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  • American Association for the Advancement of Science  (7,424)
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  • 1
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    An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome (2019)
    American Association for the Advancement of Science
    In:  EPIC3Science Advances, American Association for the Advancement of Science, 5(4), ISSN: 2375-2548
    Details
    Publication Date: 2020-02-12
    Description: Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    Different iron storage strategies among bloom-forming diatoms (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 115(52), (2018): E12275-E12284. doi: 10.1073/pnas.1805243115.
    Description: Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage mechanisms have been previously described: the protein ferritin and vacuolar storage. To investigate the ecological role of these mechanisms among diatoms, iron addition and removal incubations were conducted using natural phytoplankton communities from varying iron environments. We show that among the predominant diatoms, Pseudo-nitzschia were favored by iron removal and displayed unique ferritin expression consistent with a long-term storage function. Meanwhile, Chaetoceros and Thalassiosira gene expression aligned with vacuolar storage mechanisms. Pseudo-nitzschia also showed exceptionally high iron storage under steady-state high and low iron conditions, as well as following iron resupply to iron-limited cells. We propose that bloom-forming diatoms use different iron storage mechanisms and that ferritin utilization may provide an advantage in areas of prolonged iron limitation with pulsed iron inputs. As iron distributions and availability change, this speculated ferritin-linked advantage may result in shifts in diatom community composition that can alter marine ecosystems and biogeochemical cycles.
    Description: We thank the captain and crew of the R/V Melville and the CCGS J. P. Tully as well as the participants of the IRNBRU (MV1405) cruise for the California-based data, particularly K. Ellis [University of North Carolina (UNC)], T. Coale (University of California, San Diego), F. Kuzminov (Rutgers), H. McNair [University of California, Santa Barbara (UCSB)], and J. Jones (UCSB). W. Burns (UNC), S. Haines (UNC), and S. Bargu (Louisiana State University) assisted with sample processing and analysis. This work was funded by the National Science Foundation Grants OCE-1334935 (to A.M.), OCE-1334632 (to B.S.T.), OCE-1333929 (to K.T.), OCE-1334387 (to M.A.B.), OCE-1259776 (to K.W.B), and DGE-1650116 (Graduate Research Fellowship to R.H.L).
    Description: 2019-06-11
    Keywords: phytoplankton ; iron limitation ; Pseudo-nitzschia ; ferritin ; metatranscriptomics
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Agreement between reconstructed and modeled boreal precipitation of the Last Interglacial (2019)
    American Association for the Advancement of Science
    In:  EPIC3Science Advances, American Association for the Advancement of Science, 5(11), pp. eaax7047, ISSN: 2375-2548
    Details
    Publication Date: 2019-11-25
    Description: The last extended time period when climate may have been warmer than today was during the Last Interglacial (LIG; ca. 129 to 120 thousand years ago). However, a global view of LIG precipitation is lacking. Here, seven new LIG climate models are compared to the first global database of proxies for LIG precipitation. In this way, models are assessed in their ability to capture important hydroclimatic processes during a different climate. The models can reproduce the proxy-based positive precipitation anomalies from the preindustrial period over much of the boreal continents. Over the Southern Hemisphere, proxy-model agreement is partial. In models, LIG boreal monsoons have 42% wider area than in the preindustrial and produce 55% more precipitation and 50% more extreme precipitation. Austral monsoons are weaker. The mechanisms behind these changes are consistent with stronger summer radiative forcing over boreal high latitudes and with the associated higher temperatures during the LIG.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Abiotic methane synthesis and serpentinization in olivine-hosted fluid inclusions (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17666-17672. doi:10.1073/pnas.1907871116.
    Description: The conditions of methane (CH4) formation in olivine-hosted secondary fluid inclusions and their prevalence in peridotite and gabbroic rocks from a wide range of geological settings were assessed using confocal Raman spectroscopy, optical and scanning electron microscopy, electron microprobe analysis, and thermodynamic modeling. Detailed examination of 160 samples from ultraslow- to fast-spreading midocean ridges, subduction zones, and ophiolites revealed that hydrogen (H2) and CH4 formation linked to serpentinization within olivine-hosted secondary fluid inclusions is a widespread process. Fluid inclusion contents are dominated by serpentine, brucite, and magnetite, as well as CH4(g) and H2(g) in varying proportions, consistent with serpentinization under strongly reducing, closed-system conditions. Thermodynamic constraints indicate that aqueous fluids entering the upper mantle or lower oceanic crust are trapped in olivine as secondary fluid inclusions at temperatures higher than ∼400 °C. When temperatures decrease below ∼340 °C, serpentinization of olivine lining the walls of the fluid inclusions leads to a near-quantitative consumption of trapped liquid H2O. The generation of molecular H2 through precipitation of Fe(III)-rich daughter minerals results in conditions that are conducive to the reduction of inorganic carbon and the formation of CH4. Once formed, CH4(g) and H2(g) can be stored over geological timescales until extracted by dissolution or fracturing of the olivine host. Fluid inclusions represent a widespread and significant source of abiotic CH4 and H2 in submarine and subaerial vent systems on Earth, and possibly elsewhere in the solar system.
    Description: We are indebted to J. Eckert for his support with FE-EMPA; to K. Aquinho and E. Codillo for providing samples from Zambales; to K. Aquinho for Raman analysis of some of the samples from Zambales and Mt. Dent; to H. Dick for providing access to his thin section collection; to the curators of the IODP core repositories for providing access to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) samples; and to the captains and crews of the many cruises without whom the collection of these samples would not have been possible. Reviews by Peter Kelemen and an anonymous referee greatly improved this manuscript. This study is supported with funds provided by the National Science Foundation (NSF-OCE Award 1634032 to F.K. and J.S.S.).
    Description: 2020-02-19
    Keywords: Abiotic methane ; Fluid inclusions ; Serpentinization ; Methane seeps ; Carbon cycling
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  • 5
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    Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones. (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(20), (2019):9925-9930, doi:10.1073/pnas.1818349116.
    Description: Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (〉30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.
    Description: We thank John Baross and Rika Anderson for helpful discussions and feedback on this project. We also thank the chief scientists of the research cruise, Al Devol and Bess Ward, as well as the captain and crew of the R/V Thomas G. Thompson. This work was supported through a NASA Earth and Space Sciences Graduate Research Fellowship to J.K.S. and National Science Foundation Grant OCE-1138368 (to G.R.).
    Description: 2019-10-29
    Keywords: Oxygen deficient zones ; Arsenic ; Chemoautotrophy ; Dissimilatory arsenate reduction ; Marine metagenome
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  • 6
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    Decadal trends in the ocean carbon sink (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (24), (2019):11646-11651, doi:10.1073/pnas.1900371116.
    Description: Measurements show large decadal variability in the rate of CO2 accumulation in the atmosphere that is not driven by CO2 emissions. The decade of the 1990s experienced enhanced carbon accumulation in the atmosphere relative to emissions, while in the 2000s, the atmospheric growth rate slowed, even though emissions grew rapidly. These variations are driven by natural sources and sinks of CO2 due to the ocean and the terrestrial biosphere. In this study, we compare three independent methods for estimating oceanic CO2 uptake and find that the ocean carbon sink could be responsible for up to 40% of the observed decadal variability in atmospheric CO2 accumulation. Data-based estimates of the ocean carbon sink from pCO2 mapping methods and decadal ocean inverse models generally agree on the magnitude and sign of decadal variability in the ocean CO2 sink at both global and regional scales. Simulations with ocean biogeochemical models confirm that climate variability drove the observed decadal trends in ocean CO2 uptake, but also demonstrate that the sensitivity of ocean CO2 uptake to climate variability may be too weak in models. Furthermore, all estimates point toward coherent decadal variability in the oceanic and terrestrial CO2 sinks, and this variability is not well-matched by current global vegetation models. Reconciling these differences will help to constrain the sensitivity of oceanic and terrestrial CO2 uptake to climate variability and lead to improved climate projections and decadal climate predictions.
    Description: We thank Rebecca Wright and Erik Buitenhuis at University of East Anglia, Norwich, for providing updated runs from the NEMO-PlankTOM5 model. T.D. was supported by NSF Grant OCE-1658392. C.L.Q. thanks the UK Natural Environment Research Council for supporting the SONATA Project (Grant NE/P021417/1). P.L. was supported by the Max Planck Society for the Advancement of Science. J.H. was supported under Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys) Grant VH-NG-1301. S.B. and R.S. were supported by the H2020 project CRESCENDO “Coordinated Research in Earth Systems and Climate: Experiments, Knowledge, Dissemination and Outreach,” which received funding from the European Union’s Horizon 2020 research and innovation program under Grant No 641816. SOCAT is an international effort, endorsed by the International Ocean Carbon Coordination Project, the Surface Ocean-Lower Atmosphere Study, and the Integrated Marine Biosphere Research program, to deliver a uniformly quality-controlled surface ocean CO2 database. The many researchers and funding agencies responsible for the collection of data and quality control are thanked for their contributions to SOCAT.
    Description: 2019-11-28
    Keywords: Carbon dioxide ; Ocean carbon sink ; Terrestrial carbon sink ; Climate variability ; Carbon budget
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  • 7
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    A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17934-17942, doi:10.1073/pnas.1910121116.
    Description: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.
    Description: We are grateful to Martin Kolisko and Fabien Burki for helpful discussion about and comments on the phylogenetic analysis; and Filip Husnik and Vittorio Boscaro for valuable comments on the manuscript. This work was supported by a grant from the National Science Foundation to R.J.G. and P.J.K. (PLR-1341362) and from the Natural Sciences and Engineering Research Council of Canada to P.J.K. (RGPIN-2014-03994).
    Description: 2020-02-19
    Keywords: plastid endosymbiosis ; kleptoplasty ; dinoflagellates ; plastid integration
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  • 8
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    NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Diaz, J. M., Plummer, S., Hansel, C. M., Andeer, P. F., Saito, M. A., & McIlvin, M. R. NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica. Proceedings of the National Academy of Sciences of the United States of America, 116 (33), (2019): 16448-16453, doi: 10.1073/pnas.1821233116.
    Description: Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.
    Description: This work was supported by a postdoctoral fellowship from the Ford Foundation (to J.M.D.), the National Science Foundation (NSF) under grants OCE 1225801 (to J.M.D.) and OCE 1246174 (to C.M.H.), a Junior Faculty Seed Grant from the University of Georgia Research Foundation (to J.M.D.), and a National Science Foundation Graduate Research Fellowship (to S.P.). The FIRe was purchased through a NSF equipment improvement grant (1624593).The authors thank Melissa Soule for assistance with LC/MS/MS analysis of peptide samples.
    Keywords: Reactive oxygen species ; Photosynthesis ; Oxidative stress ; Biogeochemistry
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  • 9
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    Rapid mixing and exchange of deep-ocean waters in an abyssal boundary current. (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(27), (2019): 13233-13238, doi: 10.1073/pnas.1904087116.
    Description: The overturning circulation of the global ocean is critically shaped by deep-ocean mixing, which transforms cold waters sinking at high latitudes into warmer, shallower waters. The effectiveness of mixing in driving this transformation is jointly set by two factors: the intensity of turbulence near topography and the rate at which well-mixed boundary waters are exchanged with the stratified ocean interior. Here, we use innovative observations of a major branch of the overturning circulation—an abyssal boundary current in the Southern Ocean—to identify a previously undocumented mixing mechanism, by which deep-ocean waters are efficiently laundered through intensified near-boundary turbulence and boundary–interior exchange. The linchpin of the mechanism is the generation of submesoscale dynamical instabilities by the flow of deep-ocean waters along a steep topographic boundary. As the conditions conducive to this mode of mixing are common to many abyssal boundary currents, our findings highlight an imperative for its representation in models of oceanic overturning.
    Description: The DynOPO project is supported by the UK Natural Environment Research Council (grants NE/K013181/1 and NE/K012843/1) and the US National Science Foundation (grants OCE-1536453 and OCE-1536779). A.C.N.G. acknowledges the support of the Royal Society and the Wolfson Foundation. S.L. acknowledges the support of award NA14OAR4320106 from the National Oceanic and Atmospheric Administration, US Department of Commerce. The statements, findings, conclusions, and recommendations are those of the authors, and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, or the US Department of Commerce. We are grateful to the scientific party, crew, and technicians on the RRS James Clark Ross for their hard work during data collection.
    Description: 2019-12-18
    Keywords: Ocean mixing ; Overturning circulation ; Submesoscale instabilities ; Turbulence
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  • 10
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    Ocean deoxygenation and zooplankton: Very small oxygen differences matter (2019)
    American Association for the Advancement of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Science Advances, 4(12), (2018): eaau5180. doi: 10.1126/sciadv.aau5180.
    Description: Oxygen minimum zones (OMZs), large midwater regions of very low oxygen, are expected to expand as a result of climate change. While oxygen is known to be important in structuring midwater ecosystems, a precise and mechanistic understanding of the effects of oxygen on zooplankton is lacking. Zooplankton are important components of midwater food webs and biogeochemical cycles. Here, we show that, in the eastern tropical North Pacific OMZ, previously undescribed submesoscale oxygen variability has a direct effect on the distribution of many major zooplankton groups. Despite extraordinary hypoxia tolerance, many zooplankton live near their physiological limits and respond to slight (≤1%) changes in oxygen. Ocean oxygen loss (deoxygenation) may, thus, elicit major unanticipated changes to midwater ecosystem structure and function.
    Description: We thank the captain and crew of the R/V Sikuliaq (University of Alaska) and Scripps Institution of Oceanography for additional technical services. Thanks also to D. Ullman and D. Casagrande for Wire Flyer assistance; C. Matson and J. Calderwood for MOCNESS upgrades; S. Gordon (professional photographer, Open Boat Films LLC) for the photographs and movies; and A. Dymowska, J. Ivory, Y. Jin, J. McGreal, and N. Redmond for help at sea. Funding: Funding was provided by the NSF grants OCE1459243 (to K.F.W., C.R., and B.A.S.), OCE1458967 (to C.D.), DGE1244657 (to M.A.B.), and OCE1460819 (URI REU SURFO program to S.R.) plus funding from our respective institutions. Author contributions: K.F.W., B.A.S., C.R., and C.D. conceived the project. K.F.W. led the writing effort, with substantial contributions from all the authors. K.F.W. directed the MOCNESS component including zooplankton abundance and biomass quantification. B.A.S. directed the metabolic experiments and Tucker trawls. C.R. directed the Wire Flyer work. B.A.S., C.D., K.A.S.M., and M.A.B. developed the MI models. D.O., C.T.S., D.M., and S.R. processed and analyzed the zooplankton data. T.J.A. processed the MOCNESS hydrographic data. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Extensive files of continuous hydrographic data from transects are available from C.R. (Wire Flyer) and K.F.W. (MOCNESS). Additional data related to this paper may be requested from the authors.
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  • 11
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    On the occurrence of cytochrome P450 in viruses (2019)
    National Academy of Sciences
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    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(25), (2019):12343-12352, doi:10.1073/pnas.1901080116.
    Description: Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.
    Description: We thank Dr. David Nes (Texas Tech University) for providing sterols and Dr. Matthieu Legendre and Dr. Chantal Abergel (CNRS, Marseille) for access to the P. celtis sequences. Drs. Irina Arkhipova, Mark Hahn, Judith Luborsky, and Ann Bucklin commented on the manuscript. The research was supported by a USA-UK Fulbright Scholarship and a Royal Society grant (to D.C.L.), the Boston University Superfund Research Program [NIH Grant 5P42ES007381 (to J.J.S. and J.V.G.) and NIH Grant 5U41HG003345 (to J.V.G.)], the European Regional Development Fund and Welsh Government Project BEACON (S.L.K.), the Woods Hole Center for Oceans and Human Health [NIH Grant P01ES021923 and National Science Foundation Grant OCE-1314642 (to J.J.S.)], and NIH Grant R01GM53753 (to T.L.P.).
    Description: 2019-12-05
    Keywords: cytochrome P450 ; virus ; evolution ; domains of life ; redox partner
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  • 12
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    Archaea dominate oxic subseafloor communities over multimillion-year time scales (2019)
    American Association for the Advancement of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).. The definitive version was published in Vuillemin, A., Wankel, S. D., Coskun, Ö. K., Magritsch, T., Vargas, S., Estes, E. R., Spivack, A. J., Smith, D. C., Pockalny, R., Murray, R. W., D'Hondt, S., & Orsi, W. D. Archaea dominate oxic subseafloor communities over multimillion-year time scales. Science Advances, 5(6), (2019): eaaw4108, doi: 10.1126/sciadv.aaw4108.
    Description: Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.
    Description: This work was supported primarily by the Deutsche Forschungsgemeinschaft (DFG) project OR 417/1-1 granted to W.D.O. Preliminary work was supported by the Center for Dark Energy Biosphere Investigations project OCE-0939564 also granted to W.D.O. Publication of the manuscript was supported by the LMU Mentoring Program. The expedition was funded by the US National Science Foundation through grant NSF-OCE-1433150 to A.J.S, S.D., and R.P. R.W.M. led the expedition. This is a contribution of the Deep Carbon Observatory (DCO). S.D.W. acknowledges partial support from NASA Exobiology (NNX15AM04G). This is Center for Dark Energy Biosphere Investigations (C-DEBI) publication number 463. Portions of this material are based on work supported while R.W.M. was serving at the National Science Foundation. A portion of this work was performed as part of the LMU Masters Program “Geobiology and Paleobiology” (MGAP).
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  • 13
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    Mesoscale eddies release pelagic sharks from thermal constraints to foraging in the ocean twilight zone (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17187-17192, doi:10.1073/pnas.1903067116.
    Description: Mesoscale eddies are critical components of the ocean’s “internal weather” system. Mixing and stirring by eddies exerts significant control on biogeochemical fluxes in the open ocean, and eddies may trap distinctive plankton communities that remain coherent for months and can be transported hundreds to thousands of kilometers. Debate regarding how and why predators use fronts and eddies, for example as a migratory cue, enhanced forage opportunities, or preferred thermal habitat, has been ongoing since the 1950s. The influence of eddies on the behavior of large pelagic fishes, however, remains largely unexplored. Here, we reconstruct movements of a pelagic predator, the blue shark (Prionace glauca), in the Gulf Stream region using electronic tags, earth-observing satellites, and data-assimilating ocean forecasting models. Based on 〉2,000 tracking days and nearly 500,000 high-resolution time series measurements collected by 15 instrumented individuals, we show that blue sharks seek out the interiors of anticyclonic eddies where they dive deep while foraging. Our observations counter the existing paradigm that anticyclonic eddies are unproductive ocean “deserts” and suggest anomalously warm temperatures in these features connect surface-oriented predators to the most abundant fish community on the planet in the mesopelagic. These results also shed light on the ecosystem services provided by mesopelagic prey. Careful consideration will be needed before biomass extraction from the ocean twilight zone to avoid interrupting a key link between planktonic production and top predators. Moreover, robust associations between targeted fish species and oceanographic features increase the prospects for effective dynamic ocean management.
    Description: We thank D. McGillicuddy, G. Lawson, and G. Flierl for helpful discussions while developing this work and 2 anonymous reviewers whose feedback significantly improved the manuscript. We also thank C. Fischer and the OCEARCH team for their support of this research. This work was funded by awards to C.D.B. from the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology; the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution; and the National Aeronatics and Space Administration (NASA) Earth and Space Science Fellowship. C.D.B. and P.G. acknowledge support from the NASA New Investigator Program Award 80NSSC18K0757, and P.G. acknowledges support from NSF Award OCE-1558809. This research is partially supported by funding to S.R.T. as part of the Audacious Project, a collaborative endeavor, housed at TED. We thank donors to the Woods Hole Oceanographic Institution (WHOI) ProjectWHOI crowdfunding campaign: The Secret Lives of Sharks. Computational support was provided by the Amazon Web Services Cloud Credits for Research program. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.
    Description: 2020-02-06
    Keywords: remote sensing ; oceanographic model ; satellite telemetry ; marine predator ; mesopelagic
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  • 14
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    A productivity collapse to end earth's great oxidation (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17207-17212, doi:10.1073/pnas.1900325116.
    Description: It has been hypothesized that the overall size of—or efficiency of carbon export from—the biosphere decreased at the end of the Great Oxidation Event (GOE) (ca. 2,400 to 2,050 Ma). However, the timing, tempo, and trigger for this decrease remain poorly constrained. Here we test this hypothesis by studying the isotope geochemistry of sulfate minerals from the Belcher Group, in subarctic Canada. Using insights from sulfur and barium isotope measurements, combined with radiometric ages from bracketing strata, we infer that the sulfate minerals studied here record ambient sulfate in the immediate aftermath of the GOE (ca. 2,018 Ma). These sulfate minerals captured negative triple-oxygen isotope anomalies as low as ∼ −0.8‰. Such negative values occurring shortly after the GOE require a rapid reduction in primary productivity of 〉80%, although even larger reductions are plausible. Given that these data imply a collapse in primary productivity rather than export efficiency, the trigger for this shift in the Earth system must reflect a change in the availability of nutrients, such as phosphorus. Cumulatively, these data highlight that Earth’s GOE is a tale of feast and famine: A geologically unprecedented reduction in the size of the biosphere occurred across the end-GOE transition.
    Description: Olivia M. J. Dagnaud assisted during fieldwork. S. V. Lalonde and E. A. Sperling provided helpful comments on an early version of the manuscript. We thank N. J. Planavsky and an anonymous reviewer for their constructive feedback. M.S.W.H. was supported by an NSERC PGS-D and student research grants from National Geographic, the APS Lewis and Clark Fund, Northern Science Training Program, McGill University Graduate Research Enhancement and Travel Awards, Geological Society of America, Mineralogical Association of Canada, and Stanford University. P.W.C. acknowledges support from the University of Colorado Boulder, the Agouron Institute Geobiology postdoctoral Fellowship program, a Natural Sciences and Engineering Council of Canada Postgraduate Scholarship–Doctoral Program scholarship, and the NSTP. Y.P. was supported by the Strategic Priority Research Program of CAS (XDB26000000). T.J.H. thanks Maureen E. Auro for laboratory assistance and the NSF for supporting isotope research in the NIRVANA Labs.
    Description: 2020-02-12
    Keywords: Proterozoic ; primary productivity ; Great Oxidation Event ; triple-oxygen isotopes ; nutrient limitation
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  • 15
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    Sustained wood burial in the Bengal Fan over the last 19 My (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(45), (2019): 22518-22525, doi:10.1073/pnas.1913714116.
    Description: The Ganges–Brahmaputra (G-B) River system transports over a billion tons of sediment every year from the Himalayan Mountains to the Bay of Bengal and has built the world’s largest active sedimentary deposit, the Bengal Fan. High sedimentation rates drive exceptional organic matter preservation that represents a long-term sink for atmospheric CO2. While much attention has been paid to organic-rich fine sediments, coarse sediments have generally been overlooked as a locus of organic carbon (OC) burial. However, International Ocean Discovery Program Expedition 354 recently discovered abundant woody debris (millimeter- to centimeter-sized fragments) preserved within the coarse sediment layers of turbidite beds recovered from 6 marine drill sites along a transect across the Bengal Fan (∼8°N, ∼3,700-m water depth) with recovery spanning 19 My. Analysis of bulk wood and lignin finds mostly lowland origins of wood delivered episodically. In the last 5 My, export included C4 plants, implying that coarse woody, lowland export continued after C4 grassland expansion, albeit in reduced amounts. Substantial export of coarse woody debris in the last 1 My included one wood-rich deposit (∼0.05 Ma) that encompassed coniferous wood transported from the headwaters. In coarse layers, we found on average 0.16 weight % OC, which is half the typical biospheric OC content of sediments exported by the modern G-B Rivers. Wood burial estimates are hampered by poor drilling recovery of sands. However, high-magnitude, low-frequency wood export events are shown to be a key mechanism for C burial in turbidites.
    Description: This work was funded by National Science Foundation Grants OCE-1401217 and COL-T354A55 to S.J.F. and OCE-1400805 to V.G. Graduate student participation in the project received support from University of Southern California Provost’s Fellowship to H.L. Samples were provided by the International Ocean Discovery Program. We are grateful for the efforts of the Expedition 354 Science Party, Carl Johnson, and Zongguang Liu. C.F.-L. and A.G. were supported by IODP-France. We thank Colin Osborne and Maria Vorontsova for helpful discussions.
    Description: 2020-04-21
    Keywords: carbon cycle ; wood ; lignin ; Himalaya ; Bengal Fan
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  • 16
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    Reproduction (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 51-68 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.000411
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  • 17
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    The Physiology of Supporting Tissue (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 103-118 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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  • 18
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    Digestive System (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 191-224 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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  • 19
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    Derivatives of Blood Plasma (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 327-356 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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  • 20
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    The Respiratory System (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 429-456 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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  • 21
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    Special Senses, Cutaneous Sensation (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 553-569 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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  • 22
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    Physiological Aspects of Genetics (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 605-628 
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    Topics: Medicine , Biology
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  • 23
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    Biological Oxidations and Reductions (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 1-34 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
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  • 24
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    Proteolytic Enzymes (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 35-54 
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  • 25
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    The Chemistry of the Carbohydrates (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 55-78 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 26
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    The Chemistry and Metabolism of the Lipids (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 79-104 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 27
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    Phosphorus Compounds (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 105-124 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Carbohydrate Metabolism (1947)
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    Annual Review of Biochemistry 16 (1947), S. 125-152 
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  • 29
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    The Metabolism of Proteins and Amino Acids (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 153-176 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Antioxidants (1947)
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    Annual Review of Biochemistry 16 (1947), S. 177-192 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
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  • 31
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    Choline (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 193-222 
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    Topics: Chemistry and Pharmacology , Biology
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  • 32
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    The Chemistry of the Proteins and Amino Acids (1947)
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    Annual Review of Biochemistry 16 (1947), S. 223-272 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
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    Mineral Metabolism (1947)
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    Annual Review of Biochemistry 16 (1947), S. 273-290 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    The Chemistry of the Hormones (1947)
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    Annual Review of Biochemistry 16 (1947), S. 291-322 
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  • 35
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    Fat-Soluble Vitamins (1947)
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    Annual Review of Biochemistry 16 (1947), S. 323-358 
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    Water-Soluble Vitamins (1947)
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    Annual Review of Biochemistry 16 (1947), S. 359-386 
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    The Use of Pteroylglutamic Acid (Liver L. Case1 Factor, Folic Acid) in Clinical Studies (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 387-402 
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  • 38
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    Nutrition (1947)
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    Annual Review of Biochemistry 16 (1947), S. 401-442 
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  • 39
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    Carotenoid and Indolic Biochromes of Animals (1947)
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    Annual Review of Biochemistry 16 (1947), S. 443-470 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 40
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    The Nitrogenous Constituents of Plants (1947)
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    Annual Review of Biochemistry 16 (1947), S. 471-502 
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  • 41
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    Mineral Nutrition of Plants (1947)
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    Annual Review of Biochemistry 16 (1947), S. 503-528 
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  • 42
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    Growth Substances in Higher Plants (1947)
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    Annual Review of Biochemistry 16 (1947), S. 529-564 
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    Marine Bacteriology (1947)
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    Annual Review of Biochemistry 16 (1947), S. 565-586 
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    Antimalarial Drugs (1947)
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    Annual Review of Biochemistry 16 (1947), S. 587-604 
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  • 45
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    Bacterial Metabolism (1947)
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    Annual Review of Biochemistry 16 (1947), S. 605-630 
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    Use of Isotopes in Biochemical Research: Fundamental Aspects (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 631-654 
    Details
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bi.16.070147.003215
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  • 47
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    The Chemistry of the Steroids (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 16 (1947), S. 655-688 
    Details
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bi.16.070147.003255
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  • 48
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    Nerve and Synaptic Conduction (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 457-476 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.002325
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  • 49
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    The Somatic Functions of the Central Nervous System (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 525-552 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.002521
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  • 50
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    Pharmacology (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 651-672 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.003251
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  • 51
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    Metabolic Functions of the Endocrine Glands (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 69-102 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.000441
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  • 52
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    Developmental Physiology (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 19-50 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.000315
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  • 53
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    Muscle (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 119-148 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.001003
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  • 54
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    Electrical Activity of the Brain (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 507-524 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.002451
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  • 55
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    Permeability (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 581-604 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.003053
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  • 56
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    Growth (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 1-18 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.000245
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  • 57
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    The Visceral Functions of the Nervous System (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 163-190 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.001115
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  • 58
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    Heart (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 301-326 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.001505
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  • 59
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    Physiological Effects of Heat and Cold (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 409-428 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.002205
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  • 60
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    Kidney (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 225-254 
    Details
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.001301
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  • 61
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    Blood Gas Transport (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 357-380 
    Details
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.002041
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  • 62
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    Defense Mechanisms (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 629-650 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.003213
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  • 63
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    Exercise (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 149-162 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.001053
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  • 64
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    Peripheral Circulation (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 255-300 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.001351
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  • 65
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    Water Metabolism (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 381-408 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.002121
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  • 66
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    Bioelectric Potentials in the Nervous System and in Muscle (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 477-506 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
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    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.002401
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  • 67
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    The Experimental Neurosis (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 9 (1947), S. 569-580 
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    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ph.09.030147.003033
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  • 68
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    Antigenic Variation in Protozoa and Bacteria (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 19-42 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.000315
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  • 69
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    Morphology and Cytology of Protozoa (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 1-18 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.000245
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  • 70
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    Variation in Phytopathogenic Fungi (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 61-84 
    Details
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.000425
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  • 71
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    Life Cycle of Malarial Parasites (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 43-60 
    Details
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.000355
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  • 72
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    Variation in Phytopathogenic Viruses (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 85-100 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.000505
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  • 73
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    Some Aspects of the Problem of Growth Factors for Protozoa (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 101-114 
    Details
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.000533
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  • 74
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    Nitrogen Metabolism (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 141-158 
    Details
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001041
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  • 75
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    Bacterial Metabolism (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 115-140 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.000555
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  • 76
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    Industrial Fermentations (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 159-172 
    Details
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001111
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  • 77
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    Quaternary Ammonium Compounds (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 173-192 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001133
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  • 78
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    Antibiotics (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 193-236 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001205
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    Chemotherapeutic Agents (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 237-262 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001321
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  • 80
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    Immunochemistry (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 263-290 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001403
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  • 81
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    Some Aspects of Active Immunization (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 291-308 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001451
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  • 82
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    The Rickettsiae (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 333-350 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
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    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.002001
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    Respiratory Viruses (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 351-384 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.002031
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  • 84
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    Medical and Epidemiological Aspects of Enteric Infection (1947)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 1 (1947), S. 309-332 
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    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.01.100147.001521
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  • 85
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    Peptidoglycan hydrolase of an unusual cross-link cleavage specificity contributes to bacterial cell wall synthesis (2019)
    National Academy of Sciences
    Details
    Publication Date: 2019-04-02
    Description: Bacteria are surrounded by a protective exoskeleton, peptidoglycan (PG), a cross-linked mesh-like macromolecule consisting of glycan strands interlinked by short peptides. Because PG completely encases the cytoplasmic membrane, cleavage of peptide cross-links is a prerequisite to make space for incorporation of nascent glycan strands for its successful expansion during cell growth. In most bacteria, the peptides consist of l-alanine, d-glutamate, meso-diaminopimelic acid (mDAP) and d-alanine (d-Ala) with cross-links occurring either between d-Ala and mDAP or two mDAP residues. In Escherichia coli, the d-Ala−mDAP cross-links whose cleavage by specialized endopeptidases is crucial for expansion of PG predominate. However, a small proportion of mDAP−mDAP cross-links also exist, yet their role in the context of PG expansion or the hydrolase(s) capable of catalyzing their cleavage is not known. Here, we identified an ORF of unknown function, YcbK (renamed MepK), as an mDAP−mDAP cross-link cleaving endopeptidase working in conjunction with other elongation-specific endopeptidases to make space for efficient incorporation of nascent PG strands into the sacculus. E. coli mutants lacking mepK and another d-Ala−mDAP–specific endopeptidase (mepS) were synthetic sick, and the defects were abrogated by lack of l,d-transpeptidases, enzymes catalyzing the formation of mDAP cross-links. Purified MepK was able to cleave the mDAP cross-links of soluble muropeptides and of intact PG sacculi. Overall, this study describes a PG hydrolytic enzyme with a hitherto unknown substrate specificity that contributes to expansion of the PG sacculus, emphasizing the fundamental importance of cross-link cleavage in bacterial peptidoglycan synthesis.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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    Shockley–Queisser triangle predicts the thermodynamic efficiency limits of arbitrarily complex multijunction bifacial solar cells (2019)
    National Academy of Sciences
    Details
    Publication Date: 2019-11-12
    Description: As monofacial, single-junction solar cells approach their fundamental limits, there has been significant interest in tandem solar cells in the presence of concentrated sunlight or tandem bifacial solar cells with back-reflected albedo. The bandgap sequence and thermodynamic efficiency limits of these complex cell configurations require sophisticated numerical calculation. Therefore, the analyses of specialized cases are scattered throughout the literature. In this paper, we show that a powerful graphical approach called the normalized “Shockley–Queisser (S-Q) triangle” (i.e., imp=1−vmp) is sufficient to calculate the bandgap sequence and efficiency limits of arbitrarily complex photovoltaic (PV) topologies. The results are validated against a wide variety of specialized cases reported in the literature and are accurate within a few percent. We anticipate that the widespread use of the S-Q triangle will illuminate the deeper physical principles and design trade-offs involved in the design of bifacial tandem solar cells under arbitrary concentration and series resistance.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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    Insulin signaling in the hippocampus and amygdala regulates metabolism and neurobehavior (2019)
    National Academy of Sciences
    Details
    Publication Date: 2019-02-14
    Description: Previous studies have shown that insulin and IGF-1 signaling in the brain, especially the hypothalamus, is important for regulation of systemic metabolism. Here, we develop mice in which we have specifically inactivated both insulin receptors (IRs) and IGF-1 receptors (IGF1Rs) in the hippocampus (Hippo-DKO) or central amygdala (CeA-DKO) by stereotaxic delivery of AAV-Cre into IRlox/lox/IGF1Rlox/loxmice. Consequently, both Hippo-DKO and CeA-DKO mice have decreased levels of the GluA1 subunit of glutamate AMPA receptor and display increased anxiety-like behavior, impaired cognition, and metabolic abnormalities, including glucose intolerance. Hippo-DKO mice also display abnormal spatial learning and memory whereas CeA-DKO mice have impaired cold-induced thermogenesis. Thus, insulin/IGF-1 signaling has common roles in the hippocampus and central amygdala, affecting synaptic function, systemic glucose homeostasis, behavior, and cognition. In addition, in the hippocampus, insulin/IGF-1 signaling is important for spatial learning and memory whereas insulin/IGF-1 signaling in the central amygdala controls thermogenesis via regulation of neural circuits innervating interscapular brown adipose tissue.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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    A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae (2019)
    National Academy of Sciences
    Details
    Publication Date: 2019-06-17
    Description: The sunflower family, Asteraceae, comprises 10% of all flowering plant species and displays an incredible diversity of form. Asteraceae are clearly monophyletic, yet resolving phylogenetic relationships within the family has proven difficult, hindering our ability to understand its origin and diversification. Recent molecular clock dating has suggested a Cretaceous origin, but the lack of deep sampling of many genes and representative taxa from across the family has impeded the resolution of migration routes and diversifications that led to its global distribution and tremendous diversity. Here we use genomic data from 256 terminals to estimate evolutionary relationships, timing of diversification(s), and biogeographic patterns. Our study places the origin of Asteraceae at ∼83 MYA in the late Cretaceous and reveals that the family underwent a series of explosive radiations during the Eocene which were accompanied by accelerations in diversification rates. The lineages that gave rise to nearly 95% of extant species originated and began diversifying during the middle Eocene, coincident with the ensuing marked cooling during this period. Phylogenetic and biogeographic analyses support a South American origin of the family with subsequent dispersals into North America and then to Asia and Africa, later followed by multiple worldwide dispersals in many directions. The rapid mid-Eocene diversification is aligned with the biogeographic range shift to Africa where many of the modern-day tribes appear to have originated. Our robust phylogeny provides a framework for future studies aimed at understanding the role of the macroevolutionary patterns and processes that generated the enormous species diversity of Asteraceae.
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    Science, health, and cultural literacy in a rapidly changing communications landscape (2019)
    National Academy of Sciences
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    Publication Date: 2019-04-15
    Description: There is a gap between how many scientists communicate and how most people understand and interpret messages. This article argues that the extensive science communications literature needs to be joined by the health literacy literature and anthropological work on cultural variations in hearing and understanding messages. Rapid changes and differences in how people in the United States get information are also discussed. Better understanding of how people get and perceive messages, and how access to information and to health services affects their behavior, should be an iterative and interdisciplinary effort. Community involvement in developing communication strategies is strongly encouraged.
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    A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales (2019)
    National Academy of Sciences
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    Publication Date: 2019-09-30
    Description: Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.
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    Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins (2019)
    National Academy of Sciences
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    Publication Date: 2019-09-16
    Description: Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the Tetrahymena doublet microtubule by cryoelectron microscopy. The map demonstrates that the network of microtubule inner proteins weaves into the tubulin lattice and forms an inner sheath. From mass spectrometry data and de novo modeling, we identified Rib43a proteins as the filamentous microtubule inner proteins in the protofilament ribbon region. The Rib43a–tubulin interaction leads to an elongated tubulin dimer distance every 2 dimers. In addition, the tubulin lattice structure with missing microtubule inner proteins (MIPs) by sarkosyl treatment shows significant longitudinal compaction and lateral angle change between protofilaments. These results are evidence that the MIPs directly affect and stabilize the tubulin lattice. It suggests that the doublet microtubule is an intrinsically stressed filament and that this stress could be manipulated in the regulation of ciliary waveforms.
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    Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells (2019)
    National Academy of Sciences
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    Publication Date: 2019-07-01
    Description: Aberrant MYC oncogene activation is one of the most prevalent characteristics of cancer. By overlapping datasets of Drosophila genes that are insulin-responsive and also regulate nucleolus size, we enriched for Myc target genes required for cellular biosynthesis. Among these, we identified the aminoacyl tRNA synthetases (aaRSs) as essential mediators of Myc growth control in Drosophila and found that their pharmacologic inhibition is sufficient to kill MYC-overexpressing human cells, indicating that aaRS inhibitors might be used to selectively target MYC-driven cancers. We suggest a general principle in which oncogenic increases in cellular biosynthesis sensitize cells to disruption of protein homeostasis.
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    Optimizing organic electrosynthesis through controlled voltage dosing and artificial intelligence (2019)
    National Academy of Sciences
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    Publication Date: 2019-08-21
    Description: Organic electrosynthesis can transform the chemical industry by introducing electricity-driven processes that are more energy efficient and that can be easily integrated with renewable energy sources. However, their deployment is severely hindered by the difficulties of controlling selectivity and achieving a large energy conversion efficiency at high current density due to the low solubility of organic reactants in practical electrolytes. This control can be improved by carefully balancing the mass transport processes and electrocatalytic reaction rates at the electrode diffusion layer through pulsed electrochemical methods. In this study, we explore these methods in the context of the electrosynthesis of adiponitrile (ADN), the largest organic electrochemical process in industry. Systematically exploring voltage pulses in the timescale between 5 and 150 ms led to a 20% increase in production of ADN and a 250% increase in relative selectivity with respect to the state-of-the-art constant voltage process. Moreover, combining this systematic experimental investigation with artificial intelligence (AI) tools allowed us to rapidly discover drastically improved electrosynthetic conditions, reaching improvements of 30 and 325% in ADN production rates and selectivity, respectively. This powerful AI-enhanced experimental approach represents a paradigm shift in the design of electrified chemical transformations, which can accelerate the deployment of more sustainable electrochemical manufacturing processes.
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    Parallel spatial channels converge at a bottleneck in anterior word-selective cortex (2019)
    National Academy of Sciences
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    Publication Date: 2019-04-08
    Description: In most environments, the visual system is confronted with many relevant objects simultaneously. That is especially true during reading. However, behavioral data demonstrate that a serial bottleneck prevents recognition of more than one word at a time. We used fMRI to investigate how parallel spatial channels of visual processing converge into a serial bottleneck for word recognition. Participants viewed pairs of words presented simultaneously. We found that retinotopic cortex processed the two words in parallel spatial channels, one in each contralateral hemisphere. Responses were higher for attended than for ignored words but were not reduced when attention was divided. We then analyzed two word-selective regions along the occipitotemporal sulcus (OTS) of both hemispheres (subregions of the visual word form area, VWFA). Unlike retinotopic regions, each word-selective region responded to words on both sides of fixation. Nonetheless, a single region in the left hemisphere (posterior OTS) contained spatial channels for both hemifields that were independently modulated by selective attention. Thus, the left posterior VWFA supports parallel processing of multiple words. In contrast, activity in a more anterior word-selective region in the left hemisphere (mid OTS) was consistent with a single channel, showing (i) limited spatial selectivity, (ii) no effect of spatial attention on mean response amplitudes, and (iii) sensitivity to lexical properties of only one attended word. Therefore, the visual system can process two words in parallel up to a late stage in the ventral stream. The transition to a single channel is consistent with the observed bottleneck in behavior.
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    Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility (2019)
    National Academy of Sciences
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    Publication Date: 2019-06-24
    Description: Genomic analyses of patients with congenital heart disease (CHD) have identified significant contribution from mutations affecting cilia genes and chromatin remodeling genes; however, the mechanism(s) connecting chromatin remodeling to CHD is unknown. Histone H2B monoubiquitination (H2Bub1) is catalyzed by the RNF20 complex consisting of RNF20, RNF40, and UBE2B. Here, we show significant enrichment of loss-of-function mutations affecting H2Bub1 in CHD patients (enrichment 6.01,P= 1.67 × 10−03), some of whom had abnormal laterality associated with ciliary dysfunction. InXenopus, knockdown ofrnf20andrnf40results in abnormal heart looping, defective development of left–right (LR) asymmetry, and impaired cilia motility. Rnf20, Rnf40, and Ube2b affect LR patterning and cilia synergistically. Examination of global H2Bub1 level inXenopusembryos shows that H2Bub1 is developmentally regulated and requires Rnf20. To examine gene-specific H2Bub1, we performed ChIP-seq of mouse ciliated and nonciliated tissues and showed tissue-specific H2Bub1 marks significantly enriched at cilia genes including the transcription factorRfx3. Rnf20 knockdown results in decreased levels ofrfx3mRNA inXenopus, and exogenousrfx3can rescue the Rnf20 depletion phenotype. These data suggest that Rnf20 functions at theRfx3locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.
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    Deep learning predicts path-dependent plasticity (2019)
    National Academy of Sciences
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    Publication Date: 2019-12-16
    Description: Plasticity theory aims at describing the yield loci and work hardening of a material under general deformation states. Most of its complexity arises from the nontrivial dependence of the yield loci on the complete strain history of a material and its microstructure. This motivated 3 ingenious simplifications that underpinned a century of developments in this field: 1) yield criteria describing yield loci location; 2) associative or nonassociative flow rules defining the direction of plastic flow; and 3) effective stress–strain laws consistent with the plastic work equivalence principle. However, 2 key complications arise from these simplifications. First, finding equations that describe these 3 assumptions for materials with complex microstructures is not trivial. Second, yield surface evolution needs to be traced iteratively, i.e., through a return mapping algorithm. Here, we show that these assumptions are not needed in the context of sequence learning when using recurrent neural networks, diverting the above-mentioned complications. This work offers an alternative to currently established plasticity formulations by providing the foundations for finding history- and microstructure-dependent constitutive models through deep learning.
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    Graphene-like monolayer monoxides and monochlorides (2019)
    National Academy of Sciences
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    Publication Date: 2019-08-12
    Description: Two-dimensional monolayer materials, with thicknesses of up to several atoms, can be obtained from almost every layer-structured material. It is believed that the catalogs of known 2D materials are almost complete, with fewer new graphene-like materials being discovered. Here, we report 2D graphene-like monolayers from monoxides such as BeO, MgO, CaO, SrO, BaO, and rock-salt structured monochlorides such as LiCl, and NaCl using first-principle calculations. Two-dimensional materials containing d-orbital atoms such as HfO, CdO, and AgCl are predicted. Adopting the same strategy, 2D graphene-like monolayers from mononitrides such as scandium nitride (ScN) and monoselenides such as cadmium selenide (CdSe) are discovered. Stress engineering is found to help stabilize 2D monolayers, through canceling the imaginary frequency of phonon dispersion relation. These 2D monolayers show high dynamic, thermal, kinetic, and mechanic stabilities due to atomic hybridization, and electronic delocalization.
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    Light-triggered thermal conductivity switching in azobenzene polymers (2019)
    National Academy of Sciences
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    Publication Date: 2019-03-08
    Description: Materials that can be switched between low and high thermal conductivity states would advance the control and conversion of thermal energy. Employing in situ time-domain thermoreflectance (TDTR) and in situ synchrotron X-ray scattering, we report a reversible, light-responsive azobenzene polymer that switches between high (0.35 W m−1K−1) and low thermal conductivity (0.10 W m−1K−1) states. This threefold change in the thermal conductivity is achieved by modulation of chain alignment resulted from the conformational transition between planar (trans) and nonplanar (cis) azobenzene groups under UV and green light illumination. This conformational transition leads to changes in the π-π stacking geometry and drives the crystal-to-liquid transition, which is fully reversible and occurs on a time scale of tens of seconds at room temperature. This result demonstrates an effective control of the thermophysical properties of polymers by modulating interchain π-π networks by light.
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    Cell contact and Nf2/Merlin-dependent regulation of TEAD palmitoylation and activity (2019)
    National Academy of Sciences
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    Publication Date: 2019-05-01
    Description: The Hippo pathway is involved in regulating contact inhibition of proliferation and organ size control and responds to various physical and biochemical stimuli. It is a kinase cascade that negatively regulates the activity of cotranscription factors YAP and TAZ, which interact with DNA binding transcription factors including TEAD and activate the expression of target genes. In this study, we show that the palmitoylation of TEAD, which controls the activity and stability of TEAD proteins, is actively regulated by cell density independent of Lats, the key kinase of the Hippo pathway. The expression of fatty acid synthase and acetyl-CoA carboxylase involved in de novo biosynthesis of palmitate is reduced by cell density in an Nf2/Merlin-dependent manner. Depalmitoylation of TEAD is mediated by depalmitoylases including APT2 and ABHD17A. Palmitoylation-deficient TEAD4 mutant is unstable and degraded by proteasome through the activity of the E3 ubiquitin ligase CHIP. These findings show that TEAD activity is tightly controlled through the regulation of palmitoylation and stability via the orchestration of FASN, depalmitoylases, and E3 ubiquitin ligase in response to cell contact.
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    Self-regulation and theforaginggene (PRKG1) in humans (2019)
    National Academy of Sciences
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    Publication Date: 2019-02-19
    Description: Foraging is a goal-directed behavior that balances the need to explore the environment for resources with the need to exploit those resources. InDrosophila melanogaster, distinct phenotypes have been observed in relation to theforaginggene (for), labeled the rover and sitter. Adult rovers explore their environs more extensively than do adult sitters. We explored whether this distinction would be conserved in humans. We made use of a distinction from regulatory mode theory between those who “get on with it,” so-called locomotors, and those who prefer to ensure they “do the right thing,” so-called assessors. In this logic, rovers and locomotors share similarities in goal pursuit, as do sitters and assessors. We showed that genetic variation inPRKG1, the human ortholog offor, is associated with preferential adoption of a specific regulatory mode. Next, participants performed a foraging task to see whether genetic differences associated with distinct regulatory modes would be associated with distinct goal pursuit patterns. Assessors tended to hug the boundary of the foraging environment, much like behaviors seen inDrosophilaadult sitters. In a patchy foraging environment, assessors adopted more cautious search strategies maximizing exploitation. These results show that distinct patterns of goal pursuit are associated with particular genotypes ofPRKG1, the human ortholog offor.
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