Identification of alpha- and beta-Hydroxy Acid Containing Cyclodepsipeptides in Natural Peptide Mixtures Using Negative Ion Mass Spectrometry

Natural peptide libraries often contain cyclodepsipeptides containing alpha or beta hydroxy residues. Extracts of fungal hyphae of Isaria yield a microheterogenous cyclodepsipeptide mixture in which two classes of molecules can be identified by mass spectral fragmentation of negative ions. In the case of isaridins, which contain an alpha-hydroxy residue and a beta-amino acid residue, a characteristic product ion corresponding to a neutral loss of 72 Da is obtained. hi addition, neutral loss of water followed by a 72 Da loss is also observed. Two distinct modes of fragmentation rationalize the observed product ion distribution. The neutral loss of 72 Da has also been obtained for a roseotoxin component, which is also an alpha-hydroxy residue containing cyclodepsipeptide. In the case of isariins, which contain a beta-hydroxy acid residue, ring opening and subsequent loss of the terminal residue as an unsaturated ketene fragment, rationalizes the observed product ion formation. Fragmentation of negative ions provide characteristic neutral losses, which are diagnostic of the presence of alpha-hydroxy or beta-hydroxy residues.

sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.

Isolation of an 800 kb contiguous DNA fragment encompassing a 3.5-cM region of chromosome 1 in Arabidopsis using YAC clones

The apetalal mutation of Arabidopsis affects floral meristem identity and the development of sepal and petal primordia of the flower. We mapped the available RFLP markers on chromosome 1 that are in the general vicinity of apetalal on a fine structure map and then chose the closest RFLP as a starting point for contiguous DNA (contig) generation. We report here a contig of about 800 kilobases (kb) that spans a 3.5 cM region of chromosome 1. We used genomic libraries of Arabidopsis prepared in yeast artificial chromosome (YAC) vectors and the detailed characterization of 19 YACs is reported. RFLPs displayed by the end fragments from the walk were mapped to align and correlate the genetic and physical maps for this region of chromosome 1. In this segment of the genome, 1 cM corresponds to a little over 200 kb of physical distance.

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.

Implementing WWWISIS for Providing Web Access to Bibliographic Databases

CDS/ISIS, an advanced non-numerical information storage and retrieval software was developed by UNESCO. With the emergence of WWW technology, most of the information activities are becoming Web-centric. Libraries and information providers are taking advantage of these Internet developments to provide access to their resources/information on the Web. A number of tools are now available for publishing CDS/ISIS databases on the Internet. One such tool is the WWWISIS Web gateway software, developed by BIREME, Brazil. This paper illustrates porting of sample records from a bibliographic database into CDS/ISIS, and then publishing this database on the Internet using WWWISIS.

A Tutorial on Integrating CDS/ISIS Databases with the World Wide Web

With the emergence of Internet, the global connectivity of computers has become a reality. Internet has progressed to provide many user-friendly tools like Gopher, WAIS, WWW etc. for information publishing and access. The WWW, which integrates all other access tools, also provides a very convenient means for publishing and accessing multimedia and hypertext linked documents stored in computers spread across the world. With the emergence of WWW technology, most of the information activities are becoming Web-centric. Once the information is published on the Web, a user can access this information from any part of the world. A Web browser like Netscape or Internet Explorer is used as a common user interface for accessing information/databases. This will greatly relieve a user from learning the search syntax of individual information systems. Libraries are taking advantage of these developments to provide access to their resources on the Web. CDS/ISIS is a very popular bibliographic information management software used in India. In this tutorial we present details of integrating CDS/ISIS with the WWW. A number of tools are now available for making CDS/ISIS database accessible on the Internet/Web. Some of these are 1) the WAIS_ISIS Server. 2) the WWWISIS Server 3) the IQUERY Server. In this tutorial, we have explained in detail the steps involved in providing Web access to an existing CDS/ISIS database using the freely available software, WWWISIS. This software is developed, maintained and distributed by BIREME, the Latin American & Caribbean Centre on Health Sciences Information. WWWISIS acts as a server for CDS/ISIS databases in a WWW client/server environment. It supports functions for searching, formatting and data entry operations over CDS/ISIS databases. WWWISIS is available for various operating systems. We have tested this software on Windows '95, Windows NT and Red Hat Linux release 5.2 (Appolo) Kernel 2. 0. 36 on an i686. The testing was carried out using IISc's main library's OPAC containing more than 80,000 records and Current Contents issues (bibliographic data) containing more than 25,000 records. WWWISIS is fully compatible with CDS/ISIS 3.07 file structure. However, on a system running Unix or its variant, there is no guarantee of this compatibility. It is therefore safe to recreate the master and the inverted files, using utilities provided by BIREME, under Unix environment.

Voltage and Temperature Scalable Standard Cell Leakage Models Based on Stacks for Statistical Leakage Characterization

With extensive use of dynamic voltage scaling (DVS) there is increasing need for voltage scalable models. Similarly, leakage being very sensitive to temperature motivates the need for a temperature scalable model as well. We characterize standard cell libraries for statistical leakage analysis based on models for transistor stacks. Modeling stacks has the advantage of using a single model across many gates there by reducing the number of models that need to be characterized. Our experiments on 15 different gates show that we needed only 23 models to predict the leakage across 126 input vector combinations. We investigate the use of neural networks for the combined PVT model, for the stacks, which can capture the effect of inter die, intra gate variations, supply voltage(0.6-1.2 V) and temperature (0 - 100degC) on leakage. Results show that neural network based stack models can predict the PDF of leakage current across supply voltage and temperature accurately with the average error in mean being less than 2% and that in standard deviation being less than 5% across a range of voltage, temperature.

Voltage and Temperature Scalable Gate Delay and Slew Models Including Intra-Gate Variations

We investigate the feasibility of developing a comprehensive gate delay and slew models which incorporates output load, input edge slew, supply voltage, temperature, global process variations and local process variations all in the same model. We find that the standard polynomial models cannot handle such a large heterogeneous set of input variables. We instead use neural networks, which are well known for their ability to approximate any arbitrary continuous function. Our initial experiments with a small subset of standard cell gates of an industrial 65 nm library show promising results with error in mean less than 1%, error in standard deviation less than 3% and maximum error less than 11% as compared to SPICE for models covering 0.9- 1.1 V of supply, -40degC to 125degC of temperature, load, slew and global and local process parameters. Enhancing the conventional libraries to be voltage and temperature scalable with similar accuracy requires on an average 4x more SPICE characterization runs.

Voltage and Temperature Scalable Gate Delay and Slew Models Including Intra-Gate Variations

We investigate the feasibility of developing a comprehensive gate delay and slew models which incorporates output load, input edge slew, supply voltage, temperature, global process variations and local process variations all in the same model. We find that the standard polynomial models cannot handle such a large heterogeneous set of input variables. We instead use neural networks, which are well known for their ability to approximate any arbitrary continuous function. Our initial experiments with a small subset of standard cell gates of an industrial 65 nm library show promising results with error in mean less than 1%, error in standard deviation less than 3% and maximum error less than 11% as compared to SPICE for models covering 0.9- 1.1 V of supply, -40degC to 125degC of temperature, load, slew and global and local process parameters. Enhancing the conventional libraries to be voltage and temperature scalable with similar accuracy requires on an average 4x more SPICE characterization runs.

Describing Hand Postures: Inspirations from Classical Mudras

The objective of this work is to develop a systematic methodology for describing hand postures and grasps which is independent of the kinematics and geometry of the hand model which in turn can be used for developing a universal referencing scheme. It is therefore necessary that the scheme be general enough to describe the continuum of hand poses. Indian traditional classical dance form, “Bharathanatyam”, uses 28 single handed gestures, called “mudras”. A Mudra can be perceived as a hand posture with a specific pattern of finger configurations. Using modifiers, complex mudras could be constructed from relatively simple mudras. An adjacency matrix is constructed to describe the relationship among mudras. Various mudra transitions can be obtained from the graph associated with this matrix. Using this matrix, a hierarchy of the mudras is formed. A set of base mudras and modifiers are used for describing how one simple posture of hand can be transformed into another relatively complex one. A canonical set of predefined hand postures and modifiers can be used in digital human modeling to develop standard hand posture libraries.

Methods for Automatic Evaluation of Sentence Extract Summaries

This paper describes three novel techniques to automatically evaluate sentence extract summaries. Two of these techniques called FuSE and DeFuSE evaluate the quality of the generated extract summary based on the degree of similarity to the model summary. They use a fuzzy set theoretic basis to generate a match score. DeFuSE is an enhancement to FuSE and uses WordNet based hypernymy structures to detect similarity between sentences at abstracted levels. The third technique focuses on quantifying the quality of an extract summary based on the difficulty in generating such a summary. Advantages of these techniques are described with examples.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

Extending the Supramolecular Synthon Based Fragment Approach (SBFA) for Transferability of Multipole Charge Density Parameters to Monofluorobenzoic Acids and their Cocrystals with Isonicotinamide: Importance of C-H center dot center dot center dot O, C-H center dot center dot center dot F, and F center dot center dot center dot F Intermolecular Regions

An extension of the supramolecular synthon-based fragment approach (SBFA) method for transferability of multipole charge density parameters to include weak supramolecular synthons is proposed. In particular, the SBFA method is applied to C-H center dot center dot center dot O, C-H center dot center dot center dot F, and F center dot center dot center dot F containing synthons. A high resolution charge density study has been performed on 4-fluorobenzoic acid to build a synthon library for C-H center dot center dot center dot F infinite chain interactions. Libraries for C-H center dot center dot center dot O and F center dot center dot center dot F synthons were taken from earlier work. The SBFA methodology was applied successfully to 2- and 3-fluorobenzoic acids, data sets for which were collected in a routine manner at 100 K, and the modularity of the synthons was demonstrated. Cocrystals of isonicotinamide with all three fluorobenzoic acids were also studied with the SBFA method. The topological analysis of inter- and intramolecular interaction regions was performed using Bader's AIM approach. This study shows that the SBFA method is generally applicable to generate charge density maps using information from multiple intermolecular regions.