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  • 1
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    The role of ultraviolet radiation in the diel vertical migration of zooplankton: an experimental test of the transparency-regulator hypothesis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-22
    Description: Zooplankton diel vertical migration (DVM) is often explained as a balance between predator avoidance and resource acquisition. However, recent studies suggest that ultraviolet radiation (UV) may also be important in driving zooplankton DVM in some systems. Williamson et al. ( Williamson et al ., 2011 ) proposed the "transparency-regulator hypothesis," which integrates UV into our current understanding of the drivers of DVM and predicts that the relative roles of UV and visual predation pressure will vary systematically across a gradient of lake transparency. To assess this hypothesis, we conducted in situ mesocosm experiments in five different lakes: two lakes without fish and three lakes with fish that spanned a range of UV and visible light transparency. We used an open-bottomed mesocosm design that allowed for the direct manipulation of UV that did not constrain visual predators or the amplitude or timing of natural migrations. Consistent with the transparency-regulator hypothesis, we found that UV is an important driver of Daphnia DVM in highly UV transparent lakes with and without fish but not in low transparency systems. Our results also suggest that UV and visual predation pressure may interact in systems of intermediate transparency.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Mineral-chemistry quantification and petrophysical calibration for multimineral evaluations: A nonlinear approach (2015)
    American Association of Petroleum Geologists (AAPG)
    Details
    Publication Date: 2015-07-07
    Description: The mineralogical complexity of mudstone reservoirs has led to the increased usage of multimineral optimizing petrophysical models for estimating porosity, water, and hydrocarbon volumes. A key uncertainty in these models is the log response parameter assigned for each log equation related to each volumetric variable. Default parameter values are commonly used and often need to be modified by considering subjective local knowledge or intuition to achieve a result that is considered acceptable. This paper describes the methods developed at Chevron for calibration of mineral log response parameters using core data. Mineral log response parameters are controlled by the major and trace element chemistry of the individual minerals in the formation rock matrix. BestRock™ uses a nonlinear approach to optimize whole-rock chemistry with mineralogy to calculate individual mineral structural formulas and trace element associations from which certain log response parameters can then be calculated. Accurate quantitative phase analysis (QPA) to determine mineral content is a critical step in the process, which is achieved here by rigorous sample preparation methods and QPA by x-ray diffraction (QXRD). The QXRD in combination with whole-rock elemental analyses are processed using Chevron’s BestRock optimization software to provide refined quantities of the mineral species present in the formation, their structural formulas, and their predicted wireline log responses. Calibrated petrophysical models are built from the information obtained from the QXRD and BestRock results. The method described herein provides an independent and robust method for determining petrophysical parameters that is independent of the interpreter, quick to implement, and supported by quantitative measurements.
    Print ISSN: 0149-1423
    Electronic ISSN: 0149-1423
    Topics: Geosciences
    Published by American Association of Petroleum Geologists (AAPG)
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  • 3
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    Nitric oxide prevents axonal degeneration by inducing HIF-1-dependent expression of erythropoietin [Medical Sciences] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-03-23
    Description: Nitric oxide (NO) is a signaling molecule that can trigger adaptive (physiological) or maladaptive (pathological) responses to stress stimuli in a context-dependent manner. We have previously reported that NO may signal axonal injury to neighboring glial cells. In this study, we show that mice deficient in neuronal nitric oxide synthase (nNOS−/−) are more vulnerable than WT mice to toxin-induced peripheral neuropathy. The administration of NO donors to primary dorsal root ganglion cultures prevents axonal degeneration induced by acrylamide in a dose-dependent manner. We demonstrate that NO-induced axonal protection is dependent on hypoxia-inducible factor (HIF)-1–mediated transcription of erythropoietin (EPO) within glial (Schwann) cells present in the cultures. Transduction of Schwann cells with adenovirus AdCA5 encoding a constitutively active form of HIF-1α results in amelioration of acrylamide-induced axonal degeneration in an EPO-dependent manner. Mice that are partially deficient in HIF-1α (HIF-1α+/−) are also more susceptible than WT littermates to toxic neuropathy. Our results indicate that NO→HIF-1→EPO signaling represents an adaptive mechanism that protects against axonal degeneration.
    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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  • 4
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    Experimental identification of downhill protein folding (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-14
    Description: Theory predicts the existence of barrierless protein folding. Without barriers, folding should be noncooperative and the degree of native structure should be coupled to overall protein stability. We investigated the thermal unfolding of the peripheral subunit binding domain from Escherichia coli's 2-oxoglutarate dehydrogenase multienzyme complex (termed BBL) with a combination of spectroscopic techniques and calorimetry. Each technique probed a different feature of protein structure. BBL has a defined three-dimensional structure at low temperatures. However, each technique showed a distinct unfolding transition. Global analysis with a statistical mechanical model identified BBL as a downhill-folding protein. Because of BBL's biological function, we propose that downhill folders may be molecular rheostats, in which effects could be modulated by altering the distribution of an ensemble of structures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia-Mira, Maria M -- Sadqi, Mourad -- Fischer, Niels -- Sanchez-Ruiz, Jose M -- Munoz, Victor -- New York, N.Y. -- Science. 2002 Dec 13;298(5601):2191-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12481137" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*chemistry ; Calorimetry, Differential Scanning ; Circular Dichroism ; Escherichia coli/enzymology ; Fluorescence ; Fluorescence Resonance Energy Transfer ; Hydrogen-Ion Concentration ; Ketoglutarate Dehydrogenase Complex/*chemistry ; Models, Chemical ; Models, Molecular ; Multienzyme Complexes/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; Protein Denaturation ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Temperature ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Cleavage of the BMP-4 antagonist chordin by zebrafish tolloid (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-01-07
    Description: Dorsoventral patterning of vertebrate and Drosophila embryos requires bone morphogenetic proteins (BMPs) and antagonists of BMP activity. The Drosophila gene tolloid encodes a metalloprotease similar to BMP-1 that interacts genetically with decapentaplegic, the Drosophila homolog of vertebrate BMP-2/4. Zebrafish embryos overexpressing a zebrafish homolog of tolloid were shown to resemble loss-of-function mutations in chordino, the zebrafish homolog of the Xenopus BMP-4 antagonist Chordin. Furthermore, Chordin was degraded by COS cells expressing Tolloid. These data suggest that Tolloid antagonizes Chordin activity by proteolytically cleaving Chordin. A conserved function for zebrafish and Drosophila Tolloid during embryogenesis is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blader, P -- Rastegar, S -- Fischer, N -- Strahle, U -- New York, N.Y. -- Science. 1997 Dec 12;278(5345):1937-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, C.U. de Strasbourg, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9395394" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Body Patterning ; Bone Morphogenetic Protein 4 ; Bone Morphogenetic Protein Receptors ; Bone Morphogenetic Proteins/antagonists & inhibitors/*metabolism ; COS Cells ; Cell Lineage ; *Drosophila Proteins ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation, Developmental ; Glycoproteins/*metabolism ; Insect Proteins/genetics/*metabolism ; *Intercellular Signaling Peptides and Proteins ; RNA, Messenger/genetics/metabolism ; Receptors, Cell Surface/metabolism ; *Receptors, Growth Factor ; Signal Transduction ; Tolloid-Like Metalloproteinases ; Transfection ; Xenopus Proteins ; Zebrafish/*embryology/genetics/metabolism ; Zebrafish Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-07-16
    Description: The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Niels -- Konevega, Andrey L -- Wintermeyer, Wolfgang -- Rodnina, Marina V -- Stark, Holger -- England -- Nature. 2010 Jul 15;466(7304):329-33. doi: 10.1038/nature09206.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631791" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; Models, Molecular ; Molecular Conformation ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Structure of the E. coli ribosome-EF-Tu complex at 〈3 A resolution by Cs-corrected cryo-EM (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-02-25
    Description: Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 A. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 A resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 A resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 A), but provides more detailed information (2.65 A) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Niels -- Neumann, Piotr -- Konevega, Andrey L -- Bock, Lars V -- Ficner, Ralf -- Rodnina, Marina V -- Stark, Holger -- England -- Nature. 2015 Apr 23;520(7548):567-70. doi: 10.1038/nature14275. Epub 2015 Feb 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. ; Abteilung Molekulare Strukturbiologie, Institut fur Mikrobiologie und Genetik, GZMB, Georg-August Universitat Gottingen, Justus-von Liebig Weg 11, 37077 Gottingen, Germany. ; 1] Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute of National Research Centre 'Kurchatov Institute', 188300 Gatchina, Russia [2] St Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St Petersburg, Russia [3] Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. ; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. ; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. ; 1] 3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany [2] Department of 3D Electron Cryomicroscopy, Institute of Microbiology and Genetics, Georg-August Universitat, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25707802" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/chemistry/metabolism ; *Cryoelectron Microscopy/methods ; Escherichia coli/*chemistry/*ultrastructure ; Ligands ; Models, Molecular ; Peptide Elongation Factor Tu/*chemistry/metabolism/*ultrastructure ; Pyridones/chemistry/metabolism ; RNA, Bacterial/chemistry/metabolism/ultrastructure ; RNA, Ribosomal/chemistry/metabolism/ultrastructure ; RNA, Transfer/chemistry/metabolism/ultrastructure ; Ribosomes/*chemistry/metabolism/*ultrastructure
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Characteristics of the ocean simulations in MPIOM, the ocean component of the MPI-Earth system model (2013)
    Wiley
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    Publication Date: 2013-03-18
    Description: MPI-ESM is a new version of the global Earth system model developed at the Max Planck Institute for Meteorology. This paper describes the ocean state and circulation as well as basic aspects of variability in simulations contributing to the fifth phase of the Coupled Model Intercomparison Project (CMIP5). The performance of the ocean/sea-ice model MPIOM, coupled to a new version of the atmosphere model ECHAM6 and modules for land surface and ocean biogeochemistry, is assessed for two model versions with different grid resolution in the ocean. The low-resolution configuration has a nominal resolution of 1.5° whereas the higher resolution version features a quasi uniform, eddy-permitting global resolution of 0.4°. The paper focuses on important oceanic features, such as surface temperature and salinity, water mass distribution, large-scale circulation, and heat and fresh water transports. In general, these integral quantities are simulated well in comparison with observational estimates, and improvements in comparison with the predecessor system are documented, for example, for tropical variability and sea ice representation. Introducing an eddy-permitting grid configuration in the ocean leads to improvements, in particular in the representation of interior water mass properties in the Atlantic and in the representation of important ocean currents, such as the Agulhas and Equatorial current systems. In general, however, there are more similarities than differences between the two grid configurations and several shortcomings, known from earlier versions of the coupled model, prevail.
    Electronic ISSN: 1942-2466
    Topics: Geography , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
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    Abnormal ion permeation through cystic fibrosis respiratory epithelium (1983)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1983-09-09
    Description: The epithelium of nasal tissue excised from subjects with cystic fibrosis exhibited higher voltage and lower conductance than tissue from control subjects. Basal sodium ion absorption by cystic fibrosis and normal nasal epithelia equaled the short-circuit current and was amiloride-sensitive. Amiloride induced chloride ion secretion in normal but not cystic fibrosis tissue and consequently was more effective in inhibiting the short-circuit current in cystic fibrosis epithelia. Chloride ion-free solution induced a smaller hyperpolarization of cystic fibrosis tissue. The increased voltage and amiloride efficacy in cystic fibrosis reflect absorption of sodium ions across an epithelium that is relatively impermeable to chloride ions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knowles, M R -- Stutts, M J -- Spock, A -- Fischer, N -- Gatzy, J T -- Boucher, R C -- HL00787/HL/NHLBI NIH HHS/ -- HL16674/HL/NHLBI NIH HHS/ -- HL22624/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1983 Sep 9;221(4615):1067-70.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6308769" target="_blank"〉PubMed〈/a〉
    Keywords: Absorption ; Amiloride/pharmacology ; Chlorides/*metabolism ; Cystic Fibrosis/*metabolism ; Humans ; Ion Channels/metabolism ; Nasal Mucosa/*metabolism ; Sodium/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Continuous Faraday measurement of spin precession without light shifts (2017)
    American Physical Society (APS)
    Details
    Publication Date: 2017-12-02
    Description: Author(s): M. Jasperse, M. J. Kewming, S. N. Fischer, P. Pakkiam, R. P. Anderson, and L. D. Turner We describe a dispersive Faraday optical probe of atomic spin which performs a weak measurement of spin projection of a quantum gas continuously for more than one second. To date, focusing bright far-off-resonance probes onto quantum gases has proved invasive due to strong scalar and vector light sh... [Phys. Rev. A 96, 063402] Published Fri Dec 01, 2017
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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