Laboratory of Biosystem Dynamics (LBD)

The Laboratory of Biosystem Dynamics (LBD), led by Professor Andre S. Ribeiro of the Faculty of Medicine and Health Technology, Tampere University, studies the in vivo dynamics and regulatory mechanisms of bacterial gene expression and small and large scale genetic circuits at the single-cell, single-molecule level, using time-lapse microscopy, flow-cytometry, RNAseq, stochastic models, single-cell signal processing, and synthetic gene engineering. We aim to understand how genes and genetic circuits are regulated and to unravel their range of functionalities and global transcriptional programs.

Our team in May 2019

Recent highlights

2019

  • May 2019: We move our offices and laboratory to the Arvo building of Tampere University! We will now work towards sharing knowledge with our new colleagues so as to improve research capabilities.
  • April 2019: We have a new team member, Suchintak Dash, which has join our group to conduct PhD studies.
  • Our former MSc and PhD student, Jason Lloyd-Price, following a post-doc at Harvard, U.S.A., has joined Google in N.Y. We wish him all the best.
  • Mar 2019: Scientific Reports has published our work on the effects of low temperatures on the dynamics of a chromosome integrated gene.
  • Jan 2019: We congratulate Samuel Oliveira for completing his PhD studies at the LBD! (1st PhD of the new Tampere University). Samuel will now move to Boston University for post-doctoral studies. We sincerely express our gratitude and admiration for his dedication and contributions. We wish him all the best possible and beyond!

2018

  • Dec 2018: Bioinformatics has published our work on segmentation and tracking tools of cells and intracellular components from time-lapse microscopy images.
  • Dec 2018: BBA Gene Regulatory Mechanisms has accepted our work on the regulation of temporal assymetries in the kinetics of gene expression!
  • Nov 2018: The Royal Society Open Science Journal has accepted our work on stochastic models of circuits with autoregulation.
  • October 2018: We congratulate Olli-Pekka Smolander, the first alumni of the LBD to obtain a professor position (TalTech University, Estonia)
  • September 2018: We congratulate Nadia Goncalves for completing her PhD studies at the LBD! Best wishes to her.
  • August 2018: Mahendra Prajapat has completed his post-doctoral studies and joined the Vidigal Lab, National Cancer Center, WA, USA.USA. We wish him all the best.
  • July 2018: We welcome Ines Baptista to our group.
  • June 2018: We are happy to announce that the Bioinformatics Journal has accepted our new software, SCIP, a Single-Cell Image Processor toolbox.
  • April 2018: We are happy to announce that the Physical Biology Journal has accepted our work on the effects of low temperatures in the symmetry in cell division in E. coli.
  • March 2018: We received our new Flow-cytometer.
  • March 2018: Inaugural lecture of the full professorship (see audioslides section)
  • January 2018: Our laboratory in the Sähkötalo Building, BMT-TUT is now fully operational!
  • January 2018: We welcome our new PhD student Bilena Almeida!

A little history...

The LBD was established in 2009 in the Department of Signal Processing. In 2016, it moved to Biomeditech (Institute of Biosciences and Medical Technologies of Tampere, Finland) located in the Sähkötalo Building. In 2019, we moved to the Arvo building, of Tampere University, where most of the members in similar areas of expertise of the Faculty of Medicine and Health Technology (MET) are located, including the distinguished scientist Howy Jacobs, with whom we will share lab space.

Initially, our studies used computational and theoretical biology methods alone, such as detailed stochastic biophysical models and simulators of genetic circuits. In 2011, we setup a Cell and Molecular Biology Laboratory, specialized in live, single-cell, single-molecule imaging. This allowed us to combine theory and measurements. Currently, in addition to the above methodologies, we also conduct live single-cell, single-molecule microscopy and flow-cytometry measurements to study gene expression and genetic circuits dynamics, as well as other intracellular processes. Recently, we added RNAseq another valuable research tool. This has been possible due to having a highly multi-disciplinary group, that includes students with backgrounds in physics, theoretical biology, molecular and cell biology, biotechnology, biomedical engineering, signal processing, and computer science.

A detail description of some of our recent projects is available in Projects.

Above are movies produced in our lab, using time-lapse microscopy, to study cellular processes ranging from transcription dynamics to segregation of protein aggregates to the cell poles. (Left) We imaged nucleoids (red) and FtsZ proteins (green) during cell division. (Center) We observed RNAs production, one molecule at a time (bright spots), in a living cell. (Right) We observed the spatial distribution of MS2-GFP-RNA spots in live cells at 10 oC, to assess how low temperatures affect the dynamics of segregation of protein aggregates towards the cell poles.

This image illustrates a methodology used in several of our studies, which consists of microscopy measurements of RNA production dynamics, subsequently processed by state-of-the-art signal and image processing techniques, from which we design and test novel stochastic models of genes and genetic circuits expression and regulation.