Dr. rer. nat. Rudrarup Bose

Interdisciplinary scientist seeking new challenges

Dresden

Research Expertise

Synthetic Biology
Biophysics
Laboratory Automation
High Throughput Experimentation
High content data analysis

About

Dr. rer. nat. Rudrarup Bose is a highly qualified and an experienced scientist with a strong background in Synthetic Biology, Biochemistry, Biophysics, and High-Throughput Experimentation. He received his Ph.D. in Biology from TU Dresden (Germany) in 2024, where he specialized in designing and engineering novel biochemical systems for various applications. Prior to this, he completed his M.Sc. in Life Sciences from Homi Bhabha National Institute (India) in 2019. Dr. Bose has a diverse range of research experience, having worked in prestigious institutions such as the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany and the Cellular, Computational and Integrative Biology department at the University of Trento, Italy. He has also completed internships and short-term projects at ELVESYS in Paris, France, National Institute of Science Education and Research in Bhubaneswar, India, and Indian Insitute of Science Education and Research in Pune, India. During his doctoral research, Dr. Bose focused on developing novel methods for screening liquid-liquid phase separation in primitive metabolites and exploring their potential applications in the origin of life and synthetic biology. His work has been published in several peer-reviewed journals and has been presented at international conferences. Apart from his academic pursuits, Dr. Bose has also gained practical experience in the field of clinical microbiology as a Clinical Technician Assistant at Sankara Nethralaya Eye Hospital in Kolkata, India.Further, He has also worked as a Computational Chemist at the Earth-Life Science Institute, Tokyo Institute of Technology, where he developed computational models to study the origins of life on Earth. With his strong academic background and extensive research experience, Dr. Bose is a valuable asset to the scientific community. He is passionate about using his skills and knowledge to drive innovations in the field of life sciences and contribute to the advancement of scientific knowledge.

Publications

Can coacervation unify disparate hypotheses in the origin of cellular life?

Current Opinion in Colloid & Interface Science / Apr 01, 2021

Ghosh, B., Bose, R., & Tang, T.-Y. D. (2021). Can coacervation unify disparate hypotheses in the origin of cellular life? Current Opinion in Colloid & Interface Science, 52, 101415. https://doi.org/10.1016/j.cocis.2020.101415

Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets

Scientific Reports / Aug 28, 2019

Ilardo, M., Bose, R., Meringer, M., Rasulev, B., Grefenstette, N., Stephenson, J., Freeland, S., Gillams, R. J., Butch, C. J., & Cleaves, H. J. (2019). Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-47574-x

Statistical mechanics of biomolecular condensates via cavity methods

iScience / Apr 01, 2023

Lauber, N., Tichacek, O., Bose, R., Flamm, C., Leuzzi, L., Tang, T.-Y. D., Ruiz-Mirazo, K., & De Martino, D. (2023). Statistical mechanics of biomolecular condensates via cavity methods. IScience, 26(4), 106300. https://doi.org/10.1016/j.isci.2023.106300

Adaptive Properties of the Amino Acid Alphabet and its Subsets

The 2018 Conference on Artificial Life / Jan 01, 2018

Bose, R., Meringer, M., Ilardo, M., & Cleaves, H. J. (2018). Adaptive Properties of the Amino Acid Alphabet and its Subsets. The 2018 Conference on Artificial Life, 459–460. https://doi.org/10.1162/isal_a_00085

An In silico method to study structure, function, and regulatory role alteration mediated by single-nucleotide polymorphisms in gallbladder cancer

Journal of Natural Science, Biology and Medicine / Jan 01, 2018

Pradhan, A., Bose, R., Ghosh, S., & Datta, A. (2018). An In silico method to study structure, function, and regulatory role alteration mediated by single-nucleotide polymorphisms in gallbladder cancer. Journal of Natural Science, Biology and Medicine, 9(2), 137. https://doi.org/10.4103/jnsbm.jnsbm_233_17

Education

TU Dresden

Ph.D., Synthetic Biology / May, 2024

Dresden

Homi Bhabha National Institute

M.Sc., Life Sciences / May, 2019

Experience

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

Postdoctoral Research Associate / October, 2023October, 2024

During this study, I examined the effect of droplet formation via liquid-liquid phase separation of oppositely charged poly-electrolytes, a phenomenon known as complex conservation, on the non-enzymatic reduction of NAD+ to NADH, a reaction that may mimic early metabolic processes. The coacervate formation was induced using a 50-mer poly-arginine, and two reaction environments were explored: one beginning as a homogeneous solution and the other involving precipitates that later formed droplets. These environments were controlled by varying sodium bicarbonate concentrations. Using a range of analytical techniques, including HPLC, NMR, mass spectrometry, and biochemical assays, I demonstrated that coacervate droplets influence the reaction equilibrium, potentially shifting it towards enhanced NADH formation.

Doctoral Candidate / September, 2019August, 2023

In my doctoral thesis, I investigated the influence of complex coacervation, a form of electrostatically driven liquid-liquid phase separation, on primitive metabolic reactions. The phenomenon of complex coacervation occurs when oppositely charged polymers condense to form polymer-dense droplets, leaving the rest of the solution polymer-poor. I explored these compartments and integrated them with primitive metabolic reactions, i.e., reactions that are hypothesised as precursors to modern metabolic reactions, shedding light on their potential role in the origin of life. My research involved a wide array of techniques, including UV-vis, fluorescence, NMR, and Raman spectroscopy, as well as bright-field and fluorescence microscopy, FRAP, and Raman imaging. Additionally, I employed automation pipelines for chemical screening and conducted experiments in anaerobic conditions, as well as computational skills in MATLAB, KNIME, and image analysis to support my work.

ELVESYS, Paris, France

Intern / January, 2021February, 2021

During this internship, I worked in a non-academic environment, and was introduced to various concepts that are important for a start-up of their kind, such as key performance indicators and search engine optimisation. I also obtained a brief understanding of the responsibilities of the different departments in the company, such as Marketing, Sales and R&D. Furthermore, I was introduced to the fundamentals of microfluidics, including designing and preparation of PDMS chips. During this time I gained experience in microfluidics applications on cell culture.

Cellular, Computational and Integrative Biology, University of Trento, Italy

Visiting Researcher / November, 2020January, 2021

I learnt to perform the different protometabolic reactions that have been established previously by Prof. Mansy’s group, and to characterise the products using spectroscopic techniques such as NMR, Fluorescence and UV-Vis. During this research visit, I learnt to work under anoxic conditions and also to synthesis peptides. Furthermore, during this time, I also imparted my knowledge and experimental expertise, on liquid-liquid phase separation, to members of Prof. Mansy’s group.

National Institute of Science Education and Research, Bhubaneswar, India

Dissertation Student / August, 2017May, 2019

Developed and conducted in-vitro studies to investigate bacterial cytomotive proteins, focusing on Ba-TubZ (Bacillus anthracis tubulin-related protein) and EcFtsZ (E. coli FtsZ). These force-generating polymers were analyzed to explore the mechanical properties influencing their biological functions. Leveraged cell-free gene expression systems to mimic biological conditions while enabling controlled experimentation on structural properties and physiological conditions. Designed experiments to estimate bending rigidity and persistence length of an EcFtsZ mutant (EcFtsZQ47KD86K), comparing them to the wild-type protein. Hypothesized how mechanical parameters impact the formation of Z-rings and provided critical insights into structural drivers of protein behavior. This work combined expertise in biophysics, polymer mechanics, and synthetic biology to address fundamental questions in bacterial cytoskeletal dynamics.

Short Project Student / January, 2017April, 2017

In this study using in silico methods, we investigated for the first time a combination of single nucear polymorphisms (SNPs) from the coding and noncoding region leading to alteration in GBC. Different pipelines were designed for the study of SNPs. Regulatory role alteration of Synonymous and non-coding SNPs were studied using RegulomeDB, DeepSEA analysis and funcPred. Structural alteration and energy parameters for non-synonymous SNPs were studied by Swiss-PDB, Chimera and Gromacs. Protein stability analysis was done using MutPred, mCSM and I-mutant.

Indian Insitute of Science Education and Research, Pune, India

Summer Student / May, 2016July, 2016

Studies in chemical origins of life involves exploring acceptable conditions that allowed the transition from chemistry to biology on prebiotic Earth. “The RNA World” hypothesis has established the importance of formation of RNA polymers. Due to the absence of enzymes on early Earth, prebiotic polymerisation processes had to largely resort to catalysis by metal ions and mineral surfaces. In this project, we attempted to compare the catalytic properties of Montmorillonite K-10, F-bed clay and C-bed clay. Furthermore, we tried to observe the effect of lipid in clay catalysed oligomerisation reactions of Guanosine 5’-phosphorimidazolide (ImpG). The results demonstrated differences in presence and absence of lipid. HPLC results showed presence of higher oligomers in reactions containing Montmorillonite K-10.

Clinical Microbiology laboratory, Sankara Nethralaya Eye Hospital, Kolkata, India

Clinical Technician Assistant / May, 2015July, 2015

Performed ocular sample testing for microbial infections, supporting accurate diagnosis and treatment

Earth-Life Science Institute, Tokyo Institute of Technology, Japan

Computational Chemist Intern / May, 2017July, 2017

Worked in a global team of interdisciplinary scientists to conduct a chemoinformatic study of amino acid properties, resulting in 2 scientific publications and 1 international conference presentation

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