Culture fluorescence dynamics in Xanthomonas campestris

Culture (NAD(P)H) fluorescence dynamics have been used to provide information on culture behaviour when Xanthomonas campestris was grown in a bioreactor. Culture fluorescence decreased by 1150 units in response to an increase in extracellular pH from 3.1 to 7.6. A mathematical model incorporating the effect of pH on the bulk NADH depletion reaction simulated the experimental data. The rates of bulk NADH formation and depletion reactions were 1 s⁻¹ and 719 (M h⁻¹)⁻¹ s⁻¹, respectively. Subsequent to the initial NADH decrease, the culture fluorescence increased to within 200 units of its original value, with a concomitant decrease in oxygen uptake rate (OUR) from 7.3 to 3 mM h⁻¹. A mathematical model incorporating the hypothesis that the culture manipulated its OUR to increase its NADH level, simulated the experimental data. In addition, it was inferred from culture fluorescence that the intracellular oxygen availability becomes insufficient at or below 10% extracellular dissolved oxygen value. Studies on H₂O₂ addition to X. campestris, to optimize the liquid-phase oxygen supply, showed no change in metabolic state, as indicated by NADH fluorescence, until 1.4 mmol H₂O₂ (g cell)⁻¹ and a significant decrease above that. Investigations on the reasons for decreases in NADH fluorescence suggested a DNA-damaging Fenton reaction as the probable reason for the observed NADH decrease on addition of H₂O₂.     

Molecular Docking and Pharmacological Investigations of Rivastigmine-Fluoxetine and Coumarin–Tacrine hybrids against Acetyl Choline Esterase

AbbreviationsAD - Alzheimer׳s Disease, AChE - Acetyl Choline Estarase, OPLS - Optimized Potentials for Liquid Simulations, PDB - Protein Data Bank.     

A convenient 'one-pot' synthesis and in vitro microbiological evaluation of novel 2,7-diaryl-[1,4] -diazepan-5-ones

A convenient method for the 'one-pot' synthesis of novel target molecule 2,7-diaryl-[1,4]-diazepan-5-ones from the respective 2,6-diaryl-piperidin-4-ones was catalyzed by NaHSO4.Al2O3 heterogeneous catalyst in dry media under microwave irradiation in solvent-free conditions. Moreover, the catalyst could be recovered and re-used up to 4 times after washing with ethyl acetate. They were evaluated for potential antibacterial activity against Staphylococcus aureus, beta-Haemolytic streptococcus, Vibreo cholerae, Salmonella typhii, Escherichia coli, Klebsiella pneumonia, Pseudomonas and antifungal activity against Aspergillus flavus, Aspergillus fumigatus, Mucor, Candida albicans and Rhizopus. Structure-Activity Relationship (SAR) led to the conclusion that, of all the compounds 25-32 tested, compound 30 exerted strong in vitro antibacterial activity against S. aureus, S. typhii, and Pseudomonas and all the compounds 25-32 were less active against E. coli, whereas all the compounds 25-32 displayed potent in vitro antifungal activity against all the fungal strains used, except compound 30, which was more effectual against Mucor.     

QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

Background

Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs).

Methodology/Principal Findings

We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F₂ population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions.

Conclusions/Significance

The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.     

Synthesis,spectral analysis,antibacterial and antifungal activities of some 4,6-diaryl-4,5-dihydro-3-hydroxy-2[H]-indazole—a novel fused indazole derivative

A novel class of 4,6-diaryl-4,5-dihydro-3-hydroxy-2[H]-indazoles 25-32 were synthesized and evaluated for their in vitro antibacterial and antifungal activities. Four Compounds, which all possessed electron withdrawing functional groups (–Cl, –NO₂, –Br) 27, 28, 30 and 32 were more potent against the tested bacterial/fungal strains than the standard bacterial and fungal drugs ciprofloxacin and fluconazole respectively.     

Database and interaction network of genes involved in oral cancer: Version II

The oral cancer gene database has been compiled to enable fast retrieval of updated information and role of the genes implicated in oral cancer. The first version of the database with 242 genes was published in Online Journal of Bioinformatics 8(1), 41-44, 2007. In the second version, the database has been enlarged to include 374 genes by adding 132 gene entries. The architecture and format of the database is similar to the earlier version, and includes updated information and external hyperlinks for all the genes. The functional gene interaction network for important biological processes and molecular functions has been rebuilt based on 374 genes using 'String 8.3'. The database is freely available at http://www.actrec.gov.in/OCDB/index.htm and provides the scientist information and external links for the genes involved in oral cancer, interactions between them, and their role in the biology of oral cancer along with clinical relevance.     

Engineering Proteins for Thermostability with iRDP Web Server

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.