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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
Handan Ankarali, Sengul Cangur, Seyit Ankarali
In this study, when the assumptions of linearity and homogeneity of regression slopes of conventional ANCOVA are not met, a new approach named as SEYHAN has been suggested to use conventional ANCOVA instead of robust or nonlinear ANCOVA. The proposed SEYHAN's approach involves transformation of continuous covariate into categorical structure when the relationship between covariate and dependent variable is nonlinear and the regression slopes are not homogenous. A simulated data set was used to explain SEYHAN's approach...
October 18, 2016: Interdisciplinary Sciences, Computational Life Sciences
Pengmian Feng, Jidong Zhang, Hua Tang, Wei Chen, Hao Lin
Noncoding RNAs (ncRNAs) are implicated in various biological processes. Recent findings have demonstrated that the function of ncRNAs correlates with their provenance. Therefore, the recognition of ncRNAs from different organelle genomes will be helpful to understand their molecular functions. However, the weakness of experimental techniques limits the progress toward studying organellar ncRNAs and their functional relevance. As a complement of experiments, computational method provides an important choice to identify ncRNA in different organelles...
October 13, 2016: Interdisciplinary Sciences, Computational Life Sciences
Jing Li, Jing Wang, Jing Li
As a public health problem, food allergy is frequently caused by food allergy proteins, which trigger a type-I hypersensitivity reaction in the immune system of atopic individuals. The food allergens in our daily lives are mainly from crops including rice, wheat, soybean and maize. However, allergens in these main crops are far from fully uncovered. Although some bioinformatics tools or methods predicting the potential allergenicity of proteins have been proposed, each method has their limitation. In this paper, we built a novel algorithm PREAL(W), which integrated PREAL, FAO/WHO criteria and motif-based method by a weighted average score, to benefit the advantages of different methods...
October 12, 2016: Interdisciplinary Sciences, Computational Life Sciences
Cagin Kandemir-Cavas, Levent Cavas, Hakan Alyuruk
There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics...
October 7, 2016: Interdisciplinary Sciences, Computational Life Sciences
Salman Akhtar, M Kalim A Khan, Jamal M Arif
Exposure to exogenous and endogenous chemicals and subsequent cellular and molecular changes has been linked to enhanced cell proliferation and restricted apoptosis phenomenon. Though in the past decades numerous anticancer drugs inducing programmed cell death in cancer cells by targeting specific apoptotic markers have reached the market, they have been allied with unwanted side effects, ranging from mild to severe toxicity. With further understanding on the functional mechanism of p53 and MDM2 in apoptosis and in our continuous search for new and potent multi-target anticancer lead compounds, we have carried out molecular docking and inhibition studies of the selected aglycones along with selected anticancer leads, against the specific apoptotic and cell cycle markers using AutoDock Tools 4...
October 5, 2016: Interdisciplinary Sciences, Computational Life Sciences
Sonali Mishra, Abhishek Kumar, Pritish Kumar Varadwaj, Krishna Misra
Psoriasis is a chronic immune-mediated inflammatory skin disorder. Heat shock proteins (HSPs) have been witnessed as a potential drug target for inhibition of psoriatic cell differentiation. The expression level of HSP is increased when the cells get exposed to elevated temperature, oxidative stress and nutritional deficiencies and thus plays major role in psoriatic progression pathway. Immunoreactivity intensity distribution index scores for HSP70 expression is significantly higher in psoriatic patients compared to normal...
October 1, 2016: Interdisciplinary Sciences, Computational Life Sciences
S Jemimah Naine, C Subathra Devi, V Mohanasrinivasan, C George Priya Doss
Despite clinical advances in antimicrobial and anticancer therapy, there is an urge for the search of new bioactive compounds. In the present study, previously isolated Streptomyces sp. VITJS4 strain (NCIM No. 5574) (ACC No: JQ234978.1) crude extract tested for antibacterial activity showed a broad spectrum at the concentration of 20 mg/mL against pathogens. The antioxidant potential tested at 0.5 mg/mL concentration exhibited reducing power activity with a maximum of 90 % inhibition. The anticancer property by MTT assay on HeLa and HepG2 cells showed cytotoxic effect with IC50 of 50 µg/mL each...
October 1, 2016: Interdisciplinary Sciences, Computational Life Sciences
Jakaria Shawon, Akib Mahmud Khan, Adhip Rahman, Mohammad Mazharol Hoque, Mohammad Abdul Kader Khan, Mohammed G Sarwar, Mohammad A Halim
Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory...
October 1, 2016: Interdisciplinary Sciences, Computational Life Sciences
Lingtao Su, Xiangyu Meng, Qingshan Ma, Tian Bai, Guixia Liu
The importance of the construction of gene-gene interaction (GGI) network to better understand breast cancer has previously been highlighted. In this study, we propose a novel GGI network construction method called linear and probabilistic relations prediction (LPRP) and used it for gaining system level insight into breast cancer mechanisms. We construct separate genome-wide GGI networks for tumor and normal breast samples, respectively, by applying LPRP on their gene expression datasets profiled by The Cancer Genome Atlas...
September 17, 2016: Interdisciplinary Sciences, Computational Life Sciences
Sabrina Nusrat Sabah, Md Amran Gazi, Rahvia Alam Sthity, Amena Binte Husain, Salwa Abdul Quyyum, Mustafizur Rahman, Md Rezaul Islam
Human papillomavirus (HPV) is a DNA virus that belongs to the papillomavirus family and is capable of infecting humans. Currently, few vaccines are available to prevent infection by HPV. However, they are not so much effective and provide little benefit to women who have already been infected with HPV. The aim of this study was to design epitope-based vaccines of HPV58 by targeting E6 and E7 proteins of HPV58. Proteomic sequences were retrieved from different isolates at different time periods and later analyzed by performing alignment of these sequences...
September 17, 2016: Interdisciplinary Sciences, Computational Life Sciences
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