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Bioinformatics and Biology Insights

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https://www.readbyqxmd.com/read/27812283/structural-prediction-and-in-silico-physicochemical-characterization-for-mouse-caltrin-i-and-bovine-caltrin-proteins
#1
Ernesto J Grasso, Adolfo E Sottile, Carlos E Coronel
It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca(2+) uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Surface electrostatic potentials and electric fields were calculated using the Poisson-Boltzmann equation...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27812282/iterative-fragmentation-improves-the-detection-of-chip-seq-peaks-for-inactive-histone-marks
#2
Miklós Laczik, Jan Hendrickx, Anne-Clémence Veillard, Mustafa Tammoh, Sarah Marzi, Dominique Poncelet
As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication - sending the fragmented DNA after ChIP through additional round(s) of shearing - to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27695302/survey-of-genes-involved-in-biosynthesis-transport-and-signaling-of-phytohormones-with-focus-on-solanum-lycopersicum
#3
Stefan Simm, Klaus-Dieter Scharf, Sridharan Jegadeesan, Maria Luisa Chiusano, Nurit Firon, Enrico Schleiff
Phytohormones control the development and growth of plants, as well as their response to biotic and abiotic stress. The seven most well-studied phytohormone classes defined today are as follows: auxins, ethylene, cytokinin, abscisic acid, jasmonic acid, gibberellins, and brassinosteroids. The basic principle of hormone regulation is conserved in all plants, but recent results suggest adaptations of synthesis, transport, or signaling pathways to the architecture and growth environment of different plant species...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27688709/evolution-of-synonymous-codon-usage-in-the-mitogenomes-of-certain-species-of-bilaterian-lineage-with-special-reference-to-chaetognatha
#4
Sudeesh Karumathil, Vijaya R Dirisala, Uthpala Srinadh, Valaboju Nikhil, N Satya Sampath Kumar, Rahul R Nair
Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27594785/interaction-analysis-of-t7-rna-polymerase-with-heparin-and-its-low-molecular-weight-derivatives-an-in-silico-approach
#5
Subhomoi Borkotoky, Chetan Kumar Meena, Ayaluru Murali
The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27559295/in-silico-structure-prediction-of-human-fatty-acid-synthase-dehydratase-a-plausible-model-for-understanding-active-site-interactions
#6
Arun John, Vetrivel Umashankar, A Samdani, Manoharan Sangeetha, Subramanian Krishnakumar, Perinkulam Ravi Deepa
Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27499617/osg-gem-gene-expression-matrix-construction-using-the-open-science-grid
#7
William L Poehlman, Mats Rynge, Chris Branton, D Balamurugan, Frank A Feltus
High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG)...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27493475/computational-identification-of-novel-genes-current-and-future-perspectives
#8
REVIEW
Steffen Klasberg, Tristan Bitard-Feildel, Ludovic Mallet
While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Besides the theoretical breakthrough, increasing evidence accumulated that novel genes play important roles in evolutionary processes, including adaptation and speciation events...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27486314/phylogenetic-and-structural-analysis-of-the-pluripotency-factor-sex-determining-region-y-box2-gene-of-camelus-dromedarius-csox2
#9
Abdullah Alawad, Sultan Alharbi, Othman Alhazzaa, Faisal Alagrafi, Mohammed Alkhrayef, Ziyad Alhamdan, Abdullah Alenazi, Hasan Al-Johi, Ibrahim O Alanazi, Mohamed Hammad
Although the sequencing information of Sox2 cDNA for many mammalian is available, the Sox2 cDNA of Camelus dromedaries has not yet been characterized. The objective of this study was to sequence and characterize Sox2 cDNA from the brain of C. dromedarius (also known as Arabian camel). A full coding sequence of the Sox2 gene from the brain of C. dromedarius was amplified by reverse transcription PCRjmc and then sequenced using the 3730XL series platform Sequencer (Applied Biosystem) for the first time. The cDNA sequence displayed an open reading frame of 822 nucleotides, encoding a protein of 273 amino acids...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27478368/pimadb-a-database-of-protein-protein-interactions-in-huge-macromolecular-assemblies
#10
Oommen K Mathew, Ramanathan Sowdhamini
Protein-protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein-protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank. These details include the results of the quantification and analysis of all the interactions in the complex...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27478367/molecular-shape-analysis-guided-virtual-screening-platform-for-adenosine-kinase-inhibitors
#11
Savita Bhutoria, Ballari Das, Nanda Ghoshal
We propose a new application of molecular shape descriptors in hierarchical selection during virtual screening (VS). Here, a structure-based pharmacophore and docking-guided VS protocol have been evolved to identify inhibitors against adenosine kinase (AK). The knowledge gained on the shape requirements has been extrapolated in classifying active and inactive molecules against this target. This classification enabled us to pick the appropriate ligand conformation in the binding site. We have suggested a set of hierarchical filters for VS, from a simple molecular shape analysis (MSA) descriptor-based recursive models to docking scores...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27385911/s2m-a-stochastic-simulation-model-of-poliovirus-genetic-state-transition
#12
Carol L Ecale Zhou
Modeling the molecular mechanisms that govern genetic variation can be useful in understanding the dynamics that drive genetic state transition in quasispecies viruses. For example, there is considerable interest in understanding how the relatively benign vaccine strains of poliovirus eventually revert to forms that confer neurovirulence and cause disease (ie, vaccine-derived poliovirus). This report describes a stochastic simulation model, S2M, which can be used to generate hypothetical outcomes based on known mechanisms of genetic diversity...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27330281/pdbparam-online-resource-for-computing-structural-parameters-of-proteins
#13
REVIEW
R Nagarajan, A Archana, A Mary Thangakani, S Jemimah, D Velmurugan, M Michael Gromiha
Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. In this work, we have developed a web-based tool, PDBparam, for computing more than 50 structure-based features for any given protein structure...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27279736/genome-data-exploration-using-correspondence-analysis
#14
REVIEW
Fredj Tekaia
Recent developments of sequencing technologies that allow the production of massive amounts of genomic and genotyping data have highlighted the need for synthetic data representation and pattern recognition methods that can mine and help discovering biologically meaningful knowledge included in such large data sets. Correspondence analysis (CA) is an exploratory descriptive method designed to analyze two-way data tables, including some measure of association between rows and columns. It constructs linear combinations of variables, known as factors...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27199550/modeling-of-the-glycolysis-pathway-in-plasmodium-falciparum-using-petri-nets
#15
Jelili Oyelade, Itunuoluwa Isewon, Solomon Rotimi, Ifeoluwa Okunoren
Malaria is one of the deadly diseases, which affects a large number of the world's population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falci-parum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27168722/practical-approaches-for-mining-frequent-patterns-in-molecular-datasets
#16
REVIEW
Stefan Naulaerts, Sandy Moens, Kristof Engelen, Wim Vanden Berghe, Bart Goethals, Kris Laukens, Pieter Meysman
Pattern detection is an inherent task in the analysis and interpretation of complex and continuously accumulating biological data. Numerous itemset mining algorithms have been developed in the last decade to efficiently detect specific pattern classes in data. Although many of these have proven their value for addressing bioinformatics problems, several factors still slow down promising algorithms from gaining popularity in the life science community. Many of these issues stem from the low user-friendliness of these tools and the complexity of their output, which is often large, static, and consequently hard to interpret...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27147821/vaccine-design-for-h5n1-based-on-b-and-t-cell-epitope-predictions
#17
Usman Sumo Friend Tambunan, Feimmy Ruth Pratiwi Sipahutar, Arli Aditya Parikesit, Djati Kerami
From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary target to be neutralized by vaccine. Vaccine is the most effective immunologic intervention. In this study, we use the epitope-based vaccine design from hemagglutinin and neuraminidase of H5N1 Indonesian strain virus by using immunoinformatics approach in order to predict the binding of B-cell and T-cell epitopes (class I and class II human leukocyte antigen [HLA])...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27127406/use-of-metatranscriptomics-in-microbiome-research
#18
REVIEW
Stavros Bashiardes, Gili Zilberman-Schapira, Eran Elinav
The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes. As most commensal species are difficult or impossible to culture, genomic characterization of microbiome composition and function, under various environmental conditions, comprises a central tool in understanding its roles in health and disease. The first decade of microbiome research was mainly characterized by usage of DNA sequencing-based 16S rDNA and shotgun metagenome sequencing, allowing for the elucidation of microbial composition and genome structure...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/26997867/modeling-intercellular-communication-as-a-survival-strategy-of-cancer-cells-an-in-silico-approach-on-a-flexible-bioinformatics-framework
#19
Maura Cárdenas-García, Pedro P González-Pérez, Sara Montagna, Oscar Sánchez Cortés, Elena Hernández Caballero
Intercellular communication is very important for cell development and allows a group of cells to survive as a population. Cancer cells have a similar behavior, presenting the same mechanisms and characteristics of tissue formation. In this article, we model and simulate the formation of different communication channels that allow an interaction between two cells. This is a first step in order to simulate in the future processes that occur in healthy tissue when normal cells surround a cancer cell and to interrupt the communication, thus preventing the spread of malignancy into these cells...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/26848260/nematode-sodium-calcium-exchangers-a-surprising-lack-of-transport
#20
Vishal Sharma, Damien M O'Halloran
Na(+)/Ca(2+) exchangers are low-affinity, high-capacity transporters that rapidly transport calcium against a gradient of Na(+) ions. Na(+)/Ca(2+) exchangers are divided into three groups based upon substrate specificity: Na(+)/Ca(2+) exchangers (NCX), Na(+)/Ca(2+)/K(+) exchangers (NCKX), and Ca(2+)/cation exchangers (NCLX). In mammals, there are three NCX genes, five NCKX genes, and a single NCLX gene. The genome of the nematode Caenorhabditis elegans contains 10 Na(+)/Ca(2+) exchanger genes: three NCX, five NCLX, and two NCKX genes...
2016: Bioinformatics and Biology Insights
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