In Silico Biology - Volume 9, issue 5-6

Authors: Ecker, K. | Welch, L.

Article Type: Research Article

Abstract: An important concern in the attempt of understanding the functional code of eukaryotic genes is to elucidate the control structures for regulating gene activation and suppression. One objective in the attempt to understand mechanisms of gene regulation is the elucidation of the regulatory network structure. A preliminary step of a detailed network analysis is identifying the transcription factor binding sites of a regulatory network. Known as cis-regulatory module (CRM), it is understood as part of …the genome that comprises a set of short length binding sites. Gene regulatory systems are known to be quite stable during evolution, as compared to relatively frequent replication processes of genes and mutations of the coding sequences. This conservation property of regulatory code can advantageously be used for identifying cis-regulatory modules of potentially co-regulated genes. As the degree of similarity is expected to depend on the phylogenetic distance of homologs or orthologs, we favor an approach that is based on a comparison paradigm. The paper introduces a novel concept for measuring the similarity of cis-regulatory modules which can then be used in an algorithm for comparing regulatory regions. The proposed algorithm searches for pairs of similar modules, and a prototype implementation is applied to human and mouse liver sequences. The results are compared to that of random sequences, and it is shown that a clear decision about co-regulation is possible at this level. Show more

Keywords: Regulatory networks, cis-regulatory modules, phylogenetic distance, similarity of sequences

DOI: 10.3233/ISB-2009-0407

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 285-306, 2009

Authors: Khan, Sofia | Vihinen, Mauno

Article Type: Research Article

Abstract: In order to study protein function and activity structural data is required. Since experimental structures are available for just a small fraction of all known protein sequences, computational methods such as protein modelling can provide useful information. Over the last few decades we have predicted, with homology modelling methods, the structures for numerous proteins. In this study we assess the structural quality and validity of the biological and medical interpretations and predictions made based on the …models. All the models had correct scaffolding and were ranked at least as correct or good by numerical evaluators even though the sequence identity with the template was as low as 8%. The biological explanations made based on models were well in line with experimental structures and other experimental studies. Retrospective analysis of homology models indicates the power of protein modelling when made carefully from sequence alignment to model building and refinement. Modelling can be applied to studying and predicting different kinds of biological phenomena and according to our results it can be done so with success. Show more

Keywords: Protein models, homology modelling, missense mutations, biological predictions, evaluation, quality of protein models, disease-causing mutations, structural explanations for mutations

DOI: 10.3233/ISB-2009-0408

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 307-331, 2009

Authors: Whyte, David B. | Nair, Gopakumar Gopalakrishnan | Nair, Achuthsankar S. | Oommen, Oommen V.

Article Type: Research Article

Abstract: An online tool named GEN-SNiP that identifies variations in a set of test DNA sequences with respect to a standard reference sequence is developed and deployed successfully. The tool generates a list of substitutions, insertions and deletions for each test sequences, determined by the reference sequence. In the key batch mode feature, the tool allows multiple sequences to be compared and contrasted even when small insertions and deletions are present, with results sent to the user …via email. Other distinguishing features of the tool are grouping of continuous deletions or insertions in the test sequence into a single entity for better output handling, displaying of the alignment of test and reference sequence and the input sequence. The tool has been reported as unique in recent literature. Show more

Keywords: Single nucleotide polymorphism (SNP), mitochondrial DNA (mtDNA), sequence analysis, genome, revised Cambridge reference sequence

DOI: 10.3233/ISB-2009-0401

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 333-336, 2009

Authors: Nayak, Kinshuk C.

Article Type: Research Article

Abstract: In this study major factors shaping codon and amino acid usage variation in Thermobifida fusca YX are reported. It is a major degrader of plant cell walls. It produces spores that can be allergenic and has been associated with a condition called farmers lung. For comparison, two other closely related Actinobacteria, S. coelicolor and N. farcinica were considered. Correspondence analysis on RSCU (Relative Synonymous Codon Usage) showed significant correlation between the major trend …of codon usage variation and gene expression level assessed by the "Codon Adaptation Index" (CAI) values. The result was further confirmed from distribution of genes along the first axis. In addition, N_{c} (effective number of codons) plot, SCUO (synonymous codon usage order) plot and correlation analyses showed that base composition and mutational bias have a dominant role in codon usage variation. Furthermore, gene expression level, hydrophobicity and aromaticity have played a significant role in the source of variations for amino acid usage. In addition, codon preference for genes at higher expression level was found to be similar among three different genera. Notably, 14 codons optimally used by Thermobifida fusca YX and its comparative study with S. coelicolor and N. farcinica might provide some useful information for their further study of molecular evolution and genetic engineering. Show more

Keywords: Thermobifida fusca YX, RSCU values, SCUO values, correspondence analysis, GC skew, N_{c} values

DOI: 10.3233/ISB-2009-0421

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 337-353, 2009

Authors: Fernandez-Becker, Nielsen Q. | Moss, Alan C.

Article Type: Research Article

Abstract: T-bet (TBX21) is a transcription factor that regulates T-cell differentiation, and has recently been implicated in the pathogenesis of Crohn's disease (CD). The regulatory networks through which T-bet affects immune function are unknown. An NCBI gene expression profile from patients with CD and controls was analyzed. T-bet transcription factor binding sites and promoter modules were identified using promoter analysis software. Functional correlations between T-bet-containing promoters were determined using data …mining and ontological analysis. T-bet expression in CD peripheral blood mononuclear cells (PBMCs) (n=59) was significantly reduced compared to control (n=42) (p<0.0001) and ulcerative colitis PBMCs (n=26), (p=0.005). The promoter regions of all genes differentially-expressed in CD were probed for T-bet Transcription Factor Binding Sites (TFBSs). Twenty-three genes contained transcription-factor binding sites for T-bet; 8 were down-regulated, and 15 were up-regulated in CD-PBMCs. Three genes (S100A16, ABHD3 and EZH1) that were down-regulated in CD-PBMCs contained a complex promoter module consisting of T-bet and EGRF transcription-factor binding sites. Ontological analysis revealed that a significant number of differentially-expressed genes that contain T-bet binding sites are involved in innate immunity (8 genes, Z-score 4.11) and signal transduction (5 genes, Z-score 2.65). This combination of gene expression datasets and promoter analysis has identified a network of genes that contain simple T-bet binding sites, and complex T-bet promoter modules, in their promoter regions. These results implicate a mechanism through which T-bet may influence innate immunity in CD. Show more

Keywords: Protein models, homology modelling, missense mutations, biological predictions, evaluation, quality of protein models, disease-causing mutations, structural explanations for mutations

DOI: 10.3233/ISB-2009-0410

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 355-363, 2009

Authors: Mitra, Pralay | Dhar, Riddhiman | Pal, Debnath

Article Type: Research Article

Abstract: Apoptosis is a programmed mechanism of cell death that is a normal component of development and health of multi-cellular organisms. In this study, we ask if interface properties of apoptotic protein complexes are different from protein complexes in general. We find that although in apoptotic protein complexes the overall distribution of interface size, surface complementarity, hydrogen bonding, hydrophobicity are similar to general interface properties, apoptotic complexes tend to have more …fragmented interfaces and different secondary structural preferences. The statistics on the number of interfaces where specific amino acid(s) occur with significantly enhanced frequency suggest that Arg, Met and Asp are most important functional residues. The role of Met is believed to be unique, as evidenced from the existing data on hot spot potential of residues. These findings together provide insight into the possible role of various physico-chemical attributes at the protein interface in regulation of the apoptosis process. Show more

Keywords: Apoptosis, protein-protein interaction, residue propensity, protein interface, secondary structure

DOI: 10.3233/ISB-2009-0411

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 365-378, 2009

Authors: Liu, Yunkai | Ye, Sujuan | Erkine, Alexandre M.

Article Type: Research Article

Abstract: Cellular stress responses are characterized by coordinated transcriptional induction of genes encoding a group of conserved proteins known as molecular chaperones, most of which are also known as heat shock proteins (HSPs). In S. cerevisiae, transcriptional responses to stress are mediated via two trans-regulatory activators: heat shock transcription factors (HSFs) that bind to heat shock elements (HSEs), and the Msn2 and Msn4 transcription factors that bind to stress response elements (STREs). Recent …studies in S. cerevisiae demonstrated that a significant portion of the non-coding region in the genome is transcribed and this intergenic transcription could regulate the transcription of adjacent genes by transcription interference. The goal of this study was to analyze the genomic distribution of HSF and Msn2/4 binding sites and to study the potential for transcription interference regulated by stress response systems. Our genome-wide analysis revealed that 297 genes have STREs in their promoter region, whereas 310 genes contained HSEs. Twenty-five genes had both HSEs and STREs in their promoters. The first set of genes is potentially regulated by the Msn2/Msn4/STRE interaction. For the second set of genes, regulation by heat shock could be mediated through HSF/HSE regulatory mechanisms. The overlap between these groups suggests a co-regulation by the two pathways. Our study yielded 239 candidate genes, whose regulation could potentially be affected by heat-shock via transcription interference directed both from upstream and downstream areas relative to the native promoters. In addition we have categorized 924 genes containing HSE and/or STRE elements within the Open Reading Frames (ORFs), which may also affect normal transcription. Our study revealed a widespread possibility for the regulation of genes via transcriptional interference initiated by stress response. We provided a categorization of genes potentially affected at the transcriptional level by known stress-response systems. Show more

Keywords: Saccharomyces cerevisiae, heat shock transcription factors, heat shock elements, Msn2 and Msn4 transcription factors, stress response elements, genomic distribution, gene regulation, transcription interference

DOI: 10.3233/ISB-2009-0412

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 379-389, 2009

Authors: Dormer, Anton | Pauleus, Cathelina V. | Syverin, Mondy N. | Dacil, Clarissa | Smile, Peta-Gaye

Article Type: Research Article

Abstract: The application of in silico tools for the development of T-cell vaccines is crucial. Yet, due to myriad of polymorphisms of human T-lymphocytic antigen challenges, such therapeutic opportunities present unique roadblocks. There is an obvious advantage in using immunoinformatics (i.e., significantly decreasing cost related to laboratory expenses). A previous publication looked at random binding and nonbinding peptides in order to test the practicality of using such in silico tools to obtain possible …immunogenic peptides. The present in silico study applied the same basic approaches to an applicable problem that was to identify promiscuous peptide vaccine candidates for hepatitis C virus (HCV) infection. The data sets used, included the proteins HCV E1, E2 and P7 as the binders (non-self antigens) and the GAD65 and ICA69, which have an association with diabetes, as non-binders (self-antigens). The in silico tools utilized were ProPred, MHC2PRED, and RANKPEP. The resulting differences were identifiable in each of the statistical parameters examined. Variations in the outcomes were evident by the dissimilarities found among the major indices of evaluation Sensitivity, Specificity, Accuracy, Positive Predictive Value (PPV), Negative Predictive Value (NPV) and Matthews's correlation coefficient (MCC) of the percentages of the predicted promiscuous peptides to HLA-DRB1*0101, *0301, and *0401. The conclusion from this study indicates that more work needs to be done in order to enhance the predictability of programs for the identification of peptide vaccine candidates for HCV. Such programs should not be solely relied upon without in vitro assay verification. Show more

Keywords: HCV, HLA, immunoinformatics, peptide, promiscuous peptide

DOI: 10.3233/ISB-2009-0422

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 391-406, 2009

Authors: Gopal, Shubha | Srinivas, Vanishree | Zameer, Farhan | Kreft, Jürgen

Article Type: Research Article

Abstract: Thiol:disulfide redox metabolism (TDRM) is a central metabolic network in all living cells. However, numerous proteins with different biochemical functions and several structural domains are involved, making it not trivial to identify and annotate its constituents in sequenced genomes. We developed an uncomplicated approach to solve the problem using existing web-based tools and public databases with the gram-positive bacterium Listeria monocytogenes EGD-e as a model organism. A pattern search for the …Cys-Xaa-Xaa-Cys (CXXC) motif – a hallmark of TDRM proteins – in the genome sequence of the bacterium yielded 156 proteins. After initial refinement by protein and domain analysis, 14 candidate proteins remained. Subsequent detailed analyses, supported by modeling of 3D structures and data integration yielded 6 thioredoxin-like proteins plus thioredoxin reductase, glutaredoxin, one redox-sensitive regulator, one peptide methionine reductase – all typical TDRM constituents – and three putative novel components of the TDRM. For all 14 proteins orthologues were found in other Listeria species. Homology searches and phylogenetic analyses showed that related proteins are present mainly in other Firmicutes. This fast approach required minimal resources. It is immediately applicable to any genome with appropriate modifications and should be practicable also for other conserved, functionally important amino acid motifs. Show more

Keywords: CXXC motif, 3D structure, L. monocytogenes EGD-e, phylogeny, redox, thiol:disulfide

DOI: 10.3233/ISB-2009-0409

Citation: In Silico Biology, vol. 9, no. 5-6, pp. 407-414, 2009