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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/28194576/design-synthesis-and-antibacterial-activities-of-novel-heterocyclic-arylsulphonamide-derivatives
#1
Anuradha Singh, Ritika Srivastava, Ramendra K Singh
Design, synthesis, and antibacterial activities of a series of arylsulphonamide derivatives as probable peptide deformylase (PDF) inhibitors have been discussed. Compounds have been designed following Lipinski's rule and after docking into the active site of PDF protein (PDB code: 1G2A) synthesized later on. Furthermore, to assess their antibacterial activity, screening of the compound was done in vitro conditions against Gram-positive and Gram-negative bacterial strains. In silico, studies revealed these compounds as potential antibacterial agents and this fact was also supported by their prominent scoring functions...
February 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28110480/casubtype-an-r-package-to-identify-gene-sets-predictive-of-cancer-subtypes-and-clinical-outcomes
#2
Hualei Kong, Pan Tong, Xiaodong Zhao, Jielin Sun, Hua Li
In the past decade, molecular classification of cancer has gained high popularity owing to its high predictive power on clinical outcomes as compared with traditional methods commonly used in clinical practice. In particular, using gene expression profiles, recent studies have successfully identified a number of gene sets for the delineation of cancer subtypes that are associated with distinct prognosis. However, identification of such gene sets remains a laborious task due to the lack of tools with flexibility, integration and ease of use...
January 21, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28013448/change-in-glutenin-macropolymer-secondary-structure-in-wheat-sourdough-fermentation-by-ftir
#3
Jinshui Wang, Yuanyuan Yue, Tiantian Liu, Bin Zhang, Zhenlei Wang, Changfu Zhang
Wheat sourdough was prepared by fermentation with Lactobacillus plantarum M616 and yeast in the present study. The change in secondary structure of glutenin macropolymer (GMP) in wheat sourdough fermentation for 4 and 12 h was determined using Fourier transform infrared spectroscopy, and then the resultant spectra were Fourier self-deconvoluted of the amide I band in the region from 1600 to 1700 cm(-1). Significant different spectra especially in the amide I band for GMP from sourdough fermented with L. plantarum M616 (SL) and with L...
December 24, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27981429/theoretical-studies-on-azaindoles-as-human-aurora-b-kinase-inhibitors-docking-pharmacophore-and-admet-studies
#4
Rajashekar Vadlakonda, Raghunandan Nerella, Sreenivas Enaganti
Aurora kinases are the cell cycle mitotic regulators processing multiple functions during cell division. Altered mechanism of these mitotic kinases may contribute to genomic instability that is most often correlated with tumorigenesis, which has been reported in many human cancers. Selective blockage of the aberrantly expressed Aurora kinases has the potential therapeutic assessment to control the deregulated cell cycle machinery and their associated risks of cancer. Using a combination of docking-, ligand- and structure-based pharmacophore strategies, in the present study, we have tried to predict the anticancer potentiality of our synthesized compounds (A1 to A5 and B1 to B9) against human Aurora B kinase...
December 16, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27900730/understanding-the-interactions-of-high-mobility-group-of-protein-domain-b1-with-dna-adducts-generated-by-platinum-anticancer-molecules-using-in-silico-approaches
#5
Gauri Misra, Shipra Gupta, Neetu Jabalia
Platinum coordination compounds having cis geometry are frequently prescribed for various types of cancers. Protein dysregulation is one of the major factors contributing towards cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the cancers where platinum-based compounds are used either alone or in combination with radiation as therapy. The underlying interactions of these compounds with both DNA and proteins are crucial for the drug response. The compounds forms DNA adducts which are recognized by conserved, non-chromosomal high-mobility group box 1 (HMGB1) proteins...
November 30, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27896664/molecular-interactions-structural-transitions-and-alterations-in-soxb-protein-due-to-soxyz-interaction-from-two-distinct-%C3%AE-proteobacteria-an-in-silico-approach-towards-the-thiosulfate-oxidation-and-recycling-of-soxy-protein
#6
Sujay Ray, Semanti Ghosh, Angshuman Bagchi
Microbial oxidation-reduction reactions utilizing the environmental thiosulfate ions and mediated mainly by the sox operon are very much essential to maintain the sulfur balance in the environment. Majority of the previously documented wet laboratory studies show genetics behind the functionality of Sox proteins encoded by the sox operon. However, the molecular details of the involvements of the essential SoxB, SoxY and SoxZ proteins in the beta-proteobacteria have not yet been elucidated. In this work, an attempt was made to analyze the interaction profiles of the aforementioned SoxB, SoxY and SoxZ proteins to predict their roles in biological sulfur oxidation process...
November 28, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27896663/significant-role-of-segmental-duplications-and-sidd-sites-in-chromosomal-translocations-of-hematological-malignancies-a-multi-parametric-bioinformatic-analysis
#7
Aditi Daga, Afzal Ansari, Medha Pandya, Krupa Shah, Shanaya Patel, Rakesh Rawal, Valentina Umrania
Recurrent non-random chromosomal translocations are hallmark characteristics of leukemogenesis, and however, molecular mechanisms underlying these rearrangements are less explored. The fundamental question is, why and how chromosomes break and reunite so precisely in the genome. Meticulous understanding of mechanism leading to chromosomal rearrangement can be achieved by characterizing breakpoints. To address this hypothesis, a novel multi-parametric computational approach for characterization of major leukemic translocations within and around breakpoint region was performed...
November 28, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27882454/portraying-the-effect-of-calcium-binding-proteins-on-cytosolic-calcium-concentration-distribution-fractionally-in-nerve-cells
#8
Brajesh Kumar Jha, Hardik Joshi, Devanshi D Dave
Nerve cells like neurons and astrocytes in central nervous system (CNS) take part in the signaling process which means the transformation of the information from one cell to another via signals. The signaling process is affected by various external parameters like buffers calcium-binding proteins, voltage-gated calcium channel. In the present paper, the role of buffers in the cytoplasmic calcium concentration distribution is shown. The elicitation in calcium concentration is due to the presence of lower amount calcium-binding proteins which can be shown graphically...
November 23, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27272764/investigation-on-quantitative-structure-activity-relationships-of-a-series-of-inducible-nitric-oxide
#9
Mukesh C Sharma, S Sharma
A series of 2-dihydro-4-quinazolin with potent highly selective inhibitors of inducible nitric oxide synthase activities was subjected to quantitative structure activity relationships (QSAR) analysis. Statistically significant equations with high correlation coefficient (r (2) = 0.8219) were developed. The k-nearest neighbor model has showed good cross-validated correlation coefficient and external validation values of 0.7866 and 0.7133, respectively. The selected electrostatic field descriptors the presence of blue ball around R1 and R4 in the quinazolinamine moiety showed electronegative groups favorable for nitric oxide synthase activity...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27129944/online-fault-diagnosis-for-biochemical-process-based-on-fcm-and-svm
#10
Xianfang Wang, Haoze Du, Jinglu Tan
Fault diagnosis is becoming an important issue in biochemical process, and a novel online fault detection and diagnosis approach is designed by combining fuzzy c-means (FCM) and support vector machine (SVM). The samples are preprocessed via FCM algorithm to enhance the ability of classification firstly. Then, those samples are input to the SVM classifier to realize the biochemical process fault diagnosis. In this study, a glutamic acid fermentation process is chosen as an example to diagnose the fault by this method, the result shows that the diagnosis time is largely shortened, and the accuracy is extremely improved by comparing to a single SVM method...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27016253/from-fhb-resistance-qtls-to-candidate-genes-identification-in-triticum-aestivum-l
#11
Mouna Choura, Moez Hanin, Ahmed Rebaï, Khaled Masmoudi
Fusarium head blight (FHB) caused by Fusarium graminearum is a worldwide destructive disease affecting cereals such as wheat. FHB resistance is a quantitative trait, and information for FHB resistance QTLs in wheat is available. However, little is known about genes underlying the FHB resistance QTL regions. Using a computational approach in this study, we have mined eight FHB resistance QTLs in wheat and predicted the candidate genes falling within these QTL intervals based on the available sequences and markers...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27013507/screening-of-furanone-in-cucurbita-melo-and-evaluation-of-its-bioactive-potential-using-in-silico-studies
#12
Nidhi Singh, C Sudandiradoss, Jayanthi Abraham
The work presented here attempts to screen for the presence of 4-Hydroxy-2,5-dimethyl-3(2H)-furanone in fruits and also any bioactive potential present in the fruit extracts. Curcurbita melo was selected for the study, and the fruit was crushed, filtered and extracted with ethyl acetate as the solvent. The resulting extract was subjected to disk diffusion test using Kirby Bauer method for checking its antimicrobial potential. Melon extract showed promising results against different clinical pathogens, 19-mm zone being the largest against Klebsiella pneumoniae and 17 mm against Shigella dysenteriae...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26923146/genetic-markers-analyses-and-bioinformatic-approaches-to-distinguish-between-olive-tree-olea-europaea-l-cultivars
#13
Rayda Ben Ayed, Hanen Ben Hassen, Karim Ennouri, Ahmed Rebai
The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26750924/an-approach-for-identification-of-novel-drug-targets-in-streptococcus-pyogenes-sf370-through-pathway-analysis
#14
Satendra Singh, Dev Bukhsh Singh, Anamika Singh, Budhayash Gautam, Gurudayal Ram, Seema Dwivedi, Pramod W Ramteke
Streptococcus pyogenes is one of the most important pathogens as it is involved in various infections affecting upper respiratory tract and skin. Due to the emergence of multidrug resistance and cross-resistance, S. Pyogenes is becoming more pathogenic and dangerous. In the present study, an in silico comparative analysis of total 65 metabolic pathways of the host (Homo sapiens) and the pathogen was performed. Initially, 486 paralogous enzymes were identified so that they can be removed from possible drug target list...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26525889/predicting-the-binding-affinity-of-er%C3%AE-ligands-based-on-a-novel-variable-selection-method
#15
Hong-Yan Liu, Fei Zhang, Li-Tang Qin, Zhong-Sheng Yi, Xiu-Li Wang, Ling-Yun Mo
A number of descriptors were employed to characterize the molecular structures of the 128 estrogen receptor β ligands. A quantitative structure-activity relationship (QSAR) model of these compounds was developed by the variable selection method based on variable interaction. The QSAR model with five descriptors was internally and externally validated. The determination coefficient (R (2)) and the leave-one-out cross-validated correlation coefficient (Q (2)) are 0.8272 and 0.8041, respectively. The estimated correlation coefficient of the external validation is 0...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26471998/identification-of-simple-sequence-repeats-in-chloroplast-genomes-of-magnoliids-through-bioinformatics-approach
#16
Deepika Srivastava, Asheesh Shanker
Basal angiosperms or Magnoliids is an important clade of commercially important plants which mainly include spices and edible fruits. In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1-6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26454649/comparing-performances-of-multiple-comparison-methods-in-commonly-used-2%C3%A2-%C3%A3-%C3%A2-c-contingency-tables
#17
Sengul Cangur, Handan Ankarali, Ozge Pasin
This study aims at mentioning briefly multiple comparison methods such as Bonferroni, Holm-Bonferroni, Hochberg, Hommel, Marascuilo, Tukey, Benjamini-Hochberg and Gavrilov-Benjamini-Sarkar for contingency tables, through the data obtained from a medical research and examining their performances by simulation study which was constructed as the total 36 scenarios to 2 × 4 contingency table. As results of simulation, it was observed that when the sample size is more than 100, the methods which can preserve the nominal alpha level are Gavrilov-Benjamini-Sarkar, Holm-Bonferroni and Bonferroni...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26310620/comparative-inhibition-study-of-compounds-identified-in-the-methanolic-extract-of-apamarga-kshara-against-trichomonas-vaginalis-carbamate-kinase-tvck-an-enzoinformatics-approach
#18
Sibhghatulla Shaikh, Hamida Aaqil, Syed Mohd Danish Rizvi, Shazi Shakil, Adel M Abuzenadah, Pragya Gupta, Soumya Saxena, Rohit Kr Tiwari, Ajai Kumar
In the present study, we have identified ten compounds, namely dodecanol acid, myristic acid, neophytadiene, palmitic acid, heptadecanoic acid, linoleic acid, elaidic acid, 3-7-dimethyl acid, stearic acid and methyl eicos acid, of the methanolic extract of Apamarga Kshara by GC-MS analysis. Apamarga Kshara has been reported to be active against cervical erosion. Major causal organism for cervical erosion is Trichomonas vaginalis. However, there is a paucity of information about the mechanism of action and inhibitory effect of the biologically active natural compounds presented in A...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26297309/targeting-heat-shock-proteins-60-and-70-of-toxoplasma-gondii-as-a-potential-drug-target-in-silico-approach
#19
Kaur Ashwinder, Mee Teck Kho, Phui Mun Chee, Wui Zhuan Lim, Ivan K S Yap, Sy Bing Choi, Wai Keat Yam
Heat shock proteins (Hsps) 60 and 70 are postulated as a potential drug target for toxoplasmosis due to its importance in the developmental and survival of Toxoplasma gondii (T. gondii). As of today, there have been no reports on three-dimensional (3D) structure of Hsp60 and Hsp70 deposited in the Brookhaven Protein Data Bank. Hence, this study was conducted to predict 3D structures for Hsp60 and Hsp70 in T. gondii by homology modeling. Selection of the best predicted model was done based on multiple scoring functions...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26275670/computational-analysis-and-binding-site-identification-of-type-iii-secretion-system-atpase-from-pseudomonas-aeruginosa
#20
Raju Dash, S M Zahid Hosen, Tasniha Sultana, Md Junaid, Mohuya Majumder, Ismat Ara Ishat, Mir Muhammad Nasir Uddin
In many gram-negative bacteria, the type III secretion system (T3SS), as a virulence factor, is an attractive target for developing novel antibacterial. Regarding this, in our study, we aimed to identify the putative drug target for Pseudomonas aeruginosa, considering ATPase enzyme involved in the type III secretion system. Selective protein sequence of P. aeruginosa involved in the T3SS was retrieved from NCBI databases, and its homologues were subjected to phylogenetic analysis. Its association in T3SS was analyzed via STRING, and the 3D structure was determined by means of homology modeling followed by intensive optimization and validation...
December 2016: Interdisciplinary Sciences, Computational Life Sciences
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