Student team project: Software for protein determination

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

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...

Looking for PhD student

Posted on September 7, 2021November 17, 2021 by admin

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...

Summer job for students

Posted on May 6, 2021September 9, 2021 by admin

We are looking for a B.Sc. or M.Sc. student to work full or part-time during the summer and, if there is an interest, for longer. The job is to do Western blots to assess whether the phosphorylation status of some proteins is different in hearts from creatine-deficient mice. Image analysis and insertion into the database is also part of the job. The results can stand alone and form the basis for a thesis. It is an advantage to have experience with laboratory work, but we will be happy to ...

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...