Statistical significance of large gene clusters.

Consider the scenario of common gene clusters of closely related species where the cluster sizes could be as large as 400 from an alphabet of 25,000 genes. This paper addresses the problem of computing the statistical significance of such large clusters, whose individual elements occur with very low frequency (of the order of the number of species in this case) and the alphabet set of the elements is relatively large. We present a model where we study the structure of the clusters in terms of smaller nested (or otherwise) sub-clusters contained within the cluster. We give a probability estimation based on the expected cluster structure for such clusters (rather than some form of the product of individual probabilities of the elements). We also give an exact probability computation based on a dynamic programming algorithm, which runs in polynomial time.     

Ectopic expression of AmNAC1 from Avicennia marina (Forsk.) Vierh. confers multiple abiotic stress tolerance in yeast and tobacco

Plant Cell, Tissue and Organ Culture (PCTOC) - Abiotic factors like salinity, drought and cold affect agricultural productivity substantially worldwide. NAC (NAM, ATAF1/2 and CUC2) family...     

Isolation and characterization of biofilm-forming bacteria and associated extracellular polymeric substances from oral cavity

The current work deals with the studies on characterization of two biofilm-forming bacteria isolated from the oral cavity. The major constituent of biofilm other than bacterial cells is the extracellular polymeric substance (EPS) matrix, which is secreted by the bacterial cells themselves. Physical properties of biofilms such as attachment, mechanical strength, antibiotic resistance can be attributed to EPS matrix. Molecular phylogeny confirmed these two isolates as Pseudomonas aeruginosa and Bacillus subtilis. It was observed that cell attachment in both the strains was maximal when xylose was used as the sole carbon source. The EPS characterization result indicated the presence of a macromolecular complex constituting of carbohydrate, protein, lipids and nucleic acids. Test for biofilm formation in the presence of metal salts of iron and zinc showed moderate to high inhibition of biofilm formation. However, calcium, iron and copper have been found to enhance biofilm growth significantly. There was more than 50 % increase in biofilm growth by P. aeruginosa with an increase in calcium concentration up to 80 ppm (Two tailed t-test P?<?0.05), whereas ≥ 15 % increase in biofilm growth by B. subtilis was observed in the presence of 80 ppm of calcium. However, variations were significant (Two way ANOVA, P?<?0.01) between different metals in different concentrations. In this study, attempts have been made to examine the effect of different carbon sources and physiological conditions on biofilm growth.     

Molecular Epidemiology and Complete Genome Characterization of H1N1pdm Virus from India

Background

Influenza A virus is one of world’s major uncontrolled pathogen, causing seasonal epidemic as well as global pandemic. This was evidenced by recent emergence and continued prevalent 2009 swine origin pandemic H1N1 Influenza A virus, provoking first true pandemic in the past 40 years. In the course of its evolution, the virus acquired many mutations and multiple unidentified molecular determinants are likely responsible for the ability of the 2009 H1N1 virus to cause increased disease severity in humans. Availability of limited data on complete genome hampers the continuous monitoring of this type of events. Outbreaks with considerable morbidity and mortality have been reported from all parts of the country.

Methods/Results

Considering a large number of clinical cases of infection complete genome based sequence characterization of Indian H1N1pdm virus and their phylogenetic analysis with respect to circulating global viruses was undertaken, to reveal the phylodynamic pattern of H1N1pdm virus in India from 2009–2011. The Clade VII was observed as a major circulating clade in phylogenetic analysis. Selection pressure analysis revealed 18 positively selected sites in major surface proteins of H1N1pdm virus.

Conclusions

This study clearly revealed that clade VII has been identified as recent circulating clade in India as well globally. Few clade VII specific well identified markers undergone positive selection during virus evolution. Continuous monitoring of the H1N1pdm virus is warranted to track of the virus evolution and further transmission. This study will serve as a baseline data for future surveillance and also for development of suitable therapeutics.     

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity,Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species

Foxtail millet ( Setaria italica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02–0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.     

Biochemical and molecular profiling of micropropagated and conventionally grown Kaempferia galanga

Kaempferia galanga L., family Zingiberaceae, is used extensively in the preparation of both traditional and modern medicines. Buds of rhizomes of K. galanga were incubated on Murashige and Skoog (MS) medium supplemented with 1 mg/l benzyladenine and 0.5 mg/l indole-3-acetic acid (IAA) to induce shoot proliferation. Micropropagated plantlets subjected to random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker-based molecular profiling revealed uniform banding patterns similar to those of the mother plants. After 2 years of culture in vitro, plantlets were transplanted to the field, evaluated for different agronomic traits, and their rhizomes were subjected to biochemical profiling using quantitative and qualitative assays of essential oils. Gas chromatography and mass spectroscopy analysis of rhizome oil of micropropagated plants showed the presence of 10 major components which were similar to those detected in the mother plants, and accounted for 95.5% of the total compounds. The compound ethyl-p-methoxy cinnamate accounted for 59.5% of the total compounds detected, followed by ethyl cinnamate, 3-carene, pentadecane, borneol, bornyl acetate, delta-selinene, camphor, alpha-piene and immidazole, 5-carbonylvinyl-4-nitro. Biochemical and molecular profiling of micropropagated clones revealed that an in vitro micropropagation protocol could be effectively used for commercial propagation of true-to-type K. galanga for a stable supply of the medicinal compounds present in this plant species.     

Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (Setaria italica L.)

WD40 proteins play a crucial role in diverse protein-protein interactions by acting as scaffolding molecules and thus assisting in the proper activity of proteins. Hence, systematic characterization and expression profiling of these WD40 genes in foxtail millet would enable us to understand the networks of WD40 proteins and their biological processes and gene functions. In the present study, a genome-wide survey was conducted and 225 potential WD40 genes were identified. Phylogenetic analysis categorized the WD40 proteins into 5 distinct sub-families (I–V). Gene Ontology annotation revealed the biological roles of the WD40 proteins along with its cellular components and molecular functions. In silico comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of WD40 genes. Estimation of synonymous and non-synonymous substitution rates revealed its evolutionary significance in terms of gene-duplication and divergence. Expression profiling against abiotic stresses provided novel insights into specific and/or overlapping expression patterns of SiWD40 genes. Homology modeling enabled three-dimensional structure prediction was performed to understand the molecular functions of WD40 proteins. Although, recent findings had shown the importance of WD40 domains in acting as hubs for cellular networks during many biological processes, it has invited a lesser research attention unlike other common domains. Being a most promiscuous interactors, WD40 domains are versatile in mediating critical cellular functions and hence this genome-wide study especially in the model crop foxtail millet would serve as a blue-print for functional characterization of WD40s in millets and bioenergy grass species. In addition, the present analyses would also assist the research community in choosing the candidate WD40s for comprehensive studies towards crop improvement of millets and biofuel grasses.     

Effect of Temperature Pre-Exposure on the Locomotion and Chemotaxis of C. elegans

The effect of temperature pre-exposure on locomotion and chemotaxis of the soil-dwelling nematode Caenorhabditis elegans has been extensively studied. The behavior of C. elegans was quantified using a simple harmonic curvature-based model. Animals showed increased levels of activity, compared to control worms, immediately after pre-exposure to 30°C. This high level of activity in C. elegans translated into frequent turns by making ‘complex’ shapes, higher velocity of locomotion, and higher chemotaxis index () in presence of a gradient of chemoattractant. The effect of pre-exposure was observed to be persistent for about 20 minutes after which the behavior (including velocity and ) appeared to be comparable to that of control animals (maintained at 20°C). Surprisingly, after 30 minutes of recovery, the behavior of C. elegans continued to deteriorate further below that of control worms with a drastic reduction in the curvature of the worms'' body. A majority of these worms also showed negative chemotaxis index indicating a loss in their chemotaxis ability.     

Biomarkers of Inflammation,Immunosuppression and Stress Are Revealed by Metabolomic Profiling of Tuberculosis Patients

Although tuberculosis (TB) causes more deaths than any other pathogen, most infected individuals harbor the pathogen without signs of disease. We explored the metabolome of >400 small molecules in serum of uninfected individuals, latently infected healthy individuals and patients with active TB. We identified changes in amino acid, lipid and nucleotide metabolism pathways, providing evidence for anti-inflammatory metabolomic changes in TB. Metabolic profiles indicate increased activity of indoleamine 2,3 dioxygenase 1 (IDO1), decreased phospholipase activity, increased abundance of adenosine metabolism products, as well as indicators of fibrotic lesions in active disease as compared to latent infection. Consistent with our predictions, we experimentally demonstrate TB-induced IDO1 activity. Furthermore, we demonstrate a link between metabolic profiles and cytokine signaling. Finally, we show that 20 metabolites are sufficient for robust discrimination of TB patients from healthy individuals. Our results provide specific insights into the biology of TB and pave the way for the rational development of metabolic biomarkers for TB.