Genome research in the cloud

High-throughput genome research has long been associated with bioinformatics, as it assists genome sequencing and annotation projects. Along with databases, to store, properly manage, and retrieve biological data, a large number of computational tools have been developed to decode biological information from this data. However, with the advent of next-generation sequencing (NGS) technology the sequence data starts generating at a pace never before seen. Consequently researchers are facing a threat as they are experiencing a potential shortage of storage space and tools to analyze the data. Moreover, the voluminous data increases traffic in the network by uploading and downloading large data sets, and thus consume much of the network's available bandwidth. All of these obstacles have led to the solution in the form of cloud computing.     

PCR-based molecular characterization, phylogenetic analysis and secondary structure of the 28S rDNA of Thaparocleidus wallagonius (Monogenea: Dactylogyridae) �C the most primitive species of this genus from India

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.     

Identification of a cDNA clone encoding for a galactose-binding lectin from peanut (Arachis hypogaea) seedling roots.

A cDNA clone obtained from developing peanut (Arachis hypogaea) seedling roots, when expressed in Escherichia coli and insect cells (Sf9) gave a 29 kDa subunit protein. The native recombinant protein agglutinates neuraminidase treated human erythrocytes and the agglutination is inhibited by galactose. Nucleotide sequence and predicted amino acid sequence analyses indicate that it is different from peanut seed (PNA and SGL) and nodule (NGLa and NGLb) galactose-binding lectins.     

Anaerobic degradation of dalapon in waterlogged soil and river sediment

Anaerobic enrichment culture of flooded soil and river sediment demonstrated that 2,2-dichloropropionate can be degraded by a methanogenic route.     

Functional significance of Micraspis discolor (F.) (Coccinellidae: Coleoptera) in rice ecosystem

Coccinellids are key predators that are conserved and augmented in agricultural ecosystems, to achieve biological control of pests. Actual quantification of field predation has not been attempted for many of the beneficial coccinellids. Numerous reports show coccinellids as opportunistic, feeding on a variety of food material in addition to their preferred prey. Micraspis discolor is the most abundant species of coccinellid in rice ecosystems and touted as a biocontrol option for brown planthopper (BPH), Nilaparvata lugens (Stal), a key pest of rice. However, it has been reported as both entomophagous and phytophagous. Native polyacrylamide gel electrophoresis (PAGE) was used to separate esterases from whole‐body homogenates of Micraspis and its prey viz., green leafhopper (GLH) Nephotettix virescens (Distant), BPH N. lugens, whitebacked planthopper (WBPH) Sogatella furcifera (Horvath), aphid Rhopalosiphum padi L., thrips, Haplothrips sp., and pollen. Field‐collected beetles showed a range of bands, some corresponding with pollen and GLH, while others were different from prey offered, indicating a wider range of prey spectrum than envisaged. Feeding preference studies confirmed a preference for pollen and GLH in no‐choice (H = 20.724; P = 0.001) and multiple‐choice tests (H = 20.52; P < 0.001) and a significant preference for pollen over all insects offered in the paired‐choice test (t = 5.099; P = 0.007). The abundance of adult M. discolor in rice at flowering phase does not correspond to prey abundance in the field but rather reflects an inclination to pollen feeding more than entomophagy.     

Development and validation of multiplex-PCR assay for simultaneous detection of rare alleles of <Emphasis Type="Italic">crtRB1</Emphasis> and <Emphasis Type="Italic">lcyE</Emphasis> governing higher accumulation of provitamin A in maize

Vitamin A deficiency is a widely prevalent health disorder among millions of people worldwide. Introgression of crtRB1 and lcyE favourable alleles that enhance concentration of provitamin A in maize endosperm have been employed in maize biofortification programmes. To make marker-assisted selection (MAS) more effective, we have developed rapid and convenient multiplex-polymerase chain reaction (PCR) assay to simultaneously discover the allelic combinations among the segregants. Validation of the multiplex assay was done in two backcross-derived populations developed using elite inbreds viz., HKI193-1 and HKI193-2 carrying unfavourable alleles of crtRB1 (296 bp) and lcyE (300 bp) and HarvestPlus inbreds viz., HP704-22 and HP704-23 possessing favourable alleles of crtRB1 (543 bp) and lcyE (650 bp). We also standardized the uniplex-PCR assays for both the genes that gave robust and reproducible results in sub-tropical populations. Gel profiles of BC₁F₁, BC₂F₁ and BC₂F₂ revealed that these assays identified the backcross progenies homo-or hetero-zygous for the favourable- or unfavourable-alleles. Multiplex-PCR assay also precisely confirmed the results of individual uniplex assays in different backcross generations. Cost and time analyses showed that multiplex-PCR assay has potential to save 41% of cost, and 50% of time compared to two uniplex assays in a MAS programme. It has also saved 50% of the manpower. The multiplex assay possesses significant advantage over uniplex assays and enhances the efficiency of selection. This is the first report of development and validation of multiplex-PCR assay of crtRB1 and lcyE for utilization in maize biofortification programme.     

Regulation of low density lipoprotein receptor mRNA levels by estradiol 17β and chorionic gonadotropin in human placenta

Inhibition of synthesis of estradiol 17 by the addition of inhibitors of aromatase, a key enzyme in the biosynthesis of estradiol 17, or addition of tamoxifen - an estrogen receptor antagonist, to human placental minces resulted in an increase in the level of LDL-receptor mRNA. This increase could be blocked by the simultaneous addition of estradiol 17. A concentration dependent effect of estradiol 17 on the level of LDL-receptor mRNA was seen both in first trimester, and term placenta. Addition of human chorionic gonadotropin (hCG) to term placental minces also increased the LDL-receptor mRNA levels. When hCG and cycloheximide were added together, an additive effect was observed. The results obtained in this study suggest that the LDL-receptor mRNA levels in the human placenta are regulated by estradiol 17 and hCG.     

Effect of root exudates and extracts on rhizosphere fungi

Summary The effects of root exudates and extracts of Cassia tora L. and Crotalaria medicaginea Lamk., on some dominant rhizosphere fungi isolated from the plants were studied. Root extracts induced a high degree of stimulation in rate of growth of a majority of the fungi tested. Root exudates caused only a marginal effect which was positive on all the fungi except Trichoderma lignorum which was inhibited by the root exudate of C. medicaginea.