1. Postdoc in The Blank Lab, ISBt – Industrial Systems Biotechnology, iAMB RWTH Aachen University [04/2024 – Present

(PI: Univ. Prof. Dr.-Ing. Lars M. Blank, PhD)

European Innovation Council (EIC) funded HYDROCOW project at RWTH Aachen in Collaboration with Solar Food, FGen/Gingko Bioworks, and the University of Groningen (https://www.hydrocow.eu/)

Objective: To develop and demonstrate a first-of-a-kind engineered hydrogen oxidizing bacterium (eHOB), Xanthobacter sp. SoF1-based protein secretion system decoupled from agriculture, where CO2 and soon N2 are valorized into food-grade protein.

Description:

Implementing a Design-Build-Test-Learn (DBTL) cycle linked to a validation and scale-up phase allows for iterative optimization of the production of secreted protein ( https://www.iamb.rwth-aachen.de/cms/iamb/Forschung/Blank-Lab/~bgdvyy/Hydrocow/lidx/1/ )

My role: Development of comparative and pan-genomic tool-guided reconstruction of the genome-scale metabolic model of X. sp SoF1

2. PhD at School of Energy Science and Engineering, IIT Guwahati, Assam, India [07/2018 – 01/2024]

(PI: Vijayanand S. Moholkar, PhD & Lepakshi Barbora, PhD)

[Thesis submission: 03.08.2024; Viva-voce: 19.01.2024; Degree award: 22.03.2024]

Dissertation: Investigations in enhanced production of bioalcohols and their derivatives using experimental and in-silico approach

Fully funded by the prestigious Prime Minister’s Research Fellowship (PMRF; Certificate), Ministry of Education, Government of India, in the second quarter of the year 2018 (for details: https://www.pmrf.in/ )

Description:

• The thesis focuses on the challenges and advancements in bioalcohol (mainly biobutanol) synthesis through clostridia, emphasizing enhancing production efficiency from sustainable resources.

• Employing a multidisciplinary approach, the research encompasses comparative and pan-genomic analysis, in-depth exploration of cell central metabolism during Acetone-Butanol-Ethanol (ABE) fermentation in Clostridium sp., experimental examination of butanol production from lignocellulosic hydrolysates using clostridial co-culture systems, development of genome-scale metabolic models (GSMs), and innovative investigations into the production and enhancement of value-added products (n-butyl levulinate) using sono-enzymatic processes.

• This dissertation has contributed to 3 among the 17 Sustainable Development Goals (SDGs) established by the United Nations in 2015, with the aim of achieving a more sustainable and inclusive future for all: (1) Goal 7 (affordable and clean energy), (2) Goal 11 (sustainable cities and communities), and (3) Goal 13 (climate action).

• Resulted in 6 first author publications (Biotechnology & Bioengineering, Process Safety and Environmental Protection, Process Biochemistry, Biomass Conversion and Biorefinery), three more in preparation

• Received Best PhD Thesis Award, international travel grants, best oral/paper awards, young scientist, and best keynote speaker awards.

3. Graduate Research Intern at HackBio, International Research Internship Program, Online [07/2020 – 09/2020]

(PI: Sarah Carl, PhD)

Dissertation: Transcriptomic dysregulations associated with SARS-CoV-2 infection in human nasopharyngeal and peripheral blood mononuclear cell samples (https://genomics-two.carrd.co/# )

International Collaboration for Transcriptomic Analysis under the HackBio Internship Program during Corona Virus Pandemic. The project resulted in a preprint publication, and our team received the Best Project award.

Description:

Over 24 million people have been infected globally with the novel coronavirus, SARS-CoV-2, with more than 820,000 succumbing to the resulting COVID-19 disease as of the end of August 2020. The complete molecular mechanisms underlying the pathogenesis of the disease are still unclear. We aim to understand host response to SARS-CoV-2 infection from two distinct sample types obtained from COVID-19 subjects and healthy controls.

We used two publicly available gene expression datasets generated by RNA sequencing of two distinct samples; peripheral blood mononuclear cells (PBMCs) and nasopharyngeal swabs. We performed a differential gene expression analysis between COVID-19 subjects and healthy controls in the two datasets and then functionally profiled the differentially expressed genes (DEGs). The DEGs common between both sample groups were assessed for their discriminatory utility. The genes involved in innate immunity were also determined. We found a clear difference in host response to SARS-CoV-2 infection between the two sample groups. In COVID-19 subjects in the PBMC group, host response involved an upregulation of genes involved in immunoglobulin-mediated immune response and the complement system. In contrast, host response in COVID-19 subjects in the nasopharyngeal group involved upregulation of genes involved in cytokine activity and interferon signaling pathway, as well as downregulation of genes involved in oxidative phosphorylation and viral transcription. Thirteen DEGs common between both sample groups accurately discriminated the samples. Host response to SARS-CoV-2 varies in different human cells, suggesting the presence of biomarkers having diagnostic and prognostic utility in COVID-19 patients.

4. B.Tech. Thesis Main Project II, School of Biotechnology, NIT Calicut, Kerala, India [01/2018 – 04/2018]

(PI: Rathinasamy K., PhD)

Dissertation: Carbon nanoparticles enhance the antibacterial activity of tetracycline in Escherichia coli and Bacillus subtilis

This resulted in a conference presentation

Description:

Among the significant obstacles of the present time is to attain an invigorating life for all human beings. Infectious diseases are among the major challenges that today’s economy, as well as public health, faces. Nanotechnology has the potential to provide solutions for these major hurdles present in the current health and medicine sector. The ability to investigate substances at the molecular level has boosted the search for materials with outstanding properties for use in medicine. Because of the limited span of antibiotics' utility, some nanomaterials have been proposed to prevent the outbreak of these infectious diseases. Functionalized carbon-based nanostructured materials (CBNMs) have become predominant among other types of nanomaterials and have gained significant attention since their discoveries due to their unique physicochemical properties (i.e., thermal and electrical conductivity, high mechanical strength, and optical properties). In this project, we have studied the antibacterial activity of functionalized carbon nanoparticles (CNPs) with the antibiotic tetracycline on E. coli and Bacillus subtilis. We observed that CNPs alone do not have any significant antibacterial activity, whereas conjugating with commonly used antibiotics showed enhanced potency against Escherichia coli DE3 and Bacillus subtilis strains.

5. B.Tech. Thesis Main Project I, School of Biotechnology, NIT Calicut, Kerala, India [08/2017 – 10/2017]

(PI: Rathinasamy K., PhD)

Dissertation: Synthesis, characterization & conjugation of carbon quantum dots with anticancer drugs for better efficacy and internalization

Description:

Researchers and scientists around the world are more concerned with finding innovative strategies to defeat Cancer. An innovative strategy in this field utilizes drug delivery carriers, which can enhance the therapeutic effect of anticancer drugs. Carbon quantum dots (CQDs) are attractive, a new type of carbon-based nanostructures that have drawn a great deal of attention, owing to their unique properties like chemical stability, excellent water solubility, tuneable fluorescence properties, low cost, low toxicity, good biocompatibility, and environmental friendliness. These CQDs are also a useful tool for molecular imaging. In the present study, we report a simple one-step synthesis and conjugation of CQDs with anti-tumor drugs. The synthesis procedure used herein is a Hydrothermal green synthesis route for highly fluorescent CQDs with good fluorescent quantum yield. These CQDs were then used to deliver an antitumor drug, Berberine (BER) (which has been shown to have poor bioavailability in cells), to increase the bioavailability in cancerous cells. Furthermore, these CQDs were demonstrated as good fluorescent bio-imaging probes that self-localized themselves inside the nucleus. We formed the complex of CQDs and BER with the help of Linker EDC. This CQDs-BER complex formation was confirmed using UV-vis, Fluorescence, size determination using dynamic light scattering, and FTIR spectrometric analysis. In sum, biocompatible, scalable, photostable, green synthesis-based CQDs have been synthesized for Bioimaging and delivery of anti-tumor drugs to increase the therapeutic effect in cancerous cells.

6. AcSIR-Dr. APJ Abdul Kalam Summer Training Fellow 2017 [06/2017 – 07/2017]

(PI: Kausar M. Ansari, PhD)

Environmental Carcinogenesis (Food, Drug & Chemical Toxicology laboratory) at CSIR – Indian Institute of Toxicology Research, India

Dissertation: To identify the molecular target of patulin using drug affinity responsive target stability (DARTS)

Fully funded by the AcSIR – Dr. APJ Abdul Kalam Summer Training Fellowship 2017, a novel initiative by the Academy of Scientific and Innovative Research, Government of India

Description:

Among over 400 naturally occurring toxin compounds by molds, mycotoxins cover an essential class of which only a small minority have been shown to be toxic to mammals. Patulin is a major toxic chemical food contaminant and falls under the small category of mycotoxins produced by fungi Aspergillus and Penicillium species. It is found in apples and apple products that are contaminated with Penicillium expansum, the common storage-rot fungus of apples. In vivo animal studies have demonstrated its clastogenic, carcinogenic, mutagenic, teratogenic, and in higher concentrations, cytotoxic properties. Even vast studies have been performed on the molecular mechanism of toxicity induced by patulin, though its molecular target proteins are still unknown. When the direct target protein to which patulin binds is identified, both the target and patulin could be applied to anti-cancer therapeutics development, which will be very helpful in the advancement of basic science and drug development. Therefore, in this project, we aimed to identify the molecular target of patulin in IEC-6 cell lines using Drug Affinity Responsive Target Stability (DARTS).

7. B.Tech. Thesis Mini Project, School of Biotechnology, NIT Calicut, Kerala, India [01/2017 – 04/2017]

(PI: Rathinasamy K., PhD)

Dissertation: Synthesis and characterization of highly fluorescent carbon nanoparticles for fluorescence imaging

Description: 

Despite many other available techniques for synthesizing carbon nanoparticles (CNPs), this paper presents an easy and versatile technique that does not use sophisticated instruments and costly raw materials or reagents. In this paper, we propose an eco-friendly method which is sometimes also referred to as green synthesis. Hydrothermal treatment of fresh fruit juices produces water-soluble, highly fluorescent, and intense photo-luminescent CNPs. This method is advantageous over other methods available because it is easy to scale up and manage. From 50ml of fresh orange juice, we synthesized water-soluble CNPs with a

fluorescent quantum yield of 8.6%. The isolated CNPs show significant photoluminescence characteristics under UV radiation. It also showed visible fluorescence under a fluorescence microscope with different filters, DAPI, FITC, and TRITC, once again, signifying its possible utility in bio-imaging. The DLS result showed that the average size of the particle synthesized is around 380nm, and its absorbance and fluorescent properties were also observed and compared to quinine sulfate, which was used as a standard. These nanoparticles have excellent fluorescent properties, and further studies can be carried out to observe if they can be internalized in target cells.

8. Summer Research Intern at School of Biotechnology, NIT Calicut, Kerala, India [05/2016 – 07/2016]

(PI: Rathinasamy K., PhD)

Project title: Binding interaction of a synthetic compound with bovine serum albumin (BSA) using Fluorometric analysis

Description:

The project focuses on investigating the binding interaction between a synthetic compound and bovine serum albumin (BSA) through fluorometric analysis, providing valuable insights into protein-drug interactions. BSA, a well-characterized model protein, is widely used in in vitro studies to mimic human serum albumin due to its structural and functional similarities. The study employs fluorescence spectroscopy to monitor the changes in BSA's intrinsic fluorescence upon binding with the synthetic compound. This technique allows for the determination of critical parameters such as binding constants, quenching mechanisms, and thermodynamic properties, which are critical in understanding the interaction dynamics. The findings from this research can contribute to drug development by shedding light on the compound's binding affinity, stability, and potential therapeutic efficacy, laying a foundation for future pharmacokinetic and pharmacodynamic studies.

1. Supervised 3 Undergraduate students for their Final Year Project, 2 Graduate (Masters) students, and 2 Graduate (Masters) research intern in genomics, transcriptomics, and genome-scale modeling at RWTH Aachen University (2024 – Present).

2. Organized & Mentored – Winter Internship in Bioinformatics & Computational Biology (2022–23, Hybrid) – Trained 15 graduate/postgraduate students in GSM reconstruction, anaerobic fermentation, docking, MD simulations; outcome: 2 journal papers & 5 book chapters.

3. PMRF Teaching Assistant – NPTEL Course: Biochemistry (NOC23-CY30), IIT Kharagpur (Jan–Apr 2023, Prof. Swagata Dasgupta). Conducted weekly 2-hr sessions, problem-solving, and career mentoring.

4. Organized & Mentored – Virtual Internship in Mathematical Biology (2022, Online) – Trained 9 graduate/postgraduate students in GSMs, docking, life-cycle assessment; outcome: 1 journal paper.

5. PMRF Teaching Assistant – NPTEL Course: Fundamentals of Protein Chemistry (NOC22-BT62), IIT Kharagpur (Jul–Oct 2022, Prof. Swagata Dasgupta). Conducted weekly 1-hr live mentoring and Q&A sessions.

6. Guest Faculty – Analytical Chemistry I, North Gauhati College, Assam (Feb–Jun 2021). Delivered lectures and practicals for UG students; designed assignments and provided career guidance.

7. Organized & Mentored – Winter Internship in Bioinformatics & Computational Biology (2021, Online) – Trained 6 graduate/postgraduate students in comparative modeling, docking, and MD; outcome: 1 preprint & Best Oral Presentation award.

8. Doctoral Mentorship – IIT Guwahati (2018–23) – Mentored 4 UG/PG trainees in enzyme kinetics, fermentation, pangenomics, and metabolic modeling.

1. Reviewer, Environmental Science and Pollution Research (ESPR) – 2 manuscripts (2024).

2. Reviewer, Springer Nature – 1 manuscript (2024)

3. Reviewer, Metabolic engineering communications – 1 manuscript (2025)

4. Reviewer, Renewable energy – 2 manuscripts (2025) 

5. Associate Editor, Trends in Renewable Energy (U.S. Library of Congress indexing) — Apr 2024–Present.

6. Associate Editor, Frontiers in Environmental Microbiology (Science Publishing Group) — Apr 2024–Apr 2027.

7. Associate Editor, PriMera Scientific Engineering (Primera Scientific) — Jun 2023–Present.

8. Life Member, International Society for Energy, Environment and Sustainability (ISEES).

9. Life Member, Biotech Research Society of India (BRSI).

10. Member, Society for Biological Engineering (SBE).

11. Member, International Metabolic Engineering Society (IMES).

12. Member, American Institute of Chemical Engineers (AIChE).

13. Member, International Society for Computational Biology (ISCB).