International Journal for Computational Biology (IJCB)
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Combined gene expression analysis in HIV Associated Dementia, Alzheimer’s disease and Parkinson’s disease- An in-silico approach
Get PDFHuman immunodeficiency virus (HIV) Type 1 infection predominantly affects the immune system. Nevertheless, scientific studies have proven its association with the Central Nervous system (CNS) causing several neurological complications leading to HIV Associated Dementia (HAD). HAD is characterized by a progressive, disabling decline in essential CNS functions such as cognition, motor control and behavior. These are the general characteristics of the most common Neuro degenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). The genetics of AD and PD is widely studied and clinical studies have shown cohesion in the pathology of HAD, AD and PD. Analysing the concurrent expression patterns of large number of genes amongst these related diseases will aid in establishing correlations between the genes and their functions.We have analysed the gene expression datasets of HAD, AD and PD from GEO database to determine the overlapping genes and transcription factors involved. The datasets were normalized using R-Bioconductor, and statistical analysis was performed to identify the significant genes using limma and related packages in R. Although substantial amount of common proteins among HAD and other Neuro degenerative diseases have been previously reported, our findings can help in expanding the pool of target genes and further enhancing the knowledge about the convergent pathways among HAD, AD and PD. These common markers identified will provide insights into parallel pathways of disease mechanisms and further assist in the understanding of progression of HAD pathogenesis
Modelling and Computational Sequence Analysis of a Bacteriocin Isolated from Bacillus licheniformis strain BTHT8
Get PDFBacteriocins are ribosomally synthesized antimicrobial peptides displaying different mode of action. Non pathogenic Bacillus licheniformis are usually associated with plants and produce several bacteriocins. This work looks at drug designing strategies using protein modelling and bioinformatics tools. In this study computational modelling and docking studies were carried out using the 13 amino acid sequence of a previously characterized thermostable bacteriocin, BL8 produced by B. licheniformis strain BTHT8. These analyses enabled the understanding of the structure of BL8 protein domain, which was noted to belong to alpha + beta protein fold family. In addition, the docking study predicted that BL8 has properties of angiotensin-converting enzyme (ACE) inhibitor.
Meta-Analysis Of Brain And Central Nervous System Microarray Datasets
Get PDFBrain and CNS cancer are rare in comparison to other types of cancer. Currently there are no effective therapies for their treatment. In this study, meta-analysis of microarray datasets of Brain and CNS cancer was done to obtain significantly upregulated genes with increased statistical power and generalizability. A total of 130 significantly up-regulated genes were obtained. Some of the genes found during analysis have not yet been associated with this cancer. Different biological networks were created and analyzed using the significantly up-regulated genes as input. For each network, the most significant pathways have also been identified computationally.
Potential of Mean Force study on the dimerization of non-amyloid-β component of Human α-Synuclein
No full textSelf-association of α-Synuclein monomers into oligomeric species and highly ordered amyloid fibrils is linked to Parkinson’s disease (PD). The peptide fragment corresponding to region 61-95 of α-synuclein protein originally termed as non-amyloid β component (NAC) has been suggested to play a critical role in the fibrillation process. To better understand the early events of aggregation process, inter-molecular interactions between the two NAC regions during the formation of dimer is critical. Here we demonstrate the molecular dynamics and potential of mean force (PMF) techniques to study the parallel and anti-parallel dimers of the peptide corresponding to the 71-82 (71VTGVTAVAQKTV82) region of α-synuclein. From the PMF study, we noticed two basins of attraction, one at 10 Ǻ and 14 Ǻ for the parallel and only one basin near 12 Ǻ for the anti-parallel conformation of the dimer of the peptide. From docking study using SymmDock, we noticed higher side chain interactions and interface surface area for the anti-parallel conformation of the dimer of the peptide. Our results thus provide atomistic insights into the structural features of the core fibril forming NAC region during dimerization which may open the way to explore the molecular basis of this disease
An algebra for biological sequences
Get PDFIn this paper, an attempt is made at an algebraic formulation of biological sequences. An algebraic structure is constructed for a given chromosomal string and segmentation. It is shown that this algebra represents, the most common chromosomal mutational mechanisms. Interpretation of the mathematical study is based on biological knowledge. Basic results are derived from the behaviour of the chromosomal segments. This leads us to a new way of manipulating chromosomal mutation with mathematical forms and models
BLASTphp: a PHP wrapper for NCBI BLAST API
Get PDFNCBI BLAST is a most popular bioinformatics framework for finding local similarity between two or more biological sequences. It provides integrative access to various biological databases through web user interface, command-line user interface, and application programming interface. BLASTphp is a lightweight PHP library that wrap’s NCBI BLAST’s RESTful API into a custom graphical user interface BLAST. The BLASTphp program remotely executes the NCBI BLAST through the HTTP/HTTPS interface and elicits the response in HTML, XML, XML2, JSON2, Text, or Tabular (plain) format. However, it can be easily connected to a webserver and integrated with any SQL database which contain the biological sequences. BLASTphp is freely available under GNU General Public License version 3 (GPLv3), at https://github.com/AshokHub/BLASTphp
Action Potential Blocking and Directional Firing by Electrical Field Induction, Modeling and Discussion
Get PDFMany invasive and non-invasive methods have been proposed to excite a neuron in the nerves system. For non-invasive methods like Transcranial Magnetic Stimulation (TMS) there is few investigation on the shape and property of the induced electrical field and its interaction with a neuron to directionally fire or block an action potential. In this article, E-fields are generated by two capacitive plates as a source. E-fields are modified in MATLAB and induced on a pyramidal neuron to study the effect of E-field on a neuron. A method is proposed to block action potential (AP) or fire and direct it into the desired direction by a non-invasive method. Blocking AP can be useful for pain reduction or anesthesia in a desired region of the body. A full modeling investigation on required form of E-field, Hyper-polarization and depolarization values in membrane potential and induction time to directionally fire or block AP have been discussed for various dendrite diameters and channel densities in one-dimensional and two-dimensional pyramidal neurons
Computational Biology Approach for Therapeutic Intervention of Alexander Disease by Post Transcriptional Gene Silencing
Get PDFAlexander disease (AxD) primarily affects the white matter of the central nervous system (CNS). It is an astrogliopathy in which Astroglial cells involved in maintenance homeostasis and providing defence to the brain are affected. Therefore their dysfunction has been implicated in a number of neurological, neuropsychiatric and neurodegerative disorders. GFAP (Glial fibrillary acidic protein) is the major intermediate filament protein present in astrocytes whose heterozygous missense mutations have been reported to be a cause of AxD. In the absence of any effective therapeutic intervention of AxD, in the present study PTGS (Post transcriptional gene silencing) approach to knock down mutant gfap gene. Various mutations causing AxD were checked for their pathogenicity using various in silico tools and 13 mutations were shortlisted based on their pathogenicity and probability of occurrence. Thereafter siRNA were designed against the mutant genes to silence them and thereby preventing the accumulation of mutant gfap that causes the pathophysiology of AxD
