Thermodynamic properties of strongly coupled plasma in the presence of an external magnetic field

Thermodynamic properties of a Yukawa system consisting of dust particles in plasma are studied in the presence of an external magnetic field. It is assumed that dust particles interact with each other by a modified potential in the presence of a magnetic field. A molecular dynamics code is developed to calculate this internal energy for the entire system. Based on the values of the internal energy given by the code, the Helmholtz free energy and pressure are calculated for the system.     

Understanding the Effect of Secondary Structures and Aggregation on Human Protein Folding Class Evolution

Using several model organisms it has been shown earlier that protein designability is related to contact density or fraction of buried residues and influence protein evolutionary rates dramatically. Here, using Homo sapiens as a model organism, we have analyzed two main folding classes (all-α and all-β) to examine the factors affecting their evolutionary rates. Since, secondary structures are the most fundamental components of the protein folding classes, we explored the effect of protein secondary structure composition on evolution. Our results show that sheet and helix fractions exhibit positive and negative correlations, respectively, with the rate of protein evolution. On dividing the secondary structure components according to solvent accessibility, linear regression model identified two factors namely buried sheet fraction and relative aggregation propensity. Both these factors together can explain about 13.4% variability in the rate of human protein evolution, while buried sheet residues can alone account to 9.9% variability.     

Cyanobacteria in rice soils

Cyanobacteria were recovered from each of 38 soil samples collected from local rice fields. Of the 84 species belonging to 31 genera that were isolated, 42 were heterocystous diazotrophic species belonging to 14 genera and the remaining were non-heterocystous. Fischerella, Nostoc and Calothrix were widespread.Z.U.M. Khan is with the Department of Botany, Jahangirnagar University, Savar, Dhaka, Bangladesh. Z.N. Tahmida Begum and M.Z. Hossain are with the Department of Botany and R. Mandal is with the Department of Soil Science, bot at the University of Dhaka, Dhaka-1000, Bangladesh;     

Studies on the effects of protease substrate analogues on some of the actions of insulin

Added TAME (N alpha-p-tosyl-1-anginine methyl ester) or BAME (benzoyl-anginine methyl ester) inhibited insulin induced activation of glucose oxidation and fat cell PDH activation without affecting spermine action on PDH activation and glucose oxidation in fat cells. BAME inhibited insulin-induced generation of both PDH stimulator and PDH inhibitor from liver particulate fraction. In contrast, insulin-induced internalization of insulin receptors and negative cooperativity of insulin receptors were not affected by protease substrate inhibitors. These results suggest that certain actions of insulin (glucose oxidation, generation of PDH regulators) are mediated by proteolytic events, while insulin-induced down regulation and negative cooperativity of insulin receptors are not mediated by activation of endogenous proteases.     

Expression and synthesis of high mobility group chromosomal proteins in different rat skeletal cell lines during myogenesis.

The synthesis, turnover, and expression of all the major high mobility group (HMG) chromosomal proteins was studied in different rat skeletal myogenic cell lines. Whereas pulse-chase experiments revealed a similar half-life (greater than 2 cell generations) for all the HMG proteins in both L8 myoblasts and myotubes, [3H]lysine incorporation data indicated a 2- to 4-fold greater incorporation of the label in the HMG proteins in proliferating myoblasts relative to the nondividing myotubes. Analysis of the HMG-1, -14, and -17 mRNAs during myogenesis showed a significant down-regulation in L6 and L8 myotubes compared to the myoblasts. However, the timing of the shift and the extent of down-regulation was cell type-dependent, being more pronounced in L6 myotubes at fusion compared to 4 days postfusion in L8 myotubes. By contrast, L8-derived fusion-defective fu-1 cells over the same period of growth showed no change in HMG-14/17 mRNA levels. HMG-I(Y) protein isoforms, noted for the first time in rat myoblasts, like their counterparts, seemed to be stable and showed a precipitous reduction in their mRNAs during myogenesis. The results suggest a cell type-specific correlation between HMG expression and cell proliferation; they also argue for their role in maintenance of the cell's state of differentiation.     

Evaluation of biorational insecticides and DNA barcoding as tools to improve insect pest management in lablab bean (Lablab purpureus) in Bangladesh

Lablab bean (Lablab purpureus) is a popular vegetable crop in Bangladesh, but farmers growing this crop experience significant losses to insect pests despite heavy reliance on conventional insecticides. We conducted field studies to improve pest management in lablab bean by testing biorational insecticides as alternatives to conventional insecticides for the control of pod borers (Maruca vitrata) and aphids (Aphis craccivora), and characterizing flower-inhabiting thrips as an emerging pest in this crop. In field experiments, spinosad was the most promising biorational we tested, suppressing pod-boring caterpillars more effectively than thiamethoxam or quinalphos. In contrast, azadirachtin (neem) did not significantly suppress any of the insect pests we measured, although target aphid populations were generally low at our research site. Using DNA barcoding at the coxI locus combined with morphological identification, we found eight thrips taxa inhabiting lablab bean flowers, dominated by Megalurothrips usitatus and M. distalis/peculiaris. A preliminary regression analysis indicated that these flower-inhabiting thrips reduced lablab bean yield. Our results suggest that spinosad may be useful within lablab bean IPM programs, and that these programs will likely need to incorporate tactics against thrips to effectively protect yield. Finally, we found that DNA barcoding was a valuable tool for pest identification in an understudied crop and region, but that to reach its full potential will require an investment in more comprehensive reference libraries.     

pVEC hydrophobic N‐terminus is critical for antibacterial activity

Cell‐penetrating peptides (CPPs) are commonly defined by their shared ability to be internalized into eukaryotic cells, without inducing permanent membrane damage, and to improve cargo delivery. Many CPPs also possess antimicrobial action strong enough to selectively lyse microbes in infected mammalian cultures. pVEC, a CPP derived from cadherin, is able to translocate into mammalian cells, and it is also antimicrobial. Structure‐activity relationship and sequence alignment studies have suggested that the hydrophobic N‐terminus (LLIIL) of pVEC is essential for this peptide's uptake into eukaryotic cells. In this study, our aim was to examine the contribution of these residues to the antimicrobial action and the translocation mechanism of pVEC. We performed antimicrobial activity and microscopy experiments with pVEC and with del5 pVEC (N‐terminal truncated variant of pVEC) and showed that pVEC loses its antimicrobial effect upon deletion of the LLIIL residues, even though both peptides induce membrane permeability. We also calculated the free energy of the transport process using steered molecular dynamic simulations and replica exchange umbrella sampling simulations to compare the difference in uptake mechanism of the 2 peptides in atomistic detail. Despite the difference in experimentally observed antimicrobial activity, the simulations on the 2 peptides showed similar characteristics and the energetic cost of translocation of pVEC was higher than that of del5 pVEC, suggesting that pVEC uptake mechanism cannot be explained by simple passive transport. Our results suggest that LLIIL residues are key contributors to pVEC antibacterial activity because of irreversible membrane disruption.