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6. Effects of species diversity on trait expression of the clonal herb Taraxacum officinale and its relation to genotype diversity and phenotypic plasticity

Author

De Giorgi, Francesca, Roscher, Christiane, Durka, Walter, De Giorgi, Francesca, Roscher, Christiane, and Durka, Walter

Abstract

Plant species respond to varying plant species diversity and associated changes in their abiotic and biotic environment with changes in their phenotype. However, it is not clear to what degree this phenotypic differentiation is due to genotype diversity within populations or phenotypic plasticity of plant individuals. We studied individuals of 16 populations of the clonal herb Taraxacum officinale grown in plant communities of different species richness in a 17-year-old grassland biodiversity experiment (Jena Experiment). We collected 12 individuals in each population to measure phenotypic traits and identify distinct genotypes using microsatellite DNA markers. Plant species richness did not influence population-level genotype and trait diversity. However, it affected the expression of several phenotypic traits, e.g. leaf and inflorescence number, maximum leaf length and seed mass, which increased with increasing plant species richness. Moreover, population-level trait diversity correlated positively with genotype richness for leaf dry matter content (LDMC) and negatively with inflorescence number. For several traits (i.e. seed mass, germination rate, LDMC, specific leaf area (SLA)), a larger portion of variance was explained by genotype identity, while variance in other traits (i.e. number of inflorescences, leaf nitrogen concentration, leaf number, leaf length) resided within genotypes and thus was mostly due to phenotypic plasticity. Overall, our findings show that plant species richness positively affected the population means of some traits related to whole-plant performance, whose variation was achieved through both phenotypic plasticity and genotype composition of a population.

Published
2024

9. Reconsidering α-Synuclein inclusion pathology in neurons, mice, and humans with an antibody sensing NAC engagement during α-Synuclein amyloid conversion

Author

De Giorgi, Francesca, primary, Letourneur, Ænora, additional, Kashyrina, Marianna, additional, Zinghirino, Federica, additional, Dovero, Sandra, additional, Dutheil, Nathalie, additional, Largitte, Leslie-Ann, additional, Arotçarena, Marie-Laure, additional, Bezard, Erwan, additional, Canron, Marie-Hélène, additional, Meissner, Wassilios, additional, De Nuccio, Francesco, additional, Lofrumento, Dario Domenico, additional, Laferrière, Florent, additional, and Ichas, François, additional

Published
2024
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10. Identification and super-resolution imaging of ligand-activated receptor dimers in live cells

Author

Winckler, Pascale, Lartigue, Lydia, Giannone, Gregory, De Giorgi, Francesca, Ichas, François, Sibarita, Jean-Baptiste, Lounis, Brahim, and Cognet, Laurent

Subjects
Physics - Biological Physics
Abstract

Molecular interactions are key to many chemical and biological processes like protein function. In many signaling processes they occur in sub-cellular areas displaying nanoscale organizations and involving molecular assemblies. The nanometric dimensions and the dynamic nature of the interactions make their investigations complex in live cells. While super-resolution fluorescence microscopies offer live-cell molecular imaging with sub-wavelength resolutions, they lack specificity for distinguishing interacting molecule populations. Here we combine super-resolution microscopy and single-molecule F\"orster Resonance Energy Transfer (FRET) to identify dimers of receptors induced by ligand binding and provide super-resolved images of their membrane distribution in live cells. By developing a two-color universal-Point-Accumulation-In-the-Nanoscale-Topography (uPAINT) method, dimers of epidermal growth factor receptors (EGFR) activated by EGF are studied at ultra-high densities, revealing preferential cell-edge sub-localization. This methodology which is specifically devoted to the study of molecules in interaction, may find other applications in biological systems where understanding of molecular organization is crucial.

Published
2013
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12. Effects of species diversity on trait expression of the clonal herb Taraxacum officinale and its relation to genotype diversity and phenotypic plasticity.

Author

De Giorgi, Francesca, Roscher, Christiane, and Durka, Walter

Subjects
*PHENOTYPIC plasticity, *COMMON dandelion, *SPECIES diversity, *PLANT species diversity, *GENOTYPES, *ABIOTIC environment
Abstract

Plant species respond to varying plant species diversity and associated changes in their abiotic and biotic environment with changes in their phenotype. However, it is not clear to what degree this phenotypic differentiation is due to genotype diversity within populations or phenotypic plasticity of plant individuals. We studied individuals of 16 populations of the clonal herb Taraxacum officinale grown in plant communities of different species richness in a 17‐year‐old grassland biodiversity experiment (Jena Experiment). We collected 12 individuals in each population to measure phenotypic traits and identify distinct genotypes using microsatellite DNA markers. Plant species richness did not influence population‐level genotype and trait diversity. However, it affected the expression of several phenotypic traits, e.g. leaf and inflorescence number, maximum leaf length and seed mass, which increased with increasing plant species richness. Moreover, population‐level trait diversity correlated positively with genotype richness for leaf dry matter content (LDMC) and negatively with inflorescence number. For several traits (i.e. seed mass, germination rate, LDMC, specific leaf area (SLA)), a larger portion of variance was explained by genotype identity, while variance in other traits (i.e. number of inflorescences, leaf nitrogen concentration, leaf number, leaf length) resided within genotypes and thus was mostly due to phenotypic plasticity. Overall, our findings show that plant species richness positively affected the population means of some traits related to whole‐plant performance, whose variation was achieved through both phenotypic plasticity and genotype composition of a population. [ABSTRACT FROM AUTHOR]

Published
2024
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13. TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates

Author

Laferrière, Florent, Maniecka, Zuzanna, Pérez-Berlanga, Manuela, Hruska-Plochan, Marian, Gilhespy, Larissa, Hock, Eva-Maria, Wagner, Ulrich, Afroz, Tariq, Boersema, Paul J., Barmettler, Gery, Foti, Sandrine C., Asi, Yasmine T., Isaacs, Adrian M., Al-Amoudi, Ashraf, Lewis, Amanda, Stahlberg, Henning, Ravits, John, De Giorgi, Francesca, Ichas, François, Bezard, Erwan, Picotti, Paola, Lashley, Tammaryn, and Polymenidou, Magdalini

Published
2019
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14. Data from Localization of Fas/CD95 into the Lipid Rafts on Down-Modulation of the Phosphatidylinositol 3-Kinase Signaling Pathway

Author

Bénéteau, Marie, primary, Pizon, Mathieu, primary, Chaigne-Delalande, Benjamin, primary, Daburon, Sophie, primary, Moreau, Patrick, primary, De Giorgi, Francesca, primary, Ichas, François, primary, Rebillard, Amélie, primary, Dimanche-Boitrel, Marie-Thérèse, primary, Taupin, Jean-Luc, primary, Moreau, Jean-François, primary, and Legembre, Patrick, primary

Published
2023
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15. Supplementary Figures S1-S3 from Localization of Fas/CD95 into the Lipid Rafts on Down-Modulation of the Phosphatidylinositol 3-Kinase Signaling Pathway

Author

Bénéteau, Marie, primary, Pizon, Mathieu, primary, Chaigne-Delalande, Benjamin, primary, Daburon, Sophie, primary, Moreau, Patrick, primary, De Giorgi, Francesca, primary, Ichas, François, primary, Rebillard, Amélie, primary, Dimanche-Boitrel, Marie-Thérèse, primary, Taupin, Jean-Luc, primary, Moreau, Jean-François, primary, and Legembre, Patrick, primary

Published
2023
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18. Identification of Regulatory Molecular "Hot Spots" for LH/PLOD Collagen Glycosyltransferase Activity.

Author

Mattoteia, Daiana, Chiapparino, Antonella, Fumagalli, Marco, De Marco, Matteo, De Giorgi, Francesca, Negro, Lisa, Pinnola, Alberta, Faravelli, Silvia, Roscioli, Tony, Scietti, Luigi, and Forneris, Federico

Subjects
MOLECULAR structure, POST-translational modification, MOLECULAR interactions, COLLAGEN, CHOLESTEROL hydroxylase
Abstract

Hydroxylysine glycosylations are post-translational modifications (PTMs) essential for the maturation and homeostasis of fibrillar and non-fibrillar collagen molecules. The multifunctional collagen lysyl hydroxylase 3 (LH3/PLOD3) and the collagen galactosyltransferase GLT25D1 are the human enzymes that have been identified as being responsible for the glycosylation of collagen lysines, although a precise description of the contribution of each enzyme to these essential PTMs has not yet been provided in the literature. LH3/PLOD3 is thought to be capable of performing two chemically distinct collagen glycosyltransferase reactions using the same catalytic site: an inverting beta-1,O-galactosylation of hydroxylysines (Gal-T) and a retaining alpha-1,2-glucosylation of galactosyl hydroxylysines (Glc-T). In this work, we have combined indirect luminescence-based assays with direct mass spectrometry-based assays and molecular structure studies to demonstrate that LH3/PLOD3 only has Glc-T activity and that GLT25D1 only has Gal-T activity. Structure-guided mutagenesis confirmed that the Glc-T activity is defined by key residues in the first-shell environment of the glycosyltransferase catalytic site as well as by long-range contributions from residues within the same glycosyltransferase (GT) domain. By solving the molecular structures and characterizing the interactions and solving the molecular structures of human LH3/PLOD3 in complex with different UDP-sugar analogs, we show how these studies could provide insights for LH3/PLOD3 glycosyltransferase inhibitor development. Collectively, our data provide new tools for the direct investigation of collagen hydroxylysine PTMs and a comprehensive overview of the complex network of shapes, charges, and interactions that enable LH3/PLOD3 glycosyltransferase activities, expanding the molecular framework and facilitating an improved understanding and manipulation of glycosyltransferase functions in biomedical applications. [ABSTRACT FROM AUTHOR]

Published
2023
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21. A Novel C-Type Lectin Receptor-Targeted α-Synuclein-Based Parkinson Vaccine Induces Potent Immune Responses and Therapeutic Efficacy in Mice

Author

Schmidhuber, Sabine, primary, Scheiblhofer, Sandra, additional, Weiss, Richard, additional, Cserepes, Mihály, additional, Tóvári, József, additional, Gadermaier, Gabriele, additional, Bezard, Erwan, additional, De Giorgi, Francesca, additional, Ichas, François, additional, Strunk, Dirk, additional, and Mandler, Markus, additional

Published
2022
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22. A Fe2+-dependent self-inhibited state influences the druggability of human collagen lysyl hydroxylase (LH/PLOD) enzymes

Author

Scietti, Luigi, primary, Moroni, Elisabetta, additional, Mattoteia, Daiana, additional, Fumagalli, Marco, additional, De Marco, Matteo, additional, Negro, Lisa, additional, Chiapparino, Antonella, additional, Serapian, Stefano A., additional, De Giorgi, Francesca, additional, Faravelli, Silvia, additional, Colombo, Giorgio, additional, and Forneris, Federico, additional

Published
2022
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24. COVID-19 and Influenza Vaccination Campaign in a Research and University Hospital in Milan, Italy

Author

Lecce, Maurizio, primary, Biganzoli, Giacomo, additional, Agnello, Luca, additional, Belisario, Ignazio, additional, Cicconi, Giovanni, additional, D’Amico, Marilena, additional, De Giorgi, Francesca, additional, Ferilli, Angelo, additional, Ferraguzzi, Gaia, additional, Guzzardi, Fabio, additional, Lanzillotti, Danilo, additional, Lattanzio, Roberta, additional, Marrocu, Chiara, additional, Noto, Maria Emanuela, additional, Piccinelli, Sara, additional, Sabatelli, Noemi, additional, Santisteban, Sheila, additional, Sharma, Sudwaric, additional, Tognaccini, Livia, additional, and Castaldi, Silvana, additional

Published
2022
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26. Neurons with Cat’s Eyes: A Synthetic Strain of α-Synuclein Fibrils Seeding Neuronal Intranuclear Inclusions

Author

De Giorgi, Francesca, primary, Abdul-Shukkoor, Muhammed Bilal, additional, Kashyrina, Marianna, additional, Largitte, Leslie-Ann, additional, De Nuccio, Francesco, additional, Kauffmann, Brice, additional, Lends, Alons, additional, Laferrière, Florent, additional, Bonhommeau, Sébastien, additional, Lofrumento, Dario Domenico, additional, Bousset, Luc, additional, Bezard, Erwan, additional, Buffeteau, Thierry, additional, Loquet, Antoine, additional, and Ichas, François, additional

Published
2022
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31. Is there more to within-plant variation in seed size than developmental noise?

Author

Pélabon, C., De Giorgi, Francesca, Opedal, Ø.H., Bolstad, G.H., Raunsgard, A., Armbruster, W.S., Pélabon, C., De Giorgi, Francesca, Opedal, Ø.H., Bolstad, G.H., Raunsgard, A., and Armbruster, W.S.

Abstract

Within-plant variation in seed size may merely reflect developmental instability, or it may be adaptive in facilitating diversifying bet-hedging, that is, production of phenotypically diverse offspring when future environments are unpredictable. To test the latter hypothesis, we analyzed patterns of variation in seed size in 11 populations of the perennial vine Dalechampia scandens grown in a common greenhouse environment. We tested whether population differences in the mean and variation of seed size covaried with environmental predictability at two different timescales. We also tested whether within-plant variation in seed size was correlated with independent measures of floral developmental instability and increased under stressful conditions. Populations differed genetically in the amount of seed-size variation occurring among plants, among infructescences within plants, and among seeds within infructescences. Within-individual variation was not detectably correlated with measures of developmental instability and did not increase under stress, but it increased weakly with short-term environmental unpredictability of precipitation at the source-population site. These results support the hypothesis that greater variation in seed size is adaptive when environmental predictability is low.

Published
2021

32. Recombinant differential anchorage probes that tower over the spatial dimension of intracellular signals for high content screening and analysis

Author

Schembri, Laura, Zanese, Marion, Deplerre-Plinet, Gaelle, Petit, Muriel, Elkaoukabi-Chaibi, Assia, Tauzin, Loic, Florean, Cristina, Lartigue, Lydia, Medina, Chantal, Rey, Christophe, Belloc, Francis, Reiffers, Josy, Ichas, Francois, and De Giorgi, Francesca

Subjects
Molecular probes -- Electric properties, Molecular dynamics -- Research, Imaging systems -- Methods, Imaging systems -- Equipment and supplies, Technology application, Chemistry
Abstract

Recombinant fluorescent probes allow the detection of molecular events inside living cells. Many of them exploit the intracellular space to provide positional signals and, thus, require detection by single cell imaging. We describe here a novel strategy based on probes capable of encoding the spatial dimension of intracellular signals into 'all-or-none' fluorescence intensity changes (differential anchorage probes, DAPs). The resulting signals can be acquired in single cells at high throughput by automated flow cytometry, (i) bypassing image acquisition and analysis, (ii) providing a direct quantitative readout, and (iii) allowing the exploration of large experimental series. We illustrate our purpose with DAPs for Bax and the effector caspases 3 and 7, which are keys players in apoptotic cell death, and show applications in basic research, high content multiplexed library screening, compound characterization, and drug profiling. 10.1021/ac9015227

Published
2009

34. Novel self-replicating α-synuclein polymorphs that escape ThT monitoring can spontaneously emerge and acutely spread in neurons

Author

De Giorgi, Francesca, Laferrière, Florent, Zinghirino, Federica, Faggiani, Emilie, Lends, Alons, Bertoni, Mathilde, Yu, Xuan, Grélard, Axelle, Morvan, Estelle, Habenstein, Birgit, Dutheil, Nathalie, Doudnikoff, Evelyne, Daniel, Jonathan, Claverol, Stéphane, Qin, Chuan, Loquet, Antoine, Bezard, Erwan, Ichas, François, Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de neurosciences expérimentales et cliniques (LNEC), Université de Poitiers-Institut National de la Santé et de la Recherche Médicale (INSERM), Chimie et Biologie des Membranes et des Nanoobjets (CBMN), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut Européen de Chimie et Biologie (IECB), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre Génomique Fonctionnelle Bordeaux [Bordeaux] (CGFB), Institut Polytechnique de Bordeaux-Université de Bordeaux Ségalen [Bordeaux 2], Université de Bordeaux (UB), Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Laferriere, Florent

Subjects
Neurons, Amyloid, MESH: Multiple System Atrophy, Synucleinopathies, animal diseases, [SDV]Life Sciences [q-bio], [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, SciAdv r-articles, Diseases and Disorders, macromolecular substances, nervous system diseases, Mice, nervous system, Cellular Neuroscience, mental disorders, MESH: alpha-Synuclein, alpha-Synuclein, Animals, Benzothiazoles, Research Articles, MESH: Parkinson Disease, Research Article
Abstract

Stealth α-synuclein amyloids proliferate in preparations of preformed fibrils and form aggressive self-replicating strains., The conformational strain diversity characterizing α-synuclein (α-syn) amyloid fibrils is thought to determine the different clinical presentations of neurodegenerative diseases underpinned by a synucleinopathy. Experimentally, various α-syn fibril polymorphs have been obtained from distinct fibrillization conditions by altering the medium constituents and were selected by amyloid monitoring using the probe thioflavin T (ThT). We report that, concurrent with classical ThT-positive products, fibrillization in saline also gives rise to polymorphs invisible to ThT (τ−). The generation of τ− fibril polymorphs is stochastic and can skew the apparent fibrillization kinetics revealed by ThT. Their emergence has thus been ignored so far or mistaken for fibrillization inhibitions/failures. They present a yet undescribed atomic organization and show an exacerbated propensity toward self-replication in cortical neurons, and in living mice, their injection into the substantia nigra pars compacta triggers a synucleinopathy that spreads toward the dorsal striatum, the nucleus accumbens, and the insular cortex.

Published
2020

41. Reduced oligodendrocyte exosome secretion in multiple system atrophy involves SNARE dysfunction

Author

Yu, Zhenwei, primary, Shi, Min, primary, Stewart, Tessandra, primary, Fernagut, Pierre-Olivier, primary, Huang, Yang, primary, Tian, Chen, primary, Dehay, Benjamin, primary, Atik, Anzari, primary, Yang, Dishun, primary, De Giorgi, Francesca, primary, Ichas, François, primary, Canron, Marie-Hélène, primary, Ceravolo, Roberto, primary, Frosini, Daniela, primary, Kim, Han-Joon, primary, Feng, Tao, primary, Meissner, Wassilios G, primary, and Zhang, Jing, primary

Published
2020
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42. Emergence of stealth polymorphs that escape α-synuclein amyloid monitoring, take over and acutely spread in neurons

Author

De Giorgi, Francesca, primary, Laferrière, Florent, additional, Zinghirino, Federica, additional, Faggiani, Emilie, additional, Lends, Alons, additional, Bertoni, Mathilde, additional, Yu, Xuan, additional, Grélard, Axelle, additional, Morvan, Estelle, additional, Habenstein, Birgit, additional, Dutheil, Nathalie, additional, Doudnikoff, Evelyne, additional, Daniel, Jonathan, additional, Claverol, Stéphane, additional, Qin, Chuan, additional, Loquet, Antoine, additional, Bezard, Erwan, additional, and Ichas, François, additional

Published
2020
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45. Chapter 5: Targeting GFP to Organelles

Author

De Giorgi, Francesca, primary, Ahmed, Zimran, additional, Bastianutto, Carlo, additional, Brini, Marisa, additional, Jouaville, Laurence Sophie, additional, Marsault, Robert, additional, Murgia, Marta, additional, Pinton, Paolo, additional, Pozzan, Tullio, additional, and Rizzuto, Rosario, additional

Published
1998
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49. TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates

Author

Laferrière, Florent, primary, Maniecka, Zuzanna, additional, Pérez-Berlanga, Manuela, additional, Hruska-Plochan, Marian, additional, Gilhespy, Larissa, additional, Hock, Eva-Maria, additional, Wagner, Ulrich, additional, Afroz, Tariq, additional, Boersema, Paul J., additional, Barmettler, Gery, additional, Foti, Sandrine C., additional, Asi, Yasmine T., additional, Isaacs, Adrian M., additional, Al-Amoudi, Ashraf, additional, Lewis, Amanda, additional, Stahlberg, Henning, additional, Ravits, John, additional, De Giorgi, Francesca, additional, Ichas, François, additional, Bezard, Erwan, additional, Picotti, Paola, additional, Lashley, Tammaryn, additional, and Polymenidou, Magdalini, additional

Published
2018
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