of Biosystem Dynamics (LBD)
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,
using time-lapse microscopy, stochastic models, molecular biosensors, single-cell signal
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
of synthetic circuits for regulating cellular processes.
Our team in August 2017
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.
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.
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.