Use of Trinitrobenzene as a Nitrogen Source by Pseudomonas vesicularis Isolated from Soil

An aerobic Gram-negative bacterium identified as Pseudomonas vesicularis was isolated from soil contaminated with 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitrobenzene (TNB). This bacterium used TNB as the sole source of nitrogen. The TNB was metabolized within 80 h of incubation. The major metabolites produced were dinitroaniline, dinitrobenzene (DNB), nitroaniline, nitrobenzene (NB), and ammonia. The concentrations of DNB and NB produced in the culture medium were nearly stoichiometric. The ammonia concentration in the culture medium increased during the course of incubation. The end product of TNB metabolism was NB, which did not undergo further degradation even after long incubation time. This bacterium could be used in a syntrophic culture system with other NB-degrading bacteria to remove TNB completely from soil and water at contaminated sites. Received: 25 July 1996 / Accepted: 10 September 1996     

Antioxidant activity evaluation of essential oil and RAPD analysis of in vitro regenerated Blumea mollis (D. Don) Merr.

Essential oil obtained from the leaves of Blumea mollis (D. Don) Merr. was analyzed by gas chromatography and gas chromatography coupled with mass spectroscopy (GC and GC–MS). Bicyclic sesquiterpene, β-caryophyllene, was identified as a major compound which accounted for 24.54 %. Antioxidant activity of oil was significantly higher than that of methanol extract of callus. Murashige and Skoog (MS) medium supplemented with 4.4 μM BA showed multiple shoot induction after 8 weeks of culture. 4.6 μM Kin showed in vitro flowering and direct organogenesis was observed from the leaf explants on medium containing 4.4 μM BA and 5.4 μM NAA. Rooted plantlets developed on half strength MS medium fortified with 2.1 μM IBA were hardened and percentage survival was recorded up to 70. RAPD analysis revealed a little genetic variation in micropropagated plants.     

Effect of Organic Acids on Shrimp Pathogen, <Emphasis Type="Italic">Vibrio harveyi</Emphasis>

Shrimp farming accounts for more than 40% of the world shrimp production. Luminous vibriosis is a shrimp disease that causes major economic losses in the shrimp industry as a result of massive shrimp kills due to infection. Some farms in the South Asia use antibiotics to control Vibrio harveyi, a responsible pathogen for luminous vibriosis. However, the antibiotic-resistant strain was found recently in many shrimp farms, which makes it necessary to develop alternative pathogen control methods. Short-chain fatty acids are metabolic products of organisms, and they have been used as food preservatives for a long time. Organic acids are also commonly added in feeds in animal husbandry, but not in aquaculture. In this study, growth inhibitory effects of short-chain fatty acids, namely formic acid, acetic acid, propionic acid, and butyric acid, on V. harveyi were investigated. Among four acids, formic acid showed the strongest inhibitory effect followed by acetic acid, propionic acid, and butyric acid. The minimum inhibitory concentration (MIC) of 0.035% formic acid suppressed growth of V. harveyi. The major inhibitory mechanism seems to be the pH effect of organic acids. The effective concentration 50 (EC₅₀) values at 96 h inoculation for all organic acids were determined to be 0.023, 0.041, 0.03, and 0.066% for formic, acetic, propionic, and butyric acid, respectively. The laboratory study results are encouraging to formulate shrimp feeds with organic acids to control vibrio infection in shrimp aquaculture farms.     

Inhibition of tetraphenylphosphonium-induced NMR-visible lipid accumulation in human breast cells by chlorpromazine

The effects of chlorpromazine (CPZ) on the lipid accumulation induced by the cationic lipophilic compound tetraphenylphosphonium chloride (TPP) were examined using proton nuclear magnetic resonance spectroscopy (NMR), lipid extraction and thin layer chromatography (TLC), and electron microscopy (EM). Chlorpromazine at concentrations of 12 or 25 microM significantly reduced the NMR-visible lipid accumulation induced by a 48-h treatment with 6.25 microM TPP in the human breast cell line, HBL-100, without affecting cell viability. TPP caused threefold increases in whole-cell triglyceride levels that were attenuated by the addition of CPZ. Electron micrographs of TPP-treated HBL-100 cells showed that the destruction of mitochondria was accompanied by the accumulation of lipid droplets and myelinoid bodies. The addition of CPZ to TPP-treated cells reduced the occurrence of lipid droplets but not of mitochondrial destruction. Treatment with CPZ, in the presence or absence of TPP, resulted in large cytoplasmic inclusions indicating the inhibition of lysosomal metabolism. The induction and attenuation of NMR-visible lipids in conjunction with concomitant changes in both intracellular lipid droplets and whole-cell triglyceride levels provides evidence that NMR-visible lipids arise from cytoplasmic neutral lipid droplets. The observation that CPZ, a known inhibitor of lysosomal and cytosolic lipid metabolism, attenuates the formation of neutral triglycerides indicates that lysosomal processing may be a major step in the accumulation of NMR-visible lipid in breast cell lines.     

Methanogenic Activity in Human Periodontal Pocket

Samples of subgingival dental tissues were examined for the presence of methanogenic activities. Using enrichment cultures, methanogenic activities were detected in 9 of 17 individuals. A mesophilic, Gram-positive, irregular coccoid methanogen, which showed close resemblance to a Methanosarcina sp., was isolated from one sample collected from a patient with type IV periodontal pocket (the periodontal pocket is a space bounded by the tooth on one side and by ulcerated epithelium lining the soft tissue wall on the other). The isolate used methanol, methylamine, acetate, and H₂-CO₂ as the sole source of carbon. However, the isolate was unable to use formate and trimethylamine as growth substrates. The organism had an optimum pH of 6.5 and an optimum temperature of 37°C. The isolate not only used ammonia, but also used nitrate as a nitrogen source. The niche of this methanogen in periodontal pockets may be to carry out terminal oxidation of simple organic compounds such as methanol and acetate produced by other obligate anaerobes present in periodontal pockets. This methanogen may also play a vital role in interspecies hydrogen transfer, as demonstrated by its use of H₂-CO₂ as a substrate. The isolate produced significant amount of methane in vitro. Received: 27 February 2002 / Accepted: 29 March 2002     

Augmenting Chinese hamster genome assembly by identifying regions of high confidence

Chinese hamster Ovary (CHO) cell lines are the dominant industrial workhorses for therapeutic recombinant protein production. The availability of genome sequence of Chinese hamster and CHO cells will spur further genome and RNA sequencing of producing cell lines. However, the mammalian genomes assembled using shot‐gun sequencing data still contain regions of uncertain quality due to assembly errors. Identifying high confidence regions in the assembled genome will facilitate its use for cell engineering and genome engineering. We assembled two independent drafts of Chinese hamster genome by de novo assembly from shotgun sequencing reads and by re‐scaffolding and gap‐filling the draft genome from NCBI for improved scaffold lengths and gap fractions. We then used the two independent assemblies to identify high confidence regions using two different approaches. First, the two independent assemblies were compared at the sequence level to identify their consensus regions as ”high confidence regions“ which accounts for at least 78 % of the assembled genome. Further, a genome wide comparison of the Chinese hamster scaffolds with mouse chromosomes revealed scaffolds with large blocks of collinearity, which were also compiled as high‐quality scaffolds. Genome scale collinearity was complemented with EST based synteny which also revealed conserved gene order compared to mouse. As cell line sequencing becomes more commonly practiced, the approaches reported here are useful for assessing the quality of assembly and potentially facilitate the engineering of cell lines.     

Antiviral activity of selected medicinal plants and marine seaweeds on the grasserie infected larvae of silkworm,Bombyx mori

Nuclear polyhedrosis virus (NPV) is the most harmful virus responsible for the manifestation of grasserie disease in the larvae of silkworm, Bombyx mori. It causes a huge economic loss in the sericulture industry. An attempt was made in the present investigation for the screening of antiviral activity using medicinal plants such as Lantana camara, Phyllanthus amarus and marine seaweeds such as Sargassum wightii, Turbinaria ornata against BmNPV. Crude extracts were prepared using different solvents, such as hexane, ethyl acetate, methanol and water. The silkworm feeding bioassay study was carried out with the crude extracts to investigate the presence of anti-BmNPV activity after inoculating fifth instar larvae of silkworm with occlusion bodies (OBs) of BmNPV. Each extract was tested for their anti-BmNPV activity using various concentrations of crude extracts ranging from 200 μg to 1000 μg. Among the crude extracts tested, methanol and aqueous extracts of P. amarus showed significant anti-BmNPV activity.     

Effect of colchicine induced tetraploidy on morphology,cytology, essential oil composition,gene expression and antioxidant activity of Citrus limon (L.) Osbeck

Citrus limon (L.) Osbeck cultivated all over the world is a valuable source of aromatic essential oil. To develop tetraploids of C. limon, four different concentration of colchicine (0.025, 0.05, 0.1 and 0.2%; w/v) and three varied exposure time (12, 24 and 48 h) were employed. The ploidy level of diploids (2n = 2x = 18) and tetraploids (2n = 4x = 36) were determined by direct chromosome count and confirmed by flow cytometric analyses. Successful result with maximum tetraploidy frequency was observed in plantlets developed from seeds treated with 0.025% colchicine for 24 h. Morphological and stomatal characteristics indicated that tetraploids were taller with increased leaf and root length. On the other side, the leaves of tetraploids had fewer and larger stomata with a greater number of chloroplasts in guard cells in contrast with diploids. GC–GC/MS analyses showed cyclic monoterpene, limonene had increased significantly in tetraploids and was further confirmed by HPLC quantification. RT-PCR analyses revealed unaltered expression of monoterpene synthase, sesquiterpene synthase and flavone synthase and remarkable upregulation of genes such as limonene synthase, chalcone synthase and phenylalanine ammonia lyase in tetraploids. Antioxidant activity of essential oil of tetraploids was higher than diploids in all the five test systems studied. Overall, the findings of the present study prove that colchicine induced tetraploidy in C. limon could be a greater source of essential oil with improved composition and of economic significance.     

Antigen-antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures

The structures of protein antigen-antibody (Ag-Ab) interfaces contain information about how Ab recognize Ag as well as how Ag are folded to present surfaces for Ag recognition. As such, the Ab surface holds information about Ag folding that resides with the Ab-Ag interface residues and how they interact. In order to gain insight into the nature of such interactions, a data set comprised of 53 non-redundant 3D structures of Ag-Ab complexes was analyzed. We assessed the physical and biochemical features of the Ag-Ab interfaces and the degree to which favored interactions exist between amino acid residues on the corresponding interface surfaces. Amino acid compositional analysis of the interfaces confirmed the dominance of TYR in the Ab paratope-containing surface (PCS), with almost two fold greater abundance than any other residue. Additionally TYR had a much higher than expected presence in the PCS compared to the surface of the whole antibody (defined as the occurrence propensity), along with aromatics PHE, TRP, and to a lesser degree HIS and ILE. In the Ag epitope-containing surface (ECS), there were slightly increased occurrence propensities of TRP and TYR relative to the whole Ag surface, implying an increased significance over the compositionally most abundant LYS > ASN > GLU > ASP > ARG. This examination encompasses a large, diverse set of unique Ag-Ab crystal structures that help explain the biological range and specificity of Ag-Ab interactions. This analysis may also provide a measure of the significance of individual amino acid residues in phage display analysis of Ag binding.     

Stabilization of type I collagen using dialdehyde cellulose

Type I collagen from rat tail tendon (RTT) fibres was crosslinked with dialdehyde cellulose to bring about stabilization of the matrix. Dialdehyde cellulose (DAC) was prepared by periodate oxidation of hydrolyzed cellulose. Autoclaving of DAC resulted in hydrolysis and lower molecular weight oligomeric species. The formation of the crosslinked network between DAC and the collagen fibres has brought about significant thermal and enzymatic stability to collagen. DAC crosslinked collagen fibres exhibited an increase in hydrothermal stability by 20 °C with autoclaved DAC at pH 8. The collagen matrix resulted in an increase in denaturation peak temperature (T_D) and an increase in phase change of activation energy (E_a) and enthalpy change (ΔH) for the shinking process indicating intermolecular crosslinking arising from covalent interactions. Thermal stability and crosslinking efficiency was found to increase with pH and concentration of DAC. DAC treated collagen exhibited 93% resistance to collagenolytic hydrolysis.