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  • 1
    Online Resource
    Online Resource
    The Genetic Basis for Bacterial Mercury Methylation
    American Association for the Advancement of Science (AAAS) ; 2013
    In:  Science Vol. 339, No. 6125 ( 2013-03-15), p. 1332-1335
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 339, No. 6125 ( 2013-03-15), p. 1332-1335
    Abstract: Methylmercury is a potent neurotoxin produced in natural environments from inorganic mercury by anaerobic bacteria. However, until now the genes and proteins involved have remained unidentified. Here, we report a two-gene cluster, hgcA and hgcB , required for mercury methylation by Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. In either bacterium, deletion of hgcA , hgcB , or both genes abolishes mercury methylation. The genes encode a putative corrinoid protein, HgcA, and a 2[4Fe-4S] ferredoxin, HgcB, consistent with roles as a methyl carrier and an electron donor required for corrinoid cofactor reduction, respectively. Among bacteria and archaea with sequenced genomes, gene orthologs are present in confirmed methylators but absent in nonmethylators, suggesting a common mercury methylation pathway in all methylating bacteria and archaea sequenced to date.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1230667
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2013
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    detail.hit.zdb_id: 2066996-3
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  • 2
    Online Resource
    Online Resource
    The Genome of the Kinetoplastid Parasite, Leishmania major
    American Association for the Advancement of Science (AAAS) ; 2005
    In:  Science Vol. 309, No. 5733 ( 2005-07-15), p. 436-442
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 309, No. 5733 ( 2005-07-15), p. 436-442
    Abstract: Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei , and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase IIâdirected transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1112680
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2005
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  • 3
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    Online Resource
    Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 29 ( 2020-07-21), p. 16776-16781
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 29 ( 2020-07-21), p. 16776-16781
    Abstract: A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in aqueous solution. Here, neutron scattering and molecular-dynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range ( 〉 25 °C) cellulose disruption occurs only above 150 °C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (R g ∼ 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent water-rich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1922883117
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 4
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    Online Resource
    Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis
    American Association for the Advancement of Science (AAAS) ; 2007
    In:  Science Vol. 315, No. 5809 ( 2007-01-12), p. 207-212
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 315, No. 5809 ( 2007-01-12), p. 207-212
    Abstract: We describe the genome sequence of the protist Trichomonas vaginalis , a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the ∼160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1132894
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2007
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 5
    Online Resource
    Online Resource
    An open repository of real-time COVID-19 indicators
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 51 ( 2021-12-21)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 51 ( 2021-12-21)
    Abstract: The COVID-19 pandemic presented enormous data challenges in the United States. Policy makers, epidemiological modelers, and health researchers all require up-to-date data on the pandemic and relevant public behavior, ideally at fine spatial and temporal resolution. The COVIDcast API is our attempt to fill this need: Operational since April 2020, it provides open access to both traditional public health surveillance signals (cases, deaths, and hospitalizations) and many auxiliary indicators of COVID-19 activity, such as signals extracted from deidentified medical claims data, massive online surveys, cell phone mobility data, and internet search trends. These are available at a fine geographic resolution (mostly at the county level) and are updated daily. The COVIDcast API also tracks all revisions to historical data, allowing modelers to account for the frequent revisions and backfill that are common for many public health data sources. All of the data are available in a common format through the API and accompanying R and Python software packages. This paper describes the data sources and signals, and provides examples demonstrating that the auxiliary signals in the COVIDcast API present information relevant to tracking COVID activity, augmenting traditional public health reporting and empowering research and decision-making.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2111452118
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
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  • 6
    Online Resource
    Online Resource
    Structural mechanism of the recovery stroke in the Myosin molecular motor
    Proceedings of the National Academy of Sciences ; 2005
    In:  Proceedings of the National Academy of Sciences Vol. 102, No. 19 ( 2005-05-10), p. 6873-6878
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 102, No. 19 ( 2005-05-10), p. 6873-6878
    Abstract: The power stroke pulling myosin along actin filaments during muscle contraction is achieved by a large rotation (≈60°) of the myosin lever arm after ATP hydrolysis. Upon binding the next ATP, myosin dissociates from actin, but its ATPase site is still partially open and catalytically off. Myosin must then close and activate its ATPase site while returning the lever arm for the next power stroke. A mechanism for this coupling between the ATPase site and the distant lever arm is determined here by generating a continuous series of optimized intermediates between the crystallographic end-states of the recovery stroke. This yields a detailed structural model for communication between the catalytic and the force-generating regions that is consistent with experimental observations. The coupling is achieved by an amplifying cascade of conformational changes along the relay helix lying between the ATPase and the domain carrying the lever arm.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0408784102
    RVK:
    TA 1000
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    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2005
    detail.hit.zdb_id: 209104-5
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  • 7
    Online Resource
    Online Resource
    MOG autoantibodies trigger a tightly-controlled FcR and BTK-driven microglia proliferative response
    Oxford University Press (OUP) ; 2021
    In:  Brain Vol. 144, No. 8 ( 2021-09-04), p. 2361-2374
    Details
    In: Brain, Oxford University Press (OUP), Vol. 144, No. 8 ( 2021-09-04), p. 2361-2374
    Abstract: Autoantibodies are a hallmark of numerous neurological disorders, including multiple sclerosis, autoimmune encephalitides and neuromyelitis optica. Whilst well understood in peripheral myeloid cells, the pathophysiological significance of autoantibody-induced Fc receptor signalling in microglia remains unknown, in part due to the lack of a robust in vivo model. Moreover, the application of therapeutic antibodies for neurodegenerative disease also highlights the importance of understanding Fc receptor signalling in microglia. Here, we describe a novel in vivo experimental paradigm that allows for selective engagement of Fc receptors within the CNS by peripherally injecting anti-myelin oligodendrocyte glycoprotein (MOG) monoclonal antibodies into normal wild-type mice. MOG antigen-bound immunoglobulins were detected throughout the CNS and triggered a rapid and tightly regulated proliferative response in both brain and spinal cord microglia. This microglial response was abrogated when anti-MOG antibodies were deprived of Fc receptor effector function or injected into Fcγ receptor knockout mice and was associated with the downregulation of Fc receptors in microglia, but not peripheral myeloid cells, establishing that this response was dependent on central Fc receptor engagement. Downstream of the Fc receptors, BTK was a required signalling node for this response, as microglia proliferation was amplified in BtkE41K knock-in mice expressing a constitutively active form of the enzyme and blunted in mice treated with a CNS-penetrant small molecule inhibitor of BTK. Finally, this response was associated with transient and stringently regulated changes in gene expression predominantly related to cellular proliferation, which markedly differed from transcriptional programs typically associated with Fc receptor engagement in peripheral myeloid cells. Together, these results establish a physiologically-meaningful functional response to Fc receptor and BTK signalling in microglia, while providing a novel in vivo tool to further dissect the roles of microglia-specific Fc receptor and BTK-driven responses to both pathogenic and therapeutic antibodies in CNS homeostasis and disease.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
    URL: Article
    DOI: 10.1093/brain/awab231
    RVK:
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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  • 8
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    Online Resource
    Is the first hydration shell of lysozyme of higher density than bulk water?
    Proceedings of the National Academy of Sciences ; 2002
    In:  Proceedings of the National Academy of Sciences Vol. 99, No. 8 ( 2002-04-16), p. 5378-5383
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 99, No. 8 ( 2002-04-16), p. 5378-5383
    Abstract: Characterization of the physical properties of protein surface hydration water is critical for understanding protein structure and folding. Here, using molecular dynamics simulation, we provide an explanation of recent x-ray and neutron solution scattering data that indicate that the density of water on the surface of lysozyme is significantly higher than that of bulk water. The simulation-derived scattering profiles are in excellent agreement with the experiment. In the simulation, the 3-Å-thick first hydration layer is 15% denser than bulk water. About two-thirds of this increase is the result of a geometric contribution that would also be present if the water was unperturbed from the bulk. The remaining third arises from modification of the water structure and dynamics, involving approximately equal contributions from shortening of the average water–water O–O distance and an increase in the coordination number. Variation in the first hydration shell density is shown to be determined by topographical and electrostatic properties of the protein surface. On average, denser water is found in depressions on the surface in which the water dipoles tend to be aligned parallel to each other by the electrostatic field generated by the protein atoms.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.082335099
    RVK:
    TA 1000
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    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2002
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 9
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    Online Resource
    Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
    Proceedings of the National Academy of Sciences ; 2011
    In:  Proceedings of the National Academy of Sciences Vol. 108, No. 12 ( 2011-03-22), p. 4822-4827
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 108, No. 12 ( 2011-03-22), p. 4822-4827
    Abstract: There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is “dynamical fingerprints” which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1004646108
    RVK:
    TA 1000
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    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2011
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 10
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    Online Resource
    Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding
    Proceedings of the National Academy of Sciences ; 2007
    In:  Proceedings of the National Academy of Sciences Vol. 104, No. 39 ( 2007-09-25), p. 15230-15235
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 104, No. 39 ( 2007-09-25), p. 15230-15235
    Abstract: Recent work has shown that the nature of hydration of pure hydrophobic surfaces changes with the length scale considered: water hydrogen-bonding networks adapt to small exposed hydrophobic species, hydrating or “wetting” them at relatively high densities, whereas larger hydrophobic areas are “dewetted” [Chandler D (2005), Nature 29:640–647]. Here we determine whether this effect is also present in peptides by examining the folding of a β-hairpin (the 14-residue amyloidogenic prion protein H1 peptide), using microsecond time-scale molecular dynamics simulations. Two simulation models are compared, one explicitly including the water molecules, which may thus adapt locally to peptide configurations, and the other using a popular continuum approximation, the generalized Born/surface area implicit solvent model. The results obtained show that, in explicit solvent, peptide conformers with high solvent-accessible hydrophobic surface area indeed also have low hydration density around hydrophobic residues, whereas a concomitant higher hydration density around hydrophilic residues is observed. This dewetting effect stabilizes the fully folded β-hairpin state found experimentally. In contrast, the implicit solvent model destabilizes the fully folded hairpin, tending to cluster hydrophobic residues regardless of the size of the exposed hydrophobic surface. Furthermore, the rate of the conformational transitions in the implicit solvent simulation is almost doubled with respect to that of the explicit solvent. The results suggest that dehydration-driven solvent exposure of hydrophobic surfaces may be a significant factor determining peptide conformational equilibria.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0701401104
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2007
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
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