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1. The High Resolutive Detection of TiO2 Nanoparticles in Human Corneocytes via TEM/NanoSIMS Correlation

Author

Morgane Janin, Anthony Delaune, David Gibouin, Fabien Delaroche, Benjamin Klaes, Auriane Etienne, and Armelle Cabin-Flaman

Subjects
TEM, SIMS, correlation, image registration, SCP filter, nanoparticles, Technology, Engineering (General). Civil engineering (General), TA1-2040, Biology (General), QH301-705.5, Physics, QC1-999, Chemistry, QD1-999
Abstract

Titanium dioxide (TiO2) nanoparticles (NPs) are the subject of numerous studies and controversies on the risks they could pose to the environment and human health. When in contact with biological tissues, NPs can sometimes be challenging to precisely localize within subcellular structures (typically around 0.1 µm) when they exist as isolated NPs, particularly when using the SIMS approach. Indeed, the chemical signals produced by isolated NPs are very low, so they can be confused with background signals. This was the motivation behind our development of a new strategy for correlating TEM/SIMS to detect TiO2 NPs in close proximity to cutaneous corneocytes. For this purpose, we initially developed a new tool for TEM and SIMS image registration based on a non-rigid image-deformation-enabling image overlay. Combining SIMS and TEM data through this overlay enhances NP localization’s precision. Secondly, we developed an algorithm based on the statistical analysis of multiplane SIMS images to denoise them. As a result, background noise was reduced, illuminating the low yet specific signals from isolated NPs. Finally, this new correlative approach enables the precise 3D localization of isolated NPs within the analyzed volume. We consider this method a breakthrough for subcellular-scale NP localization.

Published
2023
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2. Division-Based, Growth Rate Diversity in Bacteria

Author

Ghislain Y. Gangwe Nana, Camille Ripoll, Armelle Cabin-Flaman, David Gibouin, Anthony Delaune, Laurent Janniere, Gerard Grancher, Gaelle Chagny, Corinne Loutelier-Bourhis, Esther Lentzen, Patrick Grysan, Jean-Nicolas Audinot, and Vic Norris

Subjects
heterogeneity, asymmetry, bacteria, DNA segregation, cell cycle, secondary Ion mass spectrometry, Microbiology, QR1-502
Abstract

To investigate the nature and origins of growth rate diversity in bacteria, we grew Escherichia coli and Bacillus subtilis in liquid minimal media and, after different periods of 15N-labeling, analyzed and imaged isotope distributions in individual cells with Secondary Ion Mass Spectrometry. We find a striking inter- and intra-cellular diversity, even in steady state growth. This is consistent with the strand-dependent, hyperstructure-based hypothesis that a major function of the cell cycle is to generate coherent, growth rate diversity via the semi-conservative pattern of inheritance of strands of DNA and associated macromolecular assemblies. We also propose quantitative, general, measures of growth rate diversity for studies of cell physiology that include antibiotic resistance.

Published
2018
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3. Combining combing and secondary ion mass spectrometry to study DNA on chips using 13C and 15N labeling [version 1; referees: 2 approved]

Author

Armelle Cabin-Flaman, Anne-Francoise Monnier, Yannick Coffinier, Jean-Nicolas Audinot, David Gibouin, Tom Wirtz, Rabah Boukherroub, Henri-Noël Migeon, Aaron Bensimon, Laurent Jannière, Camille Ripoll, and Victor Norris

Subjects
Structure: Transcription & Translation, Medicine, Science
Abstract

Dynamic secondary ion mass spectrometry (D-SIMS) imaging of combed DNA – the combing, imaging by SIMS or CIS method – has been developed previously using a standard NanoSIMS 50 to reveal, on the 50 nm scale, individual DNA fibers labeled with different, non-radioactive isotopes in vivo and to quantify these isotopes. This makes CIS especially suitable for determining the times, places and rates of DNA synthesis as well as the detection of the fine-scale re-arrangements of DNA and of molecules associated with combed DNA fibers. Here, we show how CIS may be extended to 13C-labeling via the detection and quantification of the 13C14N- recombinant ion and the use of the 13C:12C ratio, we discuss how CIS might permit three successive labels, and we suggest ideas that might be explored using CIS.

Published
2016
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4. 50nm-scale localization of single unmodified, isotopically enriched, proteins in cells.

Author

Anthony Delaune, Armelle Cabin-Flaman, Guillaume Legent, David Gibouin, Caroline Smet-Nocca, Fabrice Lefebvre, Arndt Benecke, Marc Vasse, and Camille Ripoll

Subjects
Medicine, Science
Abstract

Imaging single proteins within cells is challenging if the possibility of artefacts due to tagging or to recognition by antibodies is to be avoided. It is generally believed that the biological properties of proteins remain unaltered when (14)N isotopes are replaced with (15)N. (15)N-enriched proteins can be localised by dynamic Secondary Ion Mass Spectrometry (D-SIMS). We describe here a novel imaging analysis algorithm to detect a few (15)N-enriched proteins--and even a single protein--within a cell using D-SIMS. The algorithm distinguishes statistically between a low local increase in (15)N isotopic fraction due to an enriched protein and a stochastic increase due to the background. To determine the number of enriched proteins responsible for the increase in the isotopic fraction, we use sequential D-SIMS images in which we compare the measured isotopic fractions to those expected if 1, 2 or more enriched proteins are present. The number of enriched proteins is the one that gives the best fit between the measured and the expected values. We used our method to localise (15)N-enriched thymine DNA glycosylase (TDG) and retinoid X receptor α (RXRα) proteins delivered to COS-7 cells. We show that both a single TDG and a single RXRα can be detected. After 4 h incubation, both proteins were found mainly in the nucleus; RXRα as a monomer or dimer and TDG only as a monomer. After 7 h, RXRα was found in the nucleus as a monomer, dimer or tetramer, whilst TDG was no longer in the nucleus and instead formed clusters in the cytoplasm. After 24 h, RXRα formed clusters in the cytoplasm, and TDG was no longer detectable. In conclusion, single unmodified proteins in cells can be counted and localised with 50 nm resolution by combining D-SIMS with our method of analysis.

Published
2013
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5. Computing with bacterial constituents, cells and populations: from bioputing to bactoputing.

Author

Vic Norris, Abdallah Zemirline, Patrick Amar, Jean Nicolas Audinot, Pascal Ballet, Eshel Ben-Jacob, Gilles Bernot, Guillaume Beslon, Armelle Cabin, Eric Fanchon, Jean-Louis Giavitto, Nicolas Glade, Patrick Greussay, Yohann Grondin, James A. Foster, Guillaume Hutzler, Jürgen Jost, François Képès, Olivier Michel 0001, Franck Molina, Jacqueline Signorini, Pasquale Stano, and Alain R. Thierry

Published
2011
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6. Exploring fungus–plant N transfer in a tripartite ant–plant–fungus mutualism

Author

Nathalie Séjalon-Delmas, Céline Leroy, Yves Martinez, Jérôme Orivel, Armelle Cabin-Flaman, David Gibouin, and Alain Jauneau

Subjects
0106 biological sciences, 0301 basic medicine, Hypha, Nitrogen, Plant Science, Fungus, 01 natural sciences, Chrysobalanaceae, Plant use of endophytic fungi in defense, 03 medical and health sciences, Myrmecophyte, Ascomycota, Botany, Animals, Hirtella physophora, Symbiosis, Allomerus decemarticulatus, Mutualism (biology), Nitrogen Isotopes, biology, Ants, fungi, food and beverages, Original Articles, biology.organism_classification, Trichome, 030104 developmental biology, 010606 plant biology & botany
Abstract

Background and aims The plant Hirtella physophora, the ant Allomerus decemarticulatus and a fungus, Trimmatostroma sp., form a tripartite association. The ants manipulate both the plant trichomes and the fungus to build galleries under the stems of their host plant used to capture prey. In addition to its structural role, the fungus also improves nutrient uptake by the host plant. But it still remains unclear whether the fungus plays an indirect or a direct role in transferring nutrients to the plant. This study aimed to trace the transfer of N from the fungus to the plant's stem tissue. Methods Optical microscopy and transmission electron microscopy (TEM) were used to investigate the presence of fungal hyphae in the stem tissues. Then, a 15N-labelling experiment was combined with a nanoscale secondary-ion mass spectrometry (NanoSIMS 50) isotopic imaging approach to trace the movement of added 15N from the fungus to plant tissues. Key results The TEM images clearly showed hyphae inside the stem tissue in the cellular compartment. Also, fungal hyphae were seen perforating the wall of the parenchyma cell. The 15N provisioning of the fungus in the galleries resulted in significant enrichment of the 15N signature of the plant's leaves 1 d after the 15N-labelling solution was deposited on the fungus-bearing trap. Finally, NanoSIMS imaging proved that nitrogen was transferred biotrophically from the fungus to the stem tissue. Conclusions This study provides evidence that the fungi are connected endophytically to an ant-plant system and actively transfer nitrogen from 15N-labelling solution to the plant's stem tissues. Overall, this study underlines how complex the trophic structure of ant-plant interactions is due to the presence of the fungus and provides insight into the possibly important nutritional aspects and tradeoffs involved in myrmecophyte-ant mutualisms.

Published
2017
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7. Effect of zein additive on perfume evaporation

Author

P Poutrain, Anthony Delaune, A Léopoldès de Vendômois, David Gibouin, Armelle Cabin-Flaman, Y G Gangwe Nana, Camille Ripoll, S Trestour, J M Seigneuret, B Jourdain, J P Paris, P Cosette, J J Etienne, Groupe de physique des matériaux (GPM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Université de Rouen Normandie (UNIROUEN), Payan Bertrand S.A., Alban Muler International, Polymères Biopolymères Surfaces (PBS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), ATN Conseil, Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Olfactory perception, Aging, Zein, [SDV]Life Sciences [q-bio], Pharmaceutical Science, Dermatology, 01 natural sciences, Gas Chromatography-Mass Spectrometry, [SPI.MAT]Engineering Sciences [physics]/Materials, chemistry.chemical_compound, 0404 agricultural biotechnology, Colloid and Surface Chemistry, 010608 biotechnology, Drug Discovery, Humans, ComputingMilieux_MISCELLANEOUS, Chemistry, 04 agricultural and veterinary sciences, Penetration (firestop), 040401 food science, Perfume, Secondary ion mass spectrometry, Solvent, Eugenol, Chemistry (miscellaneous), Microscopy, Electron, Scanning, Nuclear chemistry
Abstract

Objective Zein is known to have filmogen properties. We wanted to show if a zein film containing eugenol (eugenol as model) would retain the fragrances, slow their evaporation and therefore produce a long-lasting perception of perfume. Methods We added corn zein to eugenol in a hydro-alcoholic solution to form a film in vitro and at the surface of the human skin. We have studied the trapping and release of eugenol from zein film by GC/MS. Also we labelled eugenol with deuterium to image specifically its distribution in the zein film using Secondary Ion Mass Spectrometry technique (NanoSIMS 50). Finally, we applied the zein/D-eugenol formulation onto skin to image the eugenol location on and in skin by SIMS (Secondary Ion Mass Spectrometry). Results We showed that eugenol evaporation from zein film can be divided in three periods. The first period (≤2 h) corresponds to the simultaneous solvent and eugenol evaporation occurring during film formation. The second period corresponds to the continuous and slow eugenol evaporation during a few hours (about 10 h) but not to its completion. The third period (at least up to 48 h) results from the trapping of eugenol in zein film. After 24 or 48 h, trapped eugenol can be released and evaporated under mechanical deformations of the film. Moreover we showed that zein addition does not favour the eugenol penetration into viable epidermis which may cause allergenic cutaneous reaction. Conclusion The zein additive is safe to use, does not impact the olfactory perception, allows a better perception of the fragrance (long-lasting effect) in a more protective way and can be used in perfume.

Published
2018
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8. Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis

Author

Hamid, Nouri, Anne-Françoise, Monnier, Solveig, Fossum-Raunehaug, Monika, Maciag-Dorszynska, Armelle, Cabin-Flaman, François, Képès, Grzegorz, Wegrzyn, Agnieszka, Szalewska-Palasz, Vic, Norris, Kirsten, Skarstad, Laurent, Janniere, Epigen Project, Centre National de la Recherche Scientifique (CNRS), 1Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, Institut National de la Recherche Agronomique (INRA), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Génopole [Evry], Université d'Évry-Val-d'Essonne (UEVE), Department of Molecular Biology, University of Gdańsk, Institut de biologie systémique et synthétique (ISSB), Université d'Évry-Val-d'Essonne (UEVE)-Génopole-Centre National de la Recherche Scientifique (CNRS), Unité Commune d'Expérimentation Animale de Vilvert (UCEA), University of Gdańsk (UG), and Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
dna replication, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV]Life Sciences [q-bio], Mutation, integrative biology, cell cycle, Full Papers, signalling, metabolism, Carbon, ComputingMilieux_MISCELLANEOUS, Bacillus subtilis, Culture Media
Abstract

International audience; DNA replication is coupled to growth by an unknown mechanism. Here, we investigated this coupling by analyzing growth and replication in 15 mutants of central carbon metabolism (CCM) cultivated in three rich media. In about one-fourth of the condition tested, defects in replication resulting from changes in initiation or elongation were detected. This uncovered 11 CCM genes important for replication and showed that some of these genes have an effect in one, two or three media. Additional results presented here and elsewhere (Janniere, L., Canceill, D., Suski, C., et al. (2007), PLoS One, 2, e447.) showed that, in the LB medium, the CCM genes important for DNA elongation (gapA and ackA) are genetically linked to the lagging strand polymerase DnaE while those important for initiation (pgk and pykA) are genetically linked to the replication enzymes DnaC (helicase), DnaG (primase) and DnaE. Our work thus shows that the coupling between growth and replication involves multiple, medium-dependent links between CCM and replication. They also suggest that changes in CCM may affect initiation by altering the functional recruitment of DnaC, DnaG and DnaE at the chromosomal origin, and may affect elongation by altering the activity of DnaE at the replication fork. The underlying mechanism is discussed.

Published
2018
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9. Division-Based, Growth Rate Diversity in Bacteria

Author

Armelle Cabin-Flaman, Corinne Loutelier-Bourhis, Patrick Grysan, Ghislain Y. Gangwe Nana, Gaelle Chagny, Laurent Jannière, Esther Lentzen, Vic Norris, G. Grancher, Camille Ripoll, David Gibouin, Anthony Delaune, Jean-Nicolas Audinot, Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Normandie Université (NU), Groupe de physique des matériaux (GPM), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie systémique et synthétique (ISSB), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques Raphaël Salem (LMRS), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut de Chimie Organique Fine (IRCOF), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Luxembourg Institute of Science and Technology (LIST), Materials Research and Technology (MRT) Department, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), secondary Ion mass spectrometry, 030106 microbiology, lcsh:QR1-502, Bacillus subtilis, DNA segregation, medicine.disease_cause, Microbiology, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, medicine, Growth rate, bacteria, Escherichia coli, isotope-labeling, Original Research, NanoSIMS 50, biology, Cell cycle, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, chemistry, Evolutionary biology, cell cycle, Steady state (chemistry), heterogeneity, human activities, Function (biology), Bacteria, DNA, asymmetry
Abstract

International audience; To investigate the nature and origins of growth rate diversity in bacteria, we grew Escherichia coli and Bacillus subtilis in liquid minimal media and, after different periods of 15N-labeling, analyzed and imaged isotope distributions in individual cells with Secondary Ion Mass Spectrometry. We find a striking inter- and intra-cellular diversity, even in steady state growth. This is consistent with the strand-dependent, hyperstructure-based hypothesis that a major function of the cell cycle is to generate coherent, growth rate diversity via the semi-conservative pattern of inheritance of strands of DNA and associated macromolecular assemblies. We also propose quantitative, general, measures of growth rate diversity for studies of cell physiology that include antibiotic resistance.

Published
2018
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10. Combining Combing and Secondary Ion Mass Spectrometry to Study DNA on Chips Using 13C and 15N Labeling

Author

Victor Norris, Tom Wirtz, Jean-Nicolas Audinot, Anne-Francoise Monnier, Yannick Coffinier, David Gibouin, Laurent Jannière, Camille Ripoll, Rabah Boukherroub, Aaron Bensimon, Henri-Noël Migeon, Armelle Cabin-Flaman, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Micro-Environnement et Régulation Cellulaire Intégrée (MERCI), Normandie Université (NU)-Normandie Université (NU), Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Luxembourg Institute of Science and Technology (LIST), genomic vision, Institut de biologie systémique et synthétique (ISSB), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Assemblages moléculaires : modélisation et imagerie SIMS (AMMIS), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Materials Research and Technology (MRT) Department, Luxembourg Institute of Science and Technology (LIST), and Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement (LMDF-SME)

Subjects
0301 basic medicine, DNA isotope labeling, [SDV]Life Sciences [q-bio], Combing, Biology, General Biochemistry, Genetics and Molecular Biology, law.invention, silicon chip, 03 medical and health sciences, chemistry.chemical_compound, law, Molecule, General Pharmacology, Toxicology and Pharmaceutics, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], DNA extraction, ComputingMilieux_MISCELLANEOUS, Genetics, General Immunology and Microbiology, DNA synthesis, Radiochemistry, Articles, General Medicine, Secondary ion mass spectrometry, Research Note, Surface coating, 030104 developmental biology, PCR, chemistry, surface coating, Recombinant DNA, Structure: Transcription & Translation, isotope recombination, DNA
Abstract

Dynamic secondary ion mass spectrometry (D-SIMS) imaging of combed DNA – the combing, imaging by SIMS or CIS method – has been developed previously using a standard NanoSIMS 50 to reveal, on the 50 nm scale, individual DNA fibers labeled with different, non-radioactive isotopes in vivo and to quantify these isotopes. This makes CIS especially suitable for determining the times, places and rates of DNA synthesis as well as the detection of the fine-scale re-arrangements of DNA and of molecules associated with combed DNA fibers. Here, we show how CIS may be extended to 13C-labeling via the detection and quantification of the 13C14N- recombinant ion and the use of the 13C:12C ratio, we discuss how CIS might permit three successive labels, and we suggest ideas that might be explored using CIS.

Published
2016
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11. NanoSIMS50 imaging of thin samples coupled with neutral cesium deposition

Author

Henri-Noël Migeon, Patrick Philipp, Armelle Cabin-Flaman, Guillaume Legent, Jean-Nicolas Audinot, and Tom Wirtz

Subjects
Ion beam, Chemistry, Analytical chemistry, Surfaces and Interfaces, General Chemistry, Condensed Matter Physics, Surfaces, Coatings and Films, Ion, Secondary ion mass spectrometry, Ion beam deposition, Sputtering, Secondary emission, Materials Chemistry, Deposition (phase transition), Thin film
Abstract

Thanks to the 50 nm of lateral resolution of the NanoSIMS50, new fields of application have been opened to Secondary Ion Mass Spectrometry. The NanoSIMS50 imaging capabilities are however often hampered by the fact that, due to a high impact energy (16 keV) and normal incidence of the primary ion beam, the steady state is only reached after sputtering several nanometers (10-20 nm) of the sample. As a consequence, the secondary ion emission is very low during the sputtering of these first nanometers. This phenomenon, which is most pronounced for organic and biologic samples, induces artifacts of measurement. In a previous study, we have shown that negative secondary ion yields can be enhanced in Secondary Ion Mass Spectrometry (SIMS) by coupling the primary ion bombardment with a simultaneous neutral cesium deposition. As this method cannot be used directly on the NanoSIM550, we propose here to perform SIMS analysis after a prior deposition of Cs 0 in a standalone UHV system. With this new method of analysis, organic thin films and proteins have been 3D monitored.

Published
2010
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12. Functional taxonomy of bacterial hyperstructures

Author

Abraham Minsky, Ding Jun Jin, Eugenia Mileykovskaya, Milton H. Saier, Roy H. Doi, Petra Anne Levin, Rasika M. Harshey, Kirsten Skarstad, Alfonso Jiménez-Sánchez, Armelle Cabin-Flaman, Vic Norris, Laurent Jannière, Tanneke den Blaauwen, and Molecular Cytology (SILS, FNWI)

Subjects
DNA, Bacterial, Bacteria, biology, DNA repair, DNA replication, Reviews, Gene Expression Regulation, Bacterial, Computational biology, Chromosomes, Bacterial, Flagellum, Bacterial Physiological Phenomena, Microbiology, MreB, Cell biology, Bacterial protein, Infectious Diseases, Bacterial Proteins, Flagella, biology.protein, FtsZ, Cytoskeleton, Molecular Biology, Metabolic Networks and Pathways
Abstract

SUMMARY The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or “nucleolar” hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell.

Published
2007

13. Hypercomplexity

Author

Vic Norris, Abdallah Zemirline, and Armelle Cabin

Subjects
Cognitive science, Computer science, Adverse conditions, Applied Mathematics, Complex system, General Medicine, Coherence (philosophical gambling strategy), Models, Theoretical, General Biochemistry, Genetics and Molecular Biology, Competition (economics), Philosophy, Escherichia coli, Selection (linguistics), General Agricultural and Biological Sciences, Archetype, General Environmental Science
Abstract

What is biological complexity? How many sorts exist? Are there levels of complexity? How are they related to one another? How is complexity related to the emergence of new phenotypes? To try to get to grips with these questions, we consider the archetype of a complex biological system, Escherichia coli. We take the position that E. coli has been selected to survive adverse conditions and to grow in favourable ones and that many other complex systems undergo similar selection. We invoke the concept of hyperstructures which constitute a level of organisation intermediate between macromolecules and cells. We also invoke a new concept, competitive coherence, to describe how phenotypes are created by a competition between maintaining a consistent story over time and creating a response that is coherent with respect to both internal and external conditions. We suggest how these concepts lead to parameters suitable for describing the rich form of complexity termed hypercomplexity and we propose a relationship between competitive coherence and emergence.

Published
2005
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14. Hypothesis: Chemotaxis in Escherichia coli Results from Hyperstructure Dynamics

Author

Milton H. Saier, Camille Ripoll, Vic Norris, and Armelle Cabin-Flaman

Subjects
chemistry.chemical_element, Chemotaxis, Biology, Calcium, biology.organism_classification, medicine.disease_cause, Applied Microbiology and Biotechnology, Microbiology, Cell biology, chemistry.chemical_compound, chemistry, Transcription (biology), Cardiolipin, medicine, Phosphorylation, Signal transduction, Molecular Biology, Escherichia coli, Bacteria, Biotechnology
Abstract

Large assemblies of different molecules and macromolecules,termed hyper structures, have been proposed to be the units of an intermediate level of organisation in bacteria. Here we propose a model for chemotaxis in Escherichia coli in which (1) the size and functioning of the chemo-signalling hyper-structure depends not only on the protein constituents but also on cardiolipin and calcium,(2) the coupled transcription, translation and insertion of nascent proteins (transertion) is a potentially powerful influence in determining the size of the chemo-signalling hyper-structure and therefore in affecting its function, and (3) a single transertional hyper-structure is jointly responsible for the synthesis of chemo-signalling and flagellar proteins so as to divorce the size of the chemo-signalling hyper-structure from the transertion of its constituents.

Published
2005
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15. Two-dimensional electrophoresis investigation of short-term response of flax seedlings to a cold shock

Author

Roland Charlionet, Marie Claire Verdus, Armelle Cabin-Flaman, Camille Ripoll, and Marc Tafforeau

Subjects
Linum, Proteome, biology, Arabidopsis Proteins, Clinical Biochemistry, biology.organism_classification, Peptide Mapping, Biochemistry, Analytical Chemistry, Shock (mechanics), Cold Temperature, Kinetics, Seedlings, Two dimensional electrophoresis, Flax, Electrophoresis, Gel, Two-Dimensional, Lack of knowledge, Protein identification, Plant Proteins, Signal Transduction
Abstract

The flax, Linum usitatissimum L., is particularly suitable for studying the transduction and long-term signal storage of environmental signals. To investigate the underlying molecular mechanisms, we have focused on the initial changes in the proteome since these offer the possibility of reflecting the plant's history of exposure to stress. In principle, this 'proteome signature' might be revealed by two-dimensional electrophoresis (2-DE). We have therefore determined the potential of 2-DE to study the kinetics of changes to the proteome of flax induced by a 1 min cold shock. Protein identification is difficult with flax because of the lack of knowledge of gene sequences. Nevertheless, 2-DE analysis can be informative providing the significance of changes can be evaluated. We have developed a stringent threshold method to determine the significance of changes in gels obtained with proteins extracted from hypocotyls at different times after cold shock. This allowed us to reliably detect and characterize the kinetics of a set of seven spots that responded to cold shock and that constitute candidates for a proteome signature of long-term signal storage.

Published
2002
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16. Hypothesis: hyperstructures regulate initiation in Escherichia coli and other bacteria

Author

Derek Raine, Maurice Demarty, Armelle Cabin-Flaman, Lois Le Sceller, Vic Norris, Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)

Subjects
DNA Replication, Cell division, [SDV]Life Sciences [q-bio], Population, Biology, Origin of replication, Biochemistry, 03 medical and health sciences, Bacterial Proteins, SeqA protein domain, Hyperstructure, Escherichia coli, education, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Binding Sites, 030306 microbiology, Cell Cycle, DNA replication, Computational Biology, General Medicine, DnaA, DNA-Binding Proteins, Gene Expression Regulation, Genes, Bacterial
Abstract

Hyperstructures or modules have been proposed to constitute a level of organisation intermediate between macromolecules and whole cells. In this model of intracellular organisation, hyperstructures compete and collaborate for existence within the membrane and cytoplasm. Those directly involved in the cell cycle include initiation, replication and division hyperstructures based on DnaA, SeqA and the 2-minute cluster, respectively. During the run-up to initiation, the mass to DNA ratio increases and, we contend, differential gene expression leads to some hyperstructures becoming more active and stable than others. This results in a drop in the diversity of hyperstructures, some of which release DnaA as they dissociate, and a DnaA-initiation hyperstructure forms. Subsequent DNA replication and cell division generate different daughter cells containing different hyperstructures. This has the advantage of increasing the phenotypic diversity of the population. In developing this model, we also invoke hyperstructures in the partitioning of origins of replication.

Published
2002
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17. Combed Single DNA Molecules Imaged by Secondary Ion Mass Spectrometry

Author

Jean-Nicolas Audinot, Armelle Cabin-Flaman, Yannick Coffinier, Vic Norris, Camille Ripoll, Laurent Jannière, Tom Wirtz, Anne-Francoise Monnier, Aaron Bensimon, Rabah Boukherroub, Henri-Noël Migeon, David Gibouin, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Dept Sci & Anal Mat, Centre de Recherche Public - Gabriel Lippmann (LUXEMBOURG), Département Science et Analyse des Matériaux - SAM (Belvaux, Luxembourg), Glycobiologie et transports chez les végétaux (GTCV), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie systémique et synthétique (ISSB), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), EU Network of Excellence, Nanobeams No. 500440, Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, Groupe de physique des matériaux (GPM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Normandie Université (NU)

Subjects
Silicon, Quantitative imaging, [SDV]Life Sciences [q-bio], Analytical chemistry, Cesium, Spectrometry, Mass, Secondary Ion, chemistry, 01 natural sciences, Analytical Chemistry, [SPI.MAT]Engineering Sciences [physics]/Materials, 03 medical and health sciences, chemistry.chemical_compound, Nanotechnology, Molecule, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Isotope, Chemistry, 010401 analytical chemistry, fungi, DNA, 0104 chemical sciences, Secondary ion mass spectrometry, Microscopy, Fluorescence, Isotope Labeling, Nucleic acid, analytical, Gold, Recombination
Abstract

International audience; Studies of replication, recombination, and rearrangements at the level of individual molecules of DNA are often limited by problems of resolution or of perturbations caused by the modifications that are needed for imaging. The Combing-Imaging by Secondary Ion Mass Spectrometry (SIMS) (CIS) method helps solve these problems by combining DNA combing, cesium flooding, and quantitative imaging via the NanoSIMS 50. We show here that CIS can reveal, on the 50 nm scale, individual DNA fibers labeled with different, nonradioactive isotopes and, moreover, that it can quantify these isotopes so as to detect and measure the length of one or more short nucleic acid fragments associated with a longer fiber.

Published
2011
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18. Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

Author

Armelle Cabin, Pascal Ballet, Jürgen Jost, Jean-Nicolas Audinot, Jacqueline Signorini, Jean-Louis Giavitto, Eric Fanchon, Yohann Grondin, Abdallah Zemirline, Patrick Greussay, Nicolas Glade, Patrick Amar, Guillaume Beslon, Pasquale Stano, Alain R. Thierry, Gilles Bernot, Vic Norris, Eshel Ben-Jacob, James A. Foster, Olivier Michel, François Képès, Franck Molina, Guillaume Hutzler, Assemblages moléculaires : modélisation et imagerie SIMS (AMMIS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique des Systèmes Complexes (LISYC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Algorithms and Models for Integrative Biology (AMIB ), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Département Science et Analyse des Matériaux - SAM (Belvaux, Luxembourg), Centre de Recherche Public - Gabriel Lippmann (LUXEMBOURG), Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO), School of Physics and Astronomy [Tel Aviv], Tel Aviv University [Tel Aviv], Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe BIOINFO, Modèles Discrets pour les Systèmes Complexes (Laboratoire I3S - MDSC), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Artificial Evolution and Computational Biology (BEAGLE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Coordination Acoustique/Musique (IRCAM), Synchronous Realtime Processing and Programming of Music Signals (MuTant), Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Inria Paris-Rocquencourt, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), AGeing and IMagery (AGIM), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique Avancée de Saint-Denis (LIASD), Université Paris 8 Vincennes-Saint-Denis (UP8), Department of Physics and Astronomy [Leicester], University of Leicester, Department of Biological Sciences [Idaho], University of Idaho [Moscow, USA], Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE), Max Planck Institute for Mathematics in the Sciences (MPI-MiS), Max-Planck-Gesellschaft, Santa Fe Institute, Génopole [Evry], Laboratoire d'Algorithmique Complexité et Logique (LACL), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Sysdiag-Modélisation et Ingénierie des Systèmes Complexes Biologiques pour le Diagnostic (SysDiag ), BIO-RAD-Centre National de la Recherche Scientifique (CNRS), Enrico Fermi - Dipartimento di Fisica, University of Pisa - Università di Pisa, Normandie Université (NU), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Inria Paris-Rocquencourt, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF), CentraleSupélec-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Laboratoire de Recherche en Informatique (LRI), CentraleSupélec-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, School of Physics and Astronomy [Tel Aviv] (TAU), Raymond and Beverly Sackler Faculty of Exact Sciences [Tel Aviv] (TAU), Tel Aviv University (TAU)-Tel Aviv University (TAU), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École Pratique des Hautes Études (EPHE), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Pierre et Marie Curie - Paris 6 (UPMC)-IRCAM-Centre National de la Recherche Scientifique (CNRS), and Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Statistics and Probability, [SDV]Life Sciences [q-bio], Computational biology, Review, Turing, Bacteriophage, 03 medical and health sciences, Synthetic biology, 0302 clinical medicine, Computer Systems, Biological computing, Origin of life, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Medicine(all), 0303 health sciences, Minimal cell, biology, Bacteria, Applied Mathematics, biology.organism_classification, Computer science, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biological materials, Philosophy of biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery
Abstract

International audience; The relevance of biological materials and processes to computing-alias bioputing-has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating.

Published
2011
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19. Endopolygalacturonase-gold complex: Parameters influencing the labelling of pectic acid in the cell walls of flax hypocotyl

Author

Claudine Morvan, Maurice Demarty, A. Jauneau, and Armelle Cabin-Flaman

Subjects
Histology, Stereochemistry, Diffusion, Analytical chemistry, Pathology and Forensic Medicine, chemistry.chemical_compound, Colloid, Adsorption, Isoelectric point, chemistry, Transmission electron microscopy, Pectic acid, Labelling, Particle
Abstract

Summary An enzyme/colloidal-gold complex was prepared using a purified endopolygalacturonase (endoPGH, E.C. 3.2.1.15). Gold particles with a radius of 4·8 nm were prepared. To stabilize the gold particles, it was necessary to add a minimal amount of enzyme (approximately 0·5 μg) at a pH higher than its isoelectric pH. Under these conditions, the number of protein molecules adsorbed per gold particle was approximately one. The parameters influencing the diffusion of the endoPGH-gold complex to its target molecules were screened and tested through quantitative approaches: (i) the labelling efficiency q was calculated according to the equation for the diffusion of gold markers from the bulk solutions to target molecules and (ii) the labelling density N/S was measured by counting gold particles on electron micrographs. The highest value of N/S was obtained by determining the optimal values for the parameters outlined in the equation for q. To obtain the highest value of N/S, it was not necessary to choose values for these parameters which gave high values for q. The specificity of the probe towards homogalacturonic acid blocks was established through controls. The localization of these blocks was illustrated throughout the walls of different kinds of flax seeding cells.

Published
1993
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20. Hypothesis: chemotaxis in Escherichia coli results from hyper-structure dynamics

Author

Armelle, Cabin-Flaman, Camille, Ripoll, Milton H, Saier, and Vic, Norris

Subjects
Ions, Membrane Lipids, Cardiolipins, Flagella, Chemotaxis, Escherichia coli Proteins, Escherichia coli, Phosphorylation, Models, Biological, Signal Transduction
Abstract

Large assemblies of different molecules and macromolecules,termed hyper structures, have been proposed to be the units of an intermediate level of organisation in bacteria. Here we propose a model for chemotaxis in Escherichia coli in which (1) the size and functioning of the chemo-signalling hyper-structure depends not only on the protein constituents but also on cardiolipin and calcium,(2) the coupled transcription, translation and insertion of nascent proteins (transertion) is a potentially powerful influence in determining the size of the chemo-signalling hyper-structure and therefore in affecting its function, and (3) a single transertional hyper-structure is jointly responsible for the synthesis of chemo-signalling and flagellar proteins so as to divorce the size of the chemo-signalling hyper-structure from the transertion of its constituents.

Published
2006

21. Modelling Bacterial Hyperstructures with Cellular Automata

Author

Vic Norris, Milton H. SaierJr., Camille Ripoll, Thomas Nyström, Lois Le Sceller, Armelle Cabin-Flamand, and Maurice Demarty

Subjects
chemistry.chemical_classification, Metabolic pathway, Enzyme, Chemistry, Cytoplasm, Nucleic acid, Biophysics, Colocalization, Metabolism, Cellular automaton, Function (biology)
Abstract

The physiology of prokaryotic and eukaryotic cells has been proposed to be determined at the level of hyperstructures [Norris et al. 1999] or modules [Hartwell et al. 1999] that would constitute a level intermediate between macromolecules and whole cells. Non-equilibrium hyperstructures include assemblies of genes, mRNA, enzymes and lipids brought together to fulfil a particular function and dismissed when no longer needed [Norris, et al. 1999]. For example, enzymes in the same or related metabolic pathways that are actively engaged in processing their substrates may have an increased probability of colocalization. To determine the values of the parameters governing the formation of hyperstructures in the membrane and cytoplasm of bacteria, we have constructed a program that, in its present version, simulates the dynamics of the formation of hyperstructures comprising enzymes responsible for the transport and metabolism of sugars due to changes in the affinities of its enzymes for one another. These changes result from the binding of enzymes to their substrates and result in increased diffusion coefficients [Norris et al. 1999]. In essence, the program uses cellular automata to represent both the cytoplasm in 3-D and the surrounding cytoplasmic membrane in 2-D. Each unit volume of the bacterium corresponds to a cellular automaton that can contain an enzyme (or, according to the size of the unit volume, another molecule such as a lipid or a stretch of nucleic acid).

Published
2006
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22. Polysaccharide distribution in the cellular junctions of immature fibre cells of flax seedlings

Author

Alain Jauneau, C. Morvan, C. Pariot, Armelle Cabin-Flaman, Michel Thellier, and Camille Ripoll

Subjects
chemistry.chemical_classification, Ruthenium red, food.ingredient, Pectin, Staining and Labeling, Histocytochemistry, chemistry.chemical_element, Cell Biology, Calcium, Plants, Polysaccharide, Cell junction, Hypocotyl, Staining, chemistry.chemical_compound, Microscopy, Electron, food, Hydroxylamine, Intercellular Junctions, chemistry, Biochemistry, Cell Wall, Polysaccharides, Anatomy, Fluorescent Dyes
Abstract

The characteristic features of the pectins present in the walls of immature fibre cells of the hypocotyl of flax seedlings have been studied by a combination of three subtractive methods (treatment with boiling water, calcium chelator, and free endopolygalacturonase), three staining reactions (periodic acid-thiocarbohydrazide-silver, Ruthenium Red, and ferric hydroxylamine) and labelling with an endopolygalacturonase-gold probe. The primary wall and the periphery of the tricellular junctions were shown to contain pectic molecules made of blocks either with free acidic functions or methyl-esterified, these molecules being removed from the wall by splitting alpha (1-4) linkages. On the contrary, the pectic molecules in the core of the tricellular junctions were mainly with free acidic groups, but with an appreciable acetylesterification of their hydroxyl groups; and they were linked with one another chiefly by calcium bonds. This unexpected constitution of the core of the tricellular junctions may be considered to be an early marker of the cells destined to give rise to the fibre bundles of the mature plant.

Published
1994

24. Functional taxonomy of bacterial hyperstructures

Author

Victor Norris, Armelle Cabin-Flaman, Laurent Janniere, Skarsdat Kirsten, Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

25. From metabolic hyperstructures to DNA replication complexes and back again

Author

Anne-Françoise Monnier, Armelle Cabin-Flaman, Guillaume Legent, Danielle Canceill, Emmanuelle Le Chatellier, Camille Ripoll, Michel Thellier, Victor Norris, Laurent Janniere, Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

26. Mise au point d'une imagerie corrélative MET/NanoSIMS pour identifier, localiser et quantifier des nanoparticules dans les tissus biologiques

Author

Janin, Morgane, Groupe de physique des matériaux (GPM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Normandie Université, and Armelle Cabin-Flaman

Subjects
Corrélation, MET, Human skiin, Nanoparticules, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], NanoSIMS, Nanoparticles, Titanium dioxide, Dioxyde de titane, Peau humaine, Correlation
Abstract

Titanium dioxide (TiO2) nanoparticles are the subject of numerous studies and controversies on the risks they could generate in the environment and on human health. They are electron dense nanoparticles that have a chemical signature and are thus detectable by Transmission Electron Microscopy (TEM) and Secondary Ion Mass Spectrometry (NanoSIMS 50). Moreover, abundant in sunscreens (for anti-ultraviolet sunscreen filter properties), they constitute a good material of study for the development of the imaging by correlation TEM/NanoSIMS.As TEM uses electrons and NanoSIMS uses ions, it was necessary to define a sample preparation protocol (sunscreen applied on human skin) adapted to both instruments for the detection, characterization and localization of few nanometers nano-objects in sections of a few tens of nanometers thickness. The data obtained and processed have allowed the development of the overlay of TEM and NanoSIMS images on the one hand and to lead to a 3D reconstruction of objects smaller than the thickness of the section on the other hand. It appears that the TEM/NanoSIMS correlation completes, reinforces and brings more results than each instrument provides, and that aggregated or isolated nanoparticles are retained by the corneocytes at the skin surface.; Les nanoparticules de dioxyde de titane (TiO2) font l’objet de nombreux travaux et controverses sur les risques qu’elles pourraient engendrer dans l’environnement et sur la santé humaine. Ce sont des nanoparticules denses aux électrons qui possèdent une signature chimique et sont ainsi repérables au Microscope Electronique à Transmission (MET) et au Spectromètre de Masse d’Ions Secondaires (NanoSIMS 50). De plus, abondantes dans les crèmes solaires (pour leurs propriétés de filtre anti ultra-violets), elles constituent un bon matériel d’étude pour la mise au point de l’imagerie par corrélation MET/NanoSIMS.Comme le MET utilise des électrons et le NanoSIMS des ions, il a fallu définir un protocole de préparation d’échantillon (crème solaire appliquée sur la peau humaine) adapté aux deux instruments pour la détection, la caractérisation et la localisation de nano-objets de quelques nanomètres dans des coupes de quelques dizaines de nanomètres d’épaisseur. Les données obtenues et traitées ont permis de mettre au point la superposition des images MET et NanoSIMS d’une part et de conduire à une reconstruction 3D d’objets de taille inférieure à l’épaisseur de la coupe d’autre part. Il en ressort que la corrélation MET/NanoSIMS complète, renforce et apporte davantage de résultats que ce que fournit chaque instrument isolément. Il ressort également que les nanoparticules isolées ou agrégées sont retenues par la barrière cornéocytaire à la surface de la peau.

Published
2023

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