Bioinformation

Published by Biomedical Informatics
Online ISSN: 0973-2063
Print ISSN: 0973-8894
Publications
In silico tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV. Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27. Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree. Mesquite was employed for ancestral state reconstruction to infer the order of amino acid substitutions in the epitopes examined. The results showed that consensus peptide identified SLAEKNITI had changes that indicated predicted escape mutation in strains of HIV responding to pressure exerted by CD8+ cells expressing HLA A*02. The predominating 9-mers IRIGPGQAF of gp120 are significantly less immunogenic toward HLA B*27 than to HLA A*02. The data confirms previous findings on the importance for efficacious binding, of an arginine residue at the 2(nd) position of the gag SL9 epitope, and extends this principle to other epitopes which interacts with HLA B*27. This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that has much relevance for the creation of personalized therapeutics for HIV treatment.
 
The stability of amidase-03 structure (a cell wall hydrolase protein) from Bacillus anthracis was studied using classical molecular dynamics (MD) simulation. This protein (GenBank accession number: NP_844822) contains an amidase-03 domain which is known to exhibit the catalytic activity of N-acetylmuramoyl-L-alanine amidase (digesting MurNAc-Lalanine linkage of bacterial cell wall). The amidase-03 enzyme has stability at high temperature due to the core formed by the combination of several secondary structure elements made of β-sheets. We used root-mean-square-displacement (RMSD) of the simulated structure from its initial state to demonstrate the unfolding of the enzyme using its secondary structural elements. Results show that amidase-03 unfolds in transition state ensemble (TSE). The data suggests that α-helices unfold before β-sheets from the core during simulation.
 
Sequence alignment of amidase-03 (PDB ID: 2IR0) with template 1XOV
Homology models of amidase-03 from Bacillus anthracis were constructed using Modeller (9v2). Modeller constructs protein models using an automated approach for comparative protein structure modeling by the satisfaction of spatial restraints. A template structure of Listeria monocytogenes bacteriophage PSA endolysin PlyPSA (PDB ID: 1XOV) was selected from protein databank (PDB) using BLASTp with BLOSUM62 sequence alignment scoring matrix. We generated five models using the Modeller default routine in which initial coordinates are randomized and evaluated by pseudo-energy parameters. The protein models were validated using PROCHECK and energy minimized using the steepest descent method in GROMACS 3.2 (flexible SPC water model in cubic box of size 1 Å instead of rigid SPC model). We used G43a1 force field in GROMACS for energy calculations and the generated structure was subsequently analyzed using the VMD software for stereo-chemistry, atomic clash and misfolding. A detailed analysis of the amidase-03 model structure from Bacillus anthracis will provide insight to the molecular design of suitable inhibitors as drug candidates.
 
The HA protein is responsible for influenza virus attachment and the subsequent fusion of viral and cellular membranes. Antigenic drift is driven by an accumulation of point mutations in the HA. And, the receptor-binding specificity of HA is responsible for the host range restriction of the virus. In April 2009, large outbreaks of novel H1N1 influenza in human population were reported from North America. The pandemic H1N1 virus originated from swine influenza virus. Evolutionary process of the pandemic virus after its introduction to human population remains to be clarified. We conducted phylogenetic analyses constructing a phylogenetic tree for and calculating site-by-site selective pressures in the HA gene. Phylogenetic tree showed that pandemic viruses were not clustered clearly by their geographical location or isolation time in the phylogenetic tree. The virus has been circulating the globe extensively with multiple introductions into most geographical areas. We found 3 sites positively selected in the HA gene for pandemic H1N1 virus. Among them, position 206 is located in an antigenic site. We did not find significant negative selection on any of the receptor binding sites. The virus has been evolving under unique selective pressure.
 
SDS-PAGE of overexpressed and purified SU40-β-1,31,4 glucanase. Lane 1, molecular weight marker (Bangalore Genei, India); Lane 2, the un-induced sonicated cell supernant of Escherichia coli pET28a+-SU40 as control; lane 3, sonicated cell supernatant after IPTG induction; Lane 4, purified β-1,3-1,4 glucanase Purification of recombinant -1,3-1,4 glucanase Purified enzyme was confirmed by SDS-PAGE (Figure 1). The molecular weight was determined as 24 kDa which is similar with the theoretically calculated molecular weight. The yield of purified enzyme was 44.88% with 37.85 U/mg of specific activity.
Molecular three-dimensional model of SU40-β-1,3-1,4 glucanase with CA ion. The predicted structure of β-1,3-1,4 glucanase exhibited the occurrence of two α-helices, 16 βstrands and 19 loop turns.
Evaluation of the trajectory 5,000 ps for the calculation of a) Potential energy; b) Root Mean Square Deviation; c) RMSF and d) Radius of gyration. The backbone RMSF of Ca 2+ free SU40-β-1,3-1,4 glucanase (red) showed fluctuation in active site residues. (Black colour-with Ca 2+ and Red colour-without Ca 2+ ).
Molecular three-dimensional model of SU40- β-1,3-1,4
glucanase with CA ion. The predicted structure of β-1,3-1,4
glucanase exhibited the occurrence of two α-helices, 16 β-
strands and 19 loop turns.
A new glucanolytic bacterial strain, SU40 was isolated, and identified as Bacillus subtilis on the basis of 16S rRNA sequence homology and phylogenetic tree analysis. The gene encoding β-1,3-1,4-glucanase was delineated, cloned into pET 28a+ vector and heterologously overexpressed in Escherichia coli BL21(DE3). The purified recombinant enzyme was about 24 kDa. The enzyme exhibited maximum activity (36.84 U/ml) at 60°C, pH 8.0 and maintained 54% activity at 80°C after incubation for 60 min. The enzyme showed activity against β-glucan, lichenan, and xylan. Amino acid sequence shared a conserved motif EIDIEF. The predicted three-dimensional homology model of the enzyme showed the presence of catalytic residues Glu105, Glu109 and Asp107, single disulphide bridge between Cys32 and Cys61 and three calcium binding site residues Pro9, Gly45 and Asp207. Presence of calcium ion improves the thermal stability of SU40 β-1,3-1,4-glucanase. Molecular dynamics simulation studies revealed that the absence of calcium ion fluctuate the active site residues which are responsible for thermostability. The high catalytic activity and its stability to temperature, pH and metal ions indicated that the enzyme β-1,3-1,4-glucanase by B. subtilis SU40 is a good candidate for biotechnological applications.
 
Screenshot of software's illustration  
Unlabelled: The small hairpin RNAs (shRNA) are useful in many ways like identification of trait specific molecular markers, gene silencing and characterization of a species. In public domain, hardly there exists any standalone software for shRNA prediction. Hence, a software shRNAPred (1.0) is proposed here to offer a user-friendly Command-line User Interface (CUI) to predict 'shRNA-like' regions from a large set of nucleotide sequences. The software is developed using PERL Version 5.12.5 taking into account the parameters such as stem and loop length combinations, specific loop sequence, GC content, melting temperature, position specific nucleotides, low complexity filter, etc. Each of the parameters is assigned with a specific score and based on which the software ranks the predicted shRNAs. The high scored shRNAs obtained from the software are depicted as potential shRNAs and provided to the user in the form of a text file. The proposed software also allows the user to customize certain parameters while predicting specific shRNAs of his interest. The shRNAPred (1.0) is open access software available for academic users. It can be downloaded freely along with user manual, example dataset and output for easy understanding and implementation. Availability: The database is available for free at http://bioinformatics.iasri.res.in/EDA/downloads/shRNAPred_v1.0.exe.
 
The Affymetrix GeneChip® Human Exon 1.0 ST array (exon array) is designed to measure both gene-level and exon-level expression in human samples. This exon array contains ~1.4 million probesets consisting of ~5.4 million probes and profiles over 17,000 well-annotated gene transcripts in the human genome. As with all expression arrays, the exon array is vulnerable to SNPs within probes, because these SNPs can affect the hybridization of the probes and thus produce misleading expression values. In some cases, this could result in dramatic fluctuations of the exon-level expression. For this reason, we performed a genome-wide search for SNPs within regions that hybridize to probes by evaluating approximately 18 million SNPs in dbSNP (Build 129) and about 5.4 million probes in the exon array. We identified 597,068 probes within 350,382 probe sets that hybridized to regions containing SNPs. These affected probes and/or probesets can be filtered in the data processing procedure thus controlling for potential false expression phenotypes when using this exon array. Availability http://cid-fb2a64e541add2be.skydrive.live.com/browse.aspx/Affy%7C_HuEx%7C_1.0ST?uc=2.
 
Molecular biology databases are an integral part of biological research. To date, many databases were established with varied options to access associated biological data. Depending on the data being annotated, some are architecturally similar while others are specialized. In order to provide a partial solution to data integration, we report Database of Databases (DoD2007), constructed using html and javascript. The database has a web-based user interface with simple global search, specific database search, keyword help as well as links to abstracts, full-text and database home pages. Majority of data were derived form Nucleic Acids Research database issue and other published resources. The current release includes 15 categories with updated descriptions and links to 1082 databases, of which, 209 are new entries. New databases included in this issue are represented with ‘+’ sign before the name and a ‘*’ symbol provided for those that remained silent. Availability The database is freely available at http://www.progenebio.in/DoD/index.htm.
 
Genomic organization of Amorpha-4, 11-diene synthase gene (ADS 3963 ). Numbers shown below the lines are the start and end positions of exons.  
Multiple sequence alignment of different amorpha-4, 11-diene synthase genes.  
Prediction of 3D model of Amorpha-4, 11-diene synthase showing N (blue) and C (Red) terminal isolated from Artemisia annua L. plant.  
Figure showing the receptor molecule with the ligand docked in six top ranking binding sites. All the six figures in different colour correspond to six binding sites containing the ligand molecule FPP docked into it.  
With the escalating prevalence of malaria in recent years, artemisinin demand has placed considerable stress on its production worldwide. At present, the relative low­yield of artemisinin (0.01­1.1 %) in the source plant (Artemisia annua L. plant) has imposed a serious limitation in commercializing the drug. Amorpha­4, 11­diene synthase (ADS) has been reported a key enzyme in enhancing the artemisinin level in Artemisia annua L. An understanding of the structural and functional correlations of Amorpha­4, 11­diene synthase (ADS) may therefore, help in the molecular up­regulation of the enzyme. In this context, an in silico approach was used to study the ADS3963 (3963 bp) gene cloned by us, from high artemisinin (0.7­0.9% dry wt basis) yielding strain of A. annua L. The full­length putative gene of ADS3963 was found to encode a protein consisting of 533 amino acid residues with conserved aspartate rich domain. The isoelectric point (pI) and molecular weight of the protein were 5.25 and 62.2 kDa, respectively. The phylogenetic analysis of ADS genes from various species revealed evolutionary conservation. Homology modeling method was used for prediction of the 3D structure of ADS3963 protein and Autodock 4.0 version was used to study the ligand binding. The predicted 3D model and docking studies may further be used in characterizing the protein in wet laboratory.
 
A bioinformatics analysis of sequences of enzymes of the glycoside hydrolase (GH) 13 family members such as α-amylase, cyclodextrin glycosyltransferase (CGTase), branching enzyme and cyclomaltodextrinase has been carried out in order to find out the sequence motifs that govern the reactions specificities of these enzymes by using hidden Markov model (HMM) profile. This analysis suggests the existence of such sequence motifs and residues of these motifs constituting the −1 to +3 catalytic subsites of the enzyme. Hence, by introducing mutations in the residues of these four subsites, one can change the reaction specificities of the enzymes. In general it has been observed that α -amylase sequence motif have low sequence conservation than rest of the motifs of the GH13 family members.
 
Enterohemorrhagic Escherichia coli (EHEC) are source of emerging infectious disease in India. Escherichia coli O157:H7 is an EHEC strain showing multiple antibiotic resistances and the cause of infantile diarrhea and hemolytic uremic syndrome worldwide. A novel strategy to counteract multiple antibiotic resistant organisms is to design drugs which specifically target metabolic pathways such as thiamine biosynthetic pathways found exclusively in prokaryotes. Homology modeling was used for model building of a terminal thiamine biosynthesis enzyme phosphoryl thymidine kinase (Thi E) using Geno3D, Swiss Model and Modeller. The best model was selected based on overall stereochemical quality. The potential ligand binding sites in the model were identified by CASTp server. The validated theoretical model of the 3D structure of the thiE protein of E. coli O157:H7 was predicted using a thiamine phosphate pyrophosphatase from Pyrococcus furiosus (PDB ID: 1X13_A) as template. The active pockets of ligand binding sites in the enzyme were identified. In this study, phosphoryl thymidine kinase (thi E), a terminal enzyme in the thiamine biosynthesis pathway in the pathogen has been modeled to be used in future as a potential drug target by the design of suitable inhibitors.
 
The figure shows modeled structures of respective
domains of ppsD (A) Proline activase, (B) Glutamine activase,
(C) Tyrosine activase. Secondary structure elements are
highlighted in different colors. Image was generated using
UCSF Chimera.
Lipopeptides have a widespread role in different pathways of Bacillus subtilis; they can act as antagonists, spreader and immunostimulators. Plipastatin, an antifungal antibiotic, is one of the most important lipopeptide nonribosomly produced by Bacillus subtilis. Plipastatin has strong fungitoxic activity and involve in inhibition of phospholipase A2 and biofilm formation. For better understanding of the molecule and pathway by which lipopeptide plipastatin is synthesized, we present a computationally predicted structure of plipastatin using homology modeling. Primary and secondary structure analysis suggested that ppsD is a hydrophilic protein containing a significant proportion of alpha helices, and subcellular localization predictions suggested it is a cytoplasmic protein. The tertiary structure of protein (plipastatin synthase subunit D) was predicted by homology modeling. The results suggest a flexible structure which is also an important characteristic of active enzymes enabling them to bind various cofactors and substrates for proper functioning. Validation of 3D structure was done using Ramachandran plot ProsA-web and QMEAN score.This predicted information will help in better understanding of mechanisms underlying plipastatin synthase subunit D synthesis. Plipastatin can be used as an inhibitor of various fungal diseases in plants.
 
Output of BPROM tool sited at SoftBerry.  
A bacterial strain, designated AcBz01, was isolated from a water sample collected from Gomti River, Lucknow, India, and identified using a molecular approach. On the basis of the bacterial 16S rRNA gene sequence phylogeny and comparison of this gene sequence with sequences in Ribosomal Database project II, evidence given in this study, it is proposed that isolate is closely related to members of the genus Acinetobacter. Identification and annotation of regulatory elements in the 16S rRNA gene and characterization of their interaction with the respective transcription factor can provide basis for better understanding of the mechanism of network of gene interaction of functionally related genes. The identification of such sites is relevant for locating promoter boundary of a gene and it also allows the prediction of specific gene expression pattern and response to disturbances in a known signaling pathway. Computational identification of regulatory elements and Transcription Factor with their binding sites in 16S rRNA gene of Acinetobacter sp. was performed using BPROM tool. We predicted the regulatory elements are TSS, -10 box, -35 box and three Transcription Factor (narP, ompR and fadR) with their binding sites in the upstream region of 16S rRNA gene of Acinetobacter sp. AcBz01. The GenBank accession number for 16S rRNA gene of Acinetobacter sp. AcBz01 is EU931637.
 
Neighbor-joining tree of selected 16S rDNA gene sequence of the
genus Escherichia coli obtained from BLAST search of the strain BzDS03
sequence for phylogenetic inference.
Neighbor-joining tree of selected 16S-23S rDNA ITS region
sequence of the genus Escherichia coli obtained from BLAST search of the
strain BzDS03 sequence for phylogenetic inference.
A bacterial strain, designated BzDS03 was isolated from water sample, collected from Dal Lake Srinagar. The strain was characterized by using 16S ribosomal RNA gene and 16S-23S rRNA internal transcribed spacer region sequences. Phylogenetic analysis showed that 16S rRNA sequence of the isolate formed a monophyletic clade with genera Escherichia. The closest phylogenetic relative was Escherichia coli with 99% 16S rRNA gene sequence similarity. The result of Ribosomal database project's classifier tool revealed that the strain BzDS03 belongs to genera Escherichia.16S rRNA sequence of isolate was deposited in GenBank with accession number FJ961336. Further analysis of 16S-23S rRNA sequence of isolate confirms that the identified strain BzDS03 be assigned as the type strain of Escherichia coli with 98% 16S-23S rRNA sequence similarity. The GenBank accession number allotted for 16S-23S rRNA intergenic spacer sequence of isolate is FJ961337.
 
Neighbour-joining tree of selected 16S rRNA gene sequences of the genus Comamonas obtained from BLAST search of the Bz02 strain sequence for phylogenetic inference. 
A bacterial strain Bz02 was isolated from a water sample collected from river Gomti at the Indian city of Lucknow. We characterized the strain using 16S rRNA sequence. Phylogenetic analysis showed that the strain formed a monophyletic clade with members of the genus Comamonas. The closest phylogenetic relative was Comamonas testosteroni with 95% 16S rRNA gene sequence similarity. It is proposed that the identified strain Bz02 be assigned as the type strain of a species of the genus Comamonas (Comamonas sp Bz02) based on 16S rRNA gene sequence search in Ribosomal Database Project, small subunit rRNA and large subunit rRNA databases together with the phylogenetic tree analysis. The sequence is deposted in GenBank with the accession number FJ211417.
 
Identity of causative agent of rhinosporidiosis (Rhinosporidium seeberi) has been controversial since the disease was described in 1900. Extensive sequence alignments and phylogenetic analyses of 16S rRNA gene detected recently by us in R. seeberi , revealed 99% similarity with 16S rDNA in chloroplasts of flowering plants. Study demonstrates R. seeberi is a pigmented prokaryote displaying some characteristics of cyanobacteria, and contains 16S rDNA present in chloroplasts of all groups of land plants. This study and our recent publication of 2006 are the first molecular studies using purified organismal DNA extracted from R. seeberi free of infected tissue. Abbreviations RB - Round body
 
Figure1: (A): Structural organization of ribosomal operon depicting distal 5'region containing regulatory motifs; (B): nucleotide sequence of functional ORF; and (C): output file indicating the predicted promoter elements and transcription factor binding sites within 5' region of 16S rRNA gene of strain SJ-101. 
Multiple clustalW alignment of-35 box,-10 box, and Shine-Dalgarno (SD) sequence upstream of ORF identified within of 5' region of 16SrRNA gene of strain SJ-101. 
Multiple sequence alignments of putative ORF and its corresponding short peptide identified within 16SrRNA gene of strain SJ-101. 
Advancement in bioinformatics with the development of computational tools has enabled the in-silico prediction and identification of transcription regulatory factors and other genetic elements with great ease. In this study, computational analysis of sequence homology of 546 bp 5' region of 16SrRNA gene of Bacillus sp. strain SJ-101 resulted in identification of promoter-like sequences within the rrn gene. Using BPROM tool, the regulatory motifs like -35 and -10 boxes were mapped at 392 and 411 positions, respectively. Furthermore, the cis-acting elements as the binding sites for transcription factors (TF) cpxR and argR were identified at positions 413 and 416 at the upstream of an open reading frame (ORF). The probable functions of the putative TFs were predicted through the Uni-Prot/Swiss-Prot protein database. Search for the Shine-Dalgarno sequence (SD) found the presence of highly conserved SD sequence (AATACC), and a short 42 bp coding sequence/ORF bounded with characteristic transcription start site (AAC) and a stop codon (TGA) at positions 426 and 465 downstream to the promoter elements. A 13 amino acid long translation product of a short ORF has exhibited 100% homology with protein sequences of Bacillus spp., while showing some degree of polymorphism with other reference strains. The comparative homology of the small protein exhibited maximum similarity with Prolyl-4 hydroxylase of Chlamydomonas reinhardtii with 4.11 ZSCORE. The highly conserved regulatory elements and the putative ORF predicted within the 16SrRNA gene may help understand the role of relatively unexplored short ORFs within rrn operon, and their functional products in genetic regulatory mechanisms in eubacteria.
 
The dataflow diagram of 'lrest' database comprising with three tables 'fishinfo', 'estinfo' and 'analysis'.
Flowchart for our method explaining functional annotation of transcriptome.  
The output of`AlignmentAnalysisof`AlignmentAnalysispì perl script showing details on transcripts alignment statistics with database Refseq_RNA.  
The output of 'AlignmentAnalysis.pl' perl script showing details of transcripts alignment statistics with database Druniqdb (D. rerio dataset of UniGene).  
A total of 1671 ESTs of Labeo rohita were retrieved from dbEST database and analysed for functional annotation using various computational approaches. The result indicated 1387 non-redundant (184 contigs and 1203 singletons) putative transcripts with an average length of 542 bp. These 1387 transcript sequences were matched with Refseq_RNA, UniGene and Swiss-Prot on high threshold cut-off for functional annotation along with help of gene ontology and SSRs markers. We developed extensive Perl programming based modules for processing all alignment files, comparing and extracting common hits from all files on a threshold, evaluating statistics for alignment results and assigning gene ontology terms. In this study, 92 putative transcripts predicted as orthologous genes and among those, 44 putative transcripts were annotated with gene ontology terms. The annotated orthologous gene of our result associated with some very important proteins of L. rohita involved in biotic and abiotic stresses and glucose metabolism of spermatogenic cells etc. The unidentified transcripts, if found important in expression profiling can be vital resource after re-sequencing. The predicted genes can further be used for enhancing productivity and controlling disease of L. rohita.
 
Sperata aor commonly called as long- whiskered cat fish or “Bada Tengan” in local fish markets harboured one new and one previously known species of genus Thaparocleidus Jain, 1952, along with two species of Cornudiscoides Kulkarni, 1969, infesting gills. Thaparocleidus aori (Rizvi, 1971) Lim, 1996, was earlier described by Rizvi therefore was briefly recorded in the present study, except the egg. The newly found species Thaparocleidus susanae n.sp was characterized by the structure of its peculiar copulatory organ. Phylogenetic relationship of the two species under study, along with 14, reterived from GenBank was established using the sequences of 28S rDNA region (Dactylogyrus Diesing, 1850 taken as an out group).
 
Multiple sequence alignment in MULTALIN [Red color represents highly conserved residue; Blue color represents weakly conserved residue; A position with no conserved residue is represented by a dot in the consensus line; Symbols:! represents either I or V;# represents any one residue of NDQEBZ]. 
Secondary structure and secondary structure elements in wheat sHSP16.9 and corresponding residues in sHSP 18S and sHSP 18P. 
Structural Overlay of sHSP18P on sHSP18S. 
In this work we are proposing Homology modeled structures of Mycobacterium leprae 18kDa heat shock protein and its mutant. The more closely related structure of the small heat shock protein (sHSP) belonging to the eukaryotic species from wheat sHSP16.9 and 16.3kDa ACR1 protein from Mycobacterium tuberculosis were used as template structures. Each model contains an N-terminal domain, alpha-crystalline domain and a C-terminal tail. The models showed that a single point mutation from serine to proline at 52(nd) position causes structural changes. The structural changes are observed in N-terminal region and alpha-crystalline domains. Serine in 52(nd) position is observed in beta4 strand and Proline in 52(nd) position is observed in loop. The number of residues contributing alpha helix at N-terminal region varies in both models. In 18S more number of residues is present in alpha helix when compared to 18P. The loop regions between beta3 and beta4 strands of both models vary in number of residues present in it. Number of residues contributing beta4 strand in both models vary. beta6 strand is absent in both models. Major functional peptide region of alpha crystalline domains of both models varies. These differences observed in secondary structures support their distinct functional roles. It also emphasizes that a point mutation can cause structural variation.
 
A mutation was induced in Aspergillus niger wild strain using ethidium bromide resulting in enhanced expression of citric acid by three folds and 112.42 mg/mL citric acid was produced under optimum conditions with 121.84 mg/mL of sugar utilization. Dendograms of 18S rDNA and citrate synthase from different fungi including sample strains were made to assess homology among different fungi and to study the correlation of citrate synthase gene with evolution of fungi. Subsequent comparative sequence analysis revealed strangeness between the citrate synthase and 18S rDNA phylogenetic trees. Furthermore, the citrate synthase movement suggests that the use of traditional marker molecule of 18S rDNA gives misleading information about the evolution of citrate synthase in different fungi as it has shown that citrate synthase gene transferred independently among different fungi having no evolutionary relationships. Random amplified polymorphic DNA (RAPD-PCR) analysis was also employed to study genetic variation between wild and mutant strains of A. niger and only 71.43% similarity was found between both the genomes. Keeping in view the importance of citric acid as a necessary constituent of various food preparations, synthetic biodegradable detergents and pharmaceuticals the enhanced production of citric acid by mutant derivative might provide significant boost in commercial scale viability of this useful product. CS - Citrate synthase, CA - Citric acid, RAPD - Random amplified polymorphic DNA, TAF - Total amplified fragments, PAF - Polymorphic amplified fragments, CAF - Common amplified fragments.
 
The present study describes the molecular phylogenetic analysis of Dactylogyroides longicirrus (Monogenea: Dactylogyridae) infecting the gill filaments of fish Puntius sophore from the site Guwahati, Assam, India. The parasite Dactylogyroides longicirrus (Tripathi, 1959) Gusev, 1976 from Northeast Indian region is presented based on sequence data of a 738 base-pair fragment of ribosomal 18S small subunit and first internal transcribed spacer (ITS 1). Phylogenetic relationships were inferred using neighbour joning and maximum parsimony methods and the results support the validation of D. longicirrus. The study is also supported by secondary structure model prediction by using minimum free energy which can be considered a promising tool for monogenean species identification. This is the first report of this parasite from Northeast region of India, with this, the 18S and ITS 1 rDNA region amplified in the study is also the first sequence of the genus Dactylogyroides.
 
2D gel images of E.coli of E.coli nissle 1917 showing the protein expression when grown in the presence without metal i.e control; of E.coli nissle 1917 showing the differential protein expression when grown in the presence of 0.02 mM 
Zoomed 2D gels in specific derived from cells exposure to 0. 1917. (a) Hypothetical UPF0169 lipo protein Conserved domain protein; (c) 50S ribosomal protein L31 type B 1; (d) 50S ribosomal protein L3 1; transcriptional regulator yih W; Homology modelling of mercury stress expressed proteins Three homology models were obtained for the mercury stress proteins based on published X These include (i) β-lactamase protein (ii) Ribosomal L31 protein (iii) Yfio proteins. 
Differently expressed proteins in probiotic Escherichia coli nissle 1917 under mercury stress identified by using a proteomic approach. We applied to separate proteins by using two-dimensional gel electrophoresis and proteins were identified using MALDI-TOF-MS using PMF, by mascot database search using the NCBI database. we identified six proteins after exposure to mercury stress with respect to different functional classes. It is useful to understand the molecular insights into mercury stress in probiotic E. coli. Next we describe a structure generated by homology modelling and functional domain identification; it is interesting to study the impact of stress on protein structures. MS characterization and computational methods together provide the opportunity to examine the impact of stress arising from mercury. The role of these proteins in metal tolerance and structure relation is discussed. To the best of our knowledge, proteomics of E. coli nissle 1917 overview of mercury stress has been reported for the first time.
 
To understand the reported cross-reactivity of the 2009 H1N1 and the 1918 H1N1 pandemic viruses we docked the crystal structure of 2D1, an antibody derived from a survivor of the 1918 pandemic, to the structures of hemaglutinin (HA) of the 2009 strain and seasonal H1 vaccine strains. Our studies revealed that 2D1 binds to the 2009 HA at antigenic site ‘Sa’, with stabilizing contacts, similar to that in an available co-crystal structure of 2D1-1918 HA. However, 2D1 failed to bind to the known antigenic sites in the HAs of seasonal strains. Our study thus reveals the molecular basis for pre-existing immunity in elderly people to the 2009 pandemic virus.
 
The emergence of new strains of Influenza virus have caused several pandemics over the last hundred years with the latest being the H1N1 Swine flu pandemic of 2009. The Hemagglutinin (HA) protein of the Influenza virus is the primary target of human immune system and is responsible for generation of protective antibodies in humans. Mutations in this protein results in change in antigenic regions (antigenic drift) which consequently leads to loss of immunity in hosts even in vaccinated population (herd immunity). This necessitates periodic changes in the Influenza vaccine composition. In this paper, we investigate the molecular basis of the reported loss of herd immunity in vaccinated population (vaccine component: Influenza A/X-31/1968 (H3N2)) which resulted in the outbreak due to strain Influenza A/Port Chalmers/1/1973 (H3N2). Also, the effects of antigenic drift in HA protein (H3N2 vaccine strains 1968-2007) on the 3D structures as well as interactions with BH151, a 1968 antibody, has been studied. Rigid body molecular docking protocol has been used to study the antigen-antibody interactions. We believe that the present study will help in better understanding of host-pathogen interactions at the molecular level.
 
List of mutations in NA protein between successive strains 
Antigenic drift and shift involving the surface proteins of Influenza virus gave rise to new strains that caused epidemics affecting millions of people worldwide over the last hundred years. Variations in the membrane proteins like Hemagglutinin (HA) and Neuraminidase (NA) necessitates new vaccine strains to be updated frequently and poses challenge to effective vaccine design. Though the HA protein, the primary target of the human immune system, has been well studied, reports on the antigenic variability in the other membrane protein NA are sparse. In this paper we investigate the molecular basis of antigenic drift in the NA protein of the Influenza A/H3N2 vaccine strains between 1968 and 2009 and proceed to establish correlation between antigenic drift and antigen-antibody interactions. Sequence alignments and phylogenetic analyses were carried out and the antigenic variability was evaluated in terms of antigenic distance. To study the effects of antigenic drift on the protein structures, 3D structure of NA from various strains were predicted. Also, rigid body docking protocol has been used to study the interactions between these NA proteins and antibody Mem5, a 1998 antibody.
 
Modeled structure of HvPR-1a as visualized by Chimera 1.6.1. The structure has been formed of four α helices and four β strands. Strand D is antiparallel with strand B and C; and short strand A is parallel with strand B. Strands A and B connected to each other with helix II that is located under the β sheets. Helices III and I are parallel, located above the β-sheets and attached as horizontal and right angle related to β-strands. Helix IV located between helices I, III and β-strands. Locating helices in two sides of the beta plane provide a tight and stable folding for protein. N shows the N-terminal and C shows the Cterminal of the protein. C-terminal is longer because it contains CRISPs family signal motifs which are important for protein function. A 310-helix located just following the helix III compromising the residues 76, 77 and 78. Discussion: Assessment of resultant structure with several model evaluation tools demonstrated high quality of the model. Ramachandran plot of the structure showed that 93.9% of residues fell in most favorite regions, and 6.1% fell in additional allowed regions; none of the residues found in the generously allowed regions and disallowed regions. This validates the quality of modeled structure. Overall average G-factor of dihedral angles and main-chain covalent forces was -0.21 that was greater than acceptable cutoff -0.5. The G-factor provides a measure of the plausibility of a stereochemical property and a high G-factor means the property corresponds to a  
Sequence alignment between query and template. Query sequence has shown the highest similarity and identity with 1CFE sequence. These observations and belonging 1CFE to PR-1 group of proteins left only 1CFE as the best potential template.
3D modeled structure of SCP_CRISP region of helothermine protein (GenBank: AAC59730.1). This structure is compromised of four antiparallel β-strands and four α helices located above and below the β plane same as the HvPR-1a protein. A short α helix also located under the β-strands.  
Pathogenesis-related protein 1a of Hordeum vulgare subsp. Vulgare (HvPR-1a) is induced by various pathogens and stress related factors. It plays important roles in plant defense system. Since the discovery of HvPR-1a a great deal of research has been focused on its isolation and characterization. However, three dimensional structure of HvPR-1a is still unknown. 3D structure can be used for determining protein function, and identifying novel protein folds and potential targets for regulation. The protein model was developed using MODELLER 9v10. Physicochemical characterization and functional annotation of the model carried out with Expasy's ProtParam server and three different conserved domain finding programs including InterProScan, Proteins Families Database (Pfam), and NCBI Conserved Domains Database (NCBI-CDD). Applying validation programs revealed that the model has good quality and the RMSD value is 0.7. The predicted model submitted in Protein Model Database, PMDB for public use. This model will be used in wide range of studies for functional analysis and improvement activity of the protein.
 
Structures of the five lead molecules with their respective Ids. 
Results for the five lead molecules and 1,2,3,4-Tetrahydroisoquinolinyl sulfamic acid, obtained using UCSF DOCK 
Binding modes of the five potential ligands to the active site of PTPIB: (a) (1,2,3,4-Tetrahydroiso quinolinyl sulfamic acid, (b) ZINC12502589, (c) ZINC13213457, (d) ZINC25721858, (e) ZINC31392733 and (f) ZINC04096400 
Protein tyrosine phosphatase 1B (PTP1B) functions as major negative regulator of insulin and leptin signaling pathways. In view of this, PTP1B is an significant target for drug development against cancer, diabetes and obesity. The aim of the current study is to identify PTP1B inhibitors by means of virtual screening with docking. 523,366 molecules from ZINC database have been screened and based on DOCK grid scores and hydrogen bonding interactions five new potential inhibitors were identified. ZINC12502589, ZINC13213457, ZINC25721858, ZINC31392733 and ZINC04096400 were identified as potential lead molecules for inhibition of PTP1B. The identified molecules were subjected to Lipinski's rule of five parameters and found that they did not violate any rule. More specific analysis of pharmacological parameters may be scrutinized through a complete ADME/Tox evaluation. Pharma algorithm was used to Calculate ADME–Tox profiles for such molecules. In general, all the molecules presented advantages and as well as disadvantages when compared to each other. No marked difference in health effects and toxicity profiles were observed among these molecules.
 
Actelion property Explorer view for drug likeliness of ligand1.  
Multiple regression plot (Linear) of ten phenol compounds against MetAP of M. tuberculosis  
Residues of target docked by ligands (L-1 to L-3) and inhibitors (I-1 to I-10)  
Docking poses of Ligand L1 against MetAp in FlexX and Autodock 4.2. Analysis of result Table 3 showed that of all three ligands, ligand L1 is the best option for MetAP1b inhibition as it has better docking scores -37.5096, with least IC50 value of 4.46µM. While choosing best ligands, the least score in docking was preferred as it indicates more stability in binding [8]. Docking pattern of ligand L1 with the receptor is presented in (Figure 4). Potency of compounds in question has been calculated as inverse logarithm of IC50 for QSAR model.  
Ligandscout binding pattern of ligand1 with MetAp  
The advent of Multi Drug Resistant (MDR) strain of Mycobacterium tuberculosis (TB) necessitated search for new drug targets for the bacterium. It is reported that 3.3% of all new tuberculosis cases had multidrug resistance (MDR-TB) in 2009 and each year, about 0.44 million MDR-TB cases are estimated to emerge and 0.15 million people with MDR-TB die. Keeping such an alarming situation under consideration we wanted to design suitable anti tubercular molecules for new target using computational tools. In the work Methionine aminopeptidase (MetAP) of Mycobacterium tuberculosis was considered as target and three non-toxic phenolic=ketonic compounds were considered as ligands. Docking was done with Flex X and AutoDock 4.2 separately. Ten proven inhibitors of MetAP were collected from literature with their IC50 and were correlated using EasyQSAR to generate QSAR model. Activity of ligands in question was predicted from QSAR. Pharmacophore for each docking was generated using Ligandscout 3.0. Toxicity of the ligands in question was predicted on Mobyle@rpbs portal and Actelion property explorer. Molecular docking with target showed that of all three ligands, 3-ammonio-3-(4-oxido-1H-imidazol-1-ium-5-yl) propane-1, 1-bis (olate) has highest affinity (- 37.5096) and lowest IC50 (4.46 µM). We therefore, propose that -3-ammonio-3-(4-oxido-1H-imidazol-1-ium-5-yl) propane-1,1- bis(olate) as a potent MetAP inhibitor may be a new anti-tubercular drug particularly in the context of Multi Drug Resistant Tuberculosis (MDR-TB).
 
3-dimensional (3D) model of HIF1α and HIF1β (A) by using SWISS MODEL homology modelling, and the result of 3D structure validation using Ramachandran plot analysis (B).  
Erythropoietin (EPO) is a glycoprotein hormone that play a role as key regulator in the production of red blood cells. The promoter region of EPO is methylated in normoxic (non-hypoxia) condition, but not in hypoxic condition. Methylation of the EPO enhancer region decline the transcription activity of EPO gene. The aim of this study is to investigate how different methylation percentage affected on the regulation and transcriptional activity of EPO gene. The DNA sequence of erythropoietin gene and protein sequence was retrieved from the sequence database of NCBI. DNA structure was constructed using 3D-DART web server and modeling structure of HIF1 predicted using SWISS-MODEL web server. Methylated DNA sequence of EPO gene using performed with YASARA View software and docking of EPO gene and transcription factor HIF1 analyzed by using HADDOCK webserver. Our result showed that binding energy in 46% methylated DNA was higher (-161,45 kcal/mol) than in unmethylated DNA (-194,16 kcal/mol) and 8% methylated DNA (-175,94 kcal/mol). So, we presume that a silencing mechanism of the Epo gene by methylation is correlated with the binding energy, which is required for interaction. A higher methylation percentage correlates with a higher binding energy which can cause an unstable interaction between DNA and transcription factor. In conclution, methylation of promoter and enhancer region of Epo gene leads to silencing.
 
Figure1: Orientation of docked pose of (a) SC-558, (b) compound 3d, and (c) compound 7d (ball & stick) respectively in the active site of COX-2. All of hydrogen atoms have been removed to improve clarity.  
COX inhibitors which selectively inhibits the inducible COX-2 is an oenzyme that causes inflammation. They are clinically effective anti-inflammatory agents with less gastrointestinal and renal toxicity. However, they lack anti-thrombotic activity and hence lead to increased incidences of adverse cardiovascular trombotic events such as myocardial infarction. Therefore, there is still a need to develop better therapeutic effect and tolerability COX-2 inhibitor. The majority of COX-2 inhibitors are diaryl heterocycles. For optimum COX-2 selectivity and inhibitory potency a -SO(3)CH(3) or a- SO(2)NH(2) substituent at the para-position of phenyl ring was essential. A wide variety of heterocycles can serve as central ring system of the diaryl heterocycles structures. We report the screening of various 2,3-disubstituted-4(3H)-quinazolinones possessing benzenesulfonamide moiety, directly or indirectly bound to the ring system, using the Protein-Ligand ANT System (PLANTS) docking software against the COX-2 enzyme. Various molecular structures of ligands were docked and scored to identify structurally similar ligands to SC-558 (reference ligand) in binding interaction to COX-2 binding site. The results show that 2,3-disubstituted-4(3H)-quinazolinones possess pbenzenesulfonamide moiety at C-2, and phenyl moiety at N-3 binds directly or indirectly to the ring system with high binding affinity. The docked ligand has orientations similar to that observed with SC-558 satisfying Lipinski's rule of five.
 
Tregs/TH17 Modulatory Balance in H1N1 Infection. (a) Cellular
immune surveillance to H1N1 infection engages the release of a spectrum of
cytokines (IFN-γ, TNF-α, IL015, IL-12p70, IL-8, IL-9, IL-6, IL-21, and TGF-
β) within the microenvironment [7,
11], which act in concert to regulate T cell
subset activation, maturation and differentiation. TGF-β plays a critical role in
the regulation of both TH17 and Tregs (CD4+CD25+FoxP3+), which blunt T
cell activation and TH17 generation and activity. This dual signaling function
of TGF-β suggests that the ultimate balance between these subsets in cellular
immune surveillance to influenza is likely due to epigenetic factors in the
microenvironment [11] 
such as consequential to, but not limited to pregnancy
[12] and immune senescence 
[10]. (b) While the proportion of TH17 cells may
be relatively low in influenza patients, compared to control subjects, the
secretion of TH17 and TH1 cytokines is vigorous, and characteristically the
reported cytokine “storms” [7]. 
(c) The cytokine “storms” cascade leads to an
increase in CD8+CD38+ CTL's, whose number and proportion correlate with
the stage of infection, as they are responsible for the elimination of virally
infected host cells.
Influenza A virus is a serious public health threat. Most recently the 2009/H1N1 pandemic virus had an inherent ability to evade the host's immune surveillance through genetic drift, shift, and genomic reassortment. Immune characterization of 2009/H1N1 utilized monoclonal antibodies, neutralizing sera, and proteomics. Increased age may have provided some degree of immunity, but vaccines against seasonal influenza viruses seldom yield cross-reactive immunity, exemplified by 2009/H1N1. Nonetheless, about 33% of individuals, over the age of 60, had cross-reactive neutralizing antibodies against 2009/H1N1, whereas only 6-9% young adults had these antibodies. Children characteristically had no detectable immunity against 2009/H1N1. Taken together, these observations suggest some degree of immune transference with at least certain strains of virus that have afflicted the human population in past decades. Because internal influenza proteins may exhibit less antigenic variation, it is possible that prior exposure to diverse strains of influenza virus provide some immunity to novel strains, including the recent pandemic strain (swine-avian A/H1N1). Current trends in immunological studies - specifically the modulation of cellular immune surveillance provided by TH17 and Tregs - also support the need for additional proteomic research for characterizing novel translational evidence-based treatment interventions based on cytokine function to help defeat the virus. Timely and critical research must characterize the impact of genetics and epigenetics of oral and systemic host immune surveillance responses to influenza A virus. The continued development and application of proteomics and gene expression across viral strains and human tissues increases our ability to combat the spread of influenza epidemics and pandemics.
 
Distribution of amino acid substitutions (AASs) from 2009 pandemic AH1N1 human influenza virus NA by active site and catalytic site. ( †) Potentially resistant AASs. (*) Confirmed resistant AASs. The number of AASs reported in each section is indicated with a gray bar. Circle color indicates residues that interact with oseltamivir (O, light blue), zanamivir (Z, light green) and sialic acid (S, black). Catalytic residues shown in red rectangles indicate direct contact with sialic acid (substrate). Based on Liu et al [34], the principal binding energy contribution for each site associated with an influenza drug or substrate is indicated with letters Z, O, and S. 
The pandemic influenza AH1N1 (2009) caused an outbreak of human infection that spread to the world. Neuraminidase (NA) is an antigenic surface glycoprotein, which is essential to the influenza infection process, and is the target of anti-flu drugs oseltamivir and zanamivir. Currently, NA inhibitors are the pillar pharmacological strategy against seasonal and global influenza. Although mutations observed after NA-inhibitor treatment are characterized by changes in conserved amino acids of the enzyme catalytic site, it is possible that specific amino acid substitutions (AASs) distant from the active site such as H274Y, could confer oseltamivir or zanamivir resistance. To better understand the molecular distribution pattern of NA AASs, we analyzed NA AASs from all available reported pandemic AH1N1 NA sequences, including those reported from America, Africa, Asia, Europe, Oceania, and specifically from Mexico. The molecular distributions of the AASs were obtained at the secondary structure domain level for both the active and catalytic sites, and compared between geographic regions. Our results showed that NA AASs from America, Asia, Europe, Oceania and Mexico followed similar molecular distribution patterns. The compiled data of this study showed that highly conserved amino acids from the NA active site and catalytic site are indeed being affected by mutations. The reported NA AASs follow a similar molecular distribution pattern worldwide. Although most AASs are distributed distantly from the active site, this study shows the emergence of mutations affecting the previously conserved active and catalytic site. A significant number of unique AASs were reported simultaneously on different continents.
 
NJ plot was made for all the 8 segments of selected influenza viruses using boot strap analyses at 500 replicates. (5) Nucleocapsid Protein,
NJ plot was made for all the 8 segments of selected influenza viruses using boot strap analyses at 500 replicates. (6) Neuraminidase
Since April 2009, a serious pandemic infection has been rapidly spread across the world. These infections are caused due to the novel swine origin influenza A (H1N1) virus and hence these are commonly called as “Swine Flu”. This new virus is the reassortment of avian, human and swine influenza viruses and thus it has a unique genome composition. There are 16 different types of hemagglutinin (HA) and 9 different types of neuraminidase (NA) that can be genetically and antigenetically differentiated. The first influenza A virus isolated from pigs was of the H1N1 subtype and these viruses have been reported to cause infection in pigs in many countries. The outbreak of this virus has been transmitted from pigs to humans. This new reassorted (exchange of genes) virus which is the cause of 2009 pandemic infections has the ability to spread from human to human. This spread of infection should be brought to an end. In this study, a phylogenetic analysis of the nucleotide sequences of the RNA segments of human H1N1 viruses was carried using MEGA version 4.0 to demonstrate the route map of infection to India. Phylogenetic analysis of the sequences from India, published in Influenza Virus Resource (a database that integrates information gathered from the Influenza Genome Sequencing Project of the National Institute of Allergy and Infectious diseases (NIAID) and the genbank of the (NCBI)) was retrieved and used for the analysis. The results showed that the various segments of the Indian isolates clustered well with the sequences from American, Asian and European countries and thus indicating the transmission of viruses from these places to India.
 
Swine Influenza Virus (H1N1) is a known causative agent of swine flu. Transmission of Swine Influenza Virus form pig to human is not a common event and may not always cause human influenza. The 2009 outbreak by subtype H1N1 in humans is due to transfer of Swine Influenza Virus from pig to human. Thus to analyze the origin of this novel virus we compared two surface proteins (HA and NA) with influenza viruses of swine, avian and humans isolates recovered from 1918 to 2008 outbreaks. Phylogenetic analyses of hemagglutinin gene from 2009 pandemic found to be clustered with swine influenza virus (H1N2) circulated in U.S.A during the 1999-2004 outbreaks. Whereas, neuraminidase gene was clustered with H1N1 strains isolated from Europe and Asia during 1992-2007 outbreaks. This study concludes that the new H1N1 strain appeared in 2009 outbreak with high pathogenicity to human was originated as result of re-assortment (exchange of gene). Moreover, our data also suggest that the virus will remain sensitive to the pre-existing therapeutic strategies.
 
Physicochemical analysis on lovastatin biosynthetic cluster proteins. The graph shows the correlation observed in aliphatic, instability index and molecular weight of lovastatin biosynthetic cluster proteins. 
Modelled structure for unknown protein sequence with accession number gi|4959959. The unknown protein sequence of accession number gi|4959959 is modeled using Modeller and the function is predicted as beta-Nacetylhexosaminidases based on structural similarity. The N-glycosylation sites are represented by shaded regions in sequence and as stick in the 3-D structure. 
Aspergillus terreus is a filamentous ascomycota, which is prominent for its production of lovastatin, an antihypercholesterolemic drug. The commercial importance of lovastatin with annual sales of billions of dollars made us to focus on lovastatin biosynthetic cluster proteins. The analysis of these lovastatin biosynthetic cluster proteins with different perspectives such as physicochemical property, structure based analysis and functional studies were done to find out the role and function of every protein involved in the lovastatin biosynthesis pathway. Several computational tools are used to predict the physicochemical properties, secondary structural features, topology, patterns, domains and cellular location. There are 8 unidentified proteins in lovastatin biosynthetic cluster, in which 6 proteins have homologous partners, and annotation transfer is done based on the closely related homologous genes, and their structures are also modeled. The two other proteins that do not have homologous partners are predicted as PQ loop repeat protein that may be involved in glycosylation machinery and as thiolase-acyl activity by the integrated functional analysis approach.
 
Effect Size [(Condition-control)/ Std. Dev.] of genes allocated to Chromosome 22. Results: 190 genes, previously shown to be significantly expressed across HAD/HIVE, HAD alone, and HIVE alone vs. HIV+ only, had known locations on 23 human chromosomes. The result of gene allocation to chromosome is shown in Table 1 (see Supplementary material). Only chromosome 22 demonstrated a nonstochastic number of ascribed genes (p ≤ 0.0001).Six genes identified on chromosome 22 are CSNK1E (casein kinase 1 epsilon), DGCR8 (Di George syndrome critical region 8), GGA1 (Golgi associated gamma adapt in ear containing ARF binding protein 1), MAPK11 (mitogen activated protein kinase 11), SMCR7L (Smith-Magenis syndrome chromosome region candidate 7like), andTBC1D22A (TBC1 domain family member 22A). One gene ascribed to chromosome 22 was unidentified. The array responses of the seven genes allocated to chromosome 22 across HAD/HIVE, HAD, and HIVE vs. HIV+, 
Pathways interconnecting 6 genes CSNK1E, DGCR8, GGA1, MAPK11, SMCR7L, and TBC1D22A as well as 69 additional nearest neighbor gene interactions. 
We analyzed RNA gene expression in neurons from 16 cases in four categories, HIV associated dementia with HIV encephalitis (HAD/HIVE), HAD alone, HIVE alone, and HIV-1-positive (HIV+)with neither HAD nor HIVE. We produced the neurons by laser capture microdissection (LCM) from cryopreserved globus pallidus. Of 55,000 gene fragments analyzed, expression of 197 genes was identified with significance (p = 0.005).We examined each gene for its position in the human genome and found a non-stochastic occurrence for only seven genes, on chromosome 22. Six of the seven genes were identified, CSNK1E (casein kinase 1 epsilon), DGCR8 (Di George syndrome critical region 8), GGA1 (Golgi associated gamma adaptin ear containing ARF binding protein 1), MAPK11 (mitogen activated protein kinase 11), SMCR7L (Smith-Magenis syndrome chromosome region candidate 7-like), andTBC1D22A (TBC1 domain family member 22A). Six genes (CSNK1E, DGCR8, GGA1, MAPK11, SMCR7L, and one unidentified gene) had similar expression profiles across HAD/HIVE, HAD, and HIVE vs. HIV+ whereas one gene (TBC1D22A) had a differing gene expression profile across these patient categories. There are several mental disease-related genes including miRNAs on chromosome 22 and two of the genes (DGCR8 and SMCR7L) identified here are mental disease-related. We speculate that dysregulation of gene expression may occur through mechanisms involving chromatin damage and remodeling. We conclude that the pathogenesis of NeuroAIDS involves dysregulation of expression of mental disease-related genes on chromosome 22 as well as additional genes on other chromosomes. The involvement of these genes as well as miRNA requires additional investigation since numerous genes appear to be involved.
 
In vivo overexpression of the ATP sulfurylase from A.
ferrooxidans 23270 in E. coli. The molecular weight standard is
indicated on the left in kilodaltons. 1 and 2, total protein
extracts of E. coli BL21 Start (DE3) with and without IPTG, 4 and
6, induction of protein expression of the ATP sulfurylase in
recombinant clones BL21-22 and BL21-42 containing the atpS
gene with histidine tail. The recombinant plasmids were used to
transform the E. coli BL21 Star (DE3) strain. In the logarithmic
growth phase, strains were grown in the presence (2, 4 & 6) or
absence (1, 3 and 5) of 1 mM IPTG for 3 h. Samples of total
protein (1 to 6) were separated by SDS-polyacrylamide
electrophoresis and stained with Coomassie blue. The right
arrow indicates the band corresponding to the induction of
ATPS protein bind to 6xHis at the C-terminal domain.
Multiple alignment of the APS kinase domain of ATPS from A. ferrooxidans (CAQ76453) and A. aeolicus (2GKS) with the
APS kinase (APSK) from P. chrysogenum (1M7H), S. cerevisiae (CAA46252) and St. epidermidis (Q5HL02). Identical amino acids
(black) and similar (gray) are indicated. The arrow indicates the conserved component of the ATPS from A. ferrooxidans:
487DPKGLYAKAVRGEITGFTGVD507. The black square indicates a P-loop region of the APS kinase that has identical sequence
GLSASGKST in the ATPS from A. ferrooxidans.
Structural alignment of the ATPS from A. ferrooxidans (CAQ76453) with ATPS of A. aeolicus (MMDB: ID44452; PDB:
2GKS). a) Active site of the ATS domain with an ADP molecule, and b) most important amino acid residues of the active site for
function and binding nucleotides are marked with numbers in the ATPS sequence from A. ferrooxidans. The molecule in sky-blue is
ADP. Identical amino acids are shown in red and similar ones in blue. The HXXH motif (in gray) stabilizes PPi and QXRN motif (in
yellow) is the catalytic motif. Residues R267, H269 and Y307 (in green) are joined with the ATP.
Comparative structural alignment of the ASK domain of ATPS from A. ferrooxidans (CAQ76453) with: a) ASK domain of
ATPS from A. aeolicus (MMDB ID 44452, PDB: 2GKS_A); b) APS kinase from P. chrysogenum (MMDB ID: 21216, PDB: IM7G_A). It is
shown the catalytic site of APS kinase domain with the P-loop motif (yellow). Red color indicates identical amino acids and blue
indicates similar ones blue in the activity of true APS kinase. In a) the molecule lies in the ADP and in b) it does in the ATP (in sky blue).
The numbering is based on the sequence of ATPS from A. ferrooxidans.
Molecular studies of enzymes involved in sulfite oxidation in Acidithiobacillus ferrooxidans have not yet been developed, especially in the ATP sulfurylase (ATPS) of these acidophilus tiobacilli that have importance in biomining. This enzyme synthesizes ATP and sulfate from adenosine phosphosulfate (APS) and pyrophosphate (PPi), final stage of the sulfite oxidation by these organisms in order to obtain energy. The atpS gene (1674 bp) encoding the ATPS from Acidithiobacillus ferrooxidans ATCC 23270 was amplified using PCR, cloned in the pET101-TOPO plasmid, sequenced and expressed in Escherichia coli obtaining a 63.5 kDa ATPS recombinant protein according to SDS-PAGE analysis. The bioinformatics and phylogenetic analyses determined that the ATPS from A. ferrooxidans presents ATP sulfurylase (ATS) and APS kinase (ASK) domains similar to ATPS of Aquifex aeolicus, probably of a more ancestral origin. Enzyme activity towards ATP formation was determined by quantification of ATP formed from E. coli cell extracts, using a bioluminescence assay based on light emission by the luciferase enzyme. Our results demonstrate that the recombinant ATP sulfurylase from A. ferrooxidans presents an enzymatic activity for the formation of ATP and sulfate, and possibly is a bifunctional enzyme due to its high homology to the ASK domain from A. aeolicus and true kinases.
 
Species of the monogenean genus Thaparocleidus are specific to freshwater siluriform fish. The infection caused by these gill parasites are a major health problem to fish. But, to focus the control strategies of these parasites, first it is important to establish an accurate discrimination by molecular methods. In the present study, phylogenetic and structural analysis of 28S region of ribosomal DNA of T. wallagonius species collected from fish Wallago attu from Meerut (U.P.), India, was carried out. In the first step, we amplified, sequenced 28S region of ribosomal DNA of T. wallagonius to establish the phylogenetic relationship with other species of this genus. T. wallagonius found on gill filaments of fish W. attu, is the most primitive parasite of this genus from India, was unequivocally discriminate from other species of the same genus in this study. A secondary-structure model of the large subunit rDNA was also predicted using a combined comparative and thermodynamic approach. Molecular morphometric and phylogenetic relationship of T. wallagonius are discussed in detailed that based on molecular analysis using bioinformatic tools.
 
The three dimensional structure of 2CA1P inhibitor (a) shows in stick conformation (b) show in ball and stick (colored by CPK).  
Comparison between hydrogen bonding interactions of X-ray structure 2CABP and docked 2CABP at the active site of RubisCO
The binding modes of the 2CA1P in the active site of Rubisco; the three highest fitness score represented in a, b, c (65.71, 64.72, and 62.04 respectively) and d Superposition between the active site of rubisco before (colored green) and after (colored bleu light) the docking of the inhibitor 2CABP (Stick).  
Ribulose-1, 5- Bisphosphate carboxylase/ oxygenase (RubisCO) catalyzes the first step in net photosynthetic assimilation and photorespiratory carbon oxidation. The activity of this enzyme is modulated in response to changes in light intensity as suggested in a number of early reports. Several studies found that the natural inhibitor 2CA1P is involved in the inhibition of the enzyme under reduced light intensity in rice (Oryza sativa). Due to the lack of studies and information on the interaction between this inhibitor and the active site of the enzyme, we attempted to predict the interaction between the amino acids in the active site and the inhibitor using both Hyperchem7.5 and GOLD software. After the docking; three possibilities having the highest fitness score were found (65.71, 64.72, 62.04), in these possibilities the inhibitor was bound to the enzyme, the phosphate and carboxylate groups in the same positions with a clear difference in the position of OH. In order to confirm the accuracy of the genetic algorithm, the artificial inhibitor 2CABP was docked back in the active site of the enzyme using the same parameters used in the case of the 2CA1P and the algorithm's predictions were compared with the experimentally observed binding mode. The results showed that the difference in the active sites before and after the docking was in the range of 0.93 A which indicated that the results were very accurate. Depending on this result it was concluded that the results obtained in the case of the 2CA1P were close to the experimental results.
 
Image analysis of two-dimensional gel electrophoresis is a key step in proteomic workflow for identifying proteins that change under different experimental conditions. Since there are usually large amount of proteins and variations shown in the gel images, the use of software for analysis of 2D gel images is inevitable. We developed open-source software with graphical user interface for differential analysis of 2D gel images. The user-friendly software, RegStatGel, contains fully automated as well as interactive procedures. It was developed and has been tested under Matlab 7.01. Availability The database is available for free at http://www.mediafire.com/FengLi/2DGelsoftware
 
Identification of exons covering amino acid sequences (Html and text format) (Protein ID: 2K05; mRNA ID: NM_001710) Primary (first line)-amino acid sequence, Secondary (second line)-secondary structure identifier, Exon (third line)-exon identifier. 
Exons visualisation covering protein structure (structure ID: 2K05; mRNA ID: NM_001710) in PayMOL; exon0-amino acid originates from two different exons; exson1is cut in the process of post-translational modifications thus does not appear in the functional protein; exon2-exon18-exons coded 2K05 protein 
Unlabelled: The web application oriented on identification and visualization of protein regions encoded by exons is presented. The Exon Visualiser can be used for visualisation on different levels of protein structure: at the primary (sequence) level and secondary structures level, as well as at the level of tertiary protein structure. The programme is suitable for processing data for all genes which have protein expressions deposited in the PDB database. The procedure steps implemented in the application: I) loading exons sequences and theirs coordinates from GenBank file as well as protein sequences: CDS from GenBank and aminoacid sequence from PDB II) consensus sequence creation (comparing amino acid sequences form PDB file with the CDS sequence from GenBank file) III) matching exon coordinates IV) visualisation in 2D and 3D protein structures. Presented web-tool among others provides the color-coded graphical display of protein sequences and chains in three dimensional protein structures which are correlated with the corresponding exons. Availability: http://149.156.12.53/ExonVisualiser/
 
Biological activity data and calculated -Log value for compounds 
A quantitative structure activity relationship study was performed on different groups of anti-tuberculosis drug compound for establishing quantitative relationship between biological activity and their physicochemical /structural properties. In recent years, a large number of herbal drugs are promoted in treatment of tuberculosis especially due to the emergence of MDR (multi drug resistance) and XDR (extensive drug resistance) tuberculosis. Multidrug-resistant TB (MDR-TB) is resistant to front-line drugs (isoniazid and rifampicin, the most powerful anti-TB drugs) and extensively drug-resistant TB (XDR-TB) is resistant to front-line and second-line drugs. The possibility of drug resistance TB increases when patient does not take prescribed drugs for defined time period. Natural products (secondary metabolites) isolated from the variety of sources including terrestrial and marine plants and animals, and microorganisms, have been recognized as having antituberculosis action and have recently been tested preclinically for their growth inhibitory activity towards Mycobacterium tuberculosis or related organisms. A quantitative structure activity relationship (QSAR) studies were performed to explore the antituberculosis compound from the derivatives of natural products . Theoretical results are in accord with the in vitro experimental data with reported growth inhibitory activity towards Mycobacterium tuberculosis or related organisms. Antitubercular activity was predicted through QSAR model, developed by forward feed multiple linear regression method with leave-one-out approach. Relationship correlating measure of QSAR model was 74% (R(2) = 0.74) and predictive accuracy was 72% (RCV(2) = 0.72). QSAR studies indicate that dipole energy and heat of formation correlate well with anti-tubercular activity. These results could offer useful references for understanding mechanisms and directing the molecular design of new lead compounds with improved anti-tubercular activity. The generated QSAR model revealed the importance of structural, thermodynamic and electro topological parameters. The quantitative structure activity relationship provides important structural insight in designing of potent antitubercular agent.
 
'Conserved hypothetical' proteins pose a challenge not just for functional genomics, but also to biology in general. As long as there are hundreds of conserved proteins with unknown function in model organisms such as Escherichia coli, Bacillus subtilis or Saccharomyces cerevisiae, any discussion towards a 'complete' understanding of these biological systems will remain a wishful thinking. Insilico approaches exhibit great promise towards attempts that enable appreciating the plausible roles of these hypothetical proteins. Among the majority of genomic proteins, two-thirds in unicellular organisms and more than 80% in metazoa, are multi-domain proteins, created as a result of gene duplication events. Aromatic ring-hydroxylating dioxygenases, also called Rieske dioxygenases (RDOs), are class of multi-domain proteins that catalyze the initial step in microbial aerobic degradation of many aromatic compounds. Investigations here address the computational characterization of hypothetical proteins containing Ferredoxin and Flavodoxin signatures. Consensus sequence of each class of oxidoreductase was obtained by a phylogenetic analysis, involving clustering methods based on evolutionary relationship. A synthetic sequence was developed by combining the consensus, which was used as the basis to search for their homologs via BLAST. The exercise yielded 129 multidomain hypothetical proteins containing both 2Fe-2S (Ferredoxin) and FNR (Flavodoxin) domains. In the current study, 17 proteins with N-terminus FNR domain and C-terminus 2Fe-2S domain are characterized, through homology modelling and docking exercises which suggest dioxygenase activity indicate their plausible roles in degradation of aromatic moieties.
 
Correlation between monomer length (ML) and subunit interface area (B/2) for three groups of homodimers. 2S: two-state; 3SDI: three-state with dimeric intermediate; 3SMI: three-state with monomeric intermediate. The two dash lines through 185 aa and 1424Å 2 represent mean monomer length and mean B/2 for all homodimers, respectively. They classify the dimers into four regions (G1, G2, G3 and G4). The distributions of 2S, 3SDI and 3SMI dimers are given for each region. The value within parentheses is hydrophobicity factor (F hp ), calculated by the equation (H inf-H surf )/(H int-H surf ), where H inf is interface hydrophobicity, H int is interior hydrophobicity and H surf is surface hydrophobicity. 
The formation of homodimer complexes for interface stability, catalysis and regulation is intriguing. The mechanisms of homodimer complexations are even more interesting. Some homodimers form without intermediates (two-state (2S)) and others through the formation of stable intermediates (three-state (3S)). Here, we analyze 41 homodimer (25 `2S` and 16 `3S`) structures determined by X-ray crystallography to estimate structural differences between them. The analysis suggests that a combination of structural properties such as monomer length, subunit interface area, ratio of interface to interior hydrophobicity can predominately distinguish 2S and 3S homodimers. These findings are useful in the prediction of homodimer folding and binding mechanisms using structural data.
 
Phylogenetic analysis of EPR proteins. Only those EPR sequences that possess carboxyl-end terminal motif X2CWX are used to align and construct the neighbor-joining tree. Each OTU is represented by the binomial name and the genbank accession number of the sequence. Bootstrap values (1000 replications) are shown on the nodes. Grouping of monocots is indicated by the green lines. 
Is EPR protein a lectin-like protein? (a) The cartoon representation of EPR protein marked with conserved domains (in red color) and structural pockets (in blue color). Functional pockets (red balls surrounded by red colored probes) that are putatively calcium-binding overlap with conserved domains as well as structural pockets. (b) Calcium binding domains of EPR protein and a legume lectin. (c) It is the same region (functional pockets 1 and 2, see Figure 4) that aligns with a plant lectin (blue frame). 
Eicosapenta peptide repeats (EPRs) occur exclusively in flowering plant genomes and exhibit very high amino acid residue conservation across occurrence. DNA and amino acid sequence searches yielded no indications about the function due to absence of similarity to known sequences. Tertiary structure of an EPR protein coded by rice (Oryza sativa japonica) cDNA (GI: 32984786) was determined based on ab initio methodology in order to draw clues on functional significance of EPRs. The resultant structure comprised of seven α-helices and thirteen anti-parallel β-sheets. Surface-mapping of conserved residues onto the structure deduced that (i) regions equivalent to β α4- the primary function of EPR protein could be Ca2+ binding, and (iii) the putative EPR Ca2+ binding domain is structurally similar to calcium-binding domains of plant lectins. Additionally, the phylogenetic analysis showed an evolving taxa-specific distribution of EPR proteins observed in some GNA-like lectins.
 
Medicinal plants used to treat hypoglycemic and hyperglycemic conditions are of considerable interest to ethno-botanical community as they are recognized to contain valuable medicinal properties in different parts of the plant. The active principles of many plant species with desired properties are isolated to cure ailments such as diabetes type-1 and type-2, respectively. Here, we describe DiaMedBase, a database containing information of medicinal plants for diabetes. Availability http://www.progenebio.in/DMP/DMP.htm
 
Details of the primers used in this study 
A) Phylogram analysis using using Maximum likelihood for 16s rDNA sequence of B.t.LDC-391. *B.anthricis strains. #pathogenic B.cereus strain. Bootstrap values indicated at the nodes. Scale bar indicates no.of substittions per site; B) 
An indigenous Bacillus thuringiensis strain B.t.LDC-391 producing cytocidal proteins against human colon cancer cell line, HCT-116, was subjected to phenotypic and genotypic characterization to evaluate its relatedness to B.anthracis. The morphological features of this strain were meta-analyzed with data of other parasporin and insecticidal protein producing Bacillus thuringiensis strains. The conventional biochemical analysis and antibiotic sensitivity test proved it as an ampicillin resistant which is a salient feature, absent in B.anthracis Ames. PCR analysis showed the absence of cyt and parasporin related genes in the genome of B.t.LDC-391. But the strain was positive for cap gene. The sequencing and bio-informatic analysis of cap gene and 16S rDNA of B.t.LDC-391 placed it closer to B.thuringiensis and revealed significant divergence from that of any B.anthracis strain. However our strain lacked β– hemolysis on human erythrocytes which is a common feature of B.anthracis strains and parasporin producers.
 
Top-cited authors
Matthias Futschik
  • Universidade do Algarve
Lokesh Kumar
Anuraj Nayarisseri
  • EMINENT BIOSCIENCES
Peter Natesan Pushparaj
  • King Abdulaziz University
Francesco Chiappelli
  • University of California, Los Angeles