PubMed | Sardar Patel University and Indian Institute of Advanced Research
Type: | Journal: Journal of biomolecular structure & dynamics | Year: 2016
Nair D.N.,Indian Institute of Advanced Research |
Singh V.,Indian Institute of Advanced Research |
Yamaguchi Y.,RIKEN |
Singh D.D.,Indian Institute of Advanced Research
Planta | Year: 2012
We have previously reported the purification and preliminary X-ray characterization of a hemagglutinin from the seeds of Jatropha curcas and, with the detailed sequencing information available now, we find that it is similar to a 2S albumin allergen isolated from the same source. Through a search of Jatropha genome database (http://www. kazusa. or. jp/jatropha/), we map it to the sequence id JcCA0234191 (now referred to as Jcr4S00619. 70 in the new version, release 4. 5) which has a conserved alpha amylase inhibitor/seed storage protein domain found in the 2S albumin allergens. The putative sequence of the small and large chains of the protein is assigned and the total mass of the two subunits matches with the intact mass 10 kDa determined through MALDI. The protein retains hemagglutination activity between pH 6-9 and up to 60 °C on heat treatment and its hemagglutination activity is inhibited by sialic acid and fetuin. Bioinformatics studies show that the isolated protein sequence clusters in close association with a 2S albumin from Ricinus communis in phylogeny analysis and has a conservation of the characteristic four disulfide linkage pattern. Hemagglutinins and lectins are known to have allergenic effects through their interaction with immunoglobulin E and histamine release and earlier studies have shown that this interaction can be inhibited by lectin-specific sugars. We hope this report bridges the plant allergens and hemagglutinins further for exploring possible mediation of allergenic activity through sialic acid and complex sugar interactions and generates further interest in the area. © 2012 Springer-Verlag.
Gnaana Saraswathi S.,Holy Cross College |
Paliwal K.,Indian Institute of Advanced Research
Journal of Environmental Biology | Year: 2011
Diurnal trends in net photosynthesis rate (P N), stomatal conductance (g s), water use efficiency (WUE) and biomass were compared in six-month-old seedlings of Albizla lebbeckand Cassia siamea, under different levels of drought stress. The potted plants were subjected to four varying drought treatment by withholding watering for 7 (D1 ), 14 (D2) and 25 (D3) days. The fourth group (C) was watered daily and treated as unstressed (control). Species differed significantly (p<0.001) in their physiological performance under varying stress conditions. Higher P N of 11.6 ± 0.05 in control followed by 4.35 ± 0.4 in D1 and 2.83 ± 0.18 μmol m 2 s -1 in D2 was observed in A. Iebbeck. A significant (p<0.001 ) reduction in P N was observed in C. siamea ( C 7.65 ± 0.5 μmol m2s -1, D1,2.56 ±0.33 μmolm 2s -1 and D2,1.4±0.01 μmolm 2s -1) at 9 hr. A positive correlation was seen between P N and g s (A. Iebbeck, r 2= 0.84; C. siamea, r 2= 0.82). Higher WUE was observed in C. siamea (D2,7.1 ± 0.18 μmol m 2 s -1; D3,8.39 ± 0.11 μmol m 2s -1) than A. Iebbeck, (control, 7.58 ± 0.3 μmol m 2s -1and D3,8.12 ± 0.15 μmol m 2 s -1). The chlorophyll and relative water content (RWC) was more in A. Iebbeck than C. siamea. Maximum biomass was produced by A. lebbeck than C. siamea. From the study, one could conclude that A lebbeck'is betterthan C. siameah adopting suitable resource management strategy and be best suited for the plantation programs in the semi-arid dry lands. © 2011 Triveni Enterprises vikas Nagar, Lucknow, INDIA.
Pandya C.,M. S. University of Baroda |
Pandya C.,Indian Institute of Advanced Research |
Pillai P.,M. S. University of Baroda |
Nampoothiri L.P.,M. S. University of Baroda |
And 3 more authors.
Andrologia | Year: 2012
The mechanism of testicular toxicity of lead (Pb) and cadmium (Cd) is poorly understood. Previous studies focused on single metal-related changes in testicular toxicity. This study points towards the possible involvement of Pb- and Cd-induced oxidative stress in the suppression of steroidogenesis. The oxidative status of testis of adult male rats exposed to Pb acetate and cadmium acetate either alone or in combination at a dose of 0.025mgkg -1 body weight of metal intraperitoneally for 15days was studied. Pb and Cd caused an increase in reactive oxygen species (ROS) by elevating testicular malondialdehydes (MDA) and decrease in activities of testicular antioxidant enzymes superoxide dismutase (SOD), catalase, glucose 6 phosphate dehydrogenase (G6PDH) and glutathione-S-transferase (GST) in mitochondrial and/or post-mitochondrial fraction. Activities of steroidogenic enzymes 3β and 17β-hydroxysteroid dehydrogenase also decreased significantly leading to altered testosterone production. Metal-exposed groups showed significantly decreased testicular and epididymal sperm count. Epididymal sperm motility and viability was also decreased on Pb and Cd exposure. Cd exposure showed more toxic effect than lead exposure, while combined exposure demonstrated least toxicity. In vitro experiments showed that vitamin C restores steroidogenic enzyme activities, suggesting that Pb- and Cd-induced ROS inhibits the testicular steroidogenesis. © 2011 Blackwell Verlag GmbH.
PubMed | M. S. University of Baroda and Indian Institute of Advanced Research
Type: | Journal: International journal of biological macromolecules | Year: 2016
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous enzyme involved in glycolysis. It is also referred to as a moonlighting protein as it has many diverse functions like regulation of apoptosis, iron homeostasis, cell-matrix interactions, adherence to human colon etc. apart from its principal role in glycolysis. Lactobacilli are lactic acid bacteria which colonize the human gut and confer various health benefits to humans. In the present study, we have cloned, expressed and purified the GAPDH from Lactobacillus acidophilus to get a recombinant product (r-LaGAPDH) and characterized it. Size exclusion chromatography shows that r-LaGAPDH exists as a tetramer in solution and have a mucin binding and hemagglutination activity indicating carbohydrate like binding adhesion mechanism. Fluorescence spectroscopy studies showed an interaction of r-LaGAPDH with mannose, galactose, N-acetylgalactosamine and N-acetylglucosamine with a Kd of 3.60.710(-3)M, 4.340.0910(-3)M, 40.8710(-3)M and 3.70.2810(-3)M respectively. We hope that this preliminary data will generate more interest in further elucidation of the roles of GAPDH in the adhesion processes of the bacteria.
Nair D.N.,Indian Institute of Advanced Research |
Suresh C.G.,CSIR - National Chemical Laboratory |
Singh D.D.,Indian Institute of Advanced Research
Acta Crystallographica Section F: Structural Biology and Crystallization Communications | Year: 2011
The plant Jatropha curcas (Euphorbiaceae) is an important source of biofuel from the inedible oil present in its toxic seeds. The toxicity arises from the presence of curcin, a ribosome-inactivating protein showing haemagglutination activity. In this communication, the purification, crystallization and preliminary X-ray characterization are reported of a small protein isolated from J. curcas seeds with a molecular mass of 10 kDa that agglutinates rabbit erythrocytes. The protein was crystallized using the hanging-drop vapour-diffusion method and also by the microbatch method in 72-well HLA plates, using PEG 8000 as the precipitant in both conditions. X-ray diffraction data collected from the rod-shaped crystals were processed in the orthorhombic space group P2 12 12 1. The crystals diffracted to 2.8 Å resolution at 103 K. © 2011 International Union of Crystallography. All rights reserved.
Heikham R.,Indian Institute of Advanced Research |
Shankar R.,Indian Institute of Advanced Research
Journal of Biosciences | Year: 2010
The non-coding elements of a genome, with many of them considered as junk earlier, have now started gaining long due respectability, with microRNAs as the best current example. MicroRNAs bind preferentially to the 3' untranslated regions (UTRs) of the target genes and negatively regulate their expression most of the time. Several microRNA:target prediction softwares have been developed based upon various assumptions and the majority of them consider the free energy of binding of a target to its microRNA and seed conservation. However, the average concordance between the predictions made by these softwares is limited and compounded by a large number of false-positive results. In this study, we describe a methodology developed by us to refine microRNA:target prediction by target prediction softwares through observations made from a comprehensive study. We incorporated the information obtained from dinucleotide content variation patterns recorded for flanking regions around the target sites using support vector machines (SVMs) trained over two different major sources of experimental data, besides other sources. We assessed the performance of our methodology with rigorous tests over four different dataset models and also compared it with a recently published refinement tool, MirTif. Our methodology attained a higher average accuracy of 0.88, average sensitivity and specificity of 0.81 and 0.94, respectively, and areas under the curves (AUCs) for all the four models scored above 0.9, suggesting better performance by our methodology and a possible role of flanking regions in microRNA targeting control. We used our methodology over genes of three different pathways - toll-like receptor (TLR), apoptosis and insulin - to finally predict the most probable targets. We also investigated their possible regulatory associations, and identified a hsa-miR-23a regulatory module. © 2010 Indian Academy of Sciences.
Bhardwaj A.K.,Indian Institute of Advanced Research |
Mohanty P.,Indian Institute of Advanced Research
Recent Patents on Anti-Infective Drug Discovery | Year: 2012
Active efflux of antibiotics is one of the major mechanisms of drug resistance in bacteria. The efflux process is mediated by membrane transporters with a large variety of unrelated compounds as their substrates. Though these pumps are responsible for the low intrinsic resistance of a bacterium to a drug, their overexpression, accumulation of mutations in these proteins and their synergy with other drug resistance mechanisms hampers effective antimicrobial treatment. As efflux pumps have been reported to play vital roles in mediating multidrug resistance in clinical isolates from varied geographic locations and varied populations, the inhibition of efflux pumps appears to be an attractive approach to combat the problem of drug resistance. Efflux pump inhibitors can be utilized for increasing the antibiotic concentration inside a pathogenic cell making these drugs more effective, reduce the accumulation of other resistance mechanisms in a cell and for diagnostic purposes to evaluate the presence and contribution of the efflux mechanism in a pathogen. A large number of inhibitors have been discovered and patented in last two decades but the process of discovery, testing and commercialization is rather slow. Some of the important inhibitors include the energy decouplers, phenothiazines, analogs of popular antibiotics, inhibitors of serotonin re-uptake, to name a few, that have been used as adjuvants in the antimicrobial chemotherapy to potentiate the activity of some important antimicrobials in deadly pathogens that have worried the mankind since long. This review describes the role of efflux pumps in governing the resistance phenotype of a pathogen, efflux pumps found in bacteria and the efflux pump inhibitors that have been studied and patented so far. © 2012 Bentham Science Publishers.
Mohanty P.,Indian Institute of Advanced Research |
Patel A.,Indian Institute of Advanced Research |
Bhardwaj A.K.,Indian Institute of Advanced Research
PLoS ONE | Year: 2012
Background: The study seeks to understand the role of efflux pumps in multidrug resistance displayed by the clinical isolates of Vibrio fluvialis, a pathogen known to cause cholera-like diarrhoea. Methodology: Two putative MATE family efflux pumps (H- and D-type) were PCR amplified from clinical isolates of V. fluvialis obtained from Kolkata, India, in 2006 and sequenced. Bioinformatic analysis of these proteins was done to predict protein structures. Subsequently, the genes were cloned and expressed in a drug hypersusceptible Escherichia coli strain KAM32 using the vector pBR322. The recombinant clones were tested for the functionality of the efflux pump proteins by MIC determination and drug transport assays using fluorimeter. Results: The sequences of the genes were found to be around 99% identical to their counterparts in V. cholerae. Protein structure predicting servers TMHMM and I-TASSER depicted ten-twelve membrane helical structures for both type of pumps. Real time PCR showed that these genes were expressed in the native V. fluvialis isolates. In the drug transport assays, the V. fluvialis clinical isolates as well as recombinant E. coli harbouring the efflux pump genes showed the energy-dependent and sodium ion-dependent drug transport activity. KAM32 cells harbouring the recombinant plasmids showed elevated MIC to the fluoroquinolones, norfloxacin and ciprofloxacin but H-type pumps VCH and VFH from V. cholerae and V. fluvialis respectively, showed decreased MIC to aminoglycosides like gentamicin, kanamycin and streptomycin. Decrease in MIC was also observed for acriflavin, ethidium bromide, safranin and nalidixic acid. Significance: Increased resistance towards fluoroquinolones exhibited due to these efflux pumps from multidrug resistant clinical isolates of V. fluvialis implies that treatment procedure may become more elaborate for this simple but highly infectious disease. To the best of our knowledge, this is the first report of cloning and characterization of efflux pumps from multidrug resistant clinical isolates of V. fluvialis. © 2012 Mohanty et al.
Bhardwaj A.K.,Indian Institute of Advanced Research |
Vinothkumar K.,Indian Institute of Advanced Research |
Rajpara N.,Indian Institute of Advanced Research
Recent Patents on Anti-Infective Drug Discovery | Year: 2013
Quorum sensing (QS) is a bacterial communication process that depends on the bacterial population density. It involves small diffusible signaling molecules which activate the expression of myriad genes that control diverse array of functions like bioluminescence, virulence, biofilm formation, sporulation, to name a few. Since QS is responsible for virulence in the clinically relevant bacteria, inhibition of QS appears to be a promising strategy to control these pathogenic bacteria. With indiscriminate use of antibiotics, there has been an alarming increase in the number of antibiotic resistant pathogens. Antibiotics are no longer the magic bullets they were once thought to be and therefore there is a need for development of new antibiotics and/or other novel strategies to combat the infections caused by multidrug resistant organisms. Quorum sensing inhibition or quorum quenching has been pursued as one of such novel strategies. While antibiotics kill or slow down the growth of bacteria, quorum sensing inhibitors (QSIs) or quorum quenchers (QQs) attenuate bacterial virulence. A large body of work on QS has been carried out in deadly pathogens like Pseudomonas aeruginosa, Staphylococcus aureus, Vibrio fischeri, V. harveyi, Escherichia coli and V. cholerae etc to unravel the mechanisms of QS as well as identify and study QSIs. This review describes various aspects of QS, QSI, different model systems to study these phenomena and recent patents on various QSIs. It suggests QSIs as attractive alternatives for controlling human, animal and plant pathogens and their utility in agriculture and other industries. © 2013 Bentham Science Publishers.