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Berlin Brandenburg

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  • 1
    Language: English
    In: Journal of the American Chemical Society, 02 March 2011, Vol.133(8), pp.2626-31
    Description: The proximities of specific subgroups of nearest-neighbor chains in glassy polymers are revealed by distance-dependent (13)C-(13)C dipolar couplings and spin diffusion. The measurement of such proximities is practical even with natural-abundance levels of (13)C using a 2D version of centerband-only detection of exchange (CODEX). Two-dimensional CODEX is a relaxation-compensated experiment that avoids the problems associated with variations in T(1)(C)'s due to dynamic site heterogeneity in the glass. Isotropic chemical shifts are encoded in the t(1) preparation times before and after mixing, and variations in T(2)'s are compensated by an S(0) reference (no mixing). Data acquisition involves acquisition of an S(0) reference signal on alternate scans, and the active control of power amplifiers, to achieve stability and accuracy over long accumulation times. The model system to calibrate spin diffusion is the polymer itself. For a mixing time of 200 ms, only (13)C-(13)C pairs separated by one or two bonds (2.5 Å) show cross peaks, which therefore identify reference intrachain proximities. For a mixing time of 1200 ms, 5 Å interchain proximities appear. The resulting cross peaks are used in a simple and direct way to compare nonrandom chain packing for two commercial polycarbonates with decidedly different mechanical properties.
    Keywords: Polycarboxylate Cement -- Chemistry
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 2
    Language: English
    In: Naturwissenschaften, 2012, Vol.99(7), pp.591-595
    Description: Metabolic scaling laws predict a variety of emergent properties of biological systems based on relationships among temperature, body size, and rates of physiological processes. These models have been criticized as being overly simplistic and not accounting for directional variability arising from evolutionary tradeoffs. I measured hatch success and egg development time at six temperatures for 12 populations throughout the latitudinal range of two broadly distributed topminnows ( Fundulus ). I asked if hatch success and development time differed between the species and northern and southern populations. Hatch success reaction norms suggested that the more broadly (and northern) distributed Fundulus notatus was more eurythermic with a lower optima and broader performance breadth than Fundulus olivaceus . Temperature explained most variability in mass-corrected development time. Development time differed between the species, but not northern and southern populations. Deviations from predictions of universal scaling laws were most pronounced away from specie's thermal optima.
    Keywords: Fundulus ; Thermal optima ; Development time ; Hatch success
    ISSN: 0028-1042
    E-ISSN: 1432-1904
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  • 3
    Language: English
    In: 2015, Vol.10(2), p.e0118742
    Description: Assessing the impacts of the Deepwater Horizon oil spill with a dependable baseline comparison can provide reliable insight into environmental stressors on organisms that were potentially affected by the spill. Fluctuating asymmetry (small, non-random deviations from perfect bilateral symmetry) is an informative metric sensitive to contaminants that can be used to assess environmental stress levels. For this study, the well-studied and common Gulf of Mexico estuarine fish, Menidia beryllina , was used with pre and post-oil spill collections. Comparisons of fluctuating asymmetry in three traits (eye diameter, pectoral fin length, and pelvic fin length) were made pre and post-oil spill across two sites (Old Fort Bayou and the Pascagoula River), as well as between years of collection (2011, 2012)-one and two years, respectfully, after the spill in 2010. We hypothesized that fluctuating asymmetry would be higher in post-Deepwater Horizon samples, and that this will be replicated in both study areas along the Mississippi Gulf coast. We also predicted that fluctuating asymmetry would decrease through time after the oil spill as the oil decomposed and/or was removed. Analyses performed on 1135 fish (220 pre and 915 post Deepwater Horizon) showed significantly higher post spill fluctuating asymmetry in the eye but no difference for the pectoral or pelvic fins. There was also higher fluctuating asymmetry in one of the two sites both pre and post-spill, indicating observed asymmetry may be the product of multiple stressors. Fluctuating asymmetry decreased in 2012 compared to 2011. Fluctuating asymmetry is a sensitive measure of sub lethal stress, and the observed variability in this study (pre vs. post-spill or between sites) could be due to a combination of oil, dispersants, or other unknown stressors.
    Keywords: Research Article
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Journal of Experimental Marine Biology and Ecology, December 2018, Vol.509, pp.82-90
    Description: The April 2010 Deepwater Horizon (DWH) oil spill released over 4 million barrels of oil into northern Gulf of Mexico ecosystems. Due to the magnitude of the spill and observed effects from previous spills, the ecological impacts were predicted to be catastrophic. While negative effects of petroleum hydrocarbon exposure to fish have been documented at the organismal scale, most studies of fish assemblages have noted few, if any, DWH impacts. Our understanding of DWH effects is therefore limited by a disconnect in results reported at different organizational levels. We used population genomic tools to test hypotheses about population-level DWH impacts to Gulf Killifish ( ) in coastal Mississippi. is one of the most abundant marsh species in the northern Gulf of Mexico, and along with the sister species , has served as a model for toxicology research. We collected genotyping by sequencing data from four populations of (two oiled and two not) to test predictions about DWH-related gene flow, demographics, genetic diversity and evidence of selection. Mississippi populations of showed clear genetic structure, but there were few indicators (e.g. reduced genetic diversity, lower N estimates) consistent with large-scale mortality or migration related to DWH oil. Only one estimate of effective population size was reduced in oil-exposed populations and of the twenty outlier loci only two were in regions with potential adaptive significance (i.e., immune functions). While the toxic effects of oil on at the organismal level is well established, the minimal impacts we detected to populations along the Mississippi coast likely reflects the complexity of the northern Gulf of Mexico and DWH oil spill. However, we do recognize that the patchiness of oil exposure and low genome coverage of the data limit our ability to conclude there were no DWH effects on these populations.
    Keywords: Gulf of Mexico ; Fish ; Population Structure ; Demographics ; Outlier Loci Analysis ; Biology ; Oceanography ; Ecology
    ISSN: 0022-0981
    E-ISSN: 1879-1697
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  • 5
    Language: English
    In: Biochemistry, 28 May 2013, Vol.52(21), pp.3651-9
    Description: Staphylococcus aureus grown in the presence of an alanine-racemase inhibitor was labeled with d-[1-(13)C]alanine and l-[(15)N]alanine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance NMR of intact whole cells was used to measure internuclear distances between (13)C and (15)N of labeled amino acids incorporated in the peptidoglycan, and from those labels to (19)F of a glycopeptide drug specifically bound to the peptidoglycan. The observed (13)C-(15)N average distance of 4.1-4.4 Å between d- and l-alanines in nearest-neighbor peptide stems is consistent with a local, tightly packed, parallel-stem architecture for a repeating structural motif within the peptidoglycan of S. aureus.
    Keywords: Nuclear Magnetic Resonance, Biomolecular -- Methods ; Peptidoglycan -- Chemistry ; Staphylococcus Aureus -- Chemistry
    ISSN: 00062960
    E-ISSN: 1520-4995
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  • 6
    Language: English
    In: Journal of the American Chemical Society, 17 November 2010, Vol.132(45), pp.16052-7
    Description: We present a new method that integrates selective biosynthetic labeling and solid-state NMR detection to identify in situ important protein cross-links in plant cell walls. We have labeled soybean cells by growth in media containing l-[ring-d(4)]tyrosine and l-[ring-4-(13)C]tyrosine, compared whole-cell and cell-wall (13)C CPMAS spectra, and examined intact cell walls using (13)C{(2)H} rotational echo double-resonance (REDOR) solid-state NMR. The proximity of (13)C and (2)H labels shows that 25% of the tyrosines in soybean cell walls are part of isodityrosine cross-links between protein chains. We also used (15)N{(13)C} REDOR of intact cell walls labeled by l-[ε-(15)N,6-(13)C]lysine and depleted in natural-abundance (15)N to establish that the side chains of lysine are not significantly involved in covalent cross-links to proteins or sugars.
    Keywords: Cell Wall -- Chemistry ; Nuclear Magnetic Resonance, Biomolecular -- Methods ; Plant Proteins -- Analysis ; Tyrosine -- Analogs & Derivatives
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 7
    Language: English
    In: Biochemistry, 21 May 2013, Vol.52(20), pp.3405-14
    Description: Glycopeptides whose aminosugars have been modified by attachment of hydrophobic side chains are frequently active against vancomycin-resistant microorganisms. We have compared the conformations of six such fluorinated glycopeptides (with side chains of varying length) complexed to cell walls labeled with d-[1-(13)C]alanine, [1-(13)C]glycine, and l-[ε-(15)N]lysine in whole cells of Staphylococcus aureus. The internuclear distances from (19)F of the bound drug to the (13)C and (15)N labels of the peptidoglycan, and to the natural abundance (31)P of lipid membranes and teichoic acids, were determined by rotational-echo double resonance NMR. The drugs did not dimerize, and their side chains did not form membrane anchors but instead became essential parts of secondary binding to pentaglycyl bridge segments of the cell-wall peptidoglycan.
    Keywords: Glycopeptides -- Chemistry ; Peptidoglycan -- Chemistry ; Staphylococcus Aureus -- Metabolism
    ISSN: 00062960
    E-ISSN: 1520-4995
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  • 8
    Language: English
    In: Biochemistry, 11 March 2014, Vol.53(9), pp.1420-7
    Description: Staphylococcus aureus FemA mutant grown in the presence of an alanine-racemase inhibitor was labeled with d-[1-(13)C]alanine, l-[3-(13)C]alanine, [2-(13)C]glycine, and l-[5-(19)F]lysine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance (REDOR) NMR of isolated cell walls was used to measure internuclear distances between (13)C-labeled alanines and (19)F-labeled lysine incorporated in the peptidoglycan. The alanyl (13)C labels were preselected for REDOR measurement by their proximity to the glycine label using (13)C-(13)C spin diffusion. The observed (13)C-(13)C and (13)C-(19)F distances are consistent with a tightly packed, hybrid architecture containing both parallel and perpendicular stems in a repeating structural motif within the peptidoglycan.
    Keywords: Peptidoglycan -- Chemistry ; Staphylococcus Aureus -- Chemistry
    ISSN: 00062960
    E-ISSN: 1520-4995
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  • 9
    Language: English
    In: Journal of the American Chemical Society, May 12, 2010, Vol.132(18), p.6335-6341
    Description: Several frequency-selective rotational-echo double-resonance (REDOR) solid-state NMR spectroscopy studies are conducted to measure the concentrations of the various glycine-glycine pairs found in proteins. The variability observed in the [C.sub.3]-plant cell-wall biosynthesis is also analyzed.
    Keywords: Carbon Dioxide -- Chemical Properties ; Glycine -- Chemical Properties ; Glycine -- Structure ; Nitrogen Fertilizers -- Chemical Properties ; Nuclear Magnetic Resonance Spectroscopy -- Usage
    ISSN: 0002-7863
    Source: Cengage Learning, Inc.
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  • 10
    Language: English
    In: Journal of the American Chemical Society, 11 August 2010, Vol.132(31), pp.10802-7
    Description: We have used a rotational-echo adiabatic-passage double-resonance (13)C{(17)O} solid-state NMR experiment to prove that the glycine produced in the oxygenase reaction of ribulose bisphosphate carboxylase-oxygenase is incorporated exclusively into protein (or protein precursors) of intact, water-stressed soybean leaves exposed to (13)CO(2) and (17)O(2). The water stress increased stomatal resistance and decreased gas exchange so that the Calvin cycle in the leaf chloroplasts was no more than 35% (13)C isotopically enriched. Labeled O(2) levels were sufficient, however, to increase the (17)O isotopic concentration of oxygenase products 20-fold over the natural-abundance level of 0.04%. The observed direct incorporation of glycine into protein shows that water stress suppresses photorespiration in soybean leaves.
    Keywords: Glycine -- Chemistry ; Oxygenases -- Chemistry ; Plant Leaves -- Enzymology ; Ribulose-Bisphosphate Carboxylase -- Chemistry ; Soybeans -- Enzymology
    ISSN: 00027863
    E-ISSN: 1520-5126
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