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131.
132.
The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data
Tanenbaum DM Goll J Murphy S Kumar P Zafar N Thiagarajan M Madupu R Davidsen T Kagan L Kravitz S Rusch DB Yooseph S 《Standards in genomic sciences》2010,2(2):229-237
The JCVI metagenomics analysis pipeline provides for the efficient and consistent annotation of shotgun metagenomics sequencing data for sampling communities of prokaryotic organisms. The process can be equally applied to individual sequence reads from traditional Sanger capillary electrophoresis sequences, newer technologies such as 454 pyrosequencing, or sequence assemblies derived from one or more of these data types. It includes the analysis of both coding and non-coding genes, whether full-length or, as is often the case for shotgun metagenomics, fragmentary. The system is designed to provide the best-supported conservative functional annotation based on a combination of trusted homology-based scientific evidence and computational assertions and an annotation value hierarchy established through extensive manual curation. The functional annotation attributes assigned by this system include gene name, gene symbol, GO terms, EC numbers, and JCVI functional role categories. 相似文献
133.
Jasmine George Sahdeo Prasad Zafar Mahmood Yogeshwer Shukla 《Journal of Proteomics》2010,73(5):951-964
Glyphosate is a widely used broad spectrum herbicide, reported to induce various toxic effects in non-target species, but its carcinogenic potential is still unknown. Here we showed the carcinogenic effects of glyphosate using 2-stage mouse skin carcinogenesis model and proteomic analysis. Carcinogenicity study revealed that glyphosate has tumor promoting activity. Proteomic analysis using 2-dimensional gel electrophoresis and mass spectrometry showed that 22 spots were differentially expressed (> 2 fold) on glyphosate, 7, 12-dimethylbenz[a]anthracene (DMBA) and 12-O-tetradecanoyl-phorbol-13-acetate (TPA) application over untreated control. Among them, 9 proteins (translation elongation factor eEF-1 alpha chain, carbonic anhydrase III, annexin II, calcyclin, fab fragment anti-VEGF antibody, peroxiredoxin-2, superoxide dismutase [Cu–Zn], stefin A3, and calgranulin-B) were common and showed similar expression pattern in glyphosate and TPA-treated mouse skin. These proteins are known to be involved in several key processes like apoptosis and growth-inhibition, anti-oxidant responses, etc. The up-regulation of calcyclin, calgranulin-B and down-regulation of superoxide dismutase [Cu–Zn] was further confirmed by immunoblotting, indicating that these proteins can be good candidate biomarkers for skin carcinogenesis induced by glyphosate. Altogether, these results suggested that glyphosate has tumor promoting potential in skin carcinogenesis and its mechanism seems to be similar to TPA. 相似文献
134.
Geminivirus disease complexes: the threat is spreading 总被引:1,自引:0,他引:1
Symptom-modulating DNA satellites associated with geminiviruses have come to our attention only recently but have proven to be widespread, associated with many diseases throughout the Old World, and economically significant, particularly in developing countries. Recent developments are elucidating the role played by these novel molecules in pathogenicity and in overcoming host plant defense. Further investigation into the promiscuous nature of these satellites and their ability to recruit further begomoviruses indicates that regions not yet affected by such begomovirus-satellite complexes are at great risk. 相似文献
135.
Leahy JG Khalid ZM Quintero EJ Jones-Meehan JM Heidelberg JF Batchelor PJ Colwell RR 《Canadian journal of microbiology》2003,49(9):569-575
In the present study, we addressed the possibility that the production of both bioemulsifiers and membrane-bound vesicles may be a common feature of the growth of Acinetobacter spp. on alkanes, and we determined the extent to which the release of extracellular products by these organisms is regulated by the concentrations of the alkane substrate and inorganic nutrients. To accomplish this objective, we grew Acinetobacter venetianus RAG-1 and Acinetobacter sp. strain HO1-N with different concentrations of nutrients and assayed for extracellular products. The results indicated that the release of vesicles, soluble protein, and bioemulsifier was promoted in various degrees by higher concentrations of hexadecane and inorganic nutrients, while the specific activities of the bioemulsifiers were enhanced with lower nutrient concentrations. Based on our findings, we propose that under conditions of nutrient excess, these strains produce membrane-bound vesicles to function in "luxury uptake" of the alkane substrate for delivery and storage in the form of inclusions. Under the same conditions, soluble bioemulsifier and protein may perform auxiliary roles in cell desorption and (or) alkane uptake. With low concentrations of nutrients, the decreased production of vesicles, protein, and bioemulsifier and the increased activity of the emulsifier may represent a mechanism for reducing biosynthetic demands and conserving cellular material. 相似文献
136.
Crystallins are recognized as one of the long-lived proteins of lens tissue that might serve as the target for several posttranslational modifications leading to cataract development. We have studied several such sites present in the human gamma-crystallins based either on PROSITE pattern search results or earlier experimental evidences. Their probabilities were examined on the basis of the database analysis of the gamma-crystallin sequences and on their specific locations in the constructed homology models. An N-glycosylation site in human gammaD-crystallin and several phosphorylation sites in all four human gamma-crystallins were predicted by the PROSITE search. Some of these sites were found to be strongly conserved in the gamma-crystallin sequences from different sources. An extensive analysis of these sites was performed to predict their probabilities as potential sites for protein modifications. Glycation studies were performed separately by attaching sugars to the human gammaB-crystallin model, and the effect of binding was analyzed. The studies showed that the major effect of alphaD-glucose (alphaD-G) and alphaD-glucose-6-phosphate (alphaD-G6P) binding was the disruption of charges not only at the surface but also within the molecule. Only a minor alteration in the distances of sulfhydryl groups of cysteines and on their positions in the three-dimensional models were observed, leading us to assume that glycation alone is not responsible for intra- and intermolecular disulfide bond formation. 相似文献
137.
BACKGROUND: Fine needle aspiration (FNA) cytologic diagnosis of toxoplasmic lymphadenitis with demonstration of a tissue cyst containing bradyzoites has been very rarely reported. CASE: A 17-year-old female presented with a mobile, painless, 2-cm-diameter swelling over the right suprascapular area. Clinical diagnosis was lipoma. FNA smears showed features of reactive lymphoid hyperplasia, including tingible body macrophages and groups of epithelioid histiocytes. A Toxoplasma cyst with bradyzoites was also demonstrated in a Papanicolaou-stained smear. Following FNA cytodiagnosis, serologic tests revealed a high titer of IgG and the presence of IgM-specific antibodies to Toxoplasma gondii, indicating active/recent disease. CONCLUSION: FNA cytology is a valuable tool for the diagnosis of toxoplasmic lymphadenitis. Papanicolaou stain is appropriate for demonstration of the parasite. Serology is an excellent adjunct in clinching the diagnosis. 相似文献
138.
The effect of sodium selenite (0.05, 0.1, and 0.2 mg/kg body weight, ip) on the contents of lipids (phospholipids, cholesterol,
esterified fatty acids, gangliosides), thiobarbituric acid reactive substance (TBARS), and thiol group in circadian rhythm
centers (preoptic area, brainstem, and posterior hypothalamus) of male Wistar rats was studied after 7 d of treatment. The
content of phospholipids was elevated significantly with a dose of 0.1 mg/kg of selenite in the preoptic area and brainstem,
but a 0.2-mg/kg dose has depleted its level significantly in these regions. The alteration of phospholipids in posterior hypothalamus
was not significant with three doses of sodium selenite. The level of cholesterol in the preoptic area was inhibited significantly
with a dose of 0.05 mg/kg sodium selenite, but its level was elevated significantly with a dose of 0.2 mg/kg selenite in the
preoptic area and brainstem. Alteration with three doses of sodium selenite in the posterior hypothalamus was not significant.
The ganglioside level in the preoptic area and brainstem was elevated significantly with a 0.1-mg dose of sodium selenite;
conversely, a 0.2 mg dose of sodium selenite caused a significant depletion on its content in these areas. In the posterior
hypothalamus, the ganglioside level was depleted significantly with a dose of 0.1 mg, but elevated significantly with a dose
of 0.2 mg of sodium selenite. The level of esterified fatty acids was decreased significantly in the preoptic area and brainstem
with a dose of 0.1 mg/kg sodium selenite, but in these regions, its level was elevated with a dose of 0.2 mg/kg sodium selenite
and its elevation was significant in the preoptic area. In the posterior hypothalamus, the alteration of esterified fatty
acids with three doses of sodium selenite was not significant. The effect of 0.1 and 0.2 mg/kg sodium selenite on the TBARS
level and thiol group in sleep centers was significantly opposite to the wakefulness center. A sodium selenite dose of 0.1
mg/kg had depleted the content of TBARS in the preoptic area and brainstem but elevated the content of the thiol group significantly
in the posterior hypothalamus. On the other hand, a 0.2-mg/kg dose of sodium selenite has significantly elevated the content
of TBARS but depleted the content of the thiol group significantly in the posterior hypothalamus. No dose-dependent alteration
was observed on the content of lipids, TBARS, and thiol group in the circadian rhythm centers of rats. 相似文献
139.
140.
Summary Immobilization of Saccharum officinarum cells within the vegetable sponge of Luffa cylindrica is reported as a new medium for the cells of higher plants. The use of biostructure of the sponge offers an alternative matrix to the ones used presently for immobilization. 相似文献