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Department of Biological Dynamics

Navigation: >> Institute of Systems Biology and Ecology >> Division of Physical Biology >> Department of Biological Dynamics

Research Units

Workgroup of Mathematical Biology
Laboratory of Physiology and Ecology
Laboratory of Cell Biology
Leader
Dr. Ladislav Nedbal
Phone: +420 386361231
Fax: +420 386361231
nedbal@nh.usbe.cas.cz
www.usbe.cas.cz

Address
Zámek 136, 37333 Nové Hrady, Czech Republic
How to reach us
Secretary
Daniela Kříhová
Phone: +420 389033806
Fax: +420 386361279
krihova@nh.usbe.cas.cz

Research

Our roots go back to sixties of the last century, to Ivan Šetlík and his colleagues studying algal physiology and biotechnology in nearby Třeboň. Photosynthesis has been one of the key focuses because of its physiological, ecological and biotechnological importance. Also, multi-disciplinarity, novel methods and development of original instrumentation (PSI) have been the hallmarks of our research since the early days. Results from our department contributed to understanding of the physiological role of cytb559 in photoprotection, to understanding of the role of mycosporine-like amino acids in protection of algae against UV-B radiation, to constructing of numerous original instruments and methods and to identification of new, information-rich chlorophyll fluorescence transient in harmonically modulated irradiance. With support of the Academy of Sciences ČR, in collaboration with the University of S.Bohemia and with inspiration from Avigdor Scherz of Weizmann Institute of Science and Hugo Scheer of Ludwig Maxmillian University, we were the first pioneer lab starting research in Academic and University Center, Nové Hrady in 2000. We organized in Nové Hrady the first international meeting „Kinetic Fluorescence Imaging of Plants 2002“, laying foundations to the present AUC Conference Center. Ladislav Nedbal is, with Martin Trtílek, co-founder of Photon Systems Instruments, spol. s r.o. We designed and initiated Schola ludus project for undergraduate and graduate students in 2002. We were co-founders of Graduate College of Biophysics in Nove Hrady.

Current Research Projects:

  • 2009-2013, GA206/09/1284 Cyanobacterial cell factory: Modeling and experimental validation of models of photosynthetic energy conversion, of growth, and of
    production. Grantová agentura České republiky (    GA ČR)
  • 2007-2012 European Science Foundation (ESF) Research Networking Programme „Functional dynamics in Complex Chemical and Biological Systems“ funcdyn.org (Nedbal)
  • 2007-2009, GAČR (Komárek, 40/3917)
  • 2007-2012, FP6-2005-Life Sciences, Genomics and Biotechnology for Health / Specific Targeted Research Project (Nedbal, ): AUTOSCREEN for cell based high-throughput and high-contentgene function analysis and drug discovery screens.
  • 2006- , NPVII (Soukupová, 30/4010)
  • 2005- , výzkumný záměr ÚSBE AV0Z60870520
  • 2005- , výzkumný záměr ÚFB JcU MSM6007665808

Links

www.psi.cz

www.e-photosynthesis.org

book.e-photosynthesis.org


References 2005-2009

Jan Červený and Ladislav Nedbal (2009) Metabolic rhythms of the cyanobacterium Cyanothece sp. ATCC 51142 correlate with modeled dynamics of circadian clock. J Biol Rhythms 24(4):9

Jan Červený, Ivan Šetlík, Martin Trtílek and Ladislav Nedbal (2009) Photobioreactor for cultivation and real-time, in-situ measurement of O2 and CO2 exchange rates, growth dynamics, and of chlorophyll fluorescence emission of photoautotrophic microorganisms. Eng Life Sci 9(3):7

Ladislav Nedbal, Martin Trtílek, Jan Červený, Ondřej Komárek and Himadri Pakrasi (2008) A photobioreactor system for precision cultivation of photoautotrophic microorganisms and for high-content analysis of suspension dynamics. Biotechnol Bioeng 100(5):902-910

Julie Soukupová, Ladislav Csefalvay, Otmar Urban, Martina Košvancová, Michal Marek, Uwe Rascher and Ladislav Nedbal (2008) Annual variation of the steady-state chlorophyll fluorescence emission of evergreen plants in temperate zone. Functional Plant Biology: 35, 1–14

Ladislav Nedbal, Jan Červený, Uwe Rascher, and Henning Schmidt (2007) E-photosynthesis: A modeling approach to understand chlorophyll fluorescence transients and complex dynamic features of photosynthesis in fluctuating light. Photosynth.Res. 93: 223-234

Aleš Holoubek, Jaroslav Večeř, Karel Sigler (2007) Monitoring of the Proton Electrochemical Gradient in Reconstituted Vesicles: Quantitative Measurements of Both Transmembrane Potential and Intravesicular pH by Ratiometric Fluorescent Probes. J Fluorescence. 17 (2): 201-213

Vácha, F., V. Sarafis, Z. Benediktyová, L. Bumba, J. Valenta, M. Vácha, Ch.-R. Sheue and L.Nedbal (2007) Identification of Photosystem I and Photosystem II enriched regions of thylakoid membrane by optical microimaging of cryo-fluorescence emission spectra and of variable fluorescence. Micron 38: 170-175.

Kumud Mishra and Ram Gopal (2007) Detection of nickel - induced stress using laser-induced fluorescence signatures from leaves of wheat seedlings. Internatl. J Remote Sens. Accepted.

Susanne Berger, Zuzana Benediktyová, Karel Matouš, Katharina Bonfig, Martin J. Mueller, Ladislav Nedbal, Thomas Roitsch (2006) Visualization of dynamics of plant-pathogen interaction by novel combination of chlorophyll fluorescence imaging and statistical analysis: Differential effects of virulent and avirulent strains of P. syringae and of oxylipins on A. thaliana (2007) J.Exp.Botany. 58 (4): 797-806.

Uwe Rascher and Ladislav Nedbal (2006) Dynamics of plant photosynthesis in fluctuating light. Curr.Opinion Plant Biol. 9: 671-678.

Karel Matous; Zuzana Benediktyova; Susanne Berger; Thomas Roitsch; Ladislav Nedbal (2006) Case study of combinatorial imaging: What protocol and what chlorophyll fluorescence image to use when visualizing infection of Arabidopsis thaliana by Pseudomonas syringae? Photosynth. Res. 90 (3): 243-253

Nedbal L. and Koblížek M. (2006) Chlorophyll fluorescence as a reporter on in vivo electron transport and regulation in plants. In: “Biochemistry and Biophysics of Chlorophylls” (Eds: B. Grimm, R. Porra, W. Rüdiger, H. Scheer), pp.507-519, Springer. ISBN 1-4020-4515-8.

Žabka, M., Drastichová, K., Jegorov, A., Soukupová, J. and Nedbal, L. (2006) Direct evidence of plant-pathogenic activity of fungal metabolites of Trichothecium roseum on apple. Mycopathologia 162 (1) 65-68.

Adamec, F., Kaftan, D. and Nedbal, L. (2005) Stress-induced filament fragmentation of Calothrix elenkinii (CYANOPHYCEAE) is facilitated by death of high-fluorescence cells. J.Phycology 41 (4): 835-839

Nedbal,L., Březina,V, Červený, J. and Trtílek, M. (2005) Photosynthesis in dynamic light: Systems biology of unconventional chlorophyll fluorescence transients in Synechocystis sp. PCC6803. Photosynth.Res. 84: 99–106

Nedbal, L., Marek, M. and Trtilek, M. (2005) Remote sensing of vegetation fluorescence can yield estimates of sunlight absorbed inside a complex canopy and sense the on/off status of the photosynthetic machinery. In: Remote sensing of vegetation fluorescence (Ed. Fletcher, K.) European Space Agency Publications Division, Noordwijk, Netherlands. ISSN 1022-6656


Department seminars (spring 2007)

  • Feb.14 2007, 14:00: Josef Lazar (Columbia University, NYC): A Genetically Encoded Optical Sensor of Membrane Voltage.
  • Feb.16 2007, 13:00: Zuzana Benedikty (UFB JcU, NH): Live-Cell Imaging of Cyanothece sp. Report on results obtained during 1 month visit to Wash.University, St.Louis.
  • March 2, 2007, 10:00: Karel Matouš and Anamika Mishra (UFB JcU, NH): Plant Species Discrimination.
  • March 2, 2007, 10:30: Ladislav Cséfalvay (UFB JcU, NH): Early detection of Plasmopara viticola (Down midley) by kinetic imaging fluorometry.
  • March 2, 2007, 11:00: Radek Tesař (UFB JcU, NH): Computer vision - Reconstruction

Department seminars (fall 2007)

  • 21/08/2007; 10 AM - Radek Tesař - An introduction to 3D- reconstruction of plant Chl-fluorescence.
  • 04/09/2007; 10 AM – Anamika Mishra - Towards discrimination of plant species by machine vision: advance statistical analysis of chlorophyll fluorescence transients.
  • 18/09/2007; 10 AM – Ladislav Cséfalvay - Early detection of Plasmopara viticola (Downy mildew) by kinetic imaging fluorometry.
  • 02/10/2007; 10 AM- Kumud B Mishra - Heterogeneity in Plants Reflectance Indices, PRI
  • 16/10/2007; 10 AM - Karel Matouš - Dimensionality-dependency of required amount of data on the number of classes and measured features
    - Zuzana Benediktyova - Visualization of plant - pathogen interaction by fluorescence imaging
  • 30/10/2007; 10 AM - Julie Soukupová - Titanium effect on the Chl fluorescence of spinach plants
  • 13/11/2007; 10 AM - Ondřej Komárek - New information from Synechocystis WT and rpaC mutant data interpretation.
  • 27/11/2007; 10 AM - Ali Reshak - Enhancing the resolution of two-photon laser scanning microscopy
    - Josef Lazar - Novel sensors of membrane protein activity
  • 11/12/2007; 10 AM - Ladislav Nedbal – On the perspectives of photosynthetic production of biofuels”

Department seminars (spring 2008)
  • 15/01/2008; 10 AM - Alexey Bondar - Microscopy of fluorescent proteins: highlights and perspectives.
  • 29/01/2008; 10 AM - Radek Tesař - 3D reconstruction plant in the computer.
  • 12/02/2008; 10 AM - Anamika Mishra - Title pending
  • 26/02/2008; 10 AM - Ladislav Cséfalvay- Title pending
  • 11/03/2008; 10 AM - Kumud B Mishra -Title pending
  • 25/03/2008; 10 AM - Karel Matouš - Autofocus algorithms
  • 08/04/2008; 10 AM - Zuzana Benediktyova-Title pending
  • 22/04/2008; 10 AM - Julie Soukupová - Title pending
  • 06/05/2008; 10 AM - Ondřej Komárek - Title pending
  • 20/05/2008; 10 AM - Ali Reshak - Title pending
  • 03/06/2008; 10 AM - Josef Lazar - Title pending
  • 17/06/2008; 10 AM - Ladislav Nedbal - Title pending

Journal clubs:
  • 28/8/2007; 10 AM - Benedikty, Zuzana - Biophotons generated spontaneously by plants infected by pathogen.
  • 11/9/2007; 10 AM - Csefalvay, Laco - Regulation of drought stress in plants.
  • 25/9/2007; 10 AM - Cerveny, Jan - Identification and Monitoring of Cyanobacteria Circadian Features
  • 09/10/2007; 10 AM - Komarek, Ondrj - Title pending
  • 23/10/2007; 10 AM - Lazer, Josef - Title pending
  • 06/11/2007; 10 AM - Matous, Karel - The Kautsky Curve Is a Built-in Barcode
  • 20/11/2007; 10 AM - Mishra, Anamika - Title pending
  • 04/12/2007; 10 AM - Mishra, Kumud - Title pending
  • 18/12/2007; 10 AM - Nedbal, Lada - Title pending
  • 08/1/2008; 10 AM - Radek, Tesar - A stereo imaging system for measuring structural parameters of plant canopies
  • 22/1/2008; 10 AM - Reshak, Ali H. - Title pending
  • 05/2/2008; 10 AM - Soukupova, Julie- Title pending
  • 04/3/2008; 10 AM - Csefalvay, Laco - Chlorophyll fluorescence imaging of photosynthetic activity in sun and shade leaves of trees.
  • 18/3/2008; 10 AM - Cerveny, Jan - Advances in understanding the cyanobacterial CO2-concentrating-mechanism (CCM)

Training courses (spring 2007):

  • April 6, 2007: Collective: Basic laboratory techniques I
  • April 20, 2007: Collective: Basic laboratory techniques II
  • May 4, 2007: Ladislav Cséfalvay (UFB JcU, NH): Pigments and spectroscopy
  • May 18, 2007: Radek Tesař (UFB JcU, NH): Avantes
  • June 1, 2007: Ali Reshak (UFB JcU, NH): Spectrofluorometer
  • June 15, 2007: Ladislav Nedbal (UFB JcU, NH): Fluorometer
  • June 29, 2007: Julie Soukupova (UFB JcU, NH): Fluorcam
  • July 13, 2007: Zuzana Benedikty (UFB JcU, NH): Olympus
  • July 27, 2007: Zuzana Benedikty (UFB JcU, NH): Imac II
Training courses (fall 2007):

Equipment

High-end fluorescence imaging techniques.
Mathematical modeling of biological dynamics.