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3. The Zinc Finger proteinSlZFP2 is essential for tomato fruit locular tissue morphogenesis

Author

Hoang, Gabriel, primary, Joana, Jorly, additional, Constantinescu, Dario, additional, Martin, Pascal G P, additional, Gadin, Stéphanie, additional, Mauxion, Jean-Philippe, additional, Brès, Cécile, additional, Garcia, Virginie, additional, Gonzalez, Nathalie, additional, Rothan, Christophe, additional, Bertin, Nadia, additional, Fernandez-Lochu, Lucie, additional, and Lemaire-Chamley, Martine, additional

Published
2024
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4. The introduction of the European fallow deer to the northern provinces of the Roman Empire: a multiproxy approach to the Herstal skeleton (Belgium)

Author

Pigiere, Fabienne, Henrard, Denis, Sykes, Naomi, Suarez-Gonzalez, Nathalie, and Sonet, Gontran

Subjects
Archaeological dating -- Analysis, Radiocarbon dating -- Analysis, Archaeology -- Analysis, Anthropology/archeology/folklore
Abstract

Many exotic animal species were introduced to Northern Europe during the Roman period, including fallow deer (Dama dama). To date, however, finds of fallow deer bones at archaeological sites in this region have been sporadic and disarticulated, leaving uncertainty over their origins. This article presents the first known articulated fallow deer skeleton from Roman North-western Europe. Osteological, ancient DNA, radiocarbon dating and stable isotope analyses confirm that the species was established in this region by the Roman period, probably originating from translocated, rather than native, Mediterranean populations. Clarifying the origins of fallow deer in Northwestern Europe is critical for understanding the dynamics of species exchange around the Roman Empire. Keywords: Roman Empire, fallow deer, animal translocation, zooarchaeology, radiocarbon dating, stable isotopes, ancient DNA, Introduction During the Roman period, many new animal species were imported into North-western Europe as a result of socio-economic, cultural, administrative and military needs. These species included camels, donkeys, mules, [...]

Published
2020
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6. Ploidy‐specific transcriptomes shed light on the heterogeneous identity and metabolism of developing tomato pericarp cells.

Author

Tourdot, Edouard, Martin, Pascal G. P., Maza, Elie, Mauxion, Jean‐Philippe, Djari, Anis, Gévaudant, Frédéric, Chevalier, Christian, Pirrello, Julien, and Gonzalez, Nathalie

Subjects
PERICARP, TOMATOES, TRANSCRIPTOMES, GENE expression, FRUIT development, PLOIDY
Abstract

SUMMARY: Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programmes that are characteristic of each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types, especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of differentially expressed genes presenting only developmental‐specific, only ploidy‐specific expression patterns or profiles resulting from an additive effect of ploidy and development. When comparing ploidy levels at a specific developmental stage, we found that non‐endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome‐based predictions were validated by quantifying ploidy levels within the pericarp tissue. This in situ ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation and gene expression patterns in the tomato pericarp. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Paleo-Genetic and Paleo-Pathological Studies at Pachacamac: Methodological Issues and Preliminary Results

Author

Suarez Gonzalez, Nathalie, Sonet, Gontran, Eeckhout, Peter, Suarez Gonzalez, Nathalie, Sonet, Gontran, and Eeckhout, Peter

Abstract

Ancient DNA (aDNA) analysis can be a useful tool for sex determination, general mitochondrial lineage (haplogroup) and disease diagnosis in human remains. However, non-endogenous DNA contamination of archaeological material is a recurrent problematic, since excavation, handling and storage usually don't fit with the precautions recommended for ancient DNA analysis. Here, we present preliminary aDNA results from several human individuals recovered by the Ychsma Project (ULB) from the monumental archaeological site of Pachacamac, Peru, a corpus dating from 500 to 1400 AD where a high proportion of diseases is suspected. Our objectives are to complete the demographic information and to characterize the health status of the population buried in this pilgrimage site dedicated to the eponymous healing god. Our preliminary results show that, despite an important human DNA contamination, a strict selection of DNA reads with short sizes and damage patterns that are typical for ancient DNA was useful to determine the sex of most individuals, and mitochondrial haplogroup of some. The data were also used to estimate the presence of several pathogens including Mycobacterium tuberculosis, Treponema pallidum and Leishmania. Our preliminary results suggest that our approach is appropriate for the detection of paleopathological conditions in this major archaeological corpus., info:eu-repo/semantics/nonPublished

Published
2023

19. Paleo-Pathological Studies at Pachacamac, Peru: Challenges and Preliminary Results

Author

10th Meeting of the International Society for Biomolecular Archaeology (ISBA) (13-16/09/2032: Tartu, Estonia), Suarez Gonzalez, Nathalie, Sonet, Gontran, Eeckhout, Peter, 10th Meeting of the International Society for Biomolecular Archaeology (ISBA) (13-16/09/2032: Tartu, Estonia), Suarez Gonzalez, Nathalie, Sonet, Gontran, and Eeckhout, Peter

Abstract

Ancient DNA (aDNA) analysis can be a useful tool for sex determination, general mitochondrial lineage (haplogroup) and disease diagnosis in human remains. However, non-endogenous DNA contamination of archaeological material is a recurrent problematic, since excavation, handling and storage usually don't fit with the precautions recommended for ancient DNA analysis. Here, we present preliminary aDNA results from several human individuals recovered by the Ychsma Project (ULB) from the monumental archaeological site of Pachacamac, Peru, a corpus dating from 500 to 1400 AD where a high proportion of diseases is suspected. Our objectives are to complete the demographic information and to characterize the health status of the population buried in this pilgrimage site dedicated to the eponymous healing god. Our preliminary results show that, despite an important modern human-DNA contamination, a strict selection of DNA reads based on short sizes and deamination damage patterns that are typical for ancient DNA, allow us to determine the genetic sex of 70% of the individuals. The challenging detection of ancient DNA form human pathogens requires additional precautions. By multiplying negatives and environmental controls and data analysis strategies, our preliminary results suggest that our approach is appropriate for the detection of paleopathological conditions in this major archaeological corpus., info:eu-repo/semantics/nonPublished

Published
2023

24. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

Author

Szakonyi, Dóra, Van Landeghem, Sofie, Baerenfaller, Katja, Baeyens, Lieven, Blomme, Jonas, Casanova-Sáez, Rubén, De Bodt, Stefanie, Esteve-Bruna, David, Fiorani, Fabio, Gonzalez, Nathalie, Grønlund, Jesper, Immink, Richard G.H., Jover-Gil, Sara, Kuwabara, Asuka, Muñoz-Nortes, Tamara, van Dijk, Aalt D.J., Wilson-Sánchez, David, Buchanan-Wollaston, Vicky, Angenent, Gerco C., Van de Peer, Yves, Inzé, Dirk, Micol, José Luis, Gruissem, Wilhelm, Walsh, Sean, and Hilson, Pierre

Published
2015
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25. A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis

Author

Gonzalez, Nathalie, Pauwels, Laurens, Baekelandt, Alexandra, De Milde, Liesbeth, Van Leene, Jelle, Besbrugge, Nienke, Heyndrickx, Ken S., Pérez, Amparo Cuéllar, Durand, Astrid Nagels, De Clercq, Rebecca, Van De Slijke, Eveline, Bossche, Robin Vanden, Eeckhout, Dominique, Gevaert, Kris, Vandepoele, Klaas, De Jaeger, Geert, Goossens, Alain, and Inzé, Dirk

Published
2015

29. Preface

Author

González, Nathalie and Inzé, Dirk

Published
2015

30. Solanum lycopersicum CLASS-II KNOX genes regulate fruit anatomy via gibberellin-dependent and independent pathways

Author

Shtern, Amit, primary, Keren-Keiserman, Alexandra, additional, Mauxion, Jean-Philippe, additional, Furumizu, Chihiro, additional, Alvarez, John Paul, additional, Amsellem, Ziva, additional, Gil, Naama, additional, Motenko, Etel, additional, Alkalai-Tuvia, Sharon, additional, Fallik, Elazar, additional, Gonzalez, Nathalie, additional, and Goldshmidt, Alexander, additional

Published
2022
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32. ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development

Author

Vercruyssen, Liesbeth, Verkest, Aurine, Gonzalez, Nathalie, Heyndrickx, Ken S., Eeckhout, Dominique, Han, Soon-Ki, Jégu, Teddy, Archacki, Rafal, Van Leene, Jelle, Andriankaja, Megan, De Bodt, Stefanie, Abeel, Thomas, Coppens, Frederik, Dhondt, Stijn, De Milde, Liesbeth, Vermeersch, Mattias, Maleux, Katrien, Gevaert, Kris, Jerzmanowski, Andrzej, Benhamed, Moussa, Wagner, Doris, Vandepoele, Klaas, De Jaeger, Geert, and Inzé, Dirk

Published
2014

33. Solanum lycopersicum CLASS-II KNOXgenes regulate fruit anatomy via gibberellin-dependent and independent pathways

Author

Shtern, Amit, primary, Keren-Keiserman, Alexandra, additional, Mauxion, Jean-Philippe, additional, Furumizu, Chihiro, additional, Alvarez, John Paul, additional, Amsellem, Ziva, additional, Gil, Naama, additional, Motenko, Etel, additional, Alkalai-Tuvia, Sharon, additional, Fallik, Elazar, additional, Gonzalez, Nathalie, additional, and Goldshmidt, Alexander, additional

Published
2022
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37. Increased Leaf Size: Different Means to an End

Author

Gonzalez, Nathalie, De Bodt, Stefanie, Sulpice, Ronan, Jikumaru, Yusuke, Chae, Eunyoung, Dhondt, Stijn, Van Daele, Twiggy, De Milde, Liesbeth, Weigel, Detlef, Kamiya, Yuji, Stitt, Mark, Beemster, Gerrit T.S., and Inzé, Dirk

Published
2010

38. Solanum lycopersicum CLASS-II KNOX genes regulate fruit anatomy via gibberellin-dependent and independent pathways.

Author

Shtern, Amit, Keren-Keiserman, Alexandra, Mauxion, Jean-Philippe, Furumizu, Chihiro, Alvarez, John Paul, Amsellem, Ziva, Gil, Naama, Motenko, Etel, Alkalai-Tuvia, Sharon, Fallik, Elazar, Gonzalez, Nathalie, and Goldshmidt, Alexander

Abstract

The pericarp is the predominant tissue determining the structural characteristics of most fruits. However, the molecular and genetic mechanisms controlling pericarp development remain only partially understood. Previous studies have identified that CLASS-II KNOX genes regulate fruit size, shape, and maturation in Arabidopsis thaliana and Solanum lycopersicum. Here we characterized the roles of the S. lycopersicum CLASS-II KNOX (TKN-II) genes in pericarp development via a detailed histological, anatomical, and karyotypical analysis of TKN-II gene clade mRNAknockdown (35S:amiR-TKN-II) fruits. We identify that 35S:amiR-TKN-II pericarps contain more cells around their equatorial perimeter and fewer cell layers than the control. In addition, the cell sizes but not the ploidy levels of these pericarps were dramatically reduced. Further, we demonstrate that fruit shape and pericarp layer number phenotypes of the 35S:amiR-TKN-II fruits can be overridden by the procera mutant, known to induce a constitutive response to the plant hormone gibberellin. However, neither the procera mutation nor exogenous gibberellin application can fully rescue the reduced pericarp width and cell size phenotype of 35S:amiR-TKN-II pericarps. Our findings establish that TKN-II genes regulate tomato fruit anatomy, acting via gibberellin to control fruit shape but utilizing a gibberellinindependent pathway to control the size of pericarp cells. [ABSTRACT FROM AUTHOR]

Published
2023
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43. Tracking the origin of worked elephant ivory of a medieval chess piece from Belgium through analysis of ancient DNA

Author

Goffette, Quentin, Suarez Gonzalez, Nathalie, Vanmechelen, Raphaël, Verheyen, Erik, Sonet, Gontran, Goffette, Quentin, Suarez Gonzalez, Nathalie, Vanmechelen, Raphaël, Verheyen, Erik, and Sonet, Gontran

Abstract

The morphological identification of raw biological material used to produce archeological artifacts is sometimes difficult or even impossible. In recent years, newly developed biochemical techniques have allowed more reliable identification of exploited animal species, even for otherwise taxonomically undiagnostic fragments, and thus can help pinpoint the geographical origin of the raw material. However, in addition to being costly, these techniques involve destructive sampling. This explains why they are rarely applied to archeological artifacts, especially those made of precious, imported raw material or those representing intact works of art. Here, we analyzed the ancient DNA (aDNA) of a medieval chess piece made of ivory of unknown origin, recovered from a medieval settlement in Jambes (Namur), Belgium. This chess piece was broken during excavation. We took this unfortunate event as an opportunity to perform aDNA extraction, to try to answer three questions: (1) What Proboscidean species does the ivory come from? (2) Can we establish the geographic origin of the ivory more precisely? and (3) Does doing so help our understanding of (part of) the trade route followed by the ivory? We sequenced two short fragments of the mitochondrial genome and compared them with publicly available DNA data. This enabled the identification of the raw material as an African elephant (genus Loxodonta). Although the results cannot exclude that the ivory comes from a forest elephant, the recovered DNA sequence is currently found only among savanna elephant DNA records. The ivory likely originates from an eastern or southern African country and was therefore probably transported along the African trade route passing through the Swahili Corridor. However, the precise itinerary followed by this ivory from the African shore of the Mediterranean Sea to Europe, and then to the archeological site from which it was recovered, remains unknown. Such identification contributes to documenting pas, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021

48. KIX8 and KIX9 are conserved repressors of organ size in the asterid species tomato

Author

Swinnen, Gwen, Baekelandt, Alexandra, De Clercq, Rebecca, Van Doorsselaere, Jan, Gonzalez, Nathalie, Inzé, Dirk, Goossens, Alain, and Pauwels, Laurens

Subjects
food and beverages
Abstract

Summary Plant organ size and shape are major agronomic traits that depend on cell division and expansion, which are tightly regulated by complex gene networks. In several eudicot species belonging to the rosid clade, organ growth is controlled by a repressor complex consisting of PEAPOD (PPD) and KINASE-INDUCIBLE DOMAIN INTERACTING (KIX) proteins. Whether the function of these proteins as regulators of organ size is conserved in asterids as well, which together with the rosids constitute most of the core eudicot species, is still unknown. Here, we demonstrate that KIX8 and KIX9 redundantly regulate organ growth in the asterid model species tomato ( Solanum lycopersicum ). Protein interaction assays in yeast revealed that KIX8 and KIX9 act as molecular bridges between the PPD repressor and TOPLESS co-repressor proteins. We found that CRISPR-Cas9 genome editing of KIX8 and KIX9 led to the production of enlarged, dome-shaped leaves and that these leaves exhibited increased expression of putative PPD target genes. Moreover, the kix8 kix9 mutants carried bigger fruits with increased pericarp thickness. Our results show that KIX8 and KIX9 are conserved regulators of organ size in distinct eudicot species and can thus provide strategies to improve yield in fruit crops.

Published
2020
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49. Understanding plant organ growth: a multidisciplinary field

Author

Nelissen, Hilde, Gonzalez, Nathalie, Department of plant Biotechnology and Bioinformatics, University of Gent, Biologie du fruit et pathologie (BFP), and Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
approche multidisciplinaire, physiologie végétale, Vegetal Biology, croissance végétale, régulation, développement de la plante, plante, approche multiscalaire, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biologie végétale
Abstract

UMR 1332 - Equipe OrFE; International audience

Published
2020
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50. The introduction of the European fallow deer to the northern provinces of the Roman Empire: A multi-proxy approach to the Herstal skeleton (Belgium)

Author

Pigière, Fabienne, Henrard, Denis, Sykes, Naomi, Suarez Gonzalez, Nathalie, Sonet, Gontran, Pigière, Fabienne, Henrard, Denis, Sykes, Naomi, Suarez Gonzalez, Nathalie, and Sonet, Gontran

Abstract

Many exotic animal species were introduced to Northern Europe during the Roman period, including fallow deer (Dama dama). To date, however, finds of fallow deer bones at archaeological sites in this region have been sporadic and disarticulated, leaving uncertainty over their origins. This article presents the first known articulated fallow deer skeleton from Roman North-western Europe. Osteological, ancient DNA, radiocarbon dating and stable isotope analyses confirm that the species was established in this region by the Roman period, probably originating from translocated, rather than native, Mediterranean populations. Clarifying the origins of fallow deer in North-western Europe is critical for understanding the dynamics of species exchange around the Roman Empire., SCOPUS: ar.j, DecretOANoAutActif, info:eu-repo/semantics/published

Published
2020

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