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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/28534166/in-silico-identification-and-validation-of-potential-micrornas-in-kinnow-mandarin-citrus-reticulata-blanco
#1
Prashant Mohanpuria, Naveen Duhan, Navraj Kaur Sarao, Manvir Kaur, Mandip Kaur
MicroRNAs (miRNAs) are a large family of 19-25 nucleotides, regulatory, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in animals and plants. Despite the important functions of miRNAs related to regulation of plant growth and development processes, metabolism, and abiotic and biotic stresses, little is known about the disease-related miRNA. Here, we present a new pipeline for miRNA analysis using expressed sequence tags (ESTs)-based bioinformatics approach in Kinnow mandarin, a commercially important citrus fruit crop...
May 22, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28527150/development-of-in-silico-protocols-to-predict-structural-insights-into-the-metabolic-activation-pathways-of-xenobiotics
#2
M Kalim A Khan, Salman Akhtar, Jamal M Arif
To establish in silico model to predict the structural insight into the metabolic bioactivation pathway of xenobiotics, we considered two specific and one non-specific mammary procarcinogen [e.g., dibenzo[a,l]pyrene (DBP), 7,12-dimethylbenz[a]anthracene (DMBA), and benzo[a]pyrene (BP)]. The CYP1A1, 1B1, 2C9, 1A2 and 2B6 reported in wet-lab studies to actively metabolize DBP also showed strong binding energies (kcal/mol) of -11.50, -10.67, -10.37, -9.76 and -9.72, respectively, with inhibition constants ranging between 0...
May 19, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28516319/quantitative-prediction-of-drug-side-effects-based-on-drug-related-features
#3
Yanqing Niu, Wen Zhang
MOTIVATION: Unexpected side effects of drugs are great concern in the drug development, and the identification of side effects is an important task. Recently, machine learning methods are proposed to predict the presence or absence of interested side effects for drugs, but it is difficult to make the accurate prediction for all of them. METHODS: In this paper, we transform side effect profiles of drugs as their quantitative scores, by summing up their side effects with weights...
May 17, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28488219/inhibition-of-gelatinases-mmp-2-and-mmp-9-by-withania-somnifera-phytochemicals-confers-neuroprotection-in-stroke-an-in-silico-analysis
#4
Gaurav Kumar, Ranjana Patnaik
A stroke or cerebrovascular accident is a serious, life-threatening medical condition that occurs when the blood supply to part of the brain is severely reduced or cut off, depriving brain tissue of oxygen and nutrients. Studies suggested that level of gelatinases (MMP-2 and MMP-9) usually increases in the brain after stroke. The elevated activity of gelatinases plays the deleterious role in ischemic stroke, hemorrhagic stroke and perinatal hypoxic-ischemic brain injury. Therefore, matrix metalloproteinase (MMP)-2 and MMP-9 inhibition have therapeutic importance in stroke condition...
May 9, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28488218/discovery-of-therapeutic-lead-molecule-against-%C3%AE-tubulin-using-computational-approach
#5
K Ramanathan, Kanika Verma, Naina Gupta, V Shanthi
Virtual screening strategy was performed against the target β-tubulin to overcome paclitaxel resistance in blood cancer types. In essence, A185T and A248V are two such important mutations frequently observed in clinical trials that confer paclitaxel resistance. In the present investigation, compounds from NPACT database were filtered by pharmacokinetics, toxicity and binding energy values. A total of 5 active compounds were identified from a list of 1574 bioactive compounds investigated in our study. Finally, we have compiled all the characteristic features into biologically meaningful clusters by hierarchical clustering algorithm...
May 9, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28478537/micelles-rods-liposomes-and-other-supramolecular-surfactant-aggregates-computational-approaches
#6
REVIEW
Serena Indelicato, David Bongiorno, Valentina Calabrese, Ugo Perricone, Anna Maria Almerico, Leopoldo Ceraulo, Daniela Piazzese, Marco Tutone
Surfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered...
May 6, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28432608/fpgasw-accelerating-large-scale-smith-waterman-sequence-alignment-application-with-backtracking-on-fpga-linear-systolic-array
#7
Xia Fei, Zou Dan, Lu Lina, Man Xin, Zhang Chunlei
The Smith-Waterman (SW) algorithm based on dynamic programming is a well-known classical method for high precision sequence matching and has become the gold standard to evaluate sequence alignment software. In this paper, we propose fine-grained parallelized SW algorithms using affine gap penalty and implement a parallel computing structures to accelerating the SW with backtracking on FPGA platform. We analysis the dynamic parallel computing features of anti-diagonal elements and storage expansion problem resulting from backtracking stage, and propose a series of optimization strategies to eliminate data dependency, reduce storage requirements, and overlap memory access latency...
April 21, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28405889/asymptotic-expansion-method-with-respect-to-small-parameter-for-ternary-diffusion-models
#8
Marek Danielewski, Henryk Leszczyński, Anna Szafrańska
Ternary diffusion models lead to strongly coupled systems of PDEs. We choose the smallest diffusion coefficient as a small parameter in a power series expansion whose components fulfill relatively simple equations. Although this series is divergent, one can use its finite sums to derive feasible numerical approximations, e.g. finite difference methods (FDMs).
April 12, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28391494/metrical-consistency-nmf-for-predicting-gene-phenotype-associations
#9
Shuai Han, Hong Cai, Dan Che, Yaogong Zhang, Yalou Huang, Maoqiang Xie
Discovering gene-phenotype associations is significant to understand the disease mechanisms. Nonnegative matrix factorization (NMF) has been widely used in computational biology for its good performance and interpretability. In this paper, we proposed a novel metrical consistency NMF (MCNMF) method for candidate gene prioritization. The MCNMF method assume that phenotype similarities, calculated from various independent ways, should be consistent in case that the associations between genes and phenotypes are completely known...
April 8, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28391493/computational-comparison-and-visualization-of-viruses-in-the-perspective-of-clinical-information
#10
António M Lopes, J A Tenreiro Machado, Alexandra M Galhano
This paper addresses the visualization of complex information using multidimensional scaling (MDS). MDS is a technique adopted for processing data with multiple features scattered in high-dimensional spaces. For illustrating the proposed techniques, the case of viral diseases is considered. The study evaluates the characteristics of 21 viruses in the perspective of clinical information. Several new schemes are proposed for improving the visualization of the MDS charts. The results follow standard clinical practice, proving that the method represents a valuable tool to study a large number of viruses...
April 8, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28374118/structural-insight-into-the-mechanism-of-dibenzo-a-l-pyrene-and-benzo-a-pyrene-mediated-cell-proliferation-using-molecular-docking-simulations
#11
M Kalim A Khan, Salman Akhtar, Jamal M Arif
In the proposed work, we have explicated the mechanism of dibenzo[a,l]pyrene (DBP) and benzo[a]pyrene (BP) modulated cell proliferation by assessing the plausible binding with CASPASES, BAX, Bcl-2, MDM2, p53, p21, p16, CylinD1-CDK4 complex, CylinE1-CDK2 complex, H-Ras, K-Ras, BRCA1, and BRCA2 through exploiting the inherent potential of AutoDock Tools 4.0. In silico findings revealed that potent carcinogenic metabolites of DBP (e.g., (-)-anti-DBPDE and (+)-syn-DBPDE) and BP (e.g., (+)-anti-BPDE) exhibited better binding interactions to Caspase-9 than Caspase-8 and Caspase-3...
April 3, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28374117/virtual-screening-for-potential-inhibitors-of-ctx-m-15-protein-of-klebsiella-pneumoniae
#12
Tayebeh Farhadi, Atefeh Fakharian, Roman S Ovchinnikov
The Gram-negative bacterium Klebsiella pneumoniae, responsible for a wide variety of nosocomial infections in immuno-deficient patients, involves the respiratory, urinary and gastrointestinal tract infections and septicemia. Extended spectrum β-lactamases (ESBL) belong to β-lactamases capable of conferring antibiotic resistance in Gram-negative bacteria. CTX-M-15, a prevalent ESBL reported from Enterobacteriaceae including K. pneumoniae, was selected as a potent anti-bacterial target. To identify the novel drug-like compounds, structure-based screening procedure was employed against downloaded drug-like compounds from ZINC database...
April 3, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28361256/computational-approaches-and-related-tools-to-identify-micrornas-in-a-species-a-bird-s-eye-view
#13
REVIEW
Anjana Rajendiran, Aniruddha Chatterjee, Archana Pan
MicroRNAs (miRNAs) are a family of non-coding RNAs that play a central role in fine-tuning gene expression regulation. Over the past decade, identification and annotation of miRNAs have become a major focus in epigenomics research. However, detection and characterization of miRNA are challenging due to its small size (~22 nucleotide-long) and susceptibility to degradation. The difficulties involved in experimental prediction and characterization of miRNA coding genes have led to the development of in silico-based approaches...
March 30, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28349439/egfr-gene-regulation-in-colorectal-cancer-cells-by-garlic-phytocompounds-with-special-emphasis-on-s-allyl-l-cysteine-sulfoxide
#14
Nabarun Roy, P A Nazeem, T D Babu, P S Abida, Arunaksharan Narayanankutty, Ravisankar Valsalan, P A Valsala, Achuthan C Raghavamenon
Colorectal cancer is one among the most common cancers in the world and a major cause of cancer related deaths. Similar to other cancers, colorectal carcinogenesis is often associated with over expression of genes related to cell growth and proliferation, especially Epidermal Growth Factor Receptor (EGFR). There is an increasing attention towards the plant derived compounds in prevention of colorectal carcinogenesis by downregulating EGFR. Among plants, garlic (Allium sativum L.) is emerging with anticancer properties by virtue of its organosulfur compounds...
March 27, 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
#15
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
#16
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/28271460/structural-evaluation-and-binding-mode-analysis-of-ccl19-and-ccr7-proteins-identification-of-novel-leads-for-rheumatic-and-autoimmune-diseases-an-insilico-study
#17
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/28247172/an-algorithm-for-sequencing-by-hybridization-based-on-an-alternating-dna-chip
#18
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/28352971/ir-spectra-of-different-o2-content-hemoglobin-from-computational-study-promising-detector-of-hemoglobin-variant-in-medical-diagnosis
#19
Su-Qin Zhou, Tu-Nan Chen, Guang-Fu Ji, En-Ren Wang
IR spectra of heme and different O2-content hemoglobin were studied by the quantum computation method at the molecule level. IR spectra of heme and different O2-content hemoglobin were quantificationally characterized from 0 to 100 THz. The IR spectra of oxy-heme and de-oxy-heme are obviously different at the frequency regions of 9.08-9.48, 38.38-39.78, 50.46-50.82, and 89.04-91.00 THz. At 24.72 THz, there exists the absorption peak for oxy-heme, whereas there is not the absorption peak for de-oxy-heme. Whether the heme contains Fe-O-O bond or not has the great influence on its IR spectra and vibration intensities of functional groups in the mid-infrared area...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28013448/change-in-glutenin-macropolymer-secondary-structure-in-wheat-sourdough-fermentation-by-ftir
#20
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...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
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