Poly-3-hydroxyoctanoate P(3HO), a medium chain length polyhydroxyalkanoate homopolymer from Pseudomonas mendocina

Pseudomonas mendocina was found to produce a unique homopolymer of poly(3-hydroxyoctanoate), P(3HO), rather than a copolymer, when grown on sodium octanoate as the sole carbon source. Although this polymer has been produced by other organisms, interestingly this is the first time an absolute homopolymer has been produced by a wild type organism. In addition, a detailed study on the effects of different extraction methods on the yield, molecular weight, thermal properties, and lipopolysaccharide content of P(3HO) has been carried out. The organism was able to accumulate P(3HO) up to 31.38% of its dry cell weight within 48 h in mineral salt medium. Characterization of the monomer was carried out using FTIR, GC-MS, (13)C, (1)H, and HSQC NMR spectroscopy. The polymer had a crystallinity of 37.5%, Young's modulus value of 11.6 MPa and contact angle of 77.3°. Microstructural studies of solvent cast polymer films revealed a smooth surface topography with a root-mean-square roughness value of 0.238 μm.     

Experiments and three phase modelling of a biofilter for the removal of toluene and trichloroethylene

Volatile organic compounds, namely, toluene, trichloroethylene, styrene, etc., disposed off by electronics and polymer industries, are very harmful. The treatment of VOC laden air through biochemical route is one of the potential options for reduction of their concentration in parts per million or parts per billion level. Under the present investigation, a 0.05-m diameter and 0.58-m high trickle bed biofilter has been studied for the removal of VOCs namely toluene and trichloroethylene from a simulated air–VOC mixture using pure strain of Pseudomonas putida (NCIM2650) in immobilized form. Inlet concentrations of VOCs have been varied in two ranges, the lower being 0.20–2.00 g/m³ and higher being 10–20 g/m³, respectively. The Monod type rate kinetics of removal of VOCs has been determined. A three-phase deterministic mathematical model has been developed taking the simultaneous reaction kinetics and interphase (gas to liquid to biofilm) mass transfer rate of VOCs into consideration. Experimentally determined kinetic parameters and mass transfer coefficients calculated using standard correlations have been used. Concentrations have been simulated for all the three phases. Simulated results based on the model have been compared with the experimental ones for both gas and liquid phases satisfactorily. The mathematical model validated through the successful comparison with experimental data may be utilized for the prediction of performance of biofilters undergoing removal of different VOCs in any further investigation and may be utilized for the scale-up of the system to industrial scale.     

<Emphasis Type="Italic">Nif</Emphasis>H-based studies on azotobacterial diversity in cotton soils of India

In order to promote the use of Azotobacter inoculants for cotton crop, a complete characterization of soil isolates of Azotobacter, isolated and screened on the basis of physiological properties, from four different cotton–wheat cropping regions of India was carried out, and their genetic diversity determined by RFLP (restriction fragment length polymorphism) analysis of the functional gene nifH. Genetic analysis of these isolates depicted a similarity coefficient of ≥80% among them, suggesting that though the isolates were obtained from different cotton soils of India, still they have large commonality in the nifH gene and constituted a homogeneous nifH population.     

Clonality Despite Sex: The Evolution of Host-Associated Sexual Neighborhoods in the Pathogenic Fungus Penicillium marneffei

Molecular genetic approaches typically detect recombination in microbes regardless of assumed asexuality. However, genetic data have shown the AIDS-associated pathogen Penicillium marneffei to have extensive spatial genetic structure at local and regional scales, and although there has been some genetic evidence that a sexual cycle is possible, this haploid fungus is thought to be genetically, as well as morphologically, asexual in nature because of its highly clonal population structure. Here we use comparative genomics, experimental mixed-genotype infections, and population genetic data to elucidate the role of recombination in natural populations of P. marneffei. Genome wide comparisons reveal that all the genes required for meiosis are present in P. marneffei, mating type genes are arranged in a similar manner to that found in other heterothallic fungi, and there is evidence of a putatively meiosis-specific mutational process. Experiments suggest that recombination between isolates of compatible mating types may occur during mammal infection. Population genetic data from 34 isolates from bamboo rats in India, Thailand and Vietnam, and 273 isolates from humans in China, India, Thailand, and Vietnam show that recombination is most likely to occur across spatially and genetically limited distances in natural populations resulting in highly clonal population structure yet sexually reproducing populations. Predicted distributions of three different spatial genetic clusters within P. marneffei overlap with three different bamboo rat host distributions suggesting that recombination within hosts may act to maintain population barriers within P. marneffei.     

Resuscitation Promoting Factors: a Family of Microbial Proteins in Survival and Resuscitation of Dormant Mycobacteria

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is an extraordinarily successful pathogen of humankind. It has been estimated that up to one-third of the world’s population is infected with M. tuberculosis, and this population is an important reservoir for disease reactivation. Resuscitation promoting factor (Rpf) is a secretory protein, which was first reported in Micrococcus luteus. There are five functionally redundant Rpf-like proteins found in M. tuberculosis. Rpf promotes the resuscitation of dormant bacilli to yield normal, viable colony forming bacteria. All Rpfs share a conserved domain of about 70 amino acids and possess a lysozyme-like activity. The structural studies of the conserved domain suggest that Rpfs could be considered as a c-type lysozyme and lytic transglycosylases. Recently a novel class of nitrophenylthiocyanates (NPT) inhibitors of the muralytic activity of Rpf were reported which opens a new approach in the study of cell-wall hydrolyzing enzymes. This review describes molecular and structural studies conducted on Rpf proteins, their role in the resuscitation of dormant bacteria, in the reactivation of latent infection and identification of low molecular weight inhibitors of resuscitation promoting factors.     

In silico modeling of ligand molecule for non structural 3 (NS3) protein target of flaviviruses

Flaviviruses are small, enveloped RNA viruses which cause a variety of diseases into animals and man. Despite the existence of licensed vaccines, yellow fever, Japanese encephalitis and tick-borne encephalitis also claim many thousands of victims each year across their vast endemic areas. A number of studies have already revealed that the non-structural NS3 serine protease is required for the maturation of the viral polyprotein and thus is a promising target for the development of antiviral inhibitors. Hence, the 3D structure of NS3 protein was modeled using homology modeling by MODELLER 9v7. Validation of the constructed NS3 protein models were done by PROCHECK, VERYFY3D and through ProSA calculations. Ligands for the catalytic triad (H51, D75, and S135) were designed using LIGBUILDER. The NS3 protein's catalytic triad was explored to find out the interactions pattern for inhibitor binding using molecular docking methodology using AUTODOCK Vina. The interactions of complex NS3protein-ligand conformations, including hydrogen bonds and the bond lengths were analyzed using Accelrys DS Visualizer software. Hence, from this observation, the novel molecule designed was observed to be the best ligand against the NS3 protein of flavivirus. This molecule may prove to be a potential identity in modulating disease manifestation for all the selected flavivirus members. ABBREVIATIONS: NCBI - National Centre for Biotechnological Information, BLAST - Basic Local Alignment Search Tool, DOPE - Discrete optimized protein energy, GROMOS96 - GROningen MOlecular Simulation package, SAVS - Structure Analysis and Validation Server.     

Higher acyclic nitrogen containing deoxy sugar derivatives: a new lead in the generation of antimycobacterial chemotherapeutics

Syntheses of higher acyclic nitrogen containing deoxy sugar derivatives via nitroaldol reaction of different nitroalkanes with 2,3-dideoxy-alpha,beta-unsaturated aldehydo sugars obtained from glycals namely acetylated glucal and galactal and their in vitro antimycobacterial activity are presented.     

Isolation of colour components from native dye-bearing plants in northeastern India

Recently dyes derived from natural sources have emerged as important alternatives to synthetic dyes. A study was initiated in the year 2000 at the RRL (CSIR), Jorhat to extract dyes from parts of five different plant species indigenous to northeastern India. The colour components responsible for dyeing were isolated and their chemical constituents were established based on chemical and spectroscopic investigations. The principal colour components from the species Morinda angustifolia Roxb., Rubia cordifolia Linn. and Tectona grandis Linn. were found to contain mainly anthraquinone moieties in their molecules. Those from the species Mimusops elengi Linn. and Terminalia arjuna (Roxb.) Wight & Arn. contained flavonoid moieties in their molecules. The absorption of dye (%) on fibres increased with increasing concentrations of dye in the dye-bath. Maximum absorption of dyes on fibres was obtained at 3% concentration of dyes obtained from R. cordfolia (35.350%), M. angustifolia (31.580%) and T. grandis (25.888%) and at 4% concentration of the dyes from M. elengi (31.917%) and T. arjuna (12.246%). The K/S values were found to increase with the increase in concentration of mordants. The colour co-ordinates of dyed samples were found to lie in the yellow-red quadrant of the colour space diagram. The dyes obtained from the native plants may be alternative sources to synthetic dyes for the dyeing of natural silk and cotton.