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Hema Sekhar Reddy Rajula, Matteo Mauri, Vassilios Fanos
Metabolomics is an expanding discipline in biology. It is the process of portraying the phenotype of a cell, tissue or species organism using a comprehensive set of metabolites. Therefore, it is of interest to understand complex systems such as metabolomics using a scale-free topology. Genetic networks and the World Wide Web (WWW) are described as networks with complex topology. Several large networks have vertex connectivity that goes beyond a scale-free power-law distribution. It is observed that (a) networks expand constantly by the addition of recent vertices, and (b) recent vertices attach preferentially to sites that are already well connected...
2018: Bioinformation
Akash Srivaths, Shyam Ramanathan, Seethalakshmi Sakthivel, Skm Habeeb
Apoptosis Inducing Factor protein has a dual role depending on its localization in mitochondrion (energy production) and nucleus (induces apoptosis). Cell damage transports this protein to nucleus which otherwise favors mitochondrion. The alteration of Nuclear Localisation Signal tags could aid nuclear translocation. In this study, apoptosis inducing factor protein (AIF) was conjugated with strong NLS tags and its binding affinity with Importin was studied using in silico approaches such as molecular modeling and docking...
2018: Bioinformation
Pragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, Vagish Mishra, Pushplatha G, Kiran P Sandhya, Nagendra Kumar Singh, Vandna Rai
Rice, a staple food crop, is often subjected to drought and salinity stresses thereby limiting its yield potential. Since there is a cross talk between these abiotic stresses, identification of common and/or overlapping regulatory elements is pivotal for generating rice cultivars that showed tolerance towards them. Analysis of the gene interaction network (GIN) facilitates identifying the role of individual genes and their interactions with others that constitute important molecular determinants in sensing and signaling cascade governing drought and/or salinity stresses...
2018: Bioinformation
Benson Otarigho, Mofolusho O Falade
The control of Staphylococcus aureus infection is being hampered by methicillin and other resistant strains. The identification of the unique antibiotic resistant genes from the genomes of various strains of S. aureus is of interest. We analyzed 11 S. aureus genomes sequences for Antibiotics Resistance Genes (ARGs) using CARD 2017 platform. We identified 32 ARGs across 11 S. aureus strains. Tet(38), norB, lmrB, mepA and mepR were present across genomes except for S. aureus strain UTSW MRSA 55. The mepA and mepR were found across 11 different genomes...
2018: Bioinformation
Gopalsamy Sarangan, Seema A Nayar, Monika Mani, Sudharsana Sundarrajan, Sathish Sankar, Gunasekaran Palani, Gracy Fathima Selvaraj, Jayachandran Damodharan, Karuppaiah Muthumani, Padma Srikanth
Chikungunya Virus (CHIKV) is a single stranded positive sense enveloped RNA virus. Re-emergence of CHIKV caused a massive outbreak with severe clinical manifestation affecting multiple organs. The genetic diversity of CHIKV, which caused recurring outbreaks in India, was studied. Blood samples were collected from suspected human cases of CHIKV infection in Chennai, Tamil Nadu and three Northern districts of Kerala in Southern India during the CHIKV outbreak in 2009. A partial E2 gene segment was amplified by RT-PCR...
2018: Bioinformation
Ibrahim Torktaz, Ali Najafi, Reza Golmohamadi, Sorour Hassani
The ToxT transcription factor mediates the transcription of the two major virulence factors in Vibrio cholerae. It has a DNA binding domain made of α4, α5, α6, α7, α8, α9 and α10 helices that is responsible for the transcription of virulence genes. Therefore, it is of interest to screen ToxT against the ZINC ligand database containing data for a million compounds. The QSAR model identified 40 top hits for ToxT. Two target protein complexes with ligands Lig N1 and Lig N2 with high score were selected for molecular dynamics simulation...
2018: Bioinformation
Gurpreet Kaur, Pratap Kumar Pati
NADPH oxidase (NOX) is a key enzyme involved in the production of apoplastic superoxide (O2-), a type of reactive oxygen species (ROS). Plant Noxes are the homologs of mammalian NADPH oxidase's catalytic subunit and are documented as respiratory burst oxidase homologs (Rbohs). A number of studies have reported their diverse functions in combating various stresses and in plant growth and development. In the present study, a total of 19 Rboh proteins (10 from Arabidopsis thaliana and 9 from Oryza sativa Japonica) were analyzed...
2018: Bioinformation
Francesco Chiappelli, Vandan R Kasar, Nicole Balenton, Allen Khakshooy
Translational science conceptualizes healthcare as a concerted set of processes that integrate research findings from the bench to the bedside. This model of healthcare is effectiveness-focused, patient-centered, and evidence-based, and yields evidence-based revisions of practice-based guidelines, which emerge from research synthesis protocols in comparative effectiveness research that are disseminated in systematic reviews. Systematic reviews produce qualitative and quantitative consensi of the best available evidence...
2018: Bioinformation
Saba Hasan, Ruba Taha, Halima El Omri
Sub population of cancer cells, referred to as Cancer stem cells (CSCs) or tumor initiating cells, have enhanced metastatic potential that drives tumor progression. CSCs have been found to hold intrinsic resistance to present chemotherapeutic strategies. This resistance is attributed to DNA reparability, slower cell cycle and high levels of detoxifying enzymes. Hence, CSCs pose an obstacle against chemotherapy. The increasing prevalence of drug resistant cancers necessitates further research and treatment development...
2018: Bioinformation
Sammer Siddiqui, Muhammad F Anwar, Sadaf Naeem, Syed Hani Abidi, Shamshad Zarina, Syed Ali
Simian virus 40 large T-antigen (SV40 LT-Ag) is a 708 amino acid nuclear phosphoprotein. Among many functions of LT-Ag is its ability to perform as an ATPase-helicase, catalyzing the unwinding of viral genome during replication. The LT-Ag has been employed in the studies of helicase structure and function, and has served as a model helicase for the screening of antiviral drugs that target viral helicase. In this study, using in vitro enzyme assays and in silico computer modeling, we screened a batch of 18 fluoroquinolones to assess their potential as antivirals by virtue of their inhibition of the LT-Ag helicase...
2018: Bioinformation
Md Kamrul Hasan, Saruar Alam, Jovan Mirkovic, Md Faruk Hossain
Previous studies showed that prolonged exposure to fluoride (F-) and aluminum (Al3+) ions is associated with numerous diseases including neurological disorders. They don't have any known biological function. But they can bind with proteins that interact with ions similar to them. Such unwanted interactions affect the normal biological function of the target proteins, as well as their downstream protein-protein interactions. Several studies show the detrimental effects posed by them including Alzheimer's disease...
2018: Bioinformation
Gabriel O Eniafe, Damilohun S Metibemu, Olaposi I Omotuyi, Adewale J Ogunleye, Olumide K Inyang, Niyi S Adelakun, Yakubu O Adeniran, Bamidele Adewumi, Ojochenemi A Enejoh, Joseph O Osunmuyiwa, Sidiqat A Shodehinde, Oluwatoba E Oyeneyin
Asthma is an inflammatory disease of the airway that poses a major threat to human health. With increase industrialization in the developed and developing countries, the incidence of asthma is on the rise. The β2-adrenergic receptor is an important target in designing anti-asthmatic drugs. The synthetic agonists of the β2-adrenergic receptor used over the years proved effective, but with indispensable side effects, thereby limiting their therapeutic use on a long-term scale. Inverse agonists of this receptor, although initially contraindicated, had been reported to have long-term beneficial effects...
2018: Bioinformation
Aisha Al-Yamani, Gauthaman Kalamegam, Farid Ahmed, Mohammed Abbas, Khalid Hussein Wali Sait, Nisreen Anfinan, Mohammad Khalid Al-Wasiyah, Etimad A Huwait, Mamdouh Gari, Mohammed Al-Qahtani
Mesenchymal stem cells (MSCs) from various sources have been used in cartilage differentiation with variable success. Therefore, it is of interest to evaluate the in vitro differentiation potential of the hWJSCs derived from the human umbilical cords into chondrocytes at the stem cell research facility at the King Abdulaziz University. hWJSCs are an attractive choice for tissue engineering and regenerative medical applications including cartilage regeneration. We evaluated the hWJSCs using classical histological and cartilage related gene expression studies...
2018: Bioinformation
Hongzhao Li, Lin Li, Lewis R Liu, Robert W Omange, Nikki Toledo, Mohammad Abul Kashem, Yan Hai, Binhua Liang, Francis A Plummer, Ma Luo
Simian immunodeficiency virus (SIV) infection of Mauritian cynomolgus macaques (MCMs) is an increasingly important nonhuman primate model for HIV vaccine research. We previously reported that in MCMs anti-SIV antibodies can be naturally developed without exogenous infection or vaccination, and that a vaccine targeting SIV protease cleavage sites (PCS) can cross-induce antibodies to non-PCS SIV antigens. We speculate that this is potentially caused by the existence of endogenous SIV-like antigens. External stimuli (such as environmental factors and vaccination) may induce expression of endogenous SIV-like antigens to elicit these antibodies...
2018: Bioinformation
Maria Pratheepa, Thiruvengadam Venkatesan, Gandhi Gracy, Sushil Kumar Jalali, Rajagopal Rangheswaran, Jomin Cruz Antony, Anil Rai
MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects...
2018: Bioinformation
Paul Shapshak
From the start, Kurt Godel observed that computer and brain paradigms were considered on a par by researchers and that researchers had misunderstood his theorems. He hailed with displeasure that the brain transcends computers. In this brief article, we point out that Artificial Intelligence (AI) comprises multitudes of human-made methodologies, systems, and languages, and implemented with computer technology. These advances enhance development in the electron and quantum realms. In the biological realm, animal neurons function, also utilizing electron flow, and are products of evolution...
2018: Bioinformation
Govindaraju Archunan
Olfaction is an important mechanism by which humans and animals communicate with environment. Odorant-binding proteins (OBPs) play crucial role in the olfactory mechanism. Here, we briefly discuss about the role of OBPs and their importance in industrial, pest management and therapeutic developments.
2018: Bioinformation
Amr T M Saeb
Bioinformatics tools and techniques analyzing next-generation sequencing (NGS) data are increasingly used for the diagnosis and monitoring of infectious diseases. It is of interest to review the application of bioinformatics tools, commonly used databases and NGS data in clinical microbiology, focusing on molecular identification, genotypic, microbiome research, antimicrobial resistance analysis and detection of unknown disease-associated pathogens in clinical specimens. This review documents available bioinformatics resources and databases that are used by medical microbiology scientists and physicians to control emerging infectious pathogens...
2018: Bioinformation
Benson Otarigho, Mofolusho O Falade
We explored 285 completed eukaryotic pathogen genomes for GABA transporter proteins as effective chemotherapy targets. We identified 8 GABA proteins that spread across 4 phyla with 5 different pathogen species; Eimeria mitis Houghton, Neospora caninum Liverpool, S. mansoni, S. haematobium and Trichinella spiralis. Sub-cellular localization prediction revealed that these proteins are integral membrane and are mostly insoluble. It is found that about 81% of these proteins are non-crystallizable and 15% are crystallizable...
2018: Bioinformation
Sindhura Gudipati, Ravi Muttineni, Archana Uday Mankad, Himanshu Aniruddha Pandya, Yogesh Trilokinath Jasrai
Noggin (NOG) a BMP (bone morphogenetic protein) antagonist plays a key role in preferentially driving a subset of breast cancer cells towards the bone and causing osteolytic lesions leading to severe pain and discomfort in the patients. Owing to its role in bone metastasis, NOG could be promising molecular target in bone metastasis and that identifying small molecule inhibitors could aid in the treatment. Towards identifying cognate inhibitors of NOG, structure based virtual screen was employed. A total of 8...
2018: Bioinformation
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