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Do you want to know everything about Chlorophyll Fluorescence Analysis, JIP-Test Method and get info on other Software and Methods in Plant Research?
If your answer is YES, then please come to visit the official web page of Biolyzer at
Here is a list of relevant scientific software written by Ronald Maldonado Rodriguez. All of the computer programs are actively used in applied technical projects and scientific research in different fields (biochemistry, photosynthesis, biophysics, ecology, ecophysiology, chemistry, chemical engineering, molecular structure determination by crystallographic methods, and other:
3. SparkPlot. Software for spectroscopic analysis of reflectance spectra. Link
4. PeakTrue. Software tools for X-Ray Powder Crystallographic Data Analysis of Polymer Materials. Link
5. Fluoromapper. Software for analysis of patterns in plant fluorescence population distributions. Link
The official distributor of former free versions of Biolyzer (version 1.0 to 4.0) is Fluoromatics Software. For getting a free copy of Biolyzer free version, please fill in the Contact Form here. If you have obtained one of the free distributed versions of Biolyzer Software, you are encouraged to register your free copy. Registration is free, it takes some minutes of your time, you don’t have to pay for your free copy and gives you access to certain advantages that Fluoromatics Software offers to all registered users of any of its software. If you own a copy of Biolyzer and you decide not to register your free copy, you put yourself alone at risk. You can read the Biolyzer License Agreement in the menu “About this program” located in the main menu of your free copy of Biolyzer. Do not support software piracy or any violations of Software Author’s Copyrights; register your free copy of Biolyzer today, now.
About Biolyzer 5.x (Commercial version)
The new version Biolyzer 5.x is a completely new re-designed professional software that can be characterized as a mature, professional, high-level fluorescence analysis tool, and an excellent cost-value effective investment. Available on request by using the Contact form at www.fluoromatics.com. If you want to download a full working demo (30-days limited trial copy) of Biolyzer, or if you want to buy a full-license of Biolyzer, BioVision or Fluoromapper please visit http://www.fluoromatics.com.
Biolyzer is able to read raw data files compatible with Hansatech UK fluorometers (PEA and HandyPEA) and the FIM fluorometer. We can adapt Biolyzer to read any other instrument data files on request and to do any kind analysis required by your own research analysis method. Automation of calculation tasks is important as it decreases dramatically the time from acquisition to final presentation of research results. We can adapt any Fluoromatics Software to your fit the software needs in your technical and research field.
About Scientific Software Design Services by Fluoromatics
On your request, we create scientific software for Fluorescence Data Analysis or ANY other special purpose, data analysis, data mining, data visualization or data processing. We study your software need and we create software fully adapted to solve your specific research needs. Good software helps to speed the way you get fast results and fast research reports and publications. Interested? Then please visit the website of Fluoromatics, already available on the Internet at http://www.fluoromatics.com. Fluoromatics Sci&Tech Software Development Team is able to create a completely new software application for you that fit absolutely all of your scientific research and engineering needs. Simulations, Artificial Neural Networks, Math & Data Plotting, Modeling with Cellular Automata, Finite Elements, Differential Equations, Compartmental models, and any other method you may prefer. Interested? Just send us an email to [email protected] or fill in the contact form at this link.
Impact of Biolyzer Software in Photosynthesis Research
Here are a few references (23) to scientific reports, scientific publications, habilitation thesis, PhD thesis and diploma works where Biolyzer has been used in for the analysis of chlorophyll a fluorescence data.
There may exist many other papers, poster proceeding and oral presentations that refer to Biolyzer, unfortunately I have not all of them in my database. In case you need some paper from the list here, please let me know and I will send a PDF copy to you by e-mail on request.
NOTE: If you are aware of a publication where Biolyzer has been used, and you do not see that reference in this list, please let me know about it at this email address: [email protected]
1. Bradford Sherman Ripley (July 2001) Page 49. PhD thesis. The
Ecophysiology of Selected Coastal Dune Pioneer Plants of the
2. K Klem, M Špundová, H Hrabalová, J Nauš, M Váňová, J Masojídek & P Tomek (2002). Comparison of chlorophyll fluorescence and whole-plant bioassays of isoproturon. European Weed Research Society. Weed Research 42, Issue 5 page 335–341 doi:10.1046/j.1365-3180.2002.00293.x
3. J.P. Zrÿd, M. Ianoz, F. Rachidi, P. Zweiacker, (2002) Influence of HF electromagnetic fields on the development and the molecular biology of the moss Physcomitrella patens and the nematode Caernorhabditis elegans, 14th International Symposium on Electromagnetic Compatibility, Proceedings Supplement pp. 179-180, February 2002
4. Maust, B. E., Espadas, F., Talavera, C., Aguilar, M., Santamaría, J. M., and Oropeza, C. (2003). Changes in carbohydrate metabolism in coconut palms infected with the lethal yellowing phytoplasma. Phytopathology Biochemistry and Cell Biology 93:976-98
5. Heiko Wagner (2003) Diplomarbeit: Vergleichende Untersuchungen zum Einfluss des transthylakoidären Protonengradienten und des Redoxzustandes des Plastochinonpools auf das nichtphotochemische Quenching und dessen Wirkung auf die variable Fluoreszenz und Thermolumineszenz von Photosystem II. Universität Leipzig Fakultät für Biowissenschaften, Pharmazie und Psychologie. Available here: http://www.uni-leipzig.de/~pflaphys/webdir/Daten/dissdipl/wagnerdipl.pdf
6. Martin G Christensen, Harald B Teicher and Jens C Streibig (2003) Linking fluorescence induction curve and biomass in herbicide screening, Pest Management Science 59:1303–1310 (online: 2003) DOI: 10.1002/ps.763
7. E. Alasonati1, E. Comino1, A. Giudice1, M. Ianoz, F. Rachidi2, Y. Saidi3, J.P. Zryd3, P. Zweiacker, (2003) USE OF THE PHOTOSYNTHESIS PERFORMANCE INDEX TO ASSESS THE EFFECTS OF HIGH FREQUENCY ELECTROMAGNETIC FIELDS ON THE MEMBRANE INTEGRITY OF THE MOSS P. PATENS. Laboratoire de Phytogénétique Cellulaire http://www2.unil.ch/lpc/docs/EMF.htm
8. FILIPPO BUSSOTTI (2003) CHLOROPHYLL A FLUORESCENCE AS DIAGNOSTIC
TOOL TO DETECT EARLY STRESS CONDITION IN LEAVES EXPOSED TO OZONE In
“Establishing Ozone Critical Levels II” (Karlsson, P.E., Selldén, G., Pleijel,
H., eds.). 2003. UNECE Workshop Report. IVL report B1523. IVL Swedish
Environmental Research Institute,
9. R.K.Sarkar, D. Panda, D.N. Rao, S.G. Sharma. (2004) Chlorophyll fluorescence parameters as indicators of submergence tolerance in rice. Crop Management and Physiology. International Rice Research Institute. International Rice Research Notes. Vol 29 Issue 1 Page 65-67 Available online at http://irri.org/publications/irrn/pdfs/vol29no1/IRRN29-1.pdf
10. Dusan Lazar (2004) The OKJIP Chlorophyll transient : Theory
and experiments. Habilitation Thesis. December 2004. PalackyUniversity
11. D. Parvanova, A. Popova, I. Zaharieva, P. Lambrev, T. Konstantinova, S. Taneva, A. Atanassov, V. Goltsev and D. Djilianov, (2004) Low Temperature Tolerance of Tobacco Plants Transformed to Accumulate Proline, Fructans, or Glycine Betaine. Variable Chlorophyll Fluorescence Evidence. Photosynthetica Springer Kluwer ISSN: 0300-3604 (Paper) 1573-9058 (Online) DOI: 10.1023/B:PHOT.0000040588.31318.0f 42 Number 2 Pages: 179 – 185
12. Filippo Bussotti (2004) Corso teorico-pratico su fluorescenza
diretta della clorofilla a e JIP-Test "determinazione delle condizioni di
stress nelle piante tramite l’analisi
13. Michel Ianoz, (July 26th 2004) The Biological and Health Effects of Electromagnetic Fields. Lecture IEEE EMC Society. E-Mail : [email protected] Meeting of the Rocky Mountain Chapter EMC Society
14. Elisabetta Gravanoa,1, Filippo Bussottia,*, Reto J. Strasserb, Marcus Schaubc, Kristopher Novakc, John Skellyd and Corrado Tania (2004) Ozone symptoms in leaves of woody plants in open-top chambers: ultrastructural and physiological characteristics PHYSIOLOGIA PLANTARUM 121: 620–633. 2004 doi: 10.1111/j.1399-3054.2004.00363.x
15. F Bussotti (2004) Assessment of stress conditions in Quercus ilex L. leaves by O-J-I-P chlorophyll a fluorescence analysis. Plant Biosystems. Volume 138, Number 2. Pages 101-109 DOI 10.1080/11263500412331283708
16. Петър Харалампиев Ламбрев (2004), ДИСЕРТАЦИЯ, ПРИЛОЖЕНИЕ НА БЪРЗАТА И ЗАБАВЕНАТА ХЛОРОФИЛНА ФЛУОРЕСЦЕНЦИЯ ЗА АНАЛИЗ ДЕЙСТВИЕТО НА ФОТОСИНТЕТИЧНИ ХЕРБИЦИДИ В ИНТАКТНИ ЛИСТА И ТИЛАКОИДНИ МЕМБРАНИ ОТ ГРАХ. СОФИЙСКИ УНИВЕРСИТЕТ „СВ. КЛИМЕНТ ОХРИДСКИ“ БИОЛОГИЧЕСКИ ФАКУЛТЕТ Катедра „Биофизика и радиобиология“. Available Online. http://www.bio21.bas.bg/ibf/lambrev
Free translation: Peter Haralampiev Lambrev. (2004). PhD Thesis.
Applications of fast and delayed chlorophyll fluorescence on the analysis of
the herbicide effects in ther photosdynthetic functioning of leaves and
thylakoid membranes of pea plants. Biophysics Faculty. Biophysics and Radiobilogy.
17. Project Report 2003-2004 Fondazione Lombardia per l'Ambiente. Effetti dell'ozono sulla vegetazione alpine. Effetti dell'inquinamento transfrontaliero da ozono sulla vegetazione dell'area transalpina tra Lombardia e Canton Ticino http://www.flanet.org/ricerca/ozono02.asp http://www.flanet.org/ricerca/ozono02_relazione_04.pdf
18. Abbaspoor, Majid, Streibig, Jens C., (2005) Clodinafop changes the chlorophyll fluorescence induction curve Issn: 0043-1745 Journal: Weed Science Volume: 53 Issue: 1 Pages: 1-9 DOI: 10.1043/0043-1745(2005)053<0001:CCTCFI>2.0.CO;2
19. Filippo Bussotti, Giovanni Agati, Rosanna Desotgiu, Paolo Matteini and Corrado Tani, (June 2005) Ozone foliar symptoms in woody plant species assessed with ultrastructural and fluorescence analysis. New Phytologist Volume 166 Issue 3 Page 941 doi:10.1111/j.1469-8137.2005.01385.x
20. J. Mala, K. Klem, A. Lukavská and J. Masojídek, (2005) Ecological Risk Assessment Degradation and Movement in Soil of the Herbicide Isoproturon Analyzed by a Photosystem II–Based Biosensor J Environ Qual 34:1780-1788 (2005) DOI: 10.2134/jeq2004.0351
21. Birgit Gielena, Hans J. De Boecka, Catherine M. H. M. Lemmensa, Roland Valcke, Ivan Nijsa and Reinhart Ceulemansa (2005) Grassland species will not necessarily benefit from future elevated air temperatures: a chlorophyll fluorescence approach to study autumn physiology Physiologia Plantarum, Volume 125, Issue 1, Page 52 doi:10.1111/j.1399-3054.2005.00539.x
22. Christian A. Lange (2005), Untersuchungen zur phytotoxischen Wirkung von Tetrachlorethen und Trichloressigsäure auf Kiefer (Pinus sylvestris L.) und Birke (Betula pendula ROTH). Fakultät Forst-, Geo- und Hydrowissenschaften der Technischen Universität Dresden. Deutschland.
23. Dušan Lazár (2006) The polyphasic chlorophyll a fluorescence rise measured under high intensity of exciting light Functional Plant Biology Volume 33 Number 1 pp. 9-30.
24. Ludwig Weissflog, Gert Krueger, Nikolai Elansky, Erich Putz, Christian A. Lange, Lida Lisitzina, Andrea Pfennigsdorff and Karsten Kotte (2006), The phytotoxic effect of C1/C2-halocarbons and trichloroacetic acid on the steppe plant Artemisia lerchiana, Chemosphere, Volume 65, Issue 6, November 2006, Pages 975-980
25. N. Çiçek and H. Çakırlar (2008), CHANGES IN SOME ANTIOXIDANT ENZYME ACTIVITIES IN SIX SOYBEAN CULTIVARS IN RESPONSE TO LONG-TERM SALINITY AT TWO DIFFERENT TEMPERATURES, Gen. Appl. Plant Physiology, Special Issue, 34, (3-4), 267-289.
26. Lambrev, Ivanov, Goltsev (2003), Effects of prolonged action of sub-herbicide concentration of atrazine on the photosynthetic function of pea plants. Comptes rendus de l’Academie bulgare des Sciences, Tome 56, No,3, page 59-62.
27. D. PARVANOVA, A. POPOVA, I. ZAHARIEVA, P. LAMBREV, T. KONSTANTINOVA, S. TANEVA, A. ATANASSOV, V. GOLTSEV, and D. DJILIANOV (2004), Low temperature tolerance of tobacco plants transformed to accumulate proline, fructans, or glycine betaine. Variable chlorophyll fluorescence evidence. PHOTOSYNTHETICA 42 (2): 179-185.
28. F. L. Marchand, Fred Kockelbergh, Bart van de Vijver, Louis Beyens and I. Nijs (2006), Are heat and cold resistance of arctic species affected by successive extreme temperature events? New Phytologist Volume 170 Issue 2, Pages 291 – 300. http://www3.interscience.wiley.com/journal/118627163/abstract
29. Abram J. Strauss, Philippus D. R. van Heerden, Misha de Beer, Gert H. J. Krüger and Reto J. Strasser(2008), Changes in O-J-I-P Fluorescence Rise Kinetics During Dark Chilling Provide Insight into Genotype-Specific Effects on Photosynthesis and N2 Fixation in Soybean, in Photosynthesis. Energy from the Sun, 14th International Congress on Photosynthesis Ed. By John F. Allen, Elisabeth Gantt, John H. Golbeck and Barry Osmond, part 24, pages 1593-1597, ISBN 978-1-4020-6707-5 (Print) 978-1-4020-6709-9 (Online), DOI 10.1007/978-1-4020-6709-9_342, Springer Netherlands.
30. Alexandra Pinior1, Gisela Grunewaldt-Stöcker1 Contact Information, Henning von Alten1 and Reto J. Strasser (2005), Mycorrhizal impact on drought stress tolerance of rose plants probed by chlorophyll a fluorescence, proline content and visual scoring, Mycorrhiza, Volume 15, Number 8 / December, 2005, 596-605, Springer.
31. J. Malya,b, K. Klemc, A. Lukavskáb,d and J. Masojídek (2005), Degradation and Movement in Soil of the Herbicide Isoproturon Analyzed by a Photosystem II–Based Biosensor, J Environ Qual 34:1780-1788 (2005), DOI: 10.2134/jeq2004.0351, http://jeq.scijournals.org/cgi/content/full/34/5/1780
32. José F.C. Gonçalves*; Ulysses M. Santos Jr.; Adamir R. Nina Jr.; Larissa R. Chevreuil (2007), Energetic flux and performance index in copaiba (Copaifera multijuga Hayne) and mahogany (Swietenia macrophylla King) seedlings grown under two irradiance environments, Brazilian Journal of Plant Physiology, vol.19 no.3 Londrina July/Sept. 2007. doi: 10.1590/S1677-04202007000300001
33. Nadine Schmidt, D I P L O M A R B E I T, DER EINFLUSS VON BIOTISCHEM STRESS AUF DIE THERMOLUMINESZENZSIGNALE VON TABAKBLÄTTERN, Universität Leipzig, Fakultät für Biowissenschaften, Pharmazie und Psychologie, 2005.
34. C.A. Rolando and K.M. Little (2007), Measuring water stress in Eucalyptus grandis Hill ex Maiden seedlings planted into pots, South African Journal of Botany, Volume 74, Issue 1, January 2008, Pages 133-138
35. Shih-May Yang1, Chia-Yen Chang1, Makoto Yanagisawa1, Il Park2, Tung-Hai Tseng3 and Maurice S. B. Ku (2008), Transgenic Rice Expressing Cyanobacterial Bicarbonate Transporter Exhibited Enhanced Photosynthesis, Growth and Grain Yield, in Photosynthesis. Energy from the Sun, 14th International Congress on Photosynthesis, Part 20, 1247-1250, Edited by John F. Allen, Elisabeth Gantt, John H. Golbeck and Barry Osmond, Springer, DOI 10.1007/978-1-4020-6709-9_269
36. Julien Louvieaux (2004) Mesure de l'efficacité d'extraits d'algues sur la vigne (Vitis vinifera L.), en conditions contrôlées et au vignoble, validée par la mesure de l'activité photosynthétique et les analyses chimiques,– Travail de Diplôma de grade en Génie Agronomique (Bioingénieur en Agronomie), Université Libre de Bruxelles (ULB), Belgique.
37. Mara Isabel Aguilar, Maryosawa G. Romero, Mara Isabel Chvez, Beatriz King-Daz and Blas Lotina-Hennsen (2008), Biflavonoids Isolated from Selaginella lepidophylla Inhibit Photosynthesis in Spinach Chloroplasts, J. Agric. Food Chem., 2008, 56 (16), pp 6994–7000, DOI: 10.1021/jf8010432 http://pubs.acs.org/doi/abs/10.1021/jf8010432
38. Alan Scarlett, Tamara S. Galloway, Martin Canty, Emma L. Smith, Johanna Nilsson, and Steven J. Rowland (2005), COMPARATIVE TOXICITY OF TWO OIL DISPERSANTS, SUPERDISPERSANT-25 AND COREXIT 9527, TO A RANGE OF COASTAL SPECIES, Environmental Toxicology and Chemistry, Volume 24, Issue 5 (May 2005), 1219–1227, http://www.setacjournals.org/perlserv/?request=get-document&doi=10.1897%2F04-334R.1&ct=1
39. Micol Rossini, Tesi di Dottorato (2006), ANALISI DELLO STATO DI SALUTE DELLA VEGETAZIONE MEDIANTE TELERILEVAMENTO IPERSPETTRALE: STIMA DI VARIABILI BIOCHIMICHE E FISIOLOGICHE A LIVELLO FOGLIARE E DI CANOPY. Dipartimento di Scienze dell’Ambiente e del Territorio, Facoltà di Scienze Matematiche, Fisiche e Naturali, UNIVERSITA’ DEGLI STUDI DI MILANO – BICOCCA
40. D. Moshou, S. Wahlen, R. Strasser, A. Schenk, J. De Baerdemaeker and H. Ramon (2005), Chlorophyll Fluorescence as a Tool for Online Quality Sorting of Apples, Biosystems Engineering, Volume 91, Issue 2, June 2005, Pages 163-172. doi:10.1016/j.biosystemseng.2005.03.008
WHO IS RONALD MALDONADO RODRIGUEZ?
Ronald is a chemical engineer who obtained a Master of Sciences degree in Chemical Engineering in Bulgaria. He is a top specialist in Organic Synthesis, Combustibles and Industrial Risk Management. After a first experience at the Central Research Laboratory of the University of Burgas and six years experience while working as a research assistant at Laboratory of Microbiology and Bioenergetics of the University of Geneva, he becomes very interested in the application of Artificial intelligence methods for the analysis of dynamic phenomena in photobiology and photophysics. Since 2001, he has been working in the analysis of different numerical simulation (in-silica) approaches for studying chlorophyll fluorescence at different levels: chloroplast, cell, leaf, whole plant, a group of trees and a whole biome. For the purposes of his modeling and simulation research work, Ronald has developed several analysis method based on cellular automata theory and artificial neural networks (Kohonen’s Self-Organizing Map). Ronald has conducted several plant research projects including the Rhin Sud INTERREG Project “Tree vitality”. Ronald has published original and coauthored scientific articles and has created several software packages related to his research work, for both, chlorophyll fluorescence analysis and pattern recognition of chlorophyll fluorescence signals. Beside his scientific interests, Ronald also has acquired solid technical and management skills after several years working as a Business Developer & Analyst, and Consultant expert in chemical and biotech industry at Lifescience Consulting SA, a Pharma & Biotech IT Swiss Company and also an excellent work experience as production chemical engineer in the pharmaceutical industry at BASF Orgamol Pharma Solutions SA, Switzerland.
As student in Bulgaria at the Higher Institute of Chemical Engineering (today University of Burgas Prof. Dr. Assen Zlatarov), Ronald was already highly interested in developing computers application in chemical engineering for process simulation. He worked with Dr. Anton Popov and Dr. Stancho Pavlov as a team leader of the Crystallographic Software Development Unit at the Central Research Laboratory of the Technological University of Burgas. While working in that research group Ronald wrote several software packages and made his first scientific publications in the field developed of X-Ray Powder Crystallography of high molecular weight polymers, which includes software for polymer molecular structure determination based on X-Ray powder diffraction analysis.
working with Prof.
While working with Prof.Aristoteles Dimov within the Ecology Department of the
on, Ronald starts to work as an assistant of Prof.
Later on, Ronald starts to work as an assistant of Prof.Reto Strasser at the Bioenergetics Laboratory of the
that time, and in collaboration with Murielle Eyletters, J.P. Delhaye from ULB Brussels and the
Infrastructure Ministry of Belgium, Ronald studied the effects of urban
pollution on city trees using mainly chlorophyll fluorescence analysis and
Infrared aerial photography. The joint-research group used infrared airborne
imaging for monitoring historically important urban trees over
With Prof. GiuseppeTorzillo (
has also worked with Dr. Francisco
Ronald has also worked with Dr. FranciscoBarja (Lab of Microbiology at the
worked with Prof. Alberto Gonzalez and Prof. Jose Luis Sanchez (The University
of Madrid and the Spanish Institute for Agricultural Research INIA,
respectively) and Dr.
Ronald worked with Prof. Alberto Gonzalez and Prof. Jose Luis Sanchez (The University of Madrid and the Spanish Institute for Agricultural Research INIA, respectively) and Dr.Stancho Pavlov (
In 2001, Ronald developed a novel
method for measuring Nitrogen content in leguminous plants based using fast
fluorescence kinetics analysis. The experimental work was done in collaboration
with Patrick Schmitz (who was diploma student at
the Bioenergetics lab at that time). They presented a poster about this
work at the International Congress of Photosynthesis in
In 2001, Ronald developed a novel method for measuring Nitrogen content in leguminous plants based using fast fluorescence kinetics analysis. The experimental work was done in collaboration with Patrick Schmitz (who was diploma student at the Bioenergetics lab at that time). They presented a poster about this work at the International Congress of Photosynthesis in
Ronald has also studied the chlorophyll fluorescence emission responses
in different types of corals living in simulated light day cycled conditions,
in order to evaluate physiological diurnal changes. The results of this work
were presented as a poster at the Photosynthesis International Congress held in
Ronald has also studied the chlorophyll fluorescence emission responses in different types of corals living in simulated light day cycled conditions, in order to evaluate physiological diurnal changes. The results of this work were presented as a poster at the Photosynthesis International Congress held in 2001 in
is winner of the prize to the BEST
STUDENT POSTER in the 13th Congress of the European
Federation of Plant Physiology Societies (
Ronald is winner of the prize to the BEST STUDENT POSTER in the 13th Congress of the European Federation of Plant Physiology Societies (Heraklion,
has collaborated with Prof. Rafael Navarro (
Ronald has collaborated with Prof. Rafael Navarro (
In collaboration with Prof. V. Goltsev and Dr. Peter Lambrev
(University of Sofia Kliment Ochridski, Bulgaria), Ronald has studied the
action and dynamics of photosynthetic herbicides (Diuron,
Atrazine) on whole Pisum
sativum plants using a novel
chlorophyll fluorescence imaging technique. A paper about this work is in the
way be prepared by Dr. Lambrev.
In collaboration with Prof. V. Goltsev and Dr. Peter Lambrev (University of Sofia Kliment Ochridski, Bulgaria), Ronald has studied the action and dynamics of photosynthetic herbicides (Diuron, Atrazine) on whole Pisum sativum plants using a novel chlorophyll fluorescence imaging technique. A paper about this work is in the way be prepared by Dr. Lambrev.
is author of several software packages like Biolyzer for analysis of fast induction
kinetics from chlorophyll containing samples also known as OJIP curves and
measured with Hansatech UK
Ronald is author of several software packages like Biolyzer for analysis of fast induction kinetics from chlorophyll containing samples also known as OJIP curves and measured with Hansatech UKfluorometers. One of the many features of this program is that it includes the full JIP-test method for calculation photosynthetic behavior in plants, algae and cianobacteria; Spark software for reflectance signals (measured with UniSpec reflectometer by Optisciences); and FluoVision Software for chlorophyll fluorescence imaging analysis. Today, Biolyzer is used in many laboratories worldwide. The versions 1 to 3 were distributed as freeware (freely available for non-profit research and academic purposes).
Ronald is also author of several other copyrighted scientific software: Fluolyzer, FluoVision, SciPlot and Miller.
For contact, send your e-mail to [email protected]
Can machines recognize stress in plants?
ISSN: 1610-3653 (Paper) 1610-3661 (Online)
Ronald Maldonado Rodríguez1, Stancho Vaelkanov Pavlov2, Alberto Gonzalez Moreno3, Abdullah Okarum1, Reto Strasser1
(1) Bioenergetics Laboratory, 10 Chemin des Embrouchis, CH-1254 Jussy, Switzerland
(2) Department of Mathematics, University Asen
(3) INIA Carretera de la Coruña, 28040 Madrid, Spain
Keywords: Artificial neural networks - Chlorophyll a fluorescence - Drought stress - JIP-test - O-J-I-P fluorescence rise - Pea - Pisum sativum - Plants - Self-organizing map – SOM - Kohonen
In this paper we show that chlorophyll a fluorescence signals analysed with the self-organizing map (SOM) can be used as a routine tool for the monitoring and classification of pea varieties (Pisum sativum) according to their degree of resistance against drought stress. Fluorescence kinetics measurements were obtained from non-stressed plants. The aim of this study is to evaluate the applicability of artificial intelligence techniques in eco-physiological research. Our goal is to provide a fast tool that will contribute to the knowledge needed to develop strategies that would help to decrease the impact of environmental stress in agriculture and forestry.
A Methodological Approach for Pattern Recognition System using discriminate analysis and artificial neural networks
Link: Proceedings of the 6th WSEAS Neural Networks, Fuzzy Systems,
Evolutionary Computing Conference held in
WSEAS Transactions Journal (Accepted for Publication July 2005)
Anna Pérez-Méndez, Elizabeth Torres-Rivas, Francklin Rivas-Echeverría, Ronald Maldonado-Rodríguez
work is the result of a scientific collaboration between the Escuela de
Estadística and the Laboratorio de Sistemas Inteligentes de la Universidad de
Keywords: - Classification, Pattern recognition, Discriminate analysis, Artificial Neural Networks
In this work it is presented a methodology for the development of a pattern recognition system using classification methods as discriminate analysis and artificial neural networks. In this methodology, the information statistical analysis is contemplated, with the purpose of retaining the observations and the important characteristics that can produce an appropriate classification, and allows, as well, to detect outliers’ observations, and multicolinearity between variables, among other things.
Pisum sativum classification based on a methodological approach for pattern recognition using discriminant analysis and neural networks
Link: Proceedings of the 6th WSEAS Neural Networks, Fuzzy Systems,
Evolutionary Computing held in
WSEAS Transactions Journal (accepted for publication 07.05)
Anna Pérez-Méndez, Ronald Maldonado-Rodríguez, Elizabeth Torres-Rivas, Franklin Rivas-Echeverría.
This work is the result of a scientific collaboration
between the Escuela de Estadística
and the Laboratorio
de Sistemas Inteligentes de la Universidad de Los Andes,
Keywords: - Classification, Pattern recognition, Discriminate analysis, Artificial Neural Networks
For this paper the authors were awarded with the Best Student Paper Prize for Fuzzy Systems at the 6th WSEAS Lisbon 2005 Conference. Read more here.
In this work a statistical analysis-based methodological approach for a pattern recognition system using discriminate analysis and neural networks is used for the classification of Pisum sativum (pea) according to the drought resistance. The statistical techniques used in the exploratory analysis are a fundamental tool in the creation of variables sets and observations for the model adjustment in the neural models and in the discriminate models.
WSEAS is The World Scientific and
Chlorophyll a fluorescence patterns of six deciduous forest tree species exposed to normal and elevated CO2
R. Maldonado Rodríguez, R. Strasser.
Bioenergetics Laboratory, 10 Chemin des Embrouchis,
Artificial Neural Networks (ANN) are able to discover
“patterns” in multivariate data. We show that ANN may offer a realistic
opportunity to automation of physiological patterns identification and plant
stress quantification by using Chlorophyll a Fluorescence (CF) signals as
network information input. Fluorescence is a widely spread technique used
in many photosynthesis and eco-physiology research laboratories, and it finds
numerous applications, from agriculture and forestry, through marine biology
and chronobiology to exobiology research. CF signals are a direct measure of
photosynthetic performance in plants and algae. Fluorescence signals are a
definitive proof for photosynthesis. Measuring fluorescence is cheap, fast, and
non-destructive. In a relative short time, thousands of fluorescence curves can
be collected. The task of identification of CF patterns that correlate with
other physiological parameters becomes a necessity. The physiological responses
of photosynthetic organisms to well-defined stimuli have been observed to be
similar, presenting well-defined patterns and indeed this characteristic
suggest the possibility to group plants, green algae and cyanobacteria into
categories or classes according to their specific fluorescence pattern. Since
pattern recognition is the primary emphasis, an ANN seems to be the most
logical method of solving this problem. Formed by simulated neurons connected
together much the same way the brain's neurons are, ANN are able to associate
and generalize without rules. They have solved problems in pattern recognition,
robotics, speech processing, financial predicting, and signal processing, to
name a few. The Self-Organizing Feature Map (SOM) is a popular ANN. We build a
SOM using plant fluorescence signals as stimulatory input and the resulting
Fluorotopic Map has shown to be a valuable tool for identification of plant
classes. Such classes may vary according to their taxonomy, functional groups,
wild type or genetically modified plants, degree of stress effects, etc. We
demonstrate a novel methodology for plant stress survey using short video
sequences of whole leaf fluorescence analyzed with a Batch-SOM. The new
developed technique includes spatio-temporal analysis of fluorescence kinetics
obtained from video processing combined with fast fluorescence induction
measurements. Using this technique, a new method for recognizing and
quantifying plant stress has been developed. We have tested the applicability
of this new technique within the Swiss Canopy Crane Project framework
Self-Organizing Map (SOM) for monitoring the evolution of Rhizobium nodulation status in Vigna unguiculata
Ronald Maldonado Rodríguez, Patrick Schmitz, Reto Strasser.
Bioenergetics Laboratory, 10 Chemin des Embrouchis, CH-1254 Jussy, Switzerland
Chlorophyll a fluorescence is a useful and non-invasive tool to screen for the effects of many biotic and abiotic parameters on photosynthesis in plants. The Chl a fluorescence emitted by leaves after excitation with red light was measured with a portable fluorometer. The collected data showing the polyphasic OJIP Chl a fluorescence rise were analysed using the JIP-test (Strasser and al. 2000) which provides biophysical parameters indicating Photosystem II properties. Seeds of Vigna unguiculata were sterilized before germination. Seedlings were planted in Magenta jars (used for hydroponic cultures) filled with a nitrate-deficient solution (B&D solution). The roots of some of the plants were inoculated with Rhizobium sp. strain NGR234 (109 bacteria/200 µl) four days after germination. The other plants were grown on various concentrations of KNO3 (0, 0.5, 1, 5, 10 and 20 mM). The plants were followed for 5 weeks. During this time fluorescence measurements were done on the first and second mature leaves. We have use an Artificial Neural Network (Kohonen's Self-Organizing Map or SOM) to analyze the raw fluorescence data. The generated map shows very well defined groups of different concentrations creating a gradient from low to high nitrate content. The Rhizobium inoculated plants in the fluorescence SOM map is moving in time according to the hypothetical nitrogen supply model. This permits us to establish a method for screening the nodulation evolution as well as nitrogen deficiency in vivo on the level of the leaves.
Ecophysiological responses to summer drought in Pinus halepensis Mill. seedlings of five provenances
Rafael Mª Navarro1, David Ariza1, Ronald Maldonado Rodríguez, Francisco Canovas.
Laboratory of Bioenergetics and Microbiology.
En este ensayo se estudia la utilidad de las medidas de la cinética de inducción de fluorescencia de la clorofila de hojas in situ para detectar la respuesta temprana a estrés hídrico moderado de cinco procedencias Pinus halepensis Mill.. Las plantas se sometieron a un ciclo de sequías de 28 días en una cámara de cultivo a 21ºC. Se han encontrado diferencias significativas de supervivencia entre las procedencias a los 21 días, pero no al final del ensayo. La variación en la fluorescencia ha mostrado que la eficiencia potencial del fotosistema II de las plantas sometidas a un estrés hídrico moderado es menor conforme aumenta el nivel de estrés (medido en potencial hídrico) y que esta diferencia varía entre procedencias, por lo que puede representar una medida indirecta del nivel de estrés en etapas previas a la aparición de perdidas generales de supervivencia.
Quality assessment of urban trees: A comparative study of physiological characterisation, airborne imaging and on site fluorescence monitoring by the JIP-test
Urban & Fischer Verlag Publishers DOI: 10.1078/0176-1617-00917
The purpose of this paper is to demonstrate the complementary utility of chlorophyll fast fluorescence OJIP transient (from 50µs to 1s) measurements in the aerial study of rows of trees. We identify limitations in photochemical events induced by urban injuries on Platanus acerfolia L., using the JIP-test procedure. The Performance Index (PIABS) showed the largest dynamic range to characterise the vitality of trees. Individual trees were graded into three quality groups based on the individual PIABS value compared to the overall average for trees in the alley. These groups are: high performers, with PIABS 50% higher than the alley average; normal trees, with a deviation from the alley average between –50% and +50%; and poor performers, whose deviation from the alley average was –50% or less. Trees also were grouped into five vitality categories on the basis of a stereoscopic and morphologic observation of the symmetry of tree crowns, percentage of defoliation and reflectance property in the visible and infra-red range. Here, we report a remarkable correlation between the airborne remote sensing data and the on-site fluorescence measurements.
Cyanobacteria have the natural ability to degrade moderate amounts of organic pollutants. However, when pollutant concentration exceeds the level of tolerance, bleaching of the cells and death occur within 24 hours. Under stress conditions, cyanobacterial response includes the short-term adaptation of the photosynthetic apparatus to light quality, named state transitions. Moreover, prolonged stresses produce changes in the functional organization of phycobilisomes and in the core-complexes of both photosystems, which can result in large changes in the PS II fluorescence yield. The localization of ferredoxin-NADP+ reductase (FNR) at the ends of some peripheral rods of the cyanobacterial phycobilisomes, makes this protein a useful marker to check phycobilisome integrity.
The goal of this work is to improve the knowledge of the mechanism of action of a very potent pesticide, lindane (γ-hexachlorocyclohexane), in the cyanobacterium Anabaena sp., which can be considered a potential candidate for bioremediation of pesticides. We have studied the effect of lindane on the photosynthetic apparatus of Anabaena using fluorescence induction studies. As ferredoxin-NADP+ reductase plays a key role in the response to oxidative stress in several systems, changes in synthesis, degradation and activity of FNR were analyzed. Immunolocalization of this enzyme was used as a marker of phycobilisome integrity. The knowledge of the changes caused by lindane in the photosynthetic apparatus is essential for rational further design of genetically-modified cyanobacteria with improved biorremediation abilities.
Polyphasic chlorophyll a fluorescence rise measurements (OJIP) have been used to evaluate the vitality and stress adaptation of the nitrogen-fixing cyanobacterium Anabaena PCC 7119 in the presence of increasing concentrations of lindane. Effects of the pesticide on the ultrastructure have been investigated by electron microscopy, and FNR has been used as a marker of phycobilisome integrity.
Cultures of Anabaena sp. treated with moderate amounts of lindane showed a decrease in growth rate followed by a recovery after 72 hours of pesticide treatment. Concentrations of lindane below 5 ppm increased the photosynthetic performance and activity of the cells. Higher amounts of pesticide caused a decrease in these activities which seems to be due to a non-competitive inhibition of PS II. Active PS II units are converted into non-QA reducing, so called heat sink centers. Specific activity and amount of FNR in lindane-treated cells were similar to the values measured in control cultures. Release of FNR from the thylakoid after 48 hours of exposure to 5 ppm of lindane towards the cytoplasm was detected by immunogold labeling and electron microscopy. Conclusions. From these results, we conclude that the photosynthetic performance and activity of the cells are slightly increased in the presence of lindane up to 5 ppm. Moreover, in those conditions, lindane did not produce significant changes in the synthesis, degradation or activity of FNR. The high capability of Anabaena to tolerate lindane makes this cyanobacterium a good candidate for phytoremediation of polluted areas.
The results of this study show that cultures of Anabaena PCC 7119 tolerate lindane up to 5 ppm, without significant changes in the photosynthetic vitality index of the cells. However, a slight increase in phycobiliprotein synthesis is observed, which is related to total protein content. This change might be due to degradation of proteins less stable than phycobiliproteins. An identification of the proteins with altered expression pattern in the presence of the pesticide remains the subject of further work and will provide valuable information for the preparation of strains which are highly tolerant to lindane.
R Maldonado-Rodriguez, A Okarom (University Of Geneva, Switzerland), S Elmadidi (Laboratoire D'etude De La Variabilité Génétique, Morocco), A Gonzales (Inia, Spain) & R J Strasser (University Of Geneva, Switzerland)
I love drawing and painting. All the graphic design included in the software that I have written has been done entirely by me. I have made some cover designs for several scientific journals. For having a look at one of these covers please follow the links below:
The Microbiology Laboratory
of the Plant Biology department at the
Fluoromatics Software Website: Scientific Software, Consulting, Chlorophyll Fluorescence Analysis, Biolyzer web page.
El Pulpo Studio. This Web site was designed for Benedicto Garcia, a graphic artist living in Geneva and good friend of Ronald.
The APTE (Association for the Application and Promotion of Electronic Technologies) published an article in the BioWorld Europe Magazine about the work that Ronald did at the Bioenergetics Laboratory of the University of Geneva, Switzerland. You can read it in English or French. It is quite interesting and very informative.
Last modification on 15 April 2009 at 16:27h