Structure-function relationships of icosahedral plant

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary organization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

Structure-function relationships of icosahedral plant viruses

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary morganization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

Characterization of the DNA-binding domain of beta protein, a component of phage lambda Red-pathway by UV catalyzed cross-linking

beta protein, a key component of Red-pathway of phage lambda is necessary for its growth and general genetic recombination in recombination-deficient mutants of Escherichia coli. To facilitate studies on structure-function relationships, we overexpressed beta protein and purified it to homogeneity. A chemical cross-linking reagent, glutaraldehyde, was used to stabilize the physical association of beta protein in solution. A 67-kDa band, corresponding to homodimer, was identified after separation by SDS-polyacrylamide gel electrophoresis. Stoichiometric measurements indicated a site-size of 1 monomer of beta protein/5 nucleotide residues. Electrophoretic gel mobility shift assays suggested that beta protein formed stable nucleoprotein complexes with 36-mer, but not with 27- or 17-mer DNA. Interestingly, the interaction of beta protein with DNA and the stability of nucleoprotein complexes was dependent on the presence of MgCl2, and the binding was abolished by 250 mM NaCl. The K-d of beta protein binding to 36-mer DNA was on the order of 1.8 x 10(-6) M. Photochemical cross-linking of native beta protein or its fragments, generated by chymotrypsin, to 36-mer DNA was performed to identify its DNA-binding domain. Characterization of the cross-linked peptide disclosed that amino acids required for DNA-binding specificity resided within a 20-kDa peptide at the N-terminal end. These findings provide a basis for further understanding oi the structure and function of beta protein.

Cross-taxon surrogacy of biodiversity in the Indian Garhwal Himalaya

Biodiversity surveys were conducted in 13, 10x50 m(2) plots located between 1400 to 3100 in abode mean sea level in a range of habitats in temperate mixed Oak and Coniferous forests through sub-alpine to the alpine grasslands in Chamoli district of Uttaranchal state in the Indian Garhwal Himalaya. Cross-taxon congruence in biodiversity (alpha-diversity and beta-diversity) across macrolichens, mosses, liverworts, woody plants (shrubs and trees) and ants was investigated, so as to examine the extent to which these group, of organisms can function as Surrogates for each other. Although woody plants provided a major substrate for macrolichens and mosses, there was no species-specific association between them. Woody plant species richness was highly positively correlated with mosses (r(2) = 0.63, P < 0.001) but the relationship, as not particularly very strong with lichens and liverworts. While there was a significant correlation in the species turnover (β-diversity) of macrolichens with mosses (r(2) = 0.21 P < 0.005). the relationship was relatively poor with the woody plants. On the other hand. negative correlations emerged in the species richness of ants with those of macrolichens, mosses and woody plants (r(2) = -0.44 P < 0.05). but most of the complementarity (turnover) relationships among them were positive, Since diversity between taxonomic hierarchies within the group was consistently significantly positively correlated in all these taxa, the higher taxonomic categories Such as genus and family may be employed as surrogates for rapid assessment and monitoring of species diversity, Although no single group other than macrolichens has emerged as a good indicator of changes in species richness in all other groups, some concordant relationships between them conform to the hypothesis that species assemblages of certain taxonomic groups could still be used as surrogates for efficient monitoring of species diversity in other groups whose distribution may further predict the importance of conserving overall biodiversity in landscapes such as the Garhwal Himalaya. (C) 2002 Elsevier Science Ltd. All rights reserved.

Cross-Guided Clustering: Transfer of Relevant Supervision across Tasks

Lack of supervision in clustering algorithms often leads to clusters that are not useful or interesting to human reviewers. We investigate if supervision can be automatically transferred for clustering a target task, by providing a relevant supervised partitioning of a dataset from a different source task. The target clustering is made more meaningful for the human user by trading-off intrinsic clustering goodness on the target task for alignment with relevant supervised partitions in the source task, wherever possible. We propose a cross-guided clustering algorithm that builds on traditional k-means by aligning the target clusters with source partitions. The alignment process makes use of a cross-task similarity measure that discovers hidden relationships across tasks. When the source and target tasks correspond to different domains with potentially different vocabularies, we propose a projection approach using pivot vocabularies for the cross-domain similarity measure. Using multiple real-world and synthetic datasets, we show that our approach improves clustering accuracy significantly over traditional k-means and state-of-the-art semi-supervised clustering baselines, over a wide range of data characteristics and parameter settings.

Scale-dependent relationships between tree species richness and ecosystem function in forests

1. The relationship between species richness and ecosystem function, as measured by productivity or biomass, is of long-standing theoretical and practical interest in ecology. This is especially true for forests, which represent a majority of global biomass, productivity and biodiversity. 2. Here, we conduct an analysis of relationships between tree species richness, biomass and productivity in 25 forest plots of area 8-50ha from across the world. The data were collected using standardized protocols, obviating the need to correct for methodological differences that plague many studies on this topic. 3. We found that at very small spatial grains (0.04ha) species richness was generally positively related to productivity and biomass within plots, with a doubling of species richness corresponding to an average 48% increase in productivity and 53% increase in biomass. At larger spatial grains (0.25ha, 1ha), results were mixed, with negative relationships becoming more common. The results were qualitatively similar but much weaker when we controlled for stem density: at the 0.04ha spatial grain, a doubling of species richness corresponded to a 5% increase in productivity and 7% increase in biomass. Productivity and biomass were themselves almost always positively related at all spatial grains. 4. Synthesis. This is the first cross-site study of the effect of tree species richness on forest biomass and productivity that systematically varies spatial grain within a controlled methodology. The scale-dependent results are consistent with theoretical models in which sampling effects and niche complementarity dominate at small scales, while environmental gradients drive patterns at large scales. Our study shows that the relationship of tree species richness with biomass and productivity changes qualitatively when moving from scales typical of forest surveys (0.04ha) to slightly larger scales (0.25 and 1ha). This needs to be recognized in forest conservation policy and management.