Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G^** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO₂ group substituted molecules, the N–N bond distance increases with the increase of NO₂ groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρ_bcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO₂ groups in the nitramine molecules. The Laplacian of electron density ▽²ρ_bcp(r) of N–NO₂ bonds [DMNA: ? 16.7 eÅ^? 5, MDA: ? 12.8 eÅ^? 5 and TNA: ? 7.9 eÅ^? 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO₂ groups; this implies that the charge concentration decreases with the increase of NO₂ groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO₂ groups. The oxygen balance OB₁₀₀ of the molecules increases as the number of NO₂ group increases in the molecules, in which, the TNA molecule having maximum OB₁₀₀ value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO₂ group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.     

Management of root-knot nematode in tomato Lycopersicon esculentum,Mill, with biogas slurry

The effect of biogas slurry application on the severity of root-knot nematode, Meloidogyne incognita, attack on tomato cv. Co-1, was tested in the green house with two levels of biogas slurry: 5% and 10% (w/w) added to soil. Both the number (3 fruits/plant) and fruit yield (35.2 g/plant) of tomato increased significantly with 10% (w/w) biogas slurry. The plants amended with biogas slurry put up more vegetative growth and tended to flower and fruit much earlier than did those of the control. The nematode population in the soil decreased thus decreasing the severity of nematode attack.     

Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations

Background  

Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient associations and are part of several complexes at different stages of a cellular process. A better understanding of this higher-order organization of proteins into overlapping complexes is an important step towards unveiling functional and evolutionary mechanisms behind biological networks.     

Analysis of growth patterns in purebred Kambing Katjang goat and its crosses with the German Fawn

The objective of this study was to investigate growth patterns of goats utilizing data from a crossbreeding program involving the exotic German Fawn (GF) and the indigenous Kambing Katjang (KK) goats. Growth curve models and growth curve parameters were compared and analyzed for different genotypes and litter types. A total of 20,393 weight–age data from 208 female goats belonging to various crossbreeding genotypes were individually fitted to four growth curve models (Brody, Bertalanffy, Gompertz and Logistic). The goodness of fit was highest in the Brody model in most cases. A comparison of R² among genotypes showed that they were highest for KK. There were no significant differences of genotypes for estimated mature weight in the Brody model. The estimated mature weights for KK were significantly lower (P < 0.05) than for GF × KK (F₁), backcrosses with 75% GF genes (BC) and F₁ × F₁ (F₂) in the other models. The correlations between estimated mature weights and the maturing rates were lowest for BC. The genotype significantly (P < 0.01) affected the age at the constant degree of maturity (67% and 90% of mature weight) in all models. The BC genotype was the youngest at maturity and KK the oldest. All models well expressed the growth pattern of the target animals when they were older than 2.5 years of age. The results from the present study showed that the growth pattern may be altered by crossbreeding of KK with the GF breed.     

Aggregation and conformational studies on a pentapeptide derivative

Most of the disease causing proteins such as beta amyloid, amylin, and huntingtin protein, which are natively disordered, readily form fibrils consisting of beta-sheet polymers. Though all amyloid fibrils are made up of beta-sheet polymers, not all peptides with predominant beta-sheet content in the native state develop into amyloid fibrils. We hypothesize that stable amyloid like fibril formation may require mixture of different conformational states in the peptide. We have tested this hypothesis on amyloid forming peptide namely HCl(Ile)(5)NH(CH(2)CH(2)O)(3)CH(3) (I). We show peptide I, has propensity to form self-assembled structures of beta-sheets in aqueous solutions. When incubated over a period of time in aqueous buffer, I self assembled into beta sheet like structures with diameters ranging from 30 to 60 A that bind with amyloidophilic dyes like Congo red and Thioflavin T. Interestingly peptide I developed into unstable fibrils after prolonged aging at higher concentration in contrast with the general mature fibril-forming propensity of various amyloid petides known to date.     

Production,isolation and partial purification of xylanases from anAspergillus sp.

AnAspergillus sp., isolated from a rubbish dump, produced 10.6 IU ml^-1 xylanase activity. Two xylanases were recognized and each was purified to homogeneity by two-stage chromatography on DEAE-and CM-Sepharose. Xylanase I had a pI of 7.2 and anM _r of 26 kDa whereas xylanase II had a pI of 4.7 and anM _r of 21 kDa. At 50°C, xylanase I was stable for 2.5 h but xylanase II was only stable for 1 h.P. Khanna is with the National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440 020, India. S. Sivakami Sundari and N. Jothi Kumar are with the National Environmental Engineering Research Institute, Madras Zonal Laboratory, CSIR Madras Complex, Taramani 600 113, India.     

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

Background  

A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been co-inherited during evolution.     

Management of root lesion nematode, Pratylenchus delattrei in crossandra using oil cakes

Selected oil cakes, neem, castor and mahua, were tried independently and in combination with a chemical nematicide (carbofuran 3G) for the management of Pratylenchus delattrei in crossandra under glass house conditions. The neem oil cake was effective compared to other oil cakes used and there was a synergistic effect when the neemcake was coupled with carbofuran 3G in the management of Pratylenchus delattrei. The treatment resulted in better establishment of seedlings, and with increased plant bio-mass and flower yield.     

Predicting protein-protein interaction by searching evolutionary tree automorphism space

MOTIVATION: Uncovering the protein-protein interaction network is a fundamental step in the quest to understand the molecular machinery of a cell. This motivates the search for efficient computational methods for predicting such interactions. Among the available predictors are those that are based on the co-evolution hypothesis "evolutionary trees of protein families (that are known to interact) are expected to have similar topologies". Many of these methods are limited by the fact that they can handle only a small number of protein sequences. Also, details on evolutionary tree topology are missing as they use similarity matrices in lieu of the trees. RESULTS: We introduce MORPH, a new algorithm for predicting protein interaction partners between members of two protein families that are known to interact. Our approach can also be seen as a new method for searching the best superposition of the corresponding evolutionary trees based on tree automorphism group. We discuss relevant facts related to the predictability of protein-protein interaction based on their co-evolution. When compared with related computational approaches, our method reduces the search space by approximately 3 x 10(5)-fold and at the same time increases the accuracy of predicting correct binding partners.