Protein chaperones and non-protein substrates: on substrate promiscuity of GroEL

Chaperonins are a group of molecular chaperones that form large multi subunit structures and are found in all forms of life. Encoded by the groEL and groES genes, bacterial chaperonins are required for appropriate folding of many cellular proteins. A significant number of bacterial species are known to express multiple copies of chaperonin genes, possibly to confer redundancy of GroEL function in these species. It is also likely that the paralogous GroELs might be undergoing diversification of function as a consequence of gene duplication. We argue in this article that different chaperonins in an organism might be involved in distinct biochemical functions that remain to be discovered, some of which might be modulated by different oligomeric states of the chaperonins

Genetic Diversity of Selected Upland Rice Genotypes (Oryza sativa L.) for Grain Yield and Related Traits

Seventy-seven upland rice genotypes including popular cultivars in Nigeria and introduced varieties selected from across rice-growing regions of the world were evaluated under optimal upland ecology. These genotypes were characterised for 10 traits and the quantitative data subjected to Pearson correlation matrix, Principal Component Analysis and cluster analysis to determine the level of diversity and degree of association existing between grain yield and its related component traits. Yield and most related component traits exhibited higher PCV compared to growth parameters. Yield had the highest PCV (41.72%) while all other parameters had low to moderate GCV. Genetic Advance (GA) ranged from 9.88% for plant height at maturity to 41.08% for yield. High heritability estimates were recorded for 1000 grain weight (88.71%), days to 50% flowering (86.67%) and days to 85% maturity (71.98%). Furthermore, grain yield showed significant positive correlation with days to 50% flowering and number of panicles m-2. Three cluster groups were obtained based on the UPGMA and the first three principal components explained about 64.55% of the total variation among the 10 characters. The PCA results suggests that characters such as grain yield, days to flowering, leaf area and plant height at maturity were the principal discriminatory traits for this rice germplasm indicating that selection in favour of these traits might be effective in this population and environment

PAR-3D: a server to predict protein active site residues

PAR-3D (http://sunserver.cdfd.org.in:8080/protease/PAR_3D/index.html) is a web-based tool that exploits the fact that relative juxtaposition of active site residues is a conserved feature in functionally related protein families. The server uses previously calculated and stored values of geometrical parameters of a set of known proteins (training set) for prediction of active site residues in a query protein structure. PAR-3D stores motifs for different classes of proteases, the ten glycolytic pathway enzymes and metal-binding sites. The server accepts the structures in the pdb format. The first step during the prediction is the extraction of probable active site residues from the query structure. Spatial arrangement of the probable active site residues is then determined in terms of geometrical parameters. These are compared with stored geometries of the different motifs. Its speed and efficiency make it a beneficial tool for structural genomics projects, especially when the biochemical function of the protein has not been characterized

75 Years of India's Independence and 80 Years of CSIR

38-44The 75th year of Indian independence is even more special to CSIR because CSIR enters its 80 years of gloriously serving the Indian society through S&T interventions

EXAFS study of intermetallics of the type RGe<SUB>2</SUB> (R=La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Ho, Er and Y) Part I: determination of Ge-Ge distances

A study of the EXAFS associated with the K x-ray absorption discontinuity of germanium in pure germanium and in the rare-earth germanides RGe2 (where R=La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Ho, Er and Y) has been carried out. The Ge-Ge distances have been obtained in these compounds. Considering the phase to the RGe2 system, the bond lengths in these compounds have been determined. The values obtained by us for the RGe2 compounds (R=La, Ce, Pr, Nd, Sm, Gd, Dy and Y) agree with those obtained earlier by crystallographic methods. The bond lengths for the compounds TbGe2, HoGe2 and ErGe2 are also being reported

The cuticle modulates ultraviolet reflectance of avian eggshells

ABSTRACT Avian eggshells are variedly coloured, yet only two pigments, biliverdin and protoporphyrin IX, are known to contribute to the dramatic diversity of their colours. By contrast, the contributions of structural or other chemical components of the eggshell are poorly understood. For example, unpigmented eggshells, which appear white to the human eye, vary in their ultraviolet (UV) reflectance, which may be detectable by birds. We investigated the proximate mechanisms for the variation in UV-reflectance of unpigmented bird eggshells using spectrophotometry, electron microscopy, chemical analyses, and experimental manipulations. We specifically tested how UV-reflectance is affected by the eggshell cuticle, the outermost layer of most avian eggshells. The chemical dissolution of the outer eggshell layers, including the cuticle, increased UV-reflectance for only eggshells that contained a cuticle. Our findings demonstrate that the outer eggshell layers, including the cuticle, absorb UV-light, probably because they contain higher levels of organic components and other chemicals, such as calcium phosphates, compared to the predominantly calcite-based eggshell matrix. These data highlight the need to examine factors other than the known pigments in studies of avian eggshell colour

Rainfall trend detection in Northern Nigeria over the period of 1970-2012

This study examined the trends in variability and spatial distribution of annual rainfall over northern Nigeria during the period 1970-2012 with a view to understand the pattern of rainfall trend (significance and magnitude), by applying various statistical tools on the data obtained from 11 weather stations. The non-parametric Mann– Kendall test was used to determine the statistical significance of trends while the magnitude of trends was derived from the Sen slope estimator of the linear trends using Kendall robust line fitting. Map of rainfall trends was generated by applying a geo-statistical interpolation technique to visualize the detected tendencies. The findings revealed that a significant positive increase of 2.16mm in rainfall was recorded in the entire northern Nigeria within the period of 1970 to 2012. It further indicated that majority of the stations revealed an upward trend, with Bauchi, Borno, Kebbi and Sokoto stations showing significant positive trends of 8.13mm, 4.30mm, 4.76mm and 4.42mm respectively. It is concluded that there is high variability in rainfall in the northern Nigeria which signifies a clear evidence of climate change in the region

Identification and Functional Characterization of Gene Components of Type VI Secretion System in Bacterial Genomes

A new secretion system, called the Type VI Secretion system (T6SS), was recently reported in Vibrio cholerae, Pseudomonas aeruginosa and Burkholderia mallei. A total of 18 genes have been identified to be belonging to this secretion system in V. cholerae. Here we attempt to identify presence of T6SS in other bacterial genomes. This includes identification of orthologous sequences, conserved motifs, domains, families, 3D folds, genomic islands containing T6SS components, phylogenetic profiles and protein-protein association of these components. Our analysis indicates presence of T6SS in 42 bacteria and its absence in most of their non-pathogenic species, suggesting the role of T6SS in imparting pathogenicity to an organism. Analysis of genomic regions containing T6SS components, phylogenetic profiles and protein-protein association of T6SS components indicate few additional genes which could be involved in this secretion system. Based on our studies, functional annotations were assigned to most of the components. Except one of the genes, we could group all the other genes of T6SS into those belonging to the puncturing device, and those located in the outer membrane, transmembrane and inner membrane. Based on our analysis, we have proposed a model of T6SS and have compared the same with the other bacterial secretion systems