A database for human Y chromosome protein data

The human Y chromosome is the sex determining chromosome. The number of proteins associated with this chromosome is 196 and 107 of the 196 proteins have yet not been characterised. Here, we describe the analysis of these 107 proteins by computing various physicochemical properties using sequence and predicted structural data to elucidate molecular function. We present the derived data in the form a form a database made freely available for download, review, refinement and update.

Availability

http://puratham.googlepages.com/ or http://puratham.googlepages.com/ftpconnection     

DDBASE2.0: updated domain database with improved identification of structural domains

MOTIVATION: Although many methods are available for the identification of structural domains from protein three-dimensional structures, accurate definition of protein domains and the curation of such data for a large number of proteins are often possible only after manual intervention. The availability of domain definitions for protein structural entries is useful for the sequence analysis of aligned domains, structure comparison, fold recognition procedures and understanding protein folding, domain stability and flexibility. RESULTS: We have improved our method of domain identification starting from the concept of clustering secondary structural elements, but with an intention of reducing the number of discontinuous segments in identified domains. The results of our modified and automatic approach have been compared with the domain definitions from other databases. On a test data set of 55 proteins, this method acquires high agreement (88%) in the number of domains with the crystallographers' definition and resources such as SCOP, CATH, DALI, 3Dee and PDP databases. This method also obtains 98% overlap score with the other resources in the definition of domain boundaries of the 55 proteins. We have examined the domain arrangements of 4592 non-redundant protein chains using the improved method to include 5409 domains leading to an update of the structural domain database. AVAILABILITY: The latest version of the domain database and online domain identification methods are available from http://www.ncbs.res.in/~faculty/mini/ddbase/ddbase.html Supplementary information: http://www.ncbs.res.in/~faculty/mini/ddbase/supplementary/supplementary.html     

Marker-aided genetic divergence analysis inBrassica

Genetic divergence was evaluated in 31 breeding lines from fourBrassica species using Mahalanobis'D ² . A new method of grouping usingD ² values was used to group the 31 lines, based on diagnostic morphological traits (called morphoqts). Isozyme variation of the individual enzymes esterase and glutamate oxaloacetate was quantified by five parameters (called isoqts) developed earlier. Grouping by the same method was also done based on the isoqts, and the grouping by isozymes was compared with that by morphoqts. Overall, there was an agreement of 73% suggesting that isoqts can be used in the choice of parents and also first stage selection of segregants in the laboratory. It was suggested that such an exercise would help to take care of season-bound and field-related problems of breeding. The new isozyme QTs, within lane variance of relative mobility and relative absorption, accounted for about 50% of the total divergence. The utility of the new method and isoqts in cost-effective breeding were highlighted.     

Vegetation analysis and tree population structure of tropical wet evergreen forests in and around Namdapha National Park,northeast India

Species composition, diversity and tree population structure were studied in three stands of the tropical wet evergreen forest in and around Namdapha National Park, Arunachal Pradesh, India. Three study stands exposed to different intensities of disturbances were identified, viz., undisturbed (2.4 ha) in the core zone of the park, moderately disturbed (2.1 ha) in the periphery of the park and highly disturbed (2.7 ha) outside the park area. In total 200 plant species belonging to 73 families were recorded in three stands. Tree density and basal area showed a declining trend with the increase in disturbance intensity. The densities of tree saplings and seedlings were lower in the disturbed stands than in the undisturbed stand. Species like Altingia excelsa, Olea dioica, Terminalia chebula, Mesua ferrea and Shorea assamica in the undisturbed stand and Albizia procera alone in the moderately disturbed stand contributed more than 50% of the total tree density in respective stands. The undisturbed stand contained young tree population. In the highly disturbed stand, the tree density was scarce, but had uncut trees of higher girth class (>210 cm GBH). Low shrub density was recorded in both disturbed stands due to frequent human disturbances; the broken canopy and direct sunlight enhanced the abundance of herbs in these stands. With a species rarity (species having <2 individuals) of ca. 50%, the tropical wet evergreenforests of the Namdapha National Park and its adjacent areas warrant more protection from human intervention and also eco-development to meet the livelihood requirements of the local inhabitants in the peripheral areas of the Namdapha National Park in order to reduce the anthropogenic pressure on the natural resources of the park.     

Gamma-interferon-inducible lysosomal thiol reductase (GILT). Maturation, activity, and mechanism of action

We recently identified a gamma-interferon-inducible lysosomal thiol reductase (GILT), constitutively expressed in antigen-presenting cells, that catalyzes disulfide bond reduction both in vitro and in vivo and is optimally active at acidic pH. GILT is synthesized as a 35-kDa precursor, and following delivery to major histocompatibility complex (MHC) class II-containing compartments (MIICs), is processed to the mature 30-kDa form via cleavage of N- and C-terminal propeptides. The generation of MHC class II epitopes requires both protein denaturation and reduction of intra- and inter-chain disulfide bonds prior to proteolysis. GILT may be important in disulfide bond reduction of proteins delivered to MIICs and consequently in antigen processing. In this report we show that, like its mature form, precursor GILT reduces disulfide bonds with an acidic pH optimum, suggesting that it may also be involved in disulfide bond reduction in the endocytic pathway. We also show that processing of precursor GILT can be mediated by multiple lysosomal proteases and provide evidence that the mechanism of action of GILT resembles that of other thiol oxidoreductases.     

Early generation intermating for yield improvement in groundnut (Arachis hypogaea L.)

Summary Seeds of 4 crosses of groundnut (Arachis hypogaea L.), Robut 33-1 x Chico, Robut 33-1 x NC Ac 17090, Robut 33-1 x PI 298115 and MK 374 x GAUG 1, were irradiated with 30 kR. In the F₁, some branches of each plant were intermated with other plants at random and others selfed in each cross to produce S₂ and F₂ seeds. They were evaluated for pod yield, shelling percentage and 100-kernel weight. The frequency of plants superior to F[in1] was much higher in S₂ than in F₂, which was, in general, true for the values of yield and its components. The S₂ and F₂ were advanced to third generation by selfing. The families descending from S₂ showed clear superiority over those from F₂. The reason for such superiority was suggested to be the recombination of genes from the upper and lower ends of the genotypic distribution under intermating.     

Biomass and production of fine and coarse roots during regrowth of a disturbed subtropical humid forest in north-east India

Seasonal variation and depthwise distribution of dry matter in roots of different diameter classes and their annual production were studied using sequential core sampling. The investigations were carried out in three stands of a subtropical humid forest of north-east India representing different stages of regrowth after tree cutting. The mean annual standing crop of fine (<2 mm in diameter) and coarse (2–15 mm diameter) roots increased gradually from 5.4 Mg ha^-1 and 0.7 Mg ha^-1 in 7-yr old regrowth to 9.4 Mg ha^-1 and 2.8 Mg ha^-1 in 16-yr old regrowth, respectively. The contribution of fine roots to the total root mass declined from 88% in 7-yr old regrowth to 77% in both 13 and 16-yr old regrowths, while that of coarse roots increased from 12 to 23%. A major portion of fine roots (59–62%) was present in 0–10 cm soil layer, but the coarse roots were concentrated in 10–20 cm soil depth (38–48%). In all the three stands, biomass of both fine and coarse roots followed a unimodal growth curve by showing a gradual increase from spring/pre-rainy season to autumn/post-rainy season. Biomass to necromass ratio increased from 2.5 in the 7-yr old to 3.2 in the 16-yr old stand. The annual fine root production increased from 5.9 Mg ha^-1 to 7.7 Mg ha^-1 and total root production from 7.6 Mg ha^-1 to 14.7 Mg ha^-1 from 7-yr to 16-yr old regrowth.     

A Comparative Evaluation of Somaclonal,Gamma Ray and EMS Induced Variation in Brassica juncea

Tissue culture induced somaclonal (SC), chemical mutagen EMS (E) and gamma ray (I) induced variation among 269 third generation families in each category generated from a popular variety of Brassica juncea were evaluated for important agronomic traits, namely flowering time, plant height, number of primary and secondary branches, seed yield per plant and per plot. The frequency of somaclonal-lines significantly superior to control was higher than such EMS or irradiated lines, in general. Somaclones also showed higher heritability values. One somaclone, SC-122, is significantly superior to control for upto five traits, simultaneously, demonstrating the practical utility of somaclonal variation in improving productivity.     

Are ‘multiple cross-multiple pollen hybrids’ an answer for productive populations in Brassica campestris (var.) Brown Sarson?

Summary A set of 167 mucromphs was evaluated in their F₁ generation for seven plant, four plot and five ratio characters. Methods of characterizing the parents and the hybrids on the basis of combining ability effects described in the first part were found to be efficient in identifying desirable cross combinations for pedigree breeding or generating composite populations. Order effects of multiple-pollen combinations were found to be potent for a number of character components. High x Low cross-combinations were found to produce a high frequency of heterotic crosses followed by High x High. Selected biparental progenies, single crosses, three-way crosses and elite varieties were successful female parents and combinations of pollen from two varieties, one variety and three varieties were successful male parents, in that order, in producing significant heterosis in mucromphs. The relationship between general and specific combining ability on the one hand and realised heterosis on the other was discussed.     

Modeling <Emphasis Type="Italic">Euglena</Emphasis> sp. growth under different conditions using an artificial neural network

Microalgae are considered as the future source of biofuels because of their high biomass productivity and neutral lipid content as triacylglycerides (TAG). Microalgae have high photosynthetic efficiency and the possibility of being cultivated in different wastewaters. The isolation of potential microalgae followed by the optimization of cultivation conditions is prerequisite for successful cultivation and accumulation of high lipid content. In the present work, a three-layer artificial neural network (ANN) model is developed to predict the essential parameters (such as pH, temperature, light intensity, photoperiod, and medium composition) based on 156 sets of laboratory experiments for achieving maximum biomass from Euglena sp. The independent parameters (viz., temperature, light intensity, photoperiod and number of days at fixed pH, and media composition) were fed as input to the ANN, and biomass yield was investigated. The comparison of the simulated environmental conditions using the ANN model and experimental results are found to have an excellent correlation coefficient of about 0.97 for the model variables used in this study. The model results established that artificial neural network design may be judiciously employed for optimization of different environmental conditions for this isolated microalga.