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Article ; Online: Les milieux humides dans le paysage des Petites Antilles

Peguy Major / Jean-Philippe Claude

VertigO, Vol 21, Iss

étude des mares de la Martinique

2021 Volume 1

Abstract: Wetland types, such as ponds, are essential aquatic biotopes in the Martinique landscape. They are characterized by the permanent or temporary presence, at very shallow depths, of fresh water by the preponderance of a hygrophile phytocenosis and by the ... ...

Abstract	Wetland types, such as ponds, are essential aquatic biotopes in the Martinique landscape. They are characterized by the permanent or temporary presence, at very shallow depths, of fresh water by the preponderance of a hygrophile phytocenosis and by the existence of a hydromorphic soil. The aim of this article is to identify these slow ecosystems from a hydrogeomorphological and floristic point of view. We have inventoried twenty-three ponds. Then we established an initial classification that resulted in the distinction of forest ponds from savannah ponds. Then we identified seven hydrophytic species and one helophyte.
Keywords	lentic ecosystem ; physical characteristics ; ponds ; Martinique ; aquatic vegetation ; Environmental sciences ; GE1-350
Language	French
Publishing date	2021-05-01T00:00:00Z
Publisher	Éditions en environnement VertigO
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq.

Philippe, Claude / Cristofari, Gael

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2607, Page(s) 127–150

Abstract: By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can ... ...

Abstract	By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can also locally influence gene expression. Comprehensive measurement of L1 DNA methylation at the locus level remains challenging. Here, we present bs-ATLAS-seq, a genome-wide approach to locate full-length L1 elements in the human genome, and assess their methylation levels at single-base and single-locus resolutions. This strategy targets the youngest, and only retrotransposition-competent family, L1HS, but also detects a significant fraction of older elements (L1PA2 to L1PA8). Bs-ATLAS-seq evaluates methylation at the first 15 CpGs of L1 5' UTR, which corresponds to the first half of the sense promoter. It relies on random fragmentation of the genomic DNA, adapter ligation, bisulfite treatment and suppression PCR, and ends by asymmetrical paired-end sequencing. A dedicated pipeline provides the location of L1 elements and their methylation status, including for non-reference loci, as well as their single-molecule DNA profiles.
MeSH term(s)	Humans ; Animals ; Long Interspersed Nucleotide Elements/genetics ; Sequence Analysis, DNA ; DNA Methylation ; Protein Processing, Post-Translational ; Ascomycota ; Mammals
Language	English
Publishing date	2022-11-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2883-6_8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Milieux propices au Coffea canephora en Martinique

Jean-Philippe Claude

VertigO, Vol 17, Iss

2017 Volume 3

Abstract: Pionnière pour la culture du café dans la Caraïbe dès 1720, connue pour son légendaire café Arabica, la Martinique n’a plus aucune filière caféière depuis le XIXe siècle. Afin de relancer la culture, un système d'information géographique (SIG) avait été ... ...

Abstract	Pionnière pour la culture du café dans la Caraïbe dès 1720, connue pour son légendaire café Arabica, la Martinique n’a plus aucune filière caféière depuis le XIXe siècle. Afin de relancer la culture, un système d'information géographique (SIG) avait été élaboré pour effectuer un zonage pédoclimatique et retrouver les milieux propices au Coffea arabica. Le zonage a abouti à une impossibilité de production pour le futur d’un café Arabica d’excellence, les précipitations représentant un facteur limitant important. La présence sur l’île d’une autre espèce exogène du genre Coffea très cultivée dans le monde (Coffea canephora Pierre ex Froehner), et l’ère caféière significative qu’aurait connue la Martinique ont justifié l’élaboration d’un nouveau zonage pédoclimatique. Les exigences édapho-climatiques du C. canephora ont alors été définies à l’aide de la littérature scientifique mondiale. Les données numériques (isohyètes, isothermes, géomorphologie) proviennent des mêmes institutions martiniquaises ayant compétences dans la production de données environnementales (IRD, IGN, Météo-France, DEAL Martinique, CTM). Ces données ont été traitées avec un logiciel de SIG : QGIS version 2.12.3. Le zonage pédoclimatique du Coffea canephora a révélé plusieurs zones propices pour sa culture contrairement à l’Arabica. A partir des prévisions des services de la Météorologie Nationale pour l’horizon 2071-2100, nous avons effectué un zonage aboutissant à une possibilité restreinte de production de ce café pour les années futures. Ces zonages ont montré les contraintes des conditions environnementales de la Martinique pour la culture caféière.
Keywords	Martinique ; Coffea canephora ; exigences édapho-climatiques ; SIG ; zonage pédoclimatique ; zonage agro-climatique ; Environmental sciences ; GE1-350
Language	French
Publishing date	2017-12-01T00:00:00Z
Publisher	Éditions en environnement VertigO
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Milieux propices au Coffea canephora en Martinique

Jean-Philippe Claude

VertigO, Vol 17, Iss

2017 Volume 3

Abstract	Pionnière pour la culture du café dans la Caraïbe dès 1720, connue pour son légendaire café Arabica, la Martinique n’a plus aucune filière caféière depuis le XIXe siècle. Afin de relancer la culture, un système d'information géographique (SIG) avait été élaboré pour effectuer un zonage pédoclimatique et retrouver les milieux propices au Coffea arabica. Le zonage a abouti à une impossibilité de production pour le futur d’un café Arabica d’excellence, les précipitations représentant un facteur limitant important. La présence sur l’île d’une autre espèce exogène du genre Coffea très cultivée dans le monde (Coffea canephora Pierre ex Froehner), et l’ère caféière significative qu’aurait connue la Martinique ont justifié l’élaboration d’un nouveau zonage pédoclimatique. Les exigences édapho-climatiques du C. canephora ont alors été définies à l’aide de la littérature scientifique mondiale. Les données numériques (isohyètes, isothermes, géomorphologie) proviennent des mêmes institutions martiniquaises ayant compétences dans la production de données environnementales (IRD, IGN, Météo-France, DEAL Martinique, CTM). Ces données ont été traitées avec un logiciel de SIG : QGIS version 2.12.3. Le zonage pédoclimatique du Coffea canephora a révélé plusieurs zones propices pour sa culture contrairement à l’Arabica. A partir des prévisions des services de la Météorologie Nationale pour l’horizon 2071-2100, nous avons effectué un zonage aboutissant à une possibilité restreinte de production de ce café pour les années futures. Ces zonages ont montré les contraintes des conditions environnementales de la Martinique pour la culture caféière.
Keywords	Martinique ; Coffea canephora ; exigences édapho-climatiques ; SIG ; zonage pédoclimatique ; zonage agro-climatique ; Environmental sciences ; GE1-350
Language	French
Publishing date	2017-12-01T00:00:00Z
Publisher	Éditions en environnement VertigO
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Patrimoines naturels, socio-économiques et culturels des sociétés insulaires de la Caraïbe

Adèle Silbande / Jean-Philippe Claude

Études Caribéennes, Vol

quel avenir ?

2018 Volume 1

Abstract: The third edition of the multidisciplinary Scientific Study Day (JES 2017) of the ADJC association invites us to question about the heritage of the island societies of the Caribbean region. With the challenges facing them, how will their future be in the ...

Abstract	The third edition of the multidisciplinary Scientific Study Day (JES 2017) of the ADJC association invites us to question about the heritage of the island societies of the Caribbean region. With the challenges facing them, how will their future be in the coming decades?At first sight, the term ‘heritage’ refers to the notion of a transmission of material goods. Nevertheless, this definition has developed over time and, nowadays, includes not only physical objects but also elements which are of an intangible nature (landscapes, traditions, languages, gastronomy, etc.). Two major categories appear: the natural heritage and the cultural heritage (Fourcade, 2007; Le Hégarat, 2015). More and more studies are interested in the natural and cultural resources related to the heritage of the island territories (Kesteloot, 2001; Abenon et al., 2002; Bardolph, 2002; Furlong, 2009; Zanoaga, 2012; Sainton et al., 2013; Joseph et al., 2018).Consider the diversity of the heritage in the scientific research becomes urgent to define better the future of our island societies that have undeniable natural and cultural wealth and to act accordingly. The researcher does not have to position any more as an observer of past, preservative and protective, but as an actor proposing alternative strategies to improve community life (Bluestone, 2000; Battiste, 2007; Silverman and Ruggles, 2007).
Keywords	heritage ; island society ; scientific research ; Latin America. Spanish America ; F1201-3799 ; Social Sciences ; H
Subject code	910
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	Université des Antilles
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Contribution écologique d’une espèce potentiellement invasive des Petites Antilles

Abati Yelji / Philippe Joseph / Yanis Jean-François / Kévine Baillard / Jean-Philippe Claude / Séverine Ely-Marius / Stéphane Sophie / Peguy Major

VertigO (2023)

Spathodea campanulata P. Beauv

2023

Abstract: Trade across the globe has led to the introduction of plant and animal species into new territories. By crossing ecosystem barriers (environmental, reproductive and dispersal), some of them manage to become invasive. Spathodea campanulata, better known ... ...

Abstract	Trade across the globe has led to the introduction of plant and animal species into new territories. By crossing ecosystem barriers (environmental, reproductive and dispersal), some of them manage to become invasive. Spathodea campanulata, better known as the tulip tree is a species native to Africa introduced for ornamental purposes. It is a species that represents a great ecological threat; it has invaded the mesophilic secondary forests of the Pacific Islands (the Cook Islands, Fiji, French Polynesia, Guam, Hawaii, New Caledonia and Vanuatu) but also Puerto Rico, Brazil and Australia. In Martinique, the species has grown considerably in the natural environment. Once planted as an ornamental tree, the species now escapes from gardens and ornamental parks and gradually colonizes open plant formations. A floristic study on the Martinique territory allowed us to decipher the main life traits of Spathodea campanulata.
Keywords	Spathodea campanulata ; Bignoniaceae ; invasive species ; Lesser Antilles ; Martinique ; biodiversity ; Environmental sciences ; GE1-350
Subject code	580
Language	French
Publishing date	2023-01-01T00:00:00Z
Publisher	Éditions en environnement VertigO
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites.

Lanciano, Sophie / Philippe, Claude / Sarkar, Arpita / Pratella, David / Domrane, Cécilia / Doucet, Aurélien J / van Essen, Dominic / Saccani, Simona / Ferry, Laure / Defossez, Pierre-Antoine / Cristofari, Gael

Cell genomics

2024 Volume 4, Issue 2, Page(s) 100498

Abstract: Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and ... ...

Abstract	Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.
MeSH term(s)	Animals ; Humans ; Retroelements/genetics ; DNA Methylation/genetics ; Long Interspersed Nucleotide Elements/genetics ; Transcription Factors/genetics ; Primates/genetics ; Epigenesis, Genetic/genetics
Chemical Substances	Retroelements ; Transcription Factors
Language	English
Publishing date	2024-02-02
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2024.100498
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A novel bioinformatic approach reveals cooperation between Cancer/Testis genes in basal-like breast tumors.

Laisné, Marthe / Rodgers, Brianna / Benlamara, Sarah / Wicinski, Julien / Nicolas, André / Djerroudi, Lounes / Gupta, Nikhil / Ferry, Laure / Kirsh, Olivier / Daher, Diana / Philippe, Claude / Okada, Yuki / Charafe-Jauffret, Emmanuelle / Cristofari, Gael / Meseure, Didier / Vincent-Salomon, Anne / Ginestier, Christophe / Defossez, Pierre-Antoine

Oncogene

2024 Volume 43, Issue 18, Page(s) 1369–1385

Abstract: Breast cancer is the most prevalent type of cancer in women worldwide. Within breast tumors, the basal-like subtype has the worst prognosis, prompting the need for new tools to understand, detect, and treat these tumors. Certain germline-restricted genes ...

Abstract	Breast cancer is the most prevalent type of cancer in women worldwide. Within breast tumors, the basal-like subtype has the worst prognosis, prompting the need for new tools to understand, detect, and treat these tumors. Certain germline-restricted genes show aberrant expression in tumors and are known as Cancer/Testis genes; their misexpression has diagnostic and therapeutic applications. Here we designed a new bioinformatic approach to examine Cancer/Testis gene misexpression in breast tumors. We identify several new markers in Luminal and HER-2 positive tumors, some of which predict response to chemotherapy. We then use machine learning to identify the two Cancer/Testis genes most associated with basal-like breast tumors: HORMAD1 and CT83. We show that these genes are expressed by tumor cells and not by the microenvironment, and that they are not expressed by normal breast progenitors; in other words, their activation occurs de novo. We find these genes are epigenetically repressed by DNA methylation, and that their activation upon DNA demethylation is irreversible, providing a memory of past epigenetic disturbances. Simultaneous expression of both genes in breast cells in vitro has a synergistic effect that increases stemness and activates a transcriptional profile also observed in double-positive tumors. Therefore, we reveal a functional cooperation between Cancer/Testis genes in basal breast tumors; these findings have consequences for the understanding, diagnosis, and therapy of the breast tumors with the worst outcomes.
MeSH term(s)	Humans ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Female ; Computational Biology/methods ; Gene Expression Regulation, Neoplastic ; DNA Methylation ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; Male ; Epigenesis, Genetic
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2024-03-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639046-8
ISSN	1476-5594 ; 0950-9232
ISSN (online)	1476-5594
ISSN	0950-9232
DOI	10.1038/s41388-024-03002-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Locus-specific chromatin profiling of evolutionarily young transposable elements.

Taylor, Darren / Lowe, Robert / Philippe, Claude / Cheng, Kevin C L / Grant, Olivia A / Zabet, Nicolae Radu / Cristofari, Gael / Branco, Miguel R

Nucleic acids research

2021 Volume 50, Issue 6, Page(s) e33

Abstract: Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is ... ...

Abstract	Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.
MeSH term(s)	Animals ; Chromatin/genetics ; DNA Transposable Elements/genetics ; Gene Expression Regulation ; Genomics ; Humans ; Mice
Chemical Substances	Chromatin ; DNA Transposable Elements
Language	English
Publishing date	2021-12-15
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab1232
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Book ; Online ; Thesis: Machine Learning and Deformation Modeling for Workflow-Compliant Image Fusion during Endovascular Aortic Repair

Breininger, Katharina [Verfasser] / Maier, Andreas [Akademischer Betreuer] / Maier, Andreas [Gutachter] / Cattin, Philippe Claude [Gutachter]

2021

Author's details	Katharina Breininger ; Gutachter: Andreas Maier, Philippe Claude Cattin ; Betreuer: Andreas Maier
Keywords	Medizin, Gesundheit ; Medicine, Health
Subject code	sg610
Language	English
Publisher	Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Publishing place	Erlangen
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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