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INFO ABOUT
BIOLYZER SOFTWARE
?
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:
1. Biolyzer. Computer program for chlorophyll a
fluorescence analysis. Link to Biolyzer Official Web Site
2.
BioVision. Software for analysis of plant
fluorescence 2D time sequenced images. Link
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.
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
in
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
http://www.bioone.org/doi/abs/10.1614/WS-04-131R?journalCode=wees
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
http://www3.interscience.wiley.com/journal/118647272/abstract
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.
http://deposit.ddb.de/cgi-bin/dokserv?idn=977715671&dok_var=d1&dok_ext=pdf&filename=977715671.pdf
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.
http://www.publish.csiro.au/paper/FP05095.htm
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
http://www.scielo.br/scielo.php?pid=S1677-04202007000300001&script=sci_arttext&tlng=ptrg
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
http://dx.doi.org doi:10.1016/j.sajb.2007.08.004
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
www.disat.unimib.it/Telerilevamento/Download/Tesi/Rossini_dott.pdf
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.
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.
During
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
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?
Link: Environmental Chemistry Letters (2003) 1(3): 201–205
Springer
ISSN: 1610-3653 (Paper) 1610-3661 (Online)
DOI: 10.1007/s10311-003-0034-7
For a PDF copy of this paper click here
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
Zlatarov, 8010
(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
Abstract
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
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
Abstract
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.
Abstract
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,
CH-1254 Jussy,
Abstract
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
(Hofstetten,
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
Abstract
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.
In
preparation
Laboratory of Bioenergetics and Microbiology.
Resumen
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
Link: Journal of Plant Physiology 160 (1):
81–90 (2003)
Urban & Fischer Verlag Publishers DOI: 10.1078/0176-1617-00917
For a PDF copy of this article click here
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.
Petar H. Lambrev,
Vassilij N. Goltsev, Ronald Maldonado
Rodríguez, Reto J. Strasser
1 Faculty of Biophysics. University of Sofia “Kliment Ohridskii”;
Sofia, Bulgaria
Effects
of Lindane on the Photosynthetic Apparatus of the Cyanobacterium Anabaena:
Fluorescence Induction Studies and Immunolocalization
of Ferredoxin-NADP+ Reductase.
Environmental Sciences & Pollution Research 11 (2)
98–106 (2004)
DOI: http://dx.doi.org/10.1065/espr2003.10.175 Link to the Publisher Web site
For a free PDF copy of this article click here
3 Bioenergetics
and Microbiology Laboratory, 10 Chemin des Embrouchis, CH-1254 Jussy,
Switzerland
Intention, Goal,
Scope, Background
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.
Software for calculation
and plotting of the membrane energetic fluxes: The pipeline model
R. Maldonado Rodriguez, R. Strasser
Fluorescence
Workshop. Institute of Plant Physiology. University of Leipzig
Oral
presentation Basel March 2000
R. Maldonado Rodriguez, R. Strasser
Swiss Canopy
Crane Project Workshop. Institute of Botany, Basel.
Oral
presentation Basel April 2001
R. Maldonado Rodriguez, R. Strasser
Swiss Canopy Crane
Project Workshop. Institute of Botany, Basel.
Oral
presentation Basel March 2003
R. Maldonado Rodriguez, R. Strasser
Swiss Canopy
Crane Project Workshop. Institute of Botany, Basel.
Oral
presentation Basel February 2004
R. Maldonado Rodriguez, R. Strasser
Swiss Canopy
Crane Project Workshop. Institute of Botany, Basel.
The JIP Test: A
New Tool in Plant Research
R. Maldonado Rodríguez, C. Hermans, R.
Strasser
Biotechnology
Start-up Workshop organized by ETH Zurich
Biosensing methods
to assess environmental stress encountered by sugar beet (Beta vulgaris
L.).
Hermans, C. Maldonado-Rodríguez R., Strasser, R. J.
Proceedings of
the 24th IIRB Congress. 26-27 June 2001. Bruges, Belgium. Page 424-428
Coral life as
probed by their fluorescence emission
F. Sinniger, R. Maldonado Rodríguez, R. J. Strasser
Link to
abstract in CSIRO PUBLISHING -
Science Access
Proceedings of
International Photosynthesis Congress.
Brisbane Convention & Exhibition
Proceedings of the 12th International Congress on
Photosynthesis. Brisbane Australia 2001 ISBN O 643 06711 6
P. Schmitz, R. Maldonado Rodríguez, R. Strasser
Link to
abstract in CSIRO PUBLISHING -
Science Access
Proceedings of
International Photosynthesis Congress.
Brisbane Convention & Exhibition
Proceedings of the 12th International Congress on
Photosynthesis. Brisbane Australia 2001 ISBN O 643 06711 6
http://www.publish.csiro.au/?act=view_file&file_id=SA0403684.pdf
Poster Czech
Republic, Novy-Hradic August 2001
R. Maldonado Rodríguez, R. Strasser
Oral
presentation Varna, Bulgaria September 2002
Goltsev, V., Zaharieva, I., Lambrev, Maldonado-Rodriguez, R., Strasser, R. J.
European Workshop on Environmental Stress and Sustainable Agriculture, 7-12 September 2002,
Alberto González Moreno1, Ronald Maldonado Rodríguez2
1 INIA Carretera de la Coruña, 28040 Madrid, Spain
Plant Physiology Workshop Cordoba July 2002 organized by the University
of Barcelona, Spain.
Artificial Neural Networks for the Characterization of Eight Varieties of
Pea (Pisum Sativum)
This
poster was awarded with the “BEST STUDENT POSTER” prize, selected among other
633 posters.
R. Maldonado Rodríguez1, A.
Gonzales2, L. Ayerbe2, J. Sanches2,
S. V. Pavlov3, R. Strasser1
2 INIA Ctra de la Coruña, 28040 Madrid, Spain
3 Department of Mathematics, University Assen
Zlatarov, 8010
How Pea Plants Respond To Elevated Temperature and Repetitive Saturating
Light Pulses
A. Okarum, R. Maldonado Rodríguez, R. J. Strasser
Characterization Of Eight Varieties Of Pea (Pisum Sativum) By the
Jip-Test
A. Gonzales1, F. Reverchon2, R. Maldonado
Rodríguez2, R. Strasser2
1 INIA Ctra de la Coruña, 28040 Madrid, Spain
Ronald Maldonado Rodríguez1, Stancho Vaelkanov Pavlov2,
Reto Strasser1
3rd European
Meeting on Environmental Chemistry EMEC3, December 11 to 17 2002 Geneva,
Switzerland.
Poster EMEC3 Geneva December 2002
P. Schmitz1,
R. Maldonado Rodríguez1, S. Pavlov2, W. Broughton3,
R. Strasser1
2 Department of Mathematics, Technological University Assen Zlatarov,
8010
3rd European Meeting on Environmental Chemistry
EMEC3, December 11 to 17 2002 Geneva, Switzerland.
Poster Geneva EMEC3 December 2002
A. Okarom, R.
Maldonado Rodríguez, S Elmadidi & R. J. Strasser
3rd European Meeting on Environmental Chemistry
EMEC3, December 11 to 17 2002 Geneva, Switzerland.
Oral presentation Cordoba March 2003
Ronald Maldonado
Rodríguez1, Stancho Pavlov2, Reto
Strasser1
(1)
Bioenergetics Laboratory, 10 Chemin des Embrouchis, CH-1254 Jussy, Switzerland
(2)
Department of Mathematics, University Asen Zlatarov, 8010
Can machines
recognize stress in plants? A neural Network Approach
Ronald Maldonado
Rodríguez1, Stancho Pavlov2, Reto
Strasser1
(1)
Bioenergetics Laboratory, 10 Chemin des Embrouchis, CH-1254 Jussy, Switzerland
(2)
Department of Mathematics, University Asen Zlatarov, 8010
Poster presentation Mallorca March 2003
Oral presentation Basel February 2004
R. Maldonado Rodríguez, R. Strasser
Bioenergetics
Laboratory, 10 Chemin des Embrouchis, CH-1254 Jussy, Switzerland
Swiss Canopy Crane Project Workshop February 2004.
Institute of Botany, Basel.
Rafael Mª Navarro Cerrillo, Ronald
Maldonado Rodríguez, David Ariza
Bioenergetics Laboratory, 10 Chemin des Embrouchis,
CH-1254 Jussy, Switzerland
Anna
Pérez-Méndez, Elizabeth Torres-Rivas, Francklin Rivas-Echeverría, Ronald
Maldonado-Rodríguez
WSEAS Neural Networks, Fuzzy Systems, Evolutionary
Computing Conference (Lisbon 2005)
Poster Presentation. Bern 4 April 2007
Ronald MALDONADO RODRIGUEZ1, Yuxin YUAN2,
Reto J. STRASSER3
1. Institute
Universitaire d’Etudes du Développement, 63 Rue de Lausanne, Genève 1202,
Suisse. e-mail: [email protected]. http://www.fluoromatics.com
2. College of
3. Laboratory of Bioenergetics, University of Geneva,
10 Ch. des Embrouchis, Jussy, Geneva CH-1254, Switzerland. email: [email protected] http://www.unige.ch/sciences/biologie/bioen
Eighth Swiss Global
Change Day. Bern 4 April 2007
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:
Functional Plant Biology Vol. 30, Number 7, 2003
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.
Last modification on 15 April 2009 at 16:27h