Indian journal of biochemistry & biophysics最新文献

{"title":"Rapid and simple method of photobleaching to reduce background autofluorescence in lung tissue sections.","authors":"B Santhosh Kumar,&nbsp;S Sandhyamani,&nbsp;Shaiju S Nazeer,&nbsp;R S Jayasree","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Autofluorescence exhibited by tissues often interferes with immunofluorescence. Using imaging and spectral analysis, we observed remarkable reduction of autofluorescence of formalin fixed paraffin embedded tissues irradiated with light prior to incubation with immunofluorescent dyes. The technique of photobleaching offers significant improvement in the quality and specificity of immunofluorescence. This has the potential for better techniques for disease diagnosis.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"107-10"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33357017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural analysis and molecular docking of potential ligands with chorismate synthase of Listeria monocytogenes: a novel antibacterial drug target.","authors":"Md Musharaf Hossain,&nbsp;Pradip Kumar Roy,&nbsp;A T M Jannatul Mosnaz,&nbsp;Shahriar Kabir Shakil,&nbsp;Md Mehedi Hasan,&nbsp;Shamsul H Prodhan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Listeriosis, in particular that caused by Listeria monocytogenes, is a major foodborne pathogen, and its control is becoming difficult because of widespread emergence of drug resistance strains. Chorismate synthase (CS), an essential enzyme of shikimate pathway present only in bacteria, fungi, plant and some apicomplexan parasites, is a validated potential antimicrobial drug target. Antimicrobial development through the elucidation of essential structural features of the CS of L. monocytogenes (LmCS), identification and prioritization of potential lead compounds targeted against LmCS were done. Structure-based virtual screening and docking studies were performed using Autodock tools to retrieve potential candidates with high affinity binding against LmCS model from several ligand repositories. The potency of binding was also checked with other structurally similar CS from Streptococcus pneumoniae (SpCS) and Mycobacterium tuberculosis (MtCS). The sequence and structural studies revealed LmCS was similar to be other CS structures (1Q1L, 1QXO, 1R52, 1R53, 1SQ1, 1UMO, 1UMF, 1ZTB, 2011, 2012, 4ECD and 2G85) with each monomer presenting β-α-β sandwich topology with a central helical core. Molecular docking studies and ADME/Tox results revealed that ZINC03803450 and ZINC20149031 were most potent molecules binding into the active site of LmCS. Other two ligands ZINC13387711-and ZINC16052528 showed a strong binding affinity score against all three structures (LmCS, SpCS and MtCS) and bind to LmCS with the predicted inhibition constant (K(i)) values of 22.94 nM and 35.84 nM, respectively. A reported benzofuran-3[2H]-one analog CHEMBL135212 with good ADME/Tox properties and experimental IC50 (nM) value of 7000 nM with SpCS could also be considered as a potential inhibitor of LmCS, as compared to previously reported 41 benzofuran-3[2H]-one analogs against SpCS. This information will assist in discovering those compounds that may act as potent CS inhibitors. Further experimental studies and evaluation of structure-activity relationship could help in the development of potential inhibitors against listeriosis, as well as antibacterial chemotherapy.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"45-59"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33238295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serum neuron-specific enolase and S-100β levels as prognostic follow-up markers for oxygen administered carbon monoxide intoxication cases.","authors":"Ali Osman Yildirim,&nbsp;Murat Eroglu,&nbsp;Umit Kaldirim,&nbsp;Yusuf Emrah Eyi,&nbsp;Kemal Simsek,&nbsp;Murat Durusu,&nbsp;Levent Yamanel,&nbsp;Ibrahim Arziman,&nbsp;Salim Kemal Tuncer,&nbsp;Mehmet Toygar,&nbsp;Arzu Balkan,&nbsp;Tuncer Cayci,&nbsp;Seref Demirbas,&nbsp;Sukru Oter,&nbsp;Cumhur Bilgi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Serum neuron-specific enolase (NSE) and S-100β levels are considered novel biochemical markers of neuronal cell injury. In this study, the initial and post-treatment levels of NSE and S-100β were compared in carbon monoxide (CO) poisoning patients, who received normorbaric oxygen (NBO) or hyperbaric oxygen (HBO) therapy. Forty consecutive patients with acute CO poisoning were enrolled in this prospective, observational study. According to their clinical symptoms and observations, twenty patients were treated with NBO, and the other twenty with HBO. Serum S-100β and NSE levels were measured both at time of admission and 6 h later (post-treatment). Serum NSE and S-100β values decreased significantly in both of the therapeutic modalities. The initial and post-treatment values of NSE and S-100β in NBO or HBO patients were comparable. A clear negative correlation was observed between the decrease of NSE and S-100β levels and initial blood carboxyhemoglobin levels. In conclusion, the present results suggested the use of serum S-100β and NSE levels as indicators for brain injury. Due to the significant increase of their values with oxygen therapy, they may also be useful as prognostic follow-up markers. However, the current findings reflected no difference between the efficacy of NBO or HBO therapy.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"29-33"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33238293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of different serine protease inhibitors in validating the 115 kDa Leishmania donovani secretory serine protease as chemotherapeutic target.","authors":"Tapati Chakraborti,&nbsp;Partha Das,&nbsp;Rajdeep Choudhury,&nbsp;Tripti De","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Proteases have been considered as an important group of targets for development of antiprotozoal drugs due to their essential roles in host-parasite interactions, parasite immune evasion, life cycle transition and pathogenesis of parasitic diseases. The development of potent and selective serine protease inhibitors targeting L. donovani secretory serine protease (pSP) could pave the way to the discovery of potential antileishmanial drugs. Here, we employed different classical serine protease inhibitors (SPIs), such as aprotinin, N-tosyl-1-phenylalanine chloromethyl ketone (TPCK), N-tosyl-lysine chloromethyl ketone (TLCK), benzamidine (Bza) and pSP-antibody to determine the role of the protease in parasitic survival, growth and infectivity. Among the different classical SPIs, aprotinin appeared to be more potent in arresting L. donovani promastigotes growth with significant morphological alterations. Furthermore, aprotinin and anti-pSP treated parasites significantly decreased the intracellular parasites and percentage of infected macrophages. These results suggest that SPIs may reduce the infectivity by targeting the serine protease activity and may prove useful to elucidate defined molecular mechanisms of pSP, as well as for the development of novel antileishmanial drugs in future.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"14-22"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33238291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Purification, characterization and synthetic application of a thermally stable laccase from Hexagonia tenuis MTCC-1119.","authors":"Pankaj Kumar Chaurasia,&nbsp;Shashi Lata Bharati,&nbsp;Sudha Yadava,&nbsp;Rama Shanker Singh Yadav","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A thermally stable laccase was purified from the culture filtrate of Hexagonia tenuis MTCC-1119. The method involved concentration of the culture filtrate by ammonium sulphate precipitation and an anion-exchange chromatography on diethylaminoethyl (DEAE) cellulose. The sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and native polyacrylamide gel electrophoresis (native-PAGE) both gave single protein bands, indicating that the enzyme preparation was pure. The molecular mass of the enzyme determined from SDS-PAGE analysis was 100 kDa. The purification fold and percentage recovery of the enzyme activity were 12.75 and 30.12%, respectively. The pH and the temperature optima were 3.5 and 45 degrees C, respectively. The enzyme was most stable at pH 4.0 when exposed for 1 h. Using 2,6-dimethoxyphenol (DMP), 2,2 [azino-bis-(3-ethylbonzthiazoline-6-sulphonic acid) diammonium salt] (ABTS) and 3,5-dimethoxy-4-hydroxybenzaldehyde azine (syringaldazine) as the substrates, the K(m), k(cat) and k(cat)/K(m) values of the laccase were 80 μM, 2.54 s(-1), 3.17 x 10(4) M(-1)s(-1), 36 μM, 2.54 s(-1), 7.05 x 10(4) M(-1)s(-1) and 87 μM, 2.54 s(-1), 2.92 x 10(4) M(-1)s(-1), respectively. The purified laccase was finally used for the selective biotransformation of aromatic methyl group to aldehyde group in presence of diammonium salt of ABTS as the mediator and products were characterized by HPLC, IR and 1H NMR. The percentage yields of these transformed products were > 91%.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"60-7"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33356571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico structural and functional analysis of protein encoded by wheat early salt-stress response gene (WESR3).","authors":"A K Mishra,&nbsp;Gitanjali Tandon,&nbsp;Rajendra Sharma,&nbsp;H Chandrasekharan,&nbsp;P S Pandey","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Salt stress is one of the major abiotic stresses limiting grain yield in wheat (Triticum aestivum L.). Wheat early salt-stress response gene (WESR3) is one of the major salt stress genes, which is affected in the first phase of salt stress. In this study, sequence and structural analysis of protein coded by WESR3 gene was carried out using various bioinformatics tools. Sequence analysis of WESR3 protein revealed the presence of highly conserved regions of Mlo gene family. Three-dimensional modeling was carried out to elucidate its structure and its active site. The sequence analysis revealed that WESR3 protein might be involved in fungal pathogen attack pathway. Thus, in addition to its involvement in abiotic stresses, it also seemed to play an important part in biotic stress pathways. Out of the three modeled protein structures obtained from I-TASSER, HHPred and QUARK, the I-TASSER protein model was the best model based on high confidence score and lesser number of bad contacts. The Ramchandran plot analysis also showed that all amino acid residues of I-TASSER model lie in the allowed region and thus indicating towards the overall good quality of the predicted model. Seventeen active sites were predicted in the protein bearing resemblance to the Mlo family conserved regions. In conclusion, a detailed analysis of WESR3 protein suggested an important role of WESR3 in biotic and abiotic stress. These results aid to the experimental data and help to build up a complete view of WESR3 proteins and their role in plant stress response.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"95-100"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33356575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beta catenin is degraded by both caspase-3 and proteasomal activity during resveratrol-induced apoptosis in HeLa cells in a GSK3β-independent manner.","authors":"Mahan Ray,&nbsp;Neha Rai,&nbsp;Kuladip Jana,&nbsp;Supratim Ghatak,&nbsp;Arnab Basu,&nbsp;Soumyajit Banerjee Mustafi,&nbsp;Sanghamitra Raha","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Increased activity of β-catenin, an important transcriptional activator for survival and proliferation-associated genes has been linked with many cancers. We examined whether β-catenin is a target of resveratrol and whether its degradation contributes to the pro-apoptotic effects of resveratrol. HeLa cells were exposed to 60 μM resveratrol for 48 h. Apoptosis was confirmed by measurement of annexin V externalization, caspase-3 activation and DNA fragmentation. Induction of apoptosis was observed as early as 12 h, when both caspase-3 activation and PARP (poly ADP ribose polymerase) cleavage occurred. Nuclear β-catenin levels remained unchanged for 48 h during resveratrol exposure. However, extranuclear cell lysate β-catenin underwent a decrease at a late stage of apoptosis namely at 36-48 h. Alterations in the phosphorylation status of Akt/GSK3β were not observed during resveratrol-induced apoptosis. Furthermore, inhibition of GSK3β activity which is. largely responsible for β-catenin degradation failed to influence β-catenin stability. However, inhibition of caspase-3 activity prevented the decline in β-catenin levels at 36-48 h of resveratrol exposure. Lactacystin, a proteosomal inhibitor also prevented the degradation of β-catenin by resveratrol. In conclusion, resveratrol induced apoptosis in HeLa cells in an Akt/GSK3β-independent manner and down-regulated β-catenin levels during apoptosis through action of caspase-3 and proteasomal degradation, independent of GSK3β-mediated phosphorylation.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"7-13"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33238290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational prediction of MHC class I epitopes for most common viral diseases in cattle (Bos taurus).","authors":"Tanmaya Kumar Sahu,&nbsp;A R Rao,&nbsp;Prabina Kumar Meher,&nbsp;Bishnu Charan Sahoo,&nbsp;Satakshi Gupta,&nbsp;Anil Rai","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Viral diseases like foot-and-mouth disease (FMD), calf scour (CS), bovine viral diarrhea (BVD), infectious bovine rhinotracheitis (IBR) etc. affect the growth and milk production of cattle (Bos taurus) causing severe economic loss. Epitope-based vaccine designing have been evolved to provide a new strategy for therapeutic application of pathogen-specific immunity in animals. Therefore, identification of major histocompatibility complex (MHC) binding peptides as potential T-cell epitopes is widely applied in peptide vaccine designing and immunotherapy. In this study, MetaMHCI tool was used with seven different algorithms to predict the potential T-cell epitopes for FMD, BVD, IBR and CS in cattle. A total of 54 protein sequences were filtered out from a total set of 6351 sequences of the pathogens causing the said diseases using bioinformatics approaches. These selected protein sequences were used as the key inputs for MetaMHCI tool to predict the epitopes for the BoLA-All MHC class I allele of B. taurus. Further, the epitopes were ranked based on a proposed principal component analysis based epitope score (PbES). The best epitope for each disease based on its predictability through maximum number of predictors and low PbES was modeled in PEP-FOLD server and docked with the BoLA-A11 protein for understanding the MHC-epitope interaction. Finally, a total of 78 epitopes were predicted, out of which 27 were for FMD, 25 for BVD, 12 for CS and 14 for IBR. These epitopes could be artificially synthesized and recommended to vaccinate the cattle for the considered diseases. Besides, the methodology adapted here could also be used to predict and analyze the epitopes for other microbial diseases of important animal species.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"34-44"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33238294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of DNA polymerase λ activity during seed germination and enhancement after salinity stress and dehydration in the plumules of indica rice (Oryza sativa L.","authors":"Sayantani Sihi,&nbsp;Sankar Bakshi,&nbsp;Dibyendu Narayan Sengupta","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>DNA polymerase λ (DNA pol λ) is the only reported X-family DNA polymerases in plants and has been shown to play a significant role in dry quiescent seeds, growth, development and nuclear DNA repair. cDNA for DNA pol λ has been reported in Arabidopsis and japonica rice cultivar and has been characterized from E. coli expressed protein, but very little is known about its activity at protein level in plants. The enzymatic activity of DNA pol λ was studied in dry, imbibed and during different germination stages of indica rice IR-8 (salt sensitive) by in-gel activity assay to determine its physiological role in important stages of growth and development. The upstream sequence was also analyzed using plantCARE database and was found to contain several cis-acting elements, including light responsive elements, dehydration responsive elements, Myb binding sites, etc. Hence, 4-day-old germinating seedlings of IR29, a salt-sensitive, but high yielding indica rice cultivar and Nonabokra, a salt-tolerant, but low yielding cultivar were treated with water (control) or 250 mM NaCl or 20% polyethyleneglycol-6000 for 4 and 8 h. The protein was analyzed by in vitro DNA pol λ activity assay, in-gel activity assay and Western blot analysis. DNA pol λ was not detected in dry seeds, but enhanced after imbibition and detectable from low level to high level during subsequent germination steps. Both salinity and dehydration stress led to the enhancement of the activity and protein level of DNA pol λ, as compared to control tissues. This is the first evidence of the salinity or dehydration stress induced enhancement of DNA pol λ activity in the plumules of rice (Oryza sativa L.) cultivars.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"86-94"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33356574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of different protein extraction methods for banana (Musa spp.) root proteome analysis by two-dimensional electrophoresis.","authors":"M Mayil Vaganan,&nbsp;S Sarumathi,&nbsp;A Nandakumar,&nbsp;I Ravi,&nbsp;M M Mustaffa","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Four protocols viz., the trichloroacetic acid-acetone (TCA), phenol-ammonium acetate (PAA), phenol/SDS-ammonium acetate (PSA) and trisbase-acetone (TBA) were evaluated with modifications for protein extraction from banana (Grand Naine) roots, considered as recalcitrant tissues for proteomic analysis. The two-dimensional electrophoresis (2-DE) separated proteins were compared based on protein yield, number of resolved proteins, sum of spot quantity, average spot intensity and proteins resolved in 4-7 pI range. The PAA protocol yielded more proteins (0.89 mg/g of tissues) and protein spots (584) in 2-DE gel than TCA and other protocols. Also, the PAA protocol was superior in terms of sum of total spot quantity and average spot intensity than TCA and other protocols, suggesting phenol as extractant and ammonium acetate as precipitant of proteins were the most suitable for banana rooteomics analysis by 2-DE. In addition, 1:3 ratios of root tissue to extraction buffer and overnight protein precipitation were most efficient to obtain maximum protein yield.</p>","PeriodicalId":13281,"journal":{"name":"Indian journal of biochemistry & biophysics","volume":"52 1","pages":"101-6"},"PeriodicalIF":1.4,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33357016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}