Lung cancer is a disease of uncontrolled cell growth in tissues of the lung. This growth may lead to metastasis, which is the invasion of adjacent tissue and infiltration beyond the lungs. The vast majority of primary lung cancers are carcinomas of the lung, derived from epithelial cells. Therefore, the present study is aimed at detecting the highly expressed genes, responsible for lung cancer through Serial Analysis of Genome Expression (SAGE) Genie at Cancer Genome Anatomy Project (CGAP). IGL@ (Immunoglobulin lambda locus) gene is predominantly highly expressed in the lung cancer and is considered to be a new target for the Cancerous diseases. The protein was retrieved from the Swissprot/Uniprot KB with accession number Q6GMX3 and was modelled using MODELLER9v7 for predicting the 3D structure of the IGL @ protein which provides an accurate and efficient module to build loops and side chains, found to be identical in sequence. Modelled structure revealed appreciable measures when subjected to structure verification and evaluation using PROCHECK. Ramachandran plot signified the present work undertaken through conformational parameters ? (phi) and ? (psi) angles calculated from model with 93.4% residues in most favoured region. Further, PROCHECK results confirmed acceptance of model through main and side-chain values. Root mean square distance of planarity was found below 0.02. Hence the model was revealed to have good stereochemistry. Structure of IGL@ Protein can be important tool for future endeavours towards structure based drug designing techniques to impel the search of new efficient inhibitors.

One of the major tasks carried by biologist today is to understand the nature of proteins. How this large protein molecule folds themselves into some form and carryout the prescribed biochemical reactions. Hydrophobic interaction is the dominant force towards this task. To understand this interaction, a simple statistical analysis on the contribution of hydrophobic residues was carried out. Large Hydrophobic Residues (LHR) such as Phenylalanine (F), Isoleucine (I), Leucine (L), Methionine (M) and Valine (V) – (FILMV) as well as small hydrophobic residues (SHR) Glycine (G), Alanine (A), Proline (P), Cysteine (C) and Tryptophan (W) - (GAPCW) were studied in all proteins of given organisms. The organisms include Homo sapiens, Macaca Mullatta, Pan troglodytes, Canis familiaris, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus, Drosophila melonogaster, Monodelphis domestica, Danio rerio, Stronglycentrolus purpuratus, Anopheles gambiae, Apis mellifera, Arabidopsis thaliana, Tribolium castaneum, Saccharomyces cerevisae, Schizosaccharomyces pombe and Caenorhabditis elegans. It is observed that the protein prefers to have 27% large hydrophobic residues to maintain the required hydrophobicity. In animal, particularly in human, it is observed less. It is interesting to note that small hydrophobic residues balance this lack in number by a factor of 1:3. So is the reason why the length of the animal proteins increases. This new finding on the contribution of hydrophobic residues in protein stability will be discussed in detail.

N-Oxides were found to have antimicrobial activity. In continuation of our work on synthesis, characterization and biological activities (in vitro method) of N-Oxides and knowing their biological activities against micro organisms, we have correlated the biological activity of these N-Oxides against the micro organisms like Staphylococcus aureus, Salmonella typhi “H”, Escherichia Coli, Pseudomonas aeruginosa, Klebsiella aerogenes, Enterobacteraerogenes, Citrobacter, Staphylococcus epidermidis, and Aeromonas hydrophila by Insilico method. The target molecules (microorganism) were taken from Protein data bank. Various soft wares were used to find out the drug likeness properties of these N-Oxides. Online software “Molinspiration” was used to calculate log P (ie) Hydrophobicity of a drug. ACD/ Chemsketch was used to draw the structures of N-Oxides. Hex 4.2, docking software was used to predict the drug activities of these N-Oxides. The drug activities were measured in terms of drug likeness property by recording the E-Total value and compared with the marketed standard drugs for the above micro organism infections. Standard drugs were taken from drug bank. As per the standard norms, it was observed that the compounds that have negative E-Total values could be used as a drug. We have selected Ceftazidime ,Cefepime and Ceftizoxime as standard drugs among the available drugs for these microorganism for correlating the drug activities of these N-Oxides. We observed that some of our N-Oxides were found to have higher drug activities compared to standard drugs.

To understand the tempo and mode of evolution at the nucleotide level it is important to estimate the spontaneous rate of each mutation type. Many molecular evolutionary studies have concluded that due to the greater number of cell divisions in the male germline than in the female germline, replication-based nucleotide substitutions in primates occur more frequently in males than in females. However, a potential sex bias in mutations other than nucleotide substitutions has not been extensively investigated. The human Alu repeats provide an ideal mechanism to further investigate the degree of replication-based indel (insertion and deletion) mutations in the human chromosomes. Results: We analyze patterns of small indel mutations (1bp) in the middle poly (A) track of Alu repeats across the entire human genome in order to elucidate the processes of mutation and fixation. This analysis adds further support for the accumulation of more mutations in the Y chromosome compared to the X chromosome. We report the male-to-female mutation ratio α in humans as ~1.5. Conclusion: Our results suggest that although small indel mutation may be primarily replication driven (as previous studies suggest) the observed value of α does not exceed the threshold necessary to conclude that contributions of replication independent factors are negligible. We also report that, with small indels (1bp) deletions outnumber insertion events. This relative excess of deletions may be an important parameter in the long-term evolution of genomic size.

Background: There is substantial evidence that replication-based nucleotide substitutions in primates occur more frequently in males than in females. There has been disagreement about the extent of this disparity. The human Alu repeats provide an ideal mechanism to further investigate the degree of replication-based error by providing tighter statistical boundaries on the male-to-female mutation ratio, α, in humans. Results: We analyze patterns of point mutations in Alu repeats across the entire human genome in order to elucidate the processes of mutation and fixation. This analysis provides substantial statistically bounded support for the accumulation of more point mutations in the Y chromosome compared to the X chromosome. We report a 99.99% confidence interval for human α between 1.280 and 1.289. Our results suggest that compared with eggs, sperm tend to carry a greater number of point mutations accumulated primarily during the production of gametes. Conclusion: Our results suggest that although mutation may be primarily replication driven (as previous studies suggest) the observed value of α does not exceed the threshold necessary to conclude that contributions of replication independent factors are negligible.

Conformational preferences of hypermodified nucleotide ‘lysidine’ in the model diphosphate (Me-p-k2Cp- Me) segment of anticodon loop of tRNAIle have been studied by using quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. The consequences of 5′-3′ diphosphate backbone on the conformation of zwitterionic, non-zwitterionic, neutral and tautomeric forms of lysidine have been investigated and compared with diphosphate backbone of cytidine nucleotide. Automated geometry optimization using semi-empirical quantum chemical RM1, quantum mechanical Hartree-Fock (HF-SCF) and Density Functional Theory (B3LYP/6-31G**) calculations have also been made to compare the salient features. The orientation of lysine moiety is found trans to the N(1) of cytidine in the predicted most stable conformations of all the four forms of lysidine in the model 5′-3′ diphosphate anticodon loop segment. The lysine substituent folds back and form hydrogen bond with 2′-hydroxyl group of ribose sugar. Lysine substituent of various diphosphate lysidine nucleotides does not interact with 5′or 3′ diphosphate backbone. All forms of lysidine nucleotides retain anti (χ=3°) glycosyl (glycosidic) torsion angle. Diphosphate cytidine nucleotide prefers (χ=33°), which could destabilize the c3′-endo sugar to the minor extent. The interaction between O(12b)----HO2′ of tautomer diphosphate nucleotide may help in maintaining the c3′-endo sugar puckering at wobble (34th) position as compared to other lysidine forms and cytidine nucleotide. Hence, tautomeric form of lysidine along with suitable hydrogen bond donoracceptor groups may also provide structural stability for the proper recognition of AUA codons instead of AUG codons.

DNA sequence search is a fundamental topic in bioinformatics. The Smith-Waterman algorithm achieved highest accuracy among various sequence alignment tools, but it usually spends much computational time to search on large DNA sequence database. On the contrary, BLAST and FASTA have improved the search speed by using heuristic approaches, by there is a possibility of missing an alignment or giving inaccurate output. This paper presents an efficient hierarchical method to improve the search speed while the accurate is being kept constant. For a given query sequence, firstly, a fast histogram based method is used to scan the sequences in the database. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results show the proposed method combining histogram information and Smith-Waterman algorithm is a more efficient algorithm for DNA sequence search.

Protein-Protein interactions (PPIs) are vital to most biological processes thus the identification of PPIs is of primary importance. In the present work, we endeavor to identify the downstream interaction partners of Mitogen Activated Protein Kinase3 (MAPK3) in Arabidopsis Thaliana using the information of protein sequences through Support Vector Machine (SVM) approach. The approach here used is supervised learning based on physiochemical properties of protein sequences through which we predict whether the MAPK3 proteins interact with downstream transcription factor proteins viz., Myb, bZIP, WRKY, Myb-related proteins, AP2/EREBP, and NAC with which its interaction is almost unknown. The Myb-related transcription factor family is showing maximum interaction percentage i.e. 71.14% with MAPK3 while minimum interaction percentage is 21.15% which is shown by NAC transcription factor family. The interaction percentage shown by the gene loci of rest transcription factor family i.e. Myb, bZIP, AP2/EREBP, WRKY are 67.78%, 68.05%, 21.91% and 58.33% respectively. The results of our study clearly revealed the complexity of MAPK3 interaction with several variants of different transcription factors and the same can be verified by different methodology of wet lab experimentation for elucidating the role in various biological processes.

Fermentation products are indigenous to many civilizations, and they have been produced by industries since a long time. Saccharomyces cerevisiae S288C (commonly known as baker's yeast) is the strain mainly used in the Glucose based fermentation industries. We have seen the use of same yeast strain at different places with different Phenotypic Constraints. The way to improve the adaptability of considered strain for desired phenotypic conditions, using smart selection of genes through cybernetic modeling is illustrated. Phylogenetic homologues for all S. cerevisiae S288c Glucose Fermentation pathway genes were screened to search evolutionarily related functional domains in other yeast strains like Saccharomyces cerevisiae YJM789, Candida glabrata CBS138, Kluyveromyces lactis NRRL Y-1140, Ashbya gossypii ATCC10895 etc., which are adapted naturally in different set of environment. We observed that Saccharomyces cerevisiae YJM789, Candida glabrata CBS138, Ashbya gossypii ATCC10895, Kluyveromyces lactis NRRL Y-1140 possess highly conserved functional domains, which can be carefully selected based on usage. This study aims at designing an algorithm to select and incorporate evolutionary homologues for genes of a considered strain, which mostly show sub-optimal performance in the desired set of experimental constraints. Such a consideration of native icroenvironment and volutionary closeness in the selection of functional homologues of the entire genetic set can thus be significantly fruitful.

Mutations in the avian influenza virus can create new pathogenic strains, which can cause future pandemics. Targeting the surface haemagglutinin can inhibit viral fusion and consequent entry. The effects of 27 single and double point mutations on the properties of the H5 haemagglutinin were studied. These mutations were then introduced individually in the PDB file of the H5, to generate mutants. 13 herbal and non-herbal lead inhibitors of H5 were screened and docked with the wild type and mutant haemagglutinins to obtain a comparative docking profile. The nature of the interactions of the inhibitors were analysed, and the binding residues determined. The latter further revealed that certain mutations in HA might be affecting inhibitor binding.

More and more computational resources for microRNAs (miRNAs) have been developed in recent years. That may lead to selective difficulty, mistakes of usage and confusion due to their confined scope of usage. Here, we summarize and classify the knowledge that has been accumulated in the fields and present a novel tool, MRST (miRNA resource store tool), for the storage of miRNA resources.

Snurps or small nuclear ribonucleoproteins (snRNPs), are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a Spliceosome, comprising of five small nuclear RNAs (snRNAs)-U1, U2, U4, U5, and U6 snRNA-as well as many protein factors, upon which splicing of pre-mRNA occurs. While, RNA pseudoknots play crucial role in protein synthesis by helping in internal ribosome entry, frameshifting, stop codon readthrough in many viral species and the 3’NCR pseudoknots helps viral RNAs to replicate, has been reported by a number of investigators, its presence in human snurps has not yet been done. The present in silico study reveals the presence of pseudoknots in the mRNAs of the proteins associated with human Spliceosome. It not only emphasizes their significance as catalytic RNA world relics but also opens the scope of research in the functional and structural associations of RNA pseudoknots in eukaryotic gene regulation.