(SI10-056) Fear Effect in a Three Species Prey-predator Food-web System With Harvesting

Some recent studies and field experiments show that predators affect their prey not only by direct capture; they also induce fear in prey species, which reduces their reproduction rate. Considering this fact, we propose a mathematical model to study the fear effect of a middle predator on its prey in a three-species food web system with harvesting. The ecological feasibility of solutions to the proposed system is guaranteed in terms of positivity and boundedness. The local stability of stationary points in the proposed system is derived. Multiple co-existing stationary points for the proposed system are observed, which makes the problem more interesting compared to the similar models studied previously. The local existence of periodic solutions through Hopf bifurcations is additionally secured numerically in the case of both unique and multiple coexisting stationary points. It is also observed that the system can exhibit strange attractors in the form of chaos. A detailed numerical simulation is performed to ensure the existence of periodic solutions and period- doubling routes to chaos. Combined effects of fear and harvesting are also discussed numerically

IDENTIFICATION OF POTENTIAL SALMONELLA TYPHI BETA-LACTAMASE TEM 1 INHIBITORS USING PEPTIDOMIMETICS, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS SIMULATIONS

Objective: The purpose of this study was to identify a potential peptidomimetic S. typhi Beta-lactamase TEM 1 inhibitor to tackle the antibiotic resistance among S. typhi.Methods: The potential peptidomimetic inhibitor was identified by in silico docking of the small peptide WFRKQLKW with S. typhi Beta-lactamase TEM 1. The 3D coordinate geometry of the residues of small peptide interacting with the active site of the receptor was generated and mimics were identified using PEP: MMs: MIMIC server. All the identified mimics were docked at the active site of the receptor using Autodock 4.2 and the best-docked complex was selected on the basis of binding energy and number of H-bonds. The complex was then subjected to molecular dynamics simulations of 30 ns using AMBER 12 software package. The stereochemical stability of the Beta-lactamase TEM 1-WFRKQLKW complex was estimated with the help of Ramachandran plot using PROCHECK tool.Results: In the present study, a new potential peptidomimetic inhibitor (ZINC05839264) of Beta-lactamase TEM 1 has been identified based on antimicrobial peptide WFRKQLKW by virtual screening of the MMsINC database. The docking and molecular simulation studies revealed that the mimic binds more tightly to the active site of the receptor than the peptide. The Ramachandran plot also shows that the Beta-lactamase TEM 1-mimic complex is stereo chemically more stable than Beta-lactamase TEM 1-WFRKQLKW complex as more number of residues (93.6%) are falling under the core region of the plot in case of the former.Conclusion: The study shows that the peptidomimetic compound can act as a potential inhibitor of S. typhi Beta-lactamase TEM 1 and further it can be developed into more effective therapeutic to tackle the problem of antibiotic resistance

Studies on the Thermodynamics of Exchange in Clays: Part II - Zinc Exchange on Na- & Ca-Illites

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A scientometric analysis and visualization of the 50 highly cited papers of Eugene Garfield

Eugene Garfield’s contributions to global informetrics and scientometrics literature is significant. In this paper, a scientometric analysis of Eugene Garfield’s 50 highly cited papers is performed. His papers were published in 32 journals including top-ranked journals such as Nature and Science. The top 15 keywords with the strongest citation bursts from 1989 to 2009 and references with strong citation bursts are presented. Co-citation analysis and bibliographic coupling analysis based on source journals using VOSviewer were carried out. The result revealed that keywords 'citation relationship', 'scientific journals', 'biological journal’ and 'self-citations' started to burst/hotspot in 2002. The term 'citation analysis' has the highest number of four years' popularity as citation burst. The study further revealed that the top 50 publications of Eugene Garfield gained 8441 citations of the total citations of 9121 from 254 published documents. Garfield has Total Link Strength of 35 and has received 8511 citations which comes to 93.31% of the total citations and proved his dominance over the collaborators. Ninety percent of the papers (45) published in the USA and above 92% of the citations (8419) were also received from the USA's publications. Just five papers in three journals received 4856 citations (53.23%) of the total 9121 citations. These three journals include three papers in Science (with 3027); one each in Journal of the American Medical Association (with 1323 citations) and The Canadian Medical Association Journal (with 606 citations)

A scientometric analysis and visualization of the 50 highly cited papers of Eugene Garfield

135-144Eugene Garfield’s contributions to global informetrics and scientometrics literature is significant. In this paper, a scientometric analysis of Eugene Garfield’s 50 highly cited papers is performed. His papers were published in 32 journals including top-ranked journals such as Nature and Science. The top 15 keywords with the strongest citation bursts from 1989 to 2009 and references with strong citation bursts are presented. Co-citation analysis and bibliographic coupling analysis based on source journals using VOSviewer were carried out. The result revealed that keywords 'citation relationship', 'scientific journals', 'biological journal’ and 'self-citations' started to burst/hotspot in 2002. The term 'citation analysis' has the highest number of four years' popularity as citation burst. The study further revealed that the top 50 publications of Eugene Garfield gained 8441 citations of the total citations of 9121 from 254 published documents. Garfield has Total Link Strength of 35 and has received 8511 citations which comes to 93.31% of the total citations and proved his dominance over the collaborators. Ninety percent of the papers (45) published in the USA and above 92% of the citations (8419) were also received from the USA's publications. Just five papers in three journals received 4856 citations (53.23%) of the total 9121 citations. These three journals include three papers in Science (with 3027); one each in Journal of the American Medical Association (with 1323 citations) and The Canadian Medical Association Journal (with 606 citations)

A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

Background: The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. Method: In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B) are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. Results: Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF½ helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s) for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. Conclusion: The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome. The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from the parasite that could provide leads to identify novel drug targets against malaria

ProtRepeatsDB: a database of amino acid repeats in genomes

BACKGROUND: Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. DESCRIPTION: ProtRepeatsDB (v1.2) consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO) annotation IDs and regular expressions (REGEXP) describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. CONCLUSION: ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific repeat markers, interspecies variations and polymorphism

Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons.

article i nfo Studies from flies and insects have reported the existence of a special class of miRNA, called mirtrons that are produced from spliced-out introns in a DROSHA-independent manner. The spliced-out lariat is debranched and refolded into a stem-loop structure resembling the pre-miRNA, which can then be processed by DICER into mature ~21 nt species. The mirtrons have not been reported from plants. In this study, we present Mir- tronPred, a web based server to predict mirtrons from intronic sequences. We have used the server to predict 70 mirtrons in rice introns that were put through a stringent selection filter to shortlist 16 best sequences. The prediction accuracy was subsequently validated by northern analysis and RT-PCR of a predicted Os- mirtron-109. The target sequences for this mirtron were also found in the rice degradome database. The pos- sible role of the mirtron in rice regulon is discussed. The MirtronPred web server is available at http://bioinfo. icgeb.res.in/mirtronPred