Project 1 : Mining the deep ocean metagenomes: Exploration of quorum quenching enzymes as cryopreservative to prevent spoilage in food processing sector Funded by: Ministry of Earth Sciences (MoES), Government of India

Summary of the Project 1 : summary not given

Total Outlay: Rs. 88.55 Lakhs

Funded by:Ministry of Earth Sciences (MoES), Government of India
Role:Principal Investigator
Duration:January 2024 – December 2026 (Ongoing)

Project 2 : Immunomodulatory properties of cryptic host defense peptides against brain residing microglia cells and their potential implications in neurodegenerative diseases Funded by: Department of Science & Technology - Science and Engineering Research Board (DST-SERB), Government of India

Summary of the Project 2 : summary not given

Total Outlay: 47.29 Lakhs

Funded by: Department of Science & Technology - Science and Engineering Research Board (DST-SERB), Government of India
Role: Co-PI (PI: Dr. Mukesh Pasupuleti, CSIR-CDRI)
Duration: September 2023 – August 2026 (Ongoing)

Project 3 : Unraveling the potentials of flavonoids as dietary supplements for effective osteoporosis management: Implications on targeting molecular pathways Funded by: Innovation in Science Pursuit for Inspired Research (INSPIRE), Department of Science & Technology, Government of India

Summary of the Project 3 : Osteoporosis, characterized by low bone mass, microstructural deterioration, and increased fragility, results in a staggering 8.9 million fractures annually worldwide. Alarmingly, 80% of India's urban population is at risk, highlighting the urgency of addressing this public health concern. The bone remodelling process, orchestrated by osteocytes, osteoblasts, and osteoclasts, hinges on delicate regulation influenced by hormones, growth factors, and signaling pathways. Imbalances in bone homeostasis, attributed to primary factors like aging and postmenopausal states, or secondary factors such as glucocorticoid therapy and vitamin deficiencies, can lead to osteoporosis. Conventional osteoporosis treatments like bisphosphonates and hormonal therapies have limitations and adverse effects, necessitating safer alternatives. Our project explores the therapeutic potential of phytochemicals, particularly flavonoids abundant in ethnomedicinal plants. Notably, India's rich biodiversity has unveiled multiple plant species with anti- osteoporotic properties in recent surveys. Flavonoids, with their antioxidative properties, have shown promise in regulating bone cells and outperforming traditional medications in long-term efficacy. These compounds exhibit multifaceted effects, promoting osteogenesis and inhibiting osteoclastogenesis through antioxidant, anti-inflammatory, and gene regulatory pathways. The complexity of osteoporosis demands a comprehensive approach. Our study's objectives include evaluating the antioxidant and osteoprotective activities of various plant-derived flavonoids through in vitro assays and in silico screening. We aim to delve into the osteoprotective activities of flavonoids in cell lines and explore their effects in lower vertebrate (Zebrafish) and mammalian (mice) models in vivo. Crucially, we seek to unravel the nutrigenomic effects of flavonoids through epigenetic analysis in animal models, offering insights into their impact on bone homeostasis. This research, with its innovative methodology and focus on multiple pathways, aspires to pave the way for future therapeutics targeting both bone formation and osteoclast resorption. By addressing the unresolved mysteries surrounding flavonoids' impact on bone health, we strive to contribute significantly to the development of effective and safe osteoporosis treatments.

Total Outlay: Rs.19.6 Lakhs

Funded by: Science and Engineering Research Board, Department of Science and Technology, Ministry of Science and Technology, Government of India
Role: Mentor (Ph.D. Student: Ms. P. Snega Priya)
Duration: October 2022 – August 2027 (Ongoing)

Project 4 : Unravelling the interkingdom signaling pathways and interaction mechanisms involved in coral (Bacteria-symbiodiniaceae) endosymbiosis

Summary of the Project 4 : : Coral reefs, vital ecosystems, are under severe threat, facing a rapid decline primarily due to escalating sea surface temperatures causing devastating bleaching events. Despite conservation efforts, projected extinction by 2050 necessitates urgent intervention. Recognizing corals as holobionts, wherein multiple symbiotic organisms function as a single entity, is crucial for understanding their resilience. The pivotal role of dinoflagellate algae (zooxanthellae) in providing energy for reef construction has been wellestablished. However, the intricate interactions within the coral holobiont, especially between symbiotic partners like bacteria and Symbiodiniaceae, remain poorly explored. This project aims to address this knowledge gap using the model organism Exaiptasia pallida (Aiptasia). While coral-zooxanthellae and coral-bacteria relationships are well-documented, the nuances of Symbiodiniaceae-bacteria interactions crucial for reef health have been overlooked. Coral-associated bacteria are anticipated to influence zooxanthellae growth and foster symbiotic associations. By unraveling these connections, the study seeks to enhance our understanding of holobiont dynamics, offering valuable insights for developing conservation strategies amid global climate change challenges. The project aligns with the Intergovernmental Panel on Climate Change (IPCC) recommendations for monitoring and mitigating global warming, highlighting the significance of preserving coral reefs for ecological balance, economic sustenance, and global biodiversity.

Total Outlay: Rs. 22.4 Lakhs

Funded by: Dr. D.S. Kothari Post-Doctoral Fellowship, University Grants Commission, Government of India)
Role: Mentor (PDF: Dr. R. Meenatchi, SRMIST)
Duration: September 2021 – August 2024 (Ongoing)

Project 5 : Genome sequencing and wastewater surveillance in open drains of Chennai City and the suburbs for predicting the future waves of the COVID-19 pandemic

Summary of the Project 5 :summary not given

Total Outlay: Rs. 42.51 Lakhs

Funded by: Science and Engineering Research Board, Department of Science and Technology, Ministry of Science and Technology, Government of India
Role: Co-Principal Investigator (PI: Dr. Paromita Chakraborthy, SRMIST)
Duration: April 2022 – March 2024 (Ongoing)

Project 6 : Metagenomic analysis of gut bacteria in healthy and diseased gut, infected with white gut disease in white shrimp Litopenaeus vannamei

Summary of the Project 6 : The architecture of the gut microbiota substantially influences the health of the host, including shrimps. White faeces syndrome (WFS) is a multifactorial shrimp disease that can cause severe financial losses in Litopenaeus vannamei aquaculture business. In addition to infection with microsporidian, Enterocytozoon hepatopenaei, gut microbiota dysbiosis in shrimps, particularly the species Vibrio, is being explored as one of the aetiologies of WFS. Hence, the present study attempts to decode the gut flora of shrimps as well as to predict the genetic enigma behind the pathophysiology of WFS through metagenomic analysis by sequencing the full-length 16S rRNA gene (V1-V9) using PacBio Sequel II platform. Significant variations in the intestinal bacterial abundance were observed between healthy and WFS affected shrimps. The disease-discriminatory bacteria that are the hallmark of shrimp health status, Vibrio parahemolyticus has been accredited as one of the etiological agents responsible for WFS through long-read sequencing approach. At the genus level, Candidatus Bacilloplasma, Photobacterium, Pirellula, Rhodobacter and Lactococcus are abundantly present in the healthy shrimps, whereas, Cyanobium PCC-6307, Staphylococcus, and Vibrio are overrepresented in WFS shrimp. Vibrio parahaemolyticus was found to be dominant in WFS samples. The functional profile of gut microbiota predicted using MEGAN/PICRUSt2 revealed that WFS is overrepresented in lipid metabolism, nucleotide metabolism, and glycan biosynthesis. Furthermore, there is a majority of gene cores associated to exosome biosynthetic pathways, which is linked to the overrepresented taxa. Our study provides insight into the gut microbial community at the species level resolution between WFS and healthy shrimps, as well as accredits the involvement of Vibrio in WFS disease aetiology and highlights the importance of pathogen related gene core analysis using high throughput transcriptomic and metabolomic approaches.

Total Outlay: Rs. 4.25 Lakhs

Funded by: SRMIST (Inst. Grant)
Role: Principal Investigator
Duration: April 2022 – March 2024 (Ongoing)

Project 7 : Virulence factors identification in fish disease [epizootic ulcerative syndrome (EUS)] causing fungus Aphanomyces invadans by transcriptome approach Funded by: Department of Biotechnology, Ministry of Science and Technology, Government of India)

Summary of the Project 7 : A. invadans infection in fish community is one of the major important diseases affecting more than 95 fish species all over the world. Therefore, in this study we aimed at identifying the key virulent genes responsible for the establishment of disease in fish. So far, we have collected infected fish with severe ulcers from different natural aquatic environment and various fungal pathogens were isolated using GP agar which is the specific isolation medium for A. invadans. As per the proposed the transcriptome library of A. invadans , which was isolated from the ulcer tissues of EUS infected C. striatus was successfully constructed. From the constructed transcriptome library of A. invadans , an in-depth search for the genes with putative virulence functions revealed well-represented virulence-associated domains containing proteins such as cellulose binding proteins, proteases, kinases, kinase inhibitor and toxins.

Based upon the data obtained, we would like to propose this putative model, to establish the sequence of the events that are likely to occur and the role of the virulence factors. Initially the fungi get attracted towards the fish mucus by the Lectin containing GH proteins. Then the fungus binds to the mucus of the fish by using the Fungal binding protein. Once the fungi is on the surface, then fungal glycohydrolase damages the carbohydrates present in the mucus, thus exposing the epidermis. Beta hexosaminidase come into picture and breaks the host cell wall, thus paying the way. Upon cell wall damage, the host produces the defence mechanism like protease and reactive oxygen species. The fungi then fight the responses by using subtilisin like protein, trypsin inhibitor, thioredoxin. As this process is going on, the fungi using glycan synthase, to increase the filament length and reach the deeper regions of the tissue. Once the enough surfaces are reached, the thioredoxin helps in the reproduction of the fungi. We believe that the success of the Aphanomyces invadans pathogen is largely due to the multiple uses of the most of the virulence factors, especially Subtilisin like protein, thioredoxin, trypsin inhibitor. Subtilisin like protein helps the fungi in penetration deep into the tissue as well as degrading the host proteins. Trypsin inhibitor inhibits the host proteases from damaging the fungi components

Total Outlay: Rs. 36.925 Lakhs

Funded by: Science and Engineering Research Board, Department of Science and Technology, Ministry of Science and Technology, Government of India
Role: Principal Investigator
Duration: August 2016 – July 2019, (Completed)

Project 8 : cDNA profiling in targeting novel immune related genes in epizootic ulcerative syndrome (EUS) infected striped murrel Channa striatus

Summary of the Project 8 : Two cDNA libraries of C. striatus. muscle (non-infected and EUS infected) were constructed using Illumina sequencing technology. From the results of differentially expressed gene pattern, it was noticed that 153 genes are involved in immune pathways, thus those genes were screened for characterization studies. Among that, it was observed that 40 genes are in full length and shortlisted for further investigation. Of which, 34 genes have been completely characterized at molecular level. Also, a disease challenge model between C. striatus and EUS causing pathogens have been established for mRNA expression analysis. The gene expression of the above said 34 genes have been studied in detail using real time PCR. Overall, the analysis observed the level of distribution of these molecules in different tissues of C. striatus. Moreover, the analysis also indicated the regulation of gene expression pattern at various times points upon fungal and bacterial infection. The coding regions of the Kazal type serine protease inhibitor, chemokine 1, chemokine 19, serine protease 1, galectin 1, thioredoxin, lily type lectin 1 and caspase 10 have been cloned in an E. coli vector, over-expressed and purified the recombinant protein. The protein activity studies have been completed for serine protease 1, interferon regulatory protein 1, galectin 1, galectin 4, interleukin 8, cathepsin D, heat shock cognate 70, thioredoxin chemokine 1, chemokine 19, lily type lectin 1, lily type lectin 2, caspase 10, mitochondrial manganese superoxide dismutase, kazal type serine protease inhibitor, tumor necrosis factor regulator 1, cathepsin B, cathepsin L, copper/zinc superoxide dismutase and lysozyme G. The results indicated that each protein have different potentials, some are antimicrobial proteins (e.g., galectin 1 and 4, serine protease 1, cathepsin B and D, lily type lectin 1 and 2, interleukin 8 and heat shock cognate 70), adjuvant (interferon regulatory factor 1), therapeutic agent (thioredoxin), involved in cell migration (chemokine 1 and 19) and so on. Overall, the activity assay showed that the characterized molecules are possessed potential immune properties and can be developed as therapeutic agent to address fungal and bacterial infection in fish.

Total Outlay: Rs. 101.6 Lakhs,

Funded by: Department of Biotechnology, Ministry of Science and Technology, Government of India
Role: Principal Investigator
Duration: June 2012 – May 2018, (Completed)

Project 9 : De nova and coparative transcriptome profilling of nitrogen deprived blue-green alage: Pathway description and gene discovery for immune stimulants.

Summary of the Project 9 : Arthrospira platensis, a protein-rich blue-green alga is utilized as feed supplements for human and animals which primarily depend upon nutrients such as carbon, nitrogen, phosphorus and sulfur in the presence of sunlight for their growth and survival. Cyanobacteria depend on sulfur for the synthesis and modification of a variety of biomolecules such as protein and cofactors, iron-sulfur proteins (ferredoxins), thiamine, biotin, lipoic acid and thiouridine. But, the exact mechanism of sulfur metabolism and the impact of sulfate deprivation on A. platensis remain unclear. In this study, we analysed the change in growth and key molecules of A. platensis during sulfate deprivation and compared the transcriptome profiles of A. platensis grown at normal and sulfate-deprived culture conditions. Observations showed that sulfate stress for ten days reduced the growth of spirulina. Transcriptome profile showed that expression profiles of different genes involved in various pathways were altered due to sulfate depletion. Major genes that are altered include iron-sulfur clusters biosynthesis; especially clusters involved four elemental sulfur were down-regulated because of the absence of sulfate. Expression of genes involved in pathways such as translation, amino acid biosynthesis, protein folding, rRNA binding were down-regulated, whereas genes involved in carbohydrate metabolism, phosphor relay sensor kinase activity, integral components of membrane, plasma membrane, thylakoid membrane, metal-ion binding, DNA repair were up-regulated during sulfate stress. Genes involved in transcription were up-regulated and hence there is more number of transcripts in A. platensis grown in sulfate depleted state, however, genes involved in translation were down-regulated, thus there is a reduction in total protein content. Overall, the results showed that the response of A. platensis was similar to the response of Emiliania huxleyi and Arabidopsis thaliana during sulfate stress. This dataset shows that A. platensis was able to sustain even in the absence of sulfate by ability to alter the gene expression profile especially the genes involved in sulfur metabolism.

Total Outlay: Rs. 4.95 Lakhs

Funded by: SRMIST (Inst. Grant)
Role: Principal Investigator
Duration: April 2016 – March 2017, (Completed)

Project 10 : 102^nd EC meeting on Science and Technology for Women

Summary of the Project 10 : summary not given

Total Outlay: Rs. 10.29 Lakhs

Funded by: Science for Equity Empowerment and Development Division (SEED), Department of Science and Technology, Ministry of Science and Technology, Government of India
Role: Principal Investigator
Duration: April 2016 – March 2017, (Completed)

Project 11 : Research Seed Grant

Summary of the Project 11 : ..

Total Outlay: Rs. 25 Lakhs

Funded by: SRMIST (Inst. Grant)
Role: Principal Investigator
Duration: April 2014 – March 2017, (Completed)

Project 12 : Molecular and Proteomic Identification on Immune Related Genes in Freshwater Prawn Macrobrachium rosenbergii

Summary of the Project 12 : cDNA library of M. rosenbergii using Genome Sequencing FLX Technology (GS-FLX™) was constructed. From the constructed cDNA library, 19 full length immune genes were identified; of which, 9 genes were completely characterized at molecular level. Based on the results, each molecule belongs to different coding system such as prophenoloxidae activating system, antioxidative enzymes, antimicrobial peptides and heat shock proteins. These immune genes were predominantly expressed in most tissues in M. rosenbergii, but the relative expression level was varied from tissue to tissue. The gene expression of these defense genes in tissues changed rapidly and dynamically in response to viral (MrNV and WSBV) and bacterial (V. harveyi and A. hydrophila) challenge, which suggested that all these genes expression correlated closely with the shrimp immune response. We successfully expressed three immune genes Cathepsin L, Glutathione S-transferase theta and Histone 2 in an E. coli expression vector and acquired a highly purified functional recombinant protein. These purified proteins were used to find out their biological activity. We also synthesized and purified three antimicrobial peptides namely Histone 4, Mannose binding lectin and Antilippopolysaccharide and studied their antimicrobial activities. Moreover, we obtained two active enzymes from Transglutaminase and Prophenoloxidase in haemocytes of M. rosenbergii. Further, we used the extracted enzyme to find out their biological activities. Conclusively, the findings indicated that all the defense genes might play an important role in the defense system of M. rosenbergii.

Total Outlay: Rs. 18.1 Lakhs

Funded by: Department of Science and Technology, Ministry of Science and Technology, Government of India
Role: Principal Investigator
Duration: August 2012 – July 2015, (Completed)