An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host-pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.

antitussive potentiality offlower extract using a cough model induced by sulfur dioxide in mice

The methanol extract of the flowers of Lagerstroemia parviflora Roxb (Family: Lythraceae) was investigated for its effect on a cough model induced by sulphur dioxide gas in mice. It exhibited significant antitussive activity when compared with the control in a dose-dependent manner. The extract (100, 200, 300 mg kg(-1)) showed maximum inhibition of cough reflex at 90 min after drug administration and the antitussive activity was comparable to that of codeine phosphate, a standard antitussive agent.

Studies on Pharmacognostical features of Curcuma domestica Val

The microscopic and macroscopic characters of the rhizome of Curcuma domestica Val. were studied. The behavior of the powdered drug in the presence of various chemicals was also studied. Preliminary phytochemical screening on the various extracts of the rhizome was done in order to ascertain the various chemical constituents present. These studies were carried out to identify this plant for future research work.

Anthelmintic activity of root bark of Carissa carandas

The anthelmintic activity of the Imethanolic extract of the root bark of Carissa carandas was evaluated on adult Indian earthworm (Pheretima posthuma) using albendazole as a reference standard. The extract caused paralysis followed by the death of worm at the tested dose level. The extract at the highest tested concentration has anthelmintic activity comparable with that of standard drug albendazole.

Antidiarrhoeal evaluation of Aegle Marmelos (Correa) Linn. root extract

A study was undertaken to evaluate the in vitro and in vivo antidiarrhoeal potential of chloroform extract of the root of Aegle marmelos (Correa) Linn. The in vitro activity was determined by agar dilution and disc diffusion techniques. The extract was studied in vivo in rats. Of the 35 tested pathogenic diarrhoea causing strains, the extract was found to be mostly active against the strains of Vibrio cholerae, followed by Escherichia coli and Shigella spp. The in vitro activity was found to be comparable to that of ciprofloxacin. Further, Aegle marmelos root extract (AMRE) treated animals showed significant inhibitory activity against castor oil-induced diarrhoea. The results so obtained thus established the efficacy of AMRE as an effective antidiarrhoeal agent.

Antimicrobial potentiality of Phyllanthus amarus against drug resistant pathogens

The antimicrobial potentiality of the methanolic extract of Phyllanthus amarus (Family: Euphorbiaceae) was studied against some drug resistant pathogenic bacterial strains by disc diffusion and agar dilution method. The extract showed significant concentration-dependent antibacterial activity particularly against gram-negative microbes. The study illustrated the claim of the usefulness of the plant in dysenteric and diarrheal infections and also suggested its use in fever. The antibacterial action was mainly due to the isolated phyllanthin.

Effect of Mesua ferrea Linn. flower extract on Salmonella

Based on its traditional uses in folk medicine, the whole flower extract of Mesua ferrea Linn. was tested for its in vitro antimicrobial efficacy against five different strains of Salmonella spp. All the strains were found to be highly sensitive to the extract, MIC of the extract against each organism being 50 microg/ml. The extract was tested in vitro for its mode of antibacterial activity against S. Typhimurium NCTC 74 and it was found to be bactericidal in action. In vivo studies of this extract offered significant protection to Swiss albino mice at doses approximately 2 and 4 mg/mouse when challenged with 50 median lethal dose of S. Typhimurium NCTC 74. Further, the extract caused statistically significant reduction in viable count of the strain in liver, spleen and heart blood of challenged mice.

PHARMACOGNOSTICAL STUDIES ON THE LEAVES OF Cassia tora Linn. (FAM. CAESALPINIACEAE)

The leaves and seeds of Cassia tora (Family Caesalpinaceae) are used in the treatment of leprosy, ring worm, flatulence, colic, dyspepsia, constipation, cough, bronchitis and cardiac disorders in the Ayurvedic systems of medicine. The present study deals with the study of macroscopic characters of the leaves, ash values, extractive values, behavior on treatment with different chemical reagents and fluorescence characters under ultraviolet light. Preliminary phytochemical studies on different extractives of the leaves were also performed. These studies will help in the identification of the plant for further research.

Evaluation of antitussive activity of Lagerstroemia parviflora leaf extract

The methanol extract of the leaves of Lagerstroemia parviflora Roxb was investigated for its effect on a cough model induced by sulfur dioxide gas in mice. It exhibited significant antitussive activity when compared with the control in a dose-dependent manner. The L. parviflora extract (100, 200, 300 mg/kg) showed maximum inhibition of cough reflex at 90 min after drug administration and the antitussive activity was comparable to that of codeine phosphate, a standard antitussive agent.

STUDIES ON PHARMCOGNOSTICAL FEATURES OF Zizyphus mauritiana LINN. ROOT (FAMILY : RHAMNACEAE)

Description of the root of the plant, Zizyphus mauritiana Linn. the microscopical characters of the powdered root, its behavior on treatment with different chemical reagents, and the fluorescence character under ultraviolet light after treatment were studied to fix some pharmacognostical parameters. Preliminary phytochemical screening on the various extracts of the root of the plant was also performed. These studies were carried out to identify this plant for further research work.

Antibacterial potentiality ofMesua ferrea Linn. flowers

The antibacterial efficacy of the methanol extract of whole flowers of Mesua ferrea Linn. was studied against various strains of bacteria. It could inhibit a large number of Gram-positive and Gram-negative bacteria at concentration ranges of 100 to 50 microg/ml, or even lower, as against vibrios and Escherichia coli. In in vivo tests, used at concentrations of 100 and 200 microg/g of body weight, it offered significant protection to Swiss strain of albino mice when challenged with 50 MLD of a virulent strain Sulmonella typhimurium ATCC 6539. Mortality in mice due to these two dosages of the extract alone was insignificant. The extract at 200 microg/g body weight dosage, could significantly reduce the viable count of the strain Sulmonella typhimurium ATCC 6539 in liver, spleen and heart blood of the extract treated challenged mice.

High efficiency degradation of tetrahydrofuran (THF) using a membrane bioreactor: identification of THF-degrading cultures of Pseudonocardia sp. strain M1 and Rhodococcus ruber isolate M2

A mixed microbial culture capable of growing aerobically on tetrahydrofuran (THF) as a sole carbon and energy source was used as the inoculum in a 10 l working volume membrane bioreactor. Following start-up, the reactor was operated in batch mode for 24 h and then switched to continuous feed with 100% biomass recycle. On average, greater than 96% of THF fed to the reactor was removed during the 8-month study. THF loading rates ranged from 0.62 to 9.07 g l(-1) day(-1) with a hydraulic retention time of 24 h. THF concentrations as high as 800 mg/l were tolerated by the culture. Biomass production averaged 0.28 kg total suspended solids/kg chemical oxygen demand removed, i.e., comparable to a conventional wastewater treatment process. Periodic batch wasting resulted in a solids retention time of 7-14 days. Reactor biomass typically ranged from 4 to 10 g/l volatile suspended solids and the effluent contained no solids. Pure THF-degrading cultures were isolated from the mixed culture based on morphological characteristics, Gram-staining and THF degradation. Based on 16S rDNA analysis the isolates were identified as Pseudonocardia sp. M1 and Rhodococcus ruber M2.

Emergence of mesua ferrea linn. Leaf extract as a potent bactericide

The methanolic extract of leaves of Mesua ferrea Linn. were tested for its antibacterial potentiality against 103 various strains of bacteria including Staphylococcus aureus, Bacillus spps. Klebsiella spps., Streptococus pneumoniae, Sarcina lutea, Lactobacilus arabinosus, Escherichia coli, shigellae, salmonellae, Proteus spps., Pseudomonas spps. and the vibrios. Significant antibacterial effects were produced by the extract against Staphylococcus aureus, Bacillus sppa., lactobacilli, Escherichia coli, shigellae and salmonellae and the results were compared with standard antibiotic ciprofloxacin. Further the extract was proved to be bacterial in its action.

Antimicrobial potentiality of a phenothiazine group of antipsychotic drug-prochlorperazine

The antipsychotic drug, prochlorperazine (Pcp), was tested for its antimicrobial efficacy against 103 strains belonging to both gram positive and gram negative bacteria. The drug was found to possess maximum activity against Staphylococcus aureus, Vibrio cholerae and Shigella spp. Pcp was moderately active against E. coli but most of the strains belonging to Bacillus spp, Klebsiella spp, Salmonella spp and Lactobacillus spp were found to be resistant to this drug. The drug was tested for its mode of antibacterial activity against Shigella dysenteriae 1 and it was found to be bacteriostatic in action. In in vivo studies, Pcp offered significant protection to Swiss albino mice at concentrations of 0.75 micro g/g (P < 0.01) and 1.5 microg/g (P < 0.001) body weight when challenged with 50 median lethal dose of Salmonella typhimurium NCTC 74. Thus the result depicts that prochlorperazine may emerge as a strong antimicrobial drug to replace the conventional antibiotics and to overcome the problem of drug resistance.

Antimicrobial activity of the mycotoxin citrinin obtained from the fungus penicillium citrinum

The mycotoxin Citrinin was obtained from the fungus Penicillium citrinum. It was tested for it's Minimum Inhibitory Concentration (MIC) against some gram positive strains viz. Staphylococcus aureus, Bacillus pumilus, Bacillus subtillis, Bacillus cereus, Klebsiella pneumoniae, Streptococcus pneumoniae, Lactobacillus arabinosus and gram negative strains E.Coli, Shigella dysenteriae, shigella sonnei, shigella boydii, Salmonella typhimurium, Proteus mirabilis and Vibrio cholerae. Further the zones of inhibition produced by the fungal extract against the bacterial strains were assayed and compared with those produced by the standard antibiotic ciprofloxacin.

ANTIMICROBIAL ACTION OF THE LEAF EXTRACT OF Lagerstroemia parviflora Roxb

The benzene extract of the leaves of Lagerstroemia paviflora Roxb was tested for its Minimum Inhibitory Concentration (MIC) against Gram Positive Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, Klebsiella pneumoniae, Streptococcus pneumoniae, Lactobacillus arabinosus and gram negative strains E.Coli, Shigella dysenteriae, shigella sonnei, shigella boydii, Salmonella typhimurium, Proteus mirabilis and Vibrio cholerae. Further the zones of inhibition Produced by the crude extract against four selected bacterial strains were measured and compared with those produced by the standard antibiotic Ciprofloxacin against the same bacterial strains.

Phytochemical observation on leaf of lagerstromia parviflora (roxb)

Phytochemical studies of leaf of the plant Lagerstroemia Parviflora Roxb (Lythraceae) reveals the presence of phytosterols, tannins, alkaloids, glycosides and absence of saponin, flavanoid and triterpenoids have been reported in this plant for the first time.

Trifluoperazine: a broad spectrum bactericide especially active on staphylococci and vibrios

Trifluoperazine showed some significant antimicrobial activity when tested against 293 strains from two Gram-positive and eight Gram-negative genera. Minimum inhibitory concentrations of the drug were measured using an agar dilution technique. Forty six of 55 strains of Staphylococcus aureus were inhibited by 10-50 microg/ml of trifluoperazine. This drug also inhibited strains of Shigella spp., Vibrio cholerae and V. parahaemolyticus at a concentration of 10-100 microg/ml. Other bacteria including Pseudomonas spp. were moderately sensitive to trifluoperazine. In the in vivo studies this compound offered significant protection to Swiss albino mice at a concentration of 30 microg/mouse (P<0.001) when challenged with 50 median lethal dose of Salmonella typhimurium NCTC 74.

Comparisons of gene colinearity in genomes using GeneOrder2.0

Comparative genomics is enhanced by data mining the rapidly expanding DNA sequence databases. Because of the immense amount of data, computational tools and methods are needed to augment traditional manual visualizations and manipulations of these data. GeneOrder2.0, a Java-based interactive software programme, organizes genome sequence data into tabular and graphical visualizations of the extent of colinearity of genes between any two chromosome genomes of < or =250 kilobases. Both GenBank and proprietary data can be analyzed with this tool.

GeneOrder: comparing the order of genes in small genomes

MOTIVATION

The recent rapid rise in the availability of whole genome DNA sequence data has led to bottlenecks in their complete analysis. Specifically, there is a need for software tools that will allow mining of gene and putative gene data at a whole genome level. These new tools will complement the current set already in use for studying specific aspects of individual genes and putative genes in detail. A key software challenge is to make them user-friendly, without losing their flexibility and capability for use in research.

RESULTS

The creation of GeneOrder-a web-based interactive, computational tool-allows researchers to compare the order of genes in two genomes. It has been tested on full genome sequence data for viruses, mitochondria and chloroplasts that were obtained from the NCBI GenBank database. It is accessible at http://www.bif.atcc.org/GENEOrder/index.html. GeneOrder prepares the comparison in table form, listing the order of similar genes. Hyperlinks are provided from this output; these lead to the 'Protein Coding Regions' in the NCBI database.

Low-substrate regulated microaerophilic behavior as a stress response of aquatic and soil bacteria

Low-substrate regulated microaerophilic behavior (LSRMB) was observed in 10-54% of the bacteria isolated from several fresh-water lakes or ponds, subsurface soils, activated sludge, and Antarctic dry valley soils. Five Pseudomonas and two Bacillus type species showed LSRMB. A subsurface Pseudomonas jessenii strain was used as a model to show the metabolic interaction between substrate and oxygen concentrations, cell band movement, and the appearance of unique stress lipids and proteins. When the oxygen in the P. jessenii culture medium was increased from 11% to 100% saturation under atmospheric condition, the concentration of 17:0 cyclopropane fatty acid, a stress indicator, increased five-fold, and four unique proteins were also detected. This stress response occurred only in low-substrate media. It is our hypothesis that LSRMB is a common but under-appreciated trait of many aquatic and soil bacteria.