Intranet Campus web

Laboratory of Biomathematics

Laboratory of Biomathematics

The Laboratory of Biomathematics is active in fields of Bioimaging and Image Analysis.

Bioimaging and Image Analysis

The laboratory 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

  • Diabetic structural changes in capillary network and connective tissue
  • Quantification of isolated pancreatic islets

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

Projects

Achievements

Publications

Novotný; T. - Eckhardt; Adam - Doubková; Martina - Knitlová; Jarmila - Vondrášek; David - Vanaskova; E. - Ošťádal; M. - Uhlík; J. - Bačáková; Lucie - Musílková; Jana . The possible role of hypoxia in the affected tissue of relapsed clubfoot . Scientific Reports. 2022; 12(1)); 4462 . IF = 4.996 [ASEP] [ doi ]
Ďúranová; H. - Valková; V. - Olexiková; L. - Radochová; Barbora - Balazi; A. - Chrenek; P. - Vašíček; J. Rabbit Endothelial Progenitor Cells Derived From Peripheral Blood and Bone Marrow: An Ultrastructural Comparative Study . Microscopy and Microanalysis. 2022; 28(3); 756-766 . IF = 4.099 [ASEP] [ doi ]
Bačáková; Lucie - Novotná; Katarína - Hadraba; Daniel - Musílková; Jana - Slepička; P. - Beran; M. Influence of Biomimetically Mineralized Collagen Scaffolds on Bone Cell Proliferation and Immune Activation . Polymers. 2022; 14(3)); 602 . IF = 4.967 [ASEP] [ doi ]
Abbondanza; Alice - Bas; Irina Ribeiro - Modrák; Martin - Čapek; Martin - Minich; Jessica - Tyshkevich; Alexandra - Naser; Shahed - Rangotis; Revan - Houdek; Pavel - Sumová; Alena - Dumas; S. - Bernard; V. - Janíčková; Helena . Nicotinic Acetylcholine Receptors Expressed by Striatal Interneurons Inhibit Striatal Activity and Control Striatal-Dependent Behaviors . Journal of Neuroscience. 2022; 42(13); 2786-2803 . IF = 6.709 [ASEP] [ doi ]
Umek; N. - Janáček; Jiří - Cvetko; E. - Eržen; I. Horizontal deformation of skeletal muscle thick sections visualised by confocal microscopy . Journal of Microscopy. 2021; 282(2); 113-122 . IF = 1.952 [ASEP] [ doi ]
Skalický; D. - Koucký; V. - Hadraba; Daniel - Vítězník; M. - Dub; M. - Lopot; F. Detection of Respiratory Phases in a Breath Sound and Their Subsequent Utilization in a Diagnosis . Applied Sciences-Basel. 2021; 11(14)); 6535 . IF = 2.838 [ASEP] [ doi ]
Lopot; F. - Dub; M. - Flek; J. - Hadraba; Daniel - Havlíček; M. - Kučera; L. - Štoček; O. - Veselý; T. - Janáček; Jiří . Gearbox Mechanical Efficiency Determination by Strain Gauges Direct Application . Applied Sciences-Basel. 2021; 11(23)); 11150 . IF = 2.838 [ASEP] [ doi ]
Knitlová; Jarmila - Doubková; Martina - Plencner; Martin - Vondrášek; David - Eckhardt; Adam - Ošťádal; M. - Musílková; Jana - Bačáková; Lucie - Novotný; T. Minoxidil decreases collagen I deposition and tissue-like contraction in clubfoot-derived cells: a way to improve conservative treatment of relapsed clubfoot? . Connective Tissue Research. 2021; 62(5); 554-569 . IF = 3.342 [ASEP] [ doi ]
Jerman; A. - Janáček; Jiří - Snoj; Ž. - Umek; N. QUANTIFICATION OF THE INTERVENTIONAL APPROACHES INTO THE PTERYGOPALATINE FOSSA BY SOLID ANGLES USING VIRTUAL REALITY . Image Analysis and Stereology. 2021; 40(2); 63-69 . IF = 0.683 [ASEP] [ doi ]
Filová; Elena - Steinerová; Marie - Trávníčková; Martina - Knitlová; Jarmila - Musílková; Jana - Eckhardt; Adam - Hadraba; Daniel - Matějka; Roman - Pražák; Šimon - Štěpanovská; Jana - Kučerová; Johanka - Riedel; Tomáš - Brynda; Eduard - Lodererová; A. - Honsová; E. - Pirk; J. - Koňařík; M. - Bačáková; Lucie . Accelerated in vitro recellularization of decellularized porcine pericardium for cardiovascular grafts . Biomedical Materials. 2021; 16(2)); 025024 . IF = 4.103 [ASEP] [ doi ]
Čapek; Martin - Blažíková; M. - Novotný; I. - Chmelová; H. - Svoboda; D. - Radochová; Barbora - Janáček; Jiří - Horváth; O. THE WAVELET-BASED DENOISING OF IMAGES IN FIJI; WITH EXAMPLE APPLICATIONS IN STRUCTURED ILLUMINATION MICROSCOPY . Image Analysis and Stereology. 2021; 40(1); 3-16 . IF = 0.683 [ASEP] [ doi ]
Čaja; Fabian - Stakheev; Dmitry - Chernyavskiy; Oleksandr - Kubínová; Lucie - Křižan; Jiří - Dvořák; Jiří - Rossmann; Pavel - Štěpánková; Renata - Makovicky; Pe. - Makovicky; Pa. - Vymetálková; Veronika - Souček; P. - Vodička; Pavel - Vodičková; Ludmila - Levý; M. - Vannucci; Luca . Local Immune Changes in Early Stages of Inflammation and Carcinogenesis Correlate with the Collagen Scaffold Changes of the Colon Mucosa . Cancers (Basel). 2021; 13(10)); 2463 . IF = 6.575 [ASEP] [ doi ]
Čaja; Fabian - Stakheev; Dmitry - Chernyavskiy; Oleksandr - Křižan; Jiří - Dvořák; Jiří - Rossmann; Pavel - Štěpánková; Renata - Makovický; Peter - Makovický; P. - Kozáková; Hana - Vannucci; Luca . Immune activation by microbiome shapes the colon mucosa: Comparison between healthy rat mucosa under conventional and germ-free conditions . Journal of Immunotoxicology. 2021; 18(1); 37-49 . IF = 3.439 [ASEP] [ doi ]
Vošahlíková; Miroslava - Roubalová; Lenka - Cechová; Kristína - Kaufman; Jonáš - Musil; Stanislav - Mikšík; Ivan - Alda; M. - Svoboda; Petr . Na+/K+-ATPase and lipid peroxidation in forebrain cortex and hippocampus of sleep-deprived rats treated with therapeutic lithium concentration for different periods of time . Progress in Neuro-Psychopharmacology & Biological Psychiatry. 2020; 102(Aug 30)); 109953 . IF = 5.067 [ASEP] [ doi ]
Ujčíková; Hana - Cechová; Kristína - Roubalová; Lenka - Brejchová; Jana - Kaufman; Jonáš - Holáň; Vladimír - Svoboda; Petr . The high-resolution proteomic analysis of protein composition of rat spleen lymphocytes stimulated by Concanavalin A; a comparison with morphine-treated cells . Journal of Neuroimmunology. 2020; 341(Apr 15)); 577191 . IF = 3.478 [ASEP] [ doi ]
Ujčíková; Hana - Cechová; Kristína - Jágr; Michal - Roubalová; Lenka - Vošahlíková; Miroslava - Svoboda; Petr . Proteomic analysis of protein composition of rat hippocampus exposed to morphine for 10 days; comparison with animals after 20 days of morphine withdrawal . PLoS ONE. 2020; 15(4)); e0231721 . IF = 3.240 [ASEP] [ doi ]
Pajorová; Julia - Skogberg; A. - Hadraba; Daniel - Brož; Antonín - Trávníčková; Martina - Zikmundová; Markéta - Honkanen; M. - Hannula; M. - Lahtinen; P. - Tomková; M. - Bačáková; Lucie - Kallio; P. Cellulose Mesh with Charged Nanocellulose Coatings as a Promising Carrier of Skin and Stem Cells for Regenerative Applications . Biomacromolecules. 2020; 21(12); 4857-4870 . IF = 6.988 [ASEP] [ doi ]
Musílková; Jana - Filová; Elena - Pala; J. - Matějka; Roman - Hadraba; Daniel - Vondrášek; David - Kaplan; Ondřej - Riedel; Tomáš - Brynda; Eduard - Kučerová; Johanka - Koňařík; M. - Lopot; F. - Pirk; J. - Bačáková; Lucie . Human decellularized and crosslinked pericardium coated with bioactive molecular assemblies . Biomedical Materials. 2020; 15(1)); 015008 . IF = 3.715 [ASEP] [ doi ]
Havelka; Daniel - Chafai; Djamel Eddine - Krivosudský; Ondrej - Klebanovych; Anastasiya - Vostárek; František - Kubínová; Lucie - Dráber; Pavel - Cifra; Michal . Nanosecond Pulsed Electric Field Lab-on-Chip Integrated in Super-Resolution Microscope for Cytoskeleton Imaging . Advanced Materials Technologies. 2020; 5(3)); 1900669 . IF = 7.848 [ASEP] [ doi ]
Filová; Elena - Staňková; Ľubica - Eckhardt; Adam - Svobodová; Jana - Musílková; Jana - Pala; J. - Hadraba; Daniel - Brynda; Eduard - Koňařík; M. - Pirk; J. - Bačáková; Lucie . Modification of Human Pericardium by Chemical Crosslinking . Physiological Research. 2020; 69(1); 49-59 . IF = 1.881 [ASEP] [ doi ]

Article photogallery

The entire photogallery

People

RNDr. Jiří Janáček, PhD.
Head of the Laboratory
Ing. Martin Čapek, PhD.
Senior Researcher (part-time)
RNDr. Barbora Radochová, PhD.
Senior Researcher
Ing. Mgr. Daniel Hadraba, Ph.D.
Postdoctoral Researcher
 

Mgr. David Kala

PhD Student

Mgr. David Vondrášek

Technician

Mgr. Zuzana Kubínová

Technician

Ing. Jitka Čočková
Project Manager
 

Davide Basello

Research Assistant