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BHARATHIDASAN UNIVERSITY, TIRUCHIRAPALLI


About the Bioinformatics Centre
 

The Bioinformatics Centre at Bharathidasan University is an offshoot of National Facility for Marine Cyanobacteria (NFMC) sponsored by DBT Govt of India is exclusively started as a Sub Centre -Distributed Information Centre (Sub-DIC) to work on the primordial organism the cyanobacteria, since its inception 2001. These photosynthetic ancestor bridges the gap between prokaryotes and eukaryotes, which inhabits all illuminated environments from Tundra to hot springs and fresh water to marine ecosystems. Cyanobacteria, in addition of fixing carbon dioxide, they also fix nitrogen. They are capable of serving as food, feed, fertilizer, fuels, fine chemicals, pharmaceuticals and also help in the abatement of pollution and contribute significantly to green, white, blue, yellow, red and grey revolutions. Amazing versatility of cyanobacteria has attracted a large number of scientists around the world.

The Centre has good infrastructure facility, which supports NFMC and Department of Marine Biotechnology and other life science students of University in Bioinformatics. The centre conducts National level workshop annually, which adds up the knowledge and man power to the field of cyanobacterial Bioinformatics. NFMC and sub DIC together had done a pioneering work in marine cyanobacteria and cyanobacterial Bioinformatics and been an eye-opener for cyanobacterial research in India, other than biofertilizers.

 
Area of specialisation: Cyanobacterial Bioinformatics
 
Objectives
  • Marine Cyanobacteria deposition and maintenance.
  • Promoting education and human resource development in Bioinformatics.
  • 24 x 7 Internet connectivity with 512 kbpsfor researchers.
 
Current area of research

 

  • Comprehensive analysis of enzymes involved in cyanobacterial lipid pathway.
  • Identification, classification and evolution of cyanobacterial detoxification enzymes glutathione – S- transferases (GST)
  • Studying the binding affinity of xenobiotic compounds and glutathione- S-transferases.
  • Cyanobacterial stress associated enzymes and signaling pathways.
  • Comparative analysis of cyanobacterial CO2 fixing enyzmes in C3 & C4 pathways.
  • Omics studies.
 
Databases/applications developed
 
Complete datasheet of cyanobacterial cultures with GPS (Global Positioning System)value available in www.nfmc.res.in
 
A a database- Cyanobacterial Knowledge Bases
Achievments at glance
Molecular characterization of marine cyanobacteria
India is one of the major marine biodiversity “hotspots” of the world with a vast coastal area of @7700 km. The diverse organisms of “hotspots” should be conserved and catalogued for prosterity.Cyanobacteria, the unique group of oxygenic photoautotrophic prokaryotes possess extensive morphological diversity ranging from single celled, colonial to differentiated multicellular forms with branching patterns. Due to their wide diversity and adaptability,they could survive in varied marine ecological niches such as estuaries, coral reefs, mangroves, salt pans, backwaters, rocky shores and sandy shores. The cyanobacterial strains of various Indian coastal areas are catalogued and conserved for various biotechnological purposes in our repository.Traditionally, cyanobacteria are classified on the basis of morphological approach but certain morphological criteria used for classification have only ecotypic value which leads to misinterpretation of identification.Hence the identification has also to be carried out at the genetic level using molecular approach which offers the possibility to estimate the biodiversity upto species level. Precise identification of cyanobacterial strains in our germplasmand to optimize the accuracy of taxonomic identification is most vital. Since NFMC has a rich marine microalgal collection of @630 strains, we are concerned in the development of foolproof identification method for cyanobacterial taxa using 3 molecular markers such as 16S rRNA, 16-23S ITS region and cpc regions along with the traditional morphological method. Gene details sequenced so far were accessible in Gene sequencing portal of NFMC website (http://www.nfmc.res.in).
Comparative analysis of cyanobacterial superoxide dismutases, a canonical form
Superoxide dismutases (SOD) are ubiquitous metalloenzymes that catalyze the disproportion of superoxide to peroxide and molecular oxygen through alternate oxidation and reduction of their metal ions. In general, SODs are classified into four forms by their catalytic metals namely; FeSOD, MnSOD, Cu/ZnSOD and NiSOD. In addition, a cambialistic form that uses Fe/Mn in its active site also exists. Cyanobacteria, the oxygen evolving photosynthetic prokaryotes, produce reactive oxygen species that can damage cellular components leading to cell death. Thus, the co-evolution of an antioxidant system was necessary for the survival of photosynthetic organisms with SOD as the initial enzyme evolved to alleviate the toxic effect. Cyanobacteria represent the first oxygenic photoautotrophs and their SOD sequences available in the databases lack clear annotation.
Our in silico analysis on the sequence conservation and structural analysis of Fe (Thermosynechococcus elongatus BP1) and MnSOD (Anabaena sp. PCC7120) reveal the sharing of N and C terminal domains. At the C terminal domain, the metal binding motif in cyanoprokaryotes is DVWEHAYY while it is D-X-[WF]-E-H-[STA]-[FY]-[FY] in other pro- and eukaryotes. The cyanobacterial FeSOD differs from MnSOD at least in three ways viz.
  • FeSOD has a metal specific signature F184X3A188Q189.......T280......F/Y303
    while, in Mn it is R184X3G188G189......G280......W303
  • Aspartate ligand forms a hydrogen bond from the active site with the outer sphere residue of W243 in Fe where as it is Q262 in MnSOD; and
  • Two unique lysine residues at positions 201 and 255 with a photosynthetic role, found only in FeSOD.
Further, most of the cyanobacterial Mn metalloforms have a specific transmembrane hydrophobic pocket that distinguishes FeSOD from Mn isoform. Cyanobacterial Cu/ZnSOD has a copper domain and two different signatures G-F-H-[ILV]-H-x-[NGT]-[GPDA]-[SQK]-C and G-[GA]-G-G-[AEG]-R-[FIL]-[AG]- C-G, while Ni isoform has an nickel containing SOD domain containing a Ni-hook HCDGPCVYDPA.
Our study or the first time have unraveled the ambiguity among cyanobacterial SOD isoforms. NiSOD is the only SOD found in lower forms; whereas, Fe and Mn occupy the higher orders of cyanobacteria. Cyanobacteria harbor either Ni alone or a combination of Fe and Ni or Fe and Mn as their catalytic active metal while Cu/Zn is rare and cambialistic form is absent. SOD is important, which produces OH radical and H2O2, which helps in decolourization of effluent. Thereby SOD is involved in killing pathogens in sewage.
a. The active site residues of Fe Superoxide dismutase of Thermosynechococcus elonagtus. (PDB: 1gv3); b. The active site residues of Mn Superoxide dismutase of Anabaena sp. ( PDB: 1my6)
 
Project titled “Over Expression of Engineered SOD Enzyme in Marine Cyanobacteria for Bioremediation Purposes”, sponsored byDBT, Govt. of India
 
Siderophore mediated uranium sequestration
Increasing contamination of the environment by uranium on account of its mining and disposal of tailings is a worldwide problem. Microbial interactions with metals form an important part of the natural biogeochemical processes and have important consequences for human society. It is therefore, vital to advance our understanding of the metal-microbe interactions that may include physical and chemical adsorption, ion exchange co ordination, complexation, chelation and micro-precipitation in order to develop suitable bioremediation strategies for metal contaminated sites. Among microbes, cyanobacteria represent a morphologically diverse group of oxygenic, gram-negative photosynthetic prokaryotes, which are widely distributed in freshwater, marine and terrestrial environments. These organisms respond and adapt to most stress conditions and are often abundant in metal contaminated environments. Siderophores, constitute a major class of naturally occurringchelators that includes hydroxamate, catecholate, and carboxylicacid functional groups secreted by microorganisms in various habitats,which bind to iron and mediate its transport to the cell. Thesemetal chaperones are majorly specific for iron. Inspite of its specification for iron complexation, marine cyanobacterium S.elongatus BDU130911 was evaluated for siderophore production and its specificity to complex with uranium through in vitro and in silico analysis. Wet lab studies corroborate the siderophore production in marine cyanobacterium S.elongatus BDU130911and were identifiedas hydroxamate type. Also hydroxamate siderophore complexation with uranium was estimated to be 50% by Chrome Azurol S modified assay. In order to substantiate wet lab analysis, in silicodocking was performed between Desferroxamine (a standard hydroxamate type) with Fe (III) and UO22+. Docking studies validates the hydroxamate siderophore to bind effectively with Fe (III) and UO22+and their binding affinity constant remains >2Aº. This finding was the first report in marine cyanobacteria to elucidate uranium siderophore complexation through in vitro and in silico analysis.
Desferroxamine – Fe(III)
Desferroxamine – UO22+
Project titled “Marine cyanobacteria – A potential candidate for uranium mining”,, sponsored by DAE, Govt. of India
 
Marine cyanobacterial carbon sequestration
Rapidly growing concern on global warming is attributed to the elevated CO2 in the atmosphere and has instigated the necessity to find an efficient way to mitigate carbon dioxide.Currently, CO2 can be sequestered by chemical, biological and geological methods. Biological carbon sequestration hasgained attention as it results in the production of biomass and energy. Cyanobacteria the oxy - phototrophs possess much higher growth rate and ability to fix CO2 while capturing the solar energy with much greater efficiency over the terrestrial plants. Having evolved at CO2 rich atmospheres, these organisms are plausible candidates for carbon sequestration. Eighteen organisms representing three different ordershave been screened from the National Facility for Marine Cyanobacteriafor their carbon dioxide tolerance. The selected plausible strain was grown with continuous flow of carbon dioxide at concentration near to flue gas. The major carbon fixing enzymes of C3 and C4 cycles are also being studied for their role in carbon fixation at higher concentration of CO2. In silicoanalysis of CO2 fixing enzymes Phosphoenol pyruvate carboxylase and Ribulose 1,5 bis phosphate carboxylase/oxygenase untangles the ambiguity among cyanobacteria which can be up-regulated for high CO2 fixing capabilities.Our current research throws light upon calcifying potentials of the cyanobacteria at continuous carbon dioxide in order to convert CO2to insoluable form as CaCO3
docking pose of PEPCase with its substrate phosphoenolpyruvate
Project titled “CO2 sequestration of marine cyanobacteria for multiple utilization potentials”, sponsored by DST, Govt. of India


About the University
 

Bharathidasan University established in February 1982, and was named after the great revolutionary Tamil Poet, Bharathidasan (1891-1968). The motto of the University "We will create a brave new world" has been framed from Bharathidasan's poetic words. The University endeavours to be true to such a vision by creating in the region a brave new world of academic innovation for social change. The year 2006-07 was the Silver Jubilee year for this great and vibrant University. The University reaccreditated by NAAC in the year of 2013 with ‘A’ Grade.The University's main Campus located in a sprawling area 500 acres in Palkalaiperur. Also, the University has a downtown campus at Khajamalai, Tiruchirappalli.
The Campus has the Central Library, Hostels, Informatics Centre, Staff Quarters, Health Centre, Canteen and others. The University has totally, 16 Schools, 34 Departments and 11 Specialized Research Centres. There are 195 faculty members catering to 2372 students and scholars in the University. The University Departments/Schools are offering 177 programmes, 31 M.Phil., 33 Ph.D., 19 P.G. Diploma, 11 Diploma and 10 Certificates. The University's supporting staff strength is 521. The University under its Distance Education mode is conducting 15 UG and 26 PG programmes. The University also has centres and facilities.
The Centre for Nonlinear Dynamics and National Facility for Marine Cyanobacteriaare supported by DST, DAE and DBT. The number of ongoing research projects at the moment in various Departments and Research Centres are 119 with a total outlay of Rs.3,200.29 lakhs. During the last 5 years, the faculty members have published 1014 papers in international journals, 476 papers in national journals and have published 46 books.
The University is an affiliating one with the jurisdiction over the eight districts of Tiruchirappalli, Pudukkottai, Karur, Perambalur, Ariyalur Thanjavur, Tiruvarur and Nagapattinam with 123 colleges affiliated to the University including Fine Arts. The student strength in the affiliated colleges is over 1.50 lakhs. The extension services rendered by the Institute of Entrepreneurship and Career Development (IECD) and the Department of Women Studies to community, especially to theunder –privileged are commendable.
 
About the Institute
Scientific exploration of Marine cyanobacteria was envisioned in Bharathidasan University, Tiruchirappalli in the form of "Microbial Technology Unit" in the Department of Botany in the year 1985 by Dr. G. Subramanian. On realizing the marine cyanobacterial wealth and its potentials elsewhere in the world, Department of Ocean Development (DOD) Govt. of India, sanctioned a project to Dr.G.Subramanian to the tune of Rs. 15. 00 Lakhs to enumerate the marine cyanobacterial wealth of coast of Tamil Nadu. The promising results further kindled interest and paved way for the establishment of National Facility for Marine Cyanobacteria, (NFMC), a Dept. of Biotechnology, Govt. of India sponsored Facility in Bharathidasan University, which is the brain child of Dr.G.Subramanian. Then on, NFMC is carrying out basic and applied research work. NFMC since 1996, till 2006 in collaboration with Department of Microbiology was offering M.Sc Microbiology course. NFMC is continuing as a research center in accordance with the regulation of the funding agency within the newly created Department of Marine Biotechnology as per the syndicate resolution from 2008.
Cyanobacteria, the oxygen evolving photosynthetic diazhotrophs are the architects for all the living organisms. Considering the biotechnological potentials of these marine microbes, National Facility for Marine Cyanobacteria, (Sponsored by Department of Biotechnology, Govt. of India) at Bharathidasan University takes pride in being the only facility in the world dedicatedsolely to the field marine cyanobacterial research, registered with World Federation Culture Collection (WDCC No. 976). The main focuses of the facility are :
  • To survey the entire coast line of India and estabilish germplasm collection of marine cyanobacteria as well as cryophilic cyanobacteria;
  • To carry out, basic and applied research resulting in both the understanding of basic biology as wel as exploitation of these organisms by way of technologies towards human welfare;
  • To carryout genome wide hunt of cyanobacterial genomes;
  • To sequence the whole genome of selected marine cyanobacterium of Indian isolate.
  • To develop a strong knowledge economy and human resource through regular workshops and conferences;
  • To provide marine cyanobacterial culture, instrumental and other facilities to needy researchers.
 
Infrastructure facilities

512 kbps round the clock internet connections.
IBM Xeon Server-1, Alpha Server – 2, Silicon Graphics fuel Workstation, Desktop computers - 13, Laptop Computers – 2, UPS – Online 10 KVA, LCD projector, Printers – 4, Color Printer,All in one Printer – 2, Photocopier – 2, Fax, 24x7 Electronic Survivance – CCTV Camera – 8

 
 
 
 
Achievments at glance
Glutathione S-Trasnferases
Cyanobacteria will serve as promising bioremediator to clean up the environment. It evolved with catabolic potential that eliminates numerous natural and synthetic compounds that are considered infallible. Glutathione S- Transferase (GST) is amultifunctional phase II detoxification enzyme that act as a first line of defense against chemically induced toxicity in all pro and eukaryotes. The current research performs a genome wide hunt to portray the presence of GST enzymes, types and its evolution and it also comprehend the binding affinity and expression toward xenobiotics compounds. Cyanobacteria, a primordial organism to harbor GSTs, give an ample understanding on immense potential of cyanobacterial glutathione S-transferases towards pollution abatement.
a. GST– Omega; b. GST– Endosulfan docking pose; c. GST - Chi
 
DBT, Govt. of India sponsored project titled “Comprehensive analysisof cyanobacterial Glutathione S- Transferases : new Insights and Prespectives”
 
Marine green alga as a potential candidate for biodiesel production
Globally, biodiesel is a firm expanding industry that is facing a growing dilemma of exploring feedstock. There are many options in this area, but unlike solar, nuclear, and fossil fuels, biodiesel have the capability of providing a fuel source ideally suited to replace fossil fuel and fulfil the existing demand. Microalgae are tiny sun light driven cell factories having been projected as one of the most promising feedstock for biodiesel production since they accumulate oil and exhibits faster growth compared to other energy crops without competing for arable land. Our research on microalgal biodiesel production was initiated with ten marine green algae from different geographical regions of south east coast in Tamil Nadu. Chlorella sp. BDUG91771 possessed approximately 23% lipid content. Biodiesel production is feasible only if hyper lipid producing promising strain is used. With this context, high lipid Chlorella sp. BDUG 91771 by external stimuli has been carried out. Out door mass cultivation to the tune of 5KL in an economic medium is also tried. Additionally, overexpressing genes responsible for enhancing lipid content in microalgae is being carried out using bioinformatics approach.
 
Project titled “Repository of marine cyanobacteria for biodiesel feed stock”, sponsored byDBT, Govt. of India
 
Marine cyanobacteria – the plausible fourth generation bioenergy feedstock
Green chemistry proposes to synthesize environmentally benign compounds with the utilization of renewable feedstocks and develops design for energy efficiency. Cyanobacteria the versatile oxygenic photosynthetic microbes were found in oil bubbles in quartz dated 1000 million years ago and are the potent fourth generation biodiesel feedstock over the conventional plant feed crops. The rich cyanobacterial diversity of National Facility for Marine Cyanobacteria representing 19 genera and 41 species has widened the arena of bioenergy research. A vast number of 250 cyanobacterial strains have been screened for their lipid production and has identified about 12 strains with a high lipid yield of 15 % and above. The fatty acid profile of these strains revealed the incidence of middle to long chain fatty acids, the prerequisite for biodiesel. Our current research focusses on the fatty acid metabolic pathway in cyanobacteria and emphases in the comprehensive analysis of key regulatory enzymes involved in the up regulation of fatty acid biosynthesis- towards the production of better quality biodiesel.
Project titled “Repository of marine cyanobacteria for biodiesel feed stock”, sponsored byDBT, Govt. of India
 
Temperature response study of psychrophilic and mesophilic cyanobacteria
Cyanobacterial diazotrophs play a major role in biogeochemical cycling of carbon and nitrogen in tundra ecosystem. Themicrobial and biological processes in tundra ecosystem are slower when compared to other ecosystems due to low soil temperature. Cyanobacteria have an inherent ability to fix atmospheric nitrogen and carbon in varied thermal extremes including Antarctic lake ice where the temperature is always below 0º C and in hot spring mats where the temperature is about 55º C. Thus, the cyanobacteria comprises of psychrophilic, psychrotolerant, mesophilic and thermophilic strains showing wide thermal adaptability. The survey of microalgal flora in the polar region Ny-Alesund, (76º53’E), Svalbard, Spitsbergen during Arctic summer IV expedition(2011-12) resulted in psychrophilic germplasm comprising about 65 psychrophilic cyanobacteria and 40 psychrophilic green algae maintained at 4 ± 2ºC and 15 ± 2ºC. As we have virtuous prosperity of both the psychrophilic and mesophilic strains, research to explore the physiological response and nitrogen metabolising abilities of psychrophilic and mesophilic strains at different temperatures regimes to understand their essential role in C and N cycle in tundra ecosystem is on.
Arctic Expedition
Cold Room and Culture Repository
Project itled “Adaptive responses of psychrophilic (Arctic) and mesophilic cyanobacterial diazotrophs to temperature regimes”, sponsored byUGC.
 
 
 
 
 
 
Recent publications

 

Vijayaraghavan Rashmi, Mohandass ShylajaNaciyar, Ramamoorthy Rajalakshmi, Stanley F. D'Souza, Dharmar Prabaharan, Lakshmanan Uma (2012) Siderophore mediated uranium sequestration by marine cyanobacterium Synechococcus elongatus BDU 130911 Bioresource Technol 130: 204 – 210, Impact factor (4.980)

Balakrishnan Priya, Reddi K Sivaprasanth, Vincent Dhivya Jensi, Lakshmanan Uma, Gopalakrishnan Subramanian, Dharmar Prabaharan (2010), Characterization of manganese superoxide dismutase from a marine cyanobacterium Leptolyngbya valderiana BDU20041. Saline systems, 6.6, Impact Factor (2.28)

Jagadeesan Premanandh, Balakrishnan Priya, Dharmar Prabaharan and Lakshmanan Uma (2009) Genetic heterogeneity of the marine cyanobacterium Leptolyngbya valderiana (Pseudanabaenaceae) evidenced by RAPD molecular markers and 16S rDNA sequence data. Journal of Plankton Research, 31 (10): 1141-1150.
Priya B, Premanandh J, Dhanalakshmi, Seethalakshmi, D, Prabaharan D, and Uma L. (2007) Comparative analysis of cyanobacterial SOD , a canonical form BMC Genomics Vol :8; 458 (4.03)
Premanandh J, Priya B, Teneva I, Balik D, Prabaharan D, Uma L. (2006) Molecular characterization of marine cyanobacteria from Indian subcontinent deduced from the sequence analysis of phycocyanin operon (cpcB- IGS- cpcA) and 16S-23S IPS region. J. Microbiology (1.06)
Rashmi, V., ShylajaNaciyar M., Rajalakshmi,R., D'Souza, S.F., Prabaharan,D., Uma, L., 2013. Siderophore mediated uranium sequestration by marine cyanobacterium Synechococcus elongatus BDU 130911. Bioresour. Technol. 130: 204-210.
Priya B, Premanandh J, Dhanalakshmi, Seethalakshmi, D, Prabaharan D, and Uma L. (2007) Comparative analysis of cyanobacterial SOD a canonical form , BMC Genomics Vol :8; 458 (4.03))
Balakrishnan Priya, Reddi K Sivaprasanth, Vincent Divya Jensi, Lakshmanan Uma, Gopalakrishnan Subramanian, Dharmar Prabaharan, (2010). Characterization of manganese superoxide dismutase from a marine cyanobacterium. Leptolyngbya valderiana BDU20041. Saline Systems 6:6(3.09).
 
 
Faculty members
Coordinator    

Dr. L. Uma
lumaprabakar@yahoo.com,
uma@nfmc.res.in

 
Co-cordinator    

Dr. D. Prabaharan
dharmarpraba@yahoo.com,
praba@nfmc.res.in

 
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