·        Labos CNRS:

LOV -Villefranche sur mer

L'automate de Villefranche comprend intrinsèquement, outre les réacteurs ou incubateurs et les systèmes d'alimentation de fluides, une série d'appareils à demeure: deux compteurs optiques laser de particules HIAC (Pacific Scientific), 2 chaînes d'analyse de sels nutritifs Technicon, un spectrophotomètre UV/Visible VARIAN, un système d'éclairement modulable, un système de mesure et de contrôle du pH et de la température, un système de régulation de la pCO₂.

Sont à disposition au sein du LOV un analyseur Carbone-Hydrogène-Azote particulaire Leico-900, Carbone total TOC-5000 Smimadzu, des compteurs à scintillation, des chaînes d'analyse de sels nutritifs Alliance, des compteurs de particules Coulter-Counter, des microscopes à épifluorescence dotés de systèmes d'analyse d'image, des oxymètres de précision, des spectrofluorimètres, spectrophotomètres Perkin, des chaînes d'analyse HPLC automatisées, des AC9 (absorption-atténuancemètre 9 longueurs d'ondes), fluorimètres en lignes PAM (Pulse Amplitude Modulated Fluor.), et FRR (Fast Repetition Rate Fluor.), Salinomètre, Photosynthétron, Autoclave, etc.

Laboratory of Photosynthesis, AVCR

Les chercheurs de la république tchèque impliqués dans ce projet disposent d'un laboratoire très bien équipé pour développer des approches biophysiques et moléculaires de la photosynthèse:

·        Biochimie de base: Ultracentrifugation Beckman, , HPLC Pharmacia, électrophorèse et équipement blotting , système HPLC avec absorption, fluorescence et/ou détection M , compteur à scintillation Packard 1500, électrodes à oxygène Clark, etc.

·        Equipement de biologie moléculaire: PCR, four à hybridation, système gel documentation, électrophorèse, etc.

·        Equipement biophysique – spectrophotomètre double faisceau Shimadzu UV 3000, spectrofluorimètre Aminco AB2, fluorimètre PAM Walz 101-103, spectrophotomètre portable Avantes, kinetic fluorimètre programmable Photon System Instruments, fluorimètre FRR, Microscope à épifluorescence,  autoclave, etc.

En venant à Villefranche-sur-mer pour utiliser les fonctionnalités de l'automate de culture, les chercheurs de Trebon trouveront un environnement adéquat à l'application de leur méthode, grâce notamment au Laboratoire de Biologie Cellulaire Marine qui occupe le même bâtiment que le LOV, et qui mettra à disposition le matériel nécessaire au déploiement des techniques de biologie moléculaire.

Moyens de calculs, INRIA-LODYC

Les moyens de calculs légers sont disponibles à travers les stations de travail HP du LOV. Les calculs lourds peuvent être effectués à l'INRIA de Nice-Sophia-Antipolis dans le cadre de l'équipe mixte CNRS/INRIA COMORE (Contrôle et Modélisation des Ressources Exploitées), ainsi qu'au LODYC.

Elles sont présentées uniquement pour les membres des équipes participant au projet, depuis 1998.

  ·        LOV

Andersen, V. and Prieur, L 2000 . High Frequency time series observations in the open Northwestern Mediterranean Sea and effects of wind events (DYNAPROC study, May 1985). Deep Sea Res. I, 47, 3, 397-422.

Arino, J., Gouzé, J.L., Sciandra, A. (en révision). A discrete, size-structured model of phytoplankton growth in the chemostat. J. Math Biol.

Babin, M., and D. Stramski (sous presse). Light absorption by aquatic particles in the near-infrared spectral region. Limnology and Oceanography, in press.

Babin, M., Stramski, D. Ferrari, G.M., Claustre, H., Bricaud, A., Obolensky, G., et N. Hoepffner (sous presse). Variations in the light absorption coefficients of phytoplankton, non-algal particles, and dissolved organic matter in coastal waters around Europe, Journal of Geophysical Research, in press.

Behrenfeld, M.J., Prasil, O., Kolber, Z.S., Babin, M. and P.G. Falkowski (1998) Changes in electron turnover rates protect photosynthesis from photoinhibition. Photosynthesis Research, 58, 259-268.

Bernard O, Sallet G, Sciandra A (1998a) Nonlinear observers for a class of biological systems: Application to validation of a phytoplanktonic growth model. IEEE - Transactions on Automatic Control 43:1056-1065

Bernard O, Sallet G, Sciandra A (1999) Use of non linear software sensors to monitore the internal state of a culture of microalgae IFAC World Congress, Beijing, pp 469-474.

Bernard, O., Sciandra, A., Sallet, G. (2001). A non-linear software sensor to monitor the internal nitrogen quota of phytoplanktonic cells. Oceanologica Acta 24: 435-442

Bernard O, Sciandra A, Sallet G (1998b) High gain nonlinear softwares to monitore a culture of microalgae From sensors to decision support systems in agriculture, food-industry and environment, CDROM, Montpellier, France

Bricaud, A., Morel, A., Babin, M., Allali, K., and H. Claustre (1998) Variations of light absorption by suspended particles with chlorophyll a concentration in oceanic 'case 1) waters: Analysis and implications for bio-optical models. Journal of Geophysical Research, 103, 31033-31044

Bruyant, F., M. Babin, A. Sciandra, D. Marie, B. Genty, H. Claustre, J. Blanchot, A. Bricaud R. Rippka, S. Boulben, F. Louis and F. Partensky (2001) An axenic cyclostat of Prochlorococcus PCC 9511 with a simulator of natural light regimes. J. Appl. Phycol., 13:135-142.

Chifflet, M., Andersen, V., Prieur, L. and I. Dekeyser 2001. One dimensional model of short term dynamics of the pelagic ecosystem in the NW Mediterranean Sea. Effects of wind events. J. Mar. Systems 30, 89-114.

Claustre H, Fell F, Oubelkheir K, Prieur L, Sciandra A, Gentili B, Babin M (2000) Continuous monitoring of surface optical properties across a geostrophic front: Biogeochemical inferences. Limnol. Oceanogr. 45:309-321

Claustre, H., Bricaud, A, Babin, M., Bruyant, F., Guillou, L., Le Gall, F, & F. (soumis) Partensky. Diel variations in Prochlorococcus optical properties. Limnology and Oceanography.

Claustre, H., Morel, A., Babin, M., Caillau, C., Marie, D., Marty, J.-C., et D. Vaulot (1999). Variability in particle attenuation and stimulated fluorescence in the tropical and equatorial Pacific : scales, patterns and some biogeochemical implications. Journal of Geophysical Research,104, 3401-3422.

Collos JY, Mornet F, Sciandra A, Waser N, Larson A, Harrisson PJ (1999) An optical method for the rapid measurement of micromolar concentrations of nitrate in marine phytoplankton cultures. J. Applied phycol. 11:189-194

Collos Y, Sciandra A, Martin-Jézéquel V, Slawick G, Garcia N (1998) Dilution of 15N in Dunaliella tertiolecta by uptake of an unidentified nitrogen compound following nitrate exhaustion. C. R. Acad. Sci. 321:673-677

Garczarek^, L^., F. Partensky, H. Irlbacher, J. Holtzendorff, M. Babin, I. Mary, J.-C. Thomas and W. R. Hess (2001) Differential expression of antenna and core genes in Prochlorococcus PCC 9511 (Oxyphotobacteria) grown under a modulated light-dark cycle. Environmental Microbiol., 3: 168-175.

Le Floc'h E, Malara G, Sciandra A (in revision) An automatic device for in vivo absorption spectra acquisition in phytoplanktonic cultures: application to the study of photoadaptation to light and nutrient variations. J. Applied Phycol.

Le Floc'h E, Sciandra A (2000) Adaptation of pigment composition to interactive effects of light and nitrogen in Rhodomonas salina (Cryptophyceae) ASLO meeting, Abulquerque

Leboulanger C, Martin-Jézéquel V, Descolas-gros C, Sciandra A, Jupin H (1998) Photorespiration in continuous cultures of Dunaliella teriolecta (Chlorophyta) : relationships between serine, glycine and extracellular glycolate. J. Phycol. 34:651-654

Maritorena, S., M. Babin, H. Claustre, C. Payri, L. Bonnafous and A. Morel (sous presse) Photoacclimation in Pocillopora verrucosa zooxanthellae: comparison with a pelagic algal community. Oceanologica Acta.

Pawlowski L, Bernard O, Le Floc'h E, Sciandra A (2002) Qualitative behaviour of phytoplankton growth model in photobioreactor 15th IFAC World Congress, Barcelona, Spain

Sciandra, A., L. Lazzara, H. Claustre and M. Babin (2000) Responses of the growth rate, pigment composition and optical properties of Cryptomonas sp. to light and nitrogen stresses. Mar. Ecol. Prog.Ser. 201: 107-120

Stramski D, Sciandra A, Claustre H (2002) Variations in the optical properties of the marine diatom Thalassiosira pseudonana induced by various sources of growth limitation. Limnol. Oceanogr. 47:00-00

Tassan, S., G.M. Ferrari, A. Bricaud and M. Babin (2000) Variability of the amplification factor of light absorption by filter-retained aquatic particles in the coastal environment. Journal of Plankton Research, 22, 659-668.

Zakardjian, B. and Prieur, L. 1998. Biological and chemical signs of upward motions in permanent geostrophic fronts of the Western Mediterranean. J. Geophys. Res., 103, C12, 27849 - 27866.

Soumis:

Babin, M., A. Morel, V. Fournier-Sicre, G.M. Ferrari, F. Fell & D. Stramski. Variations in the scattering coefficient of marine particles in coastal waters around Europe. Journal of Geophysical Research.

Bruyant, F., M. Babin, B. Genty, O. Prasil, M.J. Behrenfeld, H. Claustre, A. Bricaud, J. Holtzendorf, M. Koblizek & F. Partensky. Diel variations in the photosynthetic parameters of Prochlorococcus strain PCC 9511: combined effects of photoacclimation and cell cycle. Limnology and Oceanography.

F. Bruyant, M. Babin, L. Prieur, H. Claustre, J.-C. Marty & P. Morin. Distribution of the photosynthetic parameters over the Almeria–Oran frontal system. Deep-Sea Research.

·         AVCR

Behrenfeld, M.J., Prasil, O., Kolber, Z., Babin, M., Falkowski, P. (1998) Compensatory changes in Photosystem II electron turnover rates protect photosynthesis from photoinhibition. Photosynthesis Research, 58: 259-268.

Berman-Frank I., Lundgren P., Chen Y.B., Küpper H., Kolber Z., Bergman B., Falkowski P. (2001) Segregation Of Nitrogen Fixation And Oxygenic Photosynthesis In The Marine Cyanobacterium Trichodesmium, Science 294, 1534-1537.

Durnford, D.; Prasil, O.; Escoubas, J.-M.; Falkowski, P. (1998) Assessing the Potential for Chloroplast Redox-Regulation of Nuclear Gene Expression. Methods in Enzymology, 297: 220-234.

Kaftan D., Meszaros T., Whitmarsh J. and Nedbal L. (1999) Characterization of Photosystem II activity and heterogeneity during the cell cycle of the green alga Scenedesmus quadricauda. Plant Physiol. 120: 433-441            

Kolber, Z., Prasil, O., Falkowski, P. (1998) Measurements of variable chlorophyll fluorescence using fast repetition technique I. Defining methodology and experimental protocols. Biochimica Biophysica Acta, 1367: 88-106.

Komenda J, Masojídek J (1998) The effect of Photosystem II inhibitors DCMU and BNT on the high light induced D1 turnover in two cyanobacterial strains Synechocystis PCC 6803 and Synechococcus PCC 7942. Photosynth. Res. 57, 193-202

Komenda, J., Hassan, H.A.G., Diner, B.A., Debus, R.J., Barber, J., Nixon, P.J.: Degradation of the Photosystem II D1 and D2 proteins in strains of the cyanobacterium Synechocystis PCC 6803 varying with respect to the type and level of psbA transcript. - Plant Mol. Biol. 42: 635-645, 2000

Komenda, J., Koblížek, M., Prášil, O. (2000) Mechanisms responsible for the distinct effects of phenylurea and phenolic herbicides on the Photosystem II photoinactivation in cells of the cyanobacterium Synechococcus PCC 7942. Photosynthesis Research 63: 135-144.

Küpper H., Šetlík I., Spiller M., Küpper F.C., Prášil O. (2002) Heavy metal-induced inhibition of photosynthesis: targets of in vivo heavy metal chlorophyll formation, J. Phycology, accepted

Küpper, H., Šetlík, I., Trtílek, M., Nedbal, L.: A microscope for two-dimensional measurements of in vivo chlorophyll fluorescence kinetics using pulsed measuring radiation, continuous actinic radiation, and saturating flashes. - Photosynthetica 38 (4): 553-570, 2000

Lardans, A., Forster, B., Prasil, O., Falkowski P.G., Sobolev, V., Edelmna, M., Osmond, C.B., Gillham, N.W., Boynton, J.E. (1998) Biophysical, Biochemical and Physiological Characterization of Chlamydomonas reinhardtii mutants with Amino Acid Substitutions of the Ala251 residue in the D1 protein that result in varying levels of photosynthetic Competence. Journal of Biological Chemistry, 273: 11082-11091.

Lindell D., Erdner D., Marie D., Claustre H., Prášil O., Koblížek M., Le Gall F., Rippka R., Partensky F, Scanlan D.J., Post A.F. (2002) Contrasting expression of ntca and amt in Prochlorococcus sp. Strain PCC 9511. J. Phycology, accepted

Samson G., Prášil, O., Yaakoubd, B. (1999) Photochemical and Thermal Phases of Chlorophyll a Fluorescence. Photosynthetica 37: 163-182.

Šetlíková, E., D.Sofrová, O.Prášil, P.Budáč, M.Koblížek and I.Šetlik (1999) Integrity and activity of photosystem 2 complexes isolated from the thermophilic cyanobacterium Synechococcus elongatus using various detergents, Photosynthetica 37(2): 183-200.

Šprtová M., Marek M., Nedbal L., Prášil O. and Kalina J. (1999) Seasonal changes of photosynthetic assimilation in Norway spruce exposed to enhanced UV-B radiation. Plant Science 142: 37-45.

Steglich, C., Behrenfeld, M.J., Koblížek, M., Claustre, H., Penno, S., Prášil, O., Partensky, F., Hess, W.R.: Nitrogen deprivation strongly affects Photosystem II but not phycoerythrin level in the divinyl-chlorophyll b-containing cyanobacterium Prochlorococcus marinus. - Biochimica Biophysica Acta 1503: 341-349, 2001.

Sukenik A., Schneider J.C., Roessler P., Livne A., Berner T., Kolber Z., Wyman K., Prasil O. & Falkowski P. (1998) Photosynthetic characterization of a mutant of Nannochloropsis deficient in the synthesis of eicosapentaenoic acid. Israel J. Plant Sciences, 46: 101-108.

Tichý, M., and Vermaas, W. (1999)The in vivo role of catalase-peroxidase in Synechocystis sp. strain PCC 6803. J. Bacteriol. 181: 1875-1882.

Torzillo G, Bernardini P, Masojídek J (1998) On-line monitoring of chlorophyll fluorescence to assess the extent of photoinhibition of photosynthesis induced by high oxygen concentration and low temperature and its effect on the productivity of outdoor cultures of Spirulina platensis (Cyanobacteria), J. Phycol. 34, 504-510.

·        INRIA

Bernard, O.,Gouzé, J.L., « Transient behavior of biological loop models, with application to the Droop model », Mathematical Biosciences 127, 1995, p. 19-43.

Bernard, O., G. Sallet, Sciandra, A., « Nonlinear observers for a class of biological systems. Application to validation of a phytoplanktonic growth model. », IEEE Trans. Aut. Cont. 43, 8, 1998, p. 1056-1065.

Bernard, O., S. Souissi , Qualitative behavior of stage-structured populations: application to structural validation. J. Math. Biol. 37, 1998, p 291-308

Bernard, O.,Gouzé, J.L., Nonlinear qualitative signal processing for biological systems: application to the algal growth in bioreactors, Math. Biosciences 157, 1999, p. 357-372.

Bernard, O., Sciandra A. et Sallet G. Software sensor design to monitore a culture of microalgae. Oceanologica Acta 24, 2001, p 435-442

Bernard, O., I. Queinnec, Modèles dynamiques de procédés biochimiques, dans "Automatique des bioprocédés", Ed. D.Dochain, Hermes Science, 2001, p 23-52

Bernard, O.Gouzé, J.L., Estimation d'état, dans "Automatique des bioprocédés", Ed. D.Dochain, Hermes Science, 2001, p 87-120 ",

Bernard, O.,Gouzé, J.L., Global qualitative behavior of a class of nonlinear biological systems: application to the qualitative validation of phytoplankton growth models , Artif. Intel., à paraître en 2002.

Gouzé, J.L., Structure des modèles mathématiques en biologie , in: Analysis and optimisation of systems, A. Bensoussan, J. Lions (éditeurs), Lecture Notes in Control and Information Sciences, 111, Springer-Verlag, p. 1152-1163, 1998.

Gouzé, J.-L. (1998). Positive and negative circuits in dynamical systems. Journal Biol.

Syst., 6(1):11--15.

Touzeau, S. and Gouzé, J.-L. (1998). On the stock-recruitment relationships in fish population models.Environmental modelling and assessment, 3:87--93.

Gouzé, J. L., Rapaport, A., and Hadj-Sadok, Z. (2000). Interval observers for uncertain biological systems. Journal of Ecological modelling. 133: 45-56.

·        LODYC

Faugeras, B., Levy, M., Memery, L., Blum, J., and J. Verron (2002). Estimating the parameters of a 1D biogeochemical model to assimilate date from the DYFAMED station in the North Western Mediterranean Sea, submitted to J. Marine System.

Levy, M, Klein, P. and A.-M. Treguier (2001) Impacts of sub-mesoscale physics on phytoplankton production and subduction, J. Marine System, 59, 535-565.

Lévy, M. , Mémery, L., and J.-M. André (1998). Simulation of primary production and export fluxes in the NW Mediterranean Sea, J. Mar. Res. , 56, 197-238.

Levy, M., Estubier, A, and G. Madec (2001). Choice of an advection scheme for biogeochemical models, GRL, 3725-3728

Lévy, M., Mémery, L., and G. Madec (1998). The onset of a bloom after deep winter convection in the North Western Mediterranean Sea: mesoscale process study with a primitive equation model, J. Mar. Syst., 16, 7-21.

Lévy, M., Mémery, L., and G. Madec (1999) The onset of the spring bloom in the MEDOC area : mesoscale spatial variability, Deep-Sea Res, 46, 1137-1160.

Lévy, M., Mémery, L., and G. Madec (2000).Combined effects of mesoscale processes and atmospheric high-frequency variability on the spring bloom in the MEDOC area, Deep-Sea Res, 47, 27-53.

Lévy, M., Visbeck, M. and N. Naik (1999). Sensitivity of primary production to different eddy parameterizations : a case study of the spring bloom development in the northwestern Mediterranean Sea, J. Mar. Res.,57, 1-24.

Memery, L., Levy, M., Verant, S. and L. Merlivat (2002). The relevant time scales in estimating the air-sea CO2 exchange in a mid-latitude region : a numerical study at the Dyfamed station (NW Mediterranean Sea), Deep Sea Res., in press.

Loukos, H; Mémery, L (1999) Simulation of the nitrate seasonal cycle in the Equatorial Atlantic Ocean during 1983 and 1984. J. Geophys. Res,. 104: 155