Martine Boccara

Fredy Barneche (équipe Bowler) — 2017-08-02T12:40:54Z

Professeur émérite de Sorbonne Université
email address : mboccara chez biologie.ens.fr
Major interests :
• Developping optical method to analyze virus populations from aquatic
environments
• Studying virus multiplication and vesicle production by
diatoms

- Chris Bowler / CV - No menus

Maria Helena Cruz de Carvalho

Helena Cruz de Carvalho — 2017-08-01T08:23:40Z

Associate Professor, HDR, UPEC

Contact details

Address : Institut de Biologie de l'Ecole Normale Supérieure (IBENS)
46 rue d'Ulm, 75005 Paris, France
Phone : + (33) 144 32 35 28
E-mail : cruz chez biologie.ens.fr
Google Scholar profile

Research interests : Plankton and algal responses to environmental fluctuations 

Long noncoding RNAs

The work I have developed so far has enabled me to apprehend the multigenic nature of the environmental stress response of photosynthetic organisms, from land plants to unicellular algae. The physiological adaptation to one given stress factor is ultimately the result of a complex and precise cellular program, triggered by that stress. However, the key genomic elements that orchestrate these stress responses are yet to be found. Identifying these upstream key elements and revealing how they operate in time and space to orchestrate a response that leads to stress adaptation is the ultimate goal of fundamental stress research.

Recent evidence suggests that key cellular regulatory elements could be of different nature than what the central dogma of molecular biology may seem to suggest, and that RNA species are far more than simple messengers. Longtime considered as transcriptional noise or artifacts, noncoding RNAs are starting to be recognized as important biological actors in the regulation of cellular processes.
My present research focuses on the identification and functional characterization of regulatory non-protein coding RNA species, namely long noncoding RNAs (lncRNAs) in marine microalgae, with a particular focus on their roles in the response to nutrient fluctuations in diatoms.

Figure 1. Long non-protein coding RNAs (lncRNAs) arise from different parts of the genome and are named according to their location in relation to protein coding genes (mRNAs). lincRNAs, intergenic RNAs ; incRNAs, intronic RNAs ; lncNAT (or NATs), RNAs that are transcribed from the opposite strand of a protein-coding gene sequence.

LncRNAs in diatoms

Out of the 55 million nucleotides that make up the genome of the model marine diatom Phaeodactylum tricornutum, around 19 million correspond to putative protein coding genes (Phatr3). This means that approximately 35% of the genome codes for proteins while the remainder 65% is non-coding. In the noncoding fraction of the genome we have recently identified thousands of lncRNAs (lincRNAs and lncNATs). These are polyadenylated bona fide discrete transcripts that are expressed under specific stress conditions such as phosphate or nitrogen depletion (Cruz de Carvalho et al., 2016 ; Cruz de Carvalho & Bowler, 2020) and hyposalinity stress (Debit, Charton et al., 2023). Although expressed at lower levels than mRNAs, lncRNAs show a well defined cell-type expression specific signature in the three distinct morphotypes of P. tricornutum (Debit, Charton et al., 2023).

Figure 2.
Coding and noncoding transcripts responsive to phosphate (Pi) fluctuations in the marine diatom P. tricornutum. Coding, mRNA (messenger RNAs) ; Noncoding, lncNAT (long noncoding natural antisense RNAs), lincRNA (long intergenic noncoding RNAs). P4, 4 days Pi stress ; P8, 8 days phosphate stress ; U, up-regulated ; R4, 4 days Pi resupply after 4 days Pi stress ; D, down-regulated or =, unchanged transcripts. (Cruz de Carvalho and Bowler, 2020).

My current work involves the functional study of these noncoding genes, namely by the generation of mutant CRISPR-Cas9 and overexpressing lines for the study of the loss-of-function and gain-of-function phenotypes, respectively. I am also characterizing, on a larger scale, the coding and noncoding genome/transcriptome fractions of close to one hundred diatom species and relating this with the ecological and evolutionary relevance of this phytoplankton group.

We have recently developed a MetaTool to predict lncRNAs in a species-independent way and used it across 414 marine plankton species from 9 different phyla. The full dataset is available as a user-friendly, open-access web interface, LncPlankton.

As an associate professor at UPEC I am also involved in giving lectures to university students in the Life Sciences. The lectures I deliver range from Molecular Biology and Cellular Biology to second (L2) and third (L3) year undergraduate students to Epigenomics and Noncoding RNA Functions to Master students (M1, M2). I have also co-directed the PhD preparation of three graduate students and directed several Masters students. Additionally, I have provided research training and mentoring to 20+ undergraduate students.

Finally, in recent years I've become increasingly involved in scientific mediation and outreach activities through talks and round tables, as well as through hands-on activities, for and with the general public, including younger audiences. The aim is to encourage scientific curiosity and to bring closer to the general public the science done in the lab. I am particularly drawn to the intersection of Art & Science, which taps into an innate, sensorial potential that can reach a wide audience.

Selected Awards and Grants
2025-2026 PHC-Sakura, France-Japan (Coordinator with Y. Matsuda)
2024-2028 ANR PRC BrownLincs (Coordinator)
2020-2024 ANR PRC DiaLincs (Coordinator)
2012-2015 Marie Curie IOF (EU, FP7). Rockefeller University (USA) - CNRS/IBENS (FR)

Selected publications

• LncPlankton : a comprehensive database of candidate lncRNAs from marine microbial eukaryotes. Debit A*, Vincens P, Bowler C, Cruz de Carvalho H* (2025). *corresponding authors NAR Genomics & Bioinformatics.

• The southern gap in ocean microbiome science. Sarmento H, Huber P, Dias Santos-Júnior C, Abreu A, P. Makhalanyane T, Karenyi N, Rocke E & AtlantECO project partners (2025). Ocean Microbiology.

• DiatOmicBase : a versatile gene-centered platform for mining functional omics data in diatom research. Villar E, Zweig N, Vincens P, Cruz de Carvalho H, ... Bowler C, Falciatore (2025). Plant Journal.

• Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems. Denoeud, F., Godfroy, O., Cruaud, C., Heesch, S., Nehr, Z., Tadrent, N., ... Cock, J. M. (2024). Cell.

• Light-dependent signal transduction in the marine diatom Phaeodactylum tricornutum. Agarwal A, Levitan O, Cruz de Carvalho H, Falkowski PG (2023). PNAS 120 (11) e2216286120.

• Differential expression patterns of long noncoding RNAs in a pleiomorphic diatom and relation to hyposalinity. Debit A, Charton F, Pierre-Elies P, Bowler C, Cruz de Carvalho H* (2023).*Corresponding author Scientific Reports 13 : 2440.

• Dynamic Cell Imaging : application to the diatom Phaeodactylum tricornutum under environmental stresses. Bey H, Charton F, Cruz de Carvalho H, Liu S, Dorrell RG, Bowler C, Boccara M, Boccara C (2022). European Journal of Phycology

• Global identification of a marine diatom long noncoding natural antisense transcripts (NATs) and their response to phosphate fluctuations. Cruz de Carvalho MH*, Bowler C (2020). *Corresponding author Scientific Reports 10 : 14110.

• A potential role for epigenetic processes in the acclimation response to elevated pCO2 in the model diatom Phaeodactylum tricornutum. Huang R, Ding J, Gao K, Cruz de Carvalho MH, Tirichine L, Bowler C, Lin X (2019). Frontiers in Microbiology 9 : 3342.

• Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations. Cruz de Carvalho MH, Sun H-X, Bowler C, Chua N-H (2016). New Phytologist 210 : 497–510.

• Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after re‐watering. Zhang JY, Cruz de Carvalho MH, Torres-Jerez I, Kang Y, Allen SN, Huhman DV, Tang Y, Murray J, Sumner LW, Udvardi MK (2014). Plant, Cell & Environment 37 : 2553-76.

Chris Bowler

Fredy Barneche (équipe Bowler) — 2015-10-07T16:45:17Z

Contact details
Ecole normale supérieure, 46 rue d'Ulm, 75005 Paris, France
Phone : (+33 (0) 144 32 35 25
Fax : (+33) (0) 144 32 39 35
E-mail

Current position
– Director of Research at CNRS
– Head of Plant and Algal Genomics Lab at IBENS
– Scientific Coordinator of Tara Oceans programme
– Scientific Director of Tara Oceans Polar Circle expedition

Education and qualifications
• 1987- PhD thesis at the Laboratorium Genetika (Profs. M. Van Montagu and Dirk Inzé), Universiteit Gent, Gent (Belgium). Title of thesis : A study of the role of superoxide dismutase in plants
• 1983- University of Warwick, Coventry (UK) Degree : B.Sc. (Hons) Class 2 Division 1 in Microbiology and Microbial Technology

Career overview
• 2016- Grass Fellow at the Radcliffe Institute for Advanced Study, Harvard University, USA
• 2002- Directeur de Recherche, Classe Exceptionnelle (Director of Research) at CNRS and Head of Plant and Algal Genomics Lab at the Institut be Biologie de l'Ecole normale supérieure (IBENS), Paris, France
• 1998- "Primo Ricercatore" (Assoc. Prof.) at the Stazione Zoologica ‘Anton Dohrn,' Naples (Italy)
• 1994- Marie Curie Fellow at the Stazione Zoologica ‘Anton Dohrn,' Naples (Italy)
• 1991- Postdoctoral Research with Prof. N.-H. Chua, Rockefeller University, New York (USA)

Honours
• Elected member of the Academie d'Agriculture de France in 2018
• Grand Prix Scientifique from the Louis D Foundation (Institut de France) in 2015
• CNRS Silver Medal in 2010
• EMBO member since 1995

An updated list of Bowler publications and patents can be found here

Bowler's CV

Applications

Fredy Barneche (équipe Bowler) — 2015-02-06T15:23:51Z

Applications

To join the lab as a PhD student or for a post-doc, please contact Chris Bowler.

IBENS - ENS

Martine Boccara

Maria Helena Cruz de Carvalho

Chris Bowler

Applications