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排序方式: 共有528条查询结果,搜索用时 234 毫秒
61.
Chow V Nong G St John FJ Rice JD Dickstein E Chertkov O Bruce D Detter C Brettin T Han J Woyke T Pitluck S Nolan M Pati A Martin J Copeland A Land ML Goodwin L Jones JB Ingram LO Shanmugam KT Preston JF 《Standards in genomic sciences》2012,6(1):1-10
Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of β-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources. 相似文献
62.
A Copeland A Zeytun M Yassawong M Nolan S Lucas N Hammon S Deshpande JF Cheng C Han R Tapia LA Goodwin S Pitluck K Mavromatis K Liolios I Pagani N Ivanova N Mikhailova A Pati A Chen K Palaniappan M Land L Hauser CD Jeffries EM Brambilla M Rohde J Sikorski R Pukall M Göker JC Detter T Woyke J Bristow JA Eisen V Markowitz P Hugenholtz NC Kyrpides HP Klenk A Lapidus 《Standards in genomic sciences》2012,6(2):240-250
Deinococcus proteolyticus (ex Kobatake et al. 1973) Brook and Murray 1981 is one of currently 47 species in the genus Deinococcus within the family Deinococcaceae. Strain MRP(T) was isolated from feces of Lama glama and possesses extreme radiation resistance, a trait is shares with various other species of the genus Deinococcus, with D. proteolyticus being resistant up to 1.5 Mrad of gamma radiation. Strain MRP(T) is of further interest for its carotenoid pigment. The genome presented here is only the fifth completed genome sequence of a member of the genus Deinococcus (and the forth type strain) to be published, and will hopefully contribute to a better understanding of how members of this genus adapted to high gamma- or UV ionizing-radiation. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,886,836 bp long genome with its four large plasmids of lengths 97 kbp, 132 kbp, 196 kbp and 315 kbp harbors 2,741 protein-coding and 58 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
63.
B Abt C Han C Scheuner M Lu A Lapidus M Nolan S Lucas N Hammon S Deshpande JF Cheng R Tapia LA Goodwin S Pitluck K Liolios I Pagani N Ivanova K Mavromatis N Mikhailova M Huntemann A Pati A Chen K Palaniappan M Land L Hauser EM Brambilla M Rohde S Spring S Gronow M Göker T Woyke J Bristow JA Eisen V Markowitz P Hugenholtz NC Kyrpides HP Klenk JC Detter 《Standards in genomic sciences》2012,6(2):194-209
Spirochaeta coccoides Dröge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835, one of the oldest named genera within the Bacteria. S. coccoides is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that was isolated from the hindgut contents of the termite Neotermes castaneus. The species is of interest because it may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut. Here we provide a taxonomic re-evaluation for strain SPN1T, and based on physiological and genomic characteristics, we propose its reclassification as a novel species in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta. The 2,227,296 bp long genome of strain SPN1T with its 1,866 protein-coding and 58 RNA genes is a part of the Genomic
Encyclopedia of
Bacteria and
Archaea project. 相似文献
64.
Biological systems employing microorganisms have been used as an alternative to conventional chemical techniques for synthesizing gold nanoparticles. In the present study, gold nanoparticles have been synthesized from the supernatant broth (SB) and live cell filtrate (LCF) of the industrially important fungus Penicillium rugulosum. Additionally, potato dextrose broth (PDB) medium which is used for the growth of the fungus has also been able to synthesize gold nanoparticles. The size of the particles has been investigated by Bio-TEM before purification as well as after purification to find the difference in morphology pattern of the nanoparticles. Different characterization techniques like X-ray diffraction (XRD), infra-red (FTIR), X-ray photoelectron (XPS) and UV–vis spectroscopy have been used for analysis of the particles. SB of the fungus has yielded nanoparticles with better morphology and hence further optimization studies were conducted for controlling the size and shape of the above by altering pH and concentration of gold salt. A pH range of 4–6 has favored the synthesis process whereas increasing concentration of gold salt (beyond 2 mM) has resulted in the formation of bigger sized and aggregated nanoparticles. The optimized nanoparticles have been used to conjugate with isolated genomic DNA of bacteria Escherichia coli and Staphylococcus aureus. Visual observation of agarose gel electrophoresis images confirmed the binding of gold nanoparticles (4 μL and 6 μL) with isolated DNA (2 μL) fragments of both the organisms. The slight red shift of the surface plasmon (SP) band and minor aggregations noticed in Bio-TEM images for the DNA conjugated gold nanoparticles indicates that the genomic DNA could stabilize the particles against aggregation owing to negatively charged phosphate backbone. 相似文献
65.
Amrita A. Nagle Fei-Fei Gan Gavin Jones Choon-Leng So Geoffrey Wells Eng-Hui Chew 《PloS one》2012,7(11)
Multifunctional trans-cinnamaldehyde (CA) and its analogs display anti-cancer properties, with 2-benzoyloxycinnamaldehyde (BCA) and 5-fluoro-2-hydroxycinnamaldehyde (FHCA) being identified as the ortho-substituted analogs that possess potent anti-tumor activities. In this study, BCA, FHCA and a novel analog 5-fluoro-2-benzoyloxycinnamaldehyde (FBCA), were demonstrated to decrease growth and colony formation of human colon-derived HCT 116 and mammary-derived MCF-7 carcinoma cells under non-adhesive conditions. The 2-benzoyloxy and 5-fluoro substituents rendered FBCA more potent than BCA and equipotent to FHCA. The cellular events by which these cinnamaldehydes caused G2/M phase arrest and halted proliferation of HCT 116 cells were thereby investigated. Lack of significant accumulation of mitosis marker phospho-histone H3 in cinnamaldehyde-treated cells indicated that the analogs arrested cells in G2 phase. G2 arrest was brought about partly by cinnamaldehyde-mediated depletion of cell cycle proteins involved in regulating G2 to M transition and spindle assembly, namely cdk1, cdc25C, mad2, cdc20 and survivin. Cyclin B1 levels were found to be increased, which in the absence of active cdk1, would fail to drive cells into M phase. Concentrations of cinnamaldehydes that brought about dysregulation of levels of cell cycle proteins also caused tubulin aggregation, as evident from immunodetection of dose-dependent tubulin accumulation in the insoluble cell lysate fractions. In a cell-free system, reduced biotin-conjugated iodoacetamide (BIAM) labeling of tubulin protein pretreated with cinnamaldehydes was indicative of drug interaction with the sulfhydryl groups in tubulin. In conclusion, cinnamaldehydes treatment at proapoptotic concentrations caused tubulin aggregation and dysegulation of cell cycle regulatory proteins cdk1 and cdc25C that contributed at least in part to arresting cells at G2 phase, resulting in apoptotic cell death characterized by emergence of cleaved forms of caspase 3 and poly (ADP-ribose) polymerase (PARP). Results presented in this study have thus provided further insights into the intricate network of cellular events by which cinnamaldehydes induce tumor cell death. 相似文献
66.
Amrita Banerjee Arijit Jana Bikash R. Pati Keshab C. Mondal Pradeep K. Das Mohapatra 《The protein journal》2012,31(4):306-327
The tannase protein sequences of 149 bacteria and 36 fungi were retrieved from NCBI database. Among them only 77 bacterial
and 31 fungal tannase sequences were taken which have different amino acid compositions. These sequences were analysed for
different physical and chemical properties, superfamily search, multiple sequence alignment, phylogenetic tree construction
and motif finding to find out the functional motif and the evolutionary relationship among them. The superfamily search for
these tannase exposed the occurrence of proline iminopeptidase-like, biotin biosynthesis protein BioH, O-acetyltransferase,
carboxylesterase/thioesterase 1, carbon–carbon bond hydrolase, haloperoxidase, prolyl oligopeptidase, C-terminal domain and
mycobacterial antigens families and alpha/beta hydrolase superfamily. Some bacterial and fungal sequence showed similarity
with different families individually. The multiple sequence alignment of these tannase protein sequences showed conserved
regions at different stretches with maximum homology from amino acid residues 389–469 and 482–523 which could be used for
designing degenerate primers or probes specific for tannase producing bacterial and fungal species. Phylogenetic tree showed
two different clusters; one has only bacteria and another have both fungi and bacteria showing some relationship between these
different genera. Although in second cluster near about all fungal species were found together in a corner which indicates
the sequence level similarity among fungal genera. The distributions of fourteen motifs analysis revealed Motif 1 with a signature
amino acid sequence of 29 amino acids, i.e. GCSTGGREALKQAQRWPHDYDGIIANNPA, was uniformly observed in 83.3 % of studied tannase
sequences representing its participation with the structure and enzymatic function. 相似文献
67.
Laura J. Marinelli Mariana Piuri Zuzana Swigoňová Amrita Balachandran Lauren M. Oldfield Julia C. van Kessel Graham F. Hatfull 《PloS one》2008,3(12)
Advances in DNA sequencing technology have facilitated the determination of hundreds of complete genome sequences both for bacteria and their bacteriophages. Some of these bacteria have well-developed and facile genetic systems for constructing mutants to determine gene function, and recombineering is a particularly effective tool. However, generally applicable methods for constructing defined mutants of bacteriophages are poorly developed, in part because of the inability to use selectable markers such as drug resistance genes during viral lytic growth. Here we describe a method for simple and effective directed mutagenesis of bacteriophage genomes using Bacteriophage Recombineering of Electroporated DNA (BRED), in which a highly efficient recombineering system is utilized directly on electroporated phage DNA; no selection is required and mutants can be readily detected by PCR. We describe the use of BRED to construct unmarked gene deletions, in-frame internal deletions, base substitutions, precise gene replacements, and the addition of gene tags. 相似文献
68.
Xu Y Yasin A Tang R Scharer JM Moo-Young M Chou CP 《Applied microbiology and biotechnology》2008,81(1):79-87
Functional expression of lipase B from Pseudozyma antarctica (PalB) in the cytoplasm of Escherichia coli BL21(DE3) and its mutant derivative Origami B(DE3) was explored. Coexpression of DsbA was found to be effective in enhancing
PalB expression. The improvement was particularly pronounced with Origami B(DE3) as a host, suggesting that both folding and
disulfide bond formation may be major factors limiting PalB expression. Fusion tag technique was also explored by constructing
several PalB fusions for the evaluation of their expression performance. While the solubility was enhanced for most PalB fusions,
only the DsbA tag was effective in boosting PalB activity, possibly by both enhanced solubility and correct disulfide bond
formation. Our results suggest that PalB activity is closely associated with correct disulfide bond formation, and increased
solubilization by PalB fusions does not necessarily result in activity enhancement. 相似文献
69.
Yali Xu Amrita Yasin Thomas Wucherpfennig C. Perry Chou 《World journal of microbiology & biotechnology》2008,24(12):2827-2835
Functional expression of heterologous Pseudozyma antarctica lipase B (PalB) in the periplasm of Escherichia coli was explored using four fusion tags, i.e. DsbC, DsbA, maltose-binding protein (MBP), and FLAG in the sequence of increasing
expression efficacy. Amongst these fusion tags, FLAG and MBP appear to be the most effective ones in terms of boosting enzyme
activity and enhancing solubility of PalB, respectively. Overexpression of these PalB fusions often resulted in concomitant
formation of insoluble inclusion bodies. Coexpression of a selection of periplasmic folding factors, including DegP (and its
mutant variant of DegPS210A), FkpA, DsbA, DsbC, and a cocktail of SurA, FkpA, DsbA, and DsbC, could improve the expression performance. Coexpression
of DsbA appeared to be the most effective in reducing the formation of inclusion bodies for all the four PalB fusions, implying
that functional expression of PalB could be limited by initial bridging of disulfide bonds. Culture performance was optimized
by overexpressing FLAG-PalB with DsbA coexpression, resulting in a high volumetric PalB activity of 360 U/L. 相似文献
70.
An overview of enzymatic production of biodiesel 总被引:13,自引:0,他引:13
Biodiesel production has received considerable attention in the recent past as a biodegradable and nonpolluting fuel. The production of biodiesel by transesterification process employing alkali catalyst has been industrially accepted for its high conversion and reaction rates. Recently, enzymatic transesterification has attracted much attention for biodiesel production as it produces high purity product and enables easy separation from the byproduct, glycerol. But the cost of enzyme remains a barrier for its industrial implementation. In order to increase the cost effectiveness of the process, the enzyme (both intracellular and extracellular) is reused by immobilizing in a suitable biomass support particle and that has resulted in considerable increase in efficiency. But the activity of immobilized enzyme is inhibited by methanol and glycerol which are present in the reacting mixture. The use of tert-butanol as solvent, continuous removal of glycerol, stepwise addition of methanol are found to reduce the inhibitory effects thereby increasing the cost effectiveness of the process. The present review analyzes these methods reported in literature and also suggests a suitable method for commercialization of the enzymatic process. 相似文献