Laboratory of Biosystem Dynamics (LBD)

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About us

The Laboratory of Biosystem Dynamics (LBD), led by Professor Andre S. Ribeiro of the Biomeditech Institute at Tampere University of Technology (TUT), studies the in vivo dynamics and regulatory mechanisms of bacterial gene expression and genetic circuits at the single-cell, single-molecule level using time-lapse microscopy, stochastic models, molecular biosensors, single-cell signal processing, and synthetic gene engineering. This research aims to understand how genes and genetic circuits are regulated and unravel their range of functionalities, thereby assisting in the comprehensive engineering of synthetic circuits for regulating cellular processes.

Our team in August 2017

Recent highlights

  • 2017
  • September 2017: Our team is very happy to announce that Scientific Reports has accepted our study on the ability of promoters in E.coli to regulate and evolve the level of extrinsic noise to which their RNA and proteins are subject to: J. Mäkelä, V. Kandavalli and A.S. Ribeiro (2017) Rate-limiting steps in transcription dictate sensitivity to variability in cellular components. Scientific Reports 7:10588. DOI:10.1038/s41598-017-11257-2. [J. Mäkelä is currently a Post-doc in Oxford University, U.K.]
  • Huy Tran, PhD, a former PhD student at the LBD and currently a Post-doc in Paris, France, has given a wonderful Seminar at BMT-TUT.
  • August 2017: BMT-TUT has  decided to fund our request for a Spectrometer with internal temperature control! We thank for the support.
  • August 2017: Nadia Goncalves, our PhD student, has received a short-term funding to doctoral students to complete the PhD studies by Biomeditech-TUT.
  • August 2017: BMT-TUT has decided to fund the moving of our laboratory to the BMT-TUT building! We thank for the support.
  • August 2017: BMC Bioinformatics has published a work by Frank Emmert-Streib's team to which we contributed to. We thank Frank for the opportunity.
  • August 2017: Two new members, Vatsala Chauhan and Mahendra Prajapat, PhD. have joined our group! Welcome.
  • July 2017: A. Ribeiro becomes a tenured Professor. 
  • June 2017 ***We have moved to the Sähkötalo Building, where BMT-TUT is located, at Korkeakoulunkatu 3 (33720 Tampere) ***
  • April 2017: Mahendra Prajapat has obtained a 1 year grant for Post Doctoral studies from the Finnish Foundation for Technology Promotion!
  • April 2017: Vinodh Kandavalli has obtained a 1 year grant for PhD studies from the Finnish Cultural Foundation Pirkanmaa Regional Fund! 
  • April 2017: Marco Minoia, PhD, has joined our group as a Posdoc, to bring new knowledge and contribute to the team's improvement.
  • Jan. 2017: The Journal of Neuroscience has published a work by Leonard Khiroug and Sergei Kirov's teams to which we contributed to.
  • 2016
  • The Biophysical Journal has accepted our study on the role of the nucleoid in the polar localization of the Serine Chemoreceptors of E. coli. (pre-print here)
  • We published a paper (review) on stochastic models of genetic circuits: AS Ribeiro (2016) Delays as regulators of the dynamics of genetic circuits. Markov Processes and Related Fields 22, 573-594. PDF
  • Our work on the dissection of the dynamics of RNA production at various temperatures in E. coli has been published in PLOS Computational Biology. Warm thanks to our former team member and now collaborator Antti Hakkinen. PDF
  • The LBD has been granted the "Key project funding: Forging ahead with research" grant by the Academy of Finland (01.10.2016 - 30.09.2018) for more research and applications of ongoing research results in gene expression and genetic circuits!
  • Mohamed Bahrudeen has joined our group!
  • Eero Lihavainen has completed his PhD at the LBD and will now pursue new adventures! Best wishes to him from all of us!
  • Jarno Mäkelä has completed his PhD at the LBD and will now work as a Post-Doctoral Fellow at Oxford! Best wishes from all of us!
  • We published a work on σ factor competition effects on in vivo kinetics of transcription initiation in E. coli: VK Kandavalli, H Tran, and AS Ribeiro (2016) Effects of σ factor competition on the in vivo kinetics of transcription initiation in Escherichia coli. BBA Gene Regulatory Mechanisms 1859 (2016) 1281–8. PDF
  • The Academy of Finland has granted the LBD with a new grant (01.09.2016 - 31.08.2020) for a project on studies of transcription dynamics!
  • Huy Tran and Antti Häkkinen have completed their PhD studies at the LBD, and have now move forward for Post-doctoral positions in Paris and Helsinki, respectively. We wish them all the best in their new challenges.

A little history...

The LBD was established in 2009, as part of the Computational Systems Biology Research Group of the DSP. In 2015, it became an independent research group of the Department of Signal Processing, TUT. In 2016, it joined Biomeditech (Institute of Biosciences and Medical Technologies of Tampere, Finland). In 2017, the group physically moved its offices to the building where the Biomeditech Institute is located (Sähkötalo Building).

Initially, our studies used computational and theoretical biology methods alone. 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, we conduct live single-cell, single-molecule microscopy measurements to study gene expression and genetic circuits dynamics, as well as other intracellular processes. For this, we also perform and develop methods in image and data analysis, and design detailed stochastic models and simulators of genetic circuits dynamics. This is made possible by having a highly multi-disciplinary group that includes 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 here.

Cells_nucleoids            Spots            Clod_cells

Above are movies produced in our lab, by microscopy, which we make use of to study cellular processes ranging from transcription dynamics to segregation of protein aggregates to the cell poles. (Left) Here, we image nucleoids (red) and FtsZ proteins (green) associated with the formation of the cell wall in cell division. (Center) Here we observe RNAs production, one at a time (bright spots), in a single cell. (Right) Here, we observe the spatial distribution of MS2-GFP-RNA spots in live cells at 10 oC, to assess how lower temperatures affect the dynamics of polar segregation of protein aggregates.

WorkFig

This image illustrates a methodology used in several of our studies, which consists of measurements of RNA production dynamics processed by state-of-the-art signal and image processing techniques, from which we design and test novel models of the processes responsible for RNA production regulation.

MULTI-BAM - Multi-scaled biodata analysis and modelling Research Community

The Multi-scaled biodata analysis and modelling (MultiBAM) is a recently formed (2016) research community (RC) composed of the Laboratory of Biosystem Dynamics (LBD) of the DSP (TUT) led by Andre Ribeiro (chair of MultiBAM), the Biological Physics and Soft Matter (BIO) Group led by Ilpo Vattulainen (TUT), the Computational Biology Group (CB) of BioMediTech (UTA) led by Matti Nykter, and the Protein Dynamics Group (PD) (UTA) led by Vesa Hytönen. All these groups study, at different scales, how cells sense and respond to the environment and how information flows and is processed inside them. The new community for multi-scaled biodata analysis and modelling (MultiBAM) will combine knowledge, methods, and tools used by its groups to handle biodata at different scales of observation and from different phenomena. The goal is to study and understand dynamical processes in cells in a broad sense and to produce new computational tools and models that, by being applicable to multiple scales, can provide new comprehensive understanding of biological systems. The first and most recent external evaluation process of RC's conducted by TUT (2017) placed us as the top graded new RC at TUT.