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Welcome - Dr Desbenoit Nicolas

Nicolas Desbenoit
Dr Nicolas Desbenoit

Nicolas Desbenoit studied organic chemistry at the University of Orsay (Paris XI). He received his PhD from the University of Paris Descartes (Paris V) in 2009. After several post-doctoral stays in France (ICSN/CNRS), and in Germany (University of Justus-Liebig, and University of Bayreuth), Nicolas Desbenoit was recruited as a CNRS Chargé de Recherche in 2016 at CBMN (UMR 5248), and he joined team of Prof. M. Bonneu and Prof. J.-M. Schmitter (Spectrométrie de Masse des Macromolécules Biologiques) in January 2017.

His current research is focused on the development of the mass spectrometry imaging for the detection of lipids, metabolites, drugs, neurotransmitters present at the surface of tissue sections. He also will work on the development of the multimodal imaging combining the vibrational spectroscopies (Raman / FT-IR, collaboration with S. Lecomte team) and mass spectrometry.

Scientific seminar - Prof. Tokarski C

Professor Caroline Tokarski, Miniaturisation pour l’Analyse, la Synthèse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies, 59655 Villeneuve d’Ascq, France.

Date :  Thursday 15th June 2017, 4 pm, ENSCBP.

Title : "Art and Cultural Heritage natural polymers by bottom up and top down approaches".

Abstract : " The study of organic matter in Cultural Heritage samples is a real analytical challenge. Organic compounds are included in a complex matrix. They are submitted to environmental stress, denaturation and ageing for years. Finally, very low sample amounts are available for analysis. Considering artworks, characterization of organic compounds is an invaluable source of information for knowledge, understanding of a manufacturing process or comprehension of an artist’s technique. This information is also of main importance to propose adapted conservation conditions and best preservation/restoration treatments. In the case of archaeological and paleontological samples, information related to proteins may inform on species phylogeny, evolutionary links but also human habits.

Until recently, the organic compounds from Cultural Heritage samples were analyzed via their constitutive moieties (e.g. amino acids, fatty acids, monosaccharides) inducing a loss of information. In the early 2000s, we have successfully adapted proteomic (bottom up approach) and lipidomic methodologies to the study of few micrograms of historic art paintings or archaeological samples allowing for the first time the accurate structural identification as well as the identification of the biological species. These methodologies are currently used in the most famous international museums (e.g. Metropolitan Museum of Art, New York; Harvard Art Museum in Cambridge).

This conference will address our current challenges for analysis of Cultural Heritage samples:

(i) Because bottom up proteomics sometimes causes a loss of structural information or suffers from modifications induced by sample handling, we propose novel developments based on native protein analysis and top down proteomics. Application to the study of historic artworks (art paintings, photographs) will show how top down proteomics inform accurately on the degradation mechanisms of the organic media (e.g. protein breakdown) and protein chemical modifications such as oxidation, deamidation etc. (i.e. impact of restoration procedures and conservation conditions at molecular level). On another aspect, applied to the study of archaeological bones, relationship between protein chemical modifications, environment and ageing will be introduced (e.g. study of the 10-years frontier between forensics sciences and archaeology).

(ii) Applied to the study of historic watercolors and drawings exposed in the Metropolitan Museum of Art (New York), our metabolomic-like strategy using an enzyme cocktail will be presented through the identification of gums by structural elucidation and despite limitations such as partially unknown polymer structures and very low sample amounts.

(iii) The third example will develop potentialities of very high resolution mass spectrometry in combination with soft depolymerization experiments. This method unravel the 3D networks formed by the insoluble lipid-based film in oil-paintings. These first results provide new information related to the network structure formed between the unsaturated fatty acids in art oil painting via the detection of various multimers linked by C-C, C-O-C or C-O-O-C bonds. In particular, evidence of addition of β scission radical intermediate in the 3D framework are shown. We also observed that the hydrolysis of the bonds between the fatty acids and the glycerol results in fatty acid release known to be responsible of paint degradation by soap formation with pigment cations.

 

Short CV : Caroline Tokarski is Professor at Lille University. She is head of the MSAP laboratory (USR CNRS 3290) and member of the “Institut Universitaire de France”. She is also co-responsible of the Proteomic platform of Lille (IBISA label) and TGE FT-ICR platform of Lille. Her research activities are focused on methodological developments for analysis of proteins, lipids and carbohydrates from native or transformed biological samples using high resolution mass spectrometry. In particular, she proposed to adapt proteomics and lipidomics to cultural heritage samples to identify accurately proteins/lipids, their modifications and their biological origins. Currently these techniques are used routinely in the analytical laboratories of the most famous museums in the world (e.g. Metropolitan Museum of Art, New York; Harvard Art Museum, Cambridge). She was awarded by the Division of Analytical Chemistry of the French Chemistry Society in 2011. She is currently coordinator of Horizon 2020 JPI-JHEP ‘LeadART’ (2014-2018; 11 european partners) and coordinator of NORD_ART networks (NORD_ART links research, museums and archaeology in the Hauts de France region). Beyond her research activities, she is the study Director of the Bioanalytics’ specialty of the Chemistry and Health Sciences Master of the University of Lille (since its creation in 2010).

Contact : Jean-Marie Schmitter, jm.schmitter@cbmn.u-bordeaux.fr

Science communications 2016

Oral communications : 

  • Chaignepain S*. Structural characterization of the yeast CF IA complex through a combination of mass spectrometry approachesSymposium on Structural Proteomics, November 18th-19th 2016, Dortmund, Germany.
  • Ezzoukhry Z, Dupuy JW, Maitre M, Balabaud C, Bioulac-Sage P, Le Bail B, Raymond AA*, Saltel F. Development of a combined laser microdissection and proteomic analysis method, for identification of liver tumor signatures and targeted biomarkers quantificationSFSM, September 27th-30th 2016, Bordeaux, France.
  • Buré C*, Schmitter JM*Molecular imaging by MALDI mass spectrometry. INSERM U1034, September 15th 2016, Bordeaux, France.
  • Saucereau Y*, Valiente Moro C, Dieryckx C, Dupuy JW, Tran FH, Girard V, Potier P, Mavingui P.  Proteomic analysis of multipartite interactions in Aedes albopictus9th International Wolbachia Conference, June 28th – July 3th 2016, Queensland, Australia.
  • Rhourri-Frih B*Initiation à l’Imagerie par Spectrométrie de Masse. Workshop imagerie. May 20th 2016, Rabat, Maroc.
  • Chaignepain S*Mass spectrometry applied to proteomicsSimposio Applicaciones en proteomica y espectrometria de masa, March 11th 2016, Temuco, Chili.

 

Posters :

  • Machado ACL*, Catta-Preta CMC, Martins ACA, Lopez MG, De Souza W, Dupuy JW, Bringaud F, Motta MCM. Endosymbiosis in trypanosomatids: is the glycosome distribution and content influenced by symbiotic bacterium ? XXXI Annual Meeting of the Brazilian Society of Protozoology, November 07th-09th 2016, Caxambu, Brazil.
  • Vilain S, Le Sénéchal C, Crouzet M, Bonneu M, Schmitter JM & Buré C*Identification of Pseudomonas aeruginosa phospholipids involved in surface attachment12th gerli international lipidomics meeting, October 2016, Toulouse, France.
  • Vilain S, Le Sénéchal C, Crouzet M, Bonneu M, Schmitter JM & Buré C*Identification of Pseudomonas aeruginosa phospholipids involved in surface attachment. SFSM, September 27th-30th 2016, Bordeaux, France.
  • Milhorat L, Laporte A, Cota D, Bonneu M, Schmitter JM, Rhourri-Frih B*. Comparative study: The MALDI-TOF Mass Spectrometry Imaging and LC-MS/MS analysis of lipid profile in different organs from healthy and obese mice at three different agesSFSM, September 27th-30th 2016, Bordeaux, France.
  • Vilain S, Le Sénéchal C, Crouzet M, Bonneu M, Schmitter JM & Buré C*Identification of Pseudomonas aeruginosa phospholipids involved in surface attachment64th ASMS conference, June 5th-9th 2016, San Antonio, Texas, USA.
  • Milhorat L, Laporte A, Cota D, Bonneu M, Schmitter JM, Rhourri-Frih B*. Comparative study: The MALDI-TOF Mass Spectrometry Imaging and LC-MS/MS analysis of lipid profile in different organs from healthy and obese mice at three different agesLipidomics Impact on Metabolic, Cancer, Cardiovascular and Inflammatory Diseases, May 17th-18th 2016, La Jolla, California, USA.
  • Sy M, Moreau M, Dupuy JW, Bonneu M, Sans N, Schmitter JM, Buré C*. MALDI mass spectrometry molecular imaging of lipids in mouse brain in case of neurodevelopmental abnormalities of autistic spectrumWorkshop on Imaging Mass Spectrometry (WIMS), March 29th-31th 2016, Saint Malo, France.

 

 

 

HDR Defense - Dr Vilain Sébastien

Date : Friday 21th October 2016, 10h00, Amphitheater ENSTBB.

Title : "Study of the formation of bacterial biofilms - Analysis of the attachment phase and the molecular processes involved in Pseudomonas aeruginosa."

Abstract : The project aims to study the development of biofilms in Pseudomonas aeruginosa, and in particular to analyze the molecular events involved in the initial phase named attachment phase. A biofilm is a complex multicellular structure adhered to biotic and abiotic surface and composed of bacterial microcolonies embedded in an extracellular matrix self-generated by sessile bacteria. Sessile bacteria are characterized by an exceptional resistance to environmental stresses, particularly to antibiotics. The origin of this resistance remains poorly understood. In industry, biofilms deteriorate (bio-corrosion) or contaminate equipment (food industry, health...). These problems have a cost: the bio-corrosion costs 5 billion € per year in France. In the medical community, biofilms are associated with certain diseases (P. aeruginosa in cystic fibrosis, for instance) and are the cause of public health issues (colonization of implants, nosocomial infections). In France, 20% of inpatients contract a nosocomial disease, and in 50% of cases the infection is related to the presence of biofilms. Nosocomial infections cause 9000 deaths a year and would cost 4.5 billion € of additional care costs.

Studies in the field of Biofilmology aim to identify the molecular mechanisms involved in each phase of the development of biofilms. The associated objective is the identification of potential molecular targets to prevent biofilm formation and/or effectively fight against sessile bacteria. Many studies of mature biofilms were conducted. However, these studies were conducted under varying experimental conditions (substrate, medium, temperature ...), with different strains and biofilms of different ages (>6h to several days). This variability results in a weak correlation between studies. Therefore, few genes / proteins involved in the biofilm formation have been identified, and currently there is no effective way to fight against bacterial biofilms. It is therefore crucial to characterize in detail the molecular processes involved in all stages of the biofilm formation. Among these steps, the attachment phase is the least well characterized at the molecular level due to technical lock (insufficient biomass). Yet this critical stage of biofilm formation could be the Achilles heel of this growth mode. An original culture system was developed in the laboratory to study the early stages of bacterial attachment (Crouzet et al., 2014). This system provides, in 5 minutes, a sessile biomass sufficient to achieve comprehensive approaches to identify molecular compounds involved in the attachment phase. Among these compounds, some might be critical, and thus constitute potential molecular targets to fight against biofilms. To date, the studied molecular elements are proteins or lipids.
 

HDR Defense - Dr Buré Corinne

Date : Tuesday 17 may 2016, 14h, salle de conférences du Centre Génomique Fonctionnelle.

Title : "Analysis of biomolecules by fragmentation in mass spectrometry : from peptides to lipids".

Abstract : This work focuses on low-energy fragmentation mass spectrometry studies of various biomolecules such as peptides, proteins and lipids to meet different research problems. Thus, it is shown that the MS / MS and MS3 were used to identify and characterize a family of complex glycosylated lipids, GIPCs, then, with an additional dimension which is chromatography, LC-MS / MS has enabled identification of lipopeptides and quantification ofother lipids, such as phospholipids, estradiol and retinoic acid. Analysis of recent lipid families was used to test the reliability of the methods developed thanks to the diversity and complexity of the samples analyzed, these analyzes are conducted to answer biological questions such as studying signaling pathways ways in response to a stress, the search for new synthesis routes for PS rich in EPA and DHA for the food industry, research addressing rich phospholipid polyunsaturated fatty acids n-3 to formulate liposomes for nutritional applications, the search for new antimalarial strategies or understanding of memory decline. These lipidomic approaches will also be applied to very little explored diseases such as cystic fibrosis using Pseudomonas aeruginosa in particular at the level of the involvement of phospholipids and / or lipopolysaccharides in the initial phase (about ten minutes to 24h) of biofilm attachment. In addition, a new research topic using lipid analysis by the imaging technique using mass spectrometry (MALDI) consists on approaching the study of phospholipids involved in neurodevelopmental abnormalities of autistic-like model in mouse. In this project, the challenge is to identify markers of these lipidic anomalies, and to  locate and quantify these markers the brain, leading to a better understanding of autism.

Science communications 2017

Oral communications : 

  • Henriet E, Abou Hammoud A, Dupuy JW, Dartigues B, Ezzoukry Z, Dugot-Senant N, Leste-Lasserre T, Pallares-Lupon N, Nikolski M, Le Bail B, Blanc JF, Balabaud C, Bioulac-Sage P, Raymond AA*, Saltel F. Combined laser microdissection and proteomic analysis for identification of tumor signaturesSMMAP, October 03rd-05th 2017, Marne-la-Vallée, France.
  • Desbenoit N*, Scheier R, Löder MGJ, Schmitter JM, Laforsh C, Schmidt H, Römpp A. Multimodal imaging combining mass spectrometry and vibrational spectroscopy using a single tissue section and an integrated data processing workflow. OurCon V, September 24th-28th 2017, Doorn, The Netherlands.
  • Barlier C, Fagan J, Claverol S, Benamara H, Tavernier E, Cognasse F, Garraud O, Laradi S*. Modification du profil protéomique des plaquettes en cas d’effet indésirable receveur (EIR). XXVIII Congrès de la Société Française de Transfusion Sanguine. September 20th-22th 2017, Bordeaux France.
  • Blanc JF*, Ismaïl-Hammoud A, Henriet E, Dupuy JW, Dartigues B, Dugot-Senan N, Lebail B, Ezzoukry Z, Nikolski M, Bioulac-Sage P, Balabaud C, Raymond AA, Saltel F. Argininosuccinate Synthase 1 (Ass1) Is A Biomarker Useful To Classify Hepatocellular Adenoma By Immunohistochemistry. The International Liver Cancer Association (ILCA). September 15th-17th 2017, Seoul, South Korea.
  • Desbenoit N*, Scheier R, Löder MGJ, Schmidt H, Bonneu M, Schmitter JM, Römpp A. FT-IR/Raman imaging, & MALDI-MSI for a molecular view of the anatomical structure of biological tissues. Sfµ, July 04th-07th 2017, Bordeaux, France.
  • Desbenoit N*, Buré C, Frih B, Bathany K, Chaignepain S, Bonneu M, Schmitter JM. Label-free mass spectrometry imaging for biological applications: toward a molecular investigation without a priori. BIPSA, April 11th 2017, Bordeaux, France.
  • Desbenoit N*, Buré C, Frih B, Bathany K, Chaignepain S, Bonneu M, Schmitter JM. Mass spectrometry imaging: fundamental and applications. CBMN days, April 07th-08th 2017, Bordeaux, France.
  • Dupuy JW*. Quantitative mass spectrometry for the study of the trypanosome proteome. GlycoNov7 meeting (ANR Project), 02nd- 05th April 2017, Bombannes, France.

 

Posters :

  • Desbenoit N*, Scheier R, Loeder M, Schmidt H, Roempp A, Bonneu M, Schmitter JMLabel-free multimodal imaging for biological applications: toward a molecular investigation without a prioriSMMAP, October 03rd-05th 2017, Marne-la-Vallée, France.
  • Ezzoukhy Z, Henriet E, Cordelieres F, Dupuy JW*, Maitre M, Moreau V, Raymond AA, Saltel F. Laser capture and mass spectrometry combination for subcellular proteomicsSMMAP, October 03rd-05th 2017, Marne-la-Vallée, France.
  • Immel F*, Grison M, Fouché M, Claverol S, Bayer E. How nano-LC-MS/MS methods improve plasmodesmata proteome knowledgeSMMAP, October 03rd-05th 2017, Marne-la-Vallée, France.
  • Bathany K*, Claverol S, Oblet C, Aldigier JC, Druilhe A, Bonneu M, Schmitter JMCharacterization of N- and O-glycosylations of immunoglobulin IgA using NanoLC-MS/MS and Byonic softwareSMMAP, October 03rd-05th 2017, Marne-la-Vallée, France.
  • Desbenoit N*, Scheier R, Löder MGJ, Schmitter JM, Laforsh C, Schmidt H, Römpp A. Multimodal imaging combining mass spectrometry and vibrational spectroscopy using a single tissue section and an integrated data processing workflow. OurCon V, September 24th-28th 2017, Doorn, Pays-Bas.
  • Desbenoit N*, Buré C, Frih B, Bathany K, Chaignepain S, Bonneu M, Schmitter JM. Label-free mass spectrometry imaging for biological applications: toward a molecular investigation without a priori. TecSan, June 22th 2017, Bordeaux, France.
  • Abou Hammoud A, Henriet E, Dupuy JW, Dartigues B, Ezzoukhry Z, Dugot-Senant N, Leste-Lasserre T, Palleres-Lupon N, Nikolski M, Le Bail B, Blanc JF, Balabaud C, Bioulac-Sage P, Raymond AA*, Saltel F. Argininosuccinate synthase 1 (ASS1) immunomarker identifies unclassified hepatocellular adenoma with bleeding risk. EASL, The International Liver Congress. April 19th-23th April 2017, Amsterdam, The Netherlands.
  • Raymond AA*, Blanc JF, Dupuy JW, Le Bail B, Dugot-Senant N, Balabaud C, Bioulac-Sage P, Saltel F. Arginino succinate synthase 1 (ASS1) is a biomarker useful to classify hepatocellular adenoma by immunohistochemistry. Experience of a single French liver center. EASL, The International Liver Congress. April 19th-23th April 2017, Amsterdam, The Netherlands.