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Transferred to a remote connection – Identifying the regulatory mechanisms involved in bacterial gene expression

Tampere University
29.4.2020 12.30–16.00
Entrance feeFree of charge
Vinodh Kandavalli
This thesis is the result of a quantitative analysis of the kinetics of transcription initiation of live E. coli cells using a single cell approach centered on a technique of single RNA tagging. From results, the rates of closed and open complex formation are dissected, which provide a direct insight into the dynamics of the mechanism and the downstream effects of promoter initiation kinetics.

Gene expression is a fundamental process in living organisms, by which the information on the genetic material (DNA) is, first, transcribed into RNA and, then, translated from RNA into functional proteins. Proteins carry out the cellular functions required for survival. Cells adjust to challenging environments by tuning their gene expression patterns.

In bacteria, the regulation of gene expression is known to happen at the transcription initiation stage. This is a multi-step process and each step is regulated by specific molecular species, such as RNA polymerases, σ factors, DNA sequences, transcription factor proteins, among others.

In his thesis, Vinodh Kandavalli used the model organism E coli, and state of the art techniques of time-lapse microscopy and computational tools to dissect the steps in the transcription initiation and, from there, to better understand how their kinetics control RNA and thus Protein numbers of individual genes in various environmental conditions.

Studying these basic biological processes reveals more about how cells work and adapt to changing conditions. The experimental and computational methods developed for dissecting the rate-limiting steps in transcription initiation will help scientists to learn more about other aspects of how cells regulate the kinetics of transcription and, consequently, the distributions of RNA numbers in cell populations. Overall, this knowledge is expected to assist in the engineering of robust and sensitive synthetic circuits. This research might be of relevance especially for medicine and pharmaceutics, and possible future applications that may contribute to the betterment of the Human society.

Vinodh Kandavalli works as a doctoral researcher at the Laboratory of Biosystems Dynamics (LBD) of the Faculty of Medicine and Health Technology of Tampere University. 

The doctoral dissertation of M.Sc. Vinodh Kandavalli in the field of Biomedical Sciences and Engineering entitled Rate-limiting steps in transcription initiation are key regulatory mechanisms of Escherichia coli gene expression dynamics will be publicly examined in the Faculty of Medicine and Health Technology at Tampere University at 12:30 on Wednesday 29.4.2020. The Opponent will be Ph.D. Libor Krasny from the Institute of Microbiology, Czech Republic. Professor Andre S. Ribeiro from the Faculty of Medicine and Health Technology at Tampere University will act as chairperson. 

Due to the coronavirus situation, public defense is organized via a digital platform at Tampere University.

The dissertation is available online at:


Faculty of Medicine and Health Technology