Publications

Suut-Tuule, E., Jarg, T., Tikker, P., Lootus, K.-M., Martõnova, J., Reitalu, R., Ustrnul, L., Ward, J. S., Rjabovs, V., Shubin, K., Nallaparaju, J. V., Vendelin, M., Preis, S., Öeren, M., Rissanen, K., Kananovich, D., & Aav, R. (2024). Mechanochemically driven covalent self-assembly of a chiral mono-biotinylated hemicucurbit[8]uril. Cell Reports Physical Science, 5(9), 102161. https://doi.org/10.1016/j.xcrp.2024.102161

Jaska, L., Birkedal, R., Laasmaa, M., & Vendelin, M. (2024). Simple Analysis of Gel Images With IOCBIO Gel Software. Bio-Protocol, 14(16), e5053. https://doi.org/10.21769/BioProtoc.5053

Branovets, J., Soodla, K., Vendelin, M., & Birkedal, R. (2023). Rat and mouse cardiomyocytes show subtle differences in creatine kinase expression and compartmentalization. PLOS ONE, 18(11), e0294718. https://doi.org/10.1371/journal.pone.0294718

Kütt, J., Margus, G., Kask, L., Rätsepso, T., Soodla, K., Bernasconi, R., Birkedal, R., Järv, P., Laasmaa, M., & Vendelin, M. (2023). Simple analysis of gel images with IOCBIO Gel. BMC Biology, 21(1), 225. https://doi.org/10.1186/s12915-023-01734-8

Risti, R., Gunn, K. H., Hiis-Hommuk, K., Seeba, N.-N., Karimi, H., Villo, L., Vendelin, M., Neher, S. B., & Lõokene, A. (2023). Combined action of albumin and heparin regulates lipoprotein lipase oligomerization, stability, and ligand interactions. PLOS ONE, 18(4), e0283358. https://doi.org/10.1371/journal.pone.0283358

Laasmaa, M., Branovets, J., Stolova, J., Shen, X., Rätsepso, T., Balodis, M. J., Grahv, C., Hendrikson, E., Louch, W. E., Birkedal, R., & Vendelin, M. (2023). Cardiomyocytes from female compared to male mice have larger ryanodine receptor clusters and higher calcium spark frequency. The Journal of Physiology, 601(18), 4033–4052. https://doi.org/10.1113/JP284515

Birkedal, R., Laasmaa, M., Branovets, J., & Vendelin, M. (2022). 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, 377(1864), 20210321. https://doi.org/10.1098/rstb.2021.0321

Branovets, J., Karro, N., Barsunova, K., Laasmaa, M., Lygate, C. A., Vendelin, M., & Birkedal, R. (2021). Cardiac expression and location of hexokinase changes in a mouse model of pure creatine deficiency. American Journal of Physiology-Heart and Circulatory Physiology, 320(2), H613–H629. https://doi.org/10.1152/ajpheart.00188.2020

Laasmaa, M., Branovets, J., Barsunova, K., Karro, N., Lygate, C. A., Birkedal, R., & Vendelin, M. (2021). Altered calcium handling in cardiomyocytes from arginine-glycine amidinotransferase-knockout mice is rescued by creatine. American Journal of Physiology-Heart and Circulatory Physiology, 320(2), H805–H825. https://doi.org/10.1152/ajpheart.00300.2020

Vendelin, M., Laasmaa, M., Kalda, M., Branovets, J., Karro, N., Barsunova, K., & Birkedal, R. (2020). IOCBIO Kinetics: An open-source software solution for analysis of data traces. PLOS Computational Biology, 16(12), e1008475. https://doi.org/10.1371/journal.pcbi.1008475

Barsunova, K., Vendelin, M., & Birkedal, R. (2020). Marker enzyme activities in hindleg from creatine-deficient AGAT and GAMT KO mice – differences between models, muscles, and sexes. Scientific Reports, 10(1), 1–9. https://doi.org/10.1038/s41598-020-64740-8

Kalda, M., & Vendelin, M. (2020). Cardiac muscle regulatory units are predicted to interact stronger than neighboring cross-bridges. Scientific Reports, 10(1), 1–13. https://doi.org/10.1038/s41598-020-62452-7

Bartkova, S., Vendelin, M., Sanka, I., Pata, P., & Scheler, O. (2020). Droplet image analysis with user-friendly freeware CellProfiler. Analytical Methods. https://doi.org/10.1039/D0AY00031K

Lu, P., Veletić, M., Laasmaa, M., Vendelin, M., Louch, W. E., Halvorsen, P. S., Bergsland, J., & Balasingham, I. (2019). Multi-nodal nano-actuator pacemaker for energy-efficient stimulation of cardiomyocytes. Nano Communication Networks, 22, 100270. https://doi.org/10.1016/j.nancom.2019.100270

Laasmaa, M., Lu, P., Veletić, M., Louch, W. E., Bergsland, J., Balasingham, I., & Vendelin, M. (2019). Energy-efficiency of Cardiomyocyte Stimulation with Rectangular Pulses. Scientific Reports, 9(1), 1–9. https://doi.org/10.1038/s41598-019-49791-w

Karro, N., Laasmaa, M., Vendelin, M., & Birkedal, R. (2019). Respiration of permeabilized cardiomyocytes from mice: no sex differences, but substrate-dependent changes in the apparent ADP-affinity. Scientific Reports, 9(1), 1–11. https://doi.org/10.1038/s41598-019-48964-x

Laasmaa, M., Karro, N., Birkedal, R., & Vendelin, M. (2019). IOCBIO Sparks detection and analysis software. PeerJ, 7, e6652. https://doi.org/10.7717/peerj.6652

Laasmaa, M., Birkedal, R., & Vendelin, M. (2016). Revealing calcium fluxes by analyzing inhibition dynamics in action potential clamp. Journal of Molecular and Cellular Cardiology, 100, 93–108. https://doi.org/10.1016/j.yjmcc.2016.08.015

Karro, N., Sepp, M., Jugai, S., Laasmaa, M., Vendelin, M., & Birkedal, R. (2016). Metabolic compartmentation in rainbow trout cardiomyocytes: coupling of hexokinase but not creatine kinase to mitochondrial respiration. Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology. https://doi.org/10.1007/s00360-016-1025-x

Simson, P., Jepihhina, N., Laasmaa, M., Peterson, P., Birkedal, R., & Vendelin, M. (2016). Restricted ADP movement in cardiomyocytes: Cytosolic diffusion obstacles are complemented with a small number of open mitochondrial voltage-dependent anion channels. Journal of Molecular and Cellular Cardiology, 97, 197–203. https://doi.org/10.1016/j.yjmcc.2016.04.012

Kalda, M., Peterson, P., & Vendelin, M. (2015). Cross-Bridge Group Ensembles Describing Cooperativity in Thermodynamically Consistent Way. PLoS ONE, 10(9), e0137438. https://doi.org/10.1371/journal.pone.0137438

Sepp, M., Sokolova, N., Jugai, S., Mandel, M., Peterson, P., & Vendelin, M. (2014). Tight Coupling of Na+/K+-ATPase with Glycolysis Demonstrated in Permeabilized Rat Cardiomyocytes. PLoS ONE, 9(6), e99413. https://doi.org/10.1371/journal.pone.0099413

Birkedal, R., Laasmaa, M., & Vendelin, M. (2014). The location of energetic compartments affects energetic communication in cardiomyocytes. Frontiers in Physiology, 5, 376. https://doi.org/10.3389/fphys.2014.00376

Sokolova, N., Pan, S., Provazza, S., Beutner, G., Vendelin, M., Birkedal, R., & Sheu, S.-S. (2013). ADP Protects Cardiac Mitochondria under Severe Oxidative Stress. PLoS ONE, 8(12), e83214. https://doi.org/10.1371/journal.pone.0083214

Branovets, J., Sepp, M., Kotlyarova, S., Jepihhina, N., Sokolova, N., Aksentijevic, D., Lygate, C. A., Neubauer, S., Vendelin, M., & Birkedal, R. (2013). Unchanged mitochondrial organization and compartmentation of high-energy phosphates in creatine deficient GAMT-/- mouse heart. American Journal of Physiology - Heart and Circulatory Physiology. https://doi.org/10.1152/ajpheart.00919.2012

Peterson, P., Kalda, M., & Vendelin, M. (2013). Real-time determination of sarcomere length of a single cardiomyocyte during contraction. American Journal of Physiology - Cell Physiology, 304(6), C519–C531. https://doi.org/10.1152/ajpcell.00032.2012

Schryer, D. W., Peterson, P., Illaste, A., & Vendelin, M. (2012). Sensitivity Analysis of Flux Determination in Heart by H218O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways. PLoS Comput Biol, 8(12), e1002795. https://doi.org/10.1371/journal.pcbi.1002795

Karo, J., Peterson, P., & Vendelin, M. (2012). Molecular Dynamics Simulations of Creatine Kinase and Adenine Nucleotide Translocase in Mitochondrial Membrane Patch. Journal of Biological Chemistry, 287(10), 7467–7476. https://doi.org/10.1074/jbc.M111.332320

Illaste, A., Laasmaa, M., Peterson, P., & Vendelin, M. (2012). Analysis of Molecular Movement Reveals Latticelike Obstructions to Diffusion in Heart Muscle Cells. Biophysical Journal, 102(4), 739–748. https://doi.org/10.1016/j.bpj.2012.01.012

Jepihhina, N., Beraud, N., Sepp, M., Birkedal, R., & Vendelin, M. (2011). Permeabilized rat cardiomyocyte response demonstrates intracellular origin of diffusion obstacles. Biophysical Journal, 101(9), 2112–2121. https://doi.org/10.1016/j.bpj.2011.09.025

Laasmaa, M., Vendelin, M., & Peterson, P. (2011). Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images. Journal of Microscopy, 243(2), 124–140. https://doi.org/10.1111/j.1365-2818.2011.03486.x

Ramay, H. R., Liu, O. Z., & Sobie, E. A. (2011). Recovery of cardiac calcium release is controlled by sarcoplasmic reticulum refilling and ryanodine receptor sensitivity. Cardiovascular Research, 91(4), 598–605. https://doi.org/10.1093/cvr/cvr143

Schryer, D., Vendelin, M., & Peterson, P. (2011). Symbolic flux analysis for genome-scale metabolic networks. BMC Systems Biology, 5(1), 81. https://doi.org/10.1186/1752-0509-5-81

Vendelin, M., Mateo, P., Soboll, S., Gillet, B., Mazet, J.-L., & Hoerter, J. A. (2010). Response to Aliev et al.: PCr and ATP Export Both Participate in Energy Transfer from Mitochondria in Normoxic Heart. Journal of Biological Chemistry, 285(52), le22. https://doi.org/10.1074/jbc.N110.147116

Illaste, A., Kalda, M., Schryer, D. W., & Sepp, M. (2010). Life of mice – development of cardiac energetics. The Journal of Physiology, 588(23), 4617–4619. https://doi.org/10.1113/jphysiol.2010.199901

Vendelin, M., Hoerter, J. A., Mateo, P., Soboll, S., Gillet, B., & Mazet, J.-L. (2010). Modulation of Energy Transfer Pathways between Mitochondria and Myofibrils by Changes in Performance of Perfused Heart. Journal of Biological Chemistry, 285(48), 37240–37250. https://doi.org/10.1074/jbc.M110.147116

Sepp, M., Vendelin, M., Vija, H., & Birkedal, R. (2010). ADP Compartmentation Analysis Reveals Coupling between Pyruvate Kinase and ATPases in Heart Muscle. Biophysical Journal, 98, 2785–2793. https://doi.org/10.1016/j.bpj.2010.03.025

Ramay, H. R., & Vendelin, M. (2009). Diffusion Restrictions Surrounding Mitochondria: A Mathematical Model of Heart Muscle Fibers. Biophysical Journal, 97(2), 443–452. https://doi.org/10.1016/j.bpj.2009.04.062

Schryer, D. W., Peterson, P., Paalme, T., & Vendelin, M. (2009). Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks. International Journal of Molecular Sciences, 10, 1697–1718. https://doi.org/10.3390/ijms10041697

Beraud, N., Pelloux, S., Usson, Y., Kuznetsov, A. V., Ronot, X., Tourneur, Y., & Saks, V. (2009). Mitochondrial dynamics in heart cells: Very low amplitude high frequency fluctuations in adult cardiomyocytes and flow motion in non beating Hl-1 cells. Journal of Bioenergetics and Biomembranes, 41(2), 195–214. https://doi.org/10.1007/s10863-009-9214-x

Birkedal, R., Christopher, J., Thistlethwaite, A., & Shiels, H. (2009). Temperature acclimation has no effect on ryanodine receptor expression or subcellular localization in rainbow trout heart. Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology, 179(8), 961–969. https://doi.org/10.1007/s00360-009-0377-x

Sokolova, N., Vendelin, M., & Birkedal, R. (2009). Intracellular diffusion restrictions in isolated cardiomyocytes from rainbow trout. BMC Cell Biology, 10(1), 90. https://doi.org/10.1186/1471-2121-10-90

Peterson, P. (2009). {F2PY}: a tool for connecting {Fortran} and {Python} programs. International Journal of Computational Science and Engineering, 4(4), 296–305. https://doi.org/10.1504/IJCSE.2009.029165

Monge, C., Beraud, N., Kuznetsov, A. V., Rostovtseva, T., Sackett, D., Schlattner, U., Vendelin, M., & Saks, V. A. (2008). Regulation of respiration in brain mitochondria and synaptosomes: restrictions of ADP diffusion in situ, roles of tubulin, and mitochondrial creatine kinase. Molecular and Cellular Biochemistry, 318(1–2), 147–165. https://doi.org/10.1007/s11010-008-9865-7

Vendelin, M., & Birkedal, R. (2008). Anisotropic Diffusion of Fluorescently Labeled ATP in Rat Cardiomyocytes Determined by Raster Image Correlation Spectroscopy. American Journal of Physiology - Cell Physiology, 295(5), C1302–C1315. https://doi.org/10.1152/ajpcell.00313.2008

Saks, V., Kaambre, T., Guzun, R., Anmann, T., Sikk, P., Schlattner, U., Wallimann, T., Aliev, M., & Vendelin, M. (2007). The creatine kinase phosphotransfer network: thermodynamic and kinetic considerations, the impact of the mitochondrial outer membrane and modelling approaches. Sub-Cellular Biochemistry, 46, 27–65.

Beard, D. A., & Vendelin, M. (2006). Systems Biology of the Mitochondrion. American Journal of Physiology - Cell Physiology, 291(6), C1101–C1103. https://doi.org/10.1152/ajpcell.00481.2006

Birkedal, R., Shiels, H. A., & Vendelin, M. (2006). Three-Dimensional Mitochondrial Arrangement in Ventricular Myocytes: From Chaos to Order. American Journal of Physiology - Cell Physiology, 291(6), C1148–C1158. https://doi.org/10.1152/ajpcell.00236.2006

Saks, V., Dzeja, P., Schlattner, U., Vendelin, M., Terzic, A., & Wallimann, T. (2006). Cardiac System Bioenergetics: Metabolic Basis of the Frank-Starling Law. The Journal of Physiology, 571(2), 253–273. https://doi.org/10.1113/jphysiol.2005.101444

Guerrero, K., Wuyam, B., Mezin, P., Vivodtzev, I., Vendelin, M., Borel, J.-C., Hacini, R., Chavanon, O., Imbeaud, S., Saks, V., & Pison, C. (2005). Functional Coupling of Adenine Nucleotide Translocase and Mitochondrial Creatine Kinase Is Enhanced After Exercise Training in Lung Transplant Skeletal Muscle. American Journal of Physiology - Regulatory, Integrative and Comparative Physiology, 289(4), R1144–R1154. https://doi.org/10.1152/ajpregu.00229.2005

Saks, V. A., Vendelin, M., Aliev, M. K., Kekelidze, T., & Engelbrecht, J. (2007). 8.1 Mechanisms and Modeling of Energy Transfer Between Intracellular Compartments. In A. Lajtha, G. E. Gibson, & G. A. Dienel (Eds.), Handbook of Neurochemistry and Molecular Neurobiology (pp. 815–860). Springer US. http://link.springer.com/referenceworkentry/10.1007/978-0-387-30411-3_30

Saks, V., Dzeja, P. P., Guzun, R., Aliev, M. K., Vendelin, M., Terzic, A., & Wallimann, T. (2007). System Analysis of Cardiac Energetics–Excitation–Contraction Coupling: Integration of Mitochondrial Respiration, Phosphotransfer Pathways, Metabolic Pacing, and Substrate Supply in the Heart. In V. Saks (Ed.), Molecular System Bioenergetics (pp. 367–405). Wiley-VCH Verlag GmbH & Co. KGaA. http://onlinelibrary.wiley.com/doi/10.1002/9783527621095.ch11/summary

Engelbrecht, J., & Vendelin, M. (2006). Mathematical Modelling of Cardiac Mechanoenergetics. In P. G. A. Holzapfel & P. R. W. Ogden (Eds.), Mechanics of Biological Tissue (pp. 369–378). Springer Berlin Heidelberg. http://link.springer.com/chapter/10.1007/3-540-31184-X_26

Vendelin, M., Bovendeerd, P. H. M., Saks, V., Engelbrecht, J., & Arts, T. (2003). Simulating Cardiac Mechanoenergetics in the Left Ventricle. In I. E. Magnin, J. Montagnat, P. Clarysse, J. Nenonen, & T. Katila (Eds.), Functional Imaging and Modeling of the Heart (pp. 72–80). Springer Berlin Heidelberg. http://link.springer.com/chapter/10.1007/3-540-44883-7_8