Rikke Birkedal, Jelena Branovets, Marko Vendelin
FEBS Letters 2024 Nov;598(21):2623-2640.
PMID: 39112921
DOI: 10.1002/1873-3468.14994
Abstract
Intracellular molecules are transported by motor proteins or move by diffusion resulting from random molecular motion. Cardiomyocytes are packed with structures that are crucial for function, but also confine the diffusional spaces, providing cells with a means to control diffusion. They form compartments in which local concentrations ar...
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Published Protocol: Simple Analysis of Gel Images With IOCBIO Gel Software
Lucia Jaska, Rikke Birkedal, Martin Laasmaa, Marko Vendelin
Bio-protocol, 2024 Aug 20; 14(16):e5053
PMID: 39210956
DOI: 10.21769/BioProtoc.5053
Abstract
Gel image analyses are often difficult to reproduce, as the most commonly used software, the ImageJ Gels plugin, does not automatically record any steps in the analysis process. This protocol provides detailed steps for image analysis using IOCBIO Gel software with western blot as an example; however, the protocol is applic...
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Simple analysis of gel images with IOCBIO Gel
Jaak Kütt, Georg Margus, Lauri Kask, Triinu Rätsepso, Kärol Soodla, Romain Bernasconi, Rikke Birkedal, Priit Järv, Martin Laasmaa, Marko Vendelin
BMC Biology 2023 Oct 20;21(1):225
PMID: PMC10589977
DOI: 10.1186/s12915-023-01734-8
Abstract
Background: Current solutions for the analysis of Western Blot images lack either transparency and reproducibility or can be tedious to use if one has to ensure the reproducibility of the analysis.
Results: Here, we present an open-sou...
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Cardiomyocytes from female compared to male mice have larger ryanodine receptor clusters and higher calcium spark frequency
Martin Laasmaa, Jelena Branovets, Jekaterina Stolova, Xin Shen, Triinu Rätsepso, Mihkel Jaan Balodis, Cärolin Grahv, Eliise Hendrikson, William Edward Louch, Rikke Birkedal, Marko Vendelin
The Journal of Physiology, 601(18), 4033–4052
PMID: 37561554
DOI: 10.1113/JP284515
Abstract
Sex differences in cardiac physiology are receiving increased attention as it has become clear that men and women have different aetiologies of cardiac disease and require different treatments. The...
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Looking for PhD student: mathematical modeling
We have opened competition for a PhD student position:
Mathematical modeling of energy transfer and mechanics in theheart
In heart muscle cells, energy used by most of the processes in the muscle cells is supplied in the form ofATP by mitochondria. Within this project, you would be designing state-of-the-art mathematical models to unravel mechanisms regulating ATP production in mitochondria, selection of energy transfer pathways between mitochondria and ATP consumers, as well as working o...
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Ontogeny of cardiomyocytes: ultrastructure optimization to meet the demand for tight communication in excitation-contraction coupling and energy transfer
Rikke Birkedal, Martin Laasmaa, Jelena Branovets, Marko Vendelin
Philos Trans R Soc Lond B Biol Sci. 2022 Nov 21;377(1864):20210321.
PMID: 36189816
DOI: 10.1098/rstb.2021.0321
Abstract
The ontogeny of the heart describes its development from the fetal to the adult stage. In newborn mammals, blood pressure and thus cardiac performance are relatively low. The cardiomyocytes are thin, and with a central core of mitochondria surrounded by a ring of myofilaments, while the sarco...
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Physiology in Focus 2023
We are participating in organizing Physiology in Focus 2023, which will be held in Tallinn, Estonia, September 14-16, 2023. Physiology in Focus 2023 is the first joint physiology meeting of the Scandinavian Physiological Society (SPS), the Federation of European Physiological Societies (FEPS), and the Baltic Physiological Societies.
See more at the archived official website of the conference https://sps-feps-2023.publicon.ee/
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Thesis defense: Jelena Branovets
Jelena Branovets is defending her thesis on Energetics and Calcium Handling in Hearts from Creatine-Deficient Mice. Defense is on 29 September 2022 at 10:00 at the Department of chemistry and biotechnology, room SCI109.
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Student team project: Software for protein determination
We are looking for a student team working on proteomics gel analysis software. The software is expected to take as an input gel description and photo images containing gel measurements. As an output, software should calculate image intensities in regions that the user can interactively select. The algorithms for that will be provided but need to be implemented by the student team.
Example gel image with the marked regions of interest for analysis
Software will be released as a cross-platf...
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Looking for PhD student
We have opened competition for a PhD student position:
Tracking molecular movement to unravel diffusion barriers in cardiac cells
This is an interdisciplinary project combining physics and biology to study the intracellular environment in the heart muscle. Through the development of cutting-edge experimental and data analysis approaches, it is expected to reveal intracellular environment properties that govern molecular movements and shape its physiology.
So that the heart could produc...
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