. For most rivers, the majority of dissolved inorganic carbon is in the form of bicarbonate. The riverine bicarbonate flux originates mainly from the dissolution of rock minerals by soil water carbon dioxide, a process called chemical weathering, which controls the buffering capacity and mineral content of receiving streams and rivers. Here we introduce an unprecedented high-temporal-resolution, 100-year data set from the Mississippi River and couple it with sub-watershed and precipitation data to reveal that the large increase in bicarbonate flux that has occurred over the past 50 years (ref. 3) is clearly anthropogenically driven. We show that the increase in bicarbonate and water fluxes is caused mainly by an increase in discharge from agricultural watersheds that has not been balanced by a rise in precipitation, which is also relevant to nutrient and pesticide fluxes to the Gulf of Mexico. These findings demonstrate that alterations in chemical weathering are relevant to improving contemporary biogeochemical budgets. Furthermore, land use change and management were arguably more important than changes in climate and plant CO2 fertilization to increases in riverine water and carbon export from this large region over the past 50 years.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raymond, Peter A -- Oh, Neung-Hwan -- Turner, R Eugene -- Broussard, Whitney -- England -- Nature. 2008 Jan 24;451(7177):449-52. doi: 10.1038/nature06505.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yale School of Forestry and Environmental Studies, 21 Sachem Street, New Haven, Connecticut 06511, USA. peter.raymond@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216851" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/history ; Bicarbonates/*analysis/chemistry ; Carbon/*analysis ; Carbon Dioxide/analysis/metabolism ; Geologic Sediments/analysis/chemistry ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Human Activities/history ; Mississippi ; Rain ; Rivers/*chemistry ; Time Factors
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    Chemistry: power play (2008)
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    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borrell, Brendan -- England -- Nature. 2008 Jan 17;451(7176):240-3. doi: 10.1038/451240a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202619" target="_blank"〉PubMed〈/a〉
    Keywords: Competitive Behavior ; Computational Biology/economics/*trends ; *Computer Simulation ; Proteins/*chemistry ; Research Personnel ; Software ; Time Factors
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    A fast, robust and tunable synthetic gene oscillator (2008)
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    Publication Date: 2008-10-31
    Description: One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to 'design specifications' generated from computational modelling. This approach provides a systematic framework for exploring how a given regulatory network generates a particular phenotypic behaviour. Several fundamental gene circuits have been developed using this approach, including toggle switches and oscillators, and these have been applied in new contexts such as triggered biofilm development and cellular population control. Here we describe an engineered genetic oscillator in Escherichia coli that is fast, robust and persistent, with tunable oscillatory periods as fast as 13 min. The oscillator was designed using a previously modelled network architecture comprising linked positive and negative feedback loops. Using a microfluidic platform tailored for single-cell microscopy, we precisely control environmental conditions and monitor oscillations in individual cells through multiple cycles. Experiments reveal remarkable robustness and persistence of oscillations in the designed circuit; almost every cell exhibited large-amplitude fluorescence oscillations throughout observation runs. The oscillatory period can be tuned by altering inducer levels, temperature and the media source. Computational modelling demonstrates that the key design principle for constructing a robust oscillator is a time delay in the negative feedback loop, which can mechanistically arise from the cascade of cellular processes involved in forming a functional transcription factor. The positive feedback loop increases the robustness of the oscillations and allows for greater tunability. Examination of our refined model suggested the existence of a simplified oscillator design without positive feedback, and we construct an oscillator strain confirming this computational prediction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stricker, Jesse -- Cookson, Scott -- Bennett, Matthew R -- Mather, William H -- Tsimring, Lev S -- Hasty, Jeff -- GM69811-01/GM/NIGMS NIH HHS/ -- R01 GM069811/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Nov 27;456(7221):516-9. doi: 10.1038/nature07389. Epub 2008 Oct 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18971928" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Escherichia coli/*genetics ; Feedback ; Flow Cytometry ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks/*genetics ; Genes, Synthetic/*genetics ; *Genetic Engineering ; Luminescent Measurements ; Microfluidic Analytical Techniques ; Models, Genetic ; *Periodicity ; Sensitivity and Specificity ; Time Factors ; Transcription Factors/metabolism
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    Pacific "dwarf" bones cause controversy (2008)
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    Publication Date: 2008-03-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2008 Mar 13;452(7184):133. doi: 10.1038/452133a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337779" target="_blank"〉PubMed〈/a〉
    Keywords: *Aging ; Animals ; Biological Evolution ; Bone and Bones/*anatomy & histology ; Burial ; Child ; *Dwarfism ; *Fossils ; Geography ; Hominidae/*anatomy & histology/classification ; Humans ; *Models, Biological ; Motion Pictures as Topic ; Palau/ethnology ; Reproducibility of Results ; Time Factors
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    Entrained rhythmic activities of neuronal ensembles as perceptual memory of time interval (2008)
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    Publication Date: 2008-10-17
    Description: The ability to process temporal information is fundamental to sensory perception, cognitive processing and motor behaviour of all living organisms, from amoebae to humans. Neural circuit mechanisms based on neuronal and synaptic properties have been shown to process temporal information over the range of tens of microseconds to hundreds of milliseconds. How neural circuits process temporal information in the range of seconds to minutes is much less understood. Studies of working memory in monkeys and rats have shown that neurons in the prefrontal cortex, the parietal cortex and the thalamus exhibit ramping activities that linearly correlate with the lapse of time until the end of a specific time interval of several seconds that the animal is trained to memorize. Many organisms can also memorize the time interval of rhythmic sensory stimuli in the timescale of seconds and can coordinate motor behaviour accordingly, for example, by keeping the rhythm after exposure to the beat of music. Here we report a form of rhythmic activity among specific neuronal ensembles in the zebrafish optic tectum, which retains the memory of the time interval (in the order of seconds) of repetitive sensory stimuli for a duration of up to approximately 20 s. After repetitive visual conditioning stimulation (CS) of zebrafish larvae, we observed rhythmic post-CS activities among specific tectal neuronal ensembles, with a regular interval that closely matched the CS. Visuomotor behaviour of the zebrafish larvae also showed regular post-CS repetitions at the entrained time interval that correlated with rhythmic neuronal ensemble activities in the tectum. Thus, rhythmic activities among specific neuronal ensembles may act as an adjustable 'metronome' for time intervals in the order of seconds, and serve as a mechanism for the short-term perceptual memory of rhythmic sensory experience.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896960/" 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/PMC2896960/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sumbre, German -- Muto, Akira -- Baier, Herwig -- Poo, Mu-ming -- R01 EY012406/EY/NEI NIH HHS/ -- R01 EY012406-01/EY/NEI NIH HHS/ -- R01 EY012406-02/EY/NEI NIH HHS/ -- R01 EY012406-03/EY/NEI NIH HHS/ -- R01 EY012406-04/EY/NEI NIH HHS/ -- R01 EY012406-05/EY/NEI NIH HHS/ -- R01 EY012406-06A2/EY/NEI NIH HHS/ -- R01 EY012406-07/EY/NEI NIH HHS/ -- R01 EY012406-08/EY/NEI NIH HHS/ -- R01 EY012406-09/EY/NEI NIH HHS/ -- R01 NS053358/NS/NINDS NIH HHS/ -- R01 NS053358-01A2/NS/NINDS NIH HHS/ -- R01 NS053358-02/NS/NINDS NIH HHS/ -- R01 NS053358-02S1/NS/NINDS NIH HHS/ -- R01 NS053358-03/NS/NINDS NIH HHS/ -- R01 NS053358-04/NS/NINDS NIH HHS/ -- England -- Nature. 2008 Nov 6;456(7218):102-6. doi: 10.1038/nature07351. Epub 2008 Oct 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923391" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Conditioning (Psychology) ; Larva/physiology ; Memory/*physiology ; Neurons/*physiology ; *Periodicity ; Photic Stimulation ; Superior Colliculi/cytology/physiology ; Swimming/physiology ; Tail/physiology ; Time Factors ; Zebrafish/embryology/growth & development/*physiology
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    Fears for oldest human footprints (2008)
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    Publication Date: 2008-01-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2008 Jan 10;451(7175):118. doi: 10.1038/451118a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185553" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthropology/*methods ; *Fossils ; *Hominidae ; Humans ; *Museums ; Tanzania ; Time Factors ; *Walking ; Weather
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    Rapid cloning of high-affinity human monoclonal antibodies against influenza virus (2008)
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    Publication Date: 2008-05-02
    Description: Pre-existing neutralizing antibody provides the first line of defence against pathogens in general. For influenza virus, annual vaccinations are given to maintain protective levels of antibody against the currently circulating strains. Here we report that after booster vaccination there was a rapid and robust influenza-specific IgG+ antibody-secreting plasma cell (ASC) response that peaked at approximately day 7 and accounted for up to 6% of peripheral blood B cells. These ASCs could be distinguished from influenza-specific IgG+ memory B cells that peaked 14-21 days after vaccination and averaged 1% of all B cells. Importantly, as much as 80% of ASCs purified at the peak of the response were influenza specific. This ASC response was characterized by a highly restricted B-cell receptor (BCR) repertoire that in some donors was dominated by only a few B-cell clones. This pauci-clonal response, however, showed extensive intraclonal diversification from accumulated somatic mutations. We used the immunoglobulin variable regions isolated from sorted single ASCs to produce over 50 human monoclonal antibodies (mAbs) that bound to the three influenza vaccine strains with high affinity. This strategy demonstrates that we can generate multiple high-affinity mAbs from humans within a month after vaccination. The panel of influenza-virus-specific human mAbs allowed us to address the issue of original antigenic sin (OAS): the phenomenon where the induced antibody shows higher affinity to a previously encountered influenza virus strain compared with the virus strain present in the vaccine. However, we found that most of the influenza-virus-specific mAbs showed the highest affinity for the current vaccine strain. Thus, OAS does not seem to be a common occurrence in normal, healthy adults receiving influenza vaccination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515609/" 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/PMC2515609/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wrammert, Jens -- Smith, Kenneth -- Miller, Joe -- Langley, William A -- Kokko, Kenneth -- Larsen, Christian -- Zheng, Nai-Ying -- Mays, Israel -- Garman, Lori -- Helms, Christina -- James, Judith -- Air, Gillian M -- Capra, J Donald -- Ahmed, Rafi -- Wilson, Patrick C -- HHSN266200500026C/PHS HHS/ -- HHSN266200700006C/PHS HHS/ -- N01-AI-50025-02/AI/NIAID NIH HHS/ -- P20 RR018758/RR/NCRR NIH HHS/ -- P20 RR018758-057588/RR/NCRR NIH HHS/ -- P30 AR053483/AR/NIAMS NIH HHS/ -- R01 AI050933/AI/NIAID NIH HHS/ -- U19 AI057266/AI/NIAID NIH HHS/ -- U19 AI057266-04/AI/NIAID NIH HHS/ -- U19-AI057266-04/AI/NIAID NIH HHS/ -- UL1 TR000454/TR/NCATS NIH HHS/ -- England -- Nature. 2008 May 29;453(7195):667-71. doi: 10.1038/nature06890. Epub 2008 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18449194" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Monoclonal/*biosynthesis/genetics/*immunology ; Antibody Affinity/*immunology ; Antibody Specificity/immunology ; Clone Cells/immunology/metabolism ; Cloning, Molecular ; Humans ; Immunization, Secondary ; Immunoglobulin G/genetics/immunology ; Immunologic Memory/*immunology ; Influenza A Virus, H1N1 Subtype/immunology ; Influenza A Virus, H3N2 Subtype/immunology ; Influenza B virus/immunology ; Influenza Vaccines/immunology ; Models, Immunological ; Orthomyxoviridae/*immunology ; Plasma Cells/immunology/metabolism ; Somatic Hypermutation, Immunoglobulin/genetics ; Time Factors ; Vaccination
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    Inapparent infections and cholera dynamics (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-16
    Description: In many infectious diseases, an unknown fraction of infections produce symptoms mild enough to go unrecorded, a fact that can seriously compromise the interpretation of epidemiological records. This is true for cholera, a pandemic bacterial disease, where estimates of the ratio of asymptomatic to symptomatic infections have ranged from 3 to 100 (refs 1-5). In the absence of direct evidence, understanding of fundamental aspects of cholera transmission, immunology and control has been based on assumptions about this ratio and about the immunological consequences of inapparent infections. Here we show that a model incorporating high asymptomatic ratio and rapidly waning immunity, with infection both from human and environmental sources, explains 50 yr of mortality data from 26 districts of Bengal, the pathogen's endemic home. We find that the asymptomatic ratio in cholera is far higher than had been previously supposed and that the immunity derived from mild infections wanes much more rapidly than earlier analyses have indicated. We find, too, that the environmental reservoir (free-living pathogen) is directly responsible for relatively few infections but that it may be critical to the disease's endemicity. Our results demonstrate that inapparent infections can hold the key to interpreting the patterns of disease outbreaks. New statistical methods, which allow rigorous maximum likelihood inference based on dynamical models incorporating multiple sources and outcomes of infection, seasonality, process noise, hidden variables and measurement error, make it possible to test more precise hypotheses and obtain unexpected results. Our experience suggests that the confrontation of time-series data with mechanistic models is likely to revise our understanding of the ecology of many infectious diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Aaron A -- Ionides, Edward L -- Pascual, Mercedes -- Bouma, Menno J -- England -- Nature. 2008 Aug 14;454(7206):877-80. doi: 10.1038/nature07084.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA. kingaa@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18704085" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier State/diagnosis/epidemiology/immunology/*transmission ; Cholera/*diagnosis/*epidemiology/immunology/transmission ; Computer Simulation ; Databases, Factual ; Humans ; Immunity, Innate ; India/epidemiology ; *Models, Biological ; Seasons ; Time Factors ; Vibrio cholerae/immunology
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    Data on display. Interview by Katherine Sanderson (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bradley, Jean-Claude -- Neylon, Cameron -- BB/D00652X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2008 Sep 18;455(7211):273. doi: 10.1038/455273a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800097" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information ; *Internet ; Patents as Topic ; *Publishing/trends ; *Research Personnel ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Conformational changes in an ultrafast light-driven enzyme determine catalytic activity (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-12-19
    Description: The role of conformational changes in explaining the huge catalytic power of enzymes is currently one of the most challenging questions in biology. Although it is now widely regarded that enzymes modulate reaction rates by means of short- and long-range protein motions, it is almost impossible to distinguish between conformational changes and catalysis. We have solved this problem using the chlorophyll biosynthetic enzyme NADPH:protochlorophyllide (Pchlide) oxidoreductase, which catalyses a unique light-driven reaction involving hydride and proton transfers. Here we report that prior excitation of the enzyme-substrate complex with a laser pulse induces a more favourable conformation of the active site, enabling the coupled hydride and proton transfer reactions to occur. This effect, which is triggered during the Pchlide excited-state lifetime and persists on a long timescale, switches the enzyme into an active state characterized by a high rate and quantum yield of formation of a catalytic intermediate. The corresponding spectral changes in the mid-infrared following the absorption of one photon reveal significant conformational changes in the enzyme, illustrating the importance of flexibility and dynamics in the structure of enzymes for their function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sytina, Olga A -- Heyes, Derren J -- Hunter, C Neil -- Alexandre, Maxime T -- van Stokkum, Ivo H M -- van Grondelle, Rienk -- Groot, Marie Louise -- Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2008 Dec 18;456(7224):1001-4. doi: 10.1038/nature07354.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092933" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis/radiation effects ; Catalytic Domain/radiation effects ; *Light ; Models, Molecular ; Oxidoreductases Acting on CH-CH Group Donors/chemistry/*metabolism/*radiation ; effects ; Protein Conformation/radiation effects ; Protons ; Structure-Activity Relationship ; Synechocystis/*enzymology ; Time Factors
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    Eocene/Oligocene ocean de-acidification linked to Antarctic glaciation by sea-level fall (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-04-25
    Description: One of the most dramatic perturbations to the Earth system during the past 100 million years was the rapid onset of Antarctic glaciation near the Eocene/Oligocene epoch boundary (approximately 34 million years ago). This climate transition was accompanied by a deepening of the calcite compensation depth--the ocean depth at which the rate of calcium carbonate input from surface waters equals the rate of dissolution. Changes in the global carbon cycle, rather than changes in continental configuration, have recently been proposed as the most likely root cause of Antarctic glaciation, but the mechanism linking glaciation to the deepening of calcite compensation depth remains unclear. Here we use a global biogeochemical box model to test competing hypotheses put forward to explain the Eocene/Oligocene transition. We find that, of the candidate hypotheses, only shelf to deep sea carbonate partitioning is capable of explaining the observed changes in both carbon isotope composition and calcium carbonate accumulation at the sea floor. In our simulations, glacioeustatic sea-level fall associated with the growth of Antarctic ice sheets permanently reduces global calcium carbonate accumulation on the continental shelves, leading to an increase in pelagic burial via permanent deepening of the calcite compensation depth. At the same time, fresh limestones are exposed to erosion, thus temporarily increasing global river inputs of dissolved carbonate and increasing seawater delta13C. Our work sheds new light on the mechanisms linking glaciation and ocean acidity change across arguably the most important climate transition of the Cenozoic era.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merico, Agostino -- Tyrrell, Toby -- Wilson, Paul A -- England -- Nature. 2008 Apr 24;452(7190):979-82. doi: 10.1038/nature06853.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK. agostino.merico@gkss.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432242" target="_blank"〉PubMed〈/a〉
    Keywords: Acids/analysis ; Antarctic Regions ; Atmosphere/chemistry ; Calcium Carbonate/analysis/metabolism ; Carbon/analysis/metabolism ; Carbon Isotopes ; Diatoms/metabolism ; Geologic Sediments/chemistry ; History, Ancient ; Hydrogen-Ion Concentration ; *Ice Cover ; Models, Biological ; Oceans and Seas ; Phytoplankton/metabolism ; Seawater/*analysis/*chemistry ; Time Factors
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    Net production of oxygen in the subtropical ocean (2008)
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    Publication Date: 2008-01-19
    Description: The question of whether the plankton communities in low-nutrient regions of the ocean, comprising 80% of the global ocean surface area, are net producers or consumers of oxygen and fixed carbon is a key uncertainty in the global carbon cycle. Direct measurements in bottle experiments indicate net oxygen consumption in the sunlit zone, whereas geochemical evidence suggests that the upper ocean is a net source of oxygen. One possible resolution to this conflict is that primary production in the gyres is episodic and thus difficult to observe: in this model, oligotrophic regions would be net consumers of oxygen during most of the year, but strong, brief events with high primary production rates might produce enough fixed carbon and dissolved oxygen to yield net production as an average over the annual cycle. Here we examine the balance of oxygen production over three years at sites in the North and South Pacific subtropical gyres using the new technique of oxygen sensors deployed on profiling floats. We find that mixing events during early winter homogenize the upper water column and cause low oxygen concentrations. Oxygen then increases below the mixed layer at a nearly constant rate that is similar to independent measures of net community production. This continuous oxygen increase is consistent with an ecosystem that is a net producer of fixed carbon (net autotrophic) throughout the year, with episodic events not required to sustain positive oxygen production.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riser, Stephen C -- Johnson, Kenneth S -- England -- Nature. 2008 Jan 17;451(7176):323-5. doi: 10.1038/nature06441.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, Washington 98195, USA. riser@ocean.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202655" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon/metabolism ; Carbon Dioxide/metabolism ; Hawaii ; Oxygen/analysis/*metabolism ; Pacific Ocean ; Plankton/metabolism ; Seawater/*chemistry ; Time Factors ; Tropical Climate
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    Rapid appearance and local toxicity of amyloid-beta plaques in a mouse model of Alzheimer's disease (2008)
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    Publication Date: 2008-02-08
    Description: Senile plaques accumulate over the course of decades in the brains of patients with Alzheimer's disease. A fundamental tenet of the amyloid hypothesis of Alzheimer's disease is that the deposition of amyloid-beta precedes and induces the neuronal abnormalities that underlie dementia. This idea has been challenged, however, by the suggestion that alterations in axonal trafficking and morphological abnormalities precede and lead to senile plaques. The role of microglia in accelerating or retarding these processes has been uncertain. To investigate the temporal relation between plaque formation and the changes in local neuritic architecture, we used longitudinal in vivo multiphoton microscopy to sequentially image young APPswe/PS1d9xYFP (B6C3-YFP) transgenic mice. Here we show that plaques form extraordinarily quickly, over 24 h. Within 1-2 days of a new plaque's appearance, microglia are activated and recruited to the site. Progressive neuritic changes ensue, leading to increasingly dysmorphic neurites over the next days to weeks. These data establish plaques as a critical mediator of neuritic pathology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264491/" 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/PMC3264491/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer-Luehmann, Melanie -- Spires-Jones, Tara L -- Prada, Claudia -- Garcia-Alloza, Monica -- de Calignon, Alix -- Rozkalne, Anete -- Koenigsknecht-Talboo, Jessica -- Holtzman, David M -- Bacskai, Brian J -- Hyman, Bradley T -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-07/DK/NIDDK NIH HHS/ -- P30 DK056341-08/DK/NIDDK NIH HHS/ -- R01 AG008487/AG/NIA NIH HHS/ -- R01 AG008487-20/AG/NIA NIH HHS/ -- England -- Nature. 2008 Feb 7;451(7179):720-4. doi: 10.1038/nature06616.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Alzheimer's Disease Research Laboratory, Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256671" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/genetics/metabolism/*pathology ; Amyloid beta-Peptides/genetics/metabolism/*toxicity ; Animals ; Axons/metabolism ; *Disease Models, Animal ; Disease Progression ; Mice ; Mice, Transgenic ; Microglia/metabolism ; Neurites/metabolism/pathology ; Plaque, Amyloid/genetics/metabolism/*pathology ; Time Factors
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    Palaeoclimate: windows on the greenhouse (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brook, Ed -- England -- Nature. 2008 May 15;453(7193):291-2. doi: 10.1038/453291a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480800" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; Atmosphere/*chemistry ; Carbon Dioxide/*analysis ; Greenhouse Effect ; Greenland ; History, Ancient ; Ice Cover/*chemistry ; Methane/*analysis ; *Temperature ; Time Factors
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    Standard identifier could mobilize data and free time (2008)
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    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roberts, Dave -- Chavan, Vishwas -- England -- Nature. 2008 May 22;453(7194):449-50. doi: 10.1038/453449c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497793" target="_blank"〉PubMed〈/a〉
    Keywords: *Authorship ; *Bibliometrics ; *Databases, Factual/standards ; Internet ; *Publishing/standards ; Time Factors
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    A ghost of battles past (2008)
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    Publication Date: 2008-04-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Apr 17;452(7189):781-2. doi: 10.1038/452781b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18421317" target="_blank"〉PubMed〈/a〉
    Keywords: 2,4,5-Trichlorophenoxyacetic Acid/*poisoning ; 2,4-Dichlorophenoxyacetic Acid/*poisoning ; Chemical Warfare/*statistics & numerical data ; Databases, Factual ; Dioxins/*poisoning ; Humans ; Tetrachlorodibenzodioxin/*poisoning ; Time Factors ; United States/epidemiology/ethnology ; United States Department of Veterans Affairs/organization & administration ; Veterans/*statistics & numerical data ; Vietnam/epidemiology
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    Clathrin is a key regulator of basolateral polarity (2008)
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    Publication Date: 2008-04-11
    Description: Clathrin-coated vesicles are vehicles for intracellular trafficking in all nucleated cells, from yeasts to humans. Many studies have demonstrated their essential roles in endocytosis and cellular signalling processes at the plasma membrane. By contrast, very few of their non-endocytic trafficking roles are known, the best characterized being the transport of hydrolases from the Golgi complex to the lysosome. Here we show that clathrin is required for polarity of the basolateral plasma membrane proteins in the epithelial cell line MDCK. Clathrin knockdown depolarized most basolateral proteins, by interfering with their biosynthetic delivery and recycling, but did not affect the polarity of apical proteins. Quantitative live imaging showed that chronic and acute clathrin knockdown selectively slowed down the exit of basolateral proteins from the Golgi complex, and promoted their mis-sorting into apical carrier vesicles. Our results demonstrate a broad requirement for clathrin in basolateral protein trafficking in epithelial cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078870/" 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/PMC4078870/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deborde, Sylvie -- Perret, Emilie -- Gravotta, Diego -- Deora, Ami -- Salvarezza, Susana -- Schreiner, Ryan -- Rodriguez-Boulan, Enrique -- R01 EY008538/EY/NEI NIH HHS/ -- R01 GM034107/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 10;452(7188):719-23. doi: 10.1038/nature06828.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ophthalmology, Dyson Vision Research Institute, LC-300, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401403" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cathepsin D/metabolism ; Cell Line ; *Cell Polarity ; Clathrin/deficiency/genetics/*metabolism ; Clathrin Heavy Chains/genetics/metabolism ; Dogs ; Epithelial Cells/*cytology/metabolism ; Golgi Apparatus/metabolism ; Humans ; Inulin/metabolism ; Lysosomes/metabolism ; Protein Transport ; Receptors, LDL/metabolism ; Receptors, Transferrin/metabolism ; Tight Junctions/metabolism ; Time Factors ; trans-Golgi Network/metabolism
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    A reprogramming rush (2008)
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    Publication Date: 2008-03-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Mar 27;452(7186):388. doi: 10.1038/452388a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18368078" target="_blank"〉PubMed〈/a〉
    Keywords: Japan ; Korea ; Peer Review, Research/standards/trends ; *Pluripotent Stem Cells/cytology ; Research Personnel/*ethics/standards ; Scientific Misconduct ; Time Factors
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    Phoenix fades away (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2008 Nov 6;456(7218):8-9. doi: 10.1038/456008a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987698" target="_blank"〉PubMed〈/a〉
    Keywords: Exobiology ; Extraterrestrial Environment/*chemistry ; Ice/analysis ; Mars ; Space Flight/*instrumentation/trends ; Time Factors
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    An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics (2008)
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    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zachos, James C -- Dickens, Gerald R -- Zeebe, Richard E -- England -- Nature. 2008 Jan 17;451(7176):279-83. doi: 10.1038/nature06588.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, University of California at Santa Cruz, Santa Cruz, California 95060, USA. jzachos@es.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202643" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon/analysis/*metabolism ; Carbon Dioxide/analysis/metabolism ; Ecosystem ; *Greenhouse Effect ; History, 21st Century ; History, Ancient ; Human Activities ; Models, Theoretical ; Oceans and Seas ; Temperature ; Time Factors
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    Palaeontology: modern life in ancient mats (2008)
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    Publication Date: 2008-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tice, Michael M -- England -- Nature. 2008 Mar 6;452(7183):40-1. doi: 10.1038/452040a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322521" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; Fossils ; Geologic Sediments/*chemistry/*microbiology ; *Marine Biology ; Models, Biological ; Oceans and Seas ; Paleontology ; Seawater/*microbiology ; Silicon Dioxide/chemistry ; South Africa ; Time Factors ; Water Movements
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    Ancient water sites for next rover (2008)
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    Publication Date: 2008-10-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2008 Oct 2;455(7213):575. doi: 10.1038/455575a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18839446" target="_blank"〉PubMed〈/a〉
    Keywords: Exobiology/instrumentation/trends ; Extraterrestrial Environment/*chemistry ; *Mars ; Space Flight/*instrumentation/*trends ; Time Factors ; Water/*analysis
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    Slow development impedes the uptake of diagnostics (2008)
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    Publication Date: 2008-01-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moon, Chul-So -- Agbo, Eddy C -- Sidransky, David -- England -- Nature. 2008 Jan 3;451(7174):16. doi: 10.1038/451016c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18172474" target="_blank"〉PubMed〈/a〉
    Keywords: Biomarkers, Tumor/analysis ; Diagnostic Techniques and Procedures/*trends ; Genetic Testing ; Humans ; Neoplasms/*diagnosis/genetics ; Pharmacogenetics ; Survival Analysis ; Time Factors
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    The four-year fight for biological art. Steven Kurtz interviewed by Rachel Courtland (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-06-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kurtz, Steven -- England -- Nature. 2008 Jun 5;453(7196):707. doi: 10.1038/453707a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528358" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Art ; Biological Warfare/prevention & control ; *Federal Government ; Food, Genetically Modified ; Guinea Pigs ; History, 21st Century ; Humans ; Research Personnel ; Science/*education ; Terrorism/prevention & control ; Time Factors ; United States
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Improved estimates of upper-ocean warming and multi-decadal sea-level rise (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-06-20
    Description: Changes in the climate system's energy budget are predominantly revealed in ocean temperatures and the associated thermal expansion contribution to sea-level rise. Climate models, however, do not reproduce the large decadal variability in globally averaged ocean heat content inferred from the sparse observational database, even when volcanic and other variable climate forcings are included. The sum of the observed contributions has also not adequately explained the overall multi-decadal rise. Here we report improved estimates of near-global ocean heat content and thermal expansion for the upper 300 m and 700 m of the ocean for 1950-2003, using statistical techniques that allow for sparse data coverage and applying recent corrections to reduce systematic biases in the most common ocean temperature observations. Our ocean warming and thermal expansion trends for 1961-2003 are about 50 per cent larger than earlier estimates but about 40 per cent smaller for 1993-2003, which is consistent with the recognition that previously estimated rates for the 1990s had a positive bias as a result of instrumental errors. On average, the decadal variability of the climate models with volcanic forcing now agrees approximately with the observations, but the modelled multi-decadal trends are smaller than observed. We add our observational estimate of upper-ocean thermal expansion to other contributions to sea-level rise and find that the sum of contributions from 1961 to 2003 is about 1.5 +/- 0.4 mm yr(-1), in good agreement with our updated estimate of near-global mean sea-level rise (using techniques established in earlier studies) of 1.6 +/- 0.2 mm yr(-1).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Domingues, Catia M -- Church, John A -- White, Neil J -- Gleckler, Peter J -- Wijffels, Susan E -- Barker, Paul M -- Dunn, Jeff R -- England -- Nature. 2008 Jun 19;453(7198):1090-3. doi: 10.1038/nature07080.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Australian Weather and Climate Research, CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania 7001, Australia. catia.domingues@csiro.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563162" target="_blank"〉PubMed〈/a〉
    Keywords: Forecasting ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Hot Temperature ; Models, Theoretical ; Oceans and Seas ; Research Design ; Seawater/*analysis ; Time Factors ; Volcanic Eruptions
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    Rapid leukocyte migration by integrin-independent flowing and squeezing (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-03
    Description: All metazoan cells carry transmembrane receptors of the integrin family, which couple the contractile force of the actomyosin cytoskeleton to the extracellular environment. In agreement with this principle, rapidly migrating leukocytes use integrin-mediated adhesion when moving over two-dimensional surfaces. As migration on two-dimensional substrates naturally overemphasizes the role of adhesion, the contribution of integrins during three-dimensional movement of leukocytes within tissues has remained controversial. We studied the interplay between adhesive, contractile and protrusive forces during interstitial leukocyte chemotaxis in vivo and in vitro. We ablated all integrin heterodimers from murine leukocytes, and show here that functional integrins do not contribute to migration in three-dimensional environments. Instead, these cells migrate by the sole force of actin-network expansion, which promotes protrusive flowing of the leading edge. Myosin II-dependent contraction is only required on passage through narrow gaps, where a squeezing contraction of the trailing edge propels the rigid nucleus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lammermann, Tim -- Bader, Bernhard L -- Monkley, Susan J -- Worbs, Tim -- Wedlich-Soldner, Roland -- Hirsch, Karin -- Keller, Markus -- Forster, Reinhold -- Critchley, David R -- Fassler, Reinhard -- Sixt, Michael -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 May 1;453(7191):51-5. doi: 10.1038/nature06887.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Medicine, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451854" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Animals ; Cell Adhesion ; *Cell Movement ; Cell Nucleus/metabolism ; Cell Shape ; Chemotaxis ; Dendritic Cells/*cytology/metabolism ; Integrins/deficiency/genetics/metabolism ; Leukocytes/*cytology/metabolism ; Lymph Nodes/cytology/immunology ; Mice ; Myosin Type II/metabolism ; Time Factors
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Further delays to full Agent Orange study (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2008 Apr 17;452(7189):786-7. doi: 10.1038/452786a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18431821" target="_blank"〉PubMed〈/a〉
    Keywords: 2,4,5-Trichlorophenoxyacetic Acid/*poisoning ; 2,4-Dichlorophenoxyacetic Acid/*poisoning ; Chemical Warfare/statistics & numerical data ; Compensation and Redress ; Dioxins/poisoning ; Humans ; Tetrachlorodibenzodioxin/*poisoning ; Time Factors ; United States/epidemiology/ethnology ; United States Department of Veterans Affairs/economics/*organization & ; administration ; Veterans/*statistics & numerical data ; Vietnam/epidemiology
    Print ISSN: 0028-0836
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    Follow the leader (2008)
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    Publication Date: 2008-06-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsuji, Kaori -- Tsutani, Kiichiro -- England -- Nature. 2008 Jun 12;453(7197):851-2. doi: 10.1038/453851a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Health Care Science Institute, Akasaka NOA 5F, 3-2-12 Akasaka, Minato-ku, Tokyo 107-0052, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18548049" target="_blank"〉PubMed〈/a〉
    Keywords: Drug Approval/*organization & administration/statistics & numerical data ; Internationality ; Japan ; Time Factors
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    Frequency-modulated nuclear localization bursts coordinate gene regulation (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-27
    Description: In yeast, the transcription factor Crz1 is dephosphorylated and translocates into the nucleus in response to extracellular calcium. Here we show, using time-lapse microscopy, that Crz1 exhibits short bursts of nuclear localization (typically lasting 2 min) that occur stochastically in individual cells and propagate to the expression of downstream genes. Strikingly, calcium concentration controls the frequency, but not the duration, of localization bursts. Using an analytic model, we also show that this frequency modulation of bursts ensures proportional expression of multiple target genes across a wide dynamic range of expression levels, independent of promoter characteristics. We experimentally confirm this theory with natural and synthetic Crz1 target promoters. Another stress-response transcription factor, Msn2, exhibits similar, but largely uncorrelated, localization bursts under calcium stress suggesting that frequency-modulation regulation of localization bursts may be a general control strategy used by the cell to coordinate multi-gene responses to external signals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695983/" 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/PMC2695983/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cai, Long -- Dalal, Chiraj K -- Elowitz, Michael B -- P50 GM068763/GM/NIGMS NIH HHS/ -- P50 GM068763-050005/GM/NIGMS NIH HHS/ -- R01 GM079771/GM/NIGMS NIH HHS/ -- R01 GM079771-02/GM/NIGMS NIH HHS/ -- R01GM079771/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Sep 25;455(7212):485-90. doi: 10.1038/nature07292.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Division of Biology and Department of Applied Physics, California Institute of Technology, M/C 114-96, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818649" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus/drug effects ; Calcium/metabolism/pharmacology ; Cell Nucleus/drug effects/*metabolism ; DNA-Binding Proteins/metabolism ; *Gene Expression Regulation, Fungal/drug effects ; Models, Genetic ; Phosphorylation/drug effects ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Saccharomyces cerevisiae/*cytology/drug effects/*genetics ; Saccharomyces cerevisiae Proteins/*metabolism ; Stochastic Processes ; Time Factors ; Trans-Activators/*metabolism ; Transcription Factors/metabolism
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    Thermodynamic control by frequent quantum measurements (2008)
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    Publication Date: 2008-04-11
    Description: Heat flow between a large thermal 'bath' and a smaller system brings them progressively closer to thermal equilibrium while increasing their entropy. Fluctuations involving a small fraction of a statistical ensemble of systems interacting with the bath result in deviations from this trend. In this respect, quantum and classical thermodynamics are in agreement. Here we predict a different trend in a purely quantum mechanical setting: disturbances of thermal equilibrium between two-level systems (TLSs) and a bath, caused by frequent, brief quantum non-demolition measurements of the TLS energy states. By making the measurements increasingly frequent, we encounter first the anti-Zeno regime and then the Zeno regime (namely where the TLSs' relaxation respectively speeds up and slows down). The corresponding entropy and temperature of both the system and the bath are then found to either decrease or increase depending only on the rate of observation, contrary to the standard thermodynamical rules that hold for memory-less (Markov) baths. From a practical viewpoint, these anomalies may offer the possibility of very fast control of heat and entropy in quantum systems, allowing cooling and state purification over an interval much shorter than the time needed for thermal equilibration or for a feedback control loop.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erez, Noam -- Gordon, Goren -- Nest, Mathias -- Kurizki, Gershon -- England -- Nature. 2008 Apr 10;452(7188):724-7. doi: 10.1038/nature06873.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401404" target="_blank"〉PubMed〈/a〉
    Keywords: *Entropy ; Markov Chains ; Observation ; *Quantum Theory ; *Research Design ; *Temperature ; Time Factors
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    From landscapes into geological history (2008)
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    Publication Date: 2008-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allen, Philip A -- England -- Nature. 2008 Jan 17;451(7176):274-6. doi: 10.1038/nature06586.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Science and Engineering, Imperial College, South Kensington Campus, London SW7 2AZ, UK. philip.allen@imperial.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202641" target="_blank"〉PubMed〈/a〉
    Keywords: Earth (Planet) ; Geologic Sediments/*analysis/chemistry ; *Geology ; History, Ancient ; Ice Cover ; Oceans and Seas ; Rivers ; Temperature ; Time Factors
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    Estimating the impact of school closure on influenza transmission from Sentinel data (2008)
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    Publication Date: 2008-04-11
    Description: The threat posed by the highly pathogenic H5N1 influenza virus requires public health authorities to prepare for a human pandemic. Although pre-pandemic vaccines and antiviral drugs might significantly reduce illness rates, their stockpiling is too expensive to be practical for many countries. Consequently, alternative control strategies, based on non-pharmaceutical interventions, are a potentially attractive policy option. School closure is the measure most often considered. The high social and economic costs of closing schools for months make it an expensive and therefore controversial policy, and the current absence of quantitative data on the role of schools during influenza epidemics means there is little consensus on the probable effectiveness of school closure in reducing the impact of a pandemic. Here, from the joint analysis of surveillance data and holiday timing in France, we quantify the role of schools in influenza epidemics and predict the effect of school closure during a pandemic. We show that holidays lead to a 20-29% reduction in the rate at which influenza is transmitted to children, but that they have no detectable effect on the contact patterns of adults. Holidays prevent 16-18% of seasonal influenza cases (18-21% in children). By extrapolation, we find that prolonged school closure during a pandemic might reduce the cumulative number of cases by 13-17% (18-23% in children) and peak attack rates by up to 39-45% (47-52% in children). The impact of school closure would be reduced if it proved difficult to maintain low contact rates among children for a prolonged period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cauchemez, Simon -- Valleron, Alain-Jacques -- Boelle, Pierre-Yves -- Flahault, Antoine -- Ferguson, Neil M -- England -- Nature. 2008 Apr 10;452(7188):750-4. doi: 10.1038/nature06732.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Diseases Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401408" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Child ; *Computer Simulation ; France/epidemiology ; Holidays/statistics & numerical data ; Humans ; Incidence ; Influenza A Virus, H5N1 Subtype/physiology ; Influenza, Human/economics/epidemiology/*prevention & control/*transmission ; Schools/*organization & administration ; Seasons ; *Sentinel Surveillance ; Time Factors
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    Do female hyaenas choose mates based on tenure? (2008)
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    Publication Date: 2008-07-11
    Description: In their investigation into whether female mate-choice drives male dispersal, Honer et al. argue that female spotted hyaenas (Crocuta crocuta) prefer mates whose tenure in the social group is less than the females' age, to avoid paternal incest, and suggest that male dispersal reflects this preference. However, we are not persuaded that females choose mates on the basis of tenure because Honer et al. overlook the alternative hypothesis that dispersal status itself is important in female mate-choice, such that females prefer immigrants over natal males. Like mate-choice based on tenure, choice based on dispersal status reduces the risk of incest.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Horn, Russell C -- Watts, Heather E -- Holekamp, Kay E -- England -- Nature. 2008 Jul 10;454(7201):E1; discussion E2. doi: 10.1038/nature07122.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoological Society of San Diego, Conservation and Research for Endangered Species, P.O. Box 120551, San Diego, California 92112-0551, USA. rvanhorn@sandiegozoo.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18615020" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; Hyaenidae/*physiology ; Inbreeding ; Male ; Mating Preference, Animal/*physiology ; Reproducibility of Results ; Social Behavior ; Time Factors
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    Sediment cores reveal Antarctica's warmer past (2008)
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    Publication Date: 2008-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2008 May 1;453(7191):13. doi: 10.1038/453013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18461714" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; Geologic Sediments/*analysis ; History, Ancient ; *Ice Cover ; Rain ; Rivers ; Time Factors ; Trees
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    25 years of HIV (2008)
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    Publication Date: 2008-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fauci, Anthony S -- England -- Nature. 2008 May 15;453(7193):289-90. doi: 10.1038/453289a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Allergy and Infectious Diseases (NIAID) at the US National Institutes of Health in Bethesda, Maryland, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480799" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/history ; Anti-HIV Agents/history/supply & distribution/therapeutic use ; Drug Resistance, Viral ; HIV/drug effects/genetics/isolation & purification/physiology ; HIV Infections/drug therapy/*history/prevention & control/virology ; History, 20th Century ; History, 21st Century ; Humans ; Time Factors ; Zidovudine/history/pharmacology/therapeutic use
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    Clusters of ant colonies and robust criticality in a tropical agroecosystem (2008)
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    Publication Date: 2008-01-25
    Description: Although sometimes difficult to measure at large scales, spatial pattern is important in natural biological spaces as a determinant of key ecological properties such as species diversity, stability, resiliency and others. Here we demonstrate, at a large spatial scale, that a common species of tropical arboreal ant forms clusters of nests through a combination of local satellite colony formation and density-dependent control by natural enemies, mainly a parasitic fly. Cluster sizes fall off as a power law consistent with a so-called robust critical state. This endogenous cluster formation at a critical state is a unique example of an insect population forming a non-random pattern at a large spatial scale. Furthermore, because the species is a keystone of a larger network that contributes to the ecosystem function of pest control, this is an example of how spatial dynamics at a large scale can affect ecosystem service at a local level.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vandermeer, John -- Perfecto, Ivette -- Philpott, Stacy M -- England -- Nature. 2008 Jan 24;451(7177):457-9. doi: 10.1038/nature06477.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Kraus Natural Science Building, University of Michigan, Ann Arbor, Michigan 48109, USA. jvander@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216853" target="_blank"〉PubMed〈/a〉
    Keywords: *Agriculture ; Animals ; Ants/parasitology/*physiology ; Coffee/parasitology/physiology ; *Ecosystem ; Female ; Mexico ; Pest Control, Biological ; Population Density ; Survival Rate ; Time Factors ; Trees/parasitology/physiology ; *Tropical Climate
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    Global control of cell-cycle transcription by coupled CDK and network oscillators (2008)
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    Publication Date: 2008-05-09
    Description: A significant fraction of the Saccharomyces cerevisiae genome is transcribed periodically during the cell division cycle, indicating that properly timed gene expression is important for regulating cell-cycle events. Genomic analyses of the localization and expression dynamics of transcription factors suggest that a network of sequentially expressed transcription factors could control the temporal programme of transcription during the cell cycle. However, directed studies interrogating small numbers of genes indicate that their periodic transcription is governed by the activity of cyclin-dependent kinases (CDKs). To determine the extent to which the global cell-cycle transcription programme is controlled by cyclin-CDK complexes, we examined genome-wide transcription dynamics in budding yeast mutant cells that do not express S-phase and mitotic cyclins. Here we show that a significant fraction of periodic genes are aberrantly expressed in the cyclin mutant. Although cells lacking cyclins are blocked at the G1/S border, nearly 70% of periodic genes continued to be expressed periodically and on schedule. Our findings reveal that although CDKs have a function in the regulation of cell-cycle transcription, they are not solely responsible for establishing the global periodic transcription programme. We propose that periodic transcription is an emergent property of a transcription factor network that can function as a cell-cycle oscillator independently of, and in tandem with, the CDK oscillator.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736871/" 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/PMC2736871/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Orlando, David A -- Lin, Charles Y -- Bernard, Allister -- Wang, Jean Y -- Socolar, Joshua E S -- Iversen, Edwin S -- Hartemink, Alexander J -- Haase, Steven B -- P50 GM081883/GM/NIGMS NIH HHS/ -- P50 GM081883-020001/GM/NIGMS NIH HHS/ -- P50 GM081883-030001/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jun 12;453(7197):944-7. doi: 10.1038/nature06955. Epub 2008 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Duke University, Durham, North Carolina 27708, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18463633" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Clocks/*physiology ; Cell Cycle/*genetics ; Cyclin-Dependent Kinases/genetics/*metabolism ; Cyclins/genetics/metabolism ; G1 Phase ; *Gene Expression Regulation, Fungal ; Mutation/genetics ; Periodicity ; S Phase ; Saccharomyces cerevisiae/*cytology/*genetics ; Time Factors ; *Transcription, Genetic
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    Prolonged suppression of ecosystem carbon dioxide uptake after an anomalously warm year (2008)
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    Publication Date: 2008-09-19
    Description: Terrestrial ecosystems control carbon dioxide fluxes to and from the atmosphere through photosynthesis and respiration, a balance between net primary productivity and heterotrophic respiration, that determines whether an ecosystem is sequestering carbon or releasing it to the atmosphere. Global and site-specific data sets have demonstrated that climate and climate variability influence biogeochemical processes that determine net ecosystem carbon dioxide exchange (NEE) at multiple timescales. Experimental data necessary to quantify impacts of a single climate variable, such as temperature anomalies, on NEE and carbon sequestration of ecosystems at interannual timescales have been lacking. This derives from an inability of field studies to avoid the confounding effects of natural intra-annual and interannual variability in temperature and precipitation. Here we present results from a four-year study using replicate 12,000-kg intact tallgrass prairie monoliths located in four 184-m(3) enclosed lysimeters. We exposed 6 of 12 monoliths to an anomalously warm year in the second year of the study and continuously quantified rates of ecosystem processes, including NEE. We find that warming decreases NEE in both the extreme year and the following year by inducing drought that suppresses net primary productivity in the extreme year and by stimulating heterotrophic respiration of soil biota in the subsequent year. Our data indicate that two years are required for NEE in the previously warmed experimental ecosystems to recover to levels measured in the control ecosystems. This time lag caused net ecosystem carbon sequestration in previously warmed ecosystems to be decreased threefold over the study period, compared with control ecosystems. Our findings suggest that more frequent anomalously warm years, a possible consequence of increasing anthropogenic carbon dioxide levels, may lead to a sustained decrease in carbon dioxide uptake by terrestrial ecosystems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arnone, John A 3rd -- Verburg, Paul S J -- Johnson, Dale W -- Larsen, Jessica D -- Jasoni, Richard L -- Lucchesi, Annmarie J -- Batts, Candace M -- von Nagy, Christopher -- Coulombe, William G -- Schorran, David E -- Buck, Paul E -- Braswell, Bobby H -- Coleman, James S -- Sherry, Rebecca A -- Wallace, Linda L -- Luo, Yiqi -- Schimel, David S -- England -- Nature. 2008 Sep 18;455(7211):383-6. doi: 10.1038/nature07296.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Desert Research Institute, Reno, Nevada 89512, USA. jarnone@dri.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800137" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/*metabolism ; *Climate ; Disasters ; *Ecosystem ; *Hot Temperature ; Time Factors
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    Tracing the stepwise oxygenation of the Proterozoic ocean (2008)
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    Publication Date: 2008-03-28
    Description: Biogeochemical signatures preserved in ancient sedimentary rocks provide clues to the nature and timing of the oxygenation of the Earth's atmosphere. Geochemical data suggest that oxygenation proceeded in two broad steps near the beginning and end of the Proterozoic eon (2,500 to 542 million years ago). The oxidation state of the Proterozoic ocean between these two steps and the timing of deep-ocean oxygenation have important implications for the evolutionary course of life on Earth but remain poorly known. Here we present a new perspective on ocean oxygenation based on the authigenic accumulation of the redox-sensitive transition element molybdenum in sulphidic black shales. Accumulation of authigenic molybdenum from sea water is already seen in shales by 2,650 Myr ago; however, the small magnitudes of these enrichments reflect weak or transient sources of dissolved molybdenum before about 2,200 Myr ago, consistent with minimal oxidative weathering of the continents. Enrichments indicative of persistent and vigorous oxidative weathering appear in shales deposited at roughly 2,150 Myr ago, more than 200 million years after the initial rise in atmospheric oxygen. Subsequent expansion of sulphidic conditions after about 1,800 Myr ago (refs 8, 9) maintained a mid-Proterozoic molybdenum reservoir below 20 per cent of the modern inventory, which in turn may have acted as a nutrient feedback limiting the spatiotemporal distribution of euxinic (sulphidic) bottom waters and perhaps the evolutionary and ecological expansion of eukaryotic organisms. By 551 Myr ago, molybdenum contents reflect a greatly expanded oceanic reservoir due to oxygenation of the deep ocean and corresponding decrease in sulphidic conditions in the sediments and water column.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, C -- Lyons, T W -- Bekker, A -- Shen, Y -- Poulton, S W -- Chu, X -- Anbar, A D -- England -- Nature. 2008 Mar 27;452(7186):456-9. doi: 10.1038/nature06811.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of California, Riverside, California 92521, USA. cscot002@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18368114" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Geologic Sediments/chemistry ; History, Ancient ; Molybdenum/analysis ; Oceans and Seas ; Oxygen/*analysis/chemistry ; Seawater/*chemistry ; Sulfides/chemistry ; Time Factors
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    Human metabolic phenotype diversity and its association with diet and blood pressure (2008)
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    Publication Date: 2008-04-22
    Description: Metabolic phenotypes are the products of interactions among a variety of factors-dietary, other lifestyle/environmental, gut microbial and genetic. We use a large-scale exploratory analytical approach to investigate metabolic phenotype variation across and within four human populations, based on 1H NMR spectroscopy. Metabolites discriminating across populations are then linked to data for individuals on blood pressure, a major risk factor for coronary heart disease and stroke (leading causes of mortality worldwide). We analyse spectra from two 24-hour urine specimens for each of 4,630 participants from the INTERMAP epidemiological study, involving 17 population samples aged 40-59 in China, Japan, UK and USA. We show that urinary metabolite excretion patterns for East Asian and western population samples, with contrasting diets, diet-related major risk factors, and coronary heart disease/stroke rates, are significantly differentiated (P 〈 10(-16)), as are Chinese/Japanese metabolic phenotypes, and subgroups with differences in dietary vegetable/animal protein and blood pressure. Among discriminatory metabolites, we quantify four and show association (P 〈 0.05 to P 〈 0.0001) of mean 24-hour urinary formate excretion with blood pressure in multiple regression analyses for individuals. Mean 24-hour urinary excretion of alanine (direct) and hippurate (inverse), reflecting diet and gut microbial activities, are also associated with blood pressure of individuals. Metabolic phenotyping applied to high-quality epidemiological data offers the potential to develop an area of aetiopathogenetic knowledge involving discovery of novel biomarkers related to cardiovascular disease risk.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmes, Elaine -- Loo, Ruey Leng -- Stamler, Jeremiah -- Bictash, Magda -- Yap, Ivan K S -- Chan, Queenie -- Ebbels, Tim -- De Iorio, Maria -- Brown, Ian J -- Veselkov, Kirill A -- Daviglus, Martha L -- Kesteloot, Hugo -- Ueshima, Hirotsugu -- Zhao, Liancheng -- Nicholson, Jeremy K -- Elliott, Paul -- R01 HL084228/HL/NHLBI NIH HHS/ -- R01 HL50490/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 May 15;453(7193):396-400. doi: 10.1038/nature06882. Epub 2008 Apr 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18425110" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Alanine/urine ; Animals ; Blood Pressure/*physiology ; Cardiovascular Diseases/metabolism ; China ; *Diet ; Dietary Proteins/pharmacology ; Female ; Great Britain ; Hippurates/urine ; Humans ; Intestines/microbiology ; Japan ; Magnetic Resonance Spectroscopy ; Male ; Metabolism/*physiology ; Middle Aged ; Phenotype ; Principal Component Analysis ; Time Factors ; United States ; Vegetables/chemistry
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    Developmental biology: Serpent clocks tick faster (2008)
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    Publication Date: 2008-07-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vonk, Freek J -- Richardson, Michael K -- England -- Nature. 2008 Jul 17;454(7202):282-3. doi: 10.1038/454282a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18633402" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Patterning/*physiology ; Mice ; Snakes/*embryology ; Somites/*embryology ; Time Factors
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    Alzheimer's disease: Moving towards a vaccine (2008)
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    Publication Date: 2008-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holtzman, David M -- England -- Nature. 2008 Jul 24;454(7203):418-20. doi: 10.1038/454418a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18650906" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/*immunology/*metabolism/physiopathology/therapy ; Amyloid beta-Peptides/chemistry/immunology/metabolism ; Animals ; Antibodies/immunology ; Clinical Trials as Topic ; Disease Models, Animal ; Disease Progression ; Humans ; Mice ; Plaque, Amyloid/immunology/metabolism ; Time Factors ; Vaccines/*immunology/therapeutic use
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    Palaeobiology: the Cambrian smorgasbord (2008)
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    Publication Date: 2008-06-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frood, Arran -- England -- Nature. 2008 Jun 5;453(7196):717-8. doi: 10.1038/453717a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528369" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; Databases, Factual ; Ecology/*methods ; *Food Chain ; *Fossils ; Geologic Sediments ; *Models, Biological ; Paleontology/*methods ; Predatory Behavior ; Time Factors
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    A longer paper gathers more citations (2008)
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    Publication Date: 2008-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ball, Philip -- England -- Nature. 2008 Sep 18;455(7211):274-5. doi: 10.1038/455274a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800099" target="_blank"〉PubMed〈/a〉
    Keywords: Astronomical Phenomena ; Astronomy ; *Bibliometrics ; Peer Review, Research/standards ; Publishing/*statistics & numerical data ; Research/*statistics & numerical data ; Time Factors
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    Minimally invasive high-speed imaging of sarcomere contractile dynamics in mice and humans (2008)
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    Publication Date: 2008-07-05
    Description: Sarcomeres are the basic contractile units of striated muscle. Our knowledge about sarcomere dynamics has primarily come from in vitro studies of muscle fibres and analysis of optical diffraction patterns obtained from living muscles. Both approaches involve highly invasive procedures and neither allows examination of individual sarcomeres in live subjects. Here we report direct visualization of individual sarcomeres and their dynamical length variations using minimally invasive optical microendoscopy to observe second-harmonic frequencies of light generated in the muscle fibres of live mice and humans. Using microendoscopes as small as 350 microm in diameter, we imaged individual sarcomeres in both passive and activated muscle. Our measurements permit in vivo characterization of sarcomere length changes that occur with alterations in body posture and visualization of local variations in sarcomere length not apparent in aggregate length determinations. High-speed data acquisition enabled observation of sarcomere contractile dynamics with millisecond-scale resolution. These experiments point the way to in vivo imaging studies demonstrating how sarcomere performance varies with physical conditioning and physiological state, as well as imaging diagnostics revealing how neuromuscular diseases affect contractile dynamics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826360/" 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/PMC2826360/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Llewellyn, Michael E -- Barretto, Robert P J -- Delp, Scott L -- Schnitzer, Mark J -- R01 NS050533/NS/NINDS NIH HHS/ -- R01 NS050533-01/NS/NINDS NIH HHS/ -- R01NS050533/NS/NINDS NIH HHS/ -- England -- Nature. 2008 Aug 7;454(7205):784-8. doi: 10.1038/nature07104. Epub 2008 Jul 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bio-X Program, James H. Clark Center for Biomedical Engineering & Sciences, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18600262" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Survival ; Endoscopy/*methods ; Humans ; Mice ; Mice, Inbred C57BL ; Movement/*physiology ; Muscle Contraction/*physiology ; Optics and Photonics ; Sarcomeres/*metabolism ; Time Factors
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    Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis (2008)
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    Publication Date: 2008-11-26
    Description: In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651468/" 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/PMC2651468/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamdan, Samir M -- Loparo, Joseph J -- Takahashi, Masateru -- Richardson, Charles C -- van Oijen, Antoine M -- GM-077248/GM/NIGMS NIH HHS/ -- GM-54397/GM/NIGMS NIH HHS/ -- R01 GM077248/GM/NIGMS NIH HHS/ -- R01 GM077248-02/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jan 15;457(7227):336-9. doi: 10.1038/nature07512. Epub 2008 Nov 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19029884" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T7/*metabolism ; Bacteriophage lambda/genetics ; DNA Replication/*physiology ; DNA, Viral/analysis/*biosynthesis ; DNA-Directed DNA Polymerase/metabolism ; Microscopy, Fluorescence ; Multienzyme Complexes/metabolism ; Time Factors
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    Caenorhabditis elegans dauers need LKB1/AMPK to ration lipid reserves and ensure long-term survival (2008)
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    Publication Date: 2008-12-05
    Description: Many organisms can enter a dormant state or diapause to survive harsh environmental conditions for extended durations. When Caenorhabditis elegans larvae enter dauer they arrest feeding but remain active and motile, yet become stress-resistant, extremely long-lived and non-ageing. Entry into dauer is associated with a reduction in insulin-like signalling, the accumulation of nutritive resources and a concomitant global change in metabolism, yet the precise molecular and physiological processes that enable long-term survival in the absence of caloric intake remain largely unknown. We show here that C. elegans larvae that lack LKB1/AMPK (AMP-activated protein kinase) signalling enter dauer normally, but then rapidly consume their stored energy and prematurely expire following vital organ failure. We found that this signalling pathway acts in adipose-like tissues to downregulate triglyceride hydrolysis so that these lipid reserves are rationed to last the entire duration of the arrest. Indeed, the downregulation of adipose triglyceride lipase (ATGL-1) activity suppresses both the rapid depletion of stored lipids and reduced life span of AMPK mutant dauers, while AMPK directly phosphorylates ATGL-1. Finally, we show that the slow release of energy during dauer is critical for appropriate long-term osmoregulation, which fails as triglyceride resources become depleted. These mechanisms may be essential for survival through diapause, hibernation, or long-term fasting in diverse organisms and may also underlie AMPK-dependent life span extension.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Narbonne, Patrick -- Roy, Richard -- England -- Nature. 2009 Jan 8;457(7226):210-4. doi: 10.1038/nature07536. Epub 2008 Dec 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19052547" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/chemistry/deficiency/genetics/*metabolism ; Adaptation, Physiological/*physiology ; Animals ; Caenorhabditis elegans/*growth & development/*metabolism ; Caenorhabditis elegans Proteins/antagonists & inhibitors/genetics/*metabolism ; Fasting/physiology ; Larva/metabolism/physiology ; Life Cycle Stages/*physiology ; Lipase/antagonists & inhibitors/metabolism ; *Lipid Metabolism ; Longevity/genetics/physiology ; Phosphorylation ; Protein-Serine-Threonine Kinases/deficiency/genetics/*metabolism ; Rats ; Signal Transduction ; Subcutaneous Tissue/metabolism ; Survival Analysis ; Time Factors ; Triglycerides/metabolism ; Water-Electrolyte Balance/genetics
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    Direct observation of the nanoscale dynamics of membrane lipids in a living cell (2008)
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    Publication Date: 2008-12-23
    Description: Cholesterol-mediated lipid interactions are thought to have a functional role in many membrane-associated processes such as signalling events. Although several experiments indicate their existence, lipid nanodomains ('rafts') remain controversial owing to the lack of suitable detection techniques in living cells. The controversy is reflected in their putative size of 5-200 nm, spanning the range between the extent of a protein complex and the resolution limit of optical microscopy. Here we demonstrate the ability of stimulated emission depletion (STED) far-field fluorescence nanoscopy to detect single diffusing (lipid) molecules in nanosized areas in the plasma membrane of living cells. Tuning of the probed area to spot sizes approximately 70-fold below the diffraction barrier reveals that unlike phosphoglycerolipids, sphingolipids and glycosylphosphatidylinositol-anchored proteins are transiently ( approximately 10-20 ms) trapped in cholesterol-mediated molecular complexes dwelling within 〈20-nm diameter areas. The non-invasive optical recording of molecular time traces and fluctuation data in tunable nanoscale domains is a powerful new approach to study the dynamics of biomolecules in living cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eggeling, Christian -- Ringemann, Christian -- Medda, Rebecca -- Schwarzmann, Gunter -- Sandhoff, Konrad -- Polyakova, Svetlana -- Belov, Vladimir N -- Hein, Birka -- von Middendorff, Claas -- Schonle, Andreas -- Hell, Stefan W -- England -- Nature. 2009 Feb 26;457(7233):1159-62. doi: 10.1038/nature07596. Epub 2008 Dec 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. ceggeli@gwdg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19098897" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Cell Membrane/chemistry/*metabolism ; Cell Survival ; Cholesterol/analysis/metabolism ; Diffusion ; Epithelial Cells/cytology ; Ethanolamines/analysis/metabolism ; Glycosylphosphatidylinositols/metabolism ; Membrane Lipids/*analysis/*metabolism ; Microscopy, Fluorescence/*methods ; Nanotechnology/*methods ; Sphingomyelins/analysis/metabolism ; Time Factors
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    Counting RAD51 proteins disassembling from nucleoprotein filaments under tension (2008)
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    Publication Date: 2008-12-09
    Description: The central catalyst in eukaryotic ATP-dependent homologous recombination consists of RAD51 proteins, polymerized around single-stranded DNA. This nucleoprotein filament recognizes and invades a homologous duplex DNA segment. After strand exchange, the nucleoprotein filament should disassemble so that the recombination process can be completed. The molecular mechanism of RAD51 filament disassembly is poorly understood. Here we show, by combining optical tweezers with single-molecule fluorescence microscopy and microfluidics, that disassembly of human RAD51 nucleoprotein filaments results from the interplay between ATP hydrolysis and the release of the tension stored in the filament. By applying external tension to the DNA, we found that disassembly slows down and can even be stalled. We quantified the fluorescence of RAD51 patches and found that disassembly occurs in bursts interspersed by long pauses. After relaxation of a stalled complex, pauses were suppressed resulting in a large burst. These results indicate that tension-dependent disassembly takes place only from filament ends, after tension-independent ATP hydrolysis. This integrative single-molecule approach allowed us to dissect the mechanism of this principal homologous recombination reaction step, which in turn clarifies how disassembly can be influenced by accessory proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871861/" 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/PMC3871861/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Mameren, Joost -- Modesti, Mauro -- Kanaar, Roland -- Wyman, Claire -- Peterman, Erwin J G -- Wuite, Gijs J L -- P01 CA092584/CA/NCI NIH HHS/ -- England -- Nature. 2009 Feb 5;457(7230):745-8. doi: 10.1038/nature07581. Epub 2008 Dec 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laser Centre and Department of Physics and Astronomy, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19060884" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Bacteriophage lambda/genetics ; DNA, Viral/chemistry/metabolism ; Fluorescence ; Humans ; Hydrolysis ; Microfluidics ; Microscopy, Fluorescence ; Optical Tweezers ; Rad51 Recombinase/*chemistry/*metabolism ; Recombination, Genetic ; Time Factors
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    Detecting influenza epidemics using search engine query data (2008)
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    Details
    Publication Date: 2008-11-21
    Description: Seasonal influenza epidemics are a major public health concern, causing tens of millions of respiratory illnesses and 250,000 to 500,000 deaths worldwide each year. In addition to seasonal influenza, a new strain of influenza virus against which no previous immunity exists and that demonstrates human-to-human transmission could result in a pandemic with millions of fatalities. Early detection of disease activity, when followed by a rapid response, can reduce the impact of both seasonal and pandemic influenza. One way to improve early detection is to monitor health-seeking behaviour in the form of queries to online search engines, which are submitted by millions of users around the world each day. Here we present a method of analysing large numbers of Google search queries to track influenza-like illness in a population. Because the relative frequency of certain queries is highly correlated with the percentage of physician visits in which a patient presents with influenza-like symptoms, we can accurately estimate the current level of weekly influenza activity in each region of the United States, with a reporting lag of about one day. This approach may make it possible to use search queries to detect influenza epidemics in areas with a large population of web search users.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ginsberg, Jeremy -- Mohebbi, Matthew H -- Patel, Rajan S -- Brammer, Lynnette -- Smolinski, Mark S -- Brilliant, Larry -- England -- Nature. 2009 Feb 19;457(7232):1012-4. doi: 10.1038/nature07634.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Google Inc., 1600 Amphitheatre Parkway, Mountain View, California 94043, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020500" target="_blank"〉PubMed〈/a〉
    Keywords: Centers for Disease Control and Prevention (U.S.) ; Databases, Factual ; *Health Behavior ; Health Education/*statistics & numerical data ; Humans ; Influenza, Human/diagnosis/*epidemiology/transmission/virology ; Internationality ; Internet/*utilization ; Linear Models ; Office Visits/statistics & numerical data ; Population Surveillance/*methods ; Reproducibility of Results ; Seasons ; Time Factors ; United States ; *User-Computer Interface
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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    Clinical research. Deaths in diabetes trial challenge a long-held theory (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin, Jennifer -- New York, N.Y. -- Science. 2008 Feb 15;319(5865):884-5. doi: 10.1126/science.319.5865.884.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276854" target="_blank"〉PubMed〈/a〉
    Keywords: Blood Glucose/*analysis ; Cardiovascular Diseases/epidemiology/prevention & control ; Controlled Clinical Trials as Topic ; Diabetes Mellitus, Type 2/blood/complications/*drug therapy/mortality ; Hemoglobin A, Glycosylated/analysis ; Humans ; Hypoglycemic Agents/*therapeutic use ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Ecology. A matter of timing (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyon, Bruce E -- Chaine, Alexis S -- Winkler, David W -- New York, N.Y. -- Science. 2008 Aug 22;321(5892):1051-2. doi: 10.1126/science.1159822.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA. lyon@biology.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719273" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; *Climate ; Cues ; Environment ; Female ; Male ; *Oviposition ; Passeriformes/genetics/*physiology ; Phenotype ; Photoperiod ; Seasons ; Selection, Genetic ; Temperature ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Phanerozoic trends in the global diversity of marine invertebrates (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: It has previously been thought that there was a steep Cretaceous and Cenozoic radiation of marine invertebrates. This pattern can be replicated with a new data set of fossil occurrences representing 3.5 million specimens, but only when older analytical protocols are used. Moreover, analyses that employ sampling standardization and more robust counting methods show a modest rise in diversity with no clear trend after the mid-Cretaceous. Globally, locally, and at both high and low latitudes, diversity was less than twice as high in the Neogene as in the mid-Paleozoic. The ratio of global to local richness has changed little, and a latitudinal diversity gradient was present in the early Paleozoic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alroy, John -- Aberhan, Martin -- Bottjer, David J -- Foote, Michael -- Fursich, Franz T -- Harries, Peter J -- Hendy, Austin J W -- Holland, Steven M -- Ivany, Linda C -- Kiessling, Wolfgang -- Kosnik, Matthew A -- Marshall, Charles R -- McGowan, Alistair J -- Miller, Arnold I -- Olszewski, Thomas D -- Patzkowsky, Mark E -- Peters, Shanan E -- Villier, Loic -- Wagner, Peter J -- Bonuso, Nicole -- Borkow, Philip S -- Brenneis, Benjamin -- Clapham, Matthew E -- Fall, Leigh M -- Ferguson, Chad A -- Hanson, Victoria L -- Krug, Andrew Z -- Layou, Karen M -- Leckey, Erin H -- Nurnberg, Sabine -- Powers, Catherine M -- Sessa, Jocelyn A -- Simpson, Carl -- Tomasovych, Adam -- Visaggi, Christy C -- New York, N.Y. -- Science. 2008 Jul 4;321(5885):97-100. doi: 10.1126/science.1156963.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Ecological Analysis and Synthesis, University of California-Santa Barbara, 735 State Street, Santa Barbara, CA 93101, USA. alroy@nceas.ucsb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599780" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Biological Evolution ; Databases, Factual ; Environment ; *Fossils ; Geography ; Geologic Sediments ; *Invertebrates/classification ; *Paleontology/methods ; Population Dynamics ; Sampling Studies ; Seawater ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Climate change: a titanic challenge (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sherwood, Steven C -- New York, N.Y. -- Science. 2008 Feb 15;319(5865):900. doi: 10.1126/science.319.5865.900b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276868" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate ; *Policy Making ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Evolution. Where have all Thoreau's flowers gone? (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2008 Jul 4;321(5885):24-5. doi: 10.1126/science.321.5885.24b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599747" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; *Climate ; *Ecosystem ; Flowers/*growth & development ; Greenhouse Effect ; Massachusetts ; *Plant Development ; Seasons ; Species Specificity ; Time Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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