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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/28303531/comprehensive-analysis-of-mile-gene-expression-data-set-advances-discovery-of-leukaemia-type-and-subtype-biomarkers
#1
Wojciech Labaj, Anna Papiez, Andrzej Polanski, Joanna Polanska
Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study...
March 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28290051/construction-of-a-comprehensive-protein-protein-interaction-map-for-vitiligo-disease-to-identify-key-regulatory-elements-a-systemic-approach
#2
Anvita Gupta Malhotra, Mohit Jha, Sudha Singh, Khushhali M Pandey
Vitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters...
March 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28283929/molecular-docking-studies-to-explore-potential-binding-pockets-and-inhibitors-for-chikungunya-virus-envelope-glycoproteins
#3
Phuong T V Nguyen, Haibo Yu, Paul A Keller
The chikungunya virus (CHIKV) envelope glycoproteins are considered important potential targets for anti-CHIKV drug discovery due to their crucial roles in virus attachment and virus entry. In this study, using two available crystal structures of the immature and mature forms of envelope glycoproteins, virtual screenings based on blind dockings and focused dockings were carried out to identify potential binding pockets and hit compounds for the virus. The chemical library database of compounds, NCI Diversity Set II, was used in these docking studies...
March 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28281239/an-agent-based-clustering-approach-for-gene-selection-in-gene-expression-microarray
#4
Juan Ramos, José A Castellanos-Garzón, Alfonso González-Briones, Juan F de Paz, Juan M Corchado
Gene selection is a major research area in microarray analysis, which seeks to discover differentially expressed genes for a particular target annotation. Such genes also often called informative genes are able to differentiate tissue samples belonging to different classes of the studied disease. Despite the fact that there is a wide number of proposals, the complexity imposed by this problem remains a challenge today. This research proposes a gene selection approach by means of a clustering-based multi-agent system...
March 9, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28271460/structural-evaluation-and-binding-mode-analysis-of-ccl19-and-ccr7-proteins-identification-of-novel-leads-for-rheumatic-and-autoimmune-diseases-an-insilico-study
#5
Santhi Prada Vellanki, Ramasree Dulapalli, Bhargavi Kondagari, Navaneetha Nambigari, Rajender Vadija, Vishwanath Ramatenki, Rama Krishna Dumpati, Uma Vuruputuri
The Human Chemokine (C-C motif) ligand 19 (CCL19) protein plays a major role in rheumatic and autoimmune diseases. The 3D models of the CCL19 and its receptor CCR7 are generated using homology modeling and are validated using standard computational protocols. Disulfide bridges identified in 3D model of CCL19 protein give extra stability to the overall protein structure. The active site region of protein CCL19, containing N-terminal amino acid residues (Gly22 to Leu31), is predicted using in silico techniques...
March 7, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28255832/analysing-algorithms-and-data-sources-for-the-tissue-specific-reconstruction-of-liver-healthy-and-cancer-cells
#6
Jorge Ferreira, Sara Correia, Miguel Rocha
Genome-Scale Metabolic Models (GSMMs), mathematical representations of the cell metabolism in different organisms including humans, are resourceful tools to simulate metabolic phenotypes and understand associated diseases, such as obesity, diabetes and cancer. In the last years, different algorithms have been developed to generate tissue-specific metabolic models that simulate different phenotypes for distinct cell types. Hepatocyte cells are one of the main sites of metabolic conversions, mainly due to their diverse physiological functions...
March 2, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28247172/an-algorithm-for-sequencing-by-hybridization-based-on-an-alternating-dna-chip
#7
Marcin Radom, Piotr Formanowicz
Sequencing by hybridization allows the reconstruction of the DNA string of a given length from smaller fragments. These fragments are obtained in the hybridization experiment in which the DNA hybridizes to a DNA chip. In a classical approach, the chip consists of all oligonucleotides of a given length, with only one type of oligonucleotide for each probe of the chip. In this paper, we propose an algorithm solving the non-classical case of SBH, where the chip probes consist set of oligonucleotides described by some specific pattern...
February 28, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28238112/development-of-a-framework-for-metabolic-pathway-analysis-driven-strain-optimization-methods
#8
Vitor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
Genome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though their use brings immediate advantages, it has mostly been restricted to small scale models due to computational demands...
February 25, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28217823/novel-insight-from-computational-virtual-screening-depict-the-binding-potential-of-selected-phytotherapeutics-against-probable-drug-targets-of-clostridium-difficile
#9
Suman Kamath, Sinosh Skariyachan
This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase...
February 20, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28194576/design-synthesis-and-antibacterial-activities-of-novel-heterocyclic-arylsulphonamide-derivatives
#10
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
#11
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
#12
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
#13
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/27272764/investigation-on-quantitative-structure-activity-relationships-of-a-series-of-inducible-nitric-oxide
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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