Hydrophobic clusters in protein structures

Globular proteins fold such that the hydrophobic groups are packed inside forming hydrophobic clusters, and the hydrophilic groups are present on the surface. In this article we analyze clusters of hydrophobic groups of atoms in 781 protein structures selected from the PDB. Our analysis showed that every structure consists of two types of clusters: at least one large cluster that forms the hydrophobic core and probably dictates the protein fold; and numerous smaller clusters, which might be involved in the stabilization of the fold. We also analyzed the preference of the hydrophobic groups in each of the amino acids toward forming hydrophobic clusters. We find that hydrophobic groups from the hydrophilic amino acids also contribute toward cluster formation. Proteins 2008. © 2008 Wiley‐Liss, Inc.     

An analysis of association of components of yield and oil in safflower (Carthamus tinctorius L.)

Summary Inter-relationships of various component characters with yield and oil content were analysed using 215 entries of safflower from India and U.S.A. Correlation of capsule number per plant and capsule weight with yield per plant was pronounced and they showed large direct effects on yield. All other components influenced seed yield mainly through these two components. Seed size had little effect on yield while seed number exerted a positive influence. The proportion of hull expressed as per cent of the whole seed revealed a highly significant and inverse relationship with oil content and was mainly responsible for the observed variability in oil content in the material. Although negative association was indicated between seed size and oil content, it was observed to be due to the indirect effect of hull content and not due to direct effect of seed size. Interestingly, yield per plant and its major components, number of capsules and capsule weight, revealed a negligible relationship with oil content. Both direct as well as indirect effects of hull percent and yield per plant were responsible for the favourable effect of seed number on oil content. The correlation of plant height, days to first flowering and total crop growth period with yield and oil content was either negligible or low, offering scope for developing early maturing and dwarf varieties with high yield and oil content. Spine index showed a non-significant association with yield and oil content. Capsule number, capsule weight and hull per cent were observed to be the most important components in breeding for higher yield and oil content.     

Population and conservation of Sapria himalayana Griffith. in Namdapha national park, Arunachal Pradesh, India

Sapria himalayana Griffith. (Rafflesiaceae), a root parasitic plant, is one of the lesser known and poorly understood taxons, which is at the brink of extinction due to incessant human interventions in the natural forest environment. This note deals with the population of Sapria in the buffer zone of Namdapha national park in Arunachal Pradesh, northeastern India. The host plant was a woody climber, Tetrastigma sp. Two patches of Sapria were observed at Hornbill (primary and relatively undisturbed forest) and four patches in Zero camp (disturbed secondary forest). Presently the species is prone to extirpation due to habitat loss through encroachments and massive NTFP extraction in the park area. All attempts to reintroduce or translocate the species will be in vain due to its phytogeographical limitations and host-specificity. A viable approach could be in situ conservation by effective protected area management.     

A new approach for enhanced multiplication of arbuscular mycorrhizal fungi and isolation of ITS regions from Glomus deserticola and Laccaria fraterna

Rootlets induced from the petiole base of L. purpureus, using IAA and kinetin was used for enhanced multiplication of arbuscular mycorrhizal (AM) fungus, G. deserticula. Using conserved short arbitrary oligonucleotides, as specific primers, we amplified the ITS-region, a molecular marker for fungal identification, from the genomic DNA extracted from cultured spores of G. deserticola, and genomic DNA extracted from the mycelium of L. fraterna. The capacity of fungal colonization and subsequent spore formation of G. deserticola, compared with the natural root system was evaluated. This technology would provide a simple way to multiply AM fungi and to produce spores without microbial contamination useful for further molecular characterization.     

Applying Support Vector Machines for Gene ontology based gene function prediction

Background

The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However, these methods can either only be applied for specific subsets, or their results are not formalised, or they do not provide precise confidence estimates for their predictions.

Results

We have developed a large-scale annotation system that tackles all of these shortcomings. In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. The general performance of the system was benchmarked with a large dataset. An organism-wise cross-validation was performed to define confidence estimates, resulting in an average precision of 80% for 74% of all test sequences. The validation results show that the prediction performance was organism-independent and could reproduce the annotation of other automated systems as well as high-quality manual annotations. We applied our trained classification system to Xenopus laevis sequences, yielding functional annotation for more than half of the known expressed genome. Compared to the currently available annotation, we provided more than twice the number of contigs with good quality annotation, and additionally we assigned a confidence value to each predicted GO term.

Conclusions

We present a complete automated annotation system that overcomes many of the usual problems by applying a controlled vocabulary of Gene Ontology and an established classification method on large and well-described sequence data sets. In a case study, the function for Xenopus laevis contig sequences was predicted and the results are publicly available at ftp://genome.dkfz-heidelberg.de/pub/agd/gene_association.agd_Xenopus.

     

A Method to Rank Multiple Trait Performance of Biological Entities

Performance of biological entities are defined, in general by k inter-dependent traits whose error variances are heterogeneous. A method of arriving at “Performance Scores” for the entities along with a multivariate test of significance of k-trait differences is described. They are used to compute, for each entity, a “Performance Index” on which a ranking of the relative performance is obtained. The improvement in the present method over an earlier one is illustrated with a numerical example.     

Latitudinal gradient of nestedness and its potential drivers in stream detritivores

Understanding what mechanisms shape the diversity and composition of biological assemblages across broad‐scale gradients is central to ecology. Litter‐consuming detritivorous invertebrates in streams show an unusual diversity gradient, with α‐diversity increasing towards high latitudes but no trend in γ‐diversity. We hypothesized this pattern to be related to shifts in nestedness and several ecological processes shaping their assemblages (dispersal, environmental filtering and competition). We tested this hypothesis, using a global dataset, by examining latitudinal trends in nestedness and several indicators of the above processes along the latitudinal gradient. Our results suggest that strong environmental filtering and low dispersal in the tropics lead to often species‐poor local detritivore assemblages, nested in richer regional assemblages. At higher latitudes, dispersal becomes stronger, disrupting the nested assemblage structure and resulting in local assemblages that are generally more species‐rich and non‐nested subsets of the regional species pools. Our results provide evidence that mechanisms underlying assemblage composition and diversity of stream litter‐consuming detritivores shift across latitudes, and provide an explanation for their unusual pattern of increasing α‐diversity with latitude. When we repeated these analyses for whole invertebrate assemblages of leaf litter and for abundant taxa showing reverse or no diversity gradients we found no latitudinal patterns, suggesting that function‐based rather than taxon‐based analyses of assemblages may help elucidate the mechanisms behind diversity gradients.     

Optimal analytical conditions for catalase in fresh water prawn,Macrobrachium malcolmsonii

The cytosol of hepatopancreas was prepared from the freshwater prawn Macrobrachium malcolmsonii, and optimal assay conditions, i.e., concentration of substrate, pH, and temperature, were determined to measure basal activities and kinetic constants of catalase activity. The properties of catalase were examined in M. macolmsonii, because quantitative data on catalase are limited in crustacean species. The optimal pH for catalase was 7.0. The activation energy was 3.55 Kcal/mol and energy inhibition value was 5.16 Kcal/mol. The value of energy inhibition is higher than that of energy activation. This may be due to inhibition of catalase by some substrate other than H2O2. A Km of 66.6?mM was also determined from various concentrations of substrate.