Design and implementation of a domain specific language for phylogenetic inference

Domain experts think and reason at a high level of abstraction when they solve problems in their domain of expertise. We present the design and motivation behind a domain specific language, called phi LOG, to enable biologists to program solutions to phylogenetic inference problems at a very high level of abstraction. The implementation infrastructure (interpreter, compiler, debugger) for the DSL is automatically obtained through a software engineering framework based on Denotational Semantics and Logic Programming.     

Management of massive pulmonary embolism after jejuno-ileal bypass for morbid obesity

Four patients developed massive pulmonary embolism after jejuno-ileal bypass for morbid obesity. All patients were in Greenfield's Class IV and were in shock. Severe hypoxia was evidenced in their blood gases. The patients were managed with digitalis, diuretics, Solu-Medrol (methylprednisolone sodium succinate), oxygen, and heparin therapy. Each patient underwent partial vena cava interruption with Mobin Uddin's umbrella, and all four survived without residual complications.     

Membrane-fusions and cytoplasmic bridges in the cells of the developing cerebellum

Summary In the developing cerebellum of the neonate rats membranefusions and cytoplasmic bridges between cells were observed. These membrane-fusions were characterized by the presence of loops of membrane and cytoplasmic bridges between the two limits of the membrane-fusions. They were found between Purkinje cells, Purkinje cells and the migratory cells, mitotically potent cells of the external granular layer, and differentiating granule cells of the internal granular layer. The membrane-fusions were found to be a transient developmental phenomenon. Issues pertaining to the universality of membrane-fusions, their significance in the induction for cell differentiation, and the problem of fixation artifacts are discussed.This research was supported by N.I.H. Research Grants No. NS-08817 and CA-14650. Assistance of Mrs. Kunda Das in various aspects of electron microscopy is gratefully acknowledged     

Antimicrobial efficacy,disease inhibition and phenolic acid-inducing potential of chloroform fraction of cow urine

High-performance liquid chromatographic (HPLC) analysis of chloroform fraction (CF) of cow urine showed rich pool of phenolic acids. Antifungal and antibacterial bioassays of CF have shown its tremendous efficacy against some fungal plant pathogens as well as human pathogenic bacteria at very low concentrations. The CF also inhibited powdery mildew (Erysiphe cichoracearum) of balsam (Impatiens balsamania) under field conditions during pre- and post-inoculation treatments. HPLC analysis of pre- and post-inoculation-treated plant leaves indicated that CF induced phenolic acid synthesis as compared to control. The results revealed that CF of cow urine has the potential for controlling some important human diseases. The result on balsam powdery mildew is a good signal that CF may also be effective against other plant diseases in the field.     

Contribution to the physiology ofTrigonella infected withPeronospora trifoliorum

Some biochemical properties ofTrigonella foenum-groecum infected withPeronospora trifoliorum have been investigated. Qualitative changes were observed in lipids, coumarins, amino acids and indole compounds only. A quantitative study of the phosphate content was also carried out. Neutral lipids did not show any significant changes. In addition to the fourteen phospholipid bands, the infected leaves contained a new band corresponding in R_f to phosphatidic acid or polyglycerophosphate. Seven coumarins were present in both the extracts. In addition 3-hydroxy coumarin, 5-hydroxy-4-methylcoumarin and 7-hydroxy-4-methyl-coumarin were detected in infected leaves. Higher levels of indole acetic acid and three of its derivatives were observed due to infection. Infection altered the free amino acid content. Tryptophan appeared and the total phosphate content increased. Increase in phenols and indoles suggest a higher respiratory rate whereas a higher content of inorganic phosphate suggests uncoupling of phosphorylation from respiration.     

Inventory and classification of wetlands in India

The Indian subcontinent has a large variety of freshwater, saline and marine wetlands. Whereas the mangroves are relatively well documented, very little is known about the other wetlands, with few exceptions. Only recently an inventory of these welands has been prepared but no effort has been made to classify them. A vast majority of the inland wetlands are temporary and/or man-made, and they have been traditionally used and managed by the local human populations. In this paper, first, we evaluate the classification schemes of the IUCN, US Fish and Wildlife Services and those of the Australian wetlands, for their applicability to Indian wetlands. Then, we propose a simple hierarchical classification of wetlands based on their location (coastal or inland), salinity (saline or freshwater), physiognomy (herbaceous or woody), duration of flooding (permanent or seasonal) and the growth forms of the dominant vegetation. We stress upon the hydrological factors which determine all the structural and functional characteristics of the wetlands. We consider that the various growth forms of wetland vegetation integrate the totality of hydrological variables and therefore, can be used as the indicators of different hydrological regimes.     

Production of thermostable pullulanase by Clostridium thermosulfurogenes SV2 in solid-state fermentation: optimization of enzyme leaching conditions using response surface methodology

The optimization of parameters for the effective leaching of thermostable pullulanase from Clostridium thermosulfurogenes SV2-fermented bran was carried out using response surface methodology based on the central composite rotatable design. The design contains a total of 54 experimental trials with the first 32 organized in a fractional factorial design and experimental trials from 33-40 and 51-54 involving the replication of the central points. The design was employed by selecting solvent to wheat bran ratio (S/BB), process temperature, solvent pH, shaking (RPM) and contact time (h) as model factors. Among the five independent variables studied, the S/BB, solvent pH and shaking were found to be significant. S/BB ratio of 9.0, 200 RPM shaking and solvent pH 6.0 were identified as optimum for the leaching of thermostable pullulanase from the strain SV2-fermented bran.     

Apigenin shows synergistic anticancer activity with curcumin by binding at different sites of tubulin

Apigenin, a natural flavone, present in many plants sources, induced apoptosis and cell death in lung epithelium cancer (A549) cells with an IC₅₀ value of 93.7 ± 3.7 μM for 48 h treatment. Target identification investigations using A549 cells and also in cell-free system demonstrated that apigenin depolymerized microtubules and inhibited reassembly of cold depolymerized microtubules of A549 cells. Again apigenin inhibited polymerization of purified tubulin with an IC₅₀ value of 79.8 ± 2.4 μM. It bounds to tubulin in cell-free system and quenched the intrinsic fluorescence of tubulin in a concentration- and time-dependent manner. The interaction was temperature-dependent and kinetics of binding was biphasic in nature with binding rate constants of 11.5 × 10⁻⁷ M⁻¹ s⁻¹ and 4.0 × 10⁻⁹ M⁻¹ s⁻¹ for fast and slow phases at 37 °C, respectively. The stoichiometry of tubulin–apigenin binding was 1:1 and binding the binding constant (K_d) was 6.08 ± 0.096 μM. Interestingly, apigenin showed synergistic anti-cancer effect with another natural anti-tubulin agent curcumin. Apigenin and curcumin synergistically induced cell death and apoptosis and also blocked cell cycle progression at G₂/M phase of A549 cells. The synergistic activity of apigenin and curcumin was also apparent from their strong depolymerizing effects on interphase microtubules and inhibitory effect of reassembly of cold depolymerized microtubules when used in combinations, indicating that these ligands bind to tubulin at different sites. In silico modeling suggested apigenin bounds at the interphase of α–β-subunit of tubulin. The binding site is 19 Å in distance from the previously predicted curcumin binding site. Binding studies with purified protein also showed both apigenin and curcumin can simultaneously bind to purified tubulin. Understanding the mechanism of synergistic effect of apigenin and curcumin could be helped to develop anti-cancer combination drugs from cheap and readily available nutraceuticals.