Looking for PhD students

Posted on April 28, 2021September 9, 2021 by admin

We have opened competition for two PhD student positions: Linking energetics to muscle phenotype: the importance of intracellular microdomains on the regulation of AMP-activated kinase . The aim of this project is to study in detail how energetics affects the signaling pathways in skeletal and heart muscle tissue. You will learn how to combine experimental and theoretical approaches to extract as much information as possible from your data.Deep dive into the cardiac cell: tracking molecular ...

Altered calcium handling in cardiomyocytes from arginine-glycine amidinotransferase-knockout mice is rescued by creatine

Posted on March 4, 2021March 4, 2021 by admin

Martin Laasmaa, Jelena Branovets, Karina Barsunova, Niina Karro, Craig A Lygate, Rikke Birkedal, Marko Vendelin Am J Physiol Heart Circ Physiol. 2021 Feb 1;320(2):H805-H825 PMID: 33275525DOI: 10.1152/ajpheart.00300.2020 Abstract The creatine kinase system facilitates energy transfer between mitochondria and the major ATPases in the heart. Creatine-deficient mice, which lack arginine-glycine amidinotransferase (AGAT) to synthesize creatine and homoarginine, exhibit reduced cardiac co...

Cardiac expression and location of hexokinase changes in a mouse model of pure creatine deficiency

Posted on March 4, 2021March 4, 2021 by admin

Jelena Branovets, Niina Karro, Karina Barsunova, Martin Laasmaa, Craig A Lygate, Marko Vendelin, Rikke Birkedal Am J Physiol Heart Circ Physiol. 2021 Feb 1;320(2):H613-H629 PMID: 33337958DOI: 10.1152/ajpheart.00188.2020 Abstract Creatine kinase (CK) is considered the main phosphotransfer system in the heart, important for overcoming diffusion restrictions and regulating mitochondrial respiration. It is substrate limited in creatine-deficient mice lacking l-arginine:glycine amidinotr...

IOCBIO Kinetics: An open-source software solution for analysis of data traces

Posted on January 22, 2021September 17, 2021 by admin

Marko Vendelin, Martin Laasmaa, Mari Kalda, Jelena Branovets, Niina Karro, Karina Barsunova, Rikke Birkedal PLoS Comput Biol. 2020 Dec 22;16(12):e1008475. PMID: 33351800PMCID: PMC7787677DOI: 10.1371/journal.pcbi.1008475 Abstract Biological measurements frequently involve measuring parameters as a function of time, space, or frequency. Later, during the analysis phase of the study, the researcher splits the recorded data trace into smaller sections, analyzes each section separately b...

List of topics for BSc/MSc students

Posted on December 14, 2020September 9, 2021 by admin

We have composed a list of topics proposed for the students interested in joining the lab. List is available under Positions. This is the first version of the list and will be updated soon to include more projects for students with the different backgrounds. Feel free to ask about possible projects outside the list as well.

IOCBIO Sparks updated

Posted on November 26, 2020November 26, 2020 by admin

IOCBIO Sparks software has been updated to 1.2.0. The new version fixes an issue with displaying images on newer installations. It also brings enhancements for use with the scripts allowing you to start analysis of some specific experiment by specifying its experiment ID. In addition, you could start it also in read-write mode as well. These changes are targeting a use case where you want to review and reanalyze larger set of the data and prefer to use external script to select experiments for ...

Marker enzyme activities in hindleg from creatine-deficient AGAT and GAMT KO mice – differences between models, muscles, and sexes

Posted on May 14, 2020 by Barsunova K, Vendelin M, Birkedal R

Barsunova K, Vendelin M, Birkedal R Sci Rep 2020 May;10(1):7956 PMID: 32409787 Abstract Creatine kinase (CK) functions as an energy buffer in muscles. Its substrate, creatine, is generated by L-arginine:glycine amidinotransferase (AGAT) and guanidinoacetate N-methyltransferase (GAMT). Creatine deficiency has more severe consequences for AGAT than GAMT KO mice. In the present study, to characterize their muscle phenotype further, we recorded the weight of tibialis anterior (TA), extensor digi...

Cardiac muscle regulatory units are predicted to interact stronger than neighboring cross-bridges

Posted on March 26, 2020April 9, 2020 by Kalda M, Vendelin M

Kalda M, Vendelin M Sci Rep 2020 Mar;10(1):5530 PMID: 32218497 Full text: https://doi.org/10.1038/s41598-020-62452-7 Abstract Model simulations (top) and the scheme showing cooperativity modes Strong interactions between cross-bridges (XB) and regulatory units (RU) lead to a steep response of cardiac muscle to an increase in intracellular calcium. We developed a model to quantitatively assess the influence of different types of interactions within the sarcomere on the prope...

Energy-efficiency of Cardiomyocyte Stimulation with Rectangular Pulses

Posted on September 16, 2019 by Laasmaa M, Lu P, Veletić M, Louch WE, Bergsland J, Balasingham I, Vendelin M

Laasmaa M, Lu P, Veletić M, Louch WE, Bergsland J, Balasingham I, Vendelin M Sci Rep 2019 Sep;9(1):13307 PMID: 31527628 Abstract In cardiac pacemaker design, energy expenditure is an important issue. This work aims to explore whether varying stimulation pulse configuration is a viable optimization strategy for reducing energy consumption by the pacemaker. A single cardiomyocyte was used as an experimental model. Each cardiomyocyte was stimulated with different stimulation protocols using rec...

Respiration of permeabilized cardiomyocytes from mice: no sex differences, but substrate-dependent changes in the apparent ADP-affinity

Posted on August 29, 2019June 10, 2020 by Karro N, Laasmaa M, Vendelin M, Birkedal R

Karro N, Laasmaa M, Vendelin M, Birkedal R Sci Rep 2019 Aug;9(1):12592 PMID: 31467353 Abstract Sex differences in cardiac physiology are getting increased attention. This study assessed whether isolated, permeabilized cardiomyocytes from male and female C57BL/6 mice differ in terms of their respiration with multiple substrates and overall intracellular diffusion restriction estimated by the apparent ADP-affinity of respiration. Using respirometry, we recorded 1) the activities of respiratory...