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61.
Background
Shigella flexneri is the major cause of bacillary dysentery in the developing countries. The lipopolysaccharide (LPS) O-antigen of S. flexneri plays an important role in its pathogenesis and also divides S. flexneri into 19 serotypes. All the serotypes with an exception for serotype 6 share a common O-antigen backbone comprising of N-acetylglucosamine and three rhamnose residues. Different serotypes result from modification of the basic backbone conferred by phage-encoded glucosyltransferase and/or acetyltransferase genes, or plasmid-encoded phosphoethanolamine transferase. Recently, a new site for O-acetylation at positions 3 and 4 of RhaIII, in serotypes 1a, 1b, 2a, 5a and Y was shown to be mediated by the oacB gene. Additionally, this gene was shown to be carried by a transposon-like structure inserted upstream of the adrA region on the chromosome.Results
In this study, a novel bacteriophage Sf101, encoding the oacB gene was isolated and characterised from a serotype 7a strain. The complete sequence of its 38,742 bp genome encoding 66 open reading frames (orfs) was determined. Comparative analysis revealed that phage Sf101 has a mosaic genome, and most of its proteins were >90% identical to the proteins from 12 previously characterised lambdoid phages. In addition, the organisation of Sf101 genes was found to be highly similar to bacteriophage Sf6. Analysis of the Sf101 OacB identified two amino acid substitutions in the protein; however, results obtained by NMR spectroscopy confirmed that Sf101-OacB was functional. Inspection of the chromosomal integration site of Sf101 phage revealed that this phage integrates in the sbcB locus, thus unveiling a new site for integration of serotype-converting phages of S. flexneri, and determining an alternative location of oacB gene in the chromosome. Furthermore, this study identified oacB gene in several serotype 7a isolates from various regions providing evidence of O-acetyl modification in serotype 7a.Conclusions
This is the first report on the isolation of bacteriophage Sf101 which contains the S. flexneri O-antigen modification gene oacB. Sf101 has a highly mosaic genome and was found to integrate in the sbcB locus. These findings contribute an advance in our current knowledge of serotype converting phages of S. flexneri.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-742) contains supplementary material, which is available to authorized users. 相似文献62.
Anupam Dhasmana Qazi Mohd. Sajid Jamal Snober Shabnam Mir Madan Lal Bramha Bhatt Qamar Rahman Richa Gupta Mohd. Haris Siddiqui Mohtashim Lohani 《PloS one》2014,9(9)
Polycyclic aromatic hydrocarbons (PAH), like Benzo[alpha]Pyrene (BaP) are known to cause a number of toxic manifestations including lung cancer. As Titanium dioxide Nanoparticles (TiO2 NPs) have recently been shown to adsorb a number of PAHs from soil and water, we investigated whether TiO2 NPs could provide protection against the BaP induced toxicity in biological system. A549 cells when co-exposed with BaP (25 µM, 50 µM and 75 µM) along with 0.1 µg/ml,0.5 µg/ml and 1 µg/ml of TiO2 NPs, showed significant reduction in the toxic effects of BaP, as measured by Micronucleus Assay, MTT Assay and ROS Assay. In order to explore the mechanism of protection by TiO2 NP against BaP, we performed in silico studies. BaP and other PAHs are known to enter the cell via aromatic hydrocarbon receptor (AHR). TiO2 NP showed a much higher docking score with AHR (12074) as compared to the docking score of BaP with AHR (4600). This indicates a preferential binding of TiO2 NP with the AHR, in case if both the TiO2 NP and BaP are present. Further, we have done the docking of BaP with the TiO2 NP bound AHR-complex (score 4710), and observed that BaP showed strong adsorption on TiO2 NP itself, and not at its original binding site (at AHR). TiO2 NPs thereby prevent the entry of BaP in to the cell via AHR and hence protect cells against the deleterious effects induced by BaP. 相似文献
63.
Bhupander Kumar V. K. Verma Meenu Mishra Richa Gaur Sanjay Kumar C. S. Sharma 《人类与生态风险评估》2014,20(6):1538-1549
Dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexane (HCH), and their isomers’ levels in residential soils were determined for the assessment of health risk in Korba, India. Observed concentrations of total HCH and total DDT in soils were more or less comparable with other parts of India and the world. ΣHCH and ΣDDT concentrations ranged between 0.9–20 μg kg?1 and 2–315 μg kg?1, respectively, which were lower than recommended soil quality guidelines indicating low ecotoxicological risk. Carcinogenic and non-carcinogenic impacts of HCH and DDT on human populations through soil ingestion were evaluated and presented. The incremental lifetime cancer risk (ILCR) for adults and children ranged between 7.8 × 10?10–1.6 × 10?7 and 4.1 × 10?9–8.2 × 10?7, respectively. Non-cancer health hazard quotient (HQ) ranged between 5.9 × 10?7–1.8 × 10?3 and 3.1 × 10?6–9.4 × 10?3, respectively, for adults and children. The estimated ILCR and HQ were within the safe acceptable limits of 10?6–10?4 and ≤1.0, respectively, indicating low risk to human populations from exposure to organochlorine pesticides (HCH and DDT) in the study area. 相似文献
64.
Richa Mudgal Ramanathan Sowdhamini Nagasuma Chandra Narayanaswamy Srinivasan Sankaran Sandhya 《Journal of molecular biology》2014
Protein functional annotation relies on the identification of accurate relationships, sequence divergence being a key factor. This is especially evident when distant protein relationships are demonstrated only with three-dimensional structures. To address this challenge, we describe a computational approach to purposefully bridge gaps between related protein families through directed design of protein-like “linker” sequences. For this, we represented SCOP domain families, integrated with sequence homologues, as multiple profiles and performed HMM-HMM alignments between related domain families. Where convincing alignments were achieved, we applied a roulette wheel-based method to design 3,611,010 protein-like sequences corresponding to 374 SCOP folds. To analyze their ability to link proteins in homology searches, we used 3024 queries to search two databases, one containing only natural sequences and another one additionally containing designed sequences. Our results showed that augmented database searches showed up to 30% improvement in fold coverage for over 74% of the folds, with 52 folds achieving all theoretically possible connections. Although sequences could not be designed between some families, the availability of designed sequences between other families within the fold established the sequence continuum to demonstrate 373 difficult relationships. Ultimately, as a practical and realistic extension, we demonstrate that such protein-like sequences can be “plugged-into” routine and generic sequence database searches to empower not only remote homology detection but also fold recognition. Our richly statistically supported findings show that complementary searches in both databases will increase the effectiveness of sequence-based searches in recognizing all homologues sharing a common fold. 相似文献
65.
Richa Verma 《生物化学与生物物理学报:生物膜》2010,1798(3):461-24841
Mutations in various voltage gated cardiac ion channels are the cause of different forms of long QT syndrome (LQTS), which is an inherited arrhythmic disorder marked as a prolonged QT interval on electrocardiogram. Of these LQTS1 is associated with mutations in the gene encoding KCNQ1 (KvLQT1) channel. One responsible mutation, G269S, in the S5 segment of KvLQT1, that affects the proper expression and function of channel protein leads to LQTS1. Our objective was to study how G269S mutation interferes with the structure and function of a synthetic S5 segment of KvLQT1 channel. One wild type 22-residue peptide and another mutant peptide of the same length with G269S mutation, derived from the S5 segment were synthesized and labeled with fluorescent probes. The mutant peptide exhibited lower affinity towards phospholipid vesicles as compared to the wild type peptide and showed impaired assembly and localization onto the lipid vesicles as evidenced by membrane-binding, energy transfer and proteolytic cleavage experiments. Loss in the helical content of S5 mutant peptide in membrane-mimetic environments was observed. Furthermore, it was observed that G269S mutation significantly inhibited the ability of S5 peptide to permeabilize the lipid vesicles. The present studies show the basis of change in function of the selected S5 segment as a result of G269S mutation which is associated with LQT1 syndrome. We speculate that the structural and functional changes related to the glycine to serine amino acid substitution in the S5 segment may also influence the activity of the whole KvLQT1 channel. 相似文献
66.
Lae-Hyeon Cho Richa Pasriga Jinmi Yoon Jong-Seong Jeon Gynheung An 《Journal of Plant Biology》2018,61(3):121-130
Flowering time is influenced by environmental factors such as photosynthesis, temperature, nutrition, and water. The main products of photosynthesis are sugars that are mobilized to sink tissues to support plant growth and differentiation. They also function as signals to control various types of metabolism and developmental processes. One of the most important transitions in the plant life cycle is from the vegetative to reproductive phase. During that transition, sucrose levels rise rapidly but transiently in the phloem and shoot apexes. For several species, the addition of exogenous sucrose promotes flowering, possibly by acting as a main signal. Although other sugars, including glucose, also appear to be involved in this transition, evidence for their roles in flowering is limited. In Arabidopsis thaliana, trehalose-6-phosphate serves as a signal to induce flowering. However, its roles in other plants have not been reported. Sucrose seems to function primarily in the leaf phloem to enhance the generation of florigens such as Flowering Locus T (FT) while trehalose-6-phosphate functions in the shoot apical meristem to promote the flowering signal pathway downstream of those florigens. 相似文献
67.
Sharma Richa Roopak Sangita Pathak Nilesh kumar Uma R. Sharma R. P. 《Plasmonics (Norwell, Mass.)》2018,13(1):335-343
Plasmonics - In the present work, we report our observations drawn from the numerical simulation of absorption and scattering efficiencies of spheroid shape nanostructures using discrete dipole... 相似文献
68.
Arora Sidharth Singh Pritam Rani Richa Ghosh Sanjoy 《Bioprocess and biosystems engineering》2018,41(7):917-929
Bioprocess and Biosystems Engineering - Direct measurement of cell biomass is difficult in a solid-state fermentation (SSF) process involving filamentous fungi since the mycelium and the solid... 相似文献
69.
Akanksha Agrawal Geetha Suryakumar Richa Rathor 《Journal of cell communication and signaling》2018,12(4):645-659
The misbehaving attitude of Ca2+ signaling pathways could be the probable reason in many muscular disorders such as myopathies, systemic disorders like hypoxia, sepsis, cachexia, sarcopenia, heart failure, and dystrophy. The present review throws light upon the calcium flux regulating signaling channels like ryanodine receptor complex (RyR1), SERCA (Sarco-endoplasmic Reticulum Calcium ATPase), DHPR (Dihydropyridine Receptor) or Cav1.1 and Na+/Ca2+ exchange pump in detail and how remodelling of these channels contribute towards disturbed calcium homeostasis. Understanding these pathways will further provide an insight for establishing new therapeutic approaches for the prevention and treatment of muscle atrophy under stress conditions, targeting calcium ion channels and associated regulatory proteins. 相似文献
70.
Aheibam Loyanganba Meitei Mamta Bhattacharjee Santanu Dhar Naimisha Chowdhury Richa Sharma 《Journal of Plant Interactions》2018,13(1):231-238
The biochemical and molecular basis of the defense in a mild tolerant (ICPL-332) and susceptible (ICPL-87) cultivars of pigeon pea (Cajanus cajan) due to Helicoverpa. armigera infestation was studied. We found that feeding by the larvae generated H2O2 in a localized manner and activity was observed upto 12?h (hrs) of with a sharp decline within 24?h. Similarly, PPO activity was also detected till 12?h of treatment, which decreased after 24?h of feeding by larvae. The activity of trypsin inhibitor was detected in all the treatments when assayed at 12 and 24?h after larval feeding. The expression of defense genes like the Pre-hevein-like protein PR-4 precursor (PR-4), protease inhibitor/seed storage/LTP family protein (Ltp) were significantly up-regulated in ICPL-332 upon infestation after 12?h as compared to ICPL-87, whereas the endo 1, 4 -β-glucanase (Kor-1) gene was expressed in both the cultivars after 24?h of infestation. Both the cultivars varied with respect to the induction of defense-related genes during larval feeding, both the PR-4 and Ltp genes appeared to be important for defense against H. armigera in pigeon pea. Thus, the present study revealed an insight of herbivore-induced biochemical and molecular changes in pigeon pea. 相似文献