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Interdisciplinary Sciences, Computational Life Sciences

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
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
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
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
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
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
Kalpana Singh, Tapobrata Lahiri
For extraction of information on binding sites of a protein, the commonly known geometry-based methods utilize the corresponding PDB file to extract its surface as a first step. Finally, the surface is used to find the binding site atoms. As shown in this paper work, since none of the mostly used surface extraction methods can retrieve a sizeable percentage of the binding site atoms, the scope of development of a better method remains. In this direction, this paper presents a new benchmarking criteria based on utilization of binding site information to compare performance of these surface extraction methods...
November 22, 2016: Interdisciplinary Sciences, Computational Life Sciences
Mohsen Ebrahimi, Omidreza Firuzi, Ramin Miri, Nima Razzaghi-Asl, Ahmad Ebadi
Phospholipase A2 (PLA2) catalyzes the hydrolysis of phospholipids into arachidonic acid and lysophospholipids. Arachidonic acid is modified by cyclooxygenases into active compounds called eicosanoids that act as signaling molecules in a number of physiological processes. Excessive production of eicosanoids leads to several pathological conditions such as inflammation. In order to block the inflammatory effect of these compounds, upstream enzymes such as PLA2 are valid targets. In the present contribution, molecular dynamic analysis was performed to evaluate the binding of diclofenac, 9-hydroxy aristolochic acid (9-HAA) and indomethacin to PLA2...
November 22, 2016: Interdisciplinary Sciences, Computational Life Sciences
Vera Afreixo, João M O S Rodrigues, Carlos A C Bastos, Ana H M P Tavares, Raquel M Silva
Single-strand DNA symmetry is pointed as a universal law observed in the genomes from all living organisms. It is a somewhat broadly defined concept, which has been refined into some more specific measurable effects. Here we discuss the exceptional symmetry effect. Exceptional symmetry is the symmetry effect beyond that expected in independence contexts, and it can be measured for each word, for each equivalent composition group, or globally, combining the effects of all possible words of a given length. Global exceptional symmetry was found in several species, but there are genomic words with no exceptional symmetry effect, whereas others show a very high exceptional symmetry effect...
November 19, 2016: Interdisciplinary Sciences, Computational Life Sciences
Pu Wang, Ruiquan Ge, Xuan Xiao, Yunpeng Cai, Guoqing Wang, Fengfeng Zhou
Disease diagnosis is one of the major data mining questions by the clinicians. The current diagnosis models usually have a strong assumption that one patient has only one disease, i.e. a single-label data mining problem. But the patients, especially when at the late stages, may have more than one disease and require a multi-label diagnosis. The multi-label data mining is much more difficult than a single-label one, and very few algorithms have been developed for this situation. Deep learning is a data mining algorithm with highly dense inner structure and has achieved many successful applications in the other areas...
November 11, 2016: Interdisciplinary Sciences, Computational Life Sciences
Mayuri A Borad, Manoj N Bhoi, Sanjay K Rathwa, Mahesh S Vasava, Hitesh D Patel, Chirag N Patel, Himanshu A Pandya, Edwin A Pithawala, John J Georrge
In the current investigation, we prepared a series of novel spiro[indole-thiazolidines] derivatives (5a-5h) from 5-substituted isatin derivatives and thioglycolic acid (TGA) with ZrSiO2 as an efficient catalyst under microwave irradiation. The significant merits of this protocol have some significant merits such as simplicity in operation, simple, efficient workup, good practical yields of product and the employment of recyclable catalyst. All the new synthesized scaffold has been well characterized by various spectroscopic methods and elemental analysis...
November 11, 2016: Interdisciplinary Sciences, Computational Life Sciences
Alvin Z Yu, Stephen A Ramsey
We report an in silico method to screen for receptors or pathways that could be targeted to elicit beneficial transcriptional changes in a cellular model of a disease of interest. In our method, we integrate: (1) a dataset of transcriptome responses of a cell line to a panel of drugs; (2) two sets of genes for the disease; and (3) mappings between drugs and the receptors or pathways that they target. We carried out a gene set enrichment analysis (GSEA) test for each of the two gene sets against a list of genes ordered by fold-change in response to a drug in a relevant cell line (HL60), with the overall score for a drug being the difference of the two enrichment scores...
October 24, 2016: Interdisciplinary Sciences, Computational Life Sciences
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
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
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
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
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
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
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
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
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