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JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE


About the Bioinformatics Centre
 

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The Bioinformatics programme was initiated at JNTBGRI in 1998 by the launching of a Sub-Distributed Information Centre, as part of the Biotechnology Information System Network (BTISNET) program of Department of Biotechnology, Government of India. The program was initially aimed to establish computer and communication infrastructure facilities for promoting biotechnology based R & D. Recognising the importance of Bioinformatics on fulfilling the main objectives of JNTBGRI i.e., to prepare a comprehensive information system on plant genetic diversity of the country particularly of the Western Ghats and novel discoveries in plant science, the Institute has established the Bioinformatics R & D Centre in 2002  with financial support from DBT in a separate campus at Saraswathy Thangavelu Centre of JNTBGRI, Puthenthope, Thiruvananthapuram.  Since its inception the Centre has been focussed on biodiversity informatics, validation of drug activity in Indian medicinal plants and human resource development.  The Centre has already developed 18 databases related to plants and fungal diversity, screened thousands of plant derived molecules and identified potential lead molecules with anti-tuberculosis, hepatoprotective and anti-snake venom activities, produced 40 Post Graduate thesis and two M.Phil thesis in Bioinformatics and trained more than 200 personnels including research scholars, teachers and scientists in various aspects of Bioinformatics. Currently eight students with fellowships from various national and State funding agencies such as UGC, DST, KSCSTE, SC/ST Department are doing their Ph.D. in the Centre. For more information and database access visit www.bioinfotbgri.org

Area of Specialization: Biodiversity informatics and screening of plant derived molecules for drug discovery.


About the Institution
 
The Institute, formerly known as Tropical Botanic Garden and Research Institute (TBGRI), is an R & D Institution established in 1979 by Government of Kerala for conserving the tropical plant genetic resources and to develop strategies for their sustainable utilization. The JNTBGRI is currently functioning as one of the Institutions of the Kerala State Council for Science Technology and Environment (KSCSTE), which is an autonomous organization, established by Government of Kerala for promoting Science and Technology developments of the country particularly in Kerala State.
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The Government of India has recognized the JNTBGRI as a National Centre of Excellence. The institute is ideally located at the foot hills of the Western Ghats (at Palode, 40 km away from Thiruvananthapuram – Shencottah Road) in a 121 hectare forest land with hills and hillocks and evergreen, deciduous, marshy and riverine vegetation in addition to grasslands and rocky areas providing different microclimatic conditions for the profusion of the tropical species. There is no ideal organization at present in India with such diverse habitats and vegetation to undertake research on plant diversity conservation and sustainable utilization of plant wealth. The institute is currently conserving more than 4000 species of flowering plants and about 300 species of non-flowering angiosperms, which is the highest number of plant species conserved among the botanic gardens in Asia. The Institute has seven R & D divisions viz. (1) Biotechnology and Bioinformatics, (2) Phytochemistry and Phytopharmacology, (3) Plant Systematics and Evolutionary Science, (4) Conservation Biology, (5) Ethnomedicine and Ethnopharmacology, (6) Garden Management, Education, Information and Training, (6) Plant Genetic Resources to achieve the mandate of the Institution. For more details visit www.jntbgri.in
 
Objectives
  • To establish JNTBGRI as a National Nodal Knowledge Centre for plants and fungal diversity information particularly of the Western Ghats.

  • Bioprospecting of medicinal plants used in Indian systems of traditional medicine for novel drug discovery.

  • Promoting education and human resource development in Bioinformatics. 

  • Dissemination of biodiversity and bioinformatics information on the web
Current areas of Research

Bioprospecting of medicinal plants

India has endowed with rich source of medicinal plant diversity and vast traditional knowledge system related to the use of medicinal plants against almost all diseases so far reported. But the efficacies of these herbal formulations are not scientifically validated due to several reasons such as lack of efficient screening methods, high expense, slow and difficulties in executing the experimental works, lack of model organism for testing etc. In silico screening of phytomolecules coupled with in vitro and in vivo screening may be the best option to validate the drug activity of herbal medicine and that also give insights to the discovery of novel drugs.  In the light of these, Bioinformatics Centre of JNTBGRI is searching for lead molecules in plants through in silico, in vitro and in vivo methods.  Currently, the Centre has focussed on lead molecules having snake anti-venom, hepatoprotective and ant-tuberculosis activity.
 
Identification of lead compounds with anti-hepatitis B activity

Hepatitis B is a life-threatening infectious liver disease caused by hepatitis B virus which kills six lakhs people every year.  It is 100 times more infectious than HIV. None of the present drugs can clear the infection; they can only stop the virus replication.  Perusal of literature revealed that more than 400 plant species have been used as hepatoprotective agent in Indian systems of medicine.  The centre has already screened about 1200 chemical molecules derived from 30 such plant species and identified potential leads.  HBx protein responsible for viral replication has been used as target.  Further investigation in this line is in progress. A Ph.D. programme with KSCSTE, Government of Kerala fellowship is going on in this area of research.

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Docking between Antherasesamone B from Sesamum indicum and HBx protein
Identification of lead compounds with snake anti-venom activity
It is estimated that every year globally 20000-125000 and in India ~50,000 people die due to snake envenomation.  Anti-venom immunotherapy is the only treatment against snake bites which cause serious side effects to the victims. The majority of the snake bite victims are depends on herbal medicines and the traditional healers claimed that which have fewer side effects.  Globally ~ 600 plant species and in India ~350 plant species have been used to treat snake bites. However, its efficacy is seldom investigated.  Snake venom is a complex mixture of bioactive compounds and many of them are harmless or medicinally important but a percentage of them are toxins. Generally, 20 such toxic molecules have been reported from snake venom, of these 12 of them are common in almost all poisonous snakes.  They are Phospholipase A2, L- Amino acid oxidase, Phosphodiesterase, 5’-Nucleotidase, Phosphomonoesterase, Deoxyribonuclease, Ribonuclease, Adenosine triphosphatase, Hyaluronidase, NAD-Nucleosidase, Arylamidase and Peptidase. Currently the centre is screening phytochemicals for leads having Indian cobra (Naja naja) and Russells viper (Daboia russellii) venom neutralizing activity.  About 20 plant species have been already screened for Cobra venom and three plant species have been screened for viper venom neutralizing activity.
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Proximadiol isolated from Acorus calamus L. . docked with Cobra venome Phospholipase A2 (PDB ID IA3D)
 
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Molecular interaction of Firamperemophillane reported from Vitex nigundo L. with the active site residues of Serine protease in Cobra venome. Hydrogen bonds are represented in green dots.
 
Identification of lead compounds with anti-tuberculosis activity
Tuberculosis (TB) caused by Mycobacterium tuberculosis is the second worldwide killer infectious disease.  Globally every year 1.4 million and in India nearly 30,000 people die due to TB.  The present drugs for TB was discovered nearly half century ago and now it is less effective and contributing to the growth of drug resistant TB. In the light of these, discovery of novel drug for TB attains prima face importance.  Since time immemorial several plant based remedies have been used against tuberculosis in the traditional systems of treatment especially in India and in African countries. The Bioinformatics Centre of JNTBGRI has searching for lead molecules in those plants.  The Centre has already screened hundreds of molecules derived from selected medicinal plants and identified potential lead compounds for further investigation.  The selected target molecules for screening purpose include 4’phosphopantetheinyl transferrase (PptT), which is required for the intracellular survival of Mycobacterium and RpfB protein, which helps to surpass the host body defense mechanisms. A Ph.D. programme with DST, Govt. of India INSPIRE fellowship and two M.Sc. Integrated Biotechnology research works with Kerala Agriculture University fellowships are going on in this line. 
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Docking between Pantothenate kinase (PDBID: 4BFS), and Yohimbine, isolated from Alstonia scholaris.
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Essential cell division protein Z FtsZ enzyme (PDB ID: 2Q1X) 19-epischolaricine, an alkaloid isolated from Alstonia scholaris.
 

Biodiversity Informatics

To prepare a comprehensive information about the plants and fungal diversity of the Western Ghats the Centre has developed several databases for different categories of plants and fungi and all these databases are linked on a common web portal.  The databases developed by JNTBGRI are listed below.

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Home page of the web portal
 
Inter Institutional collaboration

The centre joins with apex centre and developed web portal site for BTISNet Publications and Library resources and BTISNET web site.  Collaboration was made with Kerala Agriculture University for conducting integrated biotechnology course sponsored by DBT and providing guidance to the thesis work of two M.Sc. Biotechnology students. 

In collaboration with Malabar Botanic Garden, Ollavana, Kozhikkode a database application package was created for documenting a comprehensive database on plant diversity of Malabar Botanic Garden.   Data of about 400 plants conserved at Malabar Botanic Garden was documented on the database.  The database is maintained at JNTBGRI web server.

 
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Database of plants conserved at Malabar Boranical Garden- Image gallery
BTISNet Publicatin and Library: An online web portal integrating the details of publication and library resources of all the centers including Centre of Exellences (CoEs), Distributed Information Centers (DICs), Sub--Distributed Information Centres (Sub-DICs) and Bioinformatics Facility Centres (BIFs) distributed all over India.
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BTISNet Publications and Library- Home page
Ongoing Ph.D. programmes
 
Validation of the efficacy of snake anti-venom activity in selected plants
In vitro mutagenesis and somaclonal variant selection in Plectranthus vettiveroides
Bioprospecting of selected medicinal plants for viper anti-venom drug
Bioprospecting  of selected medicinal plants for anti-tuberculosis drug
Standardisation of hydroponics and essential oil production in Plectranthus vettiveroides (K.C. Jacob) N.P. Singh & B.D. Sharma
In silico and in vitro screening and identification of lead compounds against Hepatitis - B in selected plants
 
Infrastructure facilities
 
Computer & Communication facility: Web server (IBM) Pentium IV- 3 units; PCs Pentium IV – 14 units; Laptop computers – 1 unit; Printers- 4 units; UPS 2KV - 2 and 5 KV – 1 units; LCD projector – 1 unit; LAN and WAN with 2 Mbps Internet connection.
 
Ongoing projects
 
Development of computational tools for digitizing JNTBGRI herbarium.
Study of parasitic fungal taxa associated with plants of sacred groves in Thiruvananthapuram,  Kollam and Kottayam districts of Kerala State and organisation of a web enabled database.
Cultivation of high value ornamental plants and income generation.
In silico validation of drug activity in plants.
Recent publications
Shefin B, Sreekumar S, Biju CK 2016. Identification of lead molecules with anti-hepatitis B activity in Bacopa monnieri (L.) Wettst. and Cassia fistula L. through in silico method.  IOSR Journal of Pharmacy and Biological Sciences (IOSR-JPBS) 11: (5 Ver. IV) 16-2.  www.iosrjournals.org.
 
N. C. Nisha, S. Sreekumar, C. K. Biju 2016. Identification of lead compounds with Cobra venom detoxification activity in Andrographis paniculata (Burm. F.) Nees through in silico method. International Journal of Pharmacy and Pharmaceutical Sciences 8(7): 212-217.
 
Subin Mathew M S, Sreekumar S, Biju C K 2016.  Identification of lead compounds against human hepatitis B viral capsid protein in three medicinal plants through in silico method. IOSR Journal of Pharmacy and Biological Sciences (IOSR-JPBS) 11(3): 01-06.
 
Nisheeda, BA, P. M. Safeer, S. Sreekumar, C. K. Biju, G. Seeja and C. Manivannan 2016. A Review on Plectranthus vettiveroides: An Endemic to South Indian High Value Aromatic Medicinal Plant. IOSR Journal of Pharmacy and Biological Sciences (IOSR-JPBS) 11(2): 01-11.
 
Deepa V., Sreekumar S, Biju C.K  2016. Validation of Russell’s Viper Venom Detoxification Activity of Azadirachta Indica through In Silico Method. IOSR Journal of Pharmacy and Biological Sciences (IOSR-JPBS) 11(2): 35-46.
 
Nimmi Haridas, Sreekumar S, Biju C.K  2016. Validation ofAnti-Tuberculosis Activity andIdentification ofLeads in Alstonia scholaris L. (R.Br.) IOSR Journal of Pharmacy and Biological Sciences (IOSR-JPBS) 11(2): 12-19.
 
P.N. Krishnan, S. Sreekumar, C.K. Biju and M. Raveendran 2015. Biodiversity informatics In Eds. Keshavachandran, R & Raji Radhakrishnan Agricultural informatics, pp 432. New India Publishing Agency, New Delhi.
 
Nisha, NC., S. Sreekumar, C.K. Biju, and P.N.Krishnan 2014. Identification of potential lead compounds against cobra venom in Rauvolfia serpentine (L.) Benth. ex Kurz. through molecular docking. Intl. J. Pharm. Res. Del. 6(08): 32-43. IF: 2.01.
 
Nisha NC, Sreekumar S, Biju C.K and Krishnan P. N 2014. Identification of lead compounds with cobra venom neutralizing activity in three Indian medicinal plants. Intl. J. Pharm pharm Sci. 6(2):536-541.
 
Safeer PM,  Sreekumar S,  Krishnan PN,  Biju  CK and Seeja G. 2013 Influence of stem cuttings, spacing, group planting, light, irrigation and harvesting period on yield in Plectranthus vettiveroides (K.C. Jacob) N. P. Singh & B. D. Sharma IOSR-JAVS 6(3): 47-53.
 
N.C. Nisha, S. Sreekumar, C.K. Biju, and P.N.Krishnan 2013. In silico approach to prevent soft rot in vegetable crops. IOSR Journal of Agriculture and Veterinary Science. 3(3):1-4.
 
P.M. Safeer, S. Sreekumar, P.N. Krishnan, C.K. Biju and G. Seeja 2013. Influence of soil texture and bed preparation on growth performance in Plectranthus vettiveroides. IOSR-JAVS 5(3): 41-45.
 
C.K. Biju, Sony Thomas, S. Sreekumar and P.N. Krishnan 2013. Additions to the Powdery Mildews of Kerala - II. IOSR-JESTFT 6(4): 31-33.
 
Hosagoudar, V.B., Biju, C.K. and D.K. Agarwal 2011 Foliicolous Fungal floara of Idukki district in Kerala state, International books and distributors, Dehradun – 248001, India. Pp. 436
 
Biju, C.K., Hosagoudar, V.B. and Sreekumar S. 2011.  Additions to the powdery mildews of Kerala, India.  Bioscience discovery 02(1) : 38-41.
 
N.C. Nisha, S. Sreekumar, C.K. Biju, and P.N. Krishnan  2010. Snake anti-venom: virtual screening of plant derived molecules. Biobytes.  Volume 6:14-22.
 
 
 
Visit:    www.jntbgri.in 
             www.bioinfotbgri.org
 
 
Achievements at a glance
Developed 18 databases and incorporated data of about 3400 plants; published six papers in peer reviewed journals, 38 papers in seminar/workshop proceedings, 4 training manuals, 3 chapters in books and one booklet, produced 40 M.Sc./M.Tech. /M.C.A dissertations and provided six months training to 24 students; organized 14 short term training and trained about 200 personnel and organized 7 National seminars; bioinformatics facility is regularly used by 300 staff of JNTBGRI and other institutions.
Biodiversity Databases
Virtual Herbarium: The Herbarium of JNTBGRI was established in 1979 and currently recognized internationally with the acronym TBGT. It comprises 20,500 specimens of flowering plants and 10,000 specimens of mushroom group for ready reference. The collection includes nearly 2000 specimens collected by Stalwarts and distinguished botanists of yesteryears like Beddome, Bourdillon, Narayanaswamy, Sankara Iyer, Venkobarao etc. In view of catering the taxonomic study the Bioinformatics and Taxonomic groups of JNTBGRI jointly started the digitizing of the valuable specimens and made available on the web for ready reference and further interaction. At present the database provides passport data and good quality scanned images of more than 3000 herbarium specimens. Data of more herbarium specimens will be disseminated on the web very shortly.
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Herbarium database - Home page
Mushrooms of Wayanad: The database provides taxonomic information including macroscopic and microscopic details, images and other information about the mushroom diversity of Wayanad district in Kerala. The information presented on the database was collected as part of a 3 year project funded by the Ministry of Environment & Forests, Govt. of India, New Delhi to analyse the diversity of mushrooms of Wayanad area. The database was created jointly by the Mushroom unit and Bioinformatics Centre of JNTBGRI.
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Data view page of Mushroom database
Fungal Database Meliolales: The database comprises information such as legitimate name of each fungal species with literature citation and systematic classification, scientific name and family of host plants, taxonomic description of each species with illustrations and images, taxonomic characteristic features in the form of digital formula and general information about fungi. Over all, currently the database provides information on 400 species of fungi under the order Meliolales reported from India, which would serve as bedrock of information for further studies.  
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Home page of the database
Plants of JNTBGRI: The database provides information about 700 tree species conserved at JNTBGRI campus. Information is arranged under the head Taxonomic details, vernacular name, habit, distribution, flowering period, fruiting period, conservation category, propagation, nature of wood, useful parts, economic importance, etc. Image zooming facility, navigation tool and dynamic search engine are the special features of the database application.
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Data view page of Plants of JNTBGRI Database
Sacredgroves of Kerala: The sacred groves of Kerala are the remnants of evergreen forest patches, protected and conserved based on religious beliefs and a great repository of many endemic, endangered and economically important plant species. The study reports revealed that floristic diversity indices of the sacred groves of Kerala are equal or nearly equal to the forests of the Western Ghats. It is also revealed that these isolated patches are self-sustainable ecosystems function as a bioresource centre and closed system for the nutrient and water cycles for the near by areas. Since 1992 JNTBGRI has been studying various aspects like floristic and vegetational types in general and ecosystem function in selected bioclimatically divergent sacred groves of Kerala and generated voluminous data. These data are organised into the database, which comprises list of sacred groves in Kerala with photographs, short history, vegetational types, associated flora and fauna, physiology/phenology and other study reports of each sacred grove.
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Details of a Kavu in Sacredgrove Database
Garden Info: Database application package for the management of day-to-day monitoring data of plants conserved in Botanic Gardens.  The key features of the database includes tools for easy storage, sequencing, analysis, interpretation and sharing of data, provision to access the list of plants conserved in the garden with up-to-date details of each plant including the scientists who are engaged in plant conservation and related R & D activities, dynamic search engine and navigation tools for easy retrieval of data, etc.  The software package can be used as a model system for the creation of botanic garden's centralised database and its sharing
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Data documenting page of Garden Info
Wild ornamental plants of the Western Ghats: The database provides detailed information on 140 promising wild ornamental plants of the Western Gahts.  The data are displayed on different heads such as Taxonomic position, vernacular name, habit, habitat, distribution, vegetation, flowering and fruiting period, altitude, propagation, attractive parts, taxonomic description and references.
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Page showing details of a wild ornamental plant
Endemic Plants of India: The endemic species are those taxa whose distribution is confined to a restricted area due to their specific ecological niches and edaphic gradients. Therefore, the habitats of endemic species are far more vulnerable than other species. Endemic species once lost, it is a loss of biodiversity of these species for ever. In India there are about 5725 endemic taxa of angiosperms (33.5% of Indian flora) which are located in 25 hot spots. The major hotspots in India which contain largest number of endemic plant species are the Southern Western Ghats and Eastern Himalayas with 1286 and 1808 endemic species respectively. The present database provides taxonomic and phenological details of 1296 endemic plant species of India.
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Database on Endemic plants showing list of endemic plant
Foliicolous fungi of JNTBGRI: An online database providing the details of foliicolous fungal wealth of Jawaharlal Nehru Tropical Botanic Garden and Research Institute. the campus of JNTBGRI is a conservatory of different group of plants including Angiosperms, Pteridophytes, Gymnosperm and Ornamental plants of various kinds. All these plants are very good substratum or hosts for a number of leaf invading fungi. This database is a comprehensive documentation of all the foliicolous fungi growing on the plants of JNTBGRI. It provides detailed description of listed taxa with its icons or images of infected plant parts.
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Database showing the details of a fungus
Rice in Kerala: Kerala is one of the States with maximum consumption of rice. Wilde varieties of rice have been cultivated by the farmers of the State. Research institutes and agricultural universities are keen towards the development of high yielding varieties, derivatives and hybrids of rice time to time. Farmers of the state are clever enough to choose the best variety for cultivation. Conversion of paddy field for other practices, lack of trained labours, and sudden change in climate demands most suitable variety of rice to choose the farmers for better production. Towards this end a database is developed to help the farmers to know the different varieties of rice and its suitable climate and season for cultivation. It provides details of all the rice varieties cultivating in Kerala.
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Rice info database - Home page
Sacred Groves of Kerala: Sacred groves are the remnants of evergreen forest,  protected and conserved based on religious beliefs.   It forms a unique repository of many endemic, endangered and economically important plant species.  The study reports revealed that floristic diversity indices of the sacred groves of Kerala are equal or nearly equal to the forest flora of the Western Ghats.  The database provides a  list of sacred groves in Kerala with photographs, short history , vegetational types, associated flora and fauna, physiology/phenology, etc.
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Sacred groves of Kerala-Home page
Sacred Fungi: Sacred groves are the model ecosystem representing producers to decomposers. Fungi are one of the major decomposers in the ecosystem. Unique climate of the sacredgrove is verymuch favorable for the growth of plant parasitic fungi. Foliicolous fungi mainly black mildews are prevelent in these habitat. 'Sacred fungi' is a comprehaensive database providing details of foliicolous fungi growing on the flowering plants of sacred groves. Here description of the taxa is supplimented with images of infected plant parts and micrographs of the fungi. The navigation and search facility are also included for the easy accession of the data.
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Sacredfungi database- data view page
SeedPack: Database application package for the management of seed bank data.  The key features of the application package are tools for cataloguing of seeds, seed storage and germination data analysis, auto generation of reports on administrative decisions, wizard for online seed request and exchange, dynamic search engine and navigation tool. 
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SeedPack database - list of Index Seminum
Software packages
LitFriend: LitFriend is a user-friendly application with advanced search options for personal storage of bibliographic data and their frequent/easy retrieval for further exploitation. This package also provides reference style customization for different journals.
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BioLit: The software package developed for the management of publications in a research centre. Using this software package the R&D centre can store and retreive individual scientists publications in standard format.
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BioLit - launching page of the software package
Coordinator:
Dr. S. Sreekumar
Senior Scientist & In-charge of Saraswathy Thangavelu Centre, JNTBGRI, Puthenthope. JNTBGRI, Palode, Thiruvananthapruam- 695564,
Mob: 919446480968 email: drsreekumar@rediffmail.com		   5
Co-coordinator:
Dr. C.K. Biju
Scientist, Biotechnology & Bioinformatics Division, Saraswathy Thangavelu Centre, JNTBGRI, Puthenthope, Thiruvananthapruam- 695586, Mob: 9495752933
email: drbijuck@gmail.com
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