From cellular structure to muscle function

We combine advanced microscopy, quantitative experiments, and mechanistic models to study muscle physiology from molecules to the beating heart.

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Welcome to the Laboratory of Systems Biology

The Laboratory of Systems Biology is a part of the Department of Cybernetics, School of Science, Tallinn University of Technology.

Aim

The main aim of the laboratory is to study the regulation of intracellular processes and understand the functional effects of intracellular interactions. For this, a mixture of experimental and theoretical approaches is used.

Specific Scientific Interests, Projects

  • Intracellular compartmentation and diffusion restrictions and their influence on bioenergetics.
  • How does the fine structure of mitochondria influence the dynamics of oxidative phosphorylation?
  • Regulation of energy transfer in different types of cells.
  • Metabolic stability of heart muscle cells.
  • Interaction between mechanics and energetics of the heart.

Approach

We use interdisciplinary approaches to tackle questions in cardiac physiology. For that, we have formed a team of researchers with backgrounds in biophysics, biology, and applied mathematics/physics. As a result, we are able to approach scientific questions on different scales, from organ to molecular level, using combinations of different experimental and theoretical techniques. When needed, we find new ways to characterize the data, develop new mathematical models, build new hardware and program it to carry out novel experimental protocols. For example, we have developed mitochondrial positioning analysis in 2D and 3D, and built a confocal microscope to study diffusion in the cell. Among the experimental techniques routinely used in the laboratory are

  • kinetic measurements,
  • fluorescence correlation spectroscopy-based techniques,
  • confocal, super-resolution, TIRF, and wide-field fluorescence imaging,
  • controlled single-cell force measurements,
  • electrophysiology and patch-clamp recording.

We have developed models

  • to study energetics and mechanics of the left ventricle as well as intracellular diffusion using finite element method,
  • to solve partial differential equations to analyze cross-bridge mechanoenergetics,
  • to use molecular dynamics to analyze interactions between proteins and the mitochondrial membrane,
  • designed multiple other models and computational techniques to analyze the experimental data.

The results of our work are distributed through publications and the open-source software that we develop.

Keywords

General and specific keywords describing our research interests and methods: keywords.

Networks

The laboratory participates in the following research networks:

Support

Research in the laboratory is financed by

  • Estonian Research Council [ETAg, 2023-2027, PSG832]
  • We participate in the following projects on Estonia's research infrastructure roadmap:

Previous funding:

Students

See the list of proposed student topics under Positions.