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Interdisciplinary Sciences, Computational Life Sciences

Wenling Li, Menglong Li, Xuemei Pu, Yanzhi Guo
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process...
November 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
Richa Jain, Sarita Singh, Santosh Kumar Verma, Ankit Jain
Campylobacteriosis is a deadly disease which has developed resistance to most of the available chemotherapeutic agents. Although various studies provide evidence of acquired immunity following exposure to Campylobacter jejuni, no effective vaccine has been developed, still. Hence, there is an urgent need to identify potential vaccine candidates for Campylobacter species. In the proposed study, Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) was taken and computational approach was employed to screen C...
November 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
V Swaminathan, Gangothri Rajaram, V Abhishek, Boosi Shashank Reddy, K Kannan
The sequencing by hybridization (SBH) of determining the order in which nucleotides should occur on a DNA string is still under discussion for enhancements on computational intelligence although the next generation of DNA sequencing has come into existence. In the last decade, many works related to graph theory-based DNA sequencing have been carried out in the literature. This paper proposes a method for SBH by integrating hypergraph with genetic algorithm (HGGA) for designing a novel analytic technique to obtain DNA sequence from its spectrum...
November 6, 2017: Interdisciplinary Sciences, Computational Life Sciences
Inderpal Singh, Gurvinder Singh, Vijeshwar Verma, Shashank Singh, Ratna Chandra
Many aggressive and metastatic cancer cell types show Warburg Effect; therefore, it is a possible adaptation helping cancer cells to rapidly divide and utilize the glycolytic intermediates for biosynthesis of ribose sugars (for nucleotide biosynthesis), fatty acid synthesis (lipids for membrane synthesis), NADPH (cellular currency for reductive biosynthesis) and lactate. This in due course results in decrease of extracellular pH, leading to acidic tumor micro-environment. EGFR is a crucial cell surface signaling receptor implicated in cancer cell survival and progression...
November 4, 2017: Interdisciplinary Sciences, Computational Life Sciences
Teresa Milano, Sebastiana Angelaccio, Angela Tramonti, Martino Luigi di Salvo, Isabel Nogues, Roberto Contestabile, Stefano Pascarella
Bacterial proteins belonging to the YczE family are predicted to be membrane proteins of yet unknown function. In many bacterial species, the yczE gene coding for the YczE protein is divergently transcribed with respect to an adjacent transcriptional regulator of the MocR family. According to in silico predictions, proteins named YczR are supposed to regulate the expression of yczE genes. These regulators linked to the yczE genes are predicted to constitute a subfamily within the MocR family. To put forward hypotheses amenable to experimental testing about the possible function of the YczE proteins, a phylogenetic profile strategy was applied...
November 2, 2017: Interdisciplinary Sciences, Computational Life Sciences
Mingzhu Zhao, Dong-Qing Wei
A rare disease refers to any disease with very low prevalence individually. Although the impacted population is small for a single disease, more than 6000 rare diseases affect millions of people across the world. Due to the small market size, high cost and possibly low return on investment, only in recent years, the research and development of rare disease drugs have gradually risen globally, in several domains including gene therapy, enzyme replacement therapy, and drug repositioning. Due to the complex etiology and heterogeneous symptoms, there is a large gap between basic research and patient unmet needs for rare disease drug discovery...
November 1, 2017: Interdisciplinary Sciences, Computational Life Sciences
Patrizia Vizza, Giuseppe Tradigo, Pietro Hiram Guzzi, Rosario Curia, Loredana Sisca, Filippo Aiello, Gionata Fragomeni, Mario Cannataro, Giuseppe Lucio Cascini, Pierangelo Veltri
The collection and analysis of clinical data are needed to investigate diseases and to define medical protocols and treatments. Bioimages, medical annotations and patient history are clinical data acquired and studied to perform a correct diagnosis and to propose an appropriate therapy. Currently, hospital departments manage these data using legacy systems which do not often allow data integration among different departments or health structures. Thus, in many cases clinical information sharing and exchange are difficult to implement...
November 1, 2017: Interdisciplinary Sciences, Computational Life Sciences
Dibyabhaba Pradhan, Monika Yadav, Rashi Verma, Noor Saba Khan, Lingaraja Jena, Arun Kumar Jain
The recent outbreaks of Zika virus and the absence of a specific therapy have necessitated to identify T-cell-stimulating antigenic peptides as potential subunit vaccine candidates. The translated ssRNA (+) genome of Zika virus was explored in EMBOSS antigenic and VaxiJen to predict 63 peptides as potential antigens. Three MHC-II binding peptide prediction tools, viz. NetMHCIIpan, PREDIVAC and immune epitope database (IEDB) were employed in consensus on 63 antigenic peptides to propose 14 T-helper cell epitopes...
November 1, 2017: Interdisciplinary Sciences, Computational Life Sciences
Malathi Shekar, Moleyur Nagarajappa Venugopal
The transcriptional adaptor zinc (TAZ) fingers are a specialized class of zinc finger domains reported to exist only in eukaryotic transcriptional coactivator proteins. A putative protein within the shrimp white spot syndrome virus (WSSV) encodes for a TAZ domain, which is unique as no virus so far has been reported for the presence of this domain. Our study shows the viral TAZ domain to be similar to TAZ2 rather than TAZ1 domain of eukaryotic CREB-binding proteins and its paralog p300 proteins. Furthermore, as with eukaryotic TAZ2 domain which interacts and binds to several transcriptional factors including the p53 tumor suppressor protein, an in silico docking study of the WSSV-TAZ and the shrimp p53 transcriptional factor showed the two protein domains to be involved in a protein-protein interaction...
October 31, 2017: Interdisciplinary Sciences, Computational Life Sciences
Pravin A Pawar, Damodar R Edla, Thierry Edoh, Vijay Shinde, Bert-Jan van Beijnum
A Mobile Patient Monitoring System (MPMS) acquires patient's biosignals and transmits them using wireless network connection to the decision-making module or healthcare professional for the assessment of patient's condition. A variety of wireless network technologies such as wireless personal area networks (e.g., Bluetooth), mobile ad-hoc networks (MANET), and infrastructure-based networks (e.g., WLAN and cellular networks) are in practice for biosignals delivery. The wireless network quality-of-service (QoS) requirements of biosignals delivery are mainly specified in terms of required bandwidth, acceptable delay, and tolerable error rate...
October 31, 2017: Interdisciplinary Sciences, Computational Life Sciences
Vijina Chakkyarath, Jeyakumar Natarajan
Enterobacter aerogenes have been reported as important opportunistic and multi-resistant bacterial pathogens for humans during the last three decades in hospital wards. The emergence of drug-resistant E. aerogenes demands the need for developing new drugs. Peptidoglycan is an important component of the cell wall of bacteria and the peptidoglycan biochemical pathway is considered as the best source of antibacterial targets. Within this pathway, four Mur ligases MurC, MurD, MurE, and MurF are responsible for the successive additions of L-alanine and suitable targets for developing novel antibacterial drugs...
October 31, 2017: Interdisciplinary Sciences, Computational Life Sciences
Rajashekar Varma Kadumuri, Ramakrishna Vadrevu
The (βα)8/TIM barrel is one of the most common folds of known protein structures facilitating diverse catalytic functions. The fold is formed by the repetition of the basic βαβ building block in which the β-strands are followed by α-helices eight times alternating in sequence and structure. αβ and βα loops connecting α-helices to the β-strands and the β-strands to the α-helices contribute to stability and function, respectively, an inherent imposition by the TIM barrel architecture itself. In this study, αβ and βα loops from a data set of 430 non-redundant, high-resolution triosephosphate isomerase (TIM) barrels bearing sequence homology of <30% were analyzed for their amino acid propensities, sequence profiles, and positional preferences of amino acids...
October 24, 2017: Interdisciplinary Sciences, Computational Life Sciences
Arnab Sadhu, Balaram Bhattacharyya
Molecular biomarkers can be potential facilitators for detection of cancer at early stage which is otherwise difficult through conventional biomarkers. Gene expression data from microarray experiments on both normal and diseased cell samples provide enormous scope to explore genetic relations of disease using computational techniques. Varied patterns of expressions of thousands of genes at different cell conditions along with inherent experimental error make the task of isolating disease related genes challenging...
October 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
Prassan Choudhary, Prem Lal Kashyap, Sanjay Kumar Goswami, Hillol Chakdar, Alok Kumar Srivastava, Anil Kumar Saxena
Microsatellites or simple sequence repeats (SSRs) have been the most widely applied class of molecular markers used in genetic studies, having applications in genetic conservation, population studies, as well as diagnostics of fungi. Mining and analysis of SSRs of the whole genome sequence have been carried out in this study for the fungus Alternaria arborescens causing early blight of tomato and well known for producing mycotoxins like alternariol (AOH), alternariol monomethyl ether (AME), etc. A total of 4097 microsatellites were identified in A...
October 3, 2017: Interdisciplinary Sciences, Computational Life Sciences
Jian Guo, Kun Qian, Gongxuan Zhang, Huijie Xu, Björn Schuller
The advent of 'Big Data' and 'Deep Learning' offers both, a great challenge and a huge opportunity for personalised health-care. In machine learning-based biomedical data analysis, feature extraction is a key step for 'feeding' the subsequent classifiers. With increasing numbers of biomedical data, extracting features from these 'big' data is an intensive and time-consuming task. In this case study, we employ a Graphics Processing Unit (GPU) via Python to extract features from a large corpus of snore sound data...
September 25, 2017: Interdisciplinary Sciences, Computational Life Sciences
Homa Azizian, Kowsar Bagherzadeh, Sophia Shahbazi, Niusha Sharifi, Massoud Amanlou
Respiratory chain ubiquinol-cytochrome (cyt) c oxidoreductase (cyt bc 1 or complex III) has been demonstrated as a promising target for numerous antibiotics and fungicide applications. In this study, a virtual screening of NCI diversity database was carried out in order to find novel Qo/Qi cyt bc 1 complex inhibitors. Structure-based virtual screening and molecular docking methodology were employed to further screen compounds with inhibition activity against cyt bc 1 complex after extensive reliability validation protocol with cross-docking method and identification of the best score functions...
September 18, 2017: Interdisciplinary Sciences, Computational Life Sciences
Mathew Saumya, E K Subin, T V Suchithra
Network analysis and visualization of genes are very important to understand large complex biological data in a better manner. Large data on genes and proteins in the biological systems are analyzed on the occurrence, interactions, co-expression, and co-regulations of various genes. Here we have visualized the genes involved in type 1 diabetes (T1D), type 2 diabetes (T2D), and foot ulcer condition to put light on the corrective measures to the problem of impaired healing. The goal of this study was to identify the important genes involved in the pathogenesis of diabetes complications and foot ulcer and its association with the free radical-producing enzyme, the myeloperoxidase (MPO)...
September 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
Ria Biswas, Angshuman Bagchi
The tumour necrosis factor (TNF) receptor-associated factor (TRAF) family of proteins having E3 ligase activity are the key molecules involved in cellular immune response pathways. TRAF6 is a unique member of the TRAF superfamily differing from other members of the family, owing to its specific interactions with molecules outside the TNF receptor superfamily. The C-terminal domain of TRAF proteins contains the catalytic residues and are known to be involved in self-oligomerization forming a mushroom-shaped trimeric structure, which is the functional form of the protein...
September 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
Nirzari Gupta, Vivek K Vyas, Bhumika D Patel, Manjunath Ghate
Deazaflavin-dependent nitroreductase (Ddn) is an emerging target in the field of anti-tuberculosis agents. In the present study, 2-nitroimidazooxazine derivatives as Ddn activators were aligned for CoMFA, CoMSIA and HQSAR analysis. The best CoMFA and CoMSIA model were generated with leave-one-out correlation coefficients (q (2)) of 0.585 and 0.571, respectively. Both the CoMFA and CoMSIA models were also validated by a test set of 11 compounds with satisfactory [Formula: see text] value of 0.701 and 0.667, respectively...
September 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
D Ruban Durairaj, P Shanmughavel
Tuberculosis (TB) is a leading infectious disease which kills a huge number of people every year over a decade, caused by Mycobacterium tuberculosis. The conventional drugs in the market are no longer effective due to the increasing mycobacterial resistance to antibiotics. Hence, the need of finding efficient drugs to solve this multiple drug resistant factor is becoming an immediate issue. The first-line drugs in current practice for the treatment of TB emphasize on mycolic acid, which protects the bacteria from an immune response generated by the host...
August 30, 2017: Interdisciplinary Sciences, Computational Life Sciences
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