Doctoral dissertation

Dissertation: Studying the effects of temperature shifts helps find the functioning limits of synthetic genetic circuits

MSc. (Tech.) Samuel M. D. Oliveira is the first doctoral candidate to defend his dissertation in the new Tampere University. His research area is in bioengineering and computational biology as he studied the adaptation of bacteria to temperature fluctuations. This information helps us better understand how bacteria survive in a wide range of environments. The study may also benefit the developers of future biological computers.

Temperature shifts and cycles in the environment affect virtually all biophysical processes inside cells. Complex organisms, such as humans, have evolved mechanisms to stabilize their temperature. Simpler organisms, for example bacteria, lack such internal controls. Thus, it is important to understand how they adapt to temperature fluctuations.

“Most studies on microbiology are performed at the optimal growth temperature for bacteria. Therefore, we lack knowledge on the limits and sensitivity of gene expression mechanisms as regards temperature shifts. I find this topic very interesting as it combines many fields of knowledge and it contributes to better understanding how bacteria can live anywhere,” Samuel Oliveira says.

In his thesis, Oliveira used a synthetic biology approach. He engineered genes and circuits to test hypotheses on how cells cope with temperature shifts. For this, he also used state-of-the-art single-cell and single-molecule computational and experimental methods in microscopy, microfluidics, signal processing and stochastic modelling.

“I believe that exploratory works such as the one presented in my thesis contribute to the field of synthetic biology by helping us better understand the plasticity of synthetic circuits and by adding new elements to the present libraries of DNA components. This information can also be used for rationally designing, building and testing the building blocks for future biological computers, for example”, Oliveira notes.

Samuel Oliveira arrived in Finland in 2011 through an exchange programme at Tampere University of Technology (TUT). He obtained his master’s degree at TUT in 2014 under the supervision of Professor Andre S. Ribeiro from the Laboratory of Biosystem Dynamics at TUT. He then proceeded to his PhD which he is now completing after 4 years. His doctoral dissertation is the first one to be completed in the new Tampere University.

Public defence of a doctoral dissertation on Friday, 4 January 2019

MSc. (Tech.) Samuel M. D. Oliveira’s doctoral dissertation in the field of bioengineering and computational biology entitled Functionality of Genetic Circuits at Fluctuating Temperatures will be publicly examined at the Faculty of Medicine and Health Technology at Tampere University in auditorium TB109 in the Tietotalo building (address: Korkeakoulunkatu 1, Tampere, Finland) at 12 noon on Friday, 4 January 2019.

The opponent will be Associate Professor Namiko Mitarai (Neils Bohr Institute of University of Copenhagen, Denmark). Professor Andre S. Ribeiro from the Faculty of Medicine and Health Technology at Tampere University will act as Chairman.

The dissertation is available online at http://urn.fi/URN:ISBN:978-952-03-0970-1 .