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4. 3D modeling of Hi-C contacts: seeing the spatial organization of fungal chromosomes

Author

Poinsignon, Thibault, Gallopin, Mélina, Grognet, Pierre, Malagnac, Fabienne, Lelandais, Gaëlle, Poulain, Pierre, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and ANR-19-CE45-0017,MinOmics,Exploration, Visualisation et Modélisation Computationnelle des Réseaux de Signalisation Redox(2019)

Subjects
3D model, Pastis, Neurospora crassa, workflow, cohesin, Saccharomyces cerevisiae, HiC-Pro, Schizosacharromyces pombe, HiC, chromatine, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3DGB, Fungal genomes
Abstract

International audience; In recent years, significant technical advances have been made to better observe the structure and the organization of chromatin. Many Hi-C data are now available in public databases, at different accuracy and resolution and for various species. Generally, the final results of Hi-C data analyses are summarized with the representation of “contact maps”. Using a color scale, these maps (heat-maps) show the frequency of contacts observed between different portions of a genome, both at short-rangeand long-range distances.Even if they are widely used, our observation is that the biological interpretation of contact maps is not trivial. It requires training and significant experience to be useful to validate or invalidate hypotheses concerning the overall organization of the studied genome. In this context, alternative tools have been developed. Some of them produce 3D models ofcontact networks, as a substitute for visualization of Hi-C outputs. By 3D models, we mean representations in a 3D space of a genome, in which euclidean distances are derived from the contact frequency matrices. The information contained in the Hi-C data is thus directly translated into distances in a 3D space. Although care must be taken in interpreting these models (they are not “pictures” of the interior of a cell), we observed they are very helpful to highlight specific structural patterns in chromatin organization, originally hidden in contact maps.Developing new strategies to visualize and integrate large scale multi-omics data is the major objective of Thibault Poinsignon’s thesis (ANR MinOmics). These led us to start building 3D models of yeasts andfilamentous fungi genomes, from Hi-C raw sequencing data. We present here our evaluations of the biological significance and the interest to use these models for projecting heterogeneous epigenomics data and hence better support their biological interpretations.

Published
2023

7. The taxonomy of the model filamentous fungus Podospora anserina

Author

Ament-Velásquez, Sandra Lorena, Johannesson, Hanna, Giraud, Tatiana, Debuchy, Robert, Saupe, Sven J., Debets, Alfons J. M., Bastiaans, Eric, Malagnac, Fabienne, Grognet, Pierre, Peraza-Reyes, Leonardo, Gladieux, Pierre, Kruys, Åsa, Silar, Philippe, Huhndorf, Sabine M., Miller, Andrew N., Vogan, Aaron A., Uppsala Universitet [Uppsala], Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research [Wageningen] (WUR), Universidad Nacional Autónoma de México (UNAM), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Interdisciplinaire des Energies de Demain (LIED (UMR_8236)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Field Museum of Natural History [Chicago, USA], Department of Electrical and Computer Engineering [Urbana] (University of Illinois), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Swedish Research CouncilFormas, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)

Subjects
Biologisk systematik, Fungi, Sordariales, Biological Systematics, PE&RC, Laboratorium voor Erfelijkheidsleer, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, lcsh:QK1-989, phylogenetics, taxonomy, Ascomycota, Triangularia, Podospora, Lasiosphaeriaceae, lcsh:Botany, Sordariomycetes, Laboratory of Genetics, Triangularia anserina, phylogenetics Podospora Podosporaceae taxonomy, Podosporaceae, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology
Abstract

The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

Published
2020

9. Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex

Author

Hartmann, Fanny E., Ament-Velásquez, Sandra Lorena, Vogan, Aaron A., Gautier, Valerie, Le Prieur, Stephanie, Berramdane, Myriam, Snirc, Alodie, Johannesson, Hanna, Grognet, Pierre, Malagnac, Fabienne, Silar, Philippe, Giraud, Tatiana, Hartmann, Fanny E., Ament-Velásquez, Sandra Lorena, Vogan, Aaron A., Gautier, Valerie, Le Prieur, Stephanie, Berramdane, Myriam, Snirc, Alodie, Johannesson, Hanna, Grognet, Pierre, Malagnac, Fabienne, Silar, Philippe, and Giraud, Tatiana

Abstract

Sex chromosomes often carry large nonrecombining regions that can extend progressively over time, generating evolutionary strata of sequence divergence. However, some sex chromosomes display an incomplete suppression of recombination. Large genomic regions without recombination and evolutionary strata have also been documented around fungal mating-type loci, but have been studied in only a few fungal systems. In the model fungus Podospora anserina (Ascomycota, Sordariomycetes), the reference S strain lacks recombination across a 0.8-Mb region around the mating-type locus. The lack of recombination in this region ensures that nuclei of opposite mating types are packaged into a single ascospore (pseudohomothallic lifecycle). We found evidence for a lack of recombination around the mating-type locus in the genomes of ten P. anserina strains and six closely related pseudohomothallic Podospora species. Importantly, the size of the nonrecombining region differed between strains and species, as indicated by the heterozygosity levels around the mating-type locus and experimental selfing. The nonrecombining region is probably labile and polymorphic, differing in size and precise location within and between species, resulting in occasional, but infrequent, recombination at a given base pair. This view is also supported by the low divergence between mating types, and the lack of strong linkage disequilibrium, chromosomal rearrangements, transspecific polymorphism and genomic degeneration. We found a pattern suggestive of evolutionary strata in P. pseudocomata. The observed heterozygosity levels indicate low but nonnull outcrossing rates in nature in these pseudohomothallic fungi. This study adds to our understanding of mating-type chromosome evolution and its relationship to mating systems.

Published
2021
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10. Sordariales 28S ribosomal RNA gene, partial sequence

Author

Ament-velásquez, S.L., Johannesson, Hanna, Giraud, Tatiana, Debuchy, Robert, Saupe, Sven J., Debets, Alfons J.M., Bastiaans, Eric, Malagnac, Fabienne, Grognet, Pierre, Peraza-reyes, Leonardo, Gladieux, Pierre, Kruys, Åsa, Silar, Philippe, Huhndorf, Sabine M., Miller, Andrew N., Vogan, Aaron A., Ament-velásquez, S.L., Johannesson, Hanna, Giraud, Tatiana, Debuchy, Robert, Saupe, Sven J., Debets, Alfons J.M., Bastiaans, Eric, Malagnac, Fabienne, Grognet, Pierre, Peraza-reyes, Leonardo, Gladieux, Pierre, Kruys, Åsa, Silar, Philippe, Huhndorf, Sabine M., Miller, Andrew N., and Vogan, Aaron A.

Published
2021

11. Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex

Author

Hartmann, Fanny E, primary, Ament-Velásquez, Sandra Lorena, additional, Vogan, Aaron A, additional, Gautier, Valérie, additional, Le Prieur, Stephanie, additional, Berramdane, Myriam, additional, Snirc, Alodie, additional, Johannesson, Hanna, additional, Grognet, Pierre, additional, Malagnac, Fabienne, additional, Silar, Philippe, additional, and Giraud, Tatiana, additional

Published
2021
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12. The taxonomy of the model filamentous fungus Podospora anserina

Author

Ament-velásquez, S.L., Johannesson, Hanna, Giraud, Tatiana, Debuchy, Robert, Saupe, Sven J., Debets, Alfons J.M., Bastiaans, Eric, Malagnac, Fabienne, Grognet, Pierre, Peraza-reyes, Leonardo, Gladieux, Pierre, Kruys, Åsa, Silar, Philippe, Huhndorf, Sabine M., Miller, Andrew N., Vogan, Aaron A., Ament-velásquez, S.L., Johannesson, Hanna, Giraud, Tatiana, Debuchy, Robert, Saupe, Sven J., Debets, Alfons J.M., Bastiaans, Eric, Malagnac, Fabienne, Grognet, Pierre, Peraza-reyes, Leonardo, Gladieux, Pierre, Kruys, Åsa, Silar, Philippe, Huhndorf, Sabine M., Miller, Andrew N., and Vogan, Aaron A.

Abstract

The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

Published
2020

14. Figure 1 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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15. Figure 3 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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16. Supplementary material 1 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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17. Figure 2 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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18. Supplementary material 5 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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19. Supplementary material 3 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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20. Supplementary material 4 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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21. Supplementary material 2 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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22. Figure 4 from: Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJM, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA (2020) The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 75: 51-69. https://doi.org/10.3897/mycokeys.75.55968

Author

Ament-Velásquez, S. Lorena, primary, Johannesson, Hanna, additional, Giraud, Tatiana, additional, Debuchy, Robert, additional, Saupe, Sven J., additional, Debets, Alfons J. M., additional, Bastiaans, Eric, additional, Malagnac, Fabienne, additional, Grognet, Pierre, additional, Peraza-Reyes, Leonardo, additional, Gladieux, Pierre, additional, Kruys, Åsa, additional, Silar, Philippe, additional, Huhndorf, Sabine M., additional, Miller, Andrew N., additional, and Vogan, Aaron A., additional

Published
2020
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26. Recombination suppression and evolutionary strata around mating‐type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes.

Author

Hartmann, Fanny E., Duhamel, Marine, Carpentier, Fantin, Hood, Michael E., Foulongne‐Oriol, Marie, Silar, Philippe, Malagnac, Fabienne, Grognet, Pierre, and Giraud, Tatiana

Subjects
SEX chromosomes, PLANT self-incompatibility, FUNGI, GENETIC drift, PODOSPORA anserina
Abstract

Summary: Genomic regions determining sexual compatibility often display recombination suppression, as occurs in sex chromosomes, plant self‐incompatibility loci and fungal mating‐type loci. Regions lacking recombination can extend beyond the genes determining sexes or mating types, by several successive steps of recombination suppression. Here we review the evidence for recombination suppression around mating‐type loci in fungi, sometimes encompassing vast regions of the mating‐type chromosomes. The suppression of recombination at mating‐type loci in fungi has long been recognized and maintains the multiallelic combinations required for correct compatibility determination. We review more recent evidence for expansions of recombination suppression beyond mating‐type genes in fungi ('evolutionary strata'), which have been little studied and may be more pervasive than commonly thought. We discuss testable hypotheses for the ultimate (evolutionary) and proximate (mechanistic) causes for such expansions of recombination suppression, including (1) antagonistic selection, (2) association of additional functions to mating‐type, such as uniparental mitochondria inheritance, (3) accumulation in the margin of nonrecombining regions of various factors, including deleterious mutations or transposable elements resulting from relaxed selection, or neutral rearrangements resulting from genetic drift. The study of recombination suppression in fungi could thus contribute to our understanding of recombination suppression expansion across a broader range of organisms. [ABSTRACT FROM AUTHOR]

Published
2021
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27. A gene graveyard in the genome of the fungus Podospora comata

Author

Silar, Philippe, primary, Dauget, Jean-Marc, additional, Gautier, Valérie, additional, Grognet, Pierre, additional, Chablat, Michelle, additional, Hermann-Le Denmat, Sylvie, additional, Couloux, Arnaud, additional, Wincker, Patrick, additional, and Debuchy, Robert, additional

Published
2018
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30. Tau monoclonal antibody generation based on humanized yeast models

Author

Rosseels, Joëlle, van den Brande, Jeff, Violet, Marie-Luce, Jacobs, Dirk, Grognet, Pierre, Lopez, Juan, Huvent, Isabelle, Caldara, Marina, Swinnen, Erwin, Papegaey, Anthony, Caillierez, Raphaelle, Buée-Scherrer, Valerie, Engelborghs, Sebastiaan, Lippens, Guy, Colin, Morvane, Buée, Luc, Galas, Marie-Christine, Vanmechelen, Eugeen, Winderickx, Joris, Vesalius College, Department of Bio-engineering Sciences, Pathologic Biochemistry and Physiology, Clinical sciences, Neurology, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U1172 Inserm - U837 (JPArc), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Lille Nord de France (COMUE)-Université de Lille, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), University of Antwerp (UA), ANR-11-LABX-0009,DISTALZ,Développement de stratégies innovantes pour une approche transdisciplinaire de la maladie d'Alzheime(2011), CHU Lille, CNRS, Université de Lille, Inserm, Catholic University of Leuven - Katholieke Universiteit Leuven [KU Leuven], Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U837 [JPArc], Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 [UGSF], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], University of Antwerp [UA], Lille Neurosciences & Cognition (LilNCog) - U 1172, Université de Lille, LillOA, Laboratoires d'excellence - Développement de stratégies innovantes pour une approche transdisciplinaire de la maladie d'Alzheime - - DISTALZ2011 - ANR-11-LABX-0009 - LABX - VALID, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U837 (JPArc), Université Lille Nord de France (COMUE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, and Université de Lille-Centre National de la Recherche Scientifique (CNRS)

Subjects
Peptide Fragments/metabolism, Protein Folding, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, mice, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Blotting, Western, tau Proteins, Enzyme-Linked Immunosorbent Assay, Mice, Transgenic, Plaque, Amyloid, Saccharomyces cerevisiae, Hippocampus, Alzheimer Disease/cerebrospinal fluid, Immunoenzyme Techniques, Membrane Microdomains, Neurobiology, Alzheimer Disease, mental disorders, Protein Oligomer, Animals, Humans, Immunoprecipitation, Disease, Biotinylation, Biology, Antibody, Tau Protein (Tau), Yeast, Medicine(all), Mice, Inbred BALB C, phosphorylation, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Brain, Antibodies, Monoclonal, tau Proteins/cerebrospinal fluid, Neurofibrillary Tangles, magnetic resonance spectroscopy, Peptide Fragments, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, Chemistry, epitope mapping, Hippocampus/immunology, Disease Progression, Immunization, Human medicine, Brain/immunology
Abstract

A link between Tau phosphorylation and aggregation has been shown in different models for Alzheimer disease, including yeast. We used human Tau purified from yeast models to generate new monoclonal antibodies, of which three were further characterized. The first antibody, ADx201, binds the Tau proline-rich region independently of the phosphorylation status, whereas the second, ADx215, detects an epitope formed by the Tau N terminus when Tau is not phosphorylated at Tyr(18). For the third antibody, ADx210, the binding site could not be determined because its epitope is probably conformational. All three antibodies stained tangle-like structures in different brain sections of THY-Tau22 transgenic mice and Alzheimer patients, and ADx201 and ADx210 also detected neuritic plaques in the cortex of the patient brains. In hippocampal homogenates from THY-Tau22 mice and cortex homogenates obtained from Alzheimer patients, ADx215 consistently stained specific low order Tau oligomers in diseased brain, which in size correspond to Tau dimers. ADx201 and ADx210 additionally reacted to higher order Tau oligomers and presumed prefibrillar structures in the patient samples. Our data further suggest that formation of the low order Tau oligomers marks an early disease stage that is initiated by Tau phosphorylation at N-terminal sites. Formation of higher order oligomers appears to require additional phosphorylation in the C terminus of Tau. When used to assess Tau levels in human cerebrospinal fluid, the antibodies permitted us to discriminate patients with Alzheimer disease or other dementia like vascular dementia, indicative that these antibodies hold promising diagnostic potential. ispartof: JOURNAL OF BIOLOGICAL CHEMISTRY vol:290 issue:7 pages:4059-4074 ispartof: location:United States status: published

Published
2015

32. Three regulators of G protein signaling differentially affect mating, morphology and virulence in the smut fungus U stilago maydis.

Author

Moretti, Marino, Wang, Lei, Grognet, Pierre, Lanver, Daniel, Link, Hannes, and Kahmann, Regine

Subjects
G protein coupled receptors, USTILAGO maydis, PHYTOPATHOGENIC fungi, MICROBIAL virulence, CYCLIC adenylic acid, HAPLOIDY, TELIOSPORES, PSYCHOLOGY
Abstract

Regulators of G protein signaling (RGS) proteins modulate heterotrimeric G protein signaling negatively. To broaden an understanding of the roles of RGS proteins in fungal pathogens, we functionally characterized the three RGS protein-encoding genes ( rgs1, rgs2 and rgs3) in the phytopathogenic fungus Ustilago maydis. It was found that RGS proteins played distinct roles in the regulation of development and virulence. rgs1 had a minor role in virulence when deleted in a solopathogenic strain. In crosses, rgs1 was dispensable for mating and filamentation, but was required for teliospore production. Haploid rgs2 mutants were affected in cell morphology, growth, mating and were unable to cause disease symptoms in crosses. However, virulence was unaffected when rgs2 was deleted in a solopathogenic strain, suggesting an exclusive involvement in pre-fusion events. These rgs2 phenotypes are likely connected to elevated intracellular cAMP levels. rgs3 mutants were severely attenuated in mating, in their response to pheromone, virulence and formation of mature teliospores. The mating defect could be traced back to reduced expression of the transcription factor rop1. It was speculated that the distinct roles of the three U. maydis RGS proteins were achieved by direct modulation of the Gα subunit-activated signaling pathways as well as through Gα-independent functions. [ABSTRACT FROM AUTHOR]

Published
2017
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36. Use of gellable pharmaceutical compositions in periodontology

Author

Fanara, Domenico, Vranckx, Henri, Deleers, Michel, Grognet, Pierre, Fanara, Domenico, Vranckx, Henri, Deleers, Michel, and Grognet, Pierre

Abstract

A method is described for preparing a fluid pharmaceutical composition which allows the controlled release of at least one active substance. The method involves mixing a therapeutically effective amount of at least one active substance, from 3 to 55% by weight of phospholipid, from 16 to 72% by..., info:eu-repo/semantics/published

Published
2004

38. Use of gellable pharmaceutical compositions in periodontology

Author

Fanara, Domenico, Vranckx, Henri, Deleers, Michel, Grognet, Pierre, Fanara, Domenico, Vranckx, Henri, Deleers, Michel, and Grognet, Pierre

Abstract

The invention concerns the use for treating periodontitis of a fluid pharmaceutical composition for controlled release of at least one active substance comprising: a) a therapeutically efficient amount of at least an active substance; b) 3 to 55 wt. % of phospholipid; c) 16 to 72 wt. % of one or..., info:eu-repo/semantics/published

Published
2003

40. Use of pharmaceutical compositions capable of being gelled in periodontology

Author

Fanara, Domenico, Vranckx, Henri, Deleers, Michel, Grognet, Pierre, Fanara, Domenico, Vranckx, Henri, Deleers, Michel, and Grognet, Pierre

Abstract

A method is described for preparing a fluid pharmaceutical composition which allows the controlled release of at least one active substance. The method involves mixing a therapeutically effective amount of at least one active substance, from 3 to 55% by weight of phospholipid, from 16 to 72% by..., 1 citation, info:eu-repo/semantics/published

Published
2002

42. P3-071: Mass spectrometric characterization of tau in cerebrospinal fluid

Author

Gobom, Johan, primary, Portelius, Erik, additional, Hansson, Sara F., additional, Tran, Ai Jun, additional, Zetterberg, Henrik, additional, Grognet, Pierre, additional, Vanmechelen, Eugeen, additional, Hoeglund, Kina, additional, Brinkmalm, Gunnar, additional, Westman-Brinkmalm, Ann, additional, Nordhoff, Eckhard, additional, and Blennow, Kaj, additional

Published
2008
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43. Characterization of Tau in Cerebrospinal Fluid Using Mass Spectrometry

Author

Portelius, Erik, primary, Hansson, Sara F., additional, Tran, Ai Jun, additional, Zetterberg, Henrik, additional, Grognet, Pierre, additional, Vanmechelen, Eugeen, additional, Höglund, Kina, additional, Brinkmalm, Gunnar, additional, Westman-Brinkmalm, Ann, additional, Nordhoff, Eckhard, additional, Blennow, Kaj, additional, and Gobom, Johan, additional

Published
2008
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44. P3–090: Potential diagnostic relevance of amino–terminally truncated beta–amyloid species in sporadic Alzheimer's disease: A prospective brain study

Author

Vanmechelen, Eugeen, primary, Vandecasteele, Lies, additional, Grognet, Pierre, additional, Catry, Cindy, additional, Ghestem, Antoine, additional, Gompel, Marie, additional, Decraemer, Hilde, additional, Callebaut, Paul, additional, Van Kerschaver, Els, additional, Vanderstichele, Hugo, additional, Sergeant, Nicolas, additional, Buee, Luc, additional, Kostanjevecki, Vesna, additional, Blennow, Kaj, additional, and Delacourte, Andre, additional

Published
2006
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45. S1-02-01 Amino-truncated abeta 42 species as early diagnostic and etiological biomarkers of Alzheimer's disease

Author

Sergeant, Nicolas, primary, Kostanjevecki, Vesna, additional, Casas, Katy, additional, Ghestem, Antoine, additional, Grognet, Pierre, additional, Drobecq, Hervé, additional, Grasland, Bénédicte, additional, Benoit, Patrick, additional, Tremp, Günter, additional, Vanderstichele, Hugo, additional, Sergheraert, Christian, additional, Blennow, Kaj, additional, Pradier, Laurent, additional, Vanmechelen, Eugeen, additional, and Dealcourte, André, additional

Published
2004
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49. Extraction, Assay and Conversion of NH 4+. A Preparative Procedure for Isotopic Enrichment Determination

Author

Grognet, Pierre, Malaisse Lagae, Francine, Sener, Abdullah, Malaisse, Willy, Grognet, Pierre, Malaisse Lagae, Francine, Sener, Abdullah, and Malaisse, Willy

Abstract

A method is described for the extraction of NH4 + from biological samples. This method can be combined with the enzymatic conversion of NH4 + to glutamate, which can then be used for measuring 15N isotopic enrichment. Emphasis is laid on the difficulties encountered when the samples contain NH4 + together with the amide derivative of monoaminodicarboxylic acids. Copyright © 1982 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
1982

50. Roger de Collerye et ses poésies dolentes, grivoises et satiriques : un émule de Coquillart / augmentées d'inédites, publiées avec sa biographie par Frédéric Lachèvre ; et suivies du traité de Pierre Grosnet, De la louange et excellence des bons facteurs (1533)

Author

Lachèvre, Frédéric (1855-1943). Éditeur scientifique, Collerye, Roger de (1470?-1540?). Auteur du texte, Grognet, Pierre (15..?-1540?). Auteur du texte, Lachèvre, Frédéric (1855-1943). Éditeur scientifique, Collerye, Roger de (1470?-1540?). Auteur du texte, and Grognet, Pierre (15..?-1540?). Auteur du texte

Abstract

Comprend : De la louange et excellence des bons facteurs, Contient une table des matières, Avec mode texte

Published
1942

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