BioMediTech Research Groups

Computational Biophysics and Imaging Group (CBIG)

Group Leader: Professor Jari Hyttinen

jari.hyttinen(at)tut.fi

About Us

The group consists of one senior researcher (Dr. Jarno Tanskanen), two post docs, thirteen PhD students, and some graduate and undergraduate students. In addition, the group works in close collaboration with the research group of Adjunct Professor Soile Nymark.

We are part of BioMediTech’s Human Spare Part programme: http://humanspareparts.fi/

Research interests and expertise

The main expertise areas at CBIG are development of bioimaging, analysis and biophysics based in-silico tools for new personalized treatments, diagnostics and drug discoveries especially those enabled by the stem cell research. We are particularly interested in understanding the biophysics in vitro and in vivo – especially electrophysiology – of cells and tissues during cell differentiation and maturation, and their function. We search for new 3D imaging methods and analysis approaches to assess biological systems to observe microscale biomaterial structures, analyse cell seeding and function in 3D biomaterials, and to establish new 3D histological tools.

Our current main research topics are: Analysis of electrical signalling and processes in neuronal networks to develop bidirectional ICT biohybrids by connecting microelectrode arrays (MEAs) with living cells; Integrating MEA electrophysiology with image based mechanical deformation analysis and in silico models to develop future personized diagnostic platforms e.g. for cardiomyocytes; Bone cell adaptation due to mechanical loading to improve cell differentiation and bone formation; Epithelial transport function and electrophysiology to understand epithelial barrier function and its control; and multiphysical imaging development. The research covers the basic research on the topic as well as applied research to develop methods for diagnosis and drug development including imaging, measurements and in silico models.

Current research projects include Tekes funded large BioMediTech collaboration Human Spare Part program (2014-2018), Academy of Finland funded project on imaging, assessment and modelling of epithelia (2016-2020), development of novel 3D multiphysical bioimaging funded by Jane and Aatos Erkko Foundation (2017-2019), development of electric imaging of stroke also funded by Erkko Foundation (2017-2020). An example of our past projects includes the EU FET-open project 3DneuroN that the group coordinated.

Achievements

We have developed:

  • Tools for in vitro assessment of cell responses for e.g. drug testing. These include various new tools for analysis of cardiomyocyte beating using MEA signaling and video based assessment.
  • A set of tools for neuronal network analysis from detection of bursting and connectivity to complex systems analysis tools and used them for in vitro networks and analysis of higher order brain functions and epilepsy.
  • In silico methods for the first hIPSC in silico models of control and some pathological cell lines and used them for assessment of drugs.
  • Novel imaging and image analysis methods to assess various biomaterials and tissue-engineered structures including use of nanomaterial in X-ray µCT imaging and optical methods for hydrogel assessment.

Infrastructure

CBIG co-operates and hosts some of the BioMediTech infrastructures, these include hosting the X-ray CT microscope facility with Zeiss-Xradia XCT 4000 µCT, 3D optical imaging with in-house build optical projection tomography (OPT) and selectrive plane illumination microscopes (SPIM) co-operation of the Electrophysiology laboratory with two Patch-Clam, CA2+ imaging systems, several multielelectrode array (MEA) systems including CMOS based MEA with over 4000 electrodes.

Collaboration offer and requests

We can offer expertise on bioelectric measurements, and analysis including electrophysiological and bioimpedance assessment of cells and tissues, X-ray, optical and electric impedance bioimaging. Further, we have expertise on in-silico simulation and image and data analysis of various biological and physiological systems. Our special interests include cardiomyocytes and heart, neuronal networks and brain and epithelia functions.

We are interested on participating projects and consortium where we can use and deepen our expertise for better understanding the biology, and to develop novel precision medicine.

Major Publications

  1. Soto A, Koivisto J, Parrag J, Silva-Correia J, Oliveira J, Reis R, Kellomäki M, Hyttinen J, Figueiras E. Optical projection tomography technique for image texture and mass transport studies in hydrogels based on gellan gum. Langmuir 2016, 32.20: 5173-5182.
  2. Kapucu F, Vornanen I, Mikkonen J, Leone C, Lenk K, Tanskanen J, Hyttinen J. Spectral entropy based neuronal network synchronicity analysis based on microelectrode array measurements. Frontiers in Computational Neuroscience, 2016, 10
  3. Paci M, Hyttinen J, Rodriguez B, Severi S. Human induced pluripotent stem cell‐derived versus adult cardiomyocytes: an in silico electrophysiological study on ionic current block effects. British journal of pharmacology. 2015, 172.21: 5147-5160.
  4. Subramaniyam N, Hyttinen J. Dynamics of intracranial electroencephalographic recordings from epilepsy patients using univariate and bivariate recurrence networks. Physical Review E, 91(2), 022927. 2015
  5. Tervonen A, Vainio I, Nymark S, Hyttinen J. 2014. Prediction of Passive Drug Permeability Across the Blood-Retinal Barrier. Pharmaceutical Research vol. 31, num. 9, 2297-2311. http://dx.doi.org/10.1007/s11095-014-1325-3
© 2018 | BioMediTech Finland. All rights reserved.