Education September 2004 - december 2007 : PhD in Marine Biology at - - PDF document

Jonathan FLYE SAINTE MARIE Born the 8 june 1980 in Bédarieux (France) LEMAR – IUEM Phone : +33(0)2 98 49 88 99 Place Nicolas Copernic Email : jonathan.flye@univ-brest.fr 29280 PLOUZANE FRANCE

Education

– September 2004 - december 2007 : PhD in Marine Biology at Université de Bretagne Occidentale, Brest, France and Vrije Universiteit, Amsterdam, The Netherlands. Title : Ecophysiology of Brown Ring Disease in the Manila clam Ruditapes philippinarum, experimental and modelling approaches. Supervisors : Fredéric JEAN (Université de Bretagne Occidentale), Sebastiaan A.L.M. KOOIJMAN (Vrije Universiteit) and Christine PAILLARD (CNRS). Laboratories : Laboratoire de sciences de l’environnement marin (LEMAR CNRS UMR 6539), European Institute for Marine Studies (IUEM), Brest, France. Departement of theoretical biology, Vrije Universiteit, Amsterdam, The Netherlands. – February - April 2005 : Third international tele-course on Dynamic Energy Budjet theory, Vrije Uni- versiteit, Amsterdam. http ://www.bio.vu.nl/thb/deb/course/deb/. – September 2004 : Scientific diving (CAH classe 1 mention B) and CNRS diving manager training course, Roscoff. – 2001-2002 : Diplôme d’Etude Approfondies (Master equivalent) in Biological Oceanography and Ma- rine Environment. Speciality : data analysis and marine trophic webs modelling. European Institute for Marine Studies (IUEM), Université de Bretagne Occidentale, Brest, France. – 2000-2001 : Maîtrise (first year of Master equivalent) in Marine Populations and Ecosystems Biology. European Institute for Marine Studies (IUEM), Université de Bretagne Occidentale, Brest, France. (Rank : 2th/68) . – 1999-2000 : 3rd Year University Degree in Organisms Biology. Université Paul Sabatier-Toulouse III, Toulouse, France. (Rank : 3th/158). – 1997-1999 : General Universitary Dilopma in Life Sciences. Université Paul Sabatier-Toulouse III, Tou- louse, France.

Marine biology and ecology background

– March - August 2004 Employment in LEMAR CNRS UMR 6539 (IUEM, Brest, France). Implementation

• f a field survey of immunity, pathologies and physiology of a Manila clam population of Gulf of Morbihan

(France). – October-december 2003 : Employment in LEMAR CNRS UMR 6539 (IUEM, Brest, France). Crepidula fornicata and Pecten maximum biological samples preparation and packaging for isotopic analysis (carbon, nitrogen). – Septembre 2003 : Employment in LEMAR CNRS UMR 6539 (IUEM, Brest, France). Marine aggregate weel development. – February-June 2003 : Employment in ECOMAR (University de la Réunion, Saint Denis, Indian Ocean, France) Water samples analysis (total alcalinity, nitrate, phosphorus, silicate) and sediment samples analysis (CHN, cholorphyll and pheopigments). Data analysis. 1

– December 2002 : Employment in LEMAR CNRS UMR 6539 (IUEM, Brest, France). Seawater samples filtration, preparation and packaging for CHN analysis. Data analysis. – February-June 2002 : Master training research project (6 months) in LEMAR CNRS UMR 6539 (IUEM, Brest, France). Development of an ecophysiological model of individual growth of the manila clam, Rudi- tapes philippinarum. Supervisor : Frédéric JEAN. – February 2001 : First year of master training research project (1 month) in LEMAR CNRS UMR 6539 (IUEM, Brest, France). Shape variation in the dog whelk, Nucella lapillus, small spatial scale variations. Supervisor : Frédéric JEAN. – October 2000 : Participation to CERPIRAD scientific cruise in Bay of Brest. Crepidula fornicata beds cartography in the Bay of Brest.

Publications and Communications

Publications Flye-Sainte-Marie, J., Jean, F., Paillard, C., Ford, S., Powell, E., Hofmann, E., Klinck, J., 2007. Ecophysiological dynamic model of individual growth of Ruditapes philippinarum. Aquaculture 266, 130–143. Flye-Sainte-Marie, J., Pouvreau, S., Paillard, C., Jean, F., 2007. Impact of Brown Ring Disease on the energy budget of the Manila clam Ruditapes philippinarum. Journal of Experimental Marine Biology and Ecology 349 (2), 378–389. Ni’Longphuirt, S., Clavier, J., and Grall, J., Chauvaud, L. Le Loc’h, F., and Le Berre, I., Flye-Sainte-Marie, J., and Richard, J., Leynaert, A., 2007. Primary production and spatial distribution of subtidal microphytoben- thos in a temperate coastal system, the Bay of Brest, France. Estuarine, Coastal and Shelf Science. 74 (3), 367–380. Flye-Sainte-Marie, J., Jean, F., Ford, S. E., Paillard, C., Accepted (in révision). Effect of sediment grain–size on development of brown ring disease in the Manila clam Ruditapes philippinarum. Aquaculture Flye Sainte Marie, J., Soudant, P., Lambert, C., Le Goïc, N., Gonçalvez, M. Travers, M.-A., Paillard, C., Jean,

• F. Variability of the hemocyte parameters of Ruditapes philippinarum in the field during an annual cycle.

Submitted. Flye Sainte Marie, J., Kooijman, S.A.L.M., Paillard, C., Jean, F. Effect of brown ring disease on the energy bud- get of the Manila clam Ruditapes philippinarum, a modelling study. In prep. Paillard, C., Ford, S., Powell, E., Flye Sainte Marie, J., Jean, F., Klinck, J., Hoffman, E. A theoretical individual model of Brown Ring Disease in Manila clams, Ruditapes philippinarum. In prep. Oral communications Flye Sainte Marie, J., Soudant, P., Lambert, C. Da Silva, M., Paillard, C. and Jean, F.. Impact of Perkinsus sp. infection on haemocyte and physiological parameters of Manila clam Ruditapes philippinarum. Workshop for the Analysis of the Impact of Perkinsosis to the European Shellfish Industry. Vigo, Spain, Spetember 12-14, 2007. Soudant, P., Flye Sainte Marie, J., Lambert, C., Da Silva, M., Park, K.-I. Jean, F., Paillard, C., Choi. K.-S.. Varia- tions saisonnières des paramètres immunitaires de palourdes japonaise, Ruditapes philippinarum, naturelle- ment infectées par le protozoaire parasite, Perkinsus olseni. Réunion du Réseau Ecologie des Interactions Durables, Brest, France, January 29-31, 2007. Soudant, P., Lambert, C., Flye Sainte Marie, J., Da Silva, M., Park, K.-I. Jean, F., Paillard, C., Choi. K.-S.. Impact

• f Perkinsus olseni infection on the physiological and hematological parameters of the clams Ruditapes
• philippinarum. 9th International Congress on Medical and Applied Malacology (ICMAM), Qingdao, China,

October 17-20 , 2006. Soudant, P., Lambert, C., Flye Sainte Marie, J., Da Silva, M., Park, K.-I. Jean, F., Paillard, C., Choi. K.-S.. Impact

• f Perkinsus olseni infection on the physiological and hematological parameters of the clams Ruditapes
• philippinarum. International Workshop on Summer Mortality of Marine Shellfish, Pusan National University,

Busan, Korea, October 11-14, 2006. Flye Sainte Marie, J., Jean, F., Paillard, C. Mieskin, S., Powell, E., Ford, S. E., Klinck, J., Hoffman, E.. Modé- lisation de la maladie de l’anneau brun chez la palourde Ruditapes philippinarum. Colloque PNEC, "Déve- loppements récents de la recherche en environnement côtier", Nantes, France, June 26-28, 2006. 2

Gonçalves, M., Flye Sainte Marie, J., Lambert, C., Jean, F., Le Goïc, N., Paillard, C., Soudant, P.. Variations saisonnières des paramètres pathologiques, immunologiques et physiologiques chez la palourde japonaise, Ruditapes philippinarum dans le Golfe du Morbihan, Morbihan, France. Colloque PNEC, "Développements récents de la recherche en environnement côtier", Nantes, France, June 26-28, 2006. Flye Sainte Marie, J., Jean, F., Paillard, C.. Modélisation de la maladie de l’anneau brun chez la palourde Ru- ditapes philippinarum. Réunion du Réseau Ecologie des Interactions Durables, Dijon, France, 9-11 janvier 2006. Flye Sainte Marie, J., , Ford, S. E. Jean. F., Powell, E., Klinck, J. Hoffman, E., Paillard, C.. Modelling Brown Ring Disease in the Manila Clam, Ruditapes philippinarum : A numerical model. textit8th Internationnal Conference on Shellfish Restoration, Brest, France, October 2-5, 2005. Flye Sainte Marie, J., Jean. F., Paillard, C., Klinck, J., Hoffman, E., Ford, S. E. Powell, E.. Modelling Brown Ring Disease in the manila clam (Ruditapes philippinarum) : The individual host model. 97th Annual Meeting of the National Shellfisheries Association, Philadelphia, USA, April 10-14, 2005. Paillard, C., Flye Sainte Marie, J., Jean, F., Ford, S. E., Powell, E., Klinck, J., Hoffman, E.. An integrated ap- proach to bacteria-bivalve interactions : developmment of a vibriosis model in the manila clam. 97th Annual Meeting of the National Shellfisheries Association, Philadelphia, USA, April 10-14, 2005. Ford, S. E., Powell, E., Paillard, C., Flye Sainte Marie, J., Jean, F., Klinck, J., Hoffman, E.. Brown Ring Disease : the integrated model. 97th Annual Meeting of the National Shellfisheries Association, Philadelphia, USA, April 10-14, 2005. Flye Sainte Marie, J., Jean, F., Ford, S. E., Powell, E., Klinck, J., Hoffman, E., Paillard, C.. Modelling Brown Ring Disease in the Manila Clam (Ruditapes philippinarum). Meeting of the Transversal Action “Impact of Parasites on Marine Organisms, Modulation by Environmental Factors“, PNEC, Brest, France, November 4-5, 2004. Paillard, C., Flye Sainte Marie, J., Jean, F., Ford, S. E., Powell, E., Klinck, J., Hoffman, E.. Climate warming and bacterial disease evolution in the marine environment : the Brown Ring Disease Model in bivalves. Confé- rences Jacques Monod ”Ecologie et évolution des relations hôte-parasite", Roscoff, France, September 4-8, 2004. Posters Flye Sainte Marie, J., and Jean, F. Energetic cost of perkinsosis in the clams Ruditapes philippinarum and Ru- ditapes decussatus, a modelling approach ?. Workshop for the Analysis of the Impact of Perkinsosis to the European Shellfish Industry. Vigo, Spain, September 12-14, 2007. Cuet, P., Clavier, J., Esbelin, C., Flye Sainte Marie, J., Frouin, P., Taddei, D. Community metabolism in soft bottoms of a coral reef affected by nutrient-enriched groundwater discharge. The Fourth WIOMSA Scientific Symposium, Grand Baie, Mauritius. August 29 – September 3, 2005 Other Flye-Sainte-Marie, J., 2007. Approche écophysiologique de la Maladie de l¿Anneau Brun chez la palourde ja- ponaise, Ruditapes philippinarum : expérimentations et modélisation. PhD Thesis of Université de Bretagne Occidentale, France, 150 p. Flye-Sainte-Marie, J., 2008. Ecophysiology of the Manila clam Ruditapes philippinarum, experimental and mo- delling approaches. PhD Thesis of Vrije Universiteit, The Netherlands, 179 p. Flye-Sainte-Marie, J., Développement d’un modèle de croissance de la palourde japonaise (Ruditapes philippi- narum), basé sur le bilan énergétique. Mémoire de DEA de l’Université de Bretagne Occidentale, 31 p.

Teaching and student tutoring

– November-December 2006 : Licence 3 in Biologic Sciences. Course and practical works in molluscs physio-

• logy. Approach of bioenergetic aspect of growth. Impact of surce to voluma ratio on the growth of Ruditapes

philippinarum and Pecten maximus (12h) – November-December 2006 : Licence 3 in Biologic Sciences. Course and practical works in molluscs phy-

• siology. A modelling approch for the growth of Pecten maximus. (8h).

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– October 2006 : Master 1 in Marine Biologic Sciences. Course and practical works in Population Biology. Growth : methods, mesurements and modelling. (13h). – January-february 2006 : Tutoring one Master 1 student in Marine Population and Ecosytem biology. Trai- ning research project (2 months) : Impact of Brown Ring Disease on the energy budget of the Manila clam Ruditapes philippinarum. – November 2005 : Master 1 in Littoral environment appraisal and gestion. Practical works in ecology. Inter- tidal zone initiation. Tutoring the field works (4h). – October 2005 : Master 1 in Marine Biologic Sciences. Course and practical works in Population Biology. Growth : methods, mesurements and modelling. (8h). – October 2005 : Master 2 in Marine Biologic Sciences. Course in ecophysiology. Aquatic animals bioener- getics (4h). – February - march 2005 : Tutoring one Master 1 student in Marine Population and Ecosytem biology. Training research project (2 months) Seasonnal evolution of brown ring disease in manila clam (Ruditapes philippi- narum) population of Bailleron island, Golfe du Morbihan, Britanny, France. – June-july 2005 : Tutoring one 3rd year University degree student in Population and Ecosytem Biology. Training research project (1 month). Size-frequency distribution evolution in the manila clam (Ruditapes philippinarum) population of Bailleron island, Golfe du Morbihan, Britanny, France. – June-july 2005 : Tutoring one Master 1 student in Marine Population and Ecosytem biology. Training re- search project (2 months) : Development of mesure modalities of respiration rate at an individual scale in Ruditapes philippinarum using ecophysiological chambers. – March 2004 : 3rd year University degree in Population and Ecosytem Biology. Practical works in ecology. Intertidal mussel bed dynamics. Tutoring the field works (8h). – March 2004 : General Universitary Dilopma in Life Sciences. Practical works in ecology. Intertidal zone ecological gradients. Tutoring the field works (8h).

Administrative tasks

– 2005-2006 : Member of the Laboratory council of LEMAR. – 2005 : Member of the Organisation Committee of the 8th Internationnal Conference on Shellfish Restora- tion, Brest, France, 2-5 October 2005.

Technical qualifications

Modelling – Energy budget modelling (Application of Dynamic Energy Budget theory and Scope for Growth concept in molluscs). – Marine trophic food webs modelling. Informatics – Operating Sytems : Linux/Unix, Windows and Macintosh. – Softwares – Office softwares : LaTeX, OpenOffice, Gnumeric, M.S. Word, M.S. Exel and M.S. Powerpoint. – Statistics softwares : R, Statistica, Statgraphics plus, Systat. – Programmation languages : Octave/Matlab, Fortran 77, Bash, CSH. 4

Analytical chemistry – Seawater analysis using automatic analyser (Technicon) : (silicate, nitrate, phosphate). – Classical seawater analysis (total Alcalinity, chlorophyll and pheopigments.. .). – Samples packaging (biologic sapmles, filters and sediment) for CHN and isotopic analysis. Other technical qualifications – Scientific diving : Scientific diver diploma (CAH classe 1 mention B), CNRS diving manager. Diving technical qualifications : – In situ benthic chambers for water-sediment fluxes measures (deployement, water sampling. . .). – Unperturbing coring. – Macrofauna and sediment sampling. – Instrumentation deployement (Water velocity measures . . .) – Research and orientation technics. – Photography and video technics. – Instrumental development : development of in situ ecophysiological chamber for individual scale mesures (respiration and filtration) on small size bivalves. – Macrofauna sampling. – Hydrologic monitoring. – Autonomous probes use and maintenance (YSI type).

Collaborations

– Susan E. FORD and E. POWELL. Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA. – Sebastian A. L. M. KOOIJMAN. Theoretical Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, Amsterdam. – Stéphane POUVREAU. IFREMER, UMR "Physiologie et Ecophysiologie des Mollusques Marins", Pres- qu’île du Vivier 29840 Argenton en Landunvez, France. – John KLINCK and Eileen HOFFMANN. Center for Coastal Physical Oceanography, Old Dominion Univer- sity, Crittendon Hall, Norfolk, VA 23529, USA.

Languages

– English : Fluent. – Spanish : School level.

Other

– French driving licence. – Coastal boat french driving licence. – Leisure activities : – Sailing, cruising. – Sailing boat renovation. – Woodwork. – Diving : One star CMAS diving instructor. – Underwater photography. 5