Positions

We are looking for postdoctoral fellows, PhD, MSc, and BSc students to join our team. For MSc and BSc students, early start is recommended as we work in an exciting interdisciplinary subjects that may require learning different techniques and looking into physiology of the heart from several angles. See below the list of the proposed topics.

At present, the candidates for postdoctoral and other senior positions would have to apply for grants to finance their positions.

Please contact Marko Vendelin for further details.

Positions for PhD students

PhD students positions are advertised through University. See the call on our page with the links to the official announcements.

Topics for BSc and MSc students

As the laboratory is interdisciplinary, we welcome students with different backgrounds, such as biology, chemistry, gene technology, physics, and IT.

The topics are given as a short outline and would be discussed and agreed upon with each candidate separately, depending on the interests and skills. The list will be updated in time and feel free to show interest in any other topic within our expertise.

Unraveling the signaling pathways linking muscle energetics to phenotype.

Creatine kinase is important for energy transfer in muscle cells. Creatine-deficient mice exhibit changes in muscle metabolism and thus overall phenotype. This project aims at understanding the signaling pathways through which energetics affect the muscle phenotype.

How substrates affect mitochondrial function and regulation

The heart is considered a “metabolic omnivore”. This means that the heart in vivo uses a variety of substrates to fuel the production of ATP. This project addresses how different substrates affect mitochondrial function and regulation.

How mechanical contraction affects energetics in single cardiomyocytes

In the heart, electrical stimulation triggers contraction of cardiomyocytes. Using state-of-the-art techniques, we are able to measure the contractile force and determine how it varies under different conditions on single cardiomyocyte. This project addresses how changes in the stimulation and mechanics affects energetics of the cell.

Calcium fluxes in cardiomyocytes

The contraction of the heart is regulated by multiple factors. Among other things, it is shaped by the calcium transient inside the cell. In this project, you will use a combination of electrophysiology and fluorescence microscopy to determine how the calcium fluxes are affected by different conditions.

Intracellular molecular movement

Within this topic, you will study how molecules move within the heart muscle cell. There are indications that the movement of the molecules is severely restricted in the heart muscle cell. The physical basis for that is not fully understood and is the aim of this research topic. Here, you will participate in the development of new methods based on fluorescence correlation spectroscopy. So far, we have built our own microscopes and designed new approaches to analyze the measured data. You will be able to work on the experimental parts of the study and data analysis.

Example studies using raster image correlation spectroscopy and mitochondrial response.

Processing of microscopy images

Optical microscopy is a tool frequently used to study live cells. When compared with the other microscopy methods, it has an advantage of being able to follow the cell while it is alive, allowing us to study the cell response to different stimuli. However, the resolution due to diffraction, noise due to the photon detection both impact the imaging. Within this topic, you will work on development of approaches to enhance resolution and signal to noise of the recorded images.

Paper on deconvolution and corresponding software.

Mathematical modeling of the heart

Within this topic, you are expected to work on the state of the art mathematical models of cardiac function. Our earlier models include models of reaction-diffusion describing cardiac energetics, models of cardiac force generation, models of mitochondrial respiration, molecular dynamics model of proteins on the mitochondrial membrane, heart ventricle contraction, and energy consumption models.

Example models of cardiac contraction and molecular dynamics simulations.

Standards-based export of laboratory database data

We have developed database-oriented approach in the several software packages used to analyze experimental data. Within this topic, you would work on establishing or applying available software for export of the data from the laboratory database to external open databases. The export would have to take care of describing the data and adjusting it using the standards-based approaches.

Primary data analysis software: Kinetics and Sparks.

Software for gel analysis

We want to improve analysis of gels, such as used to determine protein expression via Western Blotting, by writing a new software for it. Current tools are lacking ease of use or integration with the laboratory databases. In this project, you would write new user friendly tools that would help to analyze measurements on gels and integrate them with the data analysis workflow. It requires writing cross-platform GUI for gel analysis and generalize available data analysis scripts for statistics. We expect a major impact and adoption by many labs when such software will be made available.

Primary data analysis software: Kinetics and Sparks.