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S V Reshma, Nitish Sathyanarayanan, H G Nagendra
Hypothetical proteins are functionally uncharacterized proteins with assigned function using sequence annotation tools. Almost half of the coding regions of several genomes are hypothetical proteins. Therefore, it is of our interest to characterize a hypothetical protein YVRE from the model system Bacillus subtilis using known data. YVRE is assigned the function as a glucono-lactonase using prediction and phylogenetic analysis. A molecular dynamics simulated homology model of YVRE (with calcium) using human senescence marker protein 30 /SMP30 (PDB ID: 3G4E) as template is reported for functional inference...
2017: Bioinformation
Ar-Rafi Md Faisal, Syed Hassan Imtiaz, Tasnim Zerin, Tania Rahman, Hossain Uddin Shekhar
Lassa virus (LASV) is an arena virus causing hemorrhagic fever and it is endemic in several regions of West Africa. The disease-causing virus records high mortality rate in endemic regions due to lack of appropriate treatment and prevention strategies. Therefore, it is of interest to design and develop viable vaccine components against the virus. We used the Lassa virus envelope glyco-proteins as a vaccine target to identify linear peptides as potential epitopes with immunogenic properties by computer aided epitope prediction tools...
2017: Bioinformation
Yash Shah, Deepak Sehgal, Jayaraman K Valadi
The importance to develop effective alternatives to known antibiotics due to increased microbial resistance is gaining momentum in recent years. Therefore, it is of interest to predict, design and computationally model Antimicrobial Peptides (AMPs). AMPs are oligopeptides with varying size (from 5 to over100 residues) having key role in innate immunity. Thus, the potential exploitation of AMPs as novel therapeutic agents is evident. They act by causing cell death either by disrupting the microbial membrane by inhibiting extracellular polymer synthesis or by altering intra cellular polymer functions...
2017: Bioinformation
Nicole Balenton, Francesco Chiappelli
Bioinformation is at the very core of 21st-century healthcare. Telehealth consists of the range of healthcare-related services delivered through bioinformation-aided telecommunications across health-related disciplines, including nursing. Whereas it is clear that bedside patient-centered nursing can never be replaced, recent developments in bioinformation-aided telenursing will undoubtedly contribute to improving healthcare effectiveness and efficacy. Current trends show that as telenursing becomes increasingly timely and critical, healthcare professionals adopt new and improved evidence-based practices as a standard for patient care worldwide...
2017: Bioinformation
Paul Shapshak, Charurut Somboonwit, John T Sinnott
Artificial Intelligence (AI), robotics, co-robotics (cobots), quantum computers (QC), include surges of scientific endeavor to produce machines (mechanical and software) among numerous types and constructions that are accelerating progress to defeat infectious diseases. There is a plethora of additional applications and uses of these methodologies and technologies for the understanding of biomedicine through bioinformation discovery. Therefore, we briefly outline the use of such techniques in virology.
2017: Bioinformation
Charurut Somboonwit, Lynette J Menezes, Douglas A Holt, John T Sinnott, Paul Shapshak
Cholera, an acute diarrheal infection has become a major global threat. Vibrio cholerae the causative agent of cholera has been responsible for six previous pandemics since 1817 that spanned four continents and Australia with the seventh pandemic ongoing since 1961. Two serogroups of V. cholerae O1 and O139 have the ability to secrete the enterotoxin with potential to cause epidemics. The prior six pandemics were caused by the classical biotype of the O1 serogroup. However, the emergence of the El Tor biotype and subsequent variants of El Tor with classical traits are the main isolates in the seventh pandemic...
2017: Bioinformation
Haseeb Ahmad Khan
In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific biomedical problems. Many of these tools are designed and developed by biomedical scientists independently or with the support of computer experts and often made freely available for the benefit of scientific community...
2017: Bioinformation
Irena Roterman, Mateusz Banach, Leszek Konieczny
The antifreeze protein (AFP) activity is explained using two models. The first model is using ice binding and the second is using antiice structuralization of water molecules. The description of AFP function using anti-ice structuralization of water molecules is less explored. Therefore, it is of interest to explain AFP function using this model. Protein folding is often described using models where hydrophobic residues move away from water getting buried and hydrophilic residues are exposed to the surface...
2017: Bioinformation
Kadapakkam Nandabalan Sangeetha, Sundaresan Sujatha, Velusamy Shanmuganathan Muthusamy, Singaravel Anand, Kusampudi Shilpa, Posa Jyothi Kumari, Baskaran Sarathkumar, Gopal Thiyagarajan, Baddireddi Subhadra Lakshmi
Non-insulin dependent diabetes mellitus, also known as Type 2 diabetes is a polygenic disorder leading to abnormalities in the carbohydrate and lipid metabolism. The major contributors in the pathophysiology of type 2 diabetes (T2D) include resistance to insulin action, β cell dysfunction, an abnormality in glucose metabolism and storage, visceral obesity and to some extent inflammation and oxidative stress. Insulin resistance, along with a defect in insulin secretion by the pancreatic β cells is instrumental towards progression to hyperglycemia...
2017: Bioinformation
Mundla Sri Latha, Madhu Sudhana Saddala
Hypoxia inducible factor-1(HIF-1) is a bHLH-family transcription factor that control genes involved in glucolysis, angiogenesis, migration, as well as invasion factors that are important for tumor progression and metastasis. HIF-1, a hetero dimer of HIF-1α and HIF-1β, binds to the hypoxia responsive genes, such as vascular endothelial growth factor (VEGF). It is one the molecular target for angiogenesis. A series of Chalcone - like compounds described that preferentially inhibit HIF-1 dimer, which can interact with amino acids within the active site of the protein...
2017: Bioinformation
Zoozeal Thakur, Renu Dharra, Vandana Saini, Ajit Kumar, Promod K Mehta
Protein-protein interaction (PPI) network analysis is a powerful strategy to understand M. tuberculosis (Mtb) system level physiology in the identification of hub proteins. In the present study, the PPI network of 79 Mtb toxin-antitoxin (TA) systems comprising of 167 nodes and 234 edges was investigated. The topological properties of PPI network were examined by 'Network analyzer' a cytoscape plugin app and STRING database. The key enriched biological processes and the molecular functions of Mtb TA systems were analyzed by STRING...
2017: Bioinformation
Simranjit Kaur, Mahesh Kulharia
Biofilms are bacteria living in micro-colonies with a protective coating in sessile form. The biofilm protects bacteria from harsh surroundings as well as help in antibiotics resistance using a semi-fluid substance. Cellulose is the major component of biofilm, which provides the sticky appearance to bacteria for attaching to the substratum. The bacteria communicate in biofilm with the help of quorum sensing hormones Acylated Homoserine Lactones (AHL's). In Komagataeibacter xylinus the four genes Bcs A, Bcs B, Bcs C, Bcs D are associated with cellulose biosynthesis...
2017: Bioinformation
Sathish Sankar, Mageshbabu Ramamurthy, Balaji Nandagopal, Gopalan Sridharan
Mosquito (Aedes aegyptii) salivary proteins play a crucial role in facilitating viral transmission from vector-to-host due to their role in facilitating the "blood meal" of the vector. Three main proteins, D7, aegyptin and Sialokinin play a role in this process. Using in-silico programs, we identified B- and T-cell epitopes in the mosquito salivary proteins D7 long and short form. T-cell epitopes with high affinity to the most prevalent HLA MHC class-I supertypes among different population groups was chosen...
2017: Bioinformation
Naresh Kumar Manda, Venkata Bala Sai Chaitanya Thunuguntla, Chandrasekhar Bokka, Bondili Jayakumar Singh
Ymr210w was identified as a MAG (Monoacylglycerol) lipase. The accumulation of the phospholipids in the ymr210wΔ was not clearly understood. It was expressed in S. cerevisiae using pYES2/CT vector and His-tag purified recombinant protein confirmed TAG lipase activity. To further evaluate the role of YMR210w, ester hydrolase activity was also confirmed with pNP-acetate, pNP-butyrate and pNP - palmitate. GC-MS lipid profiling of ymr210wΔ showed an increase in the 15:0 Pentadecanoic acid by 76% among the total lipids...
2017: Bioinformation
Mario Rowan Sohilait, Harno Dwi Pranowo, Winarto Haryadi
Curcumin analogues were evaluated for COX-2 inhibitory as anti-inflammatory activities. The designed analogues significantly enhance COX-2 selectivity. The three compounds could dock into the active site of COX-2 successfully. The binding energies of -8.2, - 7.6 and -7.5 kcal/mol were obtained for three analogues of curcumin respectively. Molecular docking study revealed the binding orientations of curcumin analogues in the active sites of COX-2 towards the design of potent inhibitors.
2017: Bioinformation
Francesco Chiappelli, Allen Khakshooy, Nicole Balenton
Cholera remains a feared, aggressive, infectious and lethal disease today, despite several decades of intense research, concerted public health modalities designed to prevent, and to control outbreaks, availability of efficacious vaccines aimed at containing its contagious spread, and effective patient-centered medical interventions for reducing morbidity and mortality. Despite these advances, cholera still strikes communities around the world, especially in countries and regions of the globe where medical and nursing care cannot be as effectively proffered to the population at risk as in First World economies...
2017: Bioinformation
Paul Shapshak, Charurut Somboonwit, Shu Cao, John T Sinnott
Gene network analysis was performed based on published literature describing genes that are possibly interconnected with cholera vaccine responses in vitro in cell culture and in vivo in human patient punch biopsies as well as DNA extracted from blood. These studies produced divergent results. The differences should be replicated and studied further. Included in such studies, patient ethnicities, states of stress, nutrition, and health, as well as the precise characteristics of the various cholera vaccines and modes of delivery need to be considered as well...
2017: Bioinformation
Allen Khakshooy, Nicole Balenton, Francesco Chiappelli
Lubricin is a synovial glycoprotein that contributes to joint lubrication. We propose the hypothesis that lubricin is a key modulator of the psychoneuroendocrine-osteoimmune interactome, with important clinical relevance for osteoarthritic pathologies. We consider a variety of neuroendocrine-immune factors, including inflammatory cytokines and chemokines that may contribute to the modulation of lubricin in rheumatic complications. Based on our preliminary immunocytochemistry and fractal analysis data, and in the context of translational research of modern healthcare, we propose that molecular lubricin gene expression modification by means of the novel CRISPR/Cas system be considered for osteoarthritic therapies...
2017: Bioinformation
Pooja Mitra, Aishwarya Rastogi, Mayank Rajpoot, Ajay Kumar, Vivek Srivastava
Schizophrenia is a complex, chronic mental disorder, affecting about 21 million people worldwide. It is characterized by symptoms, including distortions in thinking, perception, emotions, disorganized speech, sense of self and behavior. Recently, a numbers of marketed drugs for Schizophrenia are available against dopamine D2 and serotonin 5-HT2A receptors. Here, we docked Olanzapine derivatives (collected from literature) with 5-HT2A Receptor using the program AutoDock 4.2. The docked protein inhibitor complex structure was optimized using molecular dynamics simulation for 5ps with the CHARMM-22 force field using NAMD (NAnoscale Molecular Dynamics program) incorporated in visual molecular dynamics (VMD 1...
2017: Bioinformation
Subhadip Nandi, Satyajit Hembaram, Arindam Adhikari, Basant Kumar Tiwari, Subrata Dutta
Physalis minima is an herbaceous plant and inhabitant of the porous and organic matter containing soil of bunds in crop fields, wastelands, around the houses, and on the roadsides. S. rolfsii is soil borne and it can infect over 500 plant species of different families. It is of interest to study the pathogenesis of S. rolfsii on P. minima. The S. rolfsii isolated from P. minima (physr1) was characterized by morphology and sequence of Internal Transcribed Spacer (ITS) region. The population structure determination and phylogenetic analysis showed the isolate physr1 significantly differs from other isolates...
2017: Bioinformation
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