Systems biology research group
TalTech priority area
Research classification (Frascati)
Head of the research group
Research group member
Doctoral students
Keyword
heart
biophysics
bioenergetics
electrophysiology
biomechanics
intracellular diffusion
fluorescence microscopy
fluorescence correlation spectroscopy
Overview
In the Laboratory of Systems Biology, we useinterdisciplinary approaches to tackle questions in cardiac physiology. Our team consistsof researchers with backgrounds in biophysics,biology, and applied mathematics/physics. As aresult, we are able to approach scientific questions on different scales, from organ to molecularlevel, using combinations of different experimental and theoretical techniques by focusing onquantitative analysis of the data.We study diffusion in cardiomyocytes by tracking the movement of fluorescent molecules usingextended raster image correlation spectroscopy.Our results suggest that diffusion barriers are arranged in a 3D lattice with relatively smallopenings. Based on the analysis of autofluorescence response, we demonstrated that mitochondrial outer membrane and cytosolic diffusionbarriers reduce the movement of molecules toa similar extent. We study effects of creatinedeficiency to establish the role of creatine kinaseshuttle in the heart. In the research papers published this year, we demonstrated how creatinedeficiency leads to intracellular adaptations interms of alternative energy transfer systemschanges and an impact on calcium handlingof cardiomyocytes. These studies form a basisfor our current line of research on interactionsbetween processes in cardiomyocytes.
Important results
We have been active in the development of newtechniques and distribute them as open-sourcetools: deconvolution software for enhancingconfocal imaging, symbolic flux analysis forgenome-scale metabolic networks, and real-timesarcomere length estimation techniques. This development work has raised interest in companieswith an outreach of incorporating our algorithmsand software into their products.
Related projects
Innovative digital platform tailored for AI-assisted discoveries of hidden phenomena in biological function
Processing of confocal microscopy images(collaboration with PerkinElmer, USA)
Period of activity of the research group
Related department
Teadusgrupiga seotud publikatsioonid
- Birkedal, R., Laasmaa, M., Branovets, J., Vendelin, M. Ontogeny of cardiomyocytes : ultrastructure optimization to meet the demand for tight communication in excitation–contraction coupling and energy transfer // Philosophical Transactions of the Royal Society B : Biological Sciences (2022) vol. 377, 1864, art. 20210321.
https://doi.org/10.1098/rstb.2021.0321 - Shen, X., Brink, J. van den , Bergan-Dahl, A., Kolstad, T. R., Norden, E. S., Hou, Y., Laasmaa, M., Aguilar-Sanchez, Y., Quick, A. P., Espe, E. K. S. et al. Prolonged β-adrenergic stimulation disperses ryanodine receptor clusters incardiomyocytes and has implications for heart failure // eLife (2022) vol. 11, art. e77725.
https://doi.org/10.7554/eLife.77725 - Bartkova, S., Vendelin, M., Sanka, I., Pata, P., Scheler, O. Droplet image analysis with user-friendly freeware CellProfiler // Analytical methods (2020) vol. 12, 17, p. 2287-2294 : ill.
https://doi.org/10.1039/D0AY00031K - Barsunova, K., Vendelin, M., Birkedal, R. Marker enzyme activities in hindleg from creatine-deficient AGAT and GAMT KO mice - differences between models, muscles, and sexes // Scientific reports (2020) vol. 10, 1, Art. 7956, 9 p.
https://doi.org/10.1038/s41598-020-64740-8 - Branovets, J., Karro, N., Barsunova, K., Laasmaa, M., Lygate, C.A., Vendelin, M., Birkedal, R. Cardiac expression and location of hexokinase changes in a mouse model of pure creatine deficiency // American journal of physiology-heart and circulatory physiology (2021) vol. 320, 2, p. H613−H629.
https://doi.org/10.1152/ajpheart.00188.2020 - Vendelin, M., Laasmaa, M., Kalda, M., Branovets, J., Karro, N., Barsunova, K., Birkedal, R. IOCBIO Kinetics : an open-source software solution for analysis of data traces // PLoS computational biology (2020) vol. 16, 12, art. e1008475.
https://doi.org/10.1371/journal.pcbi.1008475 - Laasmaa, M., Branovets, J., Barsunova, K., Karro, N., Lygate, C. A., Birkedal, R., Vendelin, M. Altered calcium handling in cardiomyocytes from arginine-glycine amidinotransferase-knockout mice is rescued by creatine // American journal of physiology-heart and circulatory physiology (2020) vol. 320, 2, p. H805-H825.
https://doi.org/10.1152/ajpheart.00300.2020 - Kalda, M., Vendelin, M. Cardiac muscle regulatory units are predicted to interact stronger than neighboring cross-bridges // Scientific reports (2020) vol. 10, 1, art. 5530, 13 p. : ill.
https://doi.org/10.1038/s41598-020-62452-7 - Bartkova, S., Vendelin, M., Pata, P., Scheler, O. Cellprofiler is a fit tool for droplet digital image analysis // 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2019) Basel, Switzerland, 27 – 31 October 2019. New York : Chemical and Biological Microsystems Society, 2020. art. 163704, p. 1644-1645.
https://doi.org/10.1101/811869 - Lu, P., Veletić, M., Laasmaa, M., Vendelin, M. et al. Multi-nodal nano-actuator pacemaker for energy-efficient stimulation of cardiomyocytes // Nano Communication Networks (2019) vol. 22, dec., art. 100270, 11 p. : ill.
https://doi.org/10.1016/j.nancom.2019.100270 - Karro, N., Laasmaa, M., Vendelin, M., Birkedal Nielsen, R. Respiration of permeabilized cardiomyocytes from mice: no sex differences, but substrate-dependent changes in the apparent ADP-affinity // Scientific reports (2019) vol. 9, 1, art. 12592.
https://doi.org/10.1038/s41598-019-48964-x - Laasmaa, M., Lu, P., Veletic, M., Vendelin, M. et al. Energy-efficiency of cardiomyocyte stimulation with rectangular pulses // Scientific reports (2019) vol. 9, 1, art. 13307, p. 1−9.
https://doi.org/10.1038/s41598-019-49791-w - Laasmaa, M., Karro, N., Birkedal, R., Vendelin, M. IOCBIO Sparks detection and analysis software // PeerJ (2019) vol. 7, Issue 3, art. e6652, 28 p. : ill.
https://doi.org/10.7717/peerj.6652 - Engelbrecht, J., Peets, T., Tamm, K., Laasmaa, M., Vendelin, M. On the complexity of signal propagation in nerve fibres // Proceedings of the Estonian Academy of Sciences (2018) vol. 67, 1, p. 28-38 : ill.
https://doi.org/10.3176/proc.2017.4.28 http://www.ester.ee/record=b2355998*est