2/2018

Computer built inside bacteria

Andre Sanches Ribeiro explores gene expression and gene regulatory networks in bacteria. His goal is to develop synthetic gene networks to regulate the properties and behaviour of living single-cell organisms.

Andre Sanches Ribeiro

 

Professor Andre Sanches Ribeiro says that Finland is one of the few countries where it is possible to set up a laboratory that is both theoretical and experimental. Researchers who have left his group are setting up their own laboratories outside of Finland, which makes international collaboration even easier.

 

WHO? Andre Sanches Ribeiro

  • Professor of Computational Systems Biology
  • Born in Luanda, Angola.
  • Education: Licentiate of Physics in 1999, Doctor of Physics in 2004, University of Lisbon, Portugal.
  • Joined TUT in 2004. Founder and head of the Laboratory of Biosystem Dynamics (LBD) since 2009.
  • Family: wife.
  • Hobbies: History (ask him anything about Portuguese history!) and prehistory. Computer games that provide learning experiences.
 

The regulation of genes by switches and clocks is a seemingly simple process that in reality involves complex mutual interplay. Professor Andre Sanches Ribeiro is looking to unravel these mechanisms by studying Escherichia coli.

“If we understand the functions of real-life regulatory networks, we can develop synthetic circuits for regulating cellular processes. These circuits are like tiny computers inside bacteria,” says Ribeiro.

As Ribeiro points out, the regulation of gene expression remains a huge challenge that requires collaborative effort. There are scientists all over the world racing to find the answers, but Ribeiro has an unusual approach to the problem.

“Gene regulation involves a complex series of events, but current research in the field is largely focused on protein functions. Our interests lie primarily in the mechanisms that underlie gene transcription.”

Established a decade ago, Ribeiro’s Laboratory of Biosystem Dynamics (LBD) is likewise unconventional. As cellular mechanisms are governed by the fundamental laws of biology and physics, LBD brings together expertise in both fields.

“We collect empirical data on living cells using time-lapse microscopy, refine our data using signal and image processing techniques, and analyse, model and apply the results to develop synthetic regulatory circuits.”

More friends than foes

Ribeiro says that from a strategic perspective, it is better to treat bacteria as friends rather than foes.

“Bacteria far outnumber mammals. They’ve been around for at least four billion years and sailed through all the mass extinction events that have swiped across our Earth. Bacteria are diverse, adaptable and capable of thriving in the most inhospitable conditions imaginable. They know much more about survival than we do.”

We have a symbiotic relationship with bacteria living inside our body and gut, but Ribeiro thinks that now is the time to make a more conscious effort to befriend germs.

Life-size applications

A better understanding of gene regulatory networks could help us control the properties and behaviour of bacteria. This would open up enormous potential for applications in medicine and biotechnology.

“We could learn how to utilise similar defence mechanisms that protect bacteria from other, harmful bacteria and allows them to detect malignant cells or different substances produced by the human body during an illness.”

Advances in synthetic biology are paving the way for the development of engineered bacteria that are capable of producing edible protein and sugar from cheap sources.

“Bacteria are simple organisms. As all the different species have evolved from simple life forms, bacteria can teach us about the origins and evolution of life. This information would be helpful in the search for other habitable planets. Could we combine the properties of different bacteria, so that they would eat a certain mineral and produce oxygen in a cold climate?” asks Ribeiro.

Science now, society in the future

Ribeiro’s background is in theoretical physics. His international group is made up of researchers who specialise in computer science, physics, molecular biology, signal processing or computational biology.

“Our research goals range from the development of gene construction to complex biophysical and statistical models. We pursue fundamental research that pushes science forward but may not yet provide tangible benefits to society.”

As the head of LBD, Ribeiro is meticulous with money and respects the risks taken by funding agencies. The group does exactly as promised.

“I’ve never promised to deliver a product for a company. Maybe one day I will, but not yet.” 

Text: Kati Vastamäki
Photo: Mika Kanerva

 
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