The Department of Biomathematics consists of two research groups: (1) Bioimaging and Image Analysis, and (2) Biochemistry of Membrane Receptors. Operating mainly at in situ and in vitro levels, respectively, the two groups complement each other when studying phenomena confined to the cell membrane.
1. Bioimaging and Image Analysis
The group conducts research into the 3D microanatomical aspects of physiological phenomena at mesoscopic, microscopic and ultrastructural level. It is engaged in a range of collaborative projects across the campus and beyond. If interested please contact us (jiri.janacek@fgu.cas.cz).
CURRENTLY FUNDED PROJECTS
- Brain development in birds, as relevant to the ability to fly
- The conduction system of developing murine heart
LONG-TERM PROJECTS
- Development of 3D image analysis and stereological methods including software (employed, e.g., in a volumetric analysis of Langerhans islets from human donors)
- Microscopic optical-contrasting (label-free) strategies to visualize living cells and tissues
OTHER PROJECTS (selection only)
- Effects of ionizing radiation on blood capillaries network
- Effects of elevated CO2 on the photosynthetic apparatus’ performance and ultrastructure
- Mechanisms governing the formation of extracellular matrix proteins (collagen and elastin)
IN-HOUSE IMAGING MODALITIES
- Laser scanning confocal microscopy
- Two-photon excitation microscopy
- Second harmonic generation (SHG) microscopy
- ‘White-light‘ laser and hybrid detectors (on Leica TCS SP8 WLL MP microscope)
- FRAP recording, FRET analysis, FLIM/PLIM recording including λ2 scans
- Optical projection tomography (OPT)
- Selective plane illumination (light sheet) microscopy (SPIM)
- Phase-, modulation- and interference contrast microscopy
AVAILABLE SOFTWARE AND PROTOCOLS
- Software for 3D image analysis, stereology, spatial statistics and deconvolution (Hyughens)
- Optical/chemical clearing protocols for OPT and SPIM
OPEN ACCESS TO EQUIPMENT
The group is part of the Czech BioImaging infrastructure [1] supporting open access to most of its microscopes (listed above), and implicitly also to its expertise. The portfolio includes, among other imaging equipment located at other departments, a Nipkow spinning-disk (“Carv II“) confocal microscope [2].
[1] http://www.czech-bioimaging.cz/
[2] http://www.fgu.cas.cz/en/articles/529-czech-bioimaging-2016-2019
(click on this heading to open a detailed laboratory website)
Projects
We use 3D imaging and optical mapping to analyze the cardiac conduction system and its development in mice.
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Using high-resolution imaging and geometric morphology, we study the relation between brain anatomy and capability of flying in birds.
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By appropriately modifying microscope’s optical path, unstained living cells can be optically contrasted at negligible cost.
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Achievements
Diffraction phenomena governing image formation in the microscope were employed to improve the performance of phase-contrast microscopy.
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Langerhans islets' volume measurements using optical projection tomography and the Fakir method
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Magnetic resonance and computed tomography study of avian brain compartments' volumes measured by our Fakir probe revealed sexual dimorpism in pheasant brains.
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A review article on confocal stereology comprising innovative methods invented at the Department of Biomathematics
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Publications
Vošahlíková, Miroslava - Svoboda, Petr
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Lithium - therapeutic tool endowed with multiple beneficiary effects caused by multiple mechanisms
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Acta Neurobiologiae Experimentalis. 2016, roč. 76, 1, p. 1-19
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IF = 1.708
[ASEP]
Tonar, Z. - Tomášek, P. - Loskot, P. - Janáček, Jiří - Králíčková, M. - Witter, K.
Vasa vasorum in the tunica media and tunica adventitia of the porcine aorta
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Annals of Anatomy-Anatomischer Anzeiger. 2016, roč. 205, 2016, p. 22-36
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IF = 1.308
[ASEP]
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doi
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Sládková, J. - Spáčilová, J. - Čapek, Martin - Tesařová, M. - Hansíková, H. - Honzík, T. - Martínek, J. - Zámečník, J. - Kostková, O. - Zeman, J.
Analysis of Mitochondrial Network Morphology in Cultured Myoblasts from Patients with Mitochondrial Disorders
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Ultrastructural Pathology. 2015, Vol. 39, 5, p. 340-350
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IF = 0.828
[ASEP]
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doi
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Jirák, D. - Janáček, Jiří - Kear, B. P.
A combined MR and CT study for precise quantitative analysis of the avian brain
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Scientific Reports. 2015, Vol. 5, Oct 30, p. 16002
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IF = 5.228
[ASEP]
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doi
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Roubalová, Lenka - Vošahlíková, Miroslava - Brejchová, Jana - Sýkora, Jan - Rudajev, Vladimír - Svoboda, Petr
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High Efficacy but Low Potency of delta-Opioid Receptor-G Protein Coupling in Brij-58-Treated, Low-Density Plasma Membrane Fragments
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PLoS ONE. 2015, Vol. 10, 8, e0135664
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IF = 3.057
[ASEP]
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doi
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Fernandez, V. - Buffetaut, E. - Suteethorn, V. - Rage, J. C. - Tafforeau, P. - Kundrát, Martin
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Evidence of Egg Diversity in Squamate Evolution from Cretaceous Anguimorph Embryos
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PLoS ONE. 2015, Vol. 10, 7, e0128610
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IF = 3.057
[ASEP]
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doi
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Wilhelm, Jiří - Ivica, Josko - Veselská, Zdeňka - Uhlík, Jiří - Vajner, Luděk
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Changes in the composition of fatty acids and lipofuscin-like pigments during development of rat heart
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Physiological Research. 2015, Vol. 64, 5, p. 643-651
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IF = 1.618
[ASEP]
Michálek, Jan
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Total Variation-Based Reduction of Streak Artifacts, Ring Artifacts and Noise in 3D Reconstruction from Optical Projection Tomography
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Microscopy and Microanalysis. 2015, Vol. 21, 6, p. 1602-1615
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IF = 1.73
[ASEP]
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doi
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Kubínová, Lucie - Janáček, Jiří
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Confocal stereology: an efficient tool for measurement of microscopic structures
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Cell and Tissue Research. 2015, Vol. 360, 1, p. 13-28
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IF = 2.948
[ASEP]
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doi
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Brejchová, Jana - Sýkora, Jan - Ostašov, Pavel - Merta, Ladislav - Roubalová, Lenka - Janáček, Jiří - Hof, Martin - Svoboda, Petr
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TRH-receptor mobility and function in intact and cholesterol-depleted plasma membrane of HEK293 cells stably expressing TRH-R-eGFP
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Biochimica Et Biophysica Acta-Biomembranes. 2015, Vol. 1848, 3, p. 781-796
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IF = 3.687
[ASEP]
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doi
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