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Carpenter J, Chan L, Thevathasan N, De Sousa M, Stys D, McDiarmid L. Global Health Practice Competencies: Building Health Professionals'
Capacity to Work in Global Health Contexts. Ann Glob Health 2017. [DOI: 10.1016/j.aogh.2017.03.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Cisar P, Soloviov D, Barta A, Urban J, Stys D. BioWes-from design of experiment, through protocol to repository, control, standardization and back-tracking. Biomed Eng Online 2016; 15 Suppl 1:74. [PMID: 27454467 PMCID: PMC4959364 DOI: 10.1186/s12938-016-0188-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background One of the main challenges in modern science is the amount of data produced by the experimental work; it is difficult to store, organize and share the scientific data and to extract the wealth of knowledge. Experimental method descriptions in scientific publications are often incomplete, which complicates experimental reproducibility. The proposed system was created in order to address these issues. It provides a solution for management of the experimental data and metadata to support the reproducibility. Implementation The system is implemented as a repository for experiment descriptions and experimental data. It has three main entry points: desktop application for protocol design and data processing, web interface dedicated for protocol and data management, and web-based interface for mobile devices suitable for the field experiments. The functionality of desktop client can be extended using the custom plug-ins for data extraction and data processing. The system provides several methods to support experimental reproducibility: standardized terminology support, data and metadata at a single location, standardized protocol design or protocol evolution. Results and discussion The system was tested in the framework of international infrastructure project AQUAEXCEL with five pilot installations at different institutes. The general testing in Tissue culture certified laboratory, Institute of complex systems and IFREMER verified the usability under different research infrastructures. The specific testing focused on the data processing modules and plug-ins demonstrated the modularity of the system for the specific conditions. The BioWes system represents experimental data as black box and therefore can handle any data type so as to provide broad usability for a variety of experiments and provide the data management infrastructure to improve the reproducibility and data sharing. Conclusions The proposed system provides the tools for standard data management operations and extends the support by the standardization possibilities, protocol evolution with visualization features and modularity based on the data processing modules and device communication plug-ins. The software can be used at different organization levels: from a single researcher (to improve data organization) to research consortium through the central protocols management repository. Support from the protocol design until being shared with the standardization features helps to improve the reproducibility of research work. The platform provides support from experimental protocol design to cooperation using simple sharing.
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Affiliation(s)
- Petr Cisar
- Faculty of Fisheries and Protection of Waters, Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zámek 136, 37333, Nove Hrady, Czech Republic.
| | - Dmytro Soloviov
- Faculty of Fisheries and Protection of Waters, Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zámek 136, 37333, Nove Hrady, Czech Republic
| | - Antonin Barta
- Faculty of Fisheries and Protection of Waters, Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zámek 136, 37333, Nove Hrady, Czech Republic
| | - Jan Urban
- Faculty of Fisheries and Protection of Waters, Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zámek 136, 37333, Nove Hrady, Czech Republic
| | - Dalibor Stys
- Faculty of Fisheries and Protection of Waters, Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zámek 136, 37333, Nove Hrady, Czech Republic
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Abstract
Time-lapse microscopic movies are being increasingly utilized for understanding the derivation of cell states and predicting cell future. Often, fluorescence and other types of labeling are not available or desirable, and cell state-definitions based on observable structures must be used. We present the methodology for cell behavior recognition and prediction based on the short term cell recurrent behavior analysis. This approach has theoretical justification in non-linear dynamics theory. The methodology is based on the general stochastic systems theory which allows us to define the cell states, trajectory and the system itself. We introduce the usage of a novel image content descriptor based on information contribution (gain) by each image point for the cell state characterization as the first step. The linkage between the method and the general system theory is presented as a general frame for cell behavior interpretation. We also discuss extended cell description, system theory and methodology for future development. This methodology may be used for many practical purposes, ranging from advanced, medically relevant, precise cell culture diagnostics to very utilitarian cell recognition in a noisy or uneven image background. In addition, the results are theoretically justified.
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Affiliation(s)
- Dalibor Stys
- Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic.
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Hrouzek P, Tomek P, Lukešová A, Urban J, Voloshko L, Pushparaj B, Ventura S, Lukavský J, Stys D, Kopecký J. Cytotoxicity and secondary metabolites production in terrestrial Nostoc strains, originating from different climatic/geographic regions and habitats: is their cytotoxicity environmentally dependent? Environ Toxicol 2011; 26:345-358. [PMID: 20082446 DOI: 10.1002/tox.20561] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Revised: 11/06/2009] [Accepted: 11/15/2009] [Indexed: 05/28/2023]
Abstract
Extensive selection of cyanobacterial strains (82 isolates) belonging to the genus Nostoc, isolated from different climatic regions and habitats, were screened for both their secondary metabolite content and their cytotoxic effects to mammalian cell lines. The overall occurrence of cytotoxicity was found to be 33%, which corresponds with previously published data. However, the frequency differs significantly among strains, which originate from different climatic regions and microsites (particular localities). A large fraction of intensely cytotoxic strains were found among symbiotic strains (60%) and temperate and continental climatic isolates (45%); compared with the less significant incidences in strains originating from cold regions (36%), deserts (14%), and tropical habitats (9%). The cytotoxic strains were not randomly distributed; microsites that clearly had a higher occurrence of cytotoxicity were observed. Apparently, certain natural conditions lead to the selection of cytotoxic strains, resulting in a high cytotoxicity occurrence, and vice versa. Moreover, in strains isolated from a particular microsite, the cytotoxic effects were caused by different compounds. This result supports our hypothesis for the environmental dependence of cytotoxicity. It also contradicts the hypothesis that clonality and lateral gene transfer could be the reason for this phenomenon. Enormous variability in the secondary metabolites was detected within the studied Nostoc extracts. According to their molecular masses, only 26% of these corresponded to any known structures; thus, pointing to the high potential for the use of many terrestrial cyanobacteria in both pharmacology and biotechnology.
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Affiliation(s)
- Pavel Hrouzek
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Opatovický Mlýn, 379 81 Třeboň, Czech Republic.
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Reshak AH, Stys D, Auluck S, Kityk IV. Dispersion of linear and nonlinear optical susceptibilities and the hyperpolarizability of 3-methyl-4-phenyl-5-(2-pyridyl)-1,2,4-triazole. Phys Chem Chem Phys 2011; 13:2945-52. [DOI: 10.1039/c0cp01601b] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Reshak AH, Auluck S, Stys D, Kityk IV, Kamarudin H, Berdowski J, Tylczynski Z. Dispersion of linear and non-linear optical susceptibilities for amino acid 2-aminopropanoic CH3CH(NH2)COOH single crystals: experimental and theoretical investigations. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm12361k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Stys D, Urban J, Vanek J, Císar P. Analysis of biological time-lapse microscopic experiment from the point of view of the information theory. Micron 2010; 41:478-83. [PMID: 20194026 DOI: 10.1016/j.micron.2010.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 01/29/2010] [Indexed: 10/19/2022]
Abstract
We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.
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Affiliation(s)
- Dalibor Stys
- Institute of Physical Biology, University of South Bohemia, Academic and University Center, Zámek 136, 373 33 Nové Hrady, Czech Republic.
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Reshak AH, Stys D, Auluck S, Kityk IV. Linear and Nonlinear Optical Susceptibilities of 3-Phenylamino-4-phenyl-1,2,4-triazole-5-thione. J Phys Chem B 2010; 114:1815-21. [DOI: 10.1021/jp9092755] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A H Reshak
- Institute of Physical Biology, South Bohemia University, Nove Hrady 37333, Czech Republic.
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Abstract
UNLABELLED Expertomica Cells is a program for the creation and analysis of pedigree plots from time-lapse micrographs of cell monolayers. It enables recording the basic events in a cell cycle, cell neighbourhoods and spatial migration. The output is both numeric and graphical. The software helps to lower main hurdles in the manual analysis of cell monolayer development to practical limits; it reduces the operator processing time of typical experiment containing 5000 consecutive images from the usual 3 months to 3-10 h. AVAILABILITY AND IMPLEMENTATION Freely available on the web at http://www.expertomicacells.tk or http://www.expertomicacells.wu.cz. The source code is implemented in JAVA 6 and supported by Linux, Mac and MS Windows. SUPPLEMENTARY INFORMATION Supplementary data available at Bioinformatics online.
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Affiliation(s)
- Tomás Levitner
- Institute of Physical Biology, University of South Bohemia, Academic and University Centre, Zámek 136, 373 33 Nové Hrady, Czech Republic.
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Hussain Reshak A, Stys D, Auluck S, Kityk IV. Density functional calculations of the electronic structure of 3-phenylamino-4-phenyl-1,2,4-triazole-5-thione. Phys Chem Chem Phys 2010; 12:2975-80. [DOI: 10.1039/b920743k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Reshak AH, Stys D, Auluck S, Kityk IV. Ab initio calculation of the electronic band structure, density of states and optical properties of alpha-2-methyl-1-nitroisothiourea. J Phys Chem B 2009; 113:12648-54. [PMID: 19722528 DOI: 10.1021/jp904692k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electronic and optical properties of alpha-2-methyl-1-nitroisothiourea have been studied using a full potential linear augmented plane wave method within density-functional theory along with the Engel-Vosko exchange correlation function. The structural data obtained by Vasil'ev et al. [Vasil'ev, A. D.; Astakhov, A. M.; Gelemurzina, I. V.; Stepanov, R. S. Dokl. Chem. 2001, 379, (4-6), 232-235; translated from Dokl. Akad. Nauk 2001, 379 (6), 781-784] from X-ray diffraction was used. Our calculations show that the valence band maximum (VBM) is located at the T and the conduction band minimum (CBM) is located at the R point of the Brillouin zone, resulting in an indirect energy gap of 3.1 eV. The calculated partial density of states shows that the upper valence band and the lower conduction band arise predominantly from the O-p, N-p and S-p states. The compound has a large uniaxial dielectric anisotropy and a large negative birefringence.
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Affiliation(s)
- Ali Hussain Reshak
- Institute of Physical Biology, South Bohemia University, Nove Hrady 37333, Czech Republic.
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Zelík P, Lukesová A, Voloshko LN, Stys D, Kopecký J. Screening for acetylcholinesterase inhibitory activity in cyanobacteria of the genus Nostoc. J Enzyme Inhib Med Chem 2009; 24:531-6. [PMID: 18951237 DOI: 10.1080/14756360802234836] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Fifty-four cyanobacterial strains of the genus Nostoc from different habitats were screened for acetylcholinesterase inhibitory activity. Water-methanolic extracts from freeze-dried biomasses were tested for inhibitory activity using Ellman's spectrophotometric method. Acetylcholinesterase inhibitory activity higher than 90% was found in the crude extracts of Nostoc sp. str. Lukesova 27/97 and Nostoc ellipsosporum Rabenh. str. Lukesova 51/91. Extracts from Nostoc ellipsosporum str. Lukesova 52/91 and Nostoc linckia f. muscorum (Ag.) Elenk. str. Gromov, 1988, CALU-980 inhibited AChE activity by 84.9% and 65.3% respectively. Moderate AChE inhibitory activity (29.1-37.5%) was found in extracts of Nostoc linckia Roth. str. Gromov, 1962/10, CALU-129, Nostoc muscorum Ag. str. Lukesova 127/97, Nostoc sp. str. Lhotsky, CALU-327 and Nostoc sp. str. Gromov, CALU-998. Extracts from another seven strains showed weak anti-AChE activities. The active component responsible for acetylcholinesterase inhibition was identified in a crude extract of Nostoc sp. str. Lukesova 27/97 using HPLC and found to occur in one single peak.
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Affiliation(s)
- Petr Zelík
- Faculty of Chemistry, Institute of Food Chemistry and Biotechnology, Brno University of Technology, Brno, Czech Republic
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Urban J, Vanek J, Soukup J, Stys D. Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach. Bioinformatics 2009; 25:2764-7. [DOI: 10.1093/bioinformatics/btp427] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wiesner C, Pflüger M, Kopecky J, Stys D, Entler B, Lucas R, Hundsberger H, Schütt W. Implementation of ECIS technology for the characterization of potential therapeutic drugs that promote wound-healing. GMS Krankenhhyg Interdiszip 2008; 3:Doc05. [PMID: 20204107 PMCID: PMC2831520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Christoph Wiesner
- IMC Fachhochschule Krems, Krems, Austria,*To whom correspondence should be addressed: Christoph Wiesner, IMC Fachhochschule Krems, Piaristengasse 1, 3500 Krems, Austria, E-mail:
| | | | - Jiri Kopecky
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Trebon, Czech Republic
| | - Dalibor Stys
- Institute for Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
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Wiesner C, Kopecky J, Pflueger M, Hundsberger H, Entler B, Kleber C, Atzler J, Hrouzek P, Stys D, Lukesova A, Schuett W, Lucas R. Endothelial cell-based methods for the detection of cyanobacterial anti-inflammatory and wound-healing promoting metabolites. Drug Metab Lett 2007; 1:254-60. [PMID: 19356051 DOI: 10.2174/187231207783221385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Acute lung injury is accompanied by an increased endothelial chemokine production and adhesion molecule expression, which may result in an extensive neutrophil infiltration. Moreover, a destruction of the alveolar epithelium and capillary endothelium may result in permeability edema. As such, the search for novel anti-inflammatory substances, able to downregulate these parameters as well as the tissue damage holds therapeutic promise. We therefore describe here the use of human endothelial cell-based in vitro assays for the detection of anti-inflammatory and wound-healing metabolites from cyanobacteria.
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Affiliation(s)
- Christoph Wiesner
- Vascular Biology Center, Medical College of Georgia, Augusta, GA30909, USA.
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Halbhuber Z, Petrmichlová Z, Alexciev K, Thulin E, Stys D. Overexpression and purification of recombinant membrane PsbH protein in Escherichia coli. Protein Expr Purif 2003; 32:18-27. [PMID: 14680935 DOI: 10.1016/s1046-5928(03)00188-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2002] [Revised: 05/25/2003] [Indexed: 11/28/2022]
Abstract
In this work, we featured an expression system that enables the production of sufficient quantities ( approximately mg) of low molecular weight membrane protein of photosystem II, PsbH protein, for solid-state NMR as well as other biophysical studies. PsbH gene from cyanobacterium Synechocystis sp. PCC 6803 was cloned into a plasmid expression vector, which allowed expression of the PsbH protein as a glutathione-S transferase (GST) fusion protein in Escherichia coli BL21(DE3) cells. A relatively large GST anchor overcomes foreseeable problems with the low solubility of membrane proteins and the toxicity caused by protein incorporation into the membrane of the host organism. As a result, the majority of fusion protein was obtained in a soluble state and could be purified from crude bacterial lysate by affinity chromatography on immobilized glutathione under non-denaturing conditions. The PsbH protein was cleaved from the carrier protein with Factor Xa protease and purified on DEAE-cellulose column with yields of up to 2.1 microg protein/ml of bacterial culture. The procedure as we optimized is applicable for isolation of small membrane proteins for structural studies.
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Affiliation(s)
- Zbynek Halbhuber
- Photosynthesis Research Center, Institute of Physical Biology, University of South Bohemia, Zamek 136, 373 33 Nove Hrady, Czech Republic
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Nedbal L, Brezina V, Adamec F, Stys D, Oja V, Laisk A, Govindjee. Negative feedback regulation is responsible for the non-linear modulation of photosynthetic activity in plants and cyanobacteria exposed to a dynamic light environment. Biochim Biophys Acta 2003; 1607:5-17. [PMID: 14556908 DOI: 10.1016/j.bbabio.2003.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Photosynthetic organisms exposed to a dynamic light environment exhibit complex transients of photosynthetic activities that are strongly dependent on the temporal pattern of the incident irradiance. In a harmonically modulated light of intensity I approximately const.+sin(omegat), chlorophyll fluorescence response consists of a steady-state component, a component modulated with the angular frequency of the irradiance omega and several upper harmonic components (2omega, 3omega and higher). Our earlier reverse engineering analysis suggests that the non-linear response can be caused by a negative feedback regulation of photosynthesis. Here, we present experimental evidence that the negative feedback regulation of the energetic coupling between phycobilisome and Photosystem II (PSII) in the cyanobacterium Synechocystis sp. PCC6803 indeed results in the appearance of upper harmonic modes in the chlorophyll fluorescence emission. Dynamic changes in the coupling of the phycobilisome to PSII are not accompanied by corresponding antiparallel changes in the Photosystem I (PSI) excitation, suggesting a regulation limited to PSII. Strong upper harmonic modes were also found in the kinetics of the non-photochemical quenching (NPQ) of chlorophyll fluorescence, of the P700 redox state and of the CO(2) assimilation in tobacco (Nicotiana tabaccum) exposed to harmonically modulated light. They are ascribed to negative feedback regulation of the reactions of the Calvin-Benson cycle limiting the photosynthetic electron transport. We propose that the observed non-linear response of photosynthesis may also be relevant in a natural light environment that is modulated, e.g., by ocean waves, moving canopy or by varying cloud cover. Under controlled laboratory conditions, the non-linear photosynthetic response provides a new insight into dynamics of the regulatory processes.
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Affiliation(s)
- Ladislav Nedbal
- Institute of Landscape Ecology CAS, University of S. Bohemia, Zámek 136, CZ-37333 Nové Hrady, Czech Republic.
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Stys D. Comment on Jack Parker's article 'How much is a scientist worth?' in EMBO reports, November 2002. EMBO Rep 2003; 4:102. [PMID: 12612591 PMCID: PMC1315846 DOI: 10.1038/sj.embor.embor750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Nilsson A, Stys D, Drakenberg T, Spangfort MD, Forsén S, Allen JF. Phosphorylation controls the three-dimensional structure of plant light harvesting complex II. J Biol Chem 1997; 272:18350-7. [PMID: 9218476 DOI: 10.1074/jbc.272.29.18350] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The most abundant chlorophyll-binding complex in plants is the intrinsic membrane protein light-harvesting complex II (LHC II). LHC II acts as a light-harvesting antenna and has an important role in the distribution of absorbed energy between the two photosystems of photosynthesis. We used spectroscopic techniques to study a synthetic peptide with identical sequence to the LHC IIb N terminus found in pea, with and without the phosphorylated Thr at the 5th amino acid residue, and to study both forms of the native full-length protein. Our results show that the N terminus of LHC II changes structure upon phosphorylation and that the structural change resembles that of rabbit glycogen phosphorylase, one of the few phosphoproteins where both phosphorylated and non-phosphorylated structures have been solved. Our results indicate that phosphorylation of membrane proteins may regulate their function through structural protein-protein interactions in surface-exposed domains.
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Affiliation(s)
- A Nilsson
- Plant Cell Biology, Box 7007, Lund University, S-220 07 Lund, Sweden
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Stys D, Stancek M, Cheng L, Allen JF. Complex formation in plant thylakoid membranes. Competition studies on membrane protein interactions using synthetic peptide fragments. Photosynth Res 1995; 44:277-285. [PMID: 24307098 DOI: 10.1007/bf00048601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/1994] [Accepted: 04/27/1995] [Indexed: 06/02/2023]
Abstract
Thylakoid membranes of pea were used to study competition between extra-membrane fragments and their parental membrane-bound proteins. Phosphorylated and unphosphorylated fragments of light harvesting complex II (LHC II) from higher plants were used to compete with LHC II for interactions with itself and with other thylakoid protein complexes. Effects of these peptide fragments of LHC II and of control peptides were followed by 80 K chlorophyll fluorescence spectroscopy of isolated thylakoids. The phosphorylated LHC II fragment competes with membrane-bound phosphoproteins in the phosphatase reaction. The same fragment accelerates the process of dark-to-light adaptation and decreases the rate of the light-to-dark adaptation when these are followed by fluorescence spectroscopy. In contrast, the non-phosphorylated LHC II peptide does not affect the rate of adaptation but produces results consistent with inhibition of formation of a quenching complex. In this quenching complex we propose that LHC II remains inaccessible to the LHC II kinase, explaining an observed decrease in LHC II phosphorylation in the later stages of the time-course of phosphorylation. The most conspicuous protein which is steadily phosphorylated during the time-course of phosphorylation is the 9 kDa (psbH) protein. The participation of the phosphorylated form of psbH in the quenching complex, where it is inaccessible to the phosphatase, may explain its anomalously slow dephosphorylation. The significance of the proposed complex of LHC II with phospho-psbH is discussed.
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Affiliation(s)
- D Stys
- Plant Cell Biology, Lund University, Box 7007, S-220 07, Lund, Sweden
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Stys D, Blaha I, Strop P. Structural and functional studies in vitro on the p6 protein from the HIV-1 gag open reading frame. Biochim Biophys Acta 1993; 1182:157-61. [PMID: 8357847 DOI: 10.1016/0925-4439(93)90137-p] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Protein p6 from HIV-1 gag open reading frame is reported to affect both the final phase of assembly of the viral particle and the early stage of the gag polyprotein maturation in vitro. Two separate hypotheses have been proposed, on only one of these reported effects. We think that both observations may be eventually explained if p6 protein strongly inhibits the HIV-1 proteinase. Protein p6 was synthesised by solid-phase peptide synthesis. Several methods of folding the p6 protein were tested, each resulting in the random structure according to both CD and 1D proton NMR spectra. A uniformly high exposure of NH protons to the solution was confirmed by temperature-dependent NMR spectra and isotope exchange experiments. Thus the p6 protein does not have any rigid conformation in solution. A rigid structure is not formed after further cleavage by HIV-1 proteinase as neither the protein nor its fragments are cleaved by this proteinase. In addition, the p6 protein itself does not act as inhibitor of HIV-1 proteinase. This excludes a direct role of p6 protein and supports the hypothesis that p6 is involved in forming the appropriate structure of gag polyprotein precursor. The role of slowly cleaved tight gag-proteinase in the final stage of maturation may be to slow down maturation of the precursor polyproteins prior to their transport to final location in the membrane.
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Affiliation(s)
- D Stys
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague
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Pavlícková L, Stys D, Soucek M, Urban J, Hrusková O, Sedlácek J, Strop P. 15gag proteinase of myeloblastosis-associated virus: specificity studies with substrate-based inhibitors. Arch Biochem Biophys 1992; 298:753-6. [PMID: 1417001 DOI: 10.1016/0003-9861(92)90476-d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The specificity of the proteinase of myeloblastosis-associated virus (MAV) was studied with (a) 21 substrate-based inhibitors, (b) 9 inhibitors with pseudopalindrome sequences, (c) 8 chimeric inhibitors, and (d) 3 compounds designed as human immunodeficiency virus 1 (HIV-1) proteinase inhibitors. The central inhibitory unit (transition state or cleaved bond analog) and the role of the inhibitor side chains from P4 to P4' were investigated. MAV proteinase prefers an aromatic side chain in P1 and a small aliphatic nonpolar chain in P2 and P2'. Residues in P5 and P4 positions are outside of the short catalytic cleft of the enzyme, but still influence binding considerably. The data obtained provide evidence that the MAV proteinase has generally lower specificity and poorer binding than the HIV proteinase.
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Affiliation(s)
- L Pavlícková
- Institute of Organic Chemistry and Biochemistry, Czechoslovak Academy of Science, Prague
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Strop P, Konvalinka J, Stys D, Pavlickova L, Blaha I, Velek J, Travnicek M, Kostka V, Sedlacek J. Specificity studies on retroviral proteinase from myeloblastosis-associated virus. Biochemistry 1991; 30:3437-43. [PMID: 1849425 DOI: 10.1021/bi00228a013] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The specificity of the p15 proteinase of myeloblastosis-associated virus (MAV) was tested with nonviral high molecular weight substrates and with synthetic peptides. Peptides with sequences spanning known cleavage sites in viral polyproteins of Rous sarcoma virus (RSV) and avian leukemia viruses, as well as in BSA and HSA, were synthesized, and the rate of their cleavage by the MAV proteinase was compared. Synthetic peptides require for successful cleavage at least 4 residues at the N-terminal side and 3 residues at the C-terminal side. The proteinase shows a preference for hydrophobic residues with bulky side chains (Met, Tyr, Phe) in P3, although Arg and Gln can also be accepted. Small hydrophobic residues are required in P2 and P2', and large hydrophobic residues (Tyr, Met, Phe/p-nitro-Phe) are preferred in both P1 and P1'. The difference between the specificity of the p15 proteinase and that of the HIV-1 proteinase mostly pertains to position P2' of the substrate, where bulkier side chains are accepted by the HIV-1 proteinase (Richards et al., 1990). A good chromogenic substrate for the MAV and RSV proteinases was developed and used to further characterize the MAV proteinase activity with respect to ionic strength and pH. The activity of the proteinase is strongly dependent on ionic strength and pH. Both the kcat and Km values contribute to a higher cleavage efficiency at higher salt concentrations and show a bell-shaped pH dependence curve with a sharp maximum at pH 5.5 (kcat) and 6.5 (Km).
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Affiliation(s)
- P Strop
- Institute of Organic Chemistry and Biochemistry, Czechoslovak Academy of Science, Prague
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