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排序方式: 共有249条查询结果,搜索用时 250 毫秒
41.
Amit Ghosh Jerome Nilmeier Daniel Weaver Paul D. Adams Jay D. Keasling Aindrila Mukhopadhyay Christopher J. Petzold Héctor García Martín 《PLoS computational biology》2014,10(9)
The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species. 相似文献
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43.
A. M. Winger J. L. Heazlewood L. J. G. Chan C. J. Petzold K. Permaul S. Singh 《Journal of industrial microbiology & biotechnology》2014,41(11):1687-1696
Thermomyces lanuginosus is a thermophilic fungus known for its ability to produce industrially important enzymes including large amounts of xylanase, the key enzyme in hemicellulose hydrolysis. The secretome of T. lanuginosus SSBP was profiled by shotgun proteomics to elucidate important enzymes involved in hemicellulose saccharification and to characterise the presence of other industrially interesting enzymes. This study reproducibly identified a total of 74 proteins in the supernatant following growth on corn cobs. An analysis of proteins revealed nine glycoside hydrolase (GH) enzymes including xylanase GH11, β-xylosidase GH43, β-glucosidase GH3, α-galactosidase GH36 and trehalose hydrolase GH65. Two commercially produced Thermomyces enzymes, lipase and amylase, were also identified. In addition, other industrially relevant enzymes not currently explored in Thermomyces were identified including glutaminase, fructose-bisphosphate aldolase and cyanate hydratase. Overall, these data provide insight into the novel ability of a cellulase-free fungus to utilise lignocellulosic material, ultimately producing a number of enzymes important to various industrial processes. 相似文献
44.
Martina Wendel Anna Petzold Roland Koslowski Michael Kasper Antje Augstein Lilla Knels Jörg-Uwe Bleyl Thea Koch 《Histochemistry and cell biology》2000,122(5):507-517
Pulmonary fibrosis is characterized by excessive extracellular matrix deposition with concomitant loss of gas exchange units, and endothelin-1 (ET-1) has been implicated in its pathogenesis. Increased levels of ET-1 from tissues and bronchoalveolar lavage have been reported in patients with pulmonary fibrosis and in animal models after intratracheal bleomycin. We characterized the cellular distribution of alveolar ET receptors by immunohistochemistry in bleomycin-induced pulmonary fibrosis in the rat and determined the regulation by bleomycin of ET receptor mRNA expression in isolated alveolar macrophages and rat lung fibroblasts. We found significant increases in the numbers of fibroblasts and macrophages at day 7 compared to day 28 and control animals. ETB receptor immunoreactivity was observed on fibroblasts and invading monocytes. Isolated fibroblasts expressed both ETA and ETB receptor mRNA, and ETA receptor mRNA was upregulated by bleomycin. Isolated resident alveolar macrophages expressed neither ETA nor ETB receptor mRNA which were also not induced by bleomycin. We conclude that, while ETB receptor stimulation of fibroblasts and monocytes recruited during bleomycin-induced lung injury exerts antagonistic effects on fibroblast collagen synthesis, the observed increase in the number of fibroblasts in vivo and upregulation of fibroblast ETA receptor mRNA by bleomycin in vitro point to a predominance of the profibrotic effects of ET receptor engagement. 相似文献
45.
Stephen LR Ellison Claire A English Malcolm J Burns Jacquie T Keer 《BMC biotechnology》2006,6(1):33-11
Background
Accurate quantification of DNA using quantitative real-time PCR at low levels is increasingly important for clinical, environmental and forensic applications. At low concentration levels (here referring to under 100 target copies) DNA quantification is sensitive to losses during preparation, and suffers from appreciable valid non-detection rates for sampling reasons. This paper reports studies on a real-time quantitative PCR assay targeting a region of the human SRY gene over a concentration range of 0.5 to 1000 target copies. The effects of different sample preparation and calibration methods on quantitative accuracy were investigated. 相似文献46.
Identification of minimal size requirements of DNA for activation of poly(ADP-ribose) polymerase 总被引:3,自引:0,他引:3
Poly(ADP-ribose) polymerase requires DNA as an essential enzyme activator. Using enzyme purified from lamb thymus and double-stranded deoxynucleotide oligomers of defined length, we conducted studies to identify the smallest size DNA fragment capable of successfully activating poly(ADP-ribose) polymerase. These studies revealed that a double-stranded hexadeoxynucleotide activated the enzyme 30% as effectively as highly polymerized calf thymus DNA and a double-stranded octadeoxynucleotide activated the enzyme even more effectively than calf thymus DNA. When histone H1 was also included in the reaction system, the enzyme could be activated by even smaller DNA fragments. Thus, in the presence of histone H1, a double-stranded tetradeoxynucleotide activated the enzyme 25% as effectively as calf thymus DNA, and a double-stranded hexadeoxynucleotide was equally as effective as calf thymus DNA. The time courses for activation and the stabilities of the products were identical when the enzyme was activated by a double-stranded hexadeoxynucleotide or by calf thymus DNA. Double-stranded oligodeoxynucleotides containing dephosphorylated termini were more effective activators than those containing 3'-phosphorylated termini which in turn were more effective than those containing 5'-phosphorylated termini. 相似文献
47.
Effects of (22S,23S)-Homobrassinolide and Related Compounds on Membrane Potential and Transport of Egeria Leaf Cells 总被引:1,自引:0,他引:1
Dahse I Sack H Bernstein M Petzold U Müller E Vorbrodt HM Adam G 《Plant physiology》1990,93(3):1268-1271
(22S,23S)-Homobrassinolide was tested for its effect on the electric cell potential, proton extrusion, ferricyanide reduction, and amino acid and sucrose uptake of leaves of Egeria densa Planchon. In the light, (22S,23S)-homobrassinolide and its derivative, 2α-3α-dihydroxy-5α-stigmast-22-en-6-one, were similar to each other and similar to fusicoccin in causing hyperpolarization and proton extrusion, whereas stigmasterol was less effective. In darkness, the three sterols showed comparable effects. (22S,23S)-Homobrassinolide slightly stimulated ferricyanide reduction and promoted uptake of sucrose and α-aminoisobutyric acid. The results are compatible with a stimulation of an electrogenic proton pump mechanism at the plasmalemma by (22S,23S)-homobrassinolide. 相似文献
48.
49.
A motor neuron strategy to save time and energy in neurodegeneration: adaptive protein stoichiometry
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50.
The 18S ribosomal RNAs of 21 tetrapods were sequenced and aligned with five
published tetrapod sequences. When the coelacanth was used as an outgroup,
Lissamphibia (living amphibians) and Amniota (amniotes) were found to be
statistically significant monophyletic groups. Although little resolution
was obtained among the lissamphibian taxa, the amniote sequences support a
sister-group relationship between birds and mammals. Portions of the 28S
ribosomal RNA (rRNA) molecule in 11 tetrapods also were sequenced, although
the phylogenetic results were inconclusive. In contrast to previous
studies, deletion or down- weighting of base-paired sites were found to
have little effect on phylogenetic relationships. Molecular evidence for
amniote relationships is reviewed, showing that three genes
(beta-hemoglobin, myoglobin, and 18S rRNA) unambiguously support a
bird-mammal relationship, compared with one gene (histone H2B) that favors
a bird- crocodilian clade. Separate analyses of four other genes (alpha-
crystallin A, alpha-hemoglobin, insulin, and 28S rRNA) and a combined
analysis of all sequence data are inconclusive, in that different groups
are defined in different analyses and none are strongly supported. It is
suggested that until sequences become available from a broader array of
taxa, the molecular evidence is best evaluated at the level of individual
genes, with emphasis placed on those studies with the greatest number of
taxa and sites. When this is done, a bird-mammal relationship is most
strongly supported. When regarded in combination with the morphological
evidence for this association, it must be considered at least as plausible
as a bird-crocodilian relationship.
相似文献