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  • 1
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    Novel microbial community composition and carbon biogeochemistry emerge over time following saltwater intrusion in wetlands (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Sea level rise is expected to cause saltwater intrusion into historically freshwater wetlands, leading to shifts in microbial metabolism that alter greenhouse gas emissions and soil carbon sequestration. Here, we aimed to understand the temporal changes in microbial community composition and biogeochemical activity following saltwater intrusion in a 1‐year field manipulation experiment. Our results suggest the development of a unique successional microbial community may underpin methane production following saltwater intrusion. Further, the gradual changes composition and function we observed may indicate that previously freshwater wetlands may not experience an equilibration of ecosystem function until long after initial saltwater intrusion. Abstract Sea level rise and changes in precipitation can cause saltwater intrusion into historically freshwater wetlands, leading to shifts in microbial metabolism that alter greenhouse gas emissions and soil carbon sequestration. Saltwater intrusion modifies soil physicochemistry and can immediately affect microbial metabolism, but further alterations to biogeochemical processing can occur over time as microbial communities adapt to the changed environmental conditions. To assess temporal changes in microbial community composition and biogeochemical activity due to saltwater intrusion, soil cores were transplanted from a tidal freshwater marsh to a downstream mesohaline marsh and periodically sampled over 1 year. This experimental saltwater intrusion produced immediate changes in carbon mineralization rates, whereas shifts in the community composition developed more gradually. Salinity affected the composition of the prokaryotic community but did not exert a strong influence on the community composition of fungi. After only 1 week of saltwater exposure, carbon dioxide production doubled and methane production decreased by three orders of magnitude. By 1 month, carbon dioxide production in the transplant was comparable to the saltwater controls. Over time, we observed a partial recovery in methane production which strongly correlated with an increase in the relative abundance of three orders of hydrogenotrophic methanogens. Taken together, our results suggest that ecosystem responses to saltwater intrusion are dynamic over time as complex interactions develop between microbial communities and the soil organic carbon pool. The gradual changes in microbial community structure we observed suggest that previously freshwater wetlands may not experience an equilibration of ecosystem function until long after initial saltwater intrusion. Our results suggest that during this transitional period, likely lasting years to decades, these ecosystems may exhibit enhanced greenhouse gas production through greater soil respiration and continued methanogenesis.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Published by Wiley
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  • 2
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    ICT: isotope correction toolbox (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-18
    Description: : Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences—in particular for complex isotopic systems—is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox , a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Availability and implementation: Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ Contact: { christian.jungreuthmayer@boku.ac.at , juergen.zanghellini@boku.ac.at } Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Insights into translational termination from the structure of RF2 bound to the ribosome (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-08
    Description: The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642913/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weixlbaumer, Albert -- Jin, Hong -- Neubauer, Cajetan -- Voorhees, Rebecca M -- Petry, Sabine -- Kelley, Ann C -- Ramakrishnan, Venki -- 082086/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- U.1051.04.018(78935)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Nov 7;322(5903):953-6. doi: 10.1126/science.1164840.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988853" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/chemistry/metabolism ; Biocatalysis ; *Codon, Terminator/chemistry/metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; *Peptide Chain Termination, Translational ; Peptide Termination Factors/*chemistry/metabolism ; Peptides/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Transfer/metabolism ; Ribosome Subunits/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Thermus thermophilus/*chemistry
    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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  • 4
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    Decoding in the absence of a codon by tmRNA and SmpB in the ribosome (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-17
    Description: In bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger RNA (tmRNA), a bifunctional molecule that acts as both a transfer RNA (tRNA) and a messenger RNA (mRNA), and SmpB, a small protein that works in concert with tmRNA. Here, we present the crystal structure of a tmRNA fragment, SmpB and elongation factor Tu bound to the ribosome at 3.2 angstroms resolution. The structure shows how SmpB plays the role of both the anticodon loop of tRNA and portions of mRNA to facilitate decoding in the absence of an mRNA codon in the A site of the ribosome and explains why the tmRNA-SmpB system does not interfere with normal translation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763467/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763467/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neubauer, Cajetan -- Gillet, Reynald -- Kelley, Ann C -- Ramakrishnan, V -- 082086/Wellcome Trust/United Kingdom -- 096570/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- U105184332/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1366-9. doi: 10.1126/science.1217039.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422985" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/chemistry/metabolism ; Base Sequence ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/*chemistry/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/*chemistry/*metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; RNA-Binding Proteins/*chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism/ultrastructure ; Ribosomes/*chemistry/*metabolism/ultrastructure ; Thermus thermophilus/*chemistry/genetics/metabolism/ultrastructure
    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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    Contributions of organic and inorganic matter to sediment volume and accretion in tidal wetlands at steady state (2016)
    American Geophysical Union (AGU)
    Details
    Publication Date: 2016-03-22
    Description: A mixing model derived from first principles describes the bulk density (BD) of intertidal wetland sediments as a function of loss on ignition (LOI). The model assumes the bulk volume of sediment equates to the sum of self-packing volumes of organic and mineral components or BD = 1/[LOI/ k 1 + (1-LOI)/ k 2 ], where k 1 and k 2 are the self-packing densities of the pure organic and inorganic components, respectively. The model explained 78% of the variability in total BD when fitted to 5075 measurements drawn from 33 wetlands distributed around the conterminous United States. The values of k 1 and k 2 were estimated to be 0.085 -±0.0007 g cm −3 and 1.99 ± 0.028 g cm −3 , respectively. Based on the fitted organic density ( k 1 ) and constrained by primary production, the model suggests that the maximum steady state accretion arising from the sequestration of refractory organic matter is ≤ 0.3 cm yr −1 . Thus, tidal peatlands are unlikely to survive indefinitely a higher rate of sea-level rise in the absence of a significant source of mineral sediment. Application of k 2 to a mineral sediment load typical of East and eastern Gulf Coast estuaries gives a vertical accretion rate from inorganic sediment of 0.2 cm yr −1 . Total steady state accretion is the sum of the parts and therefore should not be greater than 0.5 cm yr −1 under the assumptions of the model. Accretion rates could deviate from this value depending on variation in plant productivity, root:shoot ratio, suspended sediment concentration, sediment-capture efficiency, and episodic events.
    Electronic ISSN: 2328-4277
    Topics: Geosciences
    Published by American Geophysical Union (AGU)
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  • 6
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    Brain mechanisms associated with internally directed attention and self-generated thought (2016)
    Springer Nature
    Details
    Publication Date: 2016-03-11
    Description: Brain mechanisms associated with internally directed attention and self-generated thought Scientific Reports, Published online: 10 March 2016; doi:10.1038/srep22959
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 7
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    Component greenhouse gas fluxes and radiative balance from two deltaic marshes in Louisiana: Pairing chamber techniques and eddy covariance (2016)
    Wiley
    Details
    Publication Date: 2016-05-24
    Description: Coastal marshes take up atmospheric CO 2 while emitting CO 2 , CH 4 , and N 2 O. This ability to sequester carbon (C) is much greater for wetlands on a per-area basis than from most ecosystems, facilitating scientific, political, and economic interest in their value as greenhouse gas sinks. However, the greenhouse gas balance of Gulf of Mexico wetlands is particularly understudied. We describe the net ecosystem exchange (NEE c ) of CO 2 and CH 4 using eddy covariance (EC) in comparison with fluxes of CO 2 , CH 4 , and N 2 O using chambers from brackish and freshwater marshes in Louisiana, USA. From EC, we found that 182 g C m -2 y -1 was lost through NEE c from the brackish marsh. Of this, 11 g C m -2 y -1 resulted from net CH 4 emissions and the remaining 171 g C m -2 y -1 resulted from net CO 2 emissions. In contrast, -290 g C m 2 y -1 was taken up through NEE c by the freshwater marsh, with 47 g C m -2 y -1 emitted as CH 4 and -337 g C m -2 y -1 taken up as CO 2 . From chambers, we discovered that neither site had large fluxes of N 2 O. Sustained-flux greenhouse gas accounting metrics indicated that both marshes had a positive (warming) radiative balance, with the brackish marsh having a substantially greater warming effect than the freshwater marsh. That net respiratory emissions of CO 2 and CH 4 as estimated through chamber techniques were 2-4 times different from emissions estimated through EC requires additional understanding of the artifacts created by different spatial and temporal sampling footprints between techniques.
    Print ISSN: 0148-0227
    Topics: Biology , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
    Electronic Resource
    Electronic Resource
    Correlation between dissipative fluorescence quenching at photosystem II and 50 μs recombination luminescence
    Amsterdam : Elsevier
    FEBS Letters 258 (1989), S. 339-342 
    Details
    ISSN: 0014-5793
    Keywords: Chlorophyll fluorescence ; Fluorescence quenching ; Luminescence ; Photosystem II ; Water splitting
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0014-5793(89)81688-6
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  • 9
    Electronic Resource
    Electronic Resource
    The Molecular Biology of the Na+-Ca2+ Exchanger and Its Functional Roles in Heart, Smooth Muscle Cells, Neurons, Glia, Lymphocytes, and Nonexcitable Cellsa (1996)
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 779 (1996), S. 0 
    Details
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1749-6632.1996.tb44764.x
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  • 10
    Electronic Resource
    Electronic Resource
    Vergiftung mit einer Mischung von Morphin und Strychnin (1870)
    Springer
    Fresenius' Zeitschrift für analytische Chemie 9 (1870), S. 240-242 
    Details
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01362906
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