Integrating CDS/ISIS Databases with Greenstone Digital Library Software (GSDL)

CDS/ISIS is an advanced non-numerical information storage and retrieval software developed by UNESCO since 1985 to satisfy the need expressed by many institutions, especially in developing countries, to be able to streamline their information processing activities by using modern (and relatively inexpensive) technologies [1]. CDS/ISIS is available for MS-DOS, Windows and Unix operating system platforms. The formatting language of CDS/ISIS is one of its several strengths. It is not only used for formatting records for display but is also used for creating customized indexes. CDS/ISIS by itself does not facilitate in publishing its databases on the Internet nor does it facilitate in publishing on CD-ROMs. However, numbers of open source tools are now available, which enables in publishing CDS/ISIS databases on the Internet and also on CD-ROMs. In this paper, we have discussed the ways and means of integrating CDS/ISIS databases with GSDL, an open source digital library (DL) software.

Lipopeptides from the Banyan Endophyte, Bacillus subtilis K1: Mass Spectrometric Characterization of a Library of Fengycins

Mass spectrometric analysis of a banyan endophyte, Bacillus subtilis K1, extract showing broad spectrum antifungal activity revealed a complex mixture of lipopeptides, iturins, surfactins, and fengycins. Fractionation by reversed-phase high performance liquid chromatography (HPLC) facilitated a detailed analysis of fengycin microheterogeneity. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric studies permitted the identification of several new fengycin variants. Four major sites of heterogeneity are identified: (1) N-terminus beta-hydroxy fatty acid moiety, where chain length variation and the presence of unsaturation occur, (2) position 6 (Ala/Val/Ile/Leu), (3) position 10 (Val/Ile) within the macrocyclic ring, and (4) Gln to Glu replacement at position 8, resulting in fengycin variants that differ in mass by 1 Da. Diagnostic fragment ions provide a quick method for localizing the sites of variation in the macrocycle or the linear segment. Subsequent establishment of the sequences is achieved by MS/MS analysis of linear fengycin species produced by hydrolysis of the macrocyclic lactone. Unsaturation in the fatty acid chain and the presence of linear precursors in the B. subtilis K1 extract are also established by mass spectrometry. The anomalous distribution of intensities within isotopic multiplets is a diagnostic for Gln/Glu replacements. High resolution mass spectrometry facilitates the identification of fengycin species differing by 1 Da by localizing the variable position (Gln(8)/Glu(8)) in the fengycin variants.

Strain localization effect on system reliability based design of bridge abutments under earthquake loading

The component and system reliability based design of bridge abutments under earthquake loading is presented in the paper. Planar failure surface has been used in conjunction with pseudo-dynamic approach to compute seismic active earth pressures on an abutment. The pseudo-dynamic method, considers the effect of phase difference in shear waves, soil amplification along with the horizontal seismic accelerations, strain localization in backfill soil and associated post-peak reduction in the shear resistance from peak to residual values along a previously formed failure plane. Four modes of stability viz. sliding, overturning, eccentricity and bearing capacity of the foundation soil are considered in the analysis. The series system reliability is computed with an assumption of independent failure modes. The lower and upper bounds of system reliability are also computed by taking into account the correlations between four failure modes, which is evaluated using the direction cosines of the tangent planes at the most probable points of failure.

Assay development for identifying inhibitors of the mycobacterial FadD32 activity

FadD32, a fatty acyl-AMP ligase (FAAL32) involved in the biosynthesis of mycolic acids, major and specific lipid components of the mycobacterial cell envelope, is essential for the survival of Mycobacterium tuberculosis, the causative agent of tuberculosis. The protein catalyzes the conversion of fatty acid to acyl-adenylate (acyl-AMP) in the presence of adenosine triphosphate and is conserved in all the mycobacterial species sequenced so far, thus representing a promising target for the development of novel antituberculous drugs. Here, we describe the optimization of the protein purification procedure and the development of a high-throughput screening assay for FadD32 activity. This spectrophotometric assay measuring the release of inorganic phosphate was optimized using the Mycobacterium smegmatis FadD32 as a surrogate enzyme. We describe the use of Tm (melting temperature) shift assay, which measures the modulation of FadD32 thermal stability, as a tool for the identification of potential ligands and for validation of compounds as inhibitors. Screening of a selected library of compounds led to the identification of five novel classes of inhibitors.

Design and construction of geocell foundation to support the embankment on settled red mud

This paper presents the case history of the construction of a 3 m high embankment on the geocell foundation over the soft settled red mud. Red mud is a waste product from the Bayer process of Aluminum industry. Geotechnical problems of the site, the design of the geocell foundation based on experimental investigation and the construction sequences of the geocell foundations in the field are discussed in the paper. Based on the experimental studies, an analytical model was also developed to estimate the load carrying capacity of the soft clay bed reinforced with geocell and combination of geocell and geogrid. The results of the experimental and analytical studies revealed that the use of combination of geocell and the geogrid is always beneficial than using the geocell alone. Hence, the combination of geocell and geogrid was recommended to stabilize the embankment base. The reported embankment is located in Lanjigharh (Orissa) in India. Construction of the embankment on the geocell foundation has already been completed. The constructed embankmenthas already sustained two monsoon rains without any cracks and seepage. (C) 2013 Elsevier Ltd. All rights reserved.

A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library

With the development of deep sequencing methodologies, it has become important to construct site saturation mutant (SSM) libraries in which every nucleotide/codon in a gene is individually randomized. We describe methodologies for the rapid, efficient, and economical construction of such libraries using inverse polymerase chain reaction (PCR). We show that if the degenerate codon is in the middle of the mutagenic primer, there is an inherent PCR bias due to the thermodynamic mismatch penalty, which decreases the proportion of unique mutants. Introducing a nucleotide bias in the primer can alleviate the problem. Alternatively, if the degenerate codon is placed at the 5' end, there is no PCR bias, which results in a higher proportion of unique mutants. This also facilitates detection of deletion mutants resulting from errors during primer synthesis. This method can be used to rapidly generate SSM libraries for any gene or nucleotide sequence, which can subsequently be screened and analyzed by deep sequencing. (C) 2013 Elsevier Inc. All rights reserved.

Regioselective Synthesis of Nitrofuran Containing Novel Spiropyrrolidine Library through 1,3-Dipolar Cycloaddition Reactions

A novel series of nitrofuran containing spiropyrrolidines has been synthesized with high regioselectivity in moderate to excellent yields via 1,3-dipolar cycloaddition reaction of azomethine ylides with various substituted chalcones.

Lead selection and characterization of antitubercular compounds using the Nested Chemical Library

Discovering new drugs to treat tuberculosis more efficiently and to overcome multidrug resistance is a world health priority. To find novel antitubercular agents several approaches have been used in various institutions worldwide, including target-based approaches against several validated mycobacterial enzymes and phenotypic screens. We screened more than 17,000 compounds from Vichem's Nested Chemical Library(TM) using an integrated strategy involving whole cell-based assays with Corynebacterium glutamicum and Mycobacterium tuberculosis, and target-based assays with protein kinases PknA, PknB and PknG as well as other targets such as PimA and bacterial topoisomerases simultaneously. With the help of the target-based approach we have found very potent hits inhibiting the selected target enzymes, but good minimal inhibitory concentrations (MIC) against M. tuberculosis were not achieved. Focussing on the whole cell-based approach several potent hits were found which displayed minimal inhibitory concentrations (MIC) against M. tuberculosis below 10 mu M and were non-mutagenic, non-cytotoxic and the targets of some of the hits were also identified. The most active hits represented various scaffolds. Medicinal chemistry-based lead optimization was performed applying various strategies and, as a consequence, a series of novel potent compounds were synthesized. These efforts resulted in some effective potential antitubercular lead compounds which were confirmed in phenotypic assays. (C) 2015 Elsevier Ltd. All rights reserved.

Bearing capacity of a circular foundation on layered sand-clay media

The bearing capacity of a circular footing lying over fully cohesive strata, with an overlaying sand layer, is computed using the axisymmetric lower bound limit analysis with finite elements and linear optimization. The effects of the thickness and the internal friction angle of the sand are examined for different combinations of c(u)/(gamma b) and q, where c(u)=the undrained shear strength of the cohesive strata, gamma=the unit weight of either layer, b=the footing radius, and q=the surcharge pressure. The results are given in the form of a ratio (eta) of the bearing capacity with an overlaying sand layer to that for a footing lying directly over clayey strata. An overlaying medium dense to dense sand layer considerably improves the bearing capacity. The improvement continuously increases with decreases in c(u)/(gamma b) and increases in phi and q/(gamma b). A certain optimum thickness of the sand layer exists beyond which no further improvement occurs. This optimum thickness increases with an increase in 0 and q and with a decrease in c(u)/(gamma b). Failure patterns are also drawn to examine the inclusion of the sand layer. (C) 2015 The Japanese Geotechnical Society. Production and hosting by Elsevier B.V. All rights reserved.