7721-23 March 2011

Session ChairDr. Siti Nor Akmar AbdullahUnivrsiti Putra Malaysia, Malaysia

Session Co-ChairDr. Sanjeeva SrivastavaIndian Institute of Technology, India

Track 4

Molecular Biology and Bioinformatics

21 March 2011 (Monday )

Session Introduction

Title: Discovering opportunities from functional genomics in oil palm Dr. Siti Nor Akmar Abdullah, Univrsiti Putra Malaysia, Malaysia

Title: Gene mining from phreatophyte Prosopis juliflora for generation of transgenic rice tolerant to abiotic stresses

Dr. Suja George, M.S. Swaminathan Research Foundation, India

Title: A transcriptional signature of pathogenic and non-pathogenic mycobacteria

Dr. Prati Pal Singh, National Institute of Pharmaceutical Education and Research, India

Title: Investigating cellular functions of the calcium signaling genes in Neurospora crassa

Dr. Ranjan Tamuli, Indian Institute of Technology-Guwahati, India

Title: SPRi-NAPPA microarray platform for high-throughput study of p53 and MDM2 protein-protein interaction

Dr. Sanjeeva Srivastava, Indian Institute of Technology, India

Title: An efficient method of soil DNA isolation for construction of metagenomic libraries

Dr. Pavan Kumar Pindi, Palamuru University, India

Plenary Speaker

Title: Structurally- and dynamically-driven alteration of the catalytic machinery of the SARS 3C-like with evolutionarily acquiring an extra-domain

Dr. Jianxing Song, National University of Singapore, Singapore

BIOTECHNOLOGY-2011

7821-23 March 2011

Track 421 March 2011 (Monday )

Title: Bioinformatics ethical values and social challenges Dr. Hanuman Thota, Acharya Nagarjuna University, India

Title: Vaccine design: Identification of the putative molecular target of infectious Bursal disease virus on chicken lymphocytes using immunological and bioinformatic approach

Prof. Hari Mohan Saxena, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), India

Title: Deployment of biotechnological tools in Cassava viral disease diagnostics and control

Dr. Kenneth Monjero, Kenya Agricultural Research Institute Biotechnology Centre, Kenya

Title: Genetic engineering of Gamma Linolenic Acid (GLA): A pharmaceuti-cally important fatty acid

Dr. I. Swarnalatha Devi, Acharya N.G.Ranga Agricultural University, India

Title: Rice varietal identification by rapid chemical tests, electrophoretic variants of soluble seed proteins and DNA fingerprinting

Dr. Sambasiva Rao P, Acharya N.G.Ranga Agricultural University, India

Title: Multitemperature single-strand conformational polymorphism - a new method for detection of minute genomic changes in viral pathogens

Dr. Boguslaw Szewczyk, University of Gdansk and Medical University of Gdansk, Poland

Title: Computer aided diagnosis system for early detection of breast cancer Dr. G. R. Sinha, Shri Shankaracharya College of Engineering & Technology,

India

Title: Evaluation of seizure activity after phospho-diesterase-7 inhibition with guanylate cyclase activation and inhibition in animal model of epilepsy

Dr. Manoj G Tyagi, Christian Medical College, India

Title: Expression of Glutathione S-transferase in antibiotic resistance bacterial species (Staphylococcus sp., Streptococcus sp. and Micrococcus sp.) isolated from the poultry litter

Dr. Thamaraiselvi, Bharathidasan University, India

Title: Metagenomics : A new window to the Marine Microbiology Dr. Vijaya. Ch, Vikrama Simhapuri University, India

Title: Dissecting the interactome of RNA-binding proteins in post-transcriptional regulatory networks

Dr. Sarath Chandra Janga, University of Illinois at Urbana-Champaign, USA

Title: Solid phase peptide synthesis of Kisspeptin-13 and its purification by Reverse Phase HPLC

Dr. Vijay Kumar Saxena, Central Sheep and Wool Research Institute, India

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Discovering opportunities from functional genomics in oil palmSiti Nor Akmar AbdullahUnivrsiti Putra Malaysia, Malaysia

Malaysia and Indonesia are the largest palm oil producers accounting for 90% of world production. Palm oil industry has managed to reduce poverty and provide employment opportunities in food, oleochemical, cosmetics, and nutraceutical industries. Oil palm genes and cDNAs obtained from various treated and normal tissues serve as valuable research materials for functional characterization to unveil their potential in agriculture biotechnological applications. Profiling of selected transcripts of pathology genes following artificial infection with disease causing Ganoderma boninense and bocontrol agent Trichoderma harzianum reveiled valuable information regarding biotic and oxidative stress response in oil palm besides demonstrating the potential of these genes as biomarkers. Using reporter gene assays in transient expression using oil palm tissue slices and in heterologous transgenic model plant systems, different oil palm tissue-specific

promoters and inducible promoters with possible applications in plant genetic engineering were unveiled. It was also discovered that an oil palm metallothionein gene promoter is functional and metal inducible in prokaryotic systems suggesting valuable application as biosensors and in bioremediation. The isolated oil palm fruit-specific promoter and fatty acid biosynthetic gene promoters were used in functional dissection using 5’-deletion analysis which have resulted in the discovery of a novel regulatory motif for fruit-specificity. Using specific promoter motifs interacting transcription factors were discovered which hold the information on the coordinated control of phytohormone responsive and specific biosynthetic pathway genes. All the data that have been generated are invaluable information and can pave the way for more applied research on their applications in crop improvement.

BiographyAssoc. Prof. Dr. Siti Nor Akmar Abdulah obtained her PhD in 1999 from University

of East Anglia, UK. It was on a collaborative project between Malaysian Palm Oil Board (MPOB) and the John Innes Centre. She was a research group leader at MPOB. Now she is an Associate Professor and the Head of the Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia. Her research interest is on oil palm biotechnology focusing on transcriptional regulation of oil biosynthesis, fruit ripening, Ganoderma infection and nutrient uptake. She is active in publishing her research findings in journals of international repute. She has filed four patents and two of them have been granted in the US.

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Structurally- and dynamically-driven alteration of the catalytic machinery of the SARS 3C-like with evolutionarily acquiring an extra-domainJianxing Song and Jiahai Shi National University of Singapore, Singapore

Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century which has not only caused rapid infection and death, but also triggered a dramatic social crisis. Its 3C-like protease plays a vital role in processing two viral polyproteins and thus represents a top target for drug design. Intriguingly, the SARS protease evolutionarily acquired a C-terminal extra domain in addition to the chymotrypsin fold sufficient to host the complete catalytic machinery of the 3C protease such as from picorovirus [1]. The functional role of this extra domain had been previously unknown but shortly after the SARS outbreak, we revealed that it plays a key role in mediating the dimerization essential for catalysis [2-3]. By determining the high-resolution structure of an inactive and monomeric R298A mutant, we further established the mechanism how the extra domain controls the dimerization which can be eventually coupled to the catalytic machinery [4]. On the other hand, we also identified several other mutants on the extra domain which have no significant alteration of the dimerization properties but their activities are either significantly attenuated (N214A) or enhanced (STI/A and STIF/A). Surprisingly their crystal structures we just determined are almost identical to

that of the wild-type, thus strongly implying that the enzyme dynamics are extremely critical to the catalysis. Therefore, we launched Molecular Dynamics (MD) simulations for WT, R298, N214, STI and STIF mutants, as well as several artificial monomers. The results show that different proteases display distinctive dynamical behaviors. While in WT, the catalytic machinery stably retains in the activated state, in R298A it remains largely collapsed in the inactivated state, implying that two states are not only structurally very distinguishable [4], but also dynamically well separated. Unbelievably, in N214A the catalytic dyad becomes dynamically unstable and many residues constituting the catalytic machinery jump to sample the conformations highly resembling those of R298A. Therefore, the N214A mutation appears to trigger the dramatic change of the enzyme dynamics in the context of the dimeric form which ultimately inactivates the catalytic machinery [5]. Our MD simulations represent the longest reported so far for the SARS-CoV 3CLpro, unveiling that its catalysis is critically dependent on the dynamics, which can be amazingly modulated by the extra domain. Consequently, mediating the dynamics may offer a potential avenue to inhibit the SARS-CoV 3CLpro.

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IL-6: A differential transcriptional signature of Pathogenic and Non-pathogenic MycobacteriaPrati Pal Singh and Amit Goyal National Institute of Pharmaceutical Education and Research, India

Tuberculosis (TB) is a chronic infectious disease caused by several Mycobacterium species such as Mycobacterium tuberculosis, M. avium and M. marinum; however, some species like M. smegmatis and M. phlei are non-pathogenic to humans. Mycobacteria are intra-macrophage pathogens and, the macrophage response to mycobacteria infection includes production of cytokines such as tumor necrosis factor, IL-1, IL-6, IL-10, IL-12 p40 and IL-12 p70. We studied the in vitro production of cytokines by mouse peritoneal macrophages infected with both pathogenic and non-pathogenic mycobacteria. Levels of cytokines were

determined by using Bio-plex suspension array system. Very low amount of IL-6 was observed in non-infected wells (20.25 ± 5.3 and 14.75 ± 1.77) as compared to the infected wells (pathogenic, 552.5 ± 19.09 and 454.5 ± 16.26; non-pathogenic, 830.25 ± 35 and 547 ± 39.6) on Day 4 and Day 7, respectively. Curiously, no significant difference was observed for other cytokines viz. IL-1, IL- 10, IL-12 p40 and IL-12 p70. Apparently, these results indicate that IL-6 may play a role(s) in virulence and pathogenicity of mycobacteria. IL-6 thus can be used as signature molecule for the differentiation of pathogenic and non-pathogenic mycobacteria.

BiographyProf. Prati Pal Singh did his Ph. D. (1980) work at CDRI, Lucknow, and post-doctoral

research work at The Ohio State University, Columbus, Ohio, USA and at The Stanford University, Stanford, Palo Alto, California, USA. He is a renowned molecular biologist, immunologist and neuroimmunopharmacologist. He has made some very important contribution to control and treatment of parasitic and microbial disease of national and international importance like malaria, tuberculosis, leishmaniasis, amoebiasis and trichomoniasis. He conceptualized and reported that opiate class of drugs can be used for treatment of parasitic and microbial infections. Prof. Singh has published extensively including in Nature Medicine. He has nearly 200 publications, and 10 national and international patents including one US patent. Prof. Singh was the Editor-in-Chief of the Journal of Parasitic Diseases and is an Editorial Board Member of a US journal, Journal of Neuroimmune Pharmacology. He is a Fellow of The National Academy of Sciences, India, and Association of Microbiologists of India.

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Gene mining from phreatophyte Prosopis juliflora for generation of transgenic rice tolerant to abiotic stresses Suja GeorgeM.S. Swaminathan Research Foundation, India

Abiotic stresses cause a drop in average yields for most crops. Development of crop plants able to grow under stress conditions assumes importance in this context. Molecular dissection of stress adaptable model plants is likely to throw light on novel pathways of tolerance. This study chose Prosopis juliflora, a drought/heat/heavy metal tolerant tree of Fabaceae as the model plant for identifying and isolating genes functioning in abiotic stress tolerance. A cDNA library was created from drought stressed leaf tissue of P. juliflora seedlings. Random sequencing of 1700 clones by EST analysis resulted in the identification of several genes reported to function in tress tolerance in addition to many previously uncharacterized ones. Once a suitable stress induced EST is identified, the gene is sequenced fully and characterized by expression and biochemical analysis.

A Reverse Northern experiment of 52 previously uncharacterized genes under drought stress indicated up-regulation of many, implicating a possible function in drought stress tolerance and paving way for better molecular insights into stress tolerance mechanisms of P. juliflora. A GST gene from P. juliflora, upregulated under drought, salt, osmotic and oxidative stress was transformed into the tobacco and the stress studies revealed protective function of this gene under different abiotic stresses. This gene was transformed into Indica rice variety ADT-43 and the transgenic plants survived better under conditions of abiotic stress compared to control. The study is the first of its kind in a leguminous tree species and adds to the existing knowledge on plant abiotic stress tolerance.

BiographyDr. Suja George completed her PhD at the age of 28 from University of Madras

on her thesis ‘Genetic engineering for abiotic stress tolerance using Prosopis juliflora (Swartz) DC. as a model plant system for gene mining”. she is currently working as a senior scientist at M.S. Swaminathan Research Foundation (MSSRF), Chennai, India. She has 13 research publications including reviews, original research papers and book chapters and an international patent. She is currently Principal investigator / CO principal investigator in as many as six research proposals MSSRF has submitted to various funding agencies for financial support.

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Investigating cellular functions of the calcium signaling genes in Neurospora crassaRekha Deka, Ravi Kumar, Ravi Gedela and Ranjan TamuliIndian Institute of Technology Guwahati, India

We are investigating cellular roles of calcium signaling genes in Neurospora crassa, using knockout mutants. Our studies have revealed cellular roles for the genes NCU04379, NCU02283.2, NCU09123, NCU06650, NCU06366, NCU07075, and NCU07966. NCU04379 gene encodes a conserved Ca2+ and/or calmodulin binding protein and plays a role in growth, calcium and ultraviolet tolerance. NCU02283 and NCU09123 encode Ca2+/calmodulin-dependent protein kinases important for sexual development of N. crassa. Both NCU06366 and NCU07075 encoded Ca2+/H+ exchangers, NCU06650

as well as NCU07966 encode a novel Ca2+and/or CaM binding protein and a cation-ATPase, respectively, and these genes play a role mating mating-type-associated heterokaryon (het) incompatibility during the vegetative phase. Mating-type-associated het incompatibility is a non-self-recognition process in N. crassa analogous to histocompatibility system in invertebrates and major histocompatibility complex in mammals. Therefore, we hypothesize that calcium plays a diverse role in N. crassa ranging from cell growth to death.

BiographyRanjan Tamuli has completed his Ph.D at the age of 28 years from Centre for

Cellular and Molecular Biology (CCMB), Hyderabad and postdoctoral studies from University of Florida and Florida International University. At present, he is an Assistant Professor in the Department of Biotechnology, Indian Institute of Technology Guwahati. He has published five research papers as well as eight on-line papers. He has also served as a reviewer for reputed journals.

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An efficient method of soil DNA isolation for construction of metagenomic librariesPavan Kumar Pindi Palamuru University, India

The soil ecosystem is dynamic and composed of biotic and abiotic components. Soil represents a diverse group of microorganism, which has frequently been used to isolate and explore and exploit microbes for industrial, environmental and agriculture applications. Soil metagenomics, which comprises isolation of soil DNA and the production and screening of clone libraries, can provide a cultivation independent assessment of the largely untapped genetic reservoir of soil microbial communities. An efficient method has been developed for the isolation of heterologous DNA from environmental soils. This approach consists of the direct extraction of large fragmented nucleic acids from soil followed by purification. Cell lysis is a critical step in soil metagenomic DNA extraction. Extraction procedure was optimized with series of steps, which

involved gentle mechanical lysis and number of freeze-thawing cycles in liquid Nitrogen and the incubation period and temperature can be varied. A comparison of the optimized protocol with other existing protocols and with commercially available kit suggested that protocol described in this report would be more efficient, high quality and high yield DNA obtained from different environmental samples. In this approach DNA is directly isolated from environmental soil samples and cloned into suitable vectors to construct complex genomic libraries for screening of novel proteins and drugs that are being produced in surrogate hosts. The approach of directly cloning environmental DNA greatly enhances the opportunities to take full advantage of the enormous naturally occurring microbial resources.

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Infectious Bursal disease vaccine design: Identification of the putative molecular target of IBD virus on chicken lymphocytes using immunological and bioinformatic approachDr. Hari Mohan Saxena Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), India.

Infectious Bursal Disease (IBD) is a contagious immunodeficiency disease of chickens causing huge economic losses worldwide. IBD Virus (IBDV) destroys Bursal B cells. However, the receptor of IBDV on B cells is not known. If it is identified, it will lead to an effective vaccine. The present study aimed for identification of the target. Activation of lymphocytes with Lipopolysaccharide very significantly (p

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Genetic engineering of Gamma Linolenic Acid (GLA): A pharmaceutically important fatty acid I Swarnalatha Devi, V Dinesh Kumar*, Ansari N A and A SivasankarAcharya N G Ranga Agricultural University , India*Directorate of Oilseeds Research, India

Recent advances in plant molecular biology have facilitated the introduction of novel traits into a range of plant species. It is now possible to modify the fatty acid composition of oilseeds, which opens up the possibility of improving the nutritional qualities of plant oils. Over 300 different types of fatty acids have been reported in plants, a number of which are of interest as targets for exploitation (Loo et al., 1993). One such fatty acid is the Gamma Linolenic Acid (GLA; 18:3 (-6,9,12), which is used as a general health supplement and is also a registered pharmaceutical used for the treatment of conditions such as eczema and mastalgia (Horrobin, 1990). GLA is synthesized by a Delta-6-fatty

acid desaturase gene using linoleic acid (C18: 2 D9, 12) as a substrate. The fatty acid composition of an oilseed determines its end use and therefore its commercial value. Value can be added to certain crop species by manipulations which would allow production of rare and valuable oils. Gamma-Linolenic acid (GLA; C18: 3 D6, 9, 12) is a component of the seed oils of evening primrose (Oenothera spp.), black current (Ribes nigrum), borage (Borago officinalis L.), and some other plants. Genetic engineering also provides novel opportunities for the production of pharmaceutical fatty acids such as gamma linolenic acid which is important for human health and nutrition.

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Rice varietal identification by rapid chemical tests, electrophoretic variants of soluble seed proteins and DNA fingerprintingSambasiva Rao P, Meena Kumari KVS and Bharati MAcharya N.G. Ranga Agricultural Universit, India

Forty genotypes of cultivated rice varieties released by Acharya N.G.Ranga Agricultural University, Andhra Pradesh. India were studied using seed and seedling characteristics for their reaction to phenol, modified phenol, NaOH, GA3 and 2,4-D (auxin) tests, as well as by electrophoresis of soluble seed proteins. Though no individual chemical test was able to distinguish all the genotypes, different chemical tests in conjunction were useful in identification of varieties. The differential banding pattern of total soluble seed proteins and

DNA polymorphism revealed the qualitative and quantitative variation among the different varieties and could distinguish among closely related varieties by the presence or absence of specific bands and intensity of bands varies with their relative mobility. Seed keys for identifying forty varieties on the basis of their biochemical response and total soluble protein profiles were developed. The cluster analysis indicated the wide diversity of the varieties released from Andhra Pradesh with similarity ranging from 0.36 to 0.98.

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Evaluation of seizure activity after Phospho-Diesterase-7 Inhibition with Guanylate cyclase activation and inhibition in animal model of epilepsyManoj G Tyagi, Vinita Ernest, Nidhi Tyagi and J NandhakumarChristian Medical College, India

The role of soluble guanylate cyclase (GC) activator (A-350619) and inhibitor (methylene blue) was evaluated in the presence of phosphodiesterase-7 (PDE-7) inhibitor such as BRL-50481, in a animal model of epilepsy. Seizures were induced in the animals by subjecting them to an injection of chemical convulsant, pentylenetetrazole (PTZ). The study mainly comprises the onset of seizures, mortality/recovery, percentage of prevention of seizures (anti-convulsant) and total duration of convulsive time. The combination of methylene blue with BRL 50481 showed a delay in onset (P

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Biological synthesis of silver nanoparticles using medicinal plantsN SavithrammaSri Venkteshwara University, India

The synthesis of metal nanoparticles using biological systems is an expanding research area due to the potential applications in nanomedicines. Nanoparticles synthesized by chemical method is not eco-friendly. The biological synthesis of silver nanoparticles is convenient and extracellular method which is environmentally safe. In the present study the silver nanoparticles synthesizes rapidly by using the medicinal plants Boswellia ovalifoliolata, Svensonia hyderabadensis and Shorea tumbuggaia. After assessing the formation of silver nanoparticles with the help of UV-Visible spectroscopy and were characterized by using EDAX and SEM. Diversity has been observed in size and shape of the silver nanoparticles synthesized in three plants. These phytosynthesized silver nanoparticles were tested for their antimicrobial activity. The test cultures of bacterial species of Proteus, Pseudomonas, Klebsiella, Bacillus and E. coli and fungal sspecies of Fusarium oxysporum,

Curvularia lunata, Aspergillus niger and Rhizopus arrhizus were used. The microbial property of silver nanoparticles was analyzed by measuring the inhibitory zone. These silver nanoparticles synthesized from the plants of Boswellia ovalifoliolata showed moderately toxic to the E.coli and Pseudomonas species and highly toxic to Proteus species. Whereas the silver nanoparticles of Shorea tumbuggaia are highly toxic to Klebsiella species and moderately toxic to E.coli and Bacillus species. Svensonia hyderabadensis shows maximum inhibitory zone in Klebsiella followed by E. coli and Pseudomonas . The effect of silver nanoparticles synthesized from the selected plant species are varied on the growth of fungal species The important outcome of the study will be the development of value added products from medicinal plants of India for biomedical and nanotechnology based industries.

BiographyProf. N.Savithramma has completed her M.Phil in 1987 and Ph.D in the year 1990

from Sri Venkateswara Univerisity; Tirupati. She is having 22 years of teaching and 26 years of research experience. She is the coordinator for Internal Quality Assurance Cell of S.V.University. She has published more than 65 papers in reputed National and International journals and the author of 3 books. She served as an editorial board member of repute journals. She visited number of countries and baged 6 awards for research work. Number of Ph.D and M.Phil degrees have been awarded under her guidance and the process has been continuing . She hold administrative positions in S.V.University and discharge her duties as special officer for University development. She is the member in number of Academic Societies and also organized national workshops. Being an active Academician and Administrator she has been extending her services to community development through NGOs and different developmental societies by holding various r of positions.

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Posters

World Congress on Biotechnology21-23 March 2011 HICC, Hyderabad, India

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Crop production is threatened by global climate change. To increase yield from both irrigated and non-irrigated lands, novel varieties that are more tolerant to environmental stresses are to be developed. Excess salts adversely affect all major metabolic activities in plants including cell wall damage, accumulation of electron-dense proteinaceous particles, plasmolysis, cytoplasmic lysis and damage to endoplasmic reticulum, and overall decline in germination and seedling growth. To overcome salt stress, efforts have been made in the isolation and expression of genes controlling yield and tolerance. To facilitate the comparison and understanding of gene characteristics, genome organization, pathways, and phenotypes in cereals, there are attempts to develop a comparative genome mapping

database using the sorghum genome as an anchor (http://www.gramene.org). The present work is carried out with an objective for isolation, characterization of NHX1 gene from Sorghum bicolor, and its expression in tomato and tobacco plants. The binary vector pCAMBIA1302 harboring NHX1, GFP and hygromycin was used. Putative transgenics were confirmed by PCR, RT-PCR, Southern blotting and gene localization on the membrane by GFP. T1 transgenics are to be tested for physiological studies like ion analysis (Na+, K+ and Ca2+) separately in root, leaf blade, leaf sheath and fruit along with controls. To know the evolutionary conservation of the NHX1gene, we compared orthologs of NHX1in rice, maize, and sorghum and comparative map (cMAP) has been developed.

Cloning and characterization of sodium proton antiporter (NHX1) gene from sorghum and comparative genome analysis of its homologs among 3 grass species P Hima Kumari, Anil Kumar S, S Deshpande*, Trushar Shah*, C Tom Hash* and P B Kavi KishorOsmania University, India*ICRISAT, India

BiographyI am a Ph.D student working with Prof. P. B. Kavi Kishor from Plant Molecular Biology

lab, Department of Genetics and Biotechnology, Osmania University.

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Groundnut (Arachis hypogaea L.) is an important commercial oil seed crop rich in high quality edible oil (56%), protein (30%) and carbohydrate (20%). India produces 8 million tonnes from 7.6 million hectares. Salinity is the major limiting factor in peanut crop productivity resulting in yield loss and reduced seed quality. Salt stress has adverse influence on water relations, photosynthesis, mineral nutrition, metabolism and growth. Mechanisms that confer salt tolerance vary with the plant species; however the basic strategy works towards the maintenance of Na+  homeostasis in the cytosol. One of the possible mechanisms is to increase the solute concentration in the vacuoles of the plant cells i.e. to compartmentalize sodium ions. The accumulation of sodium ions inside the vacuoles provides a 2-fold advantage (i) reducing toxic levels of sodium in cytosol and (ii) increasing the vacuolar osmotic potential with

the concomitant generation of a more negative water potential that favors water uptake by the cell and better tissue water retention under high soil salinity. NHX1 gene was introduced into pCAMBIA1302 vector with hygromycin as the selection marker and GFP as the reporter gene, mobilized into Agrobacterium tumefaciens LBA 4404 and used for peanut transformation. The transformants were confirmed by PCR, Southern blotting and RT-PCR to confirm gene expression at the transcription level. Further evaluation of T1 and T2 plants in presence of 150 mM NaCl (including controls) for salt tolerance and ion analysis (Na+, K+ and Ca2+) in different parts of the transgenics. Our data demonstrate the potential of  NHX1  for imparting enhanced salt tolerance capability to peanut varieties to grow in saline areas.

Overexpression of Na+/H+ antiporter (NHX1) gene to enhance salt tolerance in peanut (Arachis hypogaea L.)Venkatesh K, Chakrapani P and A Roja Rani

Osmania University, India

BiographyVenkatesh K., pursuing Ph.D under the supervision of Dr. A. Roja Rani from Osmania

University has published 2 papers in reputed international journals. He has published his papers entitled “Changes in protein composition and protein phosphorylation during somatic embryogenesis and plant regeneration in peanut (Arachis hypogaea L.)” in African Journal of Biotechnology, 2009 and “Auxins and Auxin Polar Transport Inhibitor (TIBA) on Somatic Embryogenesis in Groundnut (Arachis hypogaea. L)”, in African Journal of Plant Science, 2009. His work entitled “Biochemical studies on the effect of medicinal plants Gymnema and Andrographis species on diabetes induced Wistar rats” is published in IEEE Explore ICBPE 2009. Conference proceedings, Singapore, INSPEC Accession Number: 11085790.

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Double-stranded RNA-mediated interference (RNAi) is a simple and rapid method of silencing gene expression in a range of organisms. Disease therapy now based on genetic materials is in now reality for curing many diseases mainly cancer . This technique of gene silencing often sounded as RNAi keeps our hopes alive. The main excitement stems from the power of RNAi it has the capacity to destroy genetic materials at any point of our life time in a specific type called gene knock out system. The silencing of a gene is a consequence of degradation of RNA into short RNAs that activate ribonucleases to target homologous mRNA. Specific gene silencing has been associated with regulatory processes such as transposon silencing, antiviral defense mechanisms, gene regulation, and chromosomal modification. Extensive genetic and biochemical analysis revealed a two-step mechanism of RNAi-induced gene silencing. The first step involves degradation of dsRNA into small interfering RNAs (siRNAs), 21 to 25 nucleotides long, by an RNase III-like

activity. In the second step, the siRNAs join an RNase complex, RISC (RNA-induced silencing complex), which acts on the cognate mRNA and degrades it. Several key components such as Dicer, RNA-dependent RNA polymerase, helicases, and dsRNA endonucleases have been identified in different organisms for their roles in RNAi. Some of these components also control the development of many organisms by processing many noncoding RNAs, called micro-RNAs. The biogenesis and function of micro-RNAs resemble RNAi activities to a large extent. Recent studies indicate that in the context of RNAi, the genome also undergoes alterations in the form of DNA methylation, heterochromatin formation, and programmed DNA elimination. As a result of these changes, the silencing effect of gene functions is exercised as tightly as possible. Because of its exquisite specificity and efficiency, RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes.

RNAi- A novel gene regulatory mechanismMamidi Krishna and Nagelli srujanaGITAM University, India

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Bird species can travel longer. Thus, birds have possibility to transfer genes at greater rate than mammals. Mammals although can move from one place to another place; they are limited by their niche. Blue Rock Pigeon is a local species. In spite of being local species Blue Rock Pigeon are known for their high capacity to move. However, genetic variation depends on the mating system of particular species. DNA was isolated from the faecal sample of individual Blue Rock Pigeon. The DNA was tested for purity and quantity on UV-Vis Spectrophotometer. RAPD analysis was used to analyze genetic variation.

Genetic variation among the population of wild Blue Rock pigeonJani V R, Raval D A, Mevada M S, Trivedi A V, Dave N G and Dave S MHemchandracharya North Gujarat University, India

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An improvement of our knowledge on gene composition and expression is essential to investigate the molecular basis of drought tolerant to define the gene pool involved in cross talk to different pathways at biochemical levels and molecular levels for the survival of plants during drought condition. The availability of complete genome sequences and large sets of expressed sequence tags (ESTs) from several plants has recently triggered the development of efficient and informative methods for large-scale and genome-wide analysis of genetic variation and gene expression patterns. As Cultivated Cotton Gossypium Spp. are the world’s most important fiber plants. The deposition of > 90% cellulose in the cotton fiber secondary wall makes this unique cell powerful for understanding cellulose biogenesis, a process with great importance in nature and industry. We carried out Microarray hybridization of contrasting Gossypium herbaceum germplasms using Affymetrix cotton chip. 2 germplasm of Gossypium herbaceum were used for this study 454 pyrosequencing

was used to enrich the very few sequence data currently available for the cotton species and to identify genes involved to survive the plants during drought condition. Affymetrx microarray Cotton chip was used to compare gene expression pattern in tolerant and sensitive genotype of G.herbaceum. Statistical data analysis was performed using Array assist 5.5, R Packages and SAS using criteria of p value ≤ 0.05 and fold change ≥ 2.0. In parallel we also performed deep transcriptome sequencing of two germplasms (out of five selected) with contrasting drought tolerance using Roche’s 454-GSFLX genome sequencer.. Our efforts on microarray and transcriptome sequencing with very strong statistical analysis lead to discovery of many differentially unique (germplasm specific) and novel genes, metabolic pathways, and enriched enzyme activities probably responsible for drought tolerance in Gossypium.spp. The good statistical results related to drought tolerance in Gossypium herbaceum will be presented.

Global gene expression profiling of contrasting Gossypium sp. for deciphering highly stage specific genes and metabolic pathways governing drought toleranceDeepti NigamNational Botanical Research Institute, India

BiographyI am a Senior Research Scholar (PhD student) in NBRI, in the area of Bioinformatics

(Cotton Geniomics). I have 3 international publication till yet and 2 are communicated in Plant Physiology.

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Flax or linseed (Linum usitatissimum L.) is an important oil seed crop having high nutritional as well as industrial value. It is the richest and the cheapest vegetarian source of α-linolenic acid (ALA), which is an omega-3 fatty acid. ALA is an essential dietary fatty acid for humans and serves as a precursor for biologically active longer chain poly-unsaturated fatty acids (PUFA) of omega-3 class, mainly eicosapentanoic acid (EPA) and decosahexanoic acid (DHA). Since flax is the only agricultural source of high ALA (45-65%) and there exists varietal variation in biochemical parameters, oil content and quality, it is essential to exploit it for omega-3 nutrition.

In fatty acid biosynthetic pathway, desaturases are considered to be the key enzymes that drive the

entire pathway leading to the synthesis of PUFA. Three desaturase genes (Δ9, Δ12 and Δ15) have been reported from flax, which convert the stearic acid to oleic acid (Δ9), oleic acid to linoleic acid (Δ12) and linoleic acid to α-linolenic acid (Δ15). The desaturase genes present considerable amount of variability among the plants. Hence, to know the genetic basis of low and high ALA content in the different flax varieties, real time expression analysis of the 3 desaturase genes from five low and five high ALA containing Indian flax cultivars during seed development is being carried out. The expression profiles will be compared with the fatty acid profiles for the same tissue, so as to reveal varietal specific as well as temporal expression pattern of these genes during seed development.

Differential expression of desaturase genes in developing seeds of high and low ALA containing Indian flax varietiesAshwini V Rajwade, Reema M Banarjee, Narendra Y Kadoo and Vidya S GuptaNational Chemical Laboratory, India

BiographyMrs. Ashwini V. Rajwade is pursuing her doctoral research at National Chemical

Laboratory, Pune India, under the guidance of Dr. Vidya S. Gupta. She has completed her B.Sc. and M.Sc. Zoology from Pune University and Mumbai University respectively. She is availing Senior Research Fellowship from CSIR to support her doctoral research.

doi:10.4172/jpb.1000240

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Drought is one of the major abiotic stress conditions limiting the crop productivity all over the world. Pigeonpea (Cajanus cajan (L.) Millspaugh) is a drought tolerant pulse crop, grown mainly in semi-arid regions and India ranks first in its production. Presently less genomic resources are available on pigeonpea for drought related studies at molecular level. On the contrary, significant amount of genomic information are in the domain for a closely related leguminous crop soybean (Glycine max L.). Here, we have reported an in silico analysis for the identification of differentially expressed genes (DEGs) and their signaling pathways due to drought stress. The soybean cDNA libraries of drought stressed and unstressed leaf tissues were downloaded from unigene database of NCBI. Five unstressed libraries were independently analyzed and compared to one drought stressed library. Expressed sequence tag (EST) counts per unigene were used for in silico expression analysis by online IDEG6 web statistical tool. From IDEG6, we obtained 34, 30, l1, 13

and 7 DEGs respectively by comparing independently between normal and drought library. Among these, 52 non redundant DEGs were subjected to BLAST analysis for similarity search using BioEdit local blast tool (E-values 1.0E-50) against total ESTs, genomic survey sequences (GSS) and nucleotide sequences of pigeonpea downloaded from NCBI. Out of 52 DEGs, 4 up-regulated and 30 down-regulated genes showed blast hits against pigeonpea sequences and, their relation to drought response was confirmed by comparing with the previous studies. The pathways for 34 genes were assigned based on Kyoto Encyclopedia of Genes and Genomes (KEGG), indicating 25 genes involved in 11 pathways. Photosynthesis and light harvesting proteins showed more reduction in drought stress condition. This study reveals that the genes expressed due to drought stress and the pathways triggered in soybean were similar with the pigeonpea and hence, it can be extrapolated for further biochemical analysis.

In silico analysis and evaluation of drought responsive genes in pigeonpea by comparing with the cDNA libraries of soybean leafNagaraja D, Ramesh CK, V Krishna and Santosh Kumar HS Kuvempu University, India

doi:10.4172/jpb.1000240

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Endophytic bacteria reside within plant hosts without causing disease symptoms. These bacteria generally colonize the intercellular spaces, and they have been isolated from all plant parts. One endophytic bacterium, named as KAU-EC1 was isolated from shoot cultures derived from field plants as well as in vitro seedlings of cashew (Anacardium occidentale L.). Isolation of endophytic bacteria on nutrient agar media yielded large mucoid, opaque, circular convex colonies on nutrient agar medium. Characteristics of this bacterium were studied by cultural and morphological tests. For bacterial identification, 16S rDNA sequencing is particularly important in the case of bacteria with unusual phenotypic profiles, rare bacteria, slow-growing bacteria, uncultivable bacteria and culture-negative infections. 16S rRNA molecules contain both highly conserved regions and variable regions. The highly

conserved regions provide priming sites suitable for polymerase chain reaction and sequencing applications. PCR was performed for the amplification of 16S rDNA gene. 16S rDNA gene was amplified using two universal bacterial primers: 16S43-63 and 16S1404-1387. The PCR product when checked on agarose gel indicated the presence of band 1.3 Kbp. The 16S rDNA gene from KAU-EC1 was cloned in pGEMT vector, sequenced and analysed after vector and adapter editing. In silico analysis using bioinformatics tools revealed that sequence of KAU-EC1 showed 99 per cent homology with Klebsiella pneumoniae strain SA-D6-7 16S ribosomal RNA gene. This is the first study reporting endophytic bacteria in tissue cultured cashew plants. The possible role for this bacterium in the biology of cashew plant remains unknown.

Sequencing of 16S rDNA gene: A rapid tool for identification of endophytic bacteria from In vitro cultures of cashewJusna Mariya P L, Keshavachandran R, Nazeem P A, Girija D and Surendragopal KCentre for Plant Biotechnology and Molecular Biology, India

BiographyJusna Mariya P.L. has completed her graduation and post graduation from Kerala

Agricultural University, Thrissur and currently she is doing Ph. D. in Agri. Plant Biotechnology at Kerala Agricultural University, Thrissur and pursuing her research work.

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Diabetes Mellitus is a metabolic disorder characterized by the hypoglycaemia, glycosuria, hyperlipaemia, negative nitrogen balance & sometimes ketonaemia.

Type II Noninsulin-dependent diabetes mellitus (NIDDM), maturity onset diabetes mellitus:- Cause may be (a) Abnormality in glucose receptor of beta-cell so that they respond at high glucose concentration.(b) Reduced sensitivity of peripheral tissues to insulin, reduction in number of insulin receptor, ‘down regulation of insulin receptors’.(c) Excess of hyperglycaemic hormone. Prepare a oral drugs an in-silico (Drug Designing) research has been worked-out which is based on some computational tools & on the principle of protein-protein & protein-ligands binding. Protein-protein and protein-ligand interactions are fundamental as many proteins mediate their biological function through these interactions. Many important applications follow directly from the identification of residues in the interfaces between protein-protein and protein-ligand interactions, such as drug design,

protein mimetics engineering, elucidation of molecular pathways, and understanding of disease mechanisms. The identification of interface residues can also guide the docking process to build the structural model of protein-protein complexes.

This dissertation focuses on developing computational approaches for protein-ligand and protein-protein binding site prediction and applying these predictions to improve protein-ligand docking.

The Ligand could be developed with the help of some available software of Bioinformatics like ChemSketch of ACDLabs. The Ligand must follow the Lipinski Rule. After that a Docking procedure is performed with a specified Receptor of a Ligand prepared with the help of such software like Auto-Dock, Virtual Dock.

A result that obtained when compared with the result of prescribed drug is lower, than this proved to proposed a more chance of better Ligand against that particular Protein (SUR1- NIDDM).

In-silico evalution of ligand against sur1 receptor (diabetes mellitus)Rohit Sahu Chhatrapati Shahu Ji Maharaj University, India

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Till date little success has been achieved in antiviral therapy against Dengue virus. The NS3 viral protease, required for virus replication is a potential target for antiviral drugs. This work is a computational prediction of some of the potential HIV protease inhibitors against NS3 protease of Dengue virus followed by activity study of the molecules by taking different types of molecular descriptors. Total 19 inhibitors were obtained from Pubchem database. After energy minimization of molecules the docking study was carried out with NS3 protease of dengue virus as a receptor .The docking evaluates the binding affinity and ligand having Pubchem database id CID 482206

and CID 484561 shows the highest binding affinity i.e., -400.88. All the docked ligands were observed to share a similar position and confirmation with the receptor. Although HIV and Dengue belongs to different families of virus but the docking results suggest that some HIV protease inhibitor could be used as antiviral drug against the Dengue virus. In order to study the activity of these selected potential drug molecules, QSAR analysis has been performed by taking some of the physiochemical and structural descriptors. The effect was calculated for each type of descriptors by taking Andrews affinity as a dependent variable. Multiple regression equation models were built using Minitab Tools.

In-silico docking and QSAR analysis of HIV protease inhibitors as anti-dengue drugsPrangya Ranjan Rout, G R Satpathy and Raghunath Satpathy*

National Institute of Technology - Rourkela, India*MITS Engineering College, India

BiographyMr. Prangya Ranjan Rout has completed his Bachelor Degree in engineering from

Biju Pattnaik University of Technology,(B.P.U.T) Odisha in the year 2009. At present he is a research scholar at National Institute of Technology, Rourkela pursuing his Master of Technology Degree. He is working on the Project “In-silico docking and QSAR analysis of HIV protease inhibitors against Dengue virus NS3 protease” under supervision of Prof G.R. Satpathy and Raghunath Satpathy.

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Mycobacterium tuberculosis is an intracellular pathogen, occuring in macrophages of host & persists there for a long time. In general, external proteases in bacteria are associated with bacterial pathogenic virulence, however little information is available on M. tuberculosis secreted proteins. A diagnostically important secreted antigen, Excretory Secretory-31(TB ES-31) with serine protease activity was isolated from different M. tuberculosis strains culture filtrate. It is reported that catalytic triad is similar both in serine protease and some lipase enzymes. To confirm whether the active site of ES-31 serine protease and ES-31 of lipase is same or not; its inhibition of serine protease activity by lipase inhibitor and inhibition of lipase activity by serine metallo-protease inhibitors has to confirm. Some lipases use the same catalytic triad as that of serine protease and also hydrolyze ester bond by same mechanism. Previous studies had shown that ES-31 is highly sensitive to commercial anti obesity drug Orlistat for both serine protease and lipase activity and thus orlistat can be used to inhibit the action of ES-31. Orlistat binds to the active site of pancreatic lipase,which leads to some conformational changes and abolish its activity.The exact mechanism can be studied using bioinformatics tools.

After purifying the enzyme the sequences and molecular weight can be determend using mass spectrometry,and then the sequences we will built a homology model of ES-31.. In order to validate the sequence-structure alignment, to remove bad contacts derived from homology modelling and to achieve a good starting structure, the model was subjected to exhaustive molecular dynamics simulation with software. Furthur the model quality can be assessed by the geometric quality of backbone conformation, the residues interaction, the residue contact and the energy profile of the structures using various bioinformatic tools. To evaluate the predictive ability of the M. tuberculosis ES-31 homology model and its suitability for use in the structure based drug designing a docking study was conducted. As stated ES-31 can be inhibited by Orlistat, in the present studies docking studies can be very useful to gain insights into the most probable binding conformation of ES-31 with Orlistat. In conclusion these results may help in the understanding of the mechanism of action of M. tuberculosis ES-31 antigen. Further it will provide information about more improved selective ES-31 antigen blockers for the treatment of tuberculosis disease.

Structural analysis of ES-31 serine protease from Mycobacterium tuberculosis by using bioinformatic toolsSwathi Singh

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Lungs differ considerably in structure, embryological origin and function between vertebrate groups that all lungs have a few common characteristics, viz, they are internal, fluid lined, gas holding structures that inflate and deflate cyclically [1]. As a result, all lungs face potential problems related to the surface tension of the fluid as well as protection from the potential immunological attack from pathogens, allergens and pollutants.

Pulmonary surfactant is a complex mixture of 90%

lipids and 10% proteins synthesized by the alveolar type II cells and are secreted into alveolar spaces. A total of 13 types of Surfactant Protein-D were taken from the Protein Data Bank (PDB) based on the presence of the ligands, the x-ray diffraction and 1.40 – 1.90 resolution. Out of these types of Surfactant Protein-D, 2GGU was taken for docking. After docking, the mol dock score was used as binding efficiencies between the ligand molecules as well as the protein 2GGU.

Docking studies of surfactant protein-D on mannose family membersK V S J K TejaGITAM University, India

BiographyI K.V.S.J.K.TEJA(Btech-Biotech) is a student of GITAM University Visakhapatnam.

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Grazing goats are the backbone of most of the world’s marginal land enterprises. They are capable of utilizing effectively a vast variety of plant species and vegetation types. Most of these plants contain antinutritional factors like tannin which causes inhibitory effect on ruminal microflora involved in fermentation of feed. Tannin tolerant bacterial species are able to utilize feed more effectively. The present study was focussed on identification and molecular characterization of tannin tolerant cultured ruminal bacteria from goat rumen based on sequence comparison of 16S rRNA gene of rumen bacteria and their phylogenetic analysis. Rumen liquor of goats fed with tannin rich diet was cultured in specific media and by using molecular biology techniques of PCR, DGGE, Cloning and Sequecing, the bacterial species were identified. The data was analysed by using bioinformatics tools like MEGABLAST, Taxonomic

Classifier at RDP and MEGA4. Leuconostoc citreum, Citrobacter sp., Escherichia sp., Enterococcus faecalis, Staphylococcus sp. and Enterococcaceae bacterium were found to be high tannin tolerant. Bacillus sp., Sphingomonas sp., Mycoplasma capricolum, uminobacter amylophilus showed moderate level of tolerance and Treponema sp., Zhihengliuella sp., Bacteroidales bacteria showed less tolerance to tannin. Inoculation of tannin tolerant bacteria into the rumen of unadapted goats could help in improving feed digestibility and live weight gain in the animals. Tannin tolerance is mostly by virtue of tannase enzyme production by bacteria. Tannase is industrially important enzyme which has application in beverage, pharmaceutical and paper industry. Tannin tolerant bacterial species can be used for production of tannase enzyme.

Molecular characterization and diversity of tannin tolerant ruminal bacteria of Indian goat T G Sathe, A S Kurkute and M K JhalaAnand Agricultural University, India

BiographyTejaswini Sathe has completed her B.V.Sc. & A. H. degree from Bombay Veterinary

College, Parel, Mumbai and M.V.Sc. (Animal Biotechnology) at the age of 25 years from Anand Agricultural University, Anand, Gujarat. She has done her thesis research on “Diversity and Phylogenetic relationship of tannin tolerant ruminal bacteria of goat”.

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Nitrilases are an important class of hydrolases that convert nitriles to corresponding carboxylic acids and ammonia. Nitrilases are useful biocatalysts for the organic synthesis because their eco-friendly bioconversion allows clean and mild synthesis with high selectivity and yield. Biocatalytic hydrolysis of nitriles is attractive for various sectors like pharmaceutical, fine chemical, cosmetics and food. In the pharmaceutical sector it is used in manufacturing drug/ drug intermediates like atorvastatin, pregabalin, clopidogrile

etc. However, their applicability at industrial scale is restricted as this group of enzyme possesses certain drawbacks like low catalytic activity, their inability to act in oxidative stress condition and elevated temperature. The main objective of the present work is to address these problems via protein engineering. This approach has been employed to generate ‘superior nitrilase variant’ which can efficiently act under the optimised oxidative stress condition and also at elevated temperature as compared to the parental enzyme.

Engineering nitrilase gene for the simultaneous improvement of oxidative and thermostability Anup Kubetkar, Shubhangi Kaushik and U C BanerjeeNational Institute of Pharmaceutical Education and Research, India

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Black pepper (Piper nigrum) is the most used spices because of its distinct biting quality attributed by the alkaloid, piperine. In recent decades, black pepper, its extracts and piperine, have been reported to have many physiological effects. Piperine has been documented to enhance the bioavailability of curcumin against cancers and many other diseases. More recent reports suggest that amino acids increase the bioavailability when tagged to a compound. In the present study, piperine

was conjugated with twenty different amino acids and docked using molecular docking tools such as Molegro Virtual docker against different carcinogenic activating receptors. The piperine analogues with Trp, Try, Phe, His were found to have a greater inhibiting activity than piperine itself. The amino acids analogues of piperine are being synthesized to validate the results of in silico studies.

In silico docking analysis of piperine amino acid analogues against carcinogenic activating enzymesM Taraka Ramji, K Deepthi, K Aruna Lakshmi and P Uma deviGITAM University, India

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Despite the significant advances in the structural biology, there is still a huge gap between number of protein sequences identified and their 3-D structures solved. Due to the unavailability of the crystal structure information, it is very difficult to predict the substrate specificity and also novel potential substrate for an enzyme. Screening of novel substrate for enzymatic reaction using experimental methods is both time consuming and expensive. Sufficiently accurate computational techniques like homology modeling and molecular docking could be used to understand the structure-function relationship of enzyme and binding mode of ligands. This information could be further utilized for screening of potential substrate for an enzyme and also defining its substrate specificity. Alcaligenes faecalis nitrilase (E.C. 3.5.5.1) constitute branch 1 of nitrilase superfamily. It catalyses the

conversion of nitrile compounds into acids. Their high chemical specificity and frequent enantioselectivity make them attractive biocatalysts for the production of fine chemicals and pharmaceutical drugs intermediates (mandelic acid, nicotinic acid, 4-cyano,3-hydroxy butyric acid etc.). Because of lack of crystal structure of Alcaligenes faecalis nitrilase, the utilization of its synthetic potential as a versatile biocatalyst is largely unexploited. We developed a homology model of Alcaligenes faecalis nitrilase and molecular docking of nitrile compounds was performed into the active site of enzyme. On the basis of the docking studies and pharmaceutical importance, top hit compounds were selected as a potential substrate for enzymatic reactions. Laboratory experimentation is under progress for the svalidation of computational analysis.

Computer-aided substrate screening for Alcaligenes faecalis nitrilaseKapil Jain, Vaibhav Jain, Vachan Singh Meena, P V Bharatam and U C BanerjeeNational Institute of Pharmaceutical Education and Research, India

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Banana (Musa spp.) is one of the most important fruit crops of India next to mango. Nendran (Musa AAB group) is the leading banana cultivar of Kerala, belonging to the plantain subgroup. Biodiversity in Nendran is complex. Nendran is represented by clones distinguishable by variation in plant stature, bunch, fruit morphology and degree of development of male phase. Characterisation of varieties is generally based on morphological and genomic traits which are subjected to environmental influences. So using a molecular marker that provides a powerful tool to reveal polymorphism at the DNA sequence level will be useful. RAPD (Random Amplified Polymorphic DNA and ISSR (Inter Simple Sequence Repeat) techniques are widely used for this purpose. Standardisation of DNA using 12 Nendran ecotypes from Banana Research Station Kannara,

Kerala was carried out following a standardised CTAB method. Optimum PCR condition for both RAPD and ISSR were standardised with various quantities of DNA, dNTPs, MgCl2, primers and Taq polymerase. Initially 62 RAPD and 42 ISSR primers were screened against genomic DNA of two banana cultivars (Big Ebanga and Njockkon) for their ability to amplify DNA fragments. Of all the primers, 15 RAPD and 15 ISSR primers produced robust amplification patterns and no band was detected in any negative control amplification. The PCR products obtained were separated on 1.4% and 2% agarose gel stained with ethidium bromide. The present study assesses the levels of genetic diversity in Nendran (AAB) ecotypes of banana and the genetic relationships between them.

Variability characterization in nendran ecotypes of banana (Musa spp.) using genetic markersRakeshkumar S Choudhary, R Keshavachandran, P A Nazeem, Rema Menon and D GirijaCentre for Plant Biotechnology and Molecular Biology, India

BiographyRakeshkumar S. Choudhary has completed his under graduation from Marathwada

Agricultural University, Parbhani and currently he is doing MSc in Agri. Biotechnology at Kerala Agricultural University, Thrissur and pursuing his research work.

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Bipolaris oryzae is the common causal agent of brown spot in rice (Oryza sativa L.), and infection by this fungal pathogen results in severe yield losses. A polymerase chain reaction (PCR) based diagnostic assay was developed to detect Bipolaris oryzae, the brown spot fungus in rice. Universal primers ITS1 and ITS4 were used to obtain the rDNA sequence of the available B. oryzae isolates of diverse geographic origins of India. Species-specific primers were designed based on B. oryzae ITS sequence data obtained in the present study and in comparison with other Bipolaris spp., Curvularia spp., Drechslera spp. and Exserohilum spp. in NCBI database. The specific primers designed

were employed to amplify DNA in PCR from a total of 171 isolates of Alternaria spp., Bipolaris spp., Curvularia spp., Drechslera spp., Exserohilum spp. and Magnaporthe oryzae. The species-specific primers BoVf and BoVr were used in the detection of B. oryzae that amplified a 275 bp fragment from the DNA of all B. oryzae isolates but not the DNA from other species. The primer was also used to detect B. oryzae in rice seed and successfully amplified the predicted size of the DNA fragment in the infected material. PCR detection of as little as 100 ng µl-1 to 1 fg µl-1 of B. oryzae DNA was possible. The method described here requires one day for completion, compared to 10 days required for the cultural method.

Development of a Pcr-Based diagnostic assay for detecting Bipolaris oryzae, the brown spot fungus in rice Archana B, UdayaShankar A C, ChandraNayaka S, Niranjana S R, Mortensen C N, Lund O S and Prakash H S

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For the first time, the genetic variability of southern Caspian sea population of the brackish water amphipod (Pontogammarus maeoticus) was analyzed using randomely amplified polymorphic DNA (PCR-RAPD). We analyzed 4 populations along the Mazandaran coast with 10 arbitary primers, wich produce 23 Interpretable bands. There was no significant polymorphism and 73.91% of bands were monomorphic.

These results (Genetical identification) are consistent with those of morphological identification.

This was the first time that the southern Caspian sea amphipods (p. maeoticus) has been genetically surveyed; therefore to monitor further alteration, variation, mutation and modulation, a continus, precise and great project with the guilan province coast results, is needed.

Dna fingerprinting of southern Caspian Sea population of amphipod (Pontogammarus maeoticus) Safaeeian Sh1, Ghareyazie B* and Mottaghi AAzad Islamic University, Iran*Agricultural Biotechnology Research Instit ute of Iran

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The present study describes the colony PCR assay to detect the bacterial spot disease caused by Xanthomonas axonopodis pv. vesicatoria that affects tomato. The direct method of diagnosis of spot disease has been so far by culture isolation and traditional methods by biochemical characterization which is also time consuming and fails to identify the infecting pathovars. The rhs family gene is well characterized and sequenced completely in Escherichia coli K-12 due to high degree of sequence conservation maintained among its members. However, BLAST search using the nucleotide sequences of this rhs family gene, which are deposited in GenBank database, found sequence divergence at pathovar level. One set of PCR primer was custom synthesized to amplify gene required for an rhs family gene homologous to rhsA, cell envelop. We have developed direct colony PCR assay for the detection of

Xanthomonas axonopodis pv. vesicatoria from infected samples recovered on selective media without DNA extraction. Single colony of Xanthomonas axonopodis pv. vesicatoria was picked up with a sterile pipette tip and added directly to the PCR mix as a template for DNA amplification. Successful amplification was achieved at 517 bp in over 95% of the colonies recovered from infected plant material/seed samples with species - specific primers. Application of this direct colony PCR technique for early disease diagnosis and the source of pathogen can be explored. This method can be a quantitative tool for pathogen detection that may provide more information. The use of colony PCR for specific and sensitive detection of Xanthomonas axonopodis pv. vesicatoria is discussed in the present study.

Sensitive and specific detection of Xanthomonas axonopodis Pv. vesicatoria by direct colony polymerase chain reaction (PCR)Chandan S and Umesha SUniversity of Mysore, India

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Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) is a sensitive, simple and rapid technique for the detection and identification of DNA polymorphism or sequence variation. We have adapted this technique to identify phytopathogenic Ralstonia solanacearum the bacterial wilt causing pathogen in vegetables. 56 isolates of Ralstonia solanacearum were isolated from different parts of Karnataka, India from infected plant material/soil samples, subjected to various biochemical/physiological tests, hypersensitivity test, pathogenicity tests and amplification with lpx upstream region specific primer which is designed to lpx upstream region to confirm the pathogen. PCR-SSCP technique is employed to generate DNA fingerprints of all the 56 isolates of

Ralstonia solanacearum. With the use of universal primer 16S rRNA, PCR-SSCP could discriminate bacterial wilt causing pathogen when compared to other phytobacterial pathogens. This approach employs PCR of bacterial DNA with 16S rRNA primers, and analysis of the amplified product based on the principle of SSCP. The PCR product was denatured and separated on a non-denaturing polyacrylamide gel. SSCP banding patterns were detected by silver staining of nucleic acids. The mobility of the single-strand DNA is sequence dependent and could be used to identify unknown Ralstonia solanacearum. The possible use of PCR-SSCP technique for the specific detection of bacterial wilt causing pathogen of vegetables discussed in the present study.

Development of PCR-SSCP technique to detect bacterial wilt pathogen of vegetablesChandrashekar S and Umesha SUniversity of Mysore, India

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The class of R-genes encoding a Nucleotide Binding Site (NBS) and/or a Leucine Rich Repeat (LRR) region is responsible for a mechanism of resistance to pathogens in many crops. The use of degenerate primers designed on the conserved domains would be a fast techinque for the identification of candidate R-genes. The Resistance Gene Analogs (RGAs) of the NBS-LRR class from the genomic DNA of cabbage will be isolated using degenerrate primers . PCR-generated

fragments arising from a multi-gene family will cloned into a plasmid vector. Followed by the fingerprinting using SSCP-analysis of the inserts in order to find out unique clones before sequencing. Specific-RGAs will be characterised by conformational polymorphism (SSCP analysis) in a panel of cabbge genotypes carrying different levels of resistance. The expression of R-genes in the presence or absence of Black rot pathogen will also be taken up in the present study.

Identifcation of resistance gene analogs in cabbage by PCR-SSCP analysisKaunain Roohie R and Umesha SUniversity of Mysore, India

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Tissue engineering offers an alternative technique to tissue transplantation for diseased or malfunctioned organs and donor tissue shortages. It includes three basic components like scaffolds, cells and growth factors and signals to create three-dimensional tissues. Scaffolds should be porous, biodegradable, biocompatible, non-toxic and easily colonized by cells. Scaffold architecture and its properties greatly influence the success of tissue engineering. The main aim of this work is to design composite scaffold using chitosan and wollastonite by freeze gelation method and their characterization.

Composite scaffolds are fabricated using chitosan, a

biodegradable polymer and wollastonite, an inorganic material by freeze gelation method. Thermally induced phase separation principle is involved in this method. It results in the production of isotropic, highly interconnected, and porosity-designed membranes. Addtion of wollastonite enhances the bioactivity and mechanical strength of the composite scaffold. The porosity, crystallinity and pore size can be characterized using scanning electron microscopy (SEM), differential scanning calorimeter (DSC), Mercury porosimeter, and X-ray diffraction (XRD).

Chitosan/Wollastonite composite scaffold preparation by freeze gelation methodU Sindhu, N Panda and K PramanikNational Institute of Technology - Rourkela, India

BiographyU. Sindhu, is pursuing M.Tech, Biomedical engineering at National Institute of Technology

Rourkela, Odisha. She has completed her B.Tech, Biotechnology from JNTU-H, Andhra Pradesh. She has presented a paper at “National Conference on Tissue Engineering: Prospects and Challenges” in NIT Rourkela.

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Hundred strains of Cymbella sp were isolated from Pichavaram mangrove waters, Tamilnadu, India and made its unialgal culture. All strains were grown in F/2 medium at 21°C for 21 days in 2000lux with 12:12 light: dark. Genomic DNA was isolated from all strains and 18s rRNA was sequenced and submitted to NCBI database. Fatty acid fingerprinting of 100 Cymbella strains were determined by using Innowax column in Agilent 1100 model gas chromatography. The major fatty acids were Arachidonic acid, Behenic acid, Eicosadienoic acid, Elaidic acid, Eicosanoic Acid, Heptadecanoic acid, Heneicosanoic acid, Lignoceric acid, Linolelaidic acid, Linolenic acid Myristic acid, Myristoleic acid, Non Decanoic acid, Nervonic acid, Oleic acid, Palmitoleic acid, Pentadecanoic acid, Stearic acid, Tridecanoic acid ,Tricosanoic acid. On the basis of fatty acid fingerprinting it was possible to distinguish between the Cymbella sp.

Fatty acid fingerprinting of Cymbella sp. isolated from Pichavaram mangrove watersJagannathan NVels University, India

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This talk presents some interesting topics addressing the surface effect on physical properties and potential applications of nanostructured ZnO. The surface effects including surface band bending, chemisorption/photodesorption/biosorption near surfaces, and native surface defects/states are more pronounced in the nanostructures than that in thin film and bulk counterparts due to the structural uniqueness

and the ultrahigh surface-to-volume ratio of ZnO nanostructures. The surface effect constituting the basis for developing novel applications of ZnO nanostructures trigger an increase of interest from understanding on how the physical properties are affected by shrinking dimension or size of ZnO to putting the 1D ZnO nanodevices for ultrasensitive chemical/photo/bio detection in practice.

Surface effect of ZnO Nanostructures and its Application in Ultrasensitive Chemical/Photo/Bio DetectionJose Ramon Duran Retamal, Cheng-Ying Chen and Jr Hau He*National Taiwan University, Taiwan

BiographyProf. Jr-Hau He joined Institute of Photonics and Optoelectronics, and Department of

Electrical Engineering at National Taiwan University since 2007. He puts all his efforts into the design new nanostructured architectures for the next generation of nanodevices. Dr. He’s group is also currently involving in fundamental physical properties of the nanomaterials. Dr. He has authored over 50 peerreviewed publications in journals and over 100 presentations in international conferences. His works have been highlighted by over 20 scientific magazines such as Nature, Chemical & Engineering News, and Nano Today. He serves as an editorial board member of Journal of Nanoengineering and Nanomanufacturing.

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Fe-Fe hydrogenases are focus of research due to its involvement in energy metabolism in many micro-organisms. The current global energy crisis neccesiates biological hydrogen production as an alternative source of energy. Biological hydrogen production is one of the most challenging area of biotechnology. The technological outcome of this depends on research advances focusing on engineering strains and enzymes to develop efficient hydrogen energy. Fe-only hydrogenases do have medical relevance as well since these enzymes are involved in energy metabolism in protozoa like Trichomonas vaginalis. Fe-only hydrogenase is a distinct class of hydrogen producing metalloenzyme, present in number of prokaryotes and eukaryotes (algae).Various studies on this enzyme in last two decades have led to considerable insights into the functional and structural aspects. The aim of the present

study is to use computational approaches to elucidate further the mechanism of catalysis and identify targets for engineering efficient Fe-hydrogenase. In the present study we selected the Fe-only hydrogenase from the Clostridium pasteurianum as a model to identify the putative channels for passage of hydrogen and oxygen. To identify the gas migration pathway in the enzyme the implicit ligand sampling (ILS) approach was used. The method provides complete three dimensional maps of the gas molecule placed in the protein solvate system which allows identification of the gas diffusion by docking gas molecules at the sites in protein and identify the migration pathway. The present study identifies four putative gas channels lined by hydrophobhic aminoacids which will be investigated as biotechnological engineering targets.

Computational approaches to identify the putative hydrogen and oxygen channels in Fe– only hydrogenasePratik Vikhe and Razia KuttyPravara Institute of Medical Sciences (DU), India

BiographyDr. Razia Kutty has done Ph.D in Biochemistry from National Environmental Engineering

Research Institute, Nagpur, India (Indo-Swiss Collaborative Project with EAWAG, Switzerland) and Postdoctoral Research at Centre for Cellular and Molecular Biology, Hyderabad, India as well as at Rice University, Houston, Texas.

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Glucokinase (GK) is the predominant hexokinase that controls hepatic glucose disposal and acts as a glucose sensor for insulin secretion in pancreatic β-cells. Inactivating and activating mutations in GK gene can influence the affinity for glucose that can leads to altered glucose levels in the blood and are responsible for Type 2 diabetes (MODY2). Molecular Dynamics is a powerful computational simulation technique that can produce numerical estimations of physical properties of a molecule by making use of a variety of molecular mechanics force fields. In this study the impact of a total of 42 MODY2 mutations on the confirmation of GK was studied. The list of MODY2 mutations were retrieved from SWISS PROT data base and the X-ray crystallographic structure of pancreatic Glucokinase with resolution of 1.5 Ao was obtained from PDB data base. The intact structure was optimized with Polak-Ribiere conjugate gradient algorithm at an RMS gradient of 0.1 and dynamics simulations were carried

out in AMBER force field for a period of 0.6 ps and a simulation temperature of 300 K. The same procedure was carried out by introducing the MODY2 mutations in the intact GK structure sequentially and the energy values were compared to the intact structure. All the 42 mutated structures were submitted to PDBSum to analyze the variations in the secondary confirmations that are aroused due to each mutation. The results showed there is variation in the Kinetic and Potential energies of mutated structures with respect to intact GK structure. The PDBSum results clearly showed that the induced mutations affected the intact conformation and these conformational changes were seen in Substrate and ATP binding regions also. The results allowed following the influence of mutations on conformational variations of GK structure, especially in the substrate and ATP binding regions. This can help to elucidate the variations in binding affinity of Glucose to the substrate binding region in the MODY2 condition.

Mutation induced conformational fluctuations in glucokinase: A molecular dynamics studyNanda Kumar YellapuSri Venkateswara University, India

BiographyNanda kumar has completed his post graduation in Bioinformatics from Sri Venkateswara

institute of medical science, Tirupati and worked as Lecturer and research fellow in Thapar University, Punjab. Presently pursuing his doctoral studies in Bioinformatics in department of Zoology, Sri Venkateswara University, Tirupati. He is hard working and quick grasping with good communication skills. He stood first and received best student award for his post graduation from Sri Venkateswara institute of medical sciences. He is one of the DST INSPIRE Award winners of the year 2010 and is the first person to receive this fellow ship in Sri Venkateswara University.

doi:10.4172/jpb.1000240

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The use of biodegradable materials as implants has revolutionized the way medicine is practiced today. Among many biodegradable polymers PLA and PGA have many practical applications. Accurate Modelling of such polymers plays an important role in the designing of drug delivery systems and medical implants. So the main aim of the present work is to develop a simple mathematical model to represent the complete degradation of PLA implants.

There are different models which represents the hydrolytic degradation of PLA. In all the models water

diffusion kinetics are neglected by assuming water diffusion into the PLA implant is very fast irrespective of thickness of the implant which is not true. The present work account the kinetics of water diffusion into the model which is not considered in the previous models. The model results are compared with the experimental data as well as previous models. The agreement between the predictions and experimental data is very good.

Mathematical modelling of biodegradable polymer implantsRama Subba ReddyTata Research Devolopement and Design centre, India

BiographyRama subba reddy has completed his M.E in chemical engineering from Indian Institute

of Science, Bangalore in 2009. currently working as a researcher in T.R.D.D.C, pune.

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Pharmacophore modeling studies were undertaken for a series of 1-phenyl-3-aryl-2-propen-1-one (Chalcone) and their congeners as novel potential antimalarials against chloroquine-resistant strain (W2) of Plasmodium falciparum. A four-point pharmacophore with two hydrogen bond acceptors (A) and two aromatic rings (R) as pharmacophore features was developed. The pharmacophore hypothesis yielded a 3D-QSAR model with good partial least-square (PLS) statistics results. The training set correlation is characterized by PLS factors (r2 = 0.920, SD = 0.16, F = 60.1, P = 3.395 e−011).

The test set correlation is characterized by PLS factors (Q2ext = 0.861, RMSE = 0.16, Pearson-R = 0.94). A docking study revealed the binding orientations of these inhibitors at active site amino acid residues (Gln36, Cys39, Lys37, Asp35, Trp206) of falcipain enzyme (PDB ID: 3BPF). The results of ligand-based pharmacophore hypothesis and atom-based 3D-QSAR give detailed structural insights of novel chalcone derivatives as falcipain inhibitors which may provide guidance for further lead optimization and virtual screening.

Pharmacophore modeling and 3D-QSAR of novel chalcone derivatives as Plasmodiumfalciparum growth inhibitorsNitendra K Sahu and D V KohliDr. Hari Singh Gour University, India

doi:10.4172/jpb.1000240

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CBM35-CtGH26 protein with an accession number (ABN51273.1) is a carbohydrate active modular protein and component of a vast cellulosome of Clostridium thermocellum. Its structural analyses and substrate specificity is unexplored. The molecular architecture of full length protein contains multiple domains viz. signal peptide (1-31), CBM35 (32-134), GH26 (135-507), linker (508-519) and Dockerin type I (520-590). This study mainly focuses on carbohydrate binding module (CBM35) of the protein. CBMs are non catalytic components whose function is to enhance the catalytic efficiency by keeping the substrate in close proximity of the catalytic domain. A good quality 3D structure of CBM35 was generated by using Modeller 9v7. Structure refinement and energy minimization was carried out using loop optimization class of Modeller and by Gromacs (package 2.3), respectively. Ramachandran

plot shows that 93% residues lies in most favourable region, 7% residues is in additional allowed region. Structure similarity search of modeled structure into Dali server shows similarity with PDB ID: 2W1W-B and 2VZP-B with RMSD of 1.7 and 1.8, respectively. Multiple Sequence Alignment of representative protein from CBM35s families showed many signature motif residues as conserved. Moreover, the key residues which involve in substrate binding are conserved within subfamily Man-CBM35. Secondary structure of modelled CBM35 showed that it contains 12 β strands and 2 small α helix. Topology diagram showed β-jelly roll fold. Docking study with β-1-4 linked mannotriose and mannopentose identify potential binding sites in CBM35 which shows that key conserved aromatic residues are involved in the substrate specificity.

In silico structure and substrate binding analyses of family 35 Carbohydrate binding Module (Cbm35) from cellulosome of clostridium thermocellumAnil Kumar Verma, Arabinda Ghosh and Arun GoyalIndian Institute of Technology Guwahati, India

BiographyAnil Kumar Verma had completed M.Sc. in Industrial Microbiology from the School of

Life Sciences, Devi Ahilya Vishwavidyalaya, Indore (MP) in 2009. At present, he is doing PhD at Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam-India.

doi:10.4172/jpb.1000240

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Health promoting microorganisms such as Probiotics are recently been used as food additive and therapeutic supplement in order to enhance prophylaxis and digestion. A Probiotic which can be given as a supplement to lactose intolerance people to enhance their digestion of dairy products would be of a good economic and therapeutic value. Various bacterial strains such as Lactobacilli which can ferment lactose and their viability in the stomach are greatly affected by its inability to form spore and endure adverse environment of the digestive tract. Moreover, probiotic bacteria are sensitive to thermal stress created by the gut environment and hence it is crucial to assess the thermal adaptation characteristics of a probiotic organism.

Here we report the isolation and characterization of a spore forming Probiotic Bacillus species, with the ability to ferment lactose, from dairy effluent. Biochemical test and 16S rRNA sequencing were done in order to establish the species and was found to be Bacillus subtilis strain SK09 with a unique ability to ferment lactose. This novel isolate was subjected to varying temperatures growth conditions and checked for its thermal adaptation. Experiments w