KERALA AGRICULTURAL UNIVERSITY, THRSSUR


About the Bioinformatics Centre
 

The Bioinformatics Centre at KAU, Thrissur is one among the eleven Distributed Information Centres (DIC), funded by the Department of Biotechnology, New Delhi under the Biotechnology Information System Network (BTISnet) programme. The Centre which started as a SubDIC in 1995 was upgraded to DIC during 2004 with the objective to support Plant Biotechnology research. It provides services to promote biotechnological research and development in the specialized areas of Agriculture. The Centre is involved in research across a wide range of Bioinformatics disciplines, including gene & protein sequence analysis, protein structure prediction and interaction studies, plant-pathogen interaction studies and exploitation of active compounds of medicinal plants. The Centre offer courses in Bioinformatics to post graduate Plant Biotechnology students, conduct training programmes in Bioinformatics and maintain various databases relevant to agriculture. Resources available at the centre are efficiently utilized by students, researchers and teachers of the University.
centre

 

Area of Specialization: Agricultural Biotechnology

 
Objectives
  • To provide access to scientific information in biotechnology
  • To organize suitable training programmes for the scientists and technical personnel
  • To develop databases pertaining to specialized areas of research in the host institute
  • To promote research in Bioinformatics and popularize its importance in Biotechnology
 
Achievements at a glance
  • Conducted more than 40 training programmes on various aspects of Bioinformatics
  • Over 500 researchers and students were trained in advanced aspects of Bioinformatics
  • Has developed 9 databases that are relevant in the field of agriculture.
  • Publishes quarterly e-newsletter ‘Biobits’.
  • Conducted two national level trainings
  • ICAR sponsored Winter School on “Bioinformatics and its applications” (2009)
  • National (NAIP) training on “Applications of Bioinformatics in Agriculture” (2011)
Publications
  • Journal Publications : 30
  • Books                          : 6
  • Chapters in Books       : 6
  • NCBI Accessions       : 42
 
 
Current area of research

The Centre is actively engaged in plant based research on gene and protein sequence analysis, protein structure prediction, molecular docking and metabolic pathway analysis. The key area of specialization include in silico analysis in phytochemicals of functional importance and enzymes responsible for fungal or bacterial resistance in plants. The in silico studies on medicinal plants and spices have helped in identification of chemical compounds that can act against important diseases like Alzheimer’s, Parkinson’s, Cancer, etc.

 
 
In silico docking studies of phytocompounds on PI3K/NF-?B mediated signalling pathway

Cancer cell invasion and metastasis are multistep processes influenced by the over expression of cell-secreted proteolytic enzymes such as Matrix metalloproteinases(MMPs). Phosphatidylinositide 3-kinase/Nuclear Factor of kappaB signaling pathways have been known to be involved in regulating MMP-9 expression. Synergistic targeting of these pathways using NF-κB and PI3K inhibitors may have great potential for cancer treatment. This work focuses on identifying phytocompounds having anticancer potential to effectively inhibit PI3K and NF-κB. Thirty five phytocompounds with anticancer properties were utilized for the study. After screening out using Lipinski rule of five and ADMET, five compounds namely allixin, capsaicin, eugenol, niazimicin and piperine were docked with PI3K and NF-κB proteins. Niazimicin exhibited interaction for PI3K and NF-κB with residues CYS 633, ASP 632, GLN 392 and LYS 145 respectively. Niazimicin, a phytocompound of Moringa oleifera which is an underexploited vegetable crop with medicinal properties showed maximum interaction with the targets. Further validation using wet lab analysis is in progress in collaboration with Amala Cancer Research Center, Thrissur.

Docking of PI3K with Niazimicin and Docking of NF--κB with Niazimicin

Functional Annotation of Expressed Sequence Tags in Zingiber officinale
Ginger (Zingiber officinale Rosc) of the family Zingiberaceae is an important tropical crop  valued all over the world as a spice and for its medicinal properties. Ginger rhizome is used in several traditional systems of medicine, including ayurveda, traditional chinese medicine, and western herbal medicine. Its traditional use covers a wide array of ailments including common cold, flu like symptoms, headaches, digestive disorders as well as muscular and rheumatic disorders. Despite the medicinal values of Zingiber officinale, information regarding its genome and transcriptome is limited. Many of the enzymes involved in biosynthesis of gingerol have not yet been identified. In this work expressed sequence tags (EST) from rhizomes, leaves and roots of ginger that are available in dbEST (database of expressed sequence tags) of GenBank were characterized using in silico  tools. Assembled dataset was then submitted to the EST annotation pipeline including Blast, Gene Ontology (GO) analysis and pathway enrichment analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG).
 
 
Molecular docking studies to analyze anti cancerous effects of Boerhaavia diffusa

Apoptosis or programmed cell death plays a major role in normal cell development and tissue homeostasis. The bcl-2 family of proteins regulates apoptotic pathway by the interaction of pro apoptotic and anti apoptotic proteins. They maintain a balance between newly forming cells and old dying cells. Over expressed anti apoptotic Bcl-2 will alter the ratio of pro and anti apoptotic proteins resulting in the prevention of apoptosis. Elevated levels of apoptosis-inhibitory protein Bcl-2 has frequently been detected in many forms of human cancer. Therefore, Bcl-2 appears to be a relevant target for cancer therapy. Plants have been used for treating various diseases since ancient times. Boerhaavia diffusa is an important medicinal plant used in various human ailments including cancer, diabetes, hepatoprotective and anti-inflammatory effects. The study focuses on identifying phytocompounds having anticancer potential to effectively inhibit the action of Bcl- 2 protein there by promote apoptosis.

Docking of phytocompound from Boerhaavia diffusa with BCl2

Solanaceae are the most valuable and variable crop species and the third most economically important plant taxon. Expressed sequence tags provide a powerful tool for the identification and categorization of gene and its expression in a wide variety of species. A comparative analysis of expressed sequences would reveal novel genes whose function would be difficult to study in other taxa. The most economically important genus of the family is solanum which include Tomato (Solanum lycopersicum), Eggplant (Solanum melongena) and Potato (Solanum tuberosum). The method includes a series of blast analysis to identify specific genes. Homologs commonly present in three solanum species will be identified using comparative analysis. This work also includes removal of sequences with significant homology to non solanaceae-specific transcripts, construction and searching of novel Solanum-specific motifs.

 
 
Comparative docking studies on the effect of commercial drugs on Dipeptidyl peptidase-4 (DPP-4)

Type 2 diabetes or non-insulin-dependent diabetes is the most common form of diabetes. Dipeptidyl peptidase is an important drug target for type 2 diabetes. The main function of DPP4 is to block the action of glucon like peptide (GLP-1), a hormone which stimulates the release of insulin from pancreas. Inhibition of DPP-4 increases GLP-1 levels and thus releases insulin when needed. There are several existing drugs for the treatment of type-2 diabetes. Our present study is to investigate the inhibitory activity of available drugs used for the treatment of other diseases on DPP-4 rather than the existing drugs. Now about fifty drugs which are used for other diseases were taken as ligands and docked with the target protein DPP-4 using Discovery Studio 3.5. This work is in progress.   

Acebutolol, a drug for high blood pressure is docked with DPP-4
Structural and functional prediction of hypothetical protein in Oryza sativa

Oryza sativa or Asian rice is one of the major cereal crop and staple food for nearly half of the world’s population. Rice is an important model crop with fully sequenced genome. Sequencing projects generates huge amount of gene products in which many are hypothetical proteins. Hypothetical proteins whose functions are unknown is a challenge in the field of functional genomics. Therefore proper annotation of hypothetical proteins is very crucial for better understanding. In the present study hypothetical protein B8AC57 of Oryza sativa was retrieved from Uniprot and analyzed for their functional and structural characteristics using various in silico methods. BLAST from NCBI was used to find the homologues sequences.

 
In silico docking of Hepatitis B DNA polymerase with phytocompounds of Phyllanthus niruri
Hepatitis B is a serious and common infectious disease of the liver, affecting millions of people throughout the world and needs advancement in its treatment. Phyllanthus niruri has been used widely in south India and elsewhere for the treatment of jaundice. Phyllanthus niruri inhibits endogenous DNA polymerase of hepatitis B virus and binds to the surface antigen of hepatitis B virus in vitro. Hepatitis B DNA polymerase is selected as the target of interest and the phytcomponds from the plant are selected as ligands. In silico Docking study of hepatitis B DNA Polymerase with phytocompounds present in Phyllanthus niruri is in progress to identify the unique ligands that helps in designing novel drugs against the disease.

DNA polymerase of Hepatitis B

 
Recent publications

P. James, A.M.Vipin, S. Silpa, P. Antony, P. Sudha, R.Keshavachandran and P.A.Nazeem (2013). DIACAN: Integrated Database for Antidiabetic and Anticancer Medicinal Plants, Bioinformation 9(18): 941-943.

P.A.Nazeem, L.S.Nair, M. Mohan and R.Keshavachandran (2013). In silico docking studies of phytocompounds on PI3K/NF-ΚB mediated signalling pathway. “International Journal of Pharma and Bio Sciences”, 5(1): (B) 721 – 729.

Agricultural Bioinformatics 2013 – edited by R. Keshavachandran, Kavi Kishor Springer-Verlag, New Delhi ( in press).

P.B.Naresh, P.M.Manila, A.M.Vipin and P.S.Abida (2013). Virtual screening and benchmark analysis of compounds from garlic as inhibitor of LasR Quorum sensing signaling receptor protein in Pseudomonas aeruginosa. Poster presented in International Conference on “Biotechnology and Human Welfare”, Sasthra University, Thanjavur.

P. Antony, L.S. Nair, Mekha Mohan and P.A.Nazeem (2013). Computational characterization of Hypothetical Protein in Oryza sativa. Poster presented at National Seminar on “Applications of Bioinformatics in Agriculture”, CPCRI, Kasargod.

A.M.Vipin, B. Baby, S.P. Davis and P.A. Nazeem (2013). Characterization of Disease Resistant (R) Proteins using in silico approach. Poster presented at National Seminar on “Applications of Bioinformatics in Agriculture”, CPCRI, Kasargod.

A.R.Girme, S.C.Ekatpure and P.A.Nazeem (2013). Homology modeling and Structure evaluation of defensin like protein (pSAS10) in Vigna unguiculata. Poster presented at National Seminar on “Applications of Bioinformatics in Agriculture”, CPCRI, Kasargod.

M.Mohan, B.Baby, S.Silpa, L.S.Nair, R.Keshavachandran and P.A.Nazeem (2013). Computational study on docking mode of Mycobacterial Glycosyltransferases and phytochemical compounds, BTISNET Bioinformatics National Symposium, P-4, Lucknow.

S.Silpa, L.S.Nair, R.Keshavachandran and P.A.Nazeem (2013). In silico analysis of phytocompounds as quorum sensing inhibitor against center rot disease of onion, BTISNET Bioinformatics National Symposium, P-5, Lucknow.

T.Radha, C.Harish, P.James, R.Keshavachandran and P.A.Nazeem (2013). MangoDB – Database for Mango Biodiversity in Kerala, BTISNET Bioinformatics National Symposium, P-61, Lucknow.

P.James, P.Antony, Vipin.A.M, R.Keshavachandran and P.A.Nazeem (2013). Medicinal Plant Biodiversity-A source for new drug discovery, BTISNET Bioinformatics National Symposium, P-76, Lucknow.


About the Institution
 

university

The Kerala Agricultural University is the primary and the principal instrumentality of the Kerala State in providing human resources, skills and technology, required for the sustainable development of agriculture. The activities encompass all production activities based on land and water, including crop production (agriculture), animal husbandry, forestry and fishery through conducting, interfacing and integrating education, research and outreach for the benefit of farming community. Deemed to have come into existence on February 24th 1971 by the Act 33 of 1971 of the Kerala State Legislature, entitled 'The Agricultural University Act, 1971', the Kerala Agricultural University (KAU) became operational since February 1st 1972 when the then existing two educational and 21 research institutions administered by the Departments of Agriculture and Animal Husbandry of the Government of Kerala, were brought under one umbrella for facilitating the sustainable and accelerated development of agriculture in the State. The University under the KAU Act is bestowed with responsibility and vested with jurisdiction extending to the entire geographic territory of the State in fulfilling its designated mandate. Located almost in the middle of the state at Vellanikkara in the Thrissur District on the National Highway (NH47) at about 13 km from the Thrissur Railway Station and 50 km from the International Airport, Kochi, the headquarters of KAU is easily accessible by road, rail and air.

 
Inter Institutionel collaborations
  • Computational Chemistry Group of Amrita Viswa Vidyapeetham University, Coimbatore
  • Amala Cancer Research Centre, Thrissur
  • Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram
  • Centre for Bioinformatics, Kerala University, Thiruvananthapuram
  • Jawaharlal Nehru Tropical Botanical Garden and Research Institute, Thiruvananthapuram
  • College of Agriculture, Vellayani, Thiruvanathapuram
  • Centre for E-Learning.
  • Centre for Plant Biotechnology and Molecular Biology , KAU, Thrissur
  • College of Forestry, KAU, Thrissur
  • Banana Research Station, Kannara, Thrissur
  • Mercy College, Palakkad
  • GEMS Arts and Science College, Malappuram
  • St. Marys College, Thrissur
 
Infrastructure facilites
a. Computers and Communication Facility

The Centre has one Dell Server wit0h Microsoft Windows Vista, one IBM Server with Microsoft Windows Server 2003, ISA Server for networking, and 28 Personal Computers with Local Area Networking facility.
Networking: The Centre has established a leased line connectivity of 12 Mbps speed from Reliance.

b. Scientific software packages

The centre is equipped with software packages for analysis of sequences and structures, molecular modeling, docking and molecular simulation studies. These include:

Commercial

Accelrys Discovery Studio 3.5
MATLAB7

Non-Commercial

NTSYSpc 2.1, Rasmol , Swiss PDB Viewer, Modeller, Hex, Argus lab, Phylip, Mega, Bioedit , DarWin, Mapmaker, QTL Cartographer, Tassel.

 
Ongoing Programmes
PhD Programmes
  • Gene expression analysis in relation to Fusarium wilt resistance in Banana (Musa spp.)
  • Validation of apomixis and transcriptome analysis for the detection of genes related to apomixis in black pepper (Piper nigrum L.)
  • Metabolite profiling and gene expression analysis for gingerol production in selected somaclones of ginger (Zingiber officinale Rosc.)

PG Programmes

  • Screening mapping population through Marker Assisted Selection for imparting disease resistance in tomato (Solanum lycopersicum  L.)
  • Integration of combined disease resistance for bacterial wilt and ToLCV in tomato (Solanum lycopersicum L.)
  • Induction of variability in anthurium (Anthurium anreanum Lind.) through in vitro mutagenesis
  • Molecular docking and validation of medicinal effects of coconut (Cocos nucifera L.).
  • Detection of novel metabolites in garlic (Allium sativum L.) through in silico analysis and its validation.
c. Databases and other information resources
  • Good library with more than 300 exclusive books in Bioinformatics. Facilities are provided for staff and students for database search and retrieval.
  • Access to E- Journals through CERA  ( Consortium for e – resources in agriculture)
 
Databases/applications developed:
 
DIACAN

Medicinal plants and plant derived molecules are widely used in traditional cultures all over the world and they are becoming increasingly popular among biomedical researchers and pharmaceutical companies as a natural alternative to synthetic drugs. Antidiabetic and Anticancer Medicinal Plants Database (DIACAN) developed at this centre is unique in providing a comprehensive platform for antidiabetic/anticancer medicinal plants, taxonomical hierarchy, phytoconstituents, and medicinal properties obtained through literature mining.

DIACAN : Antidiabetic and Anticancer Medicinal Plants Database

 
Ginger EST DB

Ginger ( Zingiber officinale) is consumed worldwide as a spice and flavoring agent and is attributed to have many medicinal properties. It is used extensively in Ayurveda, the traditional medicine of India, to block excessive clotting (i.e. heart disease), reduce cholesterol and fight arthritis. Ginger is also extensively consumed as a flavoring agent. It is estimated that in India,the average daily consumption is 8 -10 g of fresh ginger. The transcriptome of Ginger was analyzed using expressed sequence tag (EST) dataset (38, 169 total) deposited in public domains. Several in silico analysis were done during the annotation process. ESTs were clustered and assembled, resulting in 8624 contigs and 8821 singletons (17,441 unigenes). Assembled dataset was then annotated using a series of Bioinformatics softwares. To make the data widely available, the results were integrated into web based ginger EST database.

Ginger Expressed Sequence Database

 
KAU VARIETIES

The database narrates details of improved crop varieties released by Kerala Agricultural University (KAU). The information contain variety name, year of release, breeding method, pedigree/parentage, parent institution and other salient features. The database consist of 43 varieties released by KAU including cereals, vegetables, tuber crops, spices, plantation crops, ornamentals, fruit crops, oil seeds, aromatic and medicinal plants, pulses, cash crops, fodder crops etc.

Database on varieties released by Kerala Agricultural University

 
MangoDB
Mango, the king of fruits, is one of the most important fruits of India grown in an area of 1.23 million ha with an annual production of 10.99 million tonnes and this accounts for 57.18 percent of the total world production. The first mango fruits of the season come to the Indian markets from Kerala. Though it is not considered as a commercial crop of Kerala, mango trees are inevitable component of homesteads of the state. Mango population in Kerala is highly varied and consists of both seedling and grafted trees.  The major cultivated varieties include the local types like Muvandan, Prior and the grafted plants comprise varieties like Alphonso, Bangalora, Banganapally, Neelum etc. and hybrids evolved from elsewhere. MangoDB presents detailed information on commercial and popular varieties, hybrids, their agrotechniques, pest and disease management, harvest and postharvest handling; prospects of mango cultivated in Kerala etc. 

MangoDB: Database for mango varieties cultivated in Kerala

 
SpiceInfo

India is known as the 'The home of spices'. There is no other country in the world that produces as many kinds of spices as India. The climate of the country is suitable for almost all spices. Out of the 109 spices listed by ISO, 63 are grown in India. Spice production in India, as much of the agriculture in the country is undertaken in millions of tiny holdings  and  it determines  the  livelihood  of   a large  number  of  the rural  population, especially  in Kerala. The major spices produced by Kerala are Pepper, Vanilla, Cardamom, Clove, Turmeric, Ginger and Nutmeg. Database gives detailed information about 50 different Indian spices. Informations include common and scientific name, taxonomic hierarchy, morphology, habitat, cultivation practices, disease management, processing techniques and medicinal and edible uses.

Databse on Indian Spices

 
RiceInfo

RiceInfo is a specialized database that gives all information about rice including the Biotechnology and Bioinformatics aspects. This database is divided into three main sections - General Section, Biotechnology and Bioinformatics. General section provides information about the plant with current status, traditional information, varieties including and cultivation practices. The second section gives brief information about the application of Biotechnology in rice research with case studies, current status of biotech research etc. In the Bioinformatics section detailed information on the genome analysis is given. Different databases available on rice genome, different tools and practical applications are also given.

RiceInfo:  Genetic Database on Rice

 
Faculty Members
 

 Name

Designation

Dr. P.A. Nazeem

Professor and Coordinator

Mrs. Priyanka James

Research Associate

Ms. Priya Antony P

Senior Research Fellow

Mrs. Mekha Mohan

Junior Research Fellow

Mr. Vipin A.M

Junior Research Fellow

Ms. Bincy Baby

Research Trainee (Bioinformatics)

Mrs. Sangeetha P. Davis

Research Trainee (Bioinformatics)

Ms. Minu Simon

Research Trainee (Biotechnology)

 
Contacts:

Name of the Coordinator

:

Bioinformatics Centre, (DIC)           Kerala Agricultural University                      Vellanikkara,Thrissur, Kerala-680 656.

Phone number

:

0487-2371994       Mobile       : +91 9447126917

Email  

:

kauniv.btisnet@nic.in

Website

:

www.kaubic.in

Name of contact person  

:

Dr P.A Nazeem

Email  

:

nazeem.pa@kau.in

Contact us Site map Archive   Last updated on: 23 October 2017
© 2012 BTISNet Inc. All rights reserved                                   Created and maintained jointly by JNTBGRI, Apex Centre and NIC Cell, DBT