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991.
Wuxiuer Y Morgunova E Cols N Popov A Karshikoff A Sylte I Gonzàlez-Duarte R Ladenstein R Winberg JO 《The FEBS journal》2012,279(16):2940-2956
All drosophilid alcohol dehydrogenases contain an eight-member water chain connecting the active site with the solvent at the dimer interface. A similar water chain has also been shown to exist in other short-chain dehydrogenase/reductase (SDR) enzymes, including therapeutically important SDRs. The role of this water chain in the enzymatic reaction is unknown, but it has been proposed to be involved in a proton relay system. In the present study, a connecting link in the water chain was removed by mutating Thr114 to Val114 in Scaptodrosophila lebanonensis alcohol dehydrogenase (SlADH). This threonine is conserved in all drosophilid alcohol dehydrogenases but not in other SDRs. X-ray crystallography of the SlADH(T114V) mutant revealed a broken water chain, the overall 3D structure of the binary enzyme-NAD(+) complex was almost identical to the wild-type enzyme (SlADH(wt) ). As for the SlADH(wt) , steady-state kinetic studies revealed that catalysis by the SlADH(T114V) mutant was consistent with a compulsory ordered reaction mechanism where the co-enzyme binds to the free enzyme. The mutation caused a reduction of the k(on) velocity for NAD(+) and its binding strength to the enzyme, as well as the rate of hydride transfer (k) in the ternary enzyme-NAD(+) -alcohol complex. Furthermore, it increased the pK(a) value of the group in the binary enzyme-NAD(+) complex that regulates the k(on) velocity of alcohol and alcohol-competitive inhibitors. Overall, the results indicate that an intact water chain is essential for optimal enzyme activity and participates in a proton relay system during catalysis. 相似文献
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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing 总被引:3,自引:0,他引:3
Bankevich A Nurk S Antipov D Gurevich AA Dvorkin M Kulikov AS Lesin VM Nikolenko SI Pham S Prjibelski AD Pyshkin AV Sirotkin AV Vyahhi N Tesler G Alekseyev MA Pevzner PA 《Journal of computational biology》2012,19(5):455-477
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software. 相似文献
995.
Andrey I. Azovsky 《Ecological Complexity》2009,6(3):308-315
In this paper, definitions and measures of complexity with regard to biological communities are briefly considered. A new topological approach that considers the community's complexity in terms of groups of species coherently varied in space or time is proposed. For a given set of samples, the number of such groups is related to the minimal number M of axes necessary to represent the original configuration of the data set. I interpret this “minimal dimensionality of structure” as the number of independent factors of structural variability and its normalized value M/MMAX as a measure of the organizational complexity of a community. The M value can be estimated as the number of significant axes obtained by ordination procedures. The percentage of total variance explained by these axes, T, is used as measure of structural rigidity. This approach is applied to data on the multi-scaled spatial distribution of marine benthic ciliates and macrofauna. Both the M and the T values obtained by principal component analysis show significant scale-dependence with an evident threshold at some critical area, with values of zero below this threshold, then increasing sharply as the area extends beyond the threshold. The critical scale of community organization ranges from hundreds of meters to kilometers for macroorganisms, whereas several meters are sufficient when considering ciliates. 相似文献
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Lenka Skalska Victoria Begley Manuel Beltran Saulius Lukauskas Garima Khandelwal Peter Faull Amandeep Bhamra Manuel Tavares Rachel Wellman Andrey Tvardovskiy Benjamin M. Foster Igor Ruiz de los Mozos Javier Herrero Silvia Surinova Ambrosius P. Snijders Till Bartke Richard G. Jenner 《Molecular cell》2021,81(14):2944-2959.e10
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998.
David R. Blair Kanix Wang Svetlozar Nestorov James A. Evans Andrey Rzhetsky 《PLoS computational biology》2014,10(9)
Synonymous relationships among biomedical terms are extensively annotated within specialized terminologies, implying that synonymy is important for practical computational applications within this field. It remains unclear, however, whether text mining actually benefits from documented synonymy and whether existing biomedical thesauri provide adequate coverage of these linguistic relationships. In this study, we examine the impact and extent of undocumented synonymy within a very large compendium of biomedical thesauri. First, we demonstrate that missing synonymy has a significant negative impact on named entity normalization, an important problem within the field of biomedical text mining. To estimate the amount synonymy currently missing from thesauri, we develop a probabilistic model for the construction of synonym terminologies that is capable of handling a wide range of potential biases, and we evaluate its performance using the broader domain of near-synonymy among general English words. Our model predicts that over 90% of these relationships are currently undocumented, a result that we support experimentally through “crowd-sourcing.” Finally, we apply our model to biomedical terminologies and predict that they are missing the vast majority (>90%) of the synonymous relationships they intend to document. Overall, our results expose the dramatic incompleteness of current biomedical thesauri and suggest the need for “next-generation,” high-coverage lexical terminologies. 相似文献
999.
Wakene C. Negassa Andrey K. Guber Alexandra N. Kravchenko Terence L. Marsh Britton Hildebrandt Mark L. Rivers 《PloS one》2015,10(4)
Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes. 相似文献
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