CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

<p>Abstract</p> <p>Background</p> <p>Distantly related proteins adopt and retain similar structural scaffolds despite length variations that could be as much as two-fold in some protein superfamilies. In this paper, we describe an analysis of indel regions that accommodate length variations amongst related proteins. We have developed an algorithm CUSP, to examine multi-membered PASS2 superfamily alignments to identify indel regions in an automated manner. Further, we have used the method to characterize the length, structural type and biochemical features of indels in related protein domains.</p> <p>Results</p> <p>CUSP, examines protein domain structural alignments to distinguish regions of conserved structure common to related proteins from structurally unconserved regions that vary in length and type of structure. On a non-redundant dataset of 353 domain superfamily alignments from PASS2, we find that 'length- deviant' protein superfamilies show > 30% length variation from their average domain length. 60% of additional lengths that occur in indels are short-length structures (< 5 residues) while 6% of indels are > 15 residues in length. Structural types in indels also show class-specific trends.</p> <p>Conclusion</p> <p>The extent of length variation varies across different superfamilies and indels show class-specific trends for preferred lengths and structural types. Such indels of different lengths even within a single protein domain superfamily could have structural and functional consequences that drive their selection, underlying their importance in similarity detection and computational modelling. The availability of systematic algorithms, like CUSP, should enable decision making in a domain superfamily-specific manner.</p

Length Variations amongst Protein Domain Superfamilies and Consequences on Structure and Function

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Comparative evaluation of PCR using IS6110 and a new target in the detection of tuberculous lymphadenitis

We evaluated TRC4 primers using polymerase chain reaction (PCR) which amplify a new target sequence from Mycobacterium tuberculosis genome to diagnose tuberculous lymphadenitis and compared the results with PCR using the widely used IS6110 primers. The PCR results were also compared with conventional methods like smear, culture and histopathology. The sensitivity of PCR using both probes is higher than the conventional methods. Out of 101 samples analysed (49 fresh and 52 fixed specimens), PCR using IS6110 and TRC4 primers was positive in 64 and 70 samples, respectively, whereas results with culture and histopathology methods were positive only in 49 and 58 samples, respectively. The problem of false negativity of IS6110 due to the absence of IS6110 copy in 4 M. tuberculosis isolates was overcome by using TRC4 primers. The results indicate that with improvement in PCR techniques, PCR using both probes, IS6110 and TRC4 can be a rapid and sensitive adjunct to conventional techniques in the diagnosis of tuberculous lymphadenitis

Observation of a plastic crystalline phase in solid MBBA

Wideline and high resolution NMR studies have been carried out in MBBA in its isotropic, nematic and solid phases. Isotropie and nematic spectra correspond to what has been reported earlier. In the solid phase, contrary to expectations, very intense narrow signals similar to signals of the isotropic phase have been observed for the first time at temperatures close to the solid ↔ nematic phase transition temperature. This indicates rapid reorientational or translational motion in the system. X-ray results however confirm the existence of translational order. The results are interpreted as indicative of the existence of a plastic crystalline phase in MBBA

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding

First Succinylome Profiling of Vibrio alginolyticus Reveals Key Role of Lysine Succinylation in Cellular Metabolism and Virulence

Recent studies have shown that a key strategy of many pathogens is to use post-translational modification (PTMs) to modulate host factors critical for infection. Lysine succinylation (Ksuc) is a major PTM widespread in prokaryotic and eukaryotic cells, and is associated with the regulation of numerous important cellular processes. Vibrio alginolyticus is a common pathogen that causes serious disease problems in aquaculture. Here we used the affinity enrichment method with LC-MS/MS to report the first identification of 2082 lysine succinylation sites on 671 proteins in V. alginolyticus, and compared this with the lysine acetylation of V. alginolyticus in our previous work. The Ksuc modification of SodB and PEPCK proteins were further validated by Co-immunoprecipitation combined with Western blotting. Bioinformatics analysis showed that the identified lysine succinylated proteins are involved in various biological processes and central metabolism pathways. Moreover, a total of 1,005 (25.4%) succinyl sites on 502 (37.3%) proteins were also found to be acetylated, which indicated that an extensive crosstalk between acetylation and succinylation in V. alginolyticus occurs, especially in three central metabolic pathways: glycolysis/gluconeogenesis, TCA cycle, and pyruvate metabolism. Furthermore, we found at least 50 (7.45%) succinylated virulence factors, including LuxS, Tdh, SodB, PEPCK, ClpP, and the Sec system to play an important role in bacterial virulence. Taken together, this systematic analysis provides a basis for further study on the pathophysiological role of lysine succinylation in V. alginolyticus and provides targets for the development of attenuated vaccines

Comparative transcriptomic analysis reveals the molecular mechanisms related to oxytetracycline- resistance in strains of Aeromonas hydrophila

Antibiotic resistance among aquatic bacterial pathogens has become a serious concern in aquaculture environments, which has increased research interest to develop solutions to overcome this problem. Moreover, the activities of several Aeromonas hydrophila gene pathways have remained elusive concerning antibiotic resistance evolution. Therefore, in this study, we have performed a transcriptomic analysis to compare differentially expressed genes between oxytetracycline (OXY) susceptible and resistant strains of A. hydrophila. Compared to the A. hydrophila susceptible strain, a total of 22 and 185 genes were differentially expressed in the 4-fold minimal inhibitory concentration (MIC) and 8-fold MIC resistant strains, respectively. Furthermore, the bioinformatics analysis revealed that the sulfur metabolism-related genes were down-regulated. The genes responsible for mannitol metabolism and the efflux pump system were up-regulated in resistant strains, compared to the susceptible strain. Therefore, it suggests that these three pathways may be involved in the OXY resistance evolution in A. hydrophila. The outcome of the transcriptomic data was further validated through quantitative reverse transcription-PCR (qRT-PCR) and Western blot analysis. Overall, the obtained data provides a deeper insight into the intrinsic molecular mechanism of OXY resistance evolution in A. hydrophila

The impacts of marketing and operations capabilities on financial performance in the UK retail sector: A resource-based perspective

Drawing upon the resource-based view (RBV) of the firm, this study investigates the relationships among marketing capability, operations capability, and financial performance. Using archival data of 186 retail firms in the UK, we find that that marketing capability has a significant impact on operations capability, and that operations capability is significantly and positively related to retail efficiency. The results also suggest that operations capability fully mediates the relationship between marketing capability and financial performance. The findings of this study provide practical insights for practicing managers to consider when developing functional capabilities in order to achieve superior financial performance. © 2013 Elsevier Inc

The evolution, seasonality, and impacts of western disturbances

Western disturbances (WDs) are upper-level synoptic-scale systems embedded in the subtropical westerly jet stream (STWJ), often associated with extreme rainfall events in north India and Pakistan during boreal winter. Here, a tracking algorithm is applied to the upper-tropospheric vorticity field in 37 years of ERA-Interim reanalysis data, giving a catalogue of over 3000 events. These events are analysed in a composite framework: the vertical structure is explored across a large number of dynamic and thermodynamic fields, revealing a significant northwestward tilt with height, strong ascent ahead of the centre which sits above the maximum surface precipitation and a warm-over-cold, dry-over-moist structure among other signatures of strong baroclinicity. Evolution of the structures of cloud cover and vertical wind speed are investigated as the composite WD passes across northern India. Cloud cover in particular is found to be particularly sensitive to the presence of the Himalayan foothills, with a significant maximum at 300 hPa approximately one day after the WD reaches peak intensity. k-means clustering is used to classify WDs both according to dynamical structure and precipitation footprint, and the relationship between the two sets is explored. Finally, the statistical relationship between the STWJ position and WDs on interannual time scales is explored, showing that WD frequency in north India is highly sensitive to the jet location over Eurasia. Years with a greater number of WDs feature a STWJ shifted to the south, a pattern that is substantially more coherent and reaches as far west as North America during boreal winter. This suggests that it may be possible to predict the statistics of western disturbance events on seasonal time scales if suitable indicators of jet position can also be predicted