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21.
Shashi Sharma Paban Kumar Dash S. R. Santhosh Jyoti Shukla Manmohan Parida P. V. Lakshmana Rao 《Molecular biotechnology》2010,45(1):49-55
Chikungunya is one of the most important emerging arboviral infections of public health significance. Due to lack of a licensed
vaccine, rapid diagnosis plays an important role in early management of patients. In this study, a QC-RT–PCR assay was developed
to quantify Chikungunya virus (CHIKV) RNA by targeting the conserved region of E1 gene. A competitor molecule containing an
internal insertion was generated, which provided a stringent control of the quantification process. The introduction of 10-fold
serially diluted competitor in each reaction was further used to determine sensitivity. The applicability of this assay for
quantification of CHIKV RNA was evaluated with human clinical samples, and the results were compared with real-time quantitative
RT–PCR. The sensitivity of this assay was estimated to be 100 RNA copies per reaction with a dynamic detection range of 102 to 1010 copies. Specificity was confirmed using closely related alpha and flaviviruses. The comparison of QC-RT–PCR result with real-time
RT–PCR revealed 100% concordance for the detection of CHIKV in clinical samples. These findings demonstrated that the reported
assay is convenient, sensitive and accurate method and has the potential usefulness for clinical diagnosis due to simultaneous
detection and quantification of CHIKV in acute-phase serum samples. 相似文献
22.
In this study, the kinetics of degradation of caffeine and related methylxanthines by induced cells of Pseudomonas sp. was performed. The kinetics data showed that degradation of caffeine, theobromine, and 7-methylxanthine followed Michealis–Menten
kinetics. The values of K
m
are low for caffeine and 7-methylxanthine and high for theobromine. Degradation of caffeine and theobromine was enhanced
in the presence of NADH and NADPH, whereas the degradation of 7-methylxanthine was unaffected. Among the various metal ions
tested, Fe2+ was found to enhance the rate of degradation for all three substrates, whereas Zn2+ and Cu2+ inhibited the degradation of caffeine and theobromine but not 7-methylxanthine. The differences in kinetic parameters and
cofactor requirement suggest the possibility of the involvement of more than one N-demethylases in the caffeine catabolic
pathway in Pseudomonas sp. The induced cells can serve as effective biocatalysts for the development of biodecaffeination techniques. 相似文献
23.
Hubs in the protein-protein interaction network have been classified as "party" hubs, which are highly correlated in their mRNA expression with their partners while "date" hubs show lesser correlation. In this study, we explored the role of intrinsic disorder in date and party hub interactions. The data reveals that intrinsic disorder is significantly enriched in date hub proteins when compared with party hub proteins. Intrinsic disorder has been largely implicated in transient binding interactions. The disorder to order transition, which occurs during binding interactions in disordered regions, renders the interaction highly reversible while maintaining the high specificity. The enrichment of intrinsic disorder in date hubs may facilitate transient interactions, which might be required for date hubs to interact with different partners at different times. 相似文献
24.
Background
The alterations in skeletal muscle structure and function after prolonged periods of unloading are initiated by the chronic lack of mechanical stimulus of sufficient intensity, which is the result of a series of biochemical and metabolic interactions spanning from cellular to tissue/organ level. Reduced activation of skeletal muscle alters the gene expression of myosin heavy chain isoforms to meet the functional demands of reduced mechanical load, which results in muscle atrophy and reduced capacity to process fatty acids. In contrast, chronic loading results in the opposite pattern of adaptations. 相似文献25.
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28.
Raju Dash Mir Muhammad Nasir Uddin S.M. Zahid Hosen Zahed Bin Rahim Abu Mansur Dinar Mohammad Shah Hafez Kabir Ramiz Ahmed Sultan Ashekul Islam Md Kamrul Hossain 《Bioinformation》2015,11(12):543-549
Cyclooxygenase-2 (COX-2) catalyzed synthesis of prostaglandin E2 and it associates with tumor growth, infiltration, and metastasis
in preclinical experiments. Known inhibitors against COX-2 exhibit toxicity. Therefore, it is of interest to screen natural compounds
like flavanoids against COX-2. Molecular docking using 12 known flavanoids against COX-2 by FlexX and of ArgusLab were
performed. All compounds showed a favourable binding energy of >-10 KJ/mol in FlexX and > -8 kcal/mol in ArgusLab.
However, this data requires in vitro and in vivo verification for further consideration. 相似文献
29.
Mass spectrometry has made rapid advances in the recent past and has become the preferred method for proteomics. Although many open source algorithms for peptide identification exist, such as X!Tandem and OMSSA, it has majorly been a domain of proprietary software. There is a need for better, freely available, and configurable algorithms that can help in identifying the correct peptides while keeping the false positives to a minimum. We have developed MassWiz, a novel empirical scoring function that gives appropriate weights to major ions, continuity of b-y ions, intensities, and the supporting neutral losses based on the instrument type. We tested MassWiz accuracy on 486,882 spectra from a standard mixture of 18 proteins generated on 6 different instruments downloaded from the Seattle Proteome Center public repository. We compared the MassWiz algorithm with Mascot, Sequest, OMSSA, and X!Tandem at 1% FDR. MassWiz outperformed all in the largest data set (AGILENT XCT) and was second only to Mascot in the other data sets. MassWiz showed good performance in the analysis of high confidence peptides, i.e., those identified by at least three algorithms. We also analyzed a yeast data set containing 106,133 spectra downloaded from the NCBI Peptidome repository and got similar results. The results demonstrate that MassWiz is an effective algorithm for high-confidence peptide identification without compromising on the number of assignments. MassWiz is open-source, versatile, and easily configurable. 相似文献
30.
Kelkar DS Kumar D Kumar P Balakrishnan L Muthusamy B Yadav AK Shrivastava P Marimuthu A Anand S Sundaram H Kingsbury R Harsha HC Nair B Prasad TS Chauhan DS Katoch K Katoch VM Kumar P Chaerkady R Ramachandran S Dash D Pandey A 《Molecular & cellular proteomics : MCP》2011,10(12):M111.011627
The genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ~80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ~250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes. 相似文献