Abdur Rahaman

Mechanism and Regulation of Nuclear Expansion:

Our group is addressing two major questions in nuclear expansion using Tetrahymena thermophila  as a model organism.

1) Mechanism of nuclear expansion

The nucleus is a membrane-bound organelle that undergoes dramatic changes in size and shape during cell cycle progression. One such change is fragmentation of the nuclear envelope (NE) during mitosis. This fragmentation is a specific feature of metazoans. In yeast, for example, a "closed" mitosis without NE fragmentation requires nuclear membrane expansion to allow chromosome separation within a single intact nucleus. A more general change is the expansion of the NE in post-mitotic cells to accommodate chromatin de-condensation and DNA replication. Nuclear remodeling is a complex process requiring coordinated biosynthesis, targeting and interaction of the nuclear membrane with nuclear pores, inner nuclear membrane proteins and chromatin. How this is accomplished is not clearly understood in any system.

We use Tetrahymena thermophila as a model system to study nuclear remodeling. The unicellular, free-swimming ciliate undergoes closed mitosis, as does yeast. A striking advantage of Tetrahymena is that, nuclear envelope expansion in this organism occurs to a dramatic extent (~10-15 folds) during specific stages in cell conjugation; a process that can be highly synchronized in cell cultures. We have recently discovered that dynamin related protein 6 (Drp6) is required for nuclear remodeling in Tetrahymena. However, the mechanism by which Drp6 performs its function is not known. Therefore, one important objective is to understand the mechanism of Drp6 function in nuclear remodeling.

2) Cell cycle regulation of lipid homeostasis and membrane biogenesis

Nuclear expansion is a regulated process that occurs at a particular stage of cell cycle. A phosphatidic acid phosphatase (PAH1) regulates nuclear expansion in yeast by undergoing phosphorylation and dephosphorylation. While phosphorylated form of PAH1 is involved in nuclear expansion, its dephosphorylated form inhibits the process. The phosphorylation and dephosphorylation state of PAH1 is regulated by cell cycle related kinase (Cdk1) and phosphatase (Nem1 and Spo7 complex) respectively. We have established the role of large PAH1 homologue in lipid homeostasis and maintaining ER tubular structure in Tetrahymena and observed functional conservation with yeast homologue. However, the regulation of PAH1 is not known in Tetrahymena. We found three Nem1 homologues and would address their role in regulation of nuclear expansion, lipid homeostasis and ER structure. Since we did not find any homologue of SPO7 in Tetrahymena, we would also try to identify the protein performing the similar function in this organism.

Aniruddha Datta Roy

The contemporary distribution of biota within the Indian subcontinent must have been shaped by its unique history. The Indian subcontinent was part of Gondwanaland and had close tectonic associations with Africa, Madagascar and Seychelles before eventually colliding with Eurasia, resulting in the orogenesis of the Himalayas. The initial contact of the Indian plate with Southeast Asia may have potentially resulted in exchange of biota across these two landmasses. On the other hand, the contemporary Indian subregion reusers insular from other biogeographic zones areas owing to various geographic barriers. Prolonged insularity generally promotes diversification in lineages with limited dispersal ability, resulting in endemic radiations. Beyond bearing these unique spatial and temporal signatures in its biotic assembly, the Indian subcontinent itself is heterogeneous in its topography with about ten major river systems/ basins flowing out of the peninsula. Additionally, the Indian subcontinent has about six major hill ranges. Cumulatively, these factors would have had (or still have) a significant effect on the contemporary distribution of biota within the Indian subcontinent, resulting in an interesting mix of lineages. Indian biota may therefore be composed of ancient Gondwanan relicts to lineages that dispersed more recently from other regions. I am personally interested in South Asian herpetofauna (reptiles and amphibians), largely owing to their diversity and antiquity. However, in my lab we have a set of broad interests ranging from understanding systematics, biogeographic patterns and evolution of characters in a diverse range of taxa from the Indian subcontinent. As a lab PI, I want to usertain and inculcate a keen interest in organismal biology, ecology, natural history, systematics and biogeography.

Asima Bhattacharyya

Host-pathogen interactions, cell signalling events, immunopathogenesis of infection, cancer microenvironment, molecular events in cancer metastasis and apoptosis.

Chandan Goswami

1. Importance of the crosstalk between TRP channels and cytoskeleton in chronification of Pain: Recent results suggest that different cytoskeleton as well as multiple receptors recognizing several noxious stimuli contribute to the pain signaling. Several key molecular factors which are involved in acute and chronic pain have been identified. Among those, TRPV receptors (TRPV1-6) are important as these receptors act as non-selective cation channels and recognize several stimuli, and integrate extracellular as well as intracellular signaling events. Interestingly, involvement of microtubule cytoskeleton in the chronification of pain has been speculated for a long time. We are the first one to demonstrate the physical interaction between TRPV channels with microtubule cytoskeleton and functional relevence of such cross-talk in the context of different cellular functions.
2. Importance of TRP channels as a sub-membraneous signalling scaffold: Taxol®, a microtubule stabilizer, often used as a chemotherapeutic drug in the treatment of cancer and AIDS is known to induce severe and chronic neuropathic pain. However, the exact molecular mechanisms of Taxol®-induced strong chronic pain is currently not known. TRP ion channels act as a molecular scaffold at the sub-membranous region, interact with different cellular components including microtubule cytoskeleton and contribute to different pain signaling. Among all channels, we are interested to elucidate the role of thermo-sensitive ion channels, namely TRPV channels (TRPV1-6), TRPM8 and TRPA1 in the context of Calcium ion-dependent as well as Calcium ion-independent signaling and further cytoskeletal reorganization. Such understanding has importance in the context to chemotherapy-induced chronifiction of pain.
3. Regulation of vesicular recycling by TRP channels: Receptor-mediated uptake, exocytosis, endocytosis, vesicle trafficking and recycling are complex cellular events which control several cellular functions. For neurons, such functions in turn control synaptic functions, release and/or uptake of specific neurotransmitters. Regulation of vesicular recycling also regulates the neuronal structures and connectivity. Interestingly, different thermosensitive TRP channels regulate these aspects in a very specific and unique manner. Using high-end imaging techniques we characterize these TRP-mediated vesicular recycling and membrane organization. Such understandings have broad importance in different neuronal as well as non-neuronal systems and have immense implications to dissect pathophysiological disorder at the cellular and molecular levels.
4. TRPV-mediated channelopathy: Rare yet naturally occurring mutations in TRPV channels are known to induce several critical pathophysiological disorders due to altered channel function, regulation and/or distribution. For example, mutations in TRPV4 lead to development of CMT2 disease and other mascular dystrophies. Similarly, mutations in TRPV3 lead to "Olmsted Syndrome". Such mutations alter channels' structure-function relationship and affect cellular functions largely. We aim to understand the molecular and cellular mechanisms that go wrong in such cases.
5. Imporatnce of TRP channels in reproduction: TRP channels are present in several parts of the reproductive tissues including mature male gametes. In sperm cells, thermosensitive TRP channels seem to play diverse and complex functions such as thermosensation, Calcium signaling, capacitation, acrosomal reaction, regulation of sperm motility and fertility. We explore these functions in details. Such understandings will have both clinical and commercial importance in future as well.
6. TRP channels in immune function: Immune activation is a temperature dependent event and also needs massive Calcium influx. Indeed, so far several reports have suggested that TRP channels are present in the immune cells where diverse immune functions are regulated by this group of proteins. We investigate the importance of thermosensitive TRP ion channels in mammalian immune systems.
7. Molecular evolution of TRP channels: Genes coding for TRP channels are present in fungus to human (but so far have not been identified in plants). In all these species, TRP channels mainly act as a set of molecular tools required for different "sensory" functions. Over millions of years, such functions in turn play crucial role in the adaptation, ecological niche formation, speciation and also in evolution. Analyzing the sequences of TRP channels from different species provides useful information regarding the selection pressure and the molecular evolution of these channels. Such in silico analysis helped us to identify certain hidden motifs and characterize such motifs in details, which provides useful information regarding the molecular mechanism of these channels per se.

Debasmita Pankaj Alone

Molecular Genetics and Epigenetics of Neurodegenerative disorders: Glaucoma, Corneal endothelial dystrophies and Cancer

With the shifting demographics towards older age, there is a major concern for age-related disorders. 90% of individuals dying each year are due to age-related causes. Understanding the genome, epigenome and proteome between healthy and diseased state of these individuals pave a way for unravelling bio-markers for early diagnosis and/or therapeutics for various diseases. Our goal is to find these underlying players that change the micro-environmental niche differently in a diseased state during the developmental process of aging and hence are responsible for these age related-disorders. We are currently focusing on understanding the pathomechanism of two neurodegenerative eye disorders (Glaucoma, the leading cause of irreversible World Blindness and Corneal Endothelial Dystrophies) as well as Cancer using a pleothora of cellular, biochemical, genetics, genomics and molecular biology techniques involving human samples, Drosophila models as well as in vitro cell lines.

Harapriya Mohapatra

Studies on antibiotic resistance and virulence in gram negative bacteria

Kishore CS Panigrahi

Signaling Systems in Plants, Light perception, flowering time control, circadian rhythm and biological clock.

Agricultural Biotechnology

Manjusha Dixit

My research broadly focuses on the regulation of tumorigenesis and tumor angiogenesis. Specifically, I aim to identify novel molecular regulators involved in cancer progression, with an emphasis on uncovering therapeutic targets that are inherently less susceptible to drug resistance.

Mohammed Saleem

The following two broad problems are currently being pursued in the lab using a combination of in vitro reconstitution, cell-based experiments, advance fluorescence microscopy/spectroscopy, computational and micro-manipulation tools:

1) We are interested in understanding the interplay of cellular membrane parameters and the kinetics of aggregation of intrinsically disordered proteins (IDPs) such as Amyloid-beta, full-length human Tau and alpha-Synuclein. This will help us understand how different IDPs and host cellular membranes influence each other in terms of aggregation kinetics of the IDP or the changes in the physico-chemical parameters of the cellular membranes that might eventually drive neuronal membrane deformation resulting in neurodegeneration and propagation of amyloids from cell to cell.

2) Mechanism by which Mycobacterial secretory components manipulate host cellular membranes to evade phagosome maturation.

Palok Aich

Prof. Palok Aich is widely regarded for his innovative work at the intersection of biophysics, immunology, and microbiome science, contributing significantly to both fundamental research and its practical applications in health and disease management. With a foundational background in biophysics and molecular biology, he integrates multi-omics technologies, AI/ML-based analytics, and animal models to understand how the gut microbiome influences host metabolism, inflammation, and neuro-immunological health.

Introduction and Research Overview

Introduction

Prof. Palok Aich currently serves as the Dean of Research & Development at the National Institute of Science Education and Research (NISER), India, and is the Director of both the NISER Homi Bhabha Foundation and MicrobioTx Health. Prof. Aich holds a Ph.D. in Biophysics from the Saha Institute of Nuclear Physics and has extensive international experience, having held research and leadership positions in Canada before joining NISER in 2009.

Research Overview

Areas of Focus

Prof. Aich’s multidisciplinary research centers on understanding the profound relationship between the gut microbiome, host metabolism, immunity, and brain health. His work integrates multi-omics technologies, artificial intelligence and machine learning (AI/ML) analytics, animal models, and human studies to:

• Decipher the gut–adipose–liver–brain axis and its role in health and disease.
• Identify microbial and host-derived metabolites regulating systemic immunity and metabolic balance.
• Investigate complex diseases such as Type 2 Diabetes, Obesity, Non-Alcoholic Fatty Liver Disease (NAFLD), Inflammatory Bowel Disease (IBD), and neurodegenerative disorders.

Innovations and Impact

• Precision Probiotics & Diagnostics: Developed the world’s first non-invasive Gut Function Test (GFT) that predicts gut microbiome composition through blood metabolites, bypassing stool diagnostics. This innovation is patented, approved by CDSCO (India), and spun-off as MicrobioTx Health, which also offers personalized probiotics.
• AI/ML-based Methodologies: Harnesses regression-based data science, uni- and multivariate statistics, clustering, and network-based modeling to map microbiome-metabolome correlations, using lab-generated data from diverse fields such as metabolism, immunology, and neuroscience.
• Translational Public Health: Prof. Aich’s research bridges basic science and practical applications, impacting personalized medicine and public health. His lab has attracted both academic and industry collaborations, fostering entrepreneurship among young researchers.

Selected Achievements

• Discovery and patenting of M-DNA, a DNA form conductive when doped with transition metal ions.
• Significant publications and patents in fields ranging from gut-brain axis science, innate mucosal immunity, to bio-imaging and systems biology.
• Extensive contributions to training, teaching, and science communication, designing courses in biophysics, systems biology, and chemical biology.

Research Interests

Prof. Palok Aich’s innovative, integrative approach positions him as a pioneer in translating foundational science to real-world health solutions. His leadership at NISER continues to advance the frontiers of life sciences in India and beyond.

Research Focus and Main Contributions

Research Focus

Prof. Palok Aich is recognized for his pioneering interdisciplinary work bridging biophysics and microbiome studies. His research centers on:

• Gut Microbiome and Host Interactions: Deciphering how gut microbes influence host metabolism, immunity, and brain health.
• Multi-omics Integration: Combining metabolomics, genomics, and proteomics to understand the gut–adipose–liver–brain axis and its role in health and disease.
• Artificial Intelligence & Data Science: Applying AI/ML methods to map complex correlations between microbiome compositions and host biomarker profiles, with a focus on disease prediction and personalized interventions.

Main Contributions

• Development of Non-Invasive Diagnostics: Invented and patented the world’s first non-invasive Gut Function Test (GFT), which predicts gut microbiome states via blood metabolites rather than stool samples. This approach, now used by MicrobioTx Health, has streamlined microbiome diagnostics and facilitated the creation of precision probiotic solutions.
• Discovery of M-DNA: Identified and patented a conductive form of DNA (M-DNA) that incorporates transition metal ions, advancing the field of molecular electronics and expanding Bio-Physics applications.
• Translational Public Health Approaches: Designed methodologies for translating basic microbiome and biophysics findings into practical solutions. His focus on the gut–adipose–liver–brain axis addresses complex diseases, including Type 2 diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), inflammatory bowel disease (IBD), and neurodegenerative disorders.
• Innovative Use of AI/ML in Microbiome Science: Developed new regression-based and network modeling tools to unravel relationships within the microbiome-metabolome network, integrating insights from immunology, system biology, and neuroscience.
• Education and Science Communication: Has played a significant role in training future researchers, designing academic courses in biophysics, systems biology, and chemical biology, and promoting entrepreneurial initiatives at the intersection of academia and industry.

Summary Table

Prof. Palok Aich’s unique integration of biophysics and microbiome research has led to breakthroughs with practical impact in diagnostics, therapeutics, and personalized medicine, marking him as a leader in his field.

Key Findings from Palok Aich's Research on Microbiome Influence in Metabolic Diseases

1. Gut Microbiota Shapes Systemic Metabolism

• Adipose Tissue Browning: Aich’s studies show that metabolites derived from specific gut microbiota can induce the browning of adipose tissue (“beige fat”) in mice. Treatment of adipocyte cells with these microbial metabolites led to increased lipid metabolism and the upregulation of genes characteristic of metabolically active beige fat. These effects were comparable or superior to those from known browning agents, highlighting the potency of gut microbial metabolites in regulating energy balance and metabolic activity 1,2.
• Potential for Metabolic Disease Therapy: These findings indicate the possibility of targeting the gut microbiome or its metabolites to combat obesity and metabolic syndrome by enhancing energy expenditure and improving lipid metabolism in the host 1,2.

2. Microbiome Composition and Dysbiosis

• Diet, Antibiotics, and Microbiome Shifts: Aich’s research establishes that both diet and antibiotic interventions can significantly alter gut microbiota composition. For example, treatment with certain antibiotics caused marked shifts in the abundance of bacterial phyla such as Bacteroidetes, Verrucomicrobia, and Proteobacteria. These compositional changes directly impacted metabolic and immune responses in the host, driving or ameliorating metabolic outcomes 3,4.
• Diet-Induced Microbial Modulation: High-starch diets increased beneficial microbial diversity and populations (notably Verrucomicrobia), which correlated with improved adiposity, glycemic control, and a reversal of harmful metabolic parameters. In contrast, fat-rich diets promoted an abundance of Proteobacteria and a reduction of Bacteroidetes, which worsened metabolic health outcomes 5.

3. Impact on Metabolic Disease: Obesity, Diabetes, NAFLD

• Firmicutes/Bacteroidetes Ratio: Aich's work confirms that shifts in the relative abundance of major bacterial phyla (Firmicutes and Bacteroidetes) are linked to obesity and metabolic syndrome. An increased Firmicutes-to-Bacteroidetes ratio correlates with obesity, while the reverse is found in some inflammatory or metabolic disorders. These changes also impact key metabolites such as TMAO, implicated in metabolic risk 6,5.
• Short-Chain Fatty Acids and Dysbiosis: Disruption of the microbiome reduced production of beneficial short-chain fatty acids (SCFAs), altering host metabolism and immune status, thereby contributing to the onset or progression of metabolic diseases (such as type 2 diabetes, nonalcoholic fatty liver disease, and obesity) 3,5.

4. Translational Innovation

• Precision Probiotics for Therapy: Aich pioneered the use of tailored probiotic formulations that specifically target dysbiosis to induce favorable metabolic outcomes. For example, probiotic therapy led to significant weight loss and improved insulin sensitivity in metabolic syndrome models, indicating real-world translational potential for chronic disease management 7.
• Non-Invasive Diagnostics: He developed and patented a blood-based "Gut Function Test" that predicts microbiome health via metabolite profiling, bypassing traditional stool-based diagnostics. This enables more accessible screening for at-risk metabolic states and personalized interventions 5.

5. Critical Developmental Windows

• Neonatal Mice Studies: His lab found that mice experience a critical postnatal window (around day 14) where gut microbial shifts coincide with rapid changes in intestinal barrier function and immune development, influencing susceptibility to metabolic disturbances later in life58.

6. Integration of Multi-Omics and AI

• Systems Biology Approach: By merging multi-omics (metabolomics, genomics) with advanced analytics, Aich’s work maps complex microbe-host-metabolite interactions—uncovering systemic links between microbiota and host metabolism that underlie individual susceptibility to obesity, diabetes, and fatty liver disease 5.

Summary Table: Major Research Findings

Palok Aich’s research demonstrates a strong, causative relationship between the gut microbiome, its metabolites, and the risk and regulation of metabolic diseases, positioning microbiome-targeted therapies as a promising frontier in personalized medicine and chronic disease management1,3,5.

1. https://pubmed.ncbi.nlm.nih.gov/39142136/
2. https://www.sciencedirect.com/science/article/abs/pii/S0006291X24010544
3. https://pubmed.ncbi.nlm.nih.gov/36414091/
4. https://www.sciencedirect.com/science/article/abs/pii/S0024320522009122
5. https://www.niser.ac.in/profile/palok.aich
6. https://pmc.ncbi.nlm.nih.gov/articles/PMC10144251/
7. https://www.onlymyhealth.com/how-does-microbiome-impact-health-and-chronic-disease-management-1728968861
8. https://loop.frontiersin.org/people/785740/publications
9. https://www.tmrjournals.com/public/articlePDF/20221222/de1238b090d15c837176fc07363516e3.pdf
10. https://scholar.google.com/citations?user=IiFpDcQAAAAJ
11. https://www.imsc.res.in/~rsidd/aogcr2025/Palok_Aich.html
12. https://orcid.org/0000-0003-4927-7812
13. https://rem.bioscientifica.com/view/journals/rem/2023/1/REM-23-0016.xml
14. https://www.mdpi.com/journal/metabolites/special_issues/8BZMTX69H3
15. https://www.frontiersin.org/research-topics/43366/gut-microbiota-composition-and-dietary-interventions-implications-in-cardiometabolic-disorders-diabetes-and-atherosclerosis-risk-factors/magazine
16. https://pubmed.ncbi.nlm.nih.gov/38290571
17. https://www.sciencedirect.com/org/science/article/pii/S2755158X23000143

Our work is being widely cited by the media. A few to mention are BioVoiceNews, OnlyMyHealth, BioSpectrum, Nuffoodsspectrum, DBT-ILS, Nextedge, ANI, NEWSVOIR.

Pre-NISER Career Highlights

Academic Training and Early Research

• Ph.D. in Biophysics from the Saha Institute of Nuclear Physics, India. His doctoral research investigated the interactions between select antitumor antibiotics (Mithramycin and Chromomycin) and DNA, exploring the critical role of magnesium ions in modulating these interactions1.
• Postdoctoral Research in Sweden: At Stockholm University and Karolinska Institutet, he focused on higher-order DNA structures using advanced biophysical techniques such as 2D NMR and circular dichroism. During this period, he was introduced to and contributed to the development of Fluorescence Correlation Spectroscopy (FCS) in the ultraviolet region—an innovative application for studying DNA base pair dynamics at the single-molecule level1.

Research in Canada

• University of Saskatchewan, Canada: Chose a postdoctoral position there over offers from prestigious institutes, including the Pasteur Institute and Dana-Farber Cancer Institute. His research focused on higher-order DNA structures in vivo, especially using c-myc and c-src oncogenes.
• Discovery of M-DNA: Alongside collaborators, discovered and patented M-DNA, a novel, conductive DNA form created by doping DNA with transition metal ions. This breakthrough helped establish the concept of molecular wires in nanoelectronics and led to the founding of the company ADNAVANCE12.
• Industry and Academic Roles: Briefly led a bioimaging group in a Canadian biopharmaceutical company before returning to academic science as part of the Saskatchewan Structural Sciences Center, University of Saskatchewan.

Principal Investigator at VIDO (Canada)

• VIDO (now VIDO-InterVac): Served as a Scientist and Principal Investigator (PI) at the Vaccine and Infectious Disease Organization, focusing on innate mucosal immunity. Aich developed programs to investigate how psychological stress affects host-pathogen interactions using bovine and chicken models, while also exploring nanotechnology-based immune stimulators.
• Collaborative and Teaching Roles: As adjunct and associate faculty at the University of Saskatchewan, he designed and taught courses in systems biology, physiological genomics, and bioinformatics to senior undergraduates1.
• Project Leadership: Led multiple projects funded by Canadian agencies, which spanned basic immunology through applied translational research to enhance animal health.

Recognition and Legacy

• Palok Aich’s pre-NISER career is distinguished by pioneering interdisciplinary discoveries—from DNA nanotechnology to translational immunology—with substantial impact in molecular biophysics, biotechnology, and animal health research. His inventive spirit is underscored by his patents, innovations in instrumentation, and leadership roles bridging academia and industry123.

References:

 

1. https://www.niser.ac.in/profile/palok.aich
2. https://scholar.google.com/citations?user=IiFpDcQAAAAJ
3. https://www.youtube.com/watch?v=u1_MXtKzqCw
4. https://niser.irins.org/profile/235251
5. https://orcid.org/0000-0003-4927-7812
6. https://www.biotecnika.org/2023/02/niser-bioinformatician-recruitment-msc-candidates-can-apply/
7. https://pubmed.ncbi.nlm.nih.gov/23690978/
8. https://www.biotecnika.org/2024/10/biological-sciences-project-niser-attend-walk/
9. https://pubmed.ncbi.nlm.nih.gov/20360883/
10. https://www.niser.ac.in/events/IDMPH/
11. https://loop.frontiersin.org/people/785740
12. https://loop.frontiersin.org/people/785740/bio
13. https://www.helpbiotech.co.in/2025/04/niser-bbsr-postdoc-openings-2025-in.html
14. https://www.niser.ac.in/events/sel2023/
15. http://idr.niser.ac.in:8080/jspui/simple-search?filterquery=Aich%2C+Palok&filtername=author&filtertype=equals
16. https://shilabiotech.com/senior-project-associate-vacancy-at-niser-bhubaneswar/

In 2009, we returned to India. When I left VIDO, I had seven ongoing projects funded by various Canadian Funding Agencies. I could not bring these funds, for obvious reasons, to India. I then transferred those projects to other faculty members at VIDO.

In 2009, I joined NISER as an Associate Professor and started understanding the effects of psychological stress on humans to develop programs on innate mucosal immunity

Pankaj Vidyadhar Alone

The fundamental difference between prokaryotic and eukaryotic translation initiation is that the former uses Shine-Dalgarno (SD) sequence on the mRNA to recruit small ribosome subunit and locate AUG codon or rarely GUC, CUC or UUG codon as a translation start site, while the latter uses eIF4F complex to bind mRNA and locate AUG codon or rarely CUG, UUG or GUC as a start codon by 5` to 3` scanning mechanism. Some of the examples listed below shows the involvement of non-AUG codon as a translation start signal.

In Saccharomyces cerevisiae, GRS1 encodes two isoforms of Glycyl-tRNA synthetases, one initiates from upstream in-frame UUG codon (encoding signal sequence for mitochondrial import) while the regular cytoplasmic version initiates from downstream AUG codon. For the synthesis of Alanine t-RNA synthetase (ALA1) protein a consecutive ACG ACG codon are utilized as an alternate translation start site. It has been reported recently that MHC class-I molecule can load antigenic precursor which is synthesized by using CUG as an initiation codon recognized by leucine tRNA and non-conventional eIF2A translation initiation factor. A genome wide ribosomal profiling analysis of vivo translation study reported that translation initiation from upstream non-AUG codon is widespread in S. cerevisiae under starvation condition. However, the importance and the basic mechanism for these initiations are still unclear. A number of yeast mutants have been identified that are able to initiate at the non-AUG codons. These mutants were designated as Sui— (Suppressor of initiation) phenotypes. Sui— phenotypes are novel mutations that causes break down of AUG codon selection fidelity. Thus, Sui— mutants provide an important tool to understand the molecular mechanism of non-AUG codon selection.

The focus of our lab is to understand the molecular mechanism of non-canonical translation initiation processes in Saccharomyces cerevisiae using molecular genetic techniques.

The key questions are as follows:

• How Sui— mutants recognize UUG codon as a start codon?
• Does 18S rRNA residues play critical role in UUG codon recognition by Sui— mutant?
• Does cis-acting elements on mRNA plays critical role in non-AUG codon recognition by Sui— mutants?
• Are there special trans-acting factors involved in non-AUG codon selection?

Praful Singru

Neural circuits and behavior, Neuroendocrine regulation

Ramanujam Srinivasan

 What I cannot create, I do not understand

                                                      - Richard Feynman

So is true for Life. For nearly a century, it was believed that Humans and its close relatives such as yeast and other eukaryotes were the sole owners of the Cytoskeleton, a mechanical framework that supports cells and carries almost all essential process within. However, recent discoveries have proved this to be a myth and shown us that the cytoskeleton was an innovation of our distant ancestors - 'Bacteria'. The bacterial cytoskeleton provides the most simplistic framework to understand the mechanical basis of all cellular process such as spatial organization and compartmentalization, cell shape establishment, cell movement, DNA segregation and cell division that are vital to the propogation of life. One of the most fascinating aspects of the cytoskeleton is their remarkable ability to self-organize and assemble into a great diversity of dynamic structures.

Broadly, our research interests lie in evolution of self-organisation, form and function in biological systems and in understanding the means by which bacterial pathogens have exploited this organization in pathogenesis for their survival and reproduction. In our research laboratory, we aim to understand how tiny cells such as bacteria achieve cellular organization and how the mechanical properties of their cytoskeleton allow them to perform the cellular functions.

We pursue these research interests through studying the following process in life:

• Cell division and Spatial organization in Bacteria - Bacterial cytoskeleton dynamics, Cytokinetic ring assembly, Regulation of cell division control and anti-bacterials targeting bacterial cytoskeleton.
• Bacterial Metabolism & Biofilms - Molecular pathways by which Bacterial proteases regulate lipid metabolism & biofilm formation.
• Bacterial Pathogenesis - Molecular Mechanisms of Bacterial effectors that target and affect Eukaryotic Cytoskeleton and Cell Cycle.
• Synthetic Biology - Synthetic Protein Polymers: Evolution of synthetic cytomotive proteins for use in biological & artificial cell systems.

Given the rapid increase in the rate of multi-drug resistance, there is a resurgence of the once conquered infectious diseases. There is an urgent need for a new class of antibiotics and bacterial cell division has proved to be an attractive target. Thus we are currently actively focused on regulation of cell division and spatial organization in bacteria. We also have an ongoing effort on creating "synthetic cytomotive proteins" for use in artificial cells.

Rittik Deb

Evolutionary Ecology Lab (EEL@NISER)

I am an evolutionary ecologist interested in understanding the forces and mechanisms that shape an organism's evolutionary trajectory. Rapidly changing anthropogenic stressors introduce novel selection pressures, leading to biodiversity loss and the emergence of new coping mechanisms in certain species. The biotic interactions among communities, populations, and individual organisms are central to this adaptation, which drives evolutionary processes. Modern sequencing techniques have shown that these interactions extend beyond the macroscopic world, significantly influencing microbial communities as well. At the intersection of these realms, macroscopic hosts and their associated microbes interact, shaping each other's evolutionary paths.

My research aims to trace these biotic interactions at various organizational levels, from host communities to individual hosts, host-microbiome interactions, and microbial communities, to understand their impact on organismal evolution. By employing classical eco-evolutionary approaches and utilizing both wild and laboratory-reared insect populations as model systems, my lab is interested in uncovering how organisms adapt to novel and rapidly changing selection pressures.

Project 1: Impact of anthropogenic noise on biodiversity and ecosystem health - estimating the threat and potential coping mechanisms

The health and sustainability of an ecosystem depend on its biotic organisation. A diverse ecosystem is a good indicator of its health, as biodiversity provides resilience and redundancies that are key to ecosystem functioning. Hence, threats to biodiversity, in the form of human activities, can lead to the functional collapse of an ecosystem. Unfortunately, most research on biodiversity is patchy, intrusive, biased towards charismatic taxa, and often overlooks elusive and nocturnal species. Since over 50% of organisms, including diurnals, rely on acoustics for communication, passive recording can provide an efficient, non-invasive, yet less biased estimate of biodiversity. However, acoustic communication suffers from an omnipresent, pervasive threat, anthropogenic noise. 

Most organisms use acoustics for conspecific recognition, competition, and mate choice. This communication has evolved under conspecific and heterospecific masking (signal overlap) giving rise to coping mechanisms like spatial, temporal, spectral (pitch) separation of signallers, and selective hearing in receivers. Anthropogenic noise, which has no particular signal structure, can act as a novel selection pressure by altering the complexity of masking, rendering the existing coping mechanisms ineffective. This can lead to a communication breakdown and large-scale loss of species diversity.

We aim to understand how acoustically communicating communities cope under such pervasive anthropogenic stress. Since insects are the most diverse yet understudied taxa, we aim to use their diversity as an indicator of ecosystem health. Among insects, Ensiferans (crickets and katydids) are one such taxa that are present across a variety of habitats and have mesmerising acoustic diversity and complexity. Unfortunately, these insects are poorly studied, with almost no data on their diversity and distribution along eastern India. We aim to study the impact of anthropogenic noise on their diversity, communication patterns, and potential coping mechanisms to ascertain the threat level in these habitats.

Rudresh Acharya

Structural biology of soluble and transmembrane proteins, and De novo design of proteins.

Proteins are workhorses of a cell, engaged in a wide range of tasks comprising structural stability, cell signaling, catalysis, transporting, molecular printing, membrane fusion, regulation, etc. Understanding the mechanism that underlies the functioning of these molecular gadgets is an intriguing question, and defines the fundamentals of biological processes. This is an interdisciplinary research program as we set out to address the question using X-ray crystallographic methods coupled with biophysical, biochemical and computational approaches.

Our structural biology group aim to deduce the structure based mechanism for the functioning of cation selective channels from viruses. The structures not only enhance our current knowledge, but also provide leading point for the structure based drug design. Also, we are interested in the structural biology of bacterial two component systems, a wide spread signal transducers.

Our other research program is de novo protein design, which aim to put our understanding of principles that define protein folding and functioning into test. Here, we seek to design scaffolds that are tailored to have predetermined non-covalent interactions as well as functions.

Subhasis Chattopadhyay

Research Theme: The fundamental consequences of cellular responses associated to altered physiological processes during infection, cancer and/or tumor progression, inflammation and immunogenic responses in various cases of altered host cell functions and phenotypes are the prime interest of our ongoing research.

We have been working in the field of host cell responses and cellular immunology with special interest of ongoing immune-regulatory responses, cellular function and phenotypes associated to Cell mediated immunity (CMI) of T cells and accessory antigen presenting cells. Currently, we have major interest groups within NISER and also with external collaboration, where we are investigating functional expression of Toll like receptor (TLR) and Transient Receptor Potential Vanilloid (TRPV) Channels in cell mediated immunity (CMI), analyzing cellular and immunological response(s) of host cells during experimental Chikungunya virus (CHIKV) infection along with anti-cancer immunity as major projects.

In brief, our research focuses to dissect out the important roles of cellular and immunological aspects to decipher the cellular pathways, strategies associated to altered host cell responses for an ongoing infection, tumor progression, inflammation-immunity and immuno-regulatory processes associated to diseases biology in different contexts of cellular responses. Research with cell lines, primary cells, animal model and also with the human blood samples from normal donors and patients with due consents and National guide lines are the prime components for such experimental studies. Such understanding will be helpful towards designing immuno-therapeutic strategies to control various diseases.

Swagata Ghatak

Our research focusses on-
1. Elucidating pathophysiological mechanisms of neurological disorders focusing on ion channels.
2. Creating novel brain models using human induced pluripotent stem cells (hiPSCs) from patients
to study neurological disorders.
3. Translating novel mechanisms to develop therapy against neurological diseases.

List of Publications
Google scholar link- https://scholar.google.com/citations?user=xsEnuCEAAAAJ&hl=en

Tirumala Kumar Chowdary

My research interest is to understand structure-function relationship of viral proteins in viral entry, genome replication and packaging into capsids.

Cell-entry of alphaviruses: Chikungunya virus, an aedes mosquito-transmitted alphavirus, enters cells through receptor-mediated endocytosis, and membrane fusion in acidic pH of endosome. Two viral surface proteins, E1 and E2 facilitate entry process. E1 'pulls' apposing endosomal and cell membranes close enough, after endosome acidification, so that they fuse and open a pore. My lab is interested in understanding the acidic-pH triggering mechanism for E1 and structural changes in the protein that lead to membrane fusion.

Nucleic acid packaging in dsDNA viruses: Viruses with double stranded DNA genome pack DNA into capsids at very high densities. Some bacteriophages Human herpesviruses (one of those with large genomes) pack their genome into pre-formed capsid through concerted action of a portal complex and terminase complex. Terminase complex of herpesviruses can be a good drug-target. My lab studies structure-function relationship of terminase protein complex components to explain the mechanism of action of the complex.

Replication complexes of flaviviruses: another interest in the lab is on replication complexes of flaviviruses. Dengue virus, a member of the virus family, forms a complex of more than five different proteins (nsp1,2a, 2b, 3, 4a, 4b and 5) formed from a single polyprotein through proteolytic processing. Special membrane-bound replication complexes are formed from ER membrane surface and viral RNA is amplified inside these vesicles. We aim to characterize these complexes and study interactions amongst the proteins in complex.

V Badireenath Konkimalla

Rational drug discovery and development require a streamlined, interdisciplinary effort from researchers working in specialized areas. From active collaboration, the drug discovery process can be and has been significantly shortened by addressing bottlenecks in drug discovery (off-target effects, polypharmacology, and chemoresistance). Our research focuses on some unanswered questions that could contribute to the development of chemotherapy.

Establishing the bioactivity of a lead molecule (of any origin) from an in vitro study is the start of a long journey in the drug discovery pipeline. The pharmacological effect of the lead molecule observed in vitro may not directly correlate with the in vivo results due to the molecule's physicochemical properties, bio-pharmacokinetics, or structural mimicry. Here, we try to design suitable study models (in silico, in vitro, and/or in vivo) that can progressively help develop a reliable formulation. 

The following are the areas and related publications we presently focus on:

Drug Delivery of Poorly-soluble Phytochemicals

• Haloi P, Choudhary R, Siva Lokesh B, Konkimalla VB. Dual Drug Nanoparticle Synergistically Induced Apoptosis, Suppressed Inflammation and Protected Autophagic Response in Rheumatoid Arthritis Fibroblast-like Synoviocytes. Immunology Letters. 2024; 267, 106854.

• Haloi P, Siva Lokesh B, Chawla S, Konkimalla VB. Formulation of a dual drug-loaded nanoparticulate co-delivery hydrogel system and its validation in rheumatoid arthritis animal model. Drug Delivery. 2023; 30(1): 2184307.
• Haloi P, Chawla S and Konkimalla VB. Thermosensitive smart hydrogel of PEITC ameliorates the therapeutic efficacy in Rheumatoid arthritis. European Journal of Pharmaceutical Sciences. 2023: 181: 106367. 
• Siva Lokesh B, Haloi P, Konkimalla VB. Fabrication and Optimization of BSA-PEG-loaded Phenethyl Isothiocyanate (PEITC) nanoparticles using Box-Behnken Design for potential application in subcutaneous infection conditions. Journal of Drug Delivery Science and Technology. 2022; 104101.
• Mohanty S, Sahoo AK, Konkimalla VB, Pal A, and Si SC. Naringin in Combination with Isothiocyanates as Liposomal Formulations Potentiates the Anti-inflammatory Activity in Different Acute and Chronic Animal Models of Rheumatoid Arthritis. ACS Omega. 2020; 5(43): 28319–28332.

Interdisciplinary approaches in the development of cancer therapeutics

• Naik H, Choudhary R, Konkimalla VB. In Silico Analysis of Novel circRNA-miRNA-mRNA Axis in BRAFV600E Melanoma: Implications for Primary to Metastasis Transformation and TIME Modulation. The Journal of Gene Medicine. 2025; 27, e70023. DOI: doi.org/10.1002/jgm.70023.
• Siva Lokesh B, Ajmeera S, Choudhary R, Moharana SK, Purohit CS, Konkimalla VB. Engineering of Redox-triggered Polymeric Lipid Hybrid Nanocarriers for Selective Drug Delivery to Cancer Cells. Journal of Materials Chemistry B. 2025; 13, 1437-1458. doi.org/10.1039/D4TB01236D.

• Shinde Y, Patil R, Konkimalla VB, Merugu SB, Mokashi V, Harihar S, Marrot J, Butcher RJ, Salunke-Gawali S. Keto-enol tautomerism of hydroxynaphthoquinoneoxime ligands-Copper complexes and topoisomerase inhibition activity. Journal of Molecular Structure. 2022; 1262: 133081
• Dash TK, Konkimalla VB. Selection of P-Glycoprotein Inhibitor and Formulation of Combinational Nanoformulation Containing Selected Agent Curcumin and DOX for Reversal of Resistance in K562 Cells. Pharm Res. 2017;34(8):1741-1750.
• Dash TK, Konkimalla VB. Selection and optimization of nano-formulation of P-glycoprotein inhibitor for reversal of doxorubicin resistance in COLO205 cells. J Pharm Pharmacol. 2017;69(7):834-843.
• Dash TK, Konkimalla VB. Comparative Study of Different Nano-Formulations of Curcumin for Reversal of Doxorubicin Resistance in K562R Cells. Pharmaceutical Research. 2017;34(2):279-289.
• Dash TK, Konkimalla VB. Formulation and Optimization of Doxorubicin and Biochanin A Combinational Liposomes for Reversal of Chemoresistance. AAPS PharmSciTech. 2017;18(4):1116-1124.
• Patil R, Bhand S, Konkimalla VB, Banerjee P, Ugale B, Chadar D, Saha SK, Praharaj PP, Nagaraja, CM, Chakrovarty D. Molecular association of 2-(n-alkylamino)-1, 4-naphthoquinone derivatives: Electrochemical, DFT studies and antiproliferative activity against leukemia cell lines. Journal of Molecular Structure. 2016; 1125,272-281. 
• Pal S, Konkimalla VB*, Kathwate L, Rao SS, Gejji SP, Puranik V, Weyhermueller T, and Salunke-Gawali S. Targeting chemorefractory COLO205 (BRAF-V600E) cell lines using substituted benzo[a]phenoxazines.  RSC Adv. 2015; 5: 82549-82563.

Understanding cellular response to different ligands deriving its implications

• Pal S, Salunke-Gawali S, Konkimalla VB. Induction of Autophagic Cell Death In Apoptosis-Resistant Pancreatic Cancer Cells Using Benzo [α] Phenoxazines Derivatives, 10-Methyl-Benzo [α] Phenoxazine-5-One And Benzo [α] Phenoxazine-5-One. Anti-cancer agents in medicinal chemistry. 2016,
• Pal S and Konkimalla VB. Sulforaphane regulates phenotypic and functional switching of both induced and spontaneously differentiating human monocytes. International Immunopharmacology. 2016; 35:85-98.
• Pal S and Konkimalla VB. Data on sulforaphane treatment mediated suppression of autoreactive, inflammatory M1 macrophages. Data Brief. 2016 Apr 25;7:1560-4. â€“ Supplementary data of publication from International Immunopharmacology
• Pal S and Konkimalla VB. Hormetic potential of Sulforaphane (SFN) in switching cells' fate towards survival or death. Mini Rev Med Chem. 2016;16(12):980-95.

Other Publications

• Roy S, Haloi P, Siva Lokesh B, Chawla S, Konkimalla VB, Jaiswal A. Biocompatible quaternary pullulan functionalized 2D MoS2 glycosheet-based non-leaching and infection-resistant coatings for indwelling medical implants. Journal of Materials Chemistry B. 2023; 202311, 10418 - 10432.
• Singh P, Haloi P, Singh K, Roy S, Sarkar A, Siva Lokesh B, Choudhary R, Mohite C, Chawla S, Konkimalla VB, Sanpui P, Jaiswal A. Palladium Nanocapsules for Photothermal Therapy in the NIR-II Biological Window. ACS Applied Materials & Interfaces. 2023. 15(33), 39081-39098. 
• Roy S, Haloi P, Choudhary R, Chawla S, Kumari M, Konkimalla VB, Jaiswal A. Quaternary Pullulan functionalized 2D MoS₂ glycosheets:  A potent bactericidal nanoplatform for efficient wound disinfection and healing. ACS Applied Materials & Interfaces. 2023; 15(20), 24209–24227.
• Roy S, Kumari M, Haloi P, Chawla S, Konkimalla VB, Kumar A, Kashyap HK and Jaiswal A. Quaternary Ammonium Substituted Pullulan Accelerates Wound Healing and Disinfects Staphylococcus aureus Infected Wounds in Mouse Through an Atypical ‘Non-Pore Forming’ Pathway of Bacterial Membrane Disruption. Biomaterials Science. 2022; 10: 581-601.
• Malwal SR, Dharmarajan S, Perumal Y, Konkimalla VB and Chakrapani H. Design, Synthesis and Evaluation of Thiol-Activated Sources of Sulfur Dioxide (SO₂) as Antimycobacterial Agents. Journal of Medicinal Chemistry. 2012; 55(1):553-7.
• Polier G, Ding J, Konkimalla VB, Eick D, Ribeiro N, Köhler R, Giaisi M, Efferth T, Desaubry L, Krammer PH, Li-Weber M. Wogonin and related natural flavones are inhibitors of CDK9 that induce apoptosis in cancer cells by transcriptional suppression of Mcl-1. Cell Death and Disease. 2011; 2(7):e182.
• Youns M, Fu YJ, Zu YG, Kramer A, Konkimalla VB, Radlwimmer B, Sültmann H, Efferth T. Sensitivity and resistance towards isoliquiritigenin, doxorubicin, and methotrexate in T cell acute lymphoblastic leukemia cell lines by pharmacogenomics. Naunyn Schmiedebergs Archives in Pharmacology. 2010; 382(3):221-34.
• Konkimalla VB, Blunder M, Korn B, Soomro SA, Jansen H, Chang W, Posner GH, Bauer R and Efferth T. Effect of artemisinins and other endoperoxides on nitric oxide-related signaling pathway in RAW 264.7 mouse macrophage cells. Nitric Oxide. 2008; 19:184-191.
• Efferth T, Konkimalla VB, Wang YF, Sauerbrey A, Meinhardt S, Zintl F, Mattern J and Volm M. Prediction of Broad Spectrum Resistance of Tumors towards Anticancer Drugs`. Clinical Cancer Research. 2008; 14(8):2405-2412.
• Kelter G, Steinbach D, Konkimalla VB, Tahara T, Taketani S, Fiebig HH and Efferth T. Role of transferrin receptor and the ABC transporters ABCB6 and ABCB7 for resistance and differentiation of tumor cells towards artesunate. PLoS ONE. 2007; 2(8): e798.
• Konkimalla VB and Chandra N. Determinants of histamine recognition: implications for the design of antihistamines. Biochemical and Biophysical Research Communications. 2003; 309(2):425-31.

Review articles

• Gaikwad M, Konkimalla VB and Salunke-Gawali S. Metal complexes as topoisomerase inhibitors. Inorganica Chimica Acta. 2022; 542: 121089.
• Pal S and Konkimalla VB. Hormetic potential of Sulforaphane (SFN) in switching cells' fate towards survival or death. Mini Rev Med Chem. 2016; 16(12): 980-995.
• Satpathy R, Konkimalla VB, Ratha J. Application of bioinformatics tools and databases in microbial dehalogenation research: A review. Applied Biochemistry and Microbiology. 2015; 51(1):11-20.
• Dash TK and Konkimalla VB. Nanoformulations for Delivery of Biomolecules; Focus on Liposomal Variants for siRNA Delivery. Critical reviews in therapeutic drug delivery system. 2013; 30(6):469-493.
• Dash TK and Konkimalla VB. Polymeric modifications and its implication in drug delivery: Poly-ε-caprolactone (PCL) as a model polymer. Molecular Pharmaceutics. 2012; 9(9):2365-79.
• Dash TK and Konkimalla VB. Poly-ε-caprolactone based formulations for drug delivery and tissue engineering: a review. Journal of Controlled Release. 2011; 21; 158(1): 15-33.
• Konkimalla VB and Efferth T. Evidence-Based Chinese Medicine for Cancer Therapy. Journal of Ethnopharmacology. 2008; 116(2):207-210.
• Efferth T, Li PC, Konkimalla VB and Kaina B. From traditional Chinese medicine to rational cancer therapy. Trends in Molecular Medicine. 2007; 13(8):353-361.
• Efferth T, Fu YJ, Zu YG, Schwarz G, Konkimalla VB, and Wink M. Molecular target-guided tumor therapy with natural products derived from traditional Chinese medicine. Current Medicinal Chemistry. 2007; 14(19):2024-2032.
• Konkimalla VB, Suhas VL, Chandra NR, Gebhart E and Efferth T. Diagnosis and therapy of oral squamous cell carcinoma. Expert Reviews in Anticancer Therapy. 2007; 7(3):317-329.

Book Chapters

• Pal S, Konkimalla VB. Natural Isothiocyanates: A Powerhouse for Antioxidant Regulation in Disease Remediation. In: B. Mukherjee (Ed.). Dietary Supplements and Nutraceuticals. Springer Nature. 2025, ISBN: 978-981-97-9936-7.

• Siva Lokesh B and Konkimalla VB. Novel Strategies for Targeted Nanotherapeutics for cancer control. In: Novel molecular oncotargets and Nano-oncotherapeutics. Cambridge Scholar Publishing. 2022. 2023, pp 395-494. ISBN: 978-1-5275-0713-5.
• Ajmeera S and Konkimalla VB. Nanoformulations to Limit Challenges of Conventional Therapy against Hepatocellular Carcinoma – An Overview. In: Nanotherapeutics for the Treatment of Hepatocellular Carcinoma. Bentham Science Publishers. 2022, pp 166-218.
• Dash TK and Konkimalla VB. Modification of Cyclodextrin for Improvement of Complexation and Formulation Properties. In: Wiley-Scriverner. In: Handbook of Polymers for Pharmaceutical Technologies: Biodegradable Polymers. Vol 3. 2015, pp 205-224. ISBN: 978-1-119-04142-9.
• Konkimalla VB. Predicting Cross-Reactivity from Computational Studies for Pre-evaluation of Specific Hepatic Glycogen Phosphorylase Inhibitors. In: Springer. Bioinformatics and Biomedical Engineering. In: Lecture Notes in Computer Science. 2015, 9044, pp 674-682.
• Konkimalla VB, Kramer A, Fu Y and Efferth T. Identification of Molecular Determinants for Cytotoxicity of Isoloquiritigenin from Liquorice (Glycyrrhiza glabra) towards Leukemia Cell Lines. In: Wiley-VCH. Deutsche Forschungsgemeinschaft (DFG) (Ed.), G. Eisenbrand (Ed.). In: Risk Assessment of Phytochemicals in Food: Novel Approaches. 2010, pp 429. ISBN: 978-3-527-32929-8.
• Konkimalla VB and Efferth T. Molecular mechanisms and interactions responsible for radio- and chemoresistance of tumors and their modulation by natural products from Ayurveda. In: R. Arora (Ed.) Herbal Medicine. A cancer chemopreventive and therapeutic perspective. 2010, 7(33). 511-530.