Centre National de la Recherche Scientifique
Université Pierre et Marie Curie
Projet de Recherche 2014-2018
Laboratoire de Biologie du Développement
de Villefranche-sur-Mer
Observatoire Océanologique, Villefranche sur Mer, Septembre 2012
SECOND TOME
Projet de Recherche 2014-2018
Laboratoire de Biologie du Développement
de Villefranche-sur-mer
Vague D :
campagne d’évaluation 2012 – 2013
Unité de recherche
2.1. Projet scientifique de l’unité
Cette partie concerne la période allant du 1er janvier 2014 au 31 décembre 2018.
‘‘Laboratoire de Biologie du Développement de Villefranche-sur mer’’ (LBDV)
CONTENTS
1. Presentation of the laboratory
a. Historical context
b. Research domain
c. Organisation and internal operation of the laboratory
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2. SWOT analysis and project outline
2.1 Conclusions of the laboratory’s self-evaluation
2.2 SWOT analysis
2.3 LBDV Project
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3. Objectives and strategic actions
1. To maintain a high quantity and quality of scientific production.
2. To increase the critical mass.
3. To consolidate the technological platforms.
4. To stimulation internal collaborations
5. To stimulate other scientific collaborations
6. To increase participation in UPMC and other teaching programmes
7. To attract top level PhD students and post-docs
8. To further develop outreach activities and visibility in the local community
9. To encourage developments of partnerships for research and teaching
10. To promote the acquisition of new skills
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Individual group projects
Group 1: “Cnidarian developmental mechanisms” (Leaders E. Houliston and T. Momose).
Group 2: “Cell cycle in eggs and embryos” (Leader A. McDougall).
Group 3: “Cell fate” (Leader H. Yasuo)
Group 4: “Regeneration and pluripotency” (Leader S. Tiozzo)
Group 5: “Evolution of intercellular signaling in development” (Leader M. Schubert)
Group 6: “Genome and protein evolution in animals ” (Leader R. Copley)
Group 7: “Mitosis and spindle checkpoints” (Leader S. Castagnetti)
“Fiches Individuelles” for all scientific participants in the LBDV project (in alphabetical order)
ANNEXES 13 à 17
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1. Presentation of the laboratory
a. Historical context
The UMR 7009 “Biologie du Développement” at the Observatoire Océanologique de Villefranche-surmer (OOV) is proposing the following project for the period 2014-2018, under the updated name of
“Laboratoire de Biologie de Développement de Villefranche-sur-mer” (LBDV), or Villefranche-sur-mer
Developmental Biology Laboratory. While the LBDV vision remains rooted in its scientific tradition
and established reputation, the proposed new structure and group composition show significant changes
compared to those of the current UMR. Successful recruitment campaigns during the current contract
period (2009-2012) will lead to the installation of four new group leaders by January 2014,
compensating the retirement of five founding members of the laboratory and departure of a fourth group
leader. This renewal will provide a refreshing input of new ideas, new animal models and new
approaches, complementary to our existing strengths.
b. Research domain
The LBDV’s scientific activities fall firmly under the heading of basic research. Our ongoing projects
and future objectives concern the mechanisms that govern fundamental biological processes at different
levels, and so aim to push back of frontiers of human knowledge, providing the foundation for future
advances in biomedical research. Developmental biology is currently moving rapidly into a new era, as
technological advances are revolutionising the levels and depth of analysis possible for any given
biological processes, notably through the use of high-throughput “omics” techniques and live cell
imaging. Importantly these are no longer restricted by cost or time investment to a small number of
established experimental “model” species used by large multi-lab communities, allowing species from a
much wider range to be adopted successfully by small scientific communities or even single groups. In
parallel, there has been a recent reawakening of the realisation that the evolutionary perspective
provides an essential framework for understanding biological mechanisms. Our unique location and
access to the unrivalled animal diversity of the marine environment provides a privileged opportuity to
embrace this new era, allowing us to identify and exploit species which, through their phylogenetic
position and/or specific biological characteristics, can illuminate biological understanding.
While our research activities are not explicitly linked to identifiable applications, certain aspects have
the potential in this direction; for instance marine invertebrate models could be valuable material for
pharmacological testing, and the novel animal culture systems and imaging systems we develop have
the potential to be commercialised. Thus, while the principal audience for our research activities is thus
the scientific world itself: locally, nationally and internationally, we remain alert to will exploit contacts
at the SATT LUTECH (http://www.sattlutech.com) to explore transfer possibilities. Similarly, while our
reseach does not address social, economic or cultural issues, our study of marine animals in a publically
accessible and friendly marine station environment offers attractive possibilities for introducing the
world of biology and of basic research to non-specialist audiences of all ages and backgrounds: local
politicians, visitors to open days, school college and university students, etc. We aim to continue to
exploit this exceptional situation and the visual nature of our research to continue to mount stimulating
and informative presentations for different audiences, hoping thereby to help create a more positive
image of science and the research world. We also hope that through these activities we will promote
civil respect for the living environment, and stimulate new generations of research scientists.
c. Organisation and internal operation of the laboratory
“Organigramme”
The proposed organisation of the LBDV for January 2014 is shown in the “organigramme fonctionel
prévisionnel” (Annexe 13). We plan to maintain the existing overall organisation, comprising seven
independent but thematically overlapping research groups supported by three principle services:
Administration, the Animal Facility and the “I4” research support service (“Imagerie, Informatique,
bioInformatique et Infographie”).
The seven proposed research teams are of variable size, and are each allocated dedicated support from at
least one of our permanent technical staff. Two groups appear very small on the Organigramme because
the projected group leaders for 2014 have yet to arrive in the unit at the time of writing. Stefania
Castagnetti is currently being hired as a CNRS scientist (CR1) following successful application in 2012
to the CNRS national recruitment competition (Developmental Biology Section: old section 26), and her
arrival is planned for Spring 2013. Richard Copley has been allocated a Research Director position
(DR2-CDI) by the CNRS Institute for Biological Sciences and will join our laboratory in January 2013.
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These two groups have nominally been attributed the support of one of the existing technical staff at
50%. In practice we will continue our policy of adjusting technical staff affiliations progressively as
each group develops. This will be facilitated by the projected return of one technician (Moly Thiaw-Ba,
CNRS) between January 2013 and 2015, following temporary detachment to the Hospital service in
Guyana. The numbers of post-docs and PhD students in each LBDV group during the period 2014-18
will depend on recruitment levels and opportunities over the next years. We are taking active measures
to try to increase the size of both populations through actions such as international PhD programmes and
the DevoNet project (see Activity report, Document S2.1.1)
Internal Rules and Regulations
A copy of the Laboratory’s official “Réglement Intérieur”, covering the working hours and other
organisational issues is appended as Annexe 14. The only change since the last contract period concerns
the new section “Sujétions et Astreintes”, which lays out the conditions that allow technical staff to be
compensated financially or in terms of working hours for activities involving animal collecting or
missions at sea. This text was inserted in line with a CNRS directive in 2009. To ensure respect of the
legislation for administrative, health and safety, computing and network access issues and safeguarding
of intellectual property rights, new formal protocols have already been put in place to be executed upon
arrival and departure of all personnel, both temporary and permanent (Annexe 15).
Health and Safety
Our policy of promoting awareness and responsibility among all members of the laboratory will be
maintained. This includes regular internal discussions and training sessions on particular issues of
concern such as radioprotection, chemical risks, working out of hours etc.
Concerning specific actions to reduce risks and improve the safety of the working environment we will
continue to implement each year priority actions within the framework of the ‘Document Unique” (2012
action plan from this Document in Annexe 9). The plan of action detailed in this document is updated
anually by the internal Health and Safety committee including the laboratory director. One of the main
items in the current plan is the complete revision of the existing OOV aquarium systems, from the point
of view of electrical circuits, fluid circulation etc. This will be accomplished as part of the major
renovation work programmed in 2012-2014 for the aquariums, associated laboratory space and technical
rooms in the “Hall Vouté” (Galeriens building). The new installations will be conceived to minimise
electrical and other risks following advice of the Health and Safety officers (LBDV, OOV, CNRS).
Protection of Information Systems
The manager of our computing and network services, F. Bekkouche, will maintain responsability for
defining, implementing and managing the technical resources for information technology, to protect
confidentiality and integrity and also to ensure service availability. He has set up an “LDAP”
information directory to manage user accounts (non-permanent and permanent), limiting access to data
necessary for the individual and defined working groups. Additional safeguards are implemented for
external access. An agreement of terms form (copy in Annexe 6) must be signed by any user of the
laboratory’s computer resources and Internet services, specifying their legal responsibilies.
The network architecture is designed to prevent any non-authorised access attempt, to assure permanent
monitoring of connections and to detect any abnormal access with the help of the OOV IT department
and the CNRS IT Security Service. We have also set up an automatic system for regular data backup.
Ethical considerations
Under the proposed scientific project, no work on vertebrate species will be conducted within the
LBDV, so no animal experimentation licences will be required. The aquarium facilities will house only
invertebrates, and so will not require conformity with vertebrate animal facility legislation. We consider
our pioneering use of the use of invertebrate model species for basic research as contributing to the
search for alternative, non-vertebrate animal models in basic and biomedical research. In this context we
are partners in running in 2013 a workshop on “Emerging aquatic model species for biomedical
research“ funded by INSERM (page 10). To cover our culture of marine invertebrate species collected
from the wild, we have recently applied for the required authorisation: “Demande d’autorisation
d’ouverture d’un établissement détenant des animaux de la faune sauvage” (submitted in June 2012).
Concerning the use of genetically modified organisms, our 5-year governmental authorisation (n°5624)
was renewed in October 2010 to cover all our standard use of bacteria for molecular biology. Our
approved “L2” level laboratory for manipulation of genetically modified bacteria in the “Galerians”
building, and a second room (L1 level) dedicated to bacterial manipulation in the Jean Maetz building,
will allow all the LBDV groups to perform routine molecular biology in controlled conditions. In the
context of the EMBRC project, we aim also to develop and/or maintain transgenic strains of certain
marine models (starting with Clytia and ascidians). This will require application for specific
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authorisations, which will be possible once the dedicated new aquarium facility is constructed
(programmed for in 2013-14 as part of the new OOV Accommodation Building construction project)
For radioisotope manipulation we hold a valid authorisation from the ASN (T06268-10/6/2010)
detailing specific experimental protocols involving 2 isotopes (35S and 32P), and an authorised controlled
laboratory space in the “Galeriens” building. No expansion/ extension of these activities is anticipated in
the LBDV in the coming years.
2. SWOT Analysis and Scientific Objectives of the Laboratory
2.1 Conclusions of the UMR7009 activity report (translated from the Activity Report S2.1.1)
Under successive names over the last 30+ years, the UMR7009 “Biologie du Développement” at the
Observatoire Océanologique de Villefranche-sur-mer has forged a unique identity. Today it is
recognised internationally as a specialist in the use of marine species for molecular research in cell and
developmental biology. The quality and quantity of its scientific production as well as the visibility of
the research groups has been well maintained during the present term, with 100 peer-reviewed
publications since 2007 covering a range of notable discoveries. These include elucidation of a range of
cellular and molecular mechanisms controlling two critical periods of animal development: early
embryonic patterning (establishing axes of polarity, presumptive fate territories, cell lineages etc), and
the formation of oocytes (including polarisation, maternal mRNA localisation, meiotic divisions etc).
An important transition in group and laboratory composition has been accomplished during the current
contract period. A wave of retirements of founding unit members and the departure of an additional
group leader will by January 2014 be compensated by the introduction of four new group leaders
bringing four new research subjects, complementing the scientific strengths of three remaining group
leaders, who will lead restructured groups. The laboratory has made good progress in the four main
strategic objectives defined at the beginning of the present contract (January 2009): 1) The introduction
of additional animal models (Botryllus, Macrostomum, Branchiostoma) and of new scientific questions
(regeneration, EvoDevo, genome evolution, mitotic checkpoint control); 2) expansion of our capacity
for analysis in bioinformatics and genomics through establishment of an internal bioinformatics support
service, recruitment of a group leader specialist in genomic analysis and pooling of human and technical
bioinformatics resources and with other marine stations in France and Europe; 3) development of
technical platforms and common services; 4) renovation of the aquarium and seawater pumping
systems. Two major actions taken to achieve these objectives have been annual calls to attract new
group leaders since 2009, and heavy participation in the Marine Biology Resource infrastructure
projects EMBRC and EMBRC-Fr.
The recruitment of a first UPMC lecturer (Maître de Conférences) at the beginning of the contract
period (C. Barreau) was a very important, albeit modest, step towards our fifth objective: to increase
contacts with university students. This allows us to stabilise the traditional Masters (M2) course held in
Villefranche-sur-mer under local organisation, to add a second course at the M1 level (including
international participation) and to contribute to undergraduate teaching on the Jussieu campus. In
parallel, our strong involvement in the UPMC André Picard scientific activity network between
developmental biologists led to our coordination of an extended Labex project (“DevoNet”), which we
hope will provide the basis for cooperation in research and teaching over the coming years.
The organisation of the laboratory has allowed smooth and efficient running. In the field of health and
safety, we have maintained our policy of programming specific actions for risk reduction and of
responsibilisation of all laboratory members. Despite the declining economic climate, we have managed
to maintain our common services thanks to the ability of our groups to attract research funding through
scientific excellence, and by an active policy to share equipment and facilities.
Our continued outreach and academic attraction has been demonstrated by many fruitful scientific
collaborations and by sustained participation in national and international conferences, as well as by the
organisation of a live-cell imaging workshop at the OOV, of a conference for the international
urochordate community on a nearby site and co-organisation in 2013 of an INSERM-sponsored
practical workshop on marine model organisms at the OOV and an EMBO workshop on oocytes
maturation and fertilisation in Banyuls-sur-mer. In parallel we have increased our interactions with the
social and cultural environment through frequent and regular participation in public events, organising
class visits, animating public presentations, hosting school students for work experience weeks, and the
conception and creation of educational models and games and of multimedia documents.
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2.2 SWOT analysis
STRENGTHS
- Excellent standard of research reflected by a strong publication record (100 peer reviewed
publications between 2007-2012, including 57 with impact factor greater than 4, and 9 with impact
factors greater than 10)
- Strong thematic cohesion between groups, stimulating scirntific exchange and collaboration.
- Maintained success of the groups in attracting funding (grants obtained regularly from ANR, ARC,
FRM, Marie Curie etc )
- Highly visible participation at international and national conferences and workshops, as well as
through organisation of workshops and conferences locally.
- Multiple national and international scientific collaborations
- Well defined scientific niche as a recognised centre for molecular/cellular research using marine
invertebrate species.
- Speciality in adapting and applying live imaging technology and image processing techniques to
marine models.
- Well-developed relationship with public and private (Zeiss) developers of imaging technology.
- Expansion of scientific horizons into emerging fields, notably EvoDevo and genome analysis
- Tradition of running attractive student courses in marine developmental / cell biology.
- Commitment to multiple outreach activities, including innovative multimedia projects.
- Well-developed and efficient common services
- Succcesful policy of risk reduction in the area of Health and Safety .
WEAKNESSES
- Low critical mass.
- Very low representation of university teaching staff within the laboratory
- Few interactions with students, either from the UPMC or other higher education institutions
- Difficulty in funding both French and foreign post-docs wishing to join our groups
- Thematic isolation on the OOV site, reducing the possibilities for sharing technical platforms,
resources and competences with other laboratories, as well as for local scientific collaborations.
- Few possibilites for commercial exploitation of findings due to focus on basic science.
OPPORTUNITIES
- Opportunities arising from involvement in the EMBRC and EMBRC-Fr “Marine Biological
Resource” infrastructure projects. These include:
o Stimulation, by deployment of dedicated personnel and space, of activities related to the
production of biological resources (culture of established model species and potential new
models); development of transgenesis technology and of specific strains carrying useful
transgenes, initially for Clytia and Phallusia (EMBRC-Fr programme), but potentially
extendable to other models.
o Increased interactions with the UPMC and European marine station bioinformatics
communities, and opportunities for scientific exchange and sharing of resources,
infrastructures, ideas, projects etc.
o Development of interactive integrated data bases for genomic, transcriptomic, gene expression
and morphological data for selected model species to serve their respective communities
- Opportunities arising from the anticipated implementation of elements of the “DevoNet”
programme by the Paris Sorbonnes University’s ‘‘SUPER” IDEX , notably involving promotion of
synergistic projets exploiting multiple models and approaches, and the attraction and stabilisation of
international PhD students and postdocs
- Opportunities afforded by the availability of a exceptional range of marine invertebrates on the OOV
site, in the context of a reawakening interest in comparative biology.
- Emerging OOV strategy to encourage shared platforms and activities with the LOV/UMS
THREATS
- Unfavourable national context for funding of basic research. This is increasingly dangerous for the
succes of individual scientific projects, but is also making financing of medium/large scale equipment
for the laboratory common platforms (eg imaging equipment) hugely problematic.
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2.3 LBDV Project
The LBDV project will be presented in this section, and strategic actions planned to facilitate its
implementation in the following one (section 3). Our overall aim is to consolidate our existing scientific
strengths, founded on the exploitation of non-conventional models to achieve new perspectives on basic
problems in cell and developmental biology, while expanding further into the areas of evolution,
EvoDevo and genomic analysis. This perspective encompasses existing trends in the field at the
international level, and is well anchored strategically within the EMBRC and EMBRC-Fr infrastructure
development projects.
Our established laboratory structure and mode of operation will be maintained, based on independent
but interacting small-to-medium sized groups supported by active common services and a sustained
policy of acquiring, updating and operating shared common equipment and resources (see projected
“Organigramme” in Annexe 13).
An important point to note is that during the next “quinquennal” period, significant additional space will
become available to the LBDV due to major reorganisations and construction projects on the OOV site,
programmed for 2013-2015: Space will be progressively freed up in the Galeriens and Jean Maetz
buildings once the new accommodation building is completed and once other OOV activities (teaching
laboratories, restaurant, etc) are relocated following the recent departure of the “GeoAzur” UMR. As a
result, the LBDV will be able to enter a phase of consolidation and expansion. We will repeat our
successful strategy of international recruitment calls, and importantly, in parallel, encourage the smaller
existing groups to expand and stabilise through the recruitment of permanent staff as well as of PhD
students and post-docs. The main aim of these actions is to alleviate the danger of instability that has
been long inherent in the laboratory, due to the historically low critical mass.
Scientific project
The scientific focus of the new LBDV will remain on illuminating basic mechanisms in cell and
developmental biology using marine model organisms. We anticipate a continued progressive increase
in the emphasis on comparisons between species, evolutionary perspectives and genomic analysis, in
line with trends in the field. The LBDV will comprise seven groups with overlapping and
complementary interests. Their objectives and principle projects for the short, medium and longer terms
are summarised below. Detailed accounts of the projects and research perspectives for each group are
presented on pages 11 to 44.
Group 1: “Cnidarian developmental mechanisms” (Joint leaders E. Houliston and T. Momose)
This group will continue to exploit the cnidarian model Clytia to address the origins and development of
oocyte and embryonic polarity at the cellular and molecular levels. Related areas of interest are germ
line/ stem cell relationships and oogenesis. Current ANR-funded joint research and genome sequencing
projects will be pursued in collaboration with M. Manuel’s group in Paris (EvoDevo focus)
Group 2: “Cell cycle in eggs and embryos” (Leader A. McDougall).
This group will focus on understanding how cell cycle mechanisms have been adapted to carry out
specific tasks related to reproductive biology (oocytes) and developmental biology, using the ascidian
Phallusia as principal model. The main approaches are live imaging and proteomics. Funding has
recently been obtained for a collaborative study on chromosome segregation during meiosis with K.
Wassmann’s group (mouse model) in Paris (ANR), and on modification of the cell cycle during
embryogenesis (ARC).
Group 3: “Cell fate” (Leader H. Yasuo)
This group will pursue studies into how embryonic precursors are generated during development using
ascidian embryos as a model system, which enables fate specification events to be described at the level
of individual cells. They also aim to extend these analysis to understand how specific neuronal subtypes
are generated, an objective that will require prior adaptation of specific technologies such as single cell
electroporation to the ascidian system, and the culture and exploitation of transgenic lines carrying
fluorescent reporters. Current projects are funded by an ANR blanche grant.
Group 4: “Regeneration and pluripotency” (Leader S. Tiozzo)
This group will continue to explore whole body regeneration (WBR) in Botryllus schlosseri and to try to
define (1) the source of the regenerative plasticity that characterizes the WBR and (2) the source of
positional information and body patterning in a non-embryonic developmental scenario. This project has
Marie Curie Return Fellowship funding. In parallel the group will analyse neoblast behaviour in
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regenerating versus non-regenerating areas in the flat worm Macrostomum lignano, and has applied for
a joint ANR grant with Peter Ladurner (Innsbruck University) to develop this model species.
Group 5: “Evolution of intercellular signaling in development” (Leader M. Schubert)
This new group, to be established with the arrival of M. Schubert (CR1 CNRS) in October 2012, will
principally use amphioxus (Branchiostoma lanceolatum) and sea urchin (Paracentrotus lividus) as
models to define the developmental roles of intercellular signalling networks, focussing in particular on
understanding the mechanisms underlying formation and patterning of the different embryonic tissue
layers, and placing them in an evolutionary context. Current projects are funded by two ANR grants
focussed on retinoic acid signalling.
Group 6: “Genome and protein evolution in animals ” (Leader R. Copley)
This new group will be established with the arrival of R. Copley (DR2 CNRS) in early 2013. It will
focus on animal genome evolution, the development of computational methods to examine the evolution
of macromolecular structure-function relationships within the animals, and the integration of these two
themes to address questions of developmental pathway evolution within a phylogenetic framework. The
group will exploit increasingly available genome sequence data, including that generated by the other
LBDV groups, to construct robust phylogenies and to provide new understanding of the underlying
connections between genome and organismal evolution.
Group 7: “Mitosis and Spindle checkpoints” (Leader S. Castagnetti)
This new group will be established with the arrival of S. Castagnetti (CR1 CNRS) in spring 2013. Its
overall goal is to improve understanding of the mechanisms underlying mitotic progression and its
control through the spindle checkpoint, focusing on the role played by structural mitotic components,
notably the kinetochore and the centrosome. The principal experimental model of this group will
initially be the fission yeast Schizosaccharomyces pombe, building on previous work and exploiting the
power of genetic manipulation to identify and characterize the molecular players. In parallel the sea
urchin (P. lividus) embryo will be developed as a model for studies on checkpoint control during early
stages of development where spatiotemporal aspects of spindle function can be dissected more readily.
Synergies
It is clear from these brief summaries that the groups share many scientific interests, providing ample
opportunities for formal and informal collaborations. One LBDV strategic objective will be to
encourage the development of joint projects internally, in order to exploit synergies and favour joint
funding, especially in view of acquiring joint instrumentation. To indicate a few examples of potential
areas of interaction:
Early activation of Wnt/Fz/ß-catenin signalling: Over the last few years, work from the LBDV groups
has been influential in building the idea that Wnt/Fz/E-catenin signalling is an evolutionary ancient and
conserved mechanism amongst metazoan embryos for setting up the earliest regional differences,
fundamental for germ layer specification and axis formation. Exploring the regulation and roles of this
pathway will remain a major preoccupation of groups #1 (Clytia), #2 (Phallusia), #3 (Ciona) and #5
(Branciostoma/Paracentrotus). There is thus considerable scope to extend the current stimulating
discussions on these subjects between groups, for instance through writing joint review articles and
proposing explicit comparative projects on specific aspects. Other possible future collaborations across
species involving several groups could involve how Fz-PCP signalling pathways are involved in
development and cell fate establishment as well as gastrulation movements.
Spindle positioning and orientation: This is a longstanding common interest of members of the two
ascidian groups (#2 “Cell cycle in eggs and embryos” and #3 “Cell fate”), and will be developed in the
sea urchin model as well as in S. pombe by the new group #7 “Mitosis and Spindle checkpoints”.
Interactions between these groups will provide explicit comparisons. It may also be a direction to
explore in other models such as amphioxus (group #5), for instance in relationship to the influence of
Fz/Wnt signalling on spindle positioning.
Genomic analysis: The installation in 2013 of the new group 6 “Genome and protein evolution in
animals ” led by R. Copley should act as an important stimulation of research on genome organisation
and evolution in the context of developmental programmes. Several other groups have been entering
into this area but have lacked the relevant expertise / personnel to exploit fully the potential of their
systems in this regard. For instance group #1: “Cnidarian developmental mechanisms” has a project to
identify conserved gene regulatory regions relating to Wnt-dependent patterning via comparisons of
upstream non-coding regions for sets of targets genes, and through collaboration with group #6 could go
further to evaluate if such motifs are conserved between available cnidarians genome sequences.
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Similarly group 3: “Cell fate” is accumulating an exceptionally complete characterisation of neuronal
differentiation pathways in the ascidian, which could provide an excellent starting point for detailed
bioinformatics analysis of the regulatory interactions. Collaborations between the theoretical and
experimental groups on topics such as these provide considerable added value, for example allowing
predictions of regulatory elements etc to be tested experimentally.
In addition to potential collaborations on scientific projects, the installation of R. Copley will also bring
obvious benefits for groups #1, #2, #3, #4 and #5, all involved to a greater or lesser extent in genome
sequencing and annotation projects
Transcriptomics: Groups #1, #3, #4 and #5 are all currently running, or planning in the short or medium
terms, projects involving comparative transcriptomics approaches. Exchanges between these groups and
with the bioinformatics services (LBDV, OOV and our EMBRC/EMBRC-Fr partners) on technical
aspects relating to the creation (material collection, preparation, sequencing etc), management and
analysis (pipelines for assembly, mapping, curation etc) of transcriptomic data will clearly aid
efficiency.
Applying live imaging technology to marine models: LBDV members in many of the proposed groups
(#1, #2, #3 #4 and #5), along with Christian Rouvière, who runs the imaging platform, have
considerable experience and recognised expertise in this area. This will be continued to be shared
between groups both through direct interactions and through activities animated by the imaging
platform. Our common interest in live imaging could also be exploited towards the development of new
imaging techniques and tools, such as the ‘portable SPIM’ development project currently being explored
(project submitted to IBISA) with our MICA platform colleague F. Brau (Sophia Antipolis)
The above list of common interests is clearly not exhaustive. Given the rapid progress in technology
development and scientific concepts and knowledge, new areas will certainly emerge. Our aim is thus to
provide a framework in which interactions and collaborations are encouraged in an ongoing manner.
3. Objectives and strategic actions
Based in the SWOT analysis, we have defined ten strategic objectives for the LBDV, and propose the
following actions to achieve them:
1. To maintain a high quantity and quality of scientific production. This objective, of primary
importance, will be achieved through:
- Assuring the continued scientific independence of the groups and encouraging their exploration of
imaginative approaches and novel animal models and research subjects. The unique environment
and tradition of the laboratory has grown largely from allowing member scientists to operate ‘off
the beaten track’, and this spirit is vital to maintain. Thus all groups will continue to be given the
freedom to conceive and develop their scientific projects, and encouraged to develop whatever
internal and external collaborations they wish.
- Being reactive to technological and methodological changes. Through regular internal meetings we
will exchange information on these issues and plan common investments in instrumentation and
technology to keep abreast with developments in the field.
- Encouraging publication in top ranked journals, especially open access ones (PloS Biology, PloS
Genetics etc) by using LBDV funds to subsidize their publication if required.
2. To increase the critical mass. The last AERES evaluation (2008) concluded that: “…the BioDev
unit is functioning at a sub-critical mass, and so is not in the position to divert human or space
resources to areas of research outside its direct field”. This is still the case. The success of our
recruitment campaigns and the installation of four new groups have been offset by many retirements
and the departure of one previous group leader. The overall size of the laboratory has thus remained
roughly constant. A real population increase through further recruitments during the next contract is
of utmost importance for the future stability of the LBDV. This would allow the groups to
consolidate their existing projects, allow more efficient sharing of instrumentation and other
common resources, promote wider scientific exchanges and allow increased reactivity to changes in
the scientific landscape. We plan to increase the LBDV population size in three ways:
- Stabilisation of existing groups. During the next quinquennal period we will strive to reinforce the
seven proposed research groups, particularly the newest/smallest ones. They all will be encouraged
to identify potential new staff scientists with the required level to be competitive for CNRS
recruitment at the CR2 or CR1 levels, to strengthen their groups. We strongly hope also that the
UPMC will attribute at least one additional lecturer (Maître de Conférences) position as well as a
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professor position to the LBDV in the short-medium term (see below). Specific actions to increase
the PhD student and post-doc populations are treated under objective 7. We recognise that with
increased group and laboratory size and complexity will come increased responsibility for the
group leaders: in running groups and projects, managing the personnel, and in assuming tasks in
the LBDV administration and strategic actions. We are thus committed to provide management
training for all existing and new group leaders. To this end collaboration with the two other
structures on the OOV site, the LOV and the UMS, has led to the programming, in collaboration
with the CNRS DR20, of a management training programme for all group leaders in 2013.
- New recruitment calls. As appropriate new space becomes available we will be able to integrate
one or possibly two additional groups into the LBDV. We will again proceed by organising
international calls. We will select groups well positioned scientifically in the context of current
trends in the field. Given our particular scientific niche, tradition and unique location, we will
continue to favour groups planning to use new or emerging marine model species. An important
criterion for candidate selection will of course remain the ability of new groups to obtain start-up or
equivalent funding through schemes such as ATIP-AVENIR, ERC, ANR return fellowship, Marie
Curie return fellowships etc. Coordination of calls with the calendars for these funding
opportunities as well as with CNRS recruitment cycles is thus vital.
- Expansion of common services. As explained below, expansion is planned for the bioinformatics
service and imaging platforms, for which we will need to recruit 2 new staff at the IR (‘Ingénieur
de Recherche’) level. We will also push for attribution of staff (AJT or T level) to a common
support service in experimental biology to be implemented either within the LBDV, or preferably
within the OOV within the EMBRC context (see section 3). The IR post for the bioinformatics
service has been requested to the CNRS since 2009, and was opened for internal mobility
(NOEMI) in 2010 and 2011 without success. We are requesting that a open recruitment for this
position now be organised to attract a suitably well-qualified candidate. For the imaging platform, a
second staff member specialised in imaging/image processing will be required to compensate the
retirement of P. Chang in 2013 and the anticipated expansion of the imaging activities
3. To consolidate the technological platforms. All the technological platforms currently run under the
I4 service umbrella (Computing/ Imaging/ Bioinformatics) require constant maintenance, repairs and
technical upgrading, and this will remain a priority through a commitment to investment, continuing
the policy of subsidies from the LBDV’s basic funding as much as possible. The I4 has proved to be
an efficient, reactive and highly appreciated service for the laboratory. Specific planned
improvements are as follows:
- Computing: Refine and develop better tools for study and quantification of 3D objects constructed
from images acquired in the laboratory. This objective will require one or more new analysis
stations installed with a range of dedicated software. In the long term we will need to develop a
new architecture for managing image databases, since image storage requirements are exploding
(10-20 TB/ year). We are exploring the possibility of adopting the OMERO framework
- Imaging: One of the greatest challenges we will face in the coming years is to ensure continued
functioning and quality of our platforms through replacing aging equipment. Renewal of our twelve
year-old Leica SP2 confocal microscope with a more sensitive and faster equivalent is a priority.
Given the current funding climate, there are currently no simple strategies for obtaining funding for
such an instrument. A new 5D video microscopy station is also required. We are exploring the
possibility of modifying an existing system. Concerning technology development, we are currently
submitting a proposal to IBISA for a collaborative project with the IPMC imaging platform (Sophia
Antipolis) within the Nice region imaging platform (MICA) framework, aimed at developing a
“portable” imaging system using light sheet plane illumination (SPIM) technology.
Further development of the imaging and bioinformatics infrastructures is planned within the context
of the EMBRC/EMBRC-Fr projects. A centralised computing centre in newly renovated space will
allow more efficient and reliable data management and backup possibilities, and specialised
personnel offer technical support in bioinformatics. A unified OOV imaging platform will provide
access to specialised instrumentation based in the two UMRs. A new OOV experimental support
service is also planned in the EMBRC context as part of the Marine Biology Resource provision
facility. Currently neither of the UMRs nor hosted scientists has access to basic support for
experimental molecular/ cell biology eg glassware preparation, sterilisation of media etc., which
places an extra burden on all the individual research groups technicians and research assistants.
4. To stimulate internal collaborations As highlighted in section 2.3 above, there are many areas of
common scientific interest and potential synergy between groups, providing the opportunity for
98
developing collaborations. The arrival of new groups will provide fresh momentum for the creation
of internal collaborations. This will be actively encouraged, for instance by preferential laboratory
funding for Masters students on common projects.
5. To stimulate other scientific collaborations. The LBDV groups have a proven record in external
collaborations, and we are convinced of the necessity of vigilance regarding new funding
opportunities for national and international collaborations, which could be used to strengthen them.
Within France, the recent approval of the PRES Sorbonne University’s IDEX programme will allow
the implementation of certain actions proposed in the ‘‘DevoNet’’ LabEx project. Notably these
include targeted funding of synergistic projects between network partners, aimed at exploiting more
fully the richness of a wide diversity of biological models as well as complementary knowledge and
approaches to biological questions of common interest
6. To increase participation in UPMC and other teaching programmes. The LBDV ambition is to
increase its participation in teaching at all levels, allowing it to share with a new generation the
passion and knowledge in basic biology of its members. Such involvement should help build greater
public awareness of science and inspire and attract motivated students into basic research. This
objective carries over from the last contract, during which significant progress was made thanks to
the recruitment of C. Barreau as our first UPMC lecturer (= MC for Maître de Conferences). C.
Barreau has collaborated with colleagues on the Jussieu campus to build the teaching project
outlined below. Further progress is clearly very strongly dependent on attribution of more UPMC
teaching positions: To correct the current severe under-representation of UPMC teaching staff in the
LBDV, one professor and at least one lecturer (MC) should be recruited by the end of the next
quinquennal period.
Provisionally, the following teaching programmes are planned for 2014-2018, with the Villefranche
courses continuing to mobilise a large fraction of the LBDV personnel:
A new speciality “Biologie et Bioressources Marines“ (presented in annexe 16) will be introduced
within the Masters programme BI (= Biologie Intégrative). The LBDV will intervene in two teaching
units (Unités d’Ensignement = UE):
- UE “Organismes Marins et Modèles Biologiques“ (6 ECTS), Master 1, course in Villefranche,
involving international participation of students and teachers.
- UE “Modèles Marins en Développement et Evolution“ (6 ECTS), Master 2, alternating between
Villefranche and Banyuls.
In parallel the existing two UEs of the BMC (= Biologie Moléculaire et Cellulaire) Master will be
continued.
In a separate non-UPMC project, members of the LBDV have been involved in setting up a new
“professional“ module called “Imagerie et Systèmes Appliqués en Biologie“ in the Masters 2
programme at the University of Nice-Sophia Antipolis, in which one UE (“Imagerie optique pour la
recherche en Biologie“, 6 ECTS) will be held partly in Villfranche. One of the LBDV researchers
(A. McDougall) is co-organiser of this new course.
7. To attract top level PhD students and post-docs. This vital objective carries over from the last
contract. As mentioned in the activity report document, one strategy is to try to set up an
international PhD programme under the Marie Curie ITN/IDP programme. A first project will be
submitted in November 2012. Our idea is to propose a comprehensive PhD programme built on the
strengths of our ongoing research projects and involving tight collaborations with public and private
sector partners in the fields of high-throughput sequencing, proteomics and imaging. In a second
strategy we will support the implementation of schemes to provide post-doc and PhD grants to
emerging UPMC projects in the wider field of Developmental Biology, as proposed in the
“DevoNet” proposal to be incorporated in the PRES Sorbonne University’s “SUPER” IDEX project.
8. To further develop outreach activities and visibility in the local community. The LBDV will
build on its numerous activities to educate the public, media, and political sectors about science and
scientific discoveries. Because of the link to the sea and marine animals, our work is particularly
appealing to non-specialists, and we are able to take advantage of numerous opportunities to
illustrate how fundamental research leads to progress in understanding the environment and in
combating diseases. To this end we have developed a mobile workshop for 3 species (sea urchin,
sea-squirt, jellyfish) including tactile aquarium, dissection, demonstration of fertilisation and
observation of live embryonic development. This popular workshop and our battery of posters and
exhibitions on topics such as the origin of life, marine models for biology, microscopy and the cell
will be assembled for each recurring “Fete de la Science”, open days and school visit, and “Science
99
café” type public debates. We have developed an interactive model cell, used for public
demonstrations; smaller versions could be produced and distributed to schools and day camps.
In addition to continuing these well-established activities for our local neighbours, we will take
advantage of our French Riviera location to expand our international visibility. Partnerships have
been initiated with the science director of the International School of Nice and the Oceanographic
Museum of Monaco who are interested in our participation in their science workshop days.
International baccalaureate students from the International School of Nice will partner with LBDV
members as mentors for their extended senior essay projects.
The new UMR website, to be put in place in early 2013, will have an “Outreach” section including
animations, explanations of our projects, listings of upcoming or past activities, and a wealth of
videos of living cells for the public or use in education. In the spirit of “Bio-Clips”, which are short
informative and entertaining multimedia communications about scientific results developed by C
Sardet, we intend to produce one or more YouTube videos based on our research subjects, targeting
both future students and the general public. Our participation in the Tara Ocean expedition, cofounded by C. Sardet, will be pursued through the continuation of the Plankton Chronicles project
including the release of videos and the publication of a book about plankton for the general public
To help sustain this ambitious programme of non-research activities, we hope to be successful in our
application to set up Marie Curie training program (see above), which will include targeted funding
and personnel for development of public outreach.
9. To encourage developments of partnerships for research and teaching. We will continue our
successful policy of encouraging each group to develop research partnerships on individual projects
both nationally and internationally, through collective vigilance on funding opportunities for
collaborative research
On the OOV site, the 2008 AERES committee suggested increasing interactions between the two
laboratories by the recruitment of one or more new groups at the interface between them. During the
next quinquennal period, the OOV director has proposed to implement this objective via a direct
international call, an initiative that we support.
For teaching, within the UPMC we will continue to participate where possible in initiatives by the
PRES Sorbonne University to develop innovative multi-partner projects in both research and
teaching, as we proposed in the DevoNet framework. In parallel, we are proposing associations with
private partners in the context of our proposed Marie Curie IDP “MIAMM’.
We also hope to build on our co-organization in 2013 of the practical module of the INSERMfunded Workshop “Emerging aquatic model species for biomedical research” to develop interactions
with new public and private sector partners in the bio-medical field. The two-fold objective of this
workshop is to favour multi-species research projects by encouraging researchers working on
established models to test emerging aquatic model organisms, and to boost the development and the
sharing of technologies for functional studies in model organisms between communities.
10. To promote the acquisition of new skills. Continued training of the LBDV staff, post-docs and
PhD students, to allow career development as well as to favour reactivity and efficiency in emerging
technological areas, will remain a priority. We will continue to be reactive to the training needs of
each laboratory member, largely through the elaboration and operation, in conjunction with the
CNRS DR20, of an annual ‘Plan de formation de Unité” (“PFU”: copy of the 2013 document in
Annexe 17), which compiles all the training requirements of the personnel. The most frequently
expressed training requests over the past years include mastering of specific software, management
skills, and applying specific methodologies to our research models. We are particularly aware of the
increasing need to keep track of recent bioinformatics and imaging progress in the developmental
biology field. With strong involvement of the bioinformatics service and imaging platform, we thus
plan to set up specific internal training programmes to ensure that all members of the unit acquire upto-date understanding in both areas. The bioinformatics training programme will involve seminars by
both internal experts and external speakers, and have a special emphasis on genome analysis,
transcriptome analyses, high throughput methods and molecular phylogeny.
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Individual group projects
Cnidarian developmental mechanisms
Group 1 “Cnidarian Developmental Mechanisms”
Joint group leaders: Evelyn Houliston and Tsuyoshi Momose
Additional known members in January 2014: Carine Barreau (MC, UPMC); Sandra Chevalier (AI
CNRS); Antonella Ruggiero (PhD 2011- 2014); European PhD student to start in September 2013
(ITN network ”NEPTUNE”)
During the period 2014-2018 we will continue to develop and exploit Clytia hemisphaerica as an
experimental model to understand fundamental processes in cell and developmental biology. We will
develop four principal subjects:
1) Further expansion of Clytia methods and resources
2) Oogenesis and oocyte maturation
3) Embryo Polarity and gastrulation
4) Germ cell origins
In each case we plan to pursue and extend ongoing projects described in the previous activity report,
and to initiate/ develop additional projects in the short and medium term. A current ANR grant (20092013) ‘DiploDevo’ held jointly with M. Manuel’s group covers all four themes. For 2014 we intend to
submit a new joint ANR proposal covering the same topics, broadly focussed on implication of
signalling pathways in development and body plan evolution. We have also recently submitted a
proposal to the Association Recherche contre le Cancer (ARC) focussed on Wnt signalling in polarity
and stem cell regulation.
1) Further development of Clytia methods and resources
Clytia is steadily becoming recognised internationally as an attractive experimental model. We have
already distributed vegetative ‘cuttings’ our Villefranche inbred Clytia strains to over a dozen groups
world-wide who have requested them to explore use of this model for their particular research
interests. We expect further interest to be generated once an annotated version of the genome sequence
becomes available publically (see below). We are also committed to continue our efforts to pioneer
additional technical innovations, since certain questions are currently out of the scope of available
methodologies for gene function analysis. Specifically, we currently perform routinely functional
analysis of genes implicated in embryo and larva development by microinjection into eggs and large
blastomeres of the early embryo of Morpholino antisense oligonucleotides and mRNAs, but have no
available method to address gene function at other stages of the life cycle. This limits the study of
many interesting processes accompanying medusa formation, polyp formation, oogenesis etc.
We have thus started to develop two additional approaches for gene function analysis : RNAi, which
may be applicable by feeding as in Hydra (Chera et al 2006) or soaking as in Hydractinia (Duffy et al
2010), and transgenesis, as successfully pioneered in Hydra and Nematostella (Khalturin et al 2007 ;
Nakanishi et al 2012). The development of transgenesis will be facilitated by the OOV’s participation
in the EMBCR-Fr infrastructure project, which includes provision for recruitment of personnel for
developing marine model species and the construction of purpose built aquaria. One aim of this project
is to produce and distribute specific transgenic Clytia lines carrying useful markers such as fluorescent
histones (for following nuclei) or cytoskeletal binding proteins (to follow mitoses, cell movements
etc). So far we have successfully achieved test construct insert integration into the Clytia genome
using the meganuclease-based approach as used in Nematostella, but unfortunately expression of the
incorporated transgene becomes suppressed during life cycle progression. If our attempts to overcome
this problem by using alternative promoters do not significantly improve success we will switch
approach to site directed insertions, using the emerging TALEN (or more established Zn finger
nuclease) technologies. A big advantage of this approach is that it can be used not only to introduce
transgenes but also to silence endogenous genes. We plan to target endogenous GFP gene(s) for new
construct insertion, providing a convenient screening assay and simultaneously eliminating imaging
difficulties from endogenous GFPs.
In parallel with these methodological developments, we plan to expand the available sequence
resources for the Clytia community. The whole genome sequencing and annotation project we are
currently engaged in with the Genoscope been hampered by difficulties in assembly. We hope that
these will be overcome within the next year, allowing us to proceed with the organisation of the
annotation phase with a group of international colleagues, an activity which will certainly occupy us
heavily for around 1 year after the web interface its set up by the Genoscope team. In parallel, we will
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Cnidarian developmental mechanisms
continue generate further transcriptomic data and to integrate them into a publically-accessible
databases, developed within the EMBRC-Fr framework. Some of this data will be accumulate through
our various planned Digital Gene Expression projects (see below). Another specific goal is to
generate non-normalised transcriptomic data sets for developmental stages (including oogenesis), to
allow rapid identification of candidate regulators of successive developmental transitions. Building of
comprehensive Clytia transcriptomics datasets will be aided by close interactions with Ulrich
Technau’s group, who have already generated useful sequence data using high-thoughput approaches
from medusa stages and aided with the construction of joint assemblies, and Michael Manuel’s group,
who aim to perform DGE analysis on isolated medusa tissues and cell types. Longer-term projects for
resource development include construction of BAC libraries, both to improve genome sequence
assembly and to provide useful genomic resources to the community, and the development of a
‘Virtual Clytia’ web interface where genomic information is linked to gene expression patterns
mapped onto 2 or 3D representations of the developing embryo as well possibly as adult stages.
2) Oogenesis and oocyte maturation
The isolated Clytia gonad has a huge potential as an experimental system to address the regulatory
mechanisms governing successive steps of oocytes growth and maturation (see Fig.1A, B). These
include the signals and cellular responses responsible for commitment of proliferating stem cells to an
oocyte fate, their entry into the growth phase, cell polarisation during oocytes growth and maturation,
growth arrest of fully grown oocytes, light-induced spawning and oocyte maturation. Many of these
crucial regulatory steps in animal gamete production remain extremely poorly understood since they
are not easily experimentally accessible in traditional model systems such as Xenopus or mouse. We
plan in the short/medium term to pursue an ongoing project on oocyte polarity and to develop a new
one on the maturation triggering mechanism.
Figure 1 : Regulatory steps in oogenesis and oocytes maturation
A) Organisation of the female gonad, which hangs from the underside of the medusa bell. Oocytes develop from a
proliferating stem cell population, with a certain proportion committing to growth each day depending on nutrient availability.
Ovulation of fully grown oocytes is triggered by light.
B) Preliminary experiments have identified a peptide secreted by the gonad ectoderm in response to light which, after an
amplification step involving a second peptide, cause the oocytes spawn and mature.
C) The second peptide (Peptide 2) is expressed in both the gonad ectoderm and growing oocytes.
Oocyte polarity - We will continue our analysis of the acquisition of oocyte polarity, and more
specifically of the mechanisms responsible for mRNA localisation. We will build on our previous
identification of sets of maternal mRNAs that localise differentially to the animal cytoplasm during
oocytes growth (Fz1 type), to the animal (Wnt3 type) and vegetal (Fz3 type) cortices during oocyte
maturation, and to the germ plasm-like (Nanos-1 type) perinuclear region (see activity rapport for
details). We will first complete a characterisation of the timing and cytoskeletal dependence of
Nanos1 mRNA localisation as previously performed for mRNAs of the other 3 classes (Amiel and
Houliston , 20009). Bioinformatics analysis of 3’ and 5’ UTR sequences for the mRNAs of each class
will then be performed to identify potential ‘Zip-code” sequences responsible for the particular
subcellular targeting of each mRNA class. The function of these sequences will then be tested for
selected mRNAs (starting with Wnt3 and Nanos1) by using an in vivo imaging assay involving
injection of fluorescent labelled mRNAs, a technique we have applied successfully to mRNAs
localised in Xenopus ooctyes previously (Chang et al 2005) and are currently adapting to Clytia.
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Cnidarian developmental mechanisms
Triggering oocyte maturation. One major new project will be aimed at identifying the molecules and
mechanisms responsible for triggering oocyte maturation and spawning in response to light, suspected
for a long time to involve neuropeptide like molecules in Hydrozoans (Ikagami et al 1978). As in
Cytaeis (Takeda et al ref), a 1 minute light pulse following a 2hr dark period is sufficient to trigger the
oocyte maturation and spawning response in C. hemisphaerica. This treatment reliably causes oocyte
maturation in isolated gonads but not individual oocytes, consistent with the involvement of a
molecular relay from gonad somatic tissue. Preliminary studies, carried out in 2011 during a three
month visit by Noriyo Takeda (Asamushi Marine Biological Station) allowed us to identify through
analysis of our transcriptome database two peptides produced in the gonad ectoderm that can trigger
oocyte maturation at very low concentrations, and thus highly likely to represent the native maturation
hormone in this species (Fig. 1B, C). This exciting finding opens the door to identification of the
participating receptors both in the gonad ectoderm (light receptor) and for the peptide receptor in the
oocytes themselves that lead to rapid rise in cytoplasmic cAMP concentrations (Takeda et al., 2006).
Both are likely to be G protein coupled receptor (GPCR) family molecules (opsins and Gas or Gai
coupled receptors respectively). We will identify candidate GPCRs and putative downstream
signalling intermediates (Ga, Gbg, AKAP, arrestins etc) by DGE analysis comparing mRNA
populations from purified oocytes and gonad ectoderm samples; followed by in situ hybridisation
and/or Q-PCR validation. To test their involvement in we will use a combination of pharmacological
approaches and injection of specific activating or interfering molecules such as peptides (Jaffe et al.,
1993). This project will be undertaken a PhD student recruited within the successful NEPTUNE ITN
programme from September 2013, and will involve visits to Gaspar Jekeley’s group (MPI Tubingen)
to characterise the spectral characteristics of the light response. Characterisation of the responses of
somatic cells and oocytes to peptides will continue as a collaboration with Noriyo Takeda in Japan.
3) Embryo polarity and gastrulation
Polarity development during embryogenesis remains the central focus of our group. We will pursue
our analysis in the three main areas described below. Globally we hope that these studies of new and
known actors in early embryonic patterning will allow us to build progressively a detailed overall
vision of cellular and molecular regulation of polarity establishment, as well as of the oral-pole
specific developmental programme that regulates gastrulation.
Identification and characterisation of new actors in embryo polarity development. As mentioned in
the activity report, we have initiated a Differential Gene Expression (DGE) approach to identify new
actors potentially implicated in axial patterning downstream of Wnt3 (see Figure 2). This has allowed
clean identification of about 120 genes significantly up or down regulated downstream of Wnt3
function, and thus predicted be involved in patterning, morphogenesis or differentiation steps confined
to the oral or aboral poles respectively. These gene sets include a number of potential interesting
candidate signalling pathway regulators, including secreted molecules related to the BMP/Wnt
inhibitors Cerberus, sFRP and Dickkopf (Kawano and Kypta, 2003), and the Wnt signalling modulator
Notum (Flowers et al, 2012), as well as many transcription factors known for developmental
regulation (eg T-box, Homeobox, Sox, Fox and bHLH families). A surprisingly high proportion of
genes appear from sequence comparisons to be “novel “ at the homology level, either by comparison
either with all metazoan sequences or with known bilaterian sequences. We are currently
characterising the expression of about 40 of these genes by in situ hybridisation and or Q-PCR, and
will then select for functional studies a subset of these genes based on expression patterns and
suspected roles Function will be determined using our standard morpholino and mRNA injection
strategy. Of particular interest are secreted molecules and cell surface modifiers that potentially
modulate intercellular signalling at short medium and long ranges, and thus contribute to the powerful
reciprocal inhibition of oral and aboral fates acting during embryo patterning (Momose and Houliston,
2007), which may also underlie the regeneration (repatterning) phenomena well known in hydrozoan
embryos, larvae and medusae. In this field of regeneration ,our interests are converging with those of
the “Regeneration and Pluripotency” group led by Stefano Tiozzo, and we envisage future
collaborations to combine their expert background in the domain with the experimental advantages of
Clytia. An exploratory project on regeneration in Clytia planula larvae involving both groups was
performed by a Masters student in 2010/11, and we hope in the future to build on this by including
collaborative studies in submitted projects.
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Cnidarian developmental mechanisms
Figure 2 Identification of new polarity actors by the DGE approach
mRNA populations from control and aboralised early gastrula stage embryos (Wnt3 Morpholino injected– confocal images on
left) were sequenced using an Illumina platform. Mapping and statistical analysis were used to identify up and downregulated genes, putatively expressed aborally and orally respectively (points circled in red on graph).
The approach is currently being validated by in by hybridisation analysis (images right) and by Q-PCR.
TGFb signalling and gastrulation
Our preliminary findings suggest that TGFb signalling acts in parallel with Wnt signalling to regulate
specifically certain morphogenetic processes of oral territory cells during gastrulation. In a first step
cell ingression appears to require down-regulation of TGFß signalling (possibly BMP mediated) via
the inhibitory SMAD 6/7, while in a second step migration of the ingressed mesenchymal cells
towards the aboral pole requires the activity of a specific TGFEreceptor (again coded by a maternally
localised animal cortex mRNA), the ligand TGFß-1 and the SMAD2/3 cytoplasmic mediator. To
understand exactly what cellular processes are involved, we will first complete two ongoing studies: a
detailed morphological description of Clytia gastrulation (collaboration with Yulia Kraus, Moscow)
and a study of the function of the two Clytia Brachury orthologues, which appear to play nonredundant roles in cell ingression. We hope also to develop a collaboration with Jaap Kaandorp
(Utrecht) to build a 3D representation of Clytia gastrulation and explore the physical forces involved.
The functional studies of the TGFb pathway components involved in cell migration will be then
completed employing out standard approaches, and we will attempt to identify the ligand and
receptors, probably maternally supplied, whose down-regulation of required for the preceding step of
cell ingression.
Planar Cell polarity (PCP) and its links to embryonic axis establishment
We will build on our finding that Strabismus-dependent PCP develops in parallel with the molecular
programme of axis establishment in two directions. Concerning the characterisation of PCP itself, in
the short term we will complete a study of the mechanisms responsible for coordination of PCP with
global body axis, notably exploring in detail the hypothesis that Wnt3 acts as a spatial cue to orient
both Fz-PCP and WNT-bcatenin pathways, thereby providing an elegant and possibly ancestral means
to couple the cellular and molecular aspects of axis establishment. We also hope to examine in detail
by time-lapse microscopy and lineage tracing techniques the cell movements predicted to occur
perpendicular to oral-aboral axis during embryo elongation, in a process analogous to convergent
extension during gastrulation in chordates.
In parallel, we will develop a detailed study of a novel transcription regulatory role for PCP uncovered
in Clytia (project recently submitted to ARC). This is based on the unexpected finding that
Strabismus, working together with the aborally-restricted Fz3, influences gene expression in the future
aboral territory in a manner independent of ß-catenin. The first approach will be to test the
involvement in axial patterning of known “PCP effector” molecules acting downstream of the core FzPCP pathway complex such as RhoA, Cdc42, JNK and ROCK, monitoring transcription of known
targets of CheFz3 and CheStbm such as FoxQ2a and CheWnt3. For comparison we will test the role of
“Wnt/Ca2+ pathway” components including PKC and CamKII. cDNAs for all these molecules have
been identified in our EST or RNA-Seq transcriptome sequence collections, and key amino acid
residues are well conserved between Clytia and vertebrates, allowing easy design of dominantnegative and/or constitutively active forms. Morpholino antisense oligonucleotides targeting the
corresponding endogenous mRNAs will also be tested. We will then perform epistasis analyses
between these PCP effectors, CheFz3 and CheStbm to define the pathway of signal transduction. The
second approach will be to identify target genes under control of Fz3/Stbm regulation using DGE (Fig.
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Cnidarian developmental mechanisms
2) comparing expression profiles in CheFz3 (or CheStbm) depleted embryos and control embryos,
harvested at the early gastrula stage. We will compare the sets of genes up and down regulated in
CheStbm, CheWnt3 and double Morpholino embryos in order to determine specific target sets for
each pathway. These comparisons should provide a complete picture of the common and specific
WDUJHWV RI )]3&3 DQG :QWȕ-catenin signalling during aboral pole determination. To identify which
transcription factors are involved, we will focus on the target gene promoters. The genome sequences
around target genes identified by DGE will be compared to those of their orthologues in H.
magnipapillata and other hydrozoans in order to identify conserved non-coding sequences. Potential
transcription factor binding sites in the CNS regions will allow us to predict candidate transcription
factors involved in Fz3/Stbm transcriptional regulation as candidates for functional testing.
4) Germ cell origins and stem cell dynamics
We will build on our finding (Leclère et al 2012) that the multipotent germ line/stem cell population in
Clytia can probably be generated by both “Preformation“ (ie inheritance of maternal localised “Germ
plasm” mRNAs) or “Epigenetic” (ie induction via extracellular signals) mechanisms. Our
characterisation of i-cell behaviour and differentiation in Clytia embryos and larvae will first be
completed by detailed gene expression analysis across developmental stages of known stem cell
markers (Nanos1 and 2, Vasa, Piwi, PL10, etc) and potential markers of their derivatives
(nematoblasts, neuroblasts and gland cells). We then aim to trace the origin and behaviour of i cells
and definitive germ cells through the Clytia life cycle by generation of transgenic lines carrying a
fluorescent i cell marker, as successfully achieved in Hydra (Khalturinet al 2007). We have cloned
the Clytia Nanos 1 promoter as a first step. Such a transgenic line will also be useful in our attempts
to understand the regulation of i cell proliferation and differentiation in the context of embryonic
development. We will initiate this area of study by a dissection of the function of CheNanos1 by
Morpholino injection followed by detection of the different i cell derivatives. In the longer term we
hope to pursue analysis of i-cell dynamics in the context or larval and or medusa regeneration
(potential collaboration with the “Regeneration and Totipotency” group- see above), which would be
greatly facilitated by availability of Clytia transgenic strains with fluorescent i cells.
To determine the basis of i cell formation via epigenesis, we will use selected markers to determine
how the formation, proliferation and the subsequent differentiation of i-cells is affected by activation
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Fz/PCP and TGF beta signalling, using previously characterised GSK3-ȕ inhibitors and Wnt3,
Strabismus or SMAD2/3 Morpholino injection respectively. We will test whether Wnt and/or TGFb
signalling is involved in i-cell formation using the regeneration assay (Leclère et al 2012), involving
isolation of individual blastomeres at the 8-cell stage from Wnt3-MO, SMAD2/3-MO or Stbm-MO
injected embryos, and monitor the development of the stem cells and their derivatives by in situ
hybridisation and/or quantitative PCR. In parallel we will search the sets of Wntȕ-catenin and Fz-PCP
target genes identified by DGE for potential regulators of stem cell maintenance. In light of the results
obtained, additional DGE runs will be planned to identify regulators of different stages of i-cell
behaviour: initial formation, proliferation and differentiation, optimising stages and experimental
conditions in each case.
Cited literature (other than recent group publications in reference list)
Chang, P, Torres, J., Lewis, R.A., Mowry, K.L., Houliston, E., King, M.L., 2004. Localization of RNAs to the mitochondrial
cloud in Xenopus oocytes through entrapment and association with endoplasmic reticulum. Mol Biol Cell 15, 4669-4681.
Chera, S., de Rosa, R., Miljkovic-Licina, M., Dobretz, K., Ghila, L., Kaloulis, K., Galliot, B., 2006. Silencing of the hydra serine
protease inhibitor Kazal1 gene mimics the human SPINK1 pancreatic phenotype. J Cell Sci 119, 846-857.
Duffy, D.J., Plickert, G., Kuenzel, T., Tilmann, W., Frank, U., 2010. Wnt signaling promotes oral but suppresses aboral
structures in Hydractinia metamorphosis and regeneration. Development 137, 3057-3066.
Flowers, G.P., Topczewska, J.M., Topczewski, J., 2012. A zebrafish Notum homolog specifically blocks the Wnt/beta-catenin
signaling pathway. Development 139, 2416-2425.
Jaffe, L.A., Gallo, C.J., Lee, R.H., Ho, Y.K., Jones, T.L., 1993. Oocyte maturation in starfish is mediated by the beta gammasubunit complex of a G-protein. J Cell Biol 121, 775-783.
Kawano, Y., Kypta, R., 2003. Secreted antagonists of the Wnt signalling pathway. J Cell Sci 116, 2627-2634.
Khalturin, K., Anton-Erxleben, F, Milde, S, Plotz, C. Wittlieb, J, Hemmrich, G, Bosch, TC, 2007. Transgenic stem cells in Hydra
reveal an early evolutionary origin for key elements controlling self-renewal and differentiation. Dev Biol 309, 32-44.
Nakanishi, N., Renfer, E., Technau, U., Rentzsch, F., 2012. Nervous systems of the sea anemone Nematostella vectensis are
generated by ectoderm and endoderm and shaped by distinct mechanisms. Development 139, 347-357
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Cell Cycle in eggs and embryos
Group 2 "Cell cycle in eggs and embryos"
Group leader: Alex McDougall
Additional known members in January 2014: Remi Dumollard (CR1, CNRS), Janet Chenevert (CR1,
CNRS), Gérard Prulière (CR1, INSERM), Céline Hébras (T, CNRS), Lydia Besnardeau (50%, AI,
CNRS).
Overall objective
Understanding how cell cycle mechanisms have been adapted to carry out specific tasks related to
reproductive biology (oocytes) and developmental biology.
A. Funded projects that are coming to an end.
Meiotic cell cycle project : Ongoing ANR with MH Verlhac (finishes Dec. 2012)
One of the aims of this project was to characterize the proteins of metaphase I chromosomes using
ascidians as a model amenable to proteomics. These data will continue to be analyzed for the coming
years.
B. Ongoing and future funded projects
1. Meiotic cell cycle (with K. Wassmann, Jussieu, UPMC). ANR 2013-16.
Aims.
i) To better understand chromosome segregation during the two meiotic divisions in oocytes.
One of the major challenges in reproductive biology is to understand how a haploid oocyte is formed
during meiotic maturation. As well as addressing fundamental questions in biology such as
asymmetric cell division (ACD) and meiotic chromosome segregation, oocyte maturation impacts
heavily upon human health since a staggering 1 in 3 human oocytes will become aneuploid as women
approach the end of their reproductive lives (see review by Hassold and Hunt, 2001). In order to
advance our understanding of the mechanism of meiotic chromosome segregation we performed a
proteomic analysis of metaphase I chromosomes using ascidian chromosomes as starting material –
mammalian species do not provide sufficient quantities of oocytes for such an approach (millions of
oocytes are required). We also performed a yeast two hybrid screen using various proteins and found
an interesting association between Shugoshin and I2PP2A (see below). We are continuing our
analysis of the proteomic data-set and have also been studying in more detail I2PP2A (we extended
this analysis to the mouse oocyte in collaboration with Katja Wassmann's group, Jussieu, UPMC).
PP2A is a heterotrimer composed of a catalytic subunit (C), a scaffold (R1) and a regulatory subunit
(R2-R5) (Janssens and Goris, 2001). In mammals there are two catalytic subunits, two scaffold
subunits, and several isoforms of regulatory subunits (at least 13 regulatory subunits exist in humans)
giving a large array of possible heterotrimers. However, in the ascidian there is one C subunit, one R1
and six different regulatory subunits. Pulldown studies in human cell lines using Sgo 1 identified B56
(R5) containing PP2A heterotrimer (Kitajima et al., 2006). We intend to extend this approach but
Figure 1) I2PP2A is in the same complex as PP2A in meiosis II
only. Immunoprecipitation (IP) with anti-I2PP2A antibody followed
by PP2Ac Western blot detection. Ascidian extracts at the
indicated stages in meiosis were used for co-immunoprecipitation
experiments. I2PP2A and PP2Ac interact only in meiosis II,
showing for the first time a meiosis II- specific interaction partner
of PP2A by co-immunoprecipitation of endogenous proteins.
instead use ascidian oocytes rather than human cells lines to identify proteins that interact with PP2A
during meiosis. We will perform immunoprecipitation or pulldown studies of all 4 PP2A regulatory
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Cell Cycle in eggs and embryos
subunits expressed in oocytes from synchronized ascidian egg populations (focusing initially on the
two B56 regulatory isoforms required for protection of centromeric Cohesin). Moreover, since we can
synchronize large populations of ascidian eggs (Meta I, Ana I, Meta II and Ana II) we will perform
this analysis at each stage of meiosis. As proof of principle we have already performed coimmunoprecipitations of PP2A catalytic subunit and detected I2PP2A (Fig. 1).
ii) To determine how spindle rotation is controlled during the meiotic cell divisions : ARC
funded project (2012/13)
During meiosis the spindle is positioned subjacent to the oocyte cortex and rotates each time a polar
body is extruded. The mechanism regulating spindle rotation has been studied most in C. elegans
oocytes. Cdk1 inactivation is required for meiotic spindle rotation in a dynein-dependent manner in
C.elegans (Ellefson and McNally, 2011). However such a mechanism might not be conserved in
chordate eggs as we noted that complete inhibition of Cdk1 activity in the ascidian egg is not
sufficient to trigger spindle rotation. Instead we have focused on the role played by aPKC during
spindle rotation. Strikingly we have recently found that aPKC and Aurora kinases are associated with
the spindle in unfertilized eggs (Fig. 2). This suggests that the same signaling pathway might regulate
Figure 2. aPKC localization during extrusion of the first polar body. Microtubules are labelled red,
chromosomes blue and aPKC green. Note that aPKC moves from the spindle to the cortex (green arrows).
spindle rotation in the egg and in the ascidian germ lineage (see later). Two to three minutes after
fertilization and before spindle rotation, aPKC undergoes a microtubule-dependent re-localization to
form a cortical patch which appears to attach one pole of the spindle to the cortex. Recent findings by
us and others indicate that aPKC protein can move towards the plus ends of microtubules, probably
via association with a kinesin type motor (Pruliere et al 2011). We aim to determine the role of aPKC
in meiotic spindle rotation and polar body extrusion, as well as whether PAR6 and PAR3 co-localize
with aPKC during this extremely ACD as they do in the centrosome attracting body/CAB (see later
section). We found that Aurora kinase relocates from the spindle to the midbody and contractile ring
during polar body extrusion and is required for abscission. aPKC and Aurora kinases can regulate one
another during ACD. We will examine whether the aPKC/actin cortical patch is defective following
Aurora inhibition, indicating that its role is to retain one spindle pole in the polar body to extrude one
haplotype and maintain correct ploïdy. We will also analyze the consequences of the manipulations of
Cdk1 and APC/C described above on the redistribution of aPKC and Aurora during spindle rotation.
2. Mitotic cell cycle project : ARC funded project (2012-13)
To determine how the cell cycle is co-opted during development to generate embryo morphology
Xenopus and Drosophila embryos have provided a wealth of information showing how the speed of
the cell cycle slows at the midblastula transition (MBT) due to increased nuclear/cytoplasmic (N/C)
ratio (see review by Vidwans and Su, 2001). C. elegans embryos develop with a fixed number of cells
that divide in an invariant pattern due to spindle re-orientation cues. The most studied of these spindle
re-orientation mechanisms occurs at the first cleavage and led to the discovery of the cortical PAR
proteins. Like C. elegans, ascidian embryos develop with a small fixed number of cells that do not
migrate and display an invariant cleavage pattern up to the gastrula stage (Conklin, 1905). One of our
aims is to explain the mechanisms that give rise to the invariant cleavage pattern and the cell cycle
asynchrony. These mechanisms involve a combination of cell cycle asynchrony, oriented cell
division (OCD) and unequal cleavage (together with cell adhesion) which combine to generate the
morphology of the ascidian gastrula. Because the most commonly used ascidian species Ciona
intestinalis is not well-adapted for live cell imaging since it does not express well fluorescent fusion
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Cell Cycle in eggs and embryos
protein constructs from injected mRNA (Prodon et al., 2010), we developed the European ascidian
Phallusia mammillata (which does translate well exogenous mRNA) as a model for fluorescencebased live cell imaging studies (McDougall et al., 2011, 2012). To demonstrate these advantages of
Phallusia we combined fast 4D fluorescence imaging with knockdown and blastomere isolation
experiments to study unequal cleavage at the 16 cell stage. Our study not only displayed Phallusia's
usefulness for live cell imaging, but also revealed that the CAB is active in prometaphase rather than
interphase as previously thought from fixed cell data (Prodon et al., 2010). Since then we have
observed OCD, induced ACD and also how cell cycle asynchrony starting at the 16 cell stage
generates mitotic domains (Dumollard et al., in preparation).
Aims.
i) Spindle orientation during unequal cleavage
Spindles are often attracted to cortical sites during unequal cleavage and ACD and this is important for
patterning during embryonic development and the maintenance of stem cell pool size. The PAR
(Par3, Par6, aPKC) and the Pins (Pins, Galpha and Mud/NuMa) protein complexes are often involved
in ACD. These cortical complexes are activated at specific moments during the cell cycle. For
example, in one cell C.elegans embryos spindle displacement towards the posterior cortex is triggered
by a fall in Cdk1 activity brought about by the APC/C. In Drosophila larval neuroblasts, Aurora A
kinase. phosphorylates and activates Pins causing the Pins apical complex to become active during
prophase. By comparison, we have shown that the centrosome attracting body or CAB, which
contains the polarity complex PAR3/PAR6/aPKC, attracts one pole of the mitotic spindle during
prometaphase.
It is now clear that several different mechanism control spindle orientation in different organisms.
Because the ascidian cortical CAB is visible by light microscopy it is an excellent system in which to
study how a cortical structure influences microtubule behavior. Moreover, through GFP screening and
antibody labeling work we have identified more than 10 proteins that specifically localize to the CAB
(Fig. 3). In terms of the temporal control of the CAB by the cell cycle, both Polo and Aurora deserve
particular mention since
these
kinases
are
activated during mitosis
thus
providing
a
potential link between
the cell cycle timing
and
spindle
repositioning.
Interestingly, Polo has
recently been found as a
Figure 3. Unequal cleavage at the 16 cell stage. Images showing aPKC, PEM1,
partner of the CAB
Aurora and RACK1 protein immunolabeling of the CAB. Live cell imaging showing
protein
PEM1
in
Plk1::Venus , Par6::Venus, Dishevelled::mCherry, and E-catenin:Venus labelling
of the CAB.
Halocynthia and our
preliminary data show
that inhibition of Polo disrupts spindle attraction towards the CAB. In addition to studying how the
CAB functions, we will also specifically assess the role played by Aurora and Polo during unequal
cleavage. The results from these mechanistic and timing studies will lead to an understanding of the
molecular pathway connecting cell cycle progression to spindle positioning during unequal cleavage.
ii) OCD in cleavage-stage embryos and in the neural tube (in collaboration of N. Minc, Institute
Curie, Paris)
In addition to the dramatic examples of unequal cleavage described above, our time-lapse videos of
embryonic development revealed numerous other examples of spindle re-orientation or OCD. We will
focus here on the analysis the OCD occurring in the ectoderm during ascidian epiboly (32-76 cell
stage) and in the elongating nerve cord during tail morphogenesis.
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Cell Cycle in eggs and embryos
A default mechanism known as
Hertwig's rule causes spindles to
align along the longest axis of the
cell. Wilson and Sachs noted that
spherical cells often divide
orthogonal to the cell division
plane of their mothers (Wilson,
1925). Cells that do not divide
orthogonal to their mothers do so
A
because
the spindle is repositioned
in an active manner (e.g. due to
cell shape, cortical cues, cell-cell
interactions etc.). In the absence of
such cues in spherical cells there
are three orthogonal division axes,
but in ascidians all spindles are
parallel to the surface of the
Figure 4. OCD at the 32 cell stage. A. Animal view of 16, 32 and 64
embryo up to the gastrula stage
cell stages. Lineages of individual blastomeres are color coded.
thus creating only two possible 90°
White stars indicate those blastomeres where spindles are predicted
rotations. By following the
to re-orient away from the default pathway. B. Spindle re-orientation
in animal hemisphere at 32 cell stage. Note that spindles rotate in all
position of cells over two cell
three blastomeres predicted to display spindle re-orientations. Also
cycles
it
is
relatively
note that -catenin knockdown abolishes spindle rotation.
straightforward to predict all cases
in which the cells do not obey the
orthogonal rule (Fig. 4). We
predicted and also observed that
the whole mitotic spindle reoriented in
many of these cells to cause the cell to
divide in a plane roughly parallel to that of
the cell division of its mother (Fig 4).
In many organisms the planar cell polarity
(PCP) pathway is involved during later
embryonic
development
in
tissue
morphogenesis. For example, the core
PCP (non-canonical Wnt pathway)
pathway causes mitotic spindles to align
along the anterior-posterior axis causing
B along that axis (Gong et al., 2004),
OCD
while in Drosophila a variant of the PCP
pathway (the Fat/Daschous/FourJointed
system) causes OCD along the proximal
distal axis (Mao et al., 2011). In ascidian
Figure 5. OCD in the neural tube. Upper row of images
embryos we have identified several
shows microtubule (labeled green with MAP7::GFP) and
lineages which display OCD exemplified
chromosome (labeled red with HH2B::Rfp1) behavior
by the neural tube which in the trunk of the
during OCD in the neural tube. Lower row of images
displays lineage specific expression of Venus in the neural
larva forms a one cell thick tube even
tube from a CiEtr1 promoter.
though cell division is ongoing (Cole and
Meinertzhagen, 2004). We have found that
neural tube extension in the ascidian is
accompanied by successive waves of OCD in an anterior-posterior direction (Fig 5). We tested a
number of lineage-specific expression vectors based on Ciona promoters (Kubo et al., 2010) and
found that all express in the correct tissue of Phallusia (following either electroporation or plasmid
injection), and have since created lineage-specific expression vectors (Fig. 5). The major outcome of
this work will be a description of how OCD contributes towards morphogenesis.
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Cell Cycle in eggs and embryos
C. Future directions
We intend to continue to exploit some of the features of ascidian eggs and embryos that make them a
useful organism to understand the how the cell cycle operates in eggs and in embryos. Over the last
10 years we have collaborated with several groups working with mouse oocytes (Herbert , Jones,
Carroll, Verlhac and Wassmann). One advantage of the ascidian model to those working on the
mouse is that ascidians produce a large quantity of Meta I-arrested oocytes that are amenable to
biochemical and proteomic analyses not possible in the mouse. Another of our questions pertains to
how the cell cycle is co-opted by developmental processes to help create embryo morphology. Several
aspects of ascidian development are interesting from a cell cycle perspective: 1) all mitotic spindle are
aligned in a precise manner up to the gastrula stage. 2) Cell cycle asynchrony develops in a
predefined order, and 3) the ascidian tadpoles is composed of around 2600 cells comprising 36
muscle, 40 notochord, around 350 neural cells and a large number of epidermis, endoderm,
mesenchyme cells. It may be possible to understand how cell cycle exit and hence cell number is
controlled in each lineage. These questions can now be addressed by manipulating the cell cycle in
each tissue through electroporation of plasmids driving lineage-specific expression. Moreover, we
noticed that electroporation of plasmids results in mosaic expression allowing us to manipulate the cell
cycle in single cells. In most cases, spindle orientation relies on specific interactions between actin
cortical structures and microtubules. Our objective for the coming years is to understand what factors
shape the ascidian embryo at a detailed molecular level. With the genome already available for several
ascidian species, we will use bioinformatics approaches to identify the Phallusia proteins which are
known to play a role in microfilaments/microtubules interactions in other systems. Their functions will
be then dissected using biochemical/proteomics approaches. We have already identified all the
members of the Myosin family and their characterization is underway.
D. Cited literature (other than recent group publications in reference list)
Conklin, E. G. 1905. The organization and cell lineage of the ascidian egg. J. Acad. Natl. Sci. Philadephia. 13.
Cole, A. G. and Meinertzhagen, I. A. 2004. The central nervous system of the ascidian larva: mitotic history of cells forming
the neural tube in late embryonic Ciona intestinalis. Dev. Biol., 271, 239–262
Ellefson, M. L. and McNally, F. J. 2011. CDK-1 inhibits meiotic spindle shortening and dynein-dependent spindle rotation in
C. elegans. J. Cell Biol., 193, 1229–1244
Gong, Y., Mo, C., and Fraser, S. E. 2004. Planar cell polarity signalling controls cell division orientation during zebrafish
gastrulation. Nature, 430, 689–693.
Hassold, T. and Hunt, P. 2001. To err (meiotically) is human: the genesis of human aneuploidy. Nat. Rev. Genet., 2, 280–
291.
Janssens, V. and Goris, J. 2001. Protein phosphatase 2A: a highly regulated family of serine/threonine phosphatases
implicated in cell growth and signalling. Biochem. J., 353, 417–439.
Kitajima, T. S., Sakuno, T., Ishiguro, K., Iemura, S., Natsume, T., Kawashima, S. A., and Watanabe, Y. 2006. Shugoshin
collaborates with protein phosphatase 2A to protect cohesin. Nature, 441, 46–52.
Kubo, A., Suzuki, N., Yuan, X., Nakai, K., Satoh, N., Imai, K. S., and Satou, Y. 2010. Genomic cis-regulatory networks in
the early Ciona intestinalis embryo. Development, 137, 1613–1623.
Mao, Y., Tournier, A. L., Bates, P. A., Gale, J. E., Tapon, N., and Thompson, B. J. 2011. Planar polarization of the atypical
myosin Dachs orients cell divisions in Drosophila. Genes Dev., 25, 131–136.
Vidwans, S. J. and Su, T. T. 2001. Cycling through development in Drosophila and other metazoa. Nat. Cell Biol., 3, E35–
39.
Wilson, E. B. 1925. The Cell in Development and Heredity (Macmillan, New York).
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Cell fate
Group 3 “Cell fate specification and generation of the chordate body plan”
Group leader: Hitoyoshi Yasuo
Additional known members in January 2014. Clare Hudson (CR1 CNRS), Cathy Sirour (AI UPMC)
I) Background
Our group has been studying how embryonic precursors are generated during development with a
particular interest in dissecting the step-by-step sequence of specification events leading to the
acquisition of chordate-specific features. We choose to study ascidian embryogenesis as a model
system because it proceeds with a fixed cell division pattern, a small number of cells and welldescribed cell lineage, allowing analysis at the level of individually identifiable embryonic cells. We
have focused on the cell fate choices leading to the formation of the notochord and caudal neural
lineages and how the caudal neural lineage is subsequently patterned. In these lineages, we were able
to dissect every cell fate choice starting from the 16-cell stage to the neural plate stage, covering four
successive rounds of cell divisions. Importantly, our results show that most of these cell fate choices
operate in a binary mode.
During the next “quinquennal”, we propose to continue our dissection of the events that lead to the
generation of the chordate body plan in ascidian embryos. The proposed projects involve a study on
how animal cells respond in a switch like manner to the neural inducing signal (II-1), a study
developing our analysis of marginal zone formation (II-2) and two studies where we undertake a new
direction to analyse the mechanisms controlling orientation of cell divisions. For this latter subject, we
analyse the orientated divisions of the notochord/neural mother cell and its endoderm sister cell (II-3)
and we exploit the ascidian epidermis as a system to study planer cell division pattern generation (II-4).
A current ANR grant (until August 2013 but planning to request a 6 months prolongation) covers all
four themes. For 2014, we intend to submit a new ANR proposal covering the same topics, further
extending our step-by-step analysis to the formation of specific neuronal subtypes in the neural tube.
II) Proposed projects
“Cell fate specification”
II-1) ON/OFF output of the binary fate choice during the neural induction
In this proposed project, we will address the embryological and molecular basis of the ON/OFF
response of ascidian embryonic cells to the neural inducing signal. The anterior neural lineage which
forms the sensory vesicle (considered to be homologous to the vertebrate brain) originates from the
animal hemisphere and is specified via a binary fate choice between neural and epidermal fates. This
binary fate choice is controlled by FGF signals from vegetal hemisphere cells, which promote neural
fates. Every cell in the animal hemisphere is
competent to respond to the FGF signal and adopt
neural fates (Hudson and Lemaire, 2001; Bertrand et
al, 2003). In the embryo of the 32-cell stage, however,
only 4 cells among the 16 animal cells respond to FGF
and are specified as neural precursors. These four cells
are the a6.5 and the b6.5 pairs, which are anterior and
dorsal neural precursors, respectively. The specific
aim of this project is to reveal how these four cells
exclusively respond to the neural inducing FGF signal.
By reconstructing 3D virtual embryos, Tassy
et al have shown that, among the animal cells, the a6.5
and b6.5 cells have largest relative contact surfaces
with the inducing vegetal cells and proposed that
Figure 1. (1) Schematic drawings of Ciona larva
neural induction takes place as a threshold response to
(left) and the animal pole view of the 32-cell
the relative area of surface contact between the animal
stage embryo (right). Neural lineages are
cells and the neural inducing vegetal cells (Tassy et al,
coloured with the anterior neural lineage in red,
2006). Threshold responses are considered to be an
the dorsal in green and the caudal in yellow. (2)
anti-dpERK1/2 immunostaining (animal pole
important mechanism in developmental processes in
view of the 32-cell stage embryo). (3)
which cells are exposed to signalling noises or
Comparison of the cell contact areas of each
signalling gradients but have to make ON/OFF
animal cell with vegetal cells (from Tassy et al,
decisions. However, it remains largely unknown how
2006).
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Cell fate
threshold responses are achieved. ephrin-Ad is expressed in all cells of the animal hemisphere from the
16-cell to 32-cell stage and we have shown that the
ephrinAd-Eph3-RasGAP signalling cassette attenuates
ERK activation induced by FGF signals during the fate
specification of the caudal neural lineage (Picco et al,
2007; our unpublished data). We thus hypothesised that
an antagonistic relationship of FGF and ephrin signals on
ERK1/2 activation might be involved in the threshold
response of animal cells during neural induction. Indeed,
Figure 2. Expression of otx, a neural
when ephrin signals were blocked at the level of ephrinmarker, in 32-cell stage embryos,
Ad, Eph3 or RasGAP, we found that, in addition to the
following injection of dnRasGAP RNA
a6.5 and b6.5 cells, additional animal cells adopted neural
into single a4.2 cells of the 8-cell stage
fates with an almost 100% cell fate transformation of the
embryo. Dashed green line circles the
a6.7 cell, which has the third largest relative area of
four cells which are descendants of a4.2
cell.
contact with vegetal cells. We ruled out that perturbation
of the ephrin signal in this experiment could have affected
cell shapes and resulted in changes in cell contact surfaces between animal and vegetal cells. We
reconstructed 3D virtual embryos of dnEph3-injected embryos and measured the cell contact surfaces.
This analysis shows clearly that there is no change in the contact surfaces between animal and vegetal
cells when ephrin signals are compromised.
We are next planning to conduct the following experiments. If, as we predict, ascidian neural
induction act as a threshold response, the system should act in an ultrasensitive manner. In order to test
this, we will quantify the activity of ERK1/2 in isolated animal caps treated with increasing doses of
FGF proteins. The ERK activity will be measured in vitro using the sensitive and quantitative assay
based on phosphorylation of myelin basic protein (MBP). The a4.2 cell, the anterior-animal cell, of the
8-cell stage embryo, adopts epidermal fates when cultured in isolation, whereas, in the presence of a
high dose of exogenous FGF proteins, it adopts neural fate (Hudson et al, 2003; Bertrand et al, 2004).
We will treat isolated a4.1 cells with serial doses of FGF and measure ERK activation levels in the
resultant partial embryos at the equivalent of the 32-cell stage (each partial embryo consists of 4 cells).
The activation levels of ERK1/2 will be plotted in the Y-axis with the X-axis for the increasing doses
of FGF proteins. We predict that the resultant curve will be sigmoidal, indicating that the system acts
in an ultrasensitive manner. We will then repeat the same experiment on a4.2 cells derived from
embryos in which ephrin-Ad signals are compromised and ask 1) whether the reaction curve to FGF
becomes a Mchaelian curve and 2) whether a4.2-derived cells become more sensitive to respond to
FGF proteins when ephrin signals are blocked. In order to correctly interpret the results from this part
of the project, we will collaborate with enzymologists.
This project addresses a fundamental question in the discipline of developmental biology: How do
cells respond in a switch-like manner in response to a signalling gradient or in the presence of
signalling noise? We hope that our project will provide novel insights into this important issue.
II-2) Gene regulatory networks controlling the zicL gene expression in the marginal precursors
(NN cells): a defining feature of the chordate embryogenesis?
In the ascidian embryo, zicL is the first gene specifically expressed in the marginal precursors of
notochord and caudal neural fates. This gene is subsequently expressed in all neural lineages and its
knockdown results in a loss of notochord and the entire CNS. Thus, zicL is required specifically for
the two chordate specific characteristics, notochord and dorsal neural tube, during ascidian
embryogenesis. In this proposed project, we aim to reveal how zicL expression is controlled at the
level of its promoter. Our unpublished data show that both canonical and non-canonical Wnt pathways
are implicated in this process with the E-catenin/Tcf activity “negatively” controlling the zicL
expression in the endoderm precursor (E cell) and Wnt5-Ryk signals required for the expression in the
marginal precursor (NN cell). It has been shown that a -295bp upstream fragment is sufficient to drive
expression of a reporter gene in NN cells (Anno et al, 2006). We will further dissect this fragment in
order to identify short sequence elements required for both the expression in NN cells and the
repression in E cells. In terms of the negative regulation of zicL expression in E cells by the Ecatenin/Tcf complex which is generally considered to be a transcriptional activator, there is a study
demonstrating that this complex can repress expression of target genes via a binding site distinct from
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Cell fate
the classical TCF binding site (Blauwkamp et al., 2008). Interestingly, the -295bp upstream fragment
contains this “repressive” binding site in tandem. We will mutate these sites in order to address
whether they mediate the repressive activity of E-catenin/Tcf. As mentioned above, a non-canonical
Wnt5-Ryk signal is required for the zicL expression in NN cells. We have shown that this signal act as
a permissive signal to induce zicL expression. Ryk encodes an enigmatic receptor tyrosine kinase
whose kinase activity is “dead” and it remains to be known how this receptor signals intracellularly. In
parallel to the promoter analysis, we will conduct a proteomics approach to identify binding partners
of this enigmatic Wnt receptor. We will express a tagged form of Ryk using the artificial promoter
containing 12xTCF binding sites which drives gene expression in vegetal cells from the 8-cell stage.
The plasmid will be electroporated in fertilised Ciona eggs, allowing us to obtain thousands of
transgenic embryos. At the 32-cell stage, when Wnt5-Ryk signals are required for the zicL expression,
we will co-immunoprecipitate tagged Ryk receptors together with associated proteins, which will be
subsequently analysed using the LS-MS/MS system. We believe that this project will reveal the spatial
control mechanisms for marginal expression of zicL, the key transcription factor required for
specification of chordate-specific features in ascidian embryos and the molecular mechanisms of how
the canonical and non-canonical Wnt signals converge to control gene expression.
In addition to the mechanistic insight, this project might provide an interesting evolutionary
perspective in term of generation of the chordate body plan. In the vertebrate lineage, zic gene number
expanded via tandem and chromosome duplication. In the mouse, zebrafish and Xenopus embryos, zic
genes are expressed in dorsal ectoderm/mesoderm just prior to gastrulation. It has been shown that a
simultaneous knockdown of zic1 and zic3 blocks the neural program in the Xenopus embryo (Marchal
et al, 2009). It will be of great interest to address whether the notochord fate is specified in these
embryos. We will address this issue in the Xenopus model in collaboration with Dr. Laurent
Kodjabachian’s group (IBDML, Marseille). If this is proven to be the case, it strongly indicates that
zic genes play a homologous role in specification of the chordate characters.
“Oriented cell division”
Our group has been so far studying cell fate specification events during ascidian embryogenesis.
However, various morphogenetic processes such as cell migration, cell adhesion, oriented cell
divisions and cell shape changes account for shaping the embryonic body. We are particularly
interested in oriented cell divisions during ascidian embryogenesis, which we predict must be essential
to an embryo in which the mode of cell division is stereotypical. An oriented cell division becomes
particularly important when it is required to position correctly an inducing cell relative to a responding
cell (for example, stem cells in niches). Oriented cell divisions can also be responsible for establishing
a global architecture of single tissue types (for example, Drosophila wing disc and vertebrate skin).
We have initiated projects aiming to describe in detail two oriented cell divisions and to uncover the
underlying mechanisms. The projects focus on i) the notochord/neural mother cell and its sister cell,
the endoderm precursor, and ii) last cell division of epidermal cells.
II-3) Oriented cell divisions of the notochord/neural mother cell (NN cell) and the endoderm
precursor (E cell)
As described in our “Scientific report”, NN
and E cells are sister cells generated
following an asymmetric cell division of an
A5.1 or A5.2 cell which involves
differential activation of E-catenin between
the two sister cells for their differential fate
acquisition. This cell division takes place
along the animal-vegetal (A-V) axis. While
E cells are fate-restricted endoderm
precursors, NN cells divide asymmetrically
to generate one notochord and one neural
precursor. Both of NN and E cells divide
Figure 3. (top) Schematic drawings of the 32- and 44-cell stage embryos. Green and
red bars connecting two cells represent their sister cell relationship. Green bars indicate
again along the A-V axis and, for the NN
that the cell division leading to formation of the two sister cells take place perpendicular
to the previous cell division axis. In contrast, red bars indicate two successive cell
cell, this division places the neural-fated
divisions which take place in the same axis. The yellow cell in the 32-cell stage embryo
is NN cell while the blue cell corresponds to E cell. (bottom) Schematic representation of
daughter cell on the animal pole side and the
the obtained observations. Red dots represent centrosomes.
notochord-fated daughter cell on the vegetal
113
Cell fate
pole side. The asymmetric cell division of NN cell is controlled by animally-derived ephrin signals,
which promote neural fates in the daughter cell positioned on the animal pole side (Picco et al, 2007).
Thus, the cell division axis of NN cell, which is aligned along the A-V axis, might be coupled with the
fate specification. In this project, we use Phallusia mammillata, which allows us to express fluorescent
protein-fused proteins as early as unfertilised eggs following injection of mRNA (Sardet et al, 2011).
We first observed the dynamics of mitotic spindles in live ascidian embryo by using
ensconsin::3xvenus to visualise microtubules and EB3::venus for centrosomes. As summarised in
Figure 3, while the mitotic spindles of both NN and E cells align along the A-V axis at metaphase,
they do so in different manners. In the NN cell, each of the duplicated centrosomes migrates 90° to
align perpendicular to the A-V axis. During the prometaphase, however, the mitotic spindle rotates by
90° to align along the A-V axis. In contrast, the E cell, in which the pre-duplicated centrosome is
positioned at the vegetal pole side, uses a different mode to align its mitotic spindle along the A-V axis.
In the E cell, only one of the duplicated centrosomes becomes migratory and moves 180° to directly
form a mitotic spindle aligned along the A-V axis. To our knowledge, this latter mode of centrosome
behaviour has been reported only in two cases in Drosophila, which include male germline stem cells
and neuroblasts (reviewed in Yamashita and Fuller, 2008). By isolating these cells individually, we
have revealed that the spindle rotation in NN cells is a cell intrinsic process while the asymmetric
behaviour of the duplicated centrosomes in E cells does not take place in isolation. We are currently
testing the potential role of the LGN-NuMA-dynein system in the spindle rotation observed in NN
cells. As described above, the asymmetric behaviour of the duplicated centrosomes in E cells does not
take place when the cells are isolated, indicating that either cell interaction or cell shape controls this
specific behaviour of centrosomes. In order to test this,
as shown in Figure 4, we ablated one of the cells in
direct contact with the E cells at their vegetal pole side
and observed the centrosome behaviour. Interestingly, in
the E cell which contacts directly with the ablated cell,
the centrosomes exhibit the asymmetrical movement as
in control. In contrast, in the E cell positioned
contralateral to the ablated cell, the centrosomes move
Figure 4. Schematics showing the results
of the ablation experiment described in the
symmetrically. Quantification of the cell shape of these
text. The cross bars indicate the ablated
two E cells revealed that the ablation results in a
cell.
deformation of the cell shape of only the contralateral E
cell. This result indicates that the asymmetric centrosome movement observed in E cells likely
depends on its cell shape, which is elongated along the A-V axis. We are planning to conduct a
“rescue” experiment by placing isolated E cells into microwells with different forms including a
microwell in the form of an embryonic E cell. This experiment will be carried out in collaboration
with Dr. Nicholas Minc (Institut Curie), who has successfully applied the microwell technique to his
study (Minc et al, 2011). Finally, we are planning to address whether certain components of the
canonical Wnt pathway, such as APC are implicated in the asymmetric centrosome movement in E
cells, in which we have shown that the pathway is active and required for its cell fate specification. We
found that the immotile centrosome in the E cell exhibits longer astral microtubules compared to the
motile counterpart and is displaced toward the cortex on the vegetal pole side. Since APC
(adenomatous polyposis coli) is known to plays a role in the cortical attachment of astral microtubules,
our current working hypothesis is that cortically-localised APC proteins trap astral microtubules
emanating from the “would-be-immotile” centrosome and that this process depends on the elongated
cell shape of E cell which brings the cell cortex closer to the centrosomes.
II-4) Oriented cell divisions of epidermal cells
In all chordate species, the initial “egg shape” elongates along the anterior-posterior (A-P) axis and
this morphogenetic process is driven by convergent extension of the axial structures including
notochord. Interestingly, in ascidian embryos, the onset of body axis elongation coincides with the last
cell division of epidermal cells, all of which divide along the A-P axis (Ogura et al, 2011).
114
Cell fate
In order to address how the cell division axis in epidermal cells is controlled and also its role in body
axis elongation, we have initiated detailed observations of this cell division using live imaging. We
first asked whether the last cell division follows the Hertwig rule, whereby the cell division axis tends
to align along the longest axis of the cell. By observing the dynamics of mitotic spindles and cell
shapes during the last two cell divisions of the epidermal lineages, we have found that the terminal cell
divisions orient along the A-P axis independently of the
longest axis of the cell. We have found three structural
polarities in the epidermal cells during interphase leading to
the last cell division: 1) membrane invaginations (typically 1
to 2 invaginations per cell) from the posterior side of the
cells, 2) posterior positioning of the nucleus, and 3) anterior
elongation of interphase microtubules. Observation of the
dynamics of the MTOC (microtubule organizing centre) has
revealed the following sequence of events: 1) the tips of
Figure 5. (A) three polarisation
membrane invaginations appear to associate with
events which take place during the
centrosome,
2)
the
nucleus/centrosome
complex
10 cell cycle in epidermal cells. (B)
temporal sequence indicating that
subsequently moves toward the posterior direction, which
the membrane invaginations (red)
converge to centrosome (green).
correlates with shortening of the membrane invagination, 3)
the centrosome appears to be “anchored” to the posterior
cortex of epidermal cells, 4) the interphase microtubules
elongate anteriorly from the posteriorly positioned centrosome and 5) during prophase, one of the
duplicated centrosomes moves anteriorly to form a mitotic spindle aligned along the A-P axis. These
observations have led us to our current working model (Figure 5), which, to our knowledge, appears to
be a novel template of the events leading to orientated cell division. We are planning to conduct a laser
nano-dissection, in collaboration, in order to ablate membrane protrusions and observe its effect on the
centrosome positioning.
th
III) Perspectives
We would ultimately like to continue our step-by-step analysis of the formation of specific neuronal
subtypes in the neural tube and describe in detail each transient regulatory state that cells pass through
on their way to their ultimate fate commitment. In order to undertake this analysis we first need to
describe in more detail the cell lineages of the CNS. We recently carried out a pilot experiment
showing that the GABAergic/glycinergic anterior caudal inhibitory neurons (ACINs) derive from the
A11.116 lineage (Nishitsuji et al, 2012). Together with improvements in cell identification (eg Hudson
et al, 2011), this project will be feasible. This task will be greatly facilitated by the use of transgenic
ascidian lines expressing GFP under the control of neuronal subtype-specific promoters. Our research
unit, UMR7009, plans to construct an aquarium in which we will be able to maintain transgenic
marine invertebrates in the frame of the EMBRC-France project. In addition, we will continue our
effort to apply the single cell electroporation technique to the ascidian system. This technique will
allow us to conduct functional studies in a sub-neural lineage specific manner.
IV) Cited literature (other than recent group publications in reference list)
Anno C, Satou A, Fujiwara S. (2006). Transcriptional regulation of ZicL in the Ciona intestinalis embryo. Dev Genes Evol.
216:597-605.
Bertrand V, Hudson C, Caillol D, Popovici C, Lemaire P. (2003). Neural tissue in ascidian embryos is induced by
FGF9/16/20, acting via a combination of maternal GATA and Ets transcription factors. Cell 115:615-27.
Blauwkamp TA, Chang MV, Cadigan KM. (2008). Novel TCF-binding sites specify transcriptional repression by Wnt
signalling. EMBO J. 27:1436-46.
Hudson C, Lemaire P. (2001). Induction of anterior neural fates in the ascidian Ciona intestinalis. Mech Dev. 100:189-203.
Marchal L, Luxardi G, Thomé V, Kodjabachian L. (2009). BMP inhibition initiates neural induction via FGF signaling and
Zic genes. Proc Natl Acad Sci U S A 106:17437-42.
Minc N, Burgess D, Chang F. (2011). Influence of cell geometry on division-plane positioning. Cell 144:414-26.
Ogura Y, Sakaue-Sawano A, Nakagawa M, Satoh N, Miyawaki A, Sasakura Y. (2011). Coordination of mitosis and
morphogenesis: role of a prolonged G2 phase during chordate neurulation. Development 138:577-87.
Tassy O, Daian F, Hudson C, Bertrand V, Lemaire P. (2006). A quantitative approach to the study of cell shapes and
interactions during early chordate embryogenesis. Curr Biol. 16:345-58.
Yamashita YM, Fuller MT. (2008). Asymmetric centrosome behavior and the mechanisms of stem cell division. J Cell Biol.
180:261-6.
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Regeneration and pluripotency
Group 4 “Regeneration and Pluripotency”
Group leader: Stefano Tiozzo (CR1, CNRS).
Additional known members in January 2014 : Sonia Lotito (T, CNRS); Lorenzo Ricci (PhD 20122014).
Overall scientific objectives:
The main interest of the laboratory is to pursue the research on non-embryonic development analyzing
the whole body regeneration (WBR) and the asexual development (blastogenesis) in the colonial
ascidian Botryllus schlosseri and studying the partial body regeneration in the flatworm Macrostomum
lignano. In both systems, the long term aim is to analyze the dynamic of the cells responsible for the
above mentioned regenerating events, i.e. neoblasts (M.lignano) and putative pluripotent stem cells
(Botryllus). We will try to define the source of the regenerative plasticity that characterizes WBR
initiation and compare compare it with the canonical embryogenesis. As to the model we recently
introduced in the lab we are exploring the neoblasts behavior in relation to the cytoarchitecture of the
blastema in regenerating versus non-regenerating areas in the flat worm Macrostomum lignano.
In summary, in the next four years we plan to continue and develop the following projects:
1) Relationship between pluripotency and tumorogenesis (B.schlosseri)
2) Role of the Wnt pathway on early vegetative development (B.schlosseri)
3) Role of the Hippo pathway on stem cell dynamics (M.lignano)
4) Transcriptome analyses of blastogenesis (B.schlosseri)
We also started and envision collaboration with the Croll Lab (Delhausie University, Canada) and the
“Cnidarian Developmental Mechanisms” group lead by Evelyn Houliston:
5) Evolution of the olfactory system (Helix aspersa, Sepia officinalis)
6) Regeneration plasticity in planula larva (Clytia hemisphaerica)
Ongoing and submitted projects:
a) Analyzing the relationship between pluripotency and tumorogenesis: molecular insights from
a new basal chordate model
This project is funded until March 2015 by the Marie Curie Reintegration Grant (IRG) and until 2014
by the UPMC-EMERGENCE. The lab started to work on this project in 2011 and for the further years
we aim:
- To continue the morphological description of the vascular bud during the whole body regeneration of
Botryllus schlosseri providing a staging of the early bud development: complete the description of the
pattern of proliferation and add the description of pattern of apoptotic cells.
- Once discrete stages will be defined, the temporal and spatial pattern of expression of a battery of
candidate genes (maintenance of pluripotency, endomesoderm differentiation) will be analyzed in
order to provide the first insights on the dynamic of differentiation and to further characterize the
nature of the cell population responsible of the initial regenerative event.
- To develop a microsurgical technique and to assay new RNA linear amplification technique in order
to get material suitable for transcriptome analyses via RNAseq. This part of the project will be in
collaboration with De Tomaso lab, which will contribute to the sequencing and with the Dunn lab
which will help with the data analyses. The outcomes of this approach will provide data for the further
steps of this research: identification of pathways of interests, i.e. signals to define the niche where the
WBR starts; and/or highlight novel molecular pathways that regulate pluripotency maintenance and
cell differentiation conserved in vertebrates.
b) Role of the Wnt pathway on early vegetative development of Botryllus schlosseri
We plan to complete this ongoing project which aims to describe the role of Wnt/b-catenin and
potentially other Wnt driven pathways during the early blastogenesis. In order to complete this project,
which is part of a collaboration with Dr Alessandro Di Maio and the De Tomaso lab (UCSB), the
following tasks have to be completed:
- Complete the analyses of the pattern of expression during the initiation of blastogenesis of: Wnts
orthologous (Wnt5A, Wnt2B), beta-catenin and Wnt/b-catening downstream targets: FoxA and Bra
and Myc.
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Regeneration and pluripotency
- Confirm the results obtained by the chemical knock down of the Wnt/bcatenin pathway during
asexual development using siRNA approach on the same target genes.
c) Role of the Hippo pathway on stem cell dynamics: insights from a flatworm system
For this project a 3-years ANR grant (Blanc II) has been submitted in collaboration with the Ladurner
lab (Innsbruck University). The taks of the project are the following:
Task 1 Spatial-temporal characterization of Hpo Pathway components
We will build on preliminary data that indicate the presence of Hippo components in Macrostomum
and describe in adult and regenerating worms: the spatial temporal pattern of expression of the
upstream putative activators (Dachous, FAT4, Crumbs, Kimbra, Merlin), the core components (HPO,
SAV1, LATS1, MOB1) and the transcriptional co-activator of the Hippo pathway (Yap). We then
analyze the expression of target genes co-activated by the interaction of Yap with TEAD/TEF family,
ZLWK ȕ&DWHQLQ7&9/() :QW ȕ&DWHQLQ SDWKZD\ ZLWK VPDG %03 SDWKZD\ DQG 6PDG
7*)ȕ SDWKZD\ ,Q WRWDO ZH will screen the pattern of 13 genes. To detect a sub-cellular level the
activation/repression of the pathway we will generate polyclonal antibodies against Yap and observe
its nuclear (pathway inactive) or cytoplasmic (pathway active) presence. We will attempt to analyze
how the upstream signals are related to the architecture of the tissues: in particular we will screen
commercial antibodies and/or generate polyclonal antibodies against the protocadherins Dachous and
FAT4 and analyze their distribution in the regenerating blastema in association with the nuclearization
of yap.
Task 2 Characterization of Somatic Stem Cell markers
Flatworm homeostasis and regeneration are based on a population of somatic stem cells known as
neoblasts (Aboobaker et al 2011). In this task, we will seek specific markers for neoblasts that
contribute to somatic turnover and regeneration but not to the formation of the germline. We combine
high throughput sequencing and in silico subtraction with high throughput in situ hybridization
screening. According to the list of the identified candidates we will produce polyclonal antibodies that
will be used in task 3.
Task 3 Role of the Hippo Pathway on the Neoblast Dynamics
The third task will combine the output of the previous tasks in order to describe functionally the role
of Hippo pathway on neoblast behavior during tissue homeostasis and during posterior and anterior
regeneration. We will begin by generating RNAi depleted adult worms for each of the nine genes
described in task 1 and screen the phenotypes in vivo, via histological and ultrastructural analyses. The
localization of Yap will be re-assayed simultaneously with the stem cells markers produced in task 2
in wild type and knocked down worms. Proliferative markers (BrdU, HH3) will be also used. If the
RNAi of the different components of the pathway will generate overlapping phenotypes, a sub-set of
these markers will be selected to repeat the same approach on posterior and anterior regenerating
worms. At the same time, further effort will be devoted to produce a line of inducible transgenic
worms will be generated in order to overexpress YAP. If successful, the phenotypes will be then
assessed using the same toolkit used for the RNAi knocked out.
Future potential project to develop:
a) Transcriptome analyses of blastogenesis
We will adopt an unbiased approach, which hopefully will provide an overall view of similarities and
differences in gene expression between embryogenesis and blastogenesis (asexual development). The
data obtained will constitute the basis for future studies focused on genes/molecular pathways of
interest. This aim will be accomplished in collaboration with the group of Anthony De Tomaso
(UCSB). The long term goal of this aims is to take a comprehensive approach to isolate differentially
expressed genes and build transcriptional networks, then compare them in embryos, and
asexual/regenerative developmental stages. This approach should be ideal to begin to characterize the
biology underlying common and divergent developmental pathways in this organism, which has the
potential to reveal much about basic developmental and regenerative processes in the chordate.
117
Regeneration and pluripotency
Figure 1: Regeneration via asexual budding: A. Each developmental stage (A-D- described in text) represents 1 day under laboratory
conditions. Drawings represent dorsal views of zooids (green frame), primary buds (yellow frame) and secondary buds (red frame). For
simplification, each adult zooid carries only one set of buds. A secondary bud appears as a thickening of the epidermis and the peribranchial
chamber leaflet of the primary bud (stage A1), which evaginates into a closed vesicle (stage B2), followed by organogenesis (stages C1-D).
During takeover (stages C2-D), the secondary bud becomes the primary bud and a new blastogenic cycle begins for the next secondary bud.
After the second takeover event, the primary bud opens its siphons and becomes a functional adult (zooid). In fertile colonies (as illustrated
here), gonadogenesis occurs in the secondary bud from mobile precursors (blue; stages B1-C2). B. confocal cross section of a primary bud in
stage A2, visualized with DAPI, a-tubulin and phalloidin.
RNA from isolated buds at stage A1-2 and B1-2 (figure 1) will be sequenced using Illumina mRNAseq technology. From preliminary KEGG pathway analyses of the present trascriptome data the
repertoire of genes responsible for asexual development are conserved to those in embryogenesis, and
all the major pathways one would expect are present. The initial efforts will be to pick a single
genotype and conduct expression profiling at the early stage of blastogenesis. In this set of
experiments, sequences will be obtained from multiple isogeneic subclones from a single genotype.
Results from this initial round of sequencing will provide a baseline for the succeeding studies. The
goal in this initial RNA-seq analysis will be to quantify the number of differentially expressed genes at
each stage of development at specific statistical thresholds, and in addition to compare expression data
from dissected tissues to whole subclones. Cluster analysis of the temporal expression data will be
used to identify modules of co-expressed genes associated with each blastogenetic stage. In particular
we will explore the use of weighted gene co-expression network analysis (WGCNA; Zhang and
Horvath, 2005) which goes beyond standard clustering and includes outside neighbors of each
interacting gene pair. This is thought to provide a more biologically meaningful measure of gene coexpression and has the potential to identify genes that are candidate ‘hub’ genes that drive the
expression of a particular module, making them good targets for knockdown.
b) Evolution of the olfactory system: description of olfactory receptors in gasteropods (Helix
aspersa) and cephalopods (Sepia officinalis)
This project, in collaboration with Prof. Roger Croll (Dalhouse University) aims to provide the first
description of Mollusca olfactory receptors, starting from the description of the anatomy, followed by
the transcriptomic analyses of the presence/absence of the chemosensory receptor gene repertoires
Chemosensory receptors (CR) are essential for the survival of organisms that range from bacteria to
mammals. It has been shown that the numbers of functional CR genes and pseudogenes specifically
expressed in the olfactory system vary enormously among the genomes of different animal species
(Nei et al. 2008). Much of this variation can be explained by the adaptation to different environments,
but it is also clear that a substantial portion is generated by random process of gene duplication and
deletion (genomic drift). However, an exhaustive description of olfactory system and the associated
CR are mainly restricted to vertebrates, in particular to mammals and to artropods (i.e. Drosophila).
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Regeneration and pluripotency
Figure 2. A-C preliminary scheme of olfactory organ in the snail Helix aspersa: antibody anti Tyr-Hidroxylase. D details of sensory cells on
the olfactory sensory epithelium of H.aspersa. B Detail of the olfactory pit in Sepia officinalis: anti acetylated tubulin.
In order to better understand the evolution of animal CR gene repertoire members of the
Lophotrocozoans must also be described. In collaboration with the comparative neurobiology group of
Prof.Croll (Dalhouse University) we started to describe the neuroanatomy of the olfactory sensory in a
species of cephalopods and one species of terrestrial Mollusca in order to address further studies
towards the identification of the CR repertoire in members of this subphylum (figure 2). We will start
with an antibody screening for catecolaminergic, serotoninergic, FRMFergic neurons, coupled with
pan-neuronal markers (alpha/beta tubulins) targeting the CR. Once the anatomical reconstruction of
the CR will be complete, trough microsurgery we will select the area were the receptors cluster and
perform analyze the transcriptome via RNAseq. This approach will allow us to identify putative
orthologous of the CR gene repertoire present in vertebrates and hopefully will permit to better
understand the evolution of olfactory system in the metazoan.
a) Regeneration in Clytia planula larva
In 2010/2011, a pilot project on regeneration of planula larva in Clytia has been performed by a
Master student in collaboration with the “Cnidarian Developmental Mechanisms” group lead by
Evelyn Houliston. This exploratory project took advantage of the regeneration capacity of cnidarian
larvae (Freeman 2005) and aimed to explore the reciprocal inhibition of the oral and aboral
determinants (Wnt2a, FoxQ2) after transversally cut Clytia planula. As soon as the resources will be
available, we hope to continue this collaboration and complete the project. We also aim to further
explore the nature of the stem cells (i-cells) that putatively are responsible of the regenerative
plasticity of the planula. Along with the ongoing projects using B.schlosseri and M.lignano, the latter
would complete a comparative approach in order to explore the conserved and divergent features of
stem cell biology.
D. Cited literature (other than recent group publications in reference list)
Aboobaker, A.A. 2011. Planarian stem cells: a simple paradigm for regeneration. Trends in cell biology 21: 304-311.
Zhang, B., Horvath, S. 2005. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol
Biol. 4:17.
Nei, M., Niimura, Y., Nozawa, M. 2008. The evolution of animal chemosensory receptor gene repertoires: roles of chance
and necessity. Nat Rev Genet. 9(12):951-63.
Freeman, G. 2005. The effect of larval age on developmental changes in the polyp prepattern of a hydrozoan planula.
Zoology (Jena). 108(1):55-73.
119
Evolution of intercellular signalling
Group 5 “Evolution of intercellular signalling in development”
Group leader: Michael Schubert (CR1-CNRS)
Additional known members in January 2014: Jenifer Croce (CR2-CNRS); Guy Lhomond (IE1CNRS); François Lahaye (AI-CNRS); João E. Carvalho (PhD student); Elisabeth Zieger (PhD
student); Romain Sordillon (Master student)
Introduction
Developmental biology studies a highly complex question: how to create an entire organism
from a single cell? Although it does not come as a surprise that this process relies on very well
coordinated intercellular signals in metazoan animals, the discovery that a relatively small toolkit of
these signalling cascades is redeployed throughout development for the patterning and formation of
various tissues has been rather astonishing (Gilbert, 2010). Elaboration of interaction between these
signals, which include Wnt, hedgehog (Hh), fibroblast growth factor (FGF), transforming growth
IDFWRUEHWD7*)ȕERQHPRUSKRJHQLFSURWHLQ%03UHWLQRLFDFLG5$DQG'HOWD1RWFKhas been
proposed as one of the key events marking the diversification of first metazoan and subsequently
bilaterian animals (Gilbert, 2010). These specific interactions have been particularly well studied in
vertebrates, but it has become evident that these intercellular signalling cascades and their interactions
are also required outside vertebrates for a plethora of other developmental processes, which in contrast
have received significantly less attention in the past (Gilbert, 2010).
The members of our group have been very actively involved in studying the developmental
functions of both Wnt and RA signalling in various animal models located at key phylogenetic
positions within the deuterostomes (Campo-Paysaa et al., 2008; Croce and McClay, 2008; Lecroisey
et al., 2012; Carvalho and Schubert, 2012). Namely, we are working on sea urchin (Paracentrotus
lividus), amphioxus (Branchiostoma lanceolatum) and lamprey (Petromyzon marinus), respectively,
an ambulacrarian, an invertebrate chordate and an agnathan vertebrate (Fig. 1). Importantly, all three
models are amenable for experimental
developmental
studies,
with
controllable spawning and external
fertilisation. The embryos are suitable
for pharmacological treatments as well
as for microinjection allowing the
creation of transient transgenic animals
and the specific functional knockdown
or overexpression of targeted genes
(Bertrand and Escriva, 2011; McClay,
2011; Shimeld and Donoghue, 2012).
Thus, taking advantage of these three
animal models, we propose a
comparative study to assess the
evolution of Wnt and RA signalling
functions and interactions during
deuterostome
development
by
Figure 1. Simplified phylogeny of metazoan animals.
elaborating the following projects.
Ongoing projects (OPs)
OP1. Analysis of the RA signalling network in developing amphioxus: metabolism, targets,
interactions (M. Schubert; F. Lahaye; J.E. Carvalho; E. Zieger)
Previous studies of the group have established that amphioxus has a vertebrate-like RA
signalling system, both in terms of molecular composition and biological function, with the important
additional benefit of a lack of significant genetic redundancy. Thus, amphioxus has only one retinoic
acid receptor (RAR) and one retinoid X receptor (RXR), forming a single RAR/RXR heterodimer that,
like its multiple vertebrate counterparts, binds to DNA and activates target gene expression in the
presence of RA (Lecroisey et al., 2012). Furthermore, in amphioxus, like in vertebrates, anterior hox
genes (such as hox1 and hox3) are direct targets of RA signalling and are required for RA-dependent
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Evolution of intercellular signalling
anteroposterior patterning of the central nervous system, the ectoderm and the endoderm (Carvalho
and Schubert, 2012). Based on these findings, we are now characterizing the biological functions of
specific components of the amphioxus RA cascade, focussing on both upstream (RA metabolism) and
downstream (RA target genes) constituents of this signalling network.
Taking advantage of the availability of the genomes of three different amphioxus species, we
have identified, in silico, the genes contributing to retinoid/RA uptake, transport, synthesis, storage
and degradation in amphioxus (Albalat et al., 2011). The ongoing functional studies are focusing on
genes encoding RA synthesis (RALDH) and degradation enzymes (CYP26) as well as intracellular
retinoid transport proteins (CRBP and CRABP). In collaboration with José Xavier-Neto (LNBio,
Campinas, Brazil), this work will be complemented by both biochemical and structural analyses of
these enzymes and proteins and by further analyses of other components of amphioxus RA
metabolism, i.e. uptake and storage molecules (Sobreira et al., 2011). Moreover, to assess tissuespecific activity of RA signalling during amphioxus development, a RA-sensitive construct containing
RAR/RXR heterodimer binding sites linked to a fluorescent reporter will be engineered and injected
into fertilized eggs and its expression will be monitored in vivo.
In parallel, to complete our previous analyses, which exclusively studied amphioxus RAR and
RXR functions pharmacologically (Carvalho and Schubert, 2012), we are now targeting these
receptors by knockdown and overexpression experiments to assess the developmental functions of
each molecule. In these analyses, special attention is given to interactions with other intercellular
signalling cascades, such as Wnt signalling. In addition, to obtain a more comprehensive and unbiased
picture of the genes targeted by the amphioxus RAR/RXR heterodimer, we will complement these
studies with large-scale transcriptomic (RNAseq) and genomic (ChIPseq) surveys. While the RNAseq
analyses will compare transcriptomes of embryos treated or not with RA signalling agonist and
antagonist, the ChIPseq experiments targeting RAR and RXR by chromatin immunoprecipitation will
yield a genome-wide map of RAR and RXR DNA binding sites. Combination of the results from these
two experiments will thus allow the generation of an atlas of genes regulated directly and indirectly by
RA signalling during amphioxus development. The RNAseq and ChIPseq experiments will be carried
out in collaboration with Gérard Benoit (CGIMC, Lyon, France), who is currently finalizing a
comparable analysis targeting the three mouse RARs and RXRs in the embryonal carcinoma cell line
F9. The antibodies directed against amphioxus RAR and RXR needed for setting up the ChIPseq
experiments will be provided by Zbynek Kozmik (IMG, Prague, Czech Republic). Altogether, this
work will allow a detailed description of the RA signalling network in amphioxus and, as such,
provide an outline of a prototypical chordate RA signalling cascade.
OP2. Role of Frizzled9/10 and canonical Wnt signalling in maintenance of sea urchin endoderm and
mesoderm gene expression (J. Croce; G. Lhomond)
In sea urchins, activation of canonical Wnt signalling, mediated E\QXFOHDUHQWU\RIȕ-catenin,
is required for the development of all vegetal tissues, i.e. the skeletogenic mesoderm (SM), the nonskeletogenic mesoderm (NSM) and the endoderm (e.g. Logan et al., 1999). NXFOHDUȕ-catenin is first
detected during embryogenesis at the 16-cell stage in the micromeres, precursors of the SM lineage.
Then, at the 32-FHOO VWDJH ȕ-catenin accumulates also in the nuclei of the macromeres, the sole
progenitors of the NSM and endoderm lineages (Logan et al., 1999). Currently, we aim at identifying
the Wnt/Frizzled couples that trigger and subsequently maintain activation of canonical Wnt signalling
in micromeres, macromeres and their respective descendants through embryogenesis. In a preceding
study, we have identified Wnt6 and Frizzled1/2/7 (Fz1/2/7) as the ligand/receptor couple that controls
the selective nuclearisation RIȕ-catenin in the macromeres at the 32-cell stage (Lhomond et al., 2012).
We are now investigating the involvement of another Frizzled receptor, Frizzled9/10 (Fz9/10), in the
subsequent maintenDQFH RI QXFOHDU ȕ-catenin in the descendants of both the micromeres and the
macromeres and its role in vegetal tissue specification. Preliminary data involving microinjections
followed by immunostaining and in situ hybridisation assays revealed that Fz9/10 signalling is not
required at the onset of embryogenesis to trigger canonical Wnt signalling and to launch NSM and
endoderm specification, but that it is necessary afterwards to maintain both of these processes.
This analysis will be completed by assessing, first, whether all the developmental defects
associated with )]NQRFNGRZQDUHGXHWRWKHREVHUYHGLPSDLUPHQWRIȕ-catenin nuclearisation. To
this end, functional analyses combining microinjection or drug treatments with immunostaining and in
121
Evolution of intercellular signalling
situ hybridisation surveys will be carried out and the results will be compared to the phenotypes
following Fz9/10 downregulation. Second, we will determine the identity of the Wnt ligands that bind
to Fz9/10. We will hence perform co-immunoprecipitation experiments followed by Western blot
analyses and/or LS-MS/MS spectrometry. We have recently completed proof of principle studies
demonstrating the association of Wnt ligands with Frizzled receptors and we are planning to continue
this work in collaboration with Peter Lenart (EMBL, Heidelberg, Germany). Third, we also plan to
LGHQWLI\ WKH :QW)UL]]OHG FRXSOH UHVSRQVLEOH IRU ȕ-catenin nuclearisation in micromeres, which will
require functional analyses on immature oocytes, a technique that we have started to develop.
OP3. Evolutionary diversification of RA signalling in deuterostomes: insights from sea urchins,
amphioxus and lampreys (M. Schubert; J. Croce; F. Lahaye; J.E. Carvalho; E. Zieger; R. Sordillon)
RA signalling was long thought to be vertebrate-specific, but, as mentioned above, studies in
invertebrate chordates have revealed conserved roles for RA throughout the chordate phylum. Outside
the chordate lineage, though, evidence for functional roles of RA and of the RAR/RXR heterodimer
becomes much scarcer (Carvalho and Schubert, 2012). Although we have identified genes encoding
orthologues of the basic vertebrate components for synthesis (RALDH) and degradation (CYP26) of
endogenous RA and of RAR and RXR in ambulacrarians (such as hemichordates and echinoderms)
and lophotrochozoans (such as annelids and molluscs) (Marlétaz et al., 2006; Campo-Paysaa et al.,
2008), extensive experimental evidence for RA functions in these organisms is still lacking. To obtain
insights into the evolutionary diversification of RA signalling, we set out to compare the
developmental functions of RA signalling in our three model animals (Fig. 1).
We are currently characterizing the developmental functions of key components of RA
signalling from sea urchins and lampreys (e.g. RAR and RXR, RALDH, CYP26, CRBP and CRABP).
In collaboration with Vincent Laudet (IGFL, Lyon, France) and José Xavier-Neto (LNBio, Campinas,
Brazil), this developmental work is complemented by a detailed molecular characterisation of each
molecule, which constitutes the PhD project of Juliana Gutierrez-Mazariegos, a graduate student codirected by Vincent Laudet and Michael Schubert (Sobreira et al., 2011). This work is supported by
collaborations with Maria Ina Arnone (Stazione Zoologica, Naples, Italy), Sylvie Mazan (SBR,
Roscoff, France) and Maureen A. Kane (University of Maryland, Baltimore, USA). In sea urchins, we
have already established that the RAR/RXR heterodimer binds DNA and, upon association with RA,
activates target gene transcription. We have also identified biological functions of RA signalling in the
developing sea urchin endoderm. In lampreys, we have isolated four RARs, which contribute to the
regionalisation of the brain through a mutual inhibitory interaction with FGF signalling. This
antagonism between RA and FGF seems also to exist in the amphioxus brain, suggesting the presence
of an ancestral mechanism for patterning the chordate nervous system, a hypothesis we will be testing
in collaboration with Simona Candiani (University of Genoa, Genoa, Italy) (Candiani et al., 2012).
Future projects (FPs)
FP1. Plasticity of the early developmental programme in chordates (M. Schubert; F. Lahaye;
postdoctoral researcher to be hired)
Over 500 million years of evolution have elapsed since the appearance of the ancestral
chordate (Schubert et al., 2006). It is thus not surprising that many changes have occurred at the level
of genome structure and global biological functions in the different chordate lineages, but also
between the species of a given phylum. Therefore, it is important to elucidate, which features are
evolutionary stable and which are more subject to variations, both between phyla and within a given
phylum, and this can be ideally addressed using the cephalochordate amphioxus as a model organism.
When considering body plan organisation and developmental programme, amphioxus displays
many ancestral chordate features (Schubert et al., 2006), with sufficient evolutionary time having
elapsed since the divergence of amphioxus and vertebrates and between different amphioxus species
to provide a strong contrast between stable and variable genetic and developmental features.
Moreover, amphioxus offers the rare opportunity to compare genomes, transcriptomes and,
developmental processes in three model species (B. lanceolatum, B. floridae and B. belcheri). Thus, in
collaboration with Hector Escriva (OOB, Banyuls-sur-Mer, France), Hugues Roest Crollius (IBENS,
Paris, France) and Marie Sémon (IGFL, Lyon, France), we will use genomic, transcriptomic and
embryological approaches in these three models to examine stable and variable features of the early
developmental programme of amphioxus. The overall work plan of this project will be subdivided into
122
Evolution of intercellular signalling
three parts. First, we will compare the genomes of the three amphioxus species and of various
vertebrate taxa to identify conserved and non-conserved features hence defining the ancestral chordate
condition. Second, comparative transcriptomic studies in normal and perturbed conditions during early
development of the three amphioxus species will enable a functional interpretation of the genomic
findings obtained in the first section. Third, we will exploit the data from the previous two sections to
dissect functionally the regulatory interactions responsible for body axis formation and patterning in
amphioxus. Taken together, the proposed work will provide strong elements to answer the main
question of this project pertaining to the stability or variability of genomic and biological features in
cephalochordates and, through careful comparisons, to at least some extent in all chordates.
FP2. Canonical Wnt signalling through time and space: endoderm versus mesoderm in sea urchins (J.
Croce; G. Lhomond; postdoctoral researcher to be hired)
In sea urchins, the vegetal tissues, i.e. the skeletogenic mesoderm (SM), the non-skeletogenic
mesoderm (NSM) and the endoderm, arise from the vegetal blastomeres: the SM derives from the
micromeres and both the NSM and the endoderm originate from the macromeres. Previous studies
KDYHVKRZQWKDWQXFOHDUȕ-catenin is required for the specification of all vegetal lineages (Logan et al.,
1999) and that Delta, the ligand of Notch, is essential for NSM development (Sweet et al., 2002).
However, during embryogenesis both molecules are expressed in micromeres and macromeres and we
propose thus to investigate the exact roles RI QXFOHDU ȕ-catenin and Delta/Notch signalling in
micromeres versus macromeres for the formation of NSM and endoderm. We further plan to assess
the developmental period(s), during which these signals are required in each cell type to ensure tissue
specification, and aim to resolve the regulatory relationship between the canonical Wnt and
Delta/Notch pathways in each cell type.
To this end, a series of experiments combining microinjection, microsurgeries, in situ
hybridisation and immunolocalisation will be conducted. As proof of principle, we have already
generated chimeric sea urchin embryos, in which we observed that, in terms of NSM specification,
QXFOHDU ȕ-catenin in micromeres appears necessary solely to activate Delta expression, whereas, in
macromeres, QXFOHDULVDWLRQ RI ȕ-catenin seems required in parallel to the Delta/Notch pathway.
Furthermore, the target genes of canonical Wnt and Delta/Notch signalling in micromeres and
macromeres responsible for NSM and endoderm specification will be investigated. A differential gene
expression screen will be performed using high-throughput sequencing, which will be based on the
following WKUHH REVHUYDWLRQV L LQKLELWLRQ RI ȕ-catenin nuclearisation disrupts both NSM and
endoderm gene expression, (ii) loss of Delta/Notch signalling selectively prevents NSM gene
expression, (iii) downregulation of Fz1/2/7 signalling specifically impedes endodermal gene
expression. Finally, given that cell fate specification occurs while successive mitotic divisions take
place, to fully understand the molecular mechanisms of cell fate specification it will ultimately also be
necessary to simultaneously examine cell fate progression and the transcriptional status of each cell
through embryogenesis. We will tackle this challenge in collaboration with Nadine Peyriéras (INAF,
Gif-sur-Yvette, France) by mapping onto a single virtual sea urchin embryo both cell lineage tree data
and gene expression patterns acquired at a cellular resolution in both space and time.
FP3. Evolution of intercellular patterning mechanisms in deuterostomes: differential deployment of
Wnt and RA signalling in sea urchin, amphioxus and lamprey development (M. Schubert; J. Croce; G.
Lhomond; F. Lahaye; J.E. Carvalho; E. Zieger; R. Sordillon; postdoctoral researcher to be hired)
The aim of this project is to reconcile our work on molecular roles and interactions of Wnt and
RA signalling in sea urchins, amphioxus and lampreys with the biological roles played by these
cascades during development, e.g. in embryonic axis establishment and tissue specification. Our
preliminary analyses indicate that in sea urchins and amphioxus, endoderm formation relies on both
Wnt and RA signalling for proper specification and anteroposterior regionalisation, respectively.
However, potential regulatory interactions between these two cascades in the endoderm remain to be
determined, as do their functions in lampreys. In addition, although RA signalling has been implicated
in mesodermal patterning of vertebrates, a role for RA in the amphioxus or sea urchin mesoderm is
still elusive. Finally, in both amphioxus and lampreys, RA signalling is required not only for
regionalisation of the central nervous system, but also for neuronal specification and neurogenesis
(Carvalho and Schubert, 2012). Given that these processes likely also depend on Wnt signals (Onai et
al., 2010), the question of functional interactions between the two cascades arises.
123
Evolution of intercellular signalling
With the ultimate aim of providing a detailed description of tissue-specific functions and
interactions of Wnt and RA signalling in our three animal models (Fig. 1), we will carry out classical
microinjection- and pharmacology-based experiments that will be analysed using marker gene
expression, immunostaining and Wnt or RA signalling reporter assays. These embryological analyses
will be complemented by comprehensive transcriptomic surveys to identify potential reciprocal,
parallel and/or distinct regulatory mechanisms between the two signalling cascades. Moreover, in
collaboration with Michela Plateroti (CGIMC, Lyon, France), Jean-Noël Freund (University of
Strasbourg, Strasbourg, France) and Stefan Hoppler (University of Aberdeen, Aberdeen, UK), who
use common vertebrate systems (i.e. the mouse and the frog), our work will ultimately be completed
by functional and genetic studies on selected components of the Wnt and RA pathways. Altogether,
this comprehensive investigation will shed light on the evolution of both developmental functions and
functional interactions of these two fundamental intercellular signalling pathways in deuterostomes.
Summary
The research plan proposed by
our group (Fig. 2) has been designed to
provide far-reaching insights into the
biological functions of Wnt and RA
signalling
during
deuterostome
development. Both the molecular
composition of the respective gene
cascades and their developmental output
will be studied in three model organisms
located at key positions of deuterostome
phylogeny. The data obtained will be
interpreted in a comparative context to
reveal the evolutionary history of the
Wnt and RA signalling networks in the
course of deuterostome diversification.
Figure 2. Research project summary
Our group is currently funded by
(OP,
ongoing projects; FP, future projects).
two grants from the ANR, the main
French granting agency, an ANR “Blanc” grant (“EvolAx”) and an ANR “JCJC” grant
(“RAvolution”) with a total budget of €328,000, which will ensure that the project can be carried out
as proposed until at least the end of 2014 and, provided a planned extension is approved, possibly until
the end of 2015. Furthermore, we will submit grant proposals based on each of the three future
projects. As mentioned in the corresponding sections, research consortia supporting the different
projects have already been established and writing of grant proposals has been initiated. We are
already in contact with young scientists that are interested in joining our group in the future to work on
specific aspects of the proposed research. This includes graduate students (Nicolas Robert) and
postdoctoral fellows (Jacob Warner). In sum, we are confident that the strategic decisions taken by our
group will provide a reliable basis for carrying out the totality of the proposed work.
Cited literature (other than recent group publications in reference list)
Bertrand, S., Escriva, H., 2011. Evolutionary crossroads in developmental biology: amphioxus. Development 138, 4819-30.
Gilbert, S.F., 2010. Developmental Biology, 9th edition. Sinaueur Associates, Inc., Sunderland, MA.
Logan, C.Y., Miller, J.R., Ferkowicz, M.J., McClay, D.R., 1999. Nuclear beta-catenin is required to specify vegetal cell fates
in the sea urchin embryo. Development 126, 345-57.
Marlétaz, F., Holland, L.Z., Laudet, V., Schubert, M., 2006. Retinoic acid signaling and the evolution of chordates. Int J Biol
Sci 2, 38-47.
McClay, D.R., 2011. Evolutionary crossroads in developmental biology: sea urchins. Development 138, 2639-48.
Schubert, M., Escriva, H., Xavier-Neto, J., and Laudet, V., 2006. Amphioxus and tunicates as evolutionary model systems.
Trends Ecol Evol 21, 269-77.
Shimeld, S.M. and Donoghue, P.C., 2012. Evolutionary crossroads in developmental biology: cyclostomes (lamprey and
hagfish). Development 139, 2091-99.
Sweet, H.C., Gehring, M., and Ettensohn, C.A., 2002. LvDelta is a mesoderm-inducing signal in the sea urchin embryo and
can endow blastomeres with organizer-like properties. Development 129, 1945-55.
124
Genomic perspectives on Deuterostome Evolution
Group 6 “Genome and protein evolution in animals”
Group leader: Richard Copley
Additional known members in January 2014: Philippe Dru (AI CNRS, 50%).
Overall scientific objective
Understanding the evolution of the animals in terms of evolving genome content
1. Genome sequencing projects and the development of novel analysis methods
The number of taxa for which complete genome sequence is available is still relatively small.
Although the situation is beginning to improve, there is a pressing need to increase sequence coverage
of animal groups, and produce reliable genome assemblies and gene annotation. (For instance, within
the echinoderms, genome sequences are available for the echinoid class, but not crinoids, asteroids,
ophiuroids or holothurians). This will enable a finer grained picture of the presence and absence of
particular genes on the animal phylogeny; better understanding of the patterns of evolution and lineage
specific functional constraint within the genes, and by producing genomic rather than transcriptomic
data, the potential to understand regulatory sequence evolution.
New sequencing technologies have driven down the cost of generating genomic DNA sequence to the
point where high coverage of an animal genome (e.g. < 1Gb) can be obtained for a few thousand
euros. Currently short read lengths (i.e. 100-150bp) present challenges for assembling sequence into a
complete genome, owing to an inability to bridge repetitive sequence. From a biological point of
view, however, much of the initial interest in a genome is in its protein coding content, which is likely
to be depleted in repetitive sequence. Together with Yang Li, a D.Phil student, I am currently working
on methods to assemble protein coding regions using proteins from other species (or native cDNA
sequences) as templates, and thus quickly and cheaply assay the protein coding content of an organism
from short read sequence data. We currently have a method that is capable of increasing the N50 on
our fragmented Xenoturbella assembly from approximately 3kb to 4kb; moreover, as protein
sequences are used to scaffold, we also obtain a set of less fragmented protein predictions aiding
functional interpretation of the genome sequence.
I am currently working on three next-generation genome sequencing projects: the deuterostome,
Xenoturbela bocki, and the acoel Paratomella rubra in collaboration with Max Telford, UCL, in order
to more fully investigate their deuterostome affinities; Paralvinella sulfincola, a hydrothermal vent
worm, in collaboration with Adam Claridge-Chang (A*STAR, Singapore). I am also interested in
genome sequencing of animals likely to shed special light on particular evolutionary questions – for
instance, I am involved in the Priapulus caudatus genome project - priapulids are among the most
slowly evolving protostomes, and thus may be particularly useful for reconstructing the genome
complement of the protostome / deuterostome ancestor (Webster et al. 2006).
2. Identifying orthologous and taxon specific genes.
In order to perform large scale comparisons of the gene content of different genomes, it is necessary to
distinguish orthologs (genes related by speciation events) from paralogs (those related by an intragenome gene duplication event). Whereas orthologs are likely to be direct functional equivalents
(being the same gene in different species), the presence of multiple copies of paralogs means that any
individual gene is more likely to have diverged from its original function (either in terms of its
expression pattern or its intrinsic encoded function). For example, orthologous transcription factors
are likely to share DNA binding specificities, as after a speciation event, the same genes are likely to
need regulating in both species. If the transcription factor then goes on to duplicate in one species, its
targets may be controlled by only one copy, with the other copy acquiring new DNA binding
specificities and different target genes. Aside from direct comparisons of gene content, the
identification of orthologs is vital if we wish to compare the regulatory sequence controlling gene
expression of particular genes shared between species. Typically we might want to compare the
upstream DNA sequence of genes in two species that have been identified as orthologous via a protein
comparison, in order to identify constrained sequence controlling expression.
125
Genomic perspectives on Deuterostome Evolution
Although databases of orthologs exist (e.g. Treefam, (Li et al. 2006)), as third party resources they are
not directly applicable to newly sequenced genomes. My primary aim in this area is not to be
comprehensive within genomes, (i.e. inclusive of all genes) but to develop high quality data sets of
cross-phylum orthologous genes suitable for further detailed evolutionary analysis, focusing
particularly on those of developmental / regulatory relevance, such as transcription factors, paracrine
factors and chromatin modification proteins; and in addition genes that are associated with particular
kinds of cell types e.g. neuron associated ion channels or specific G-protein coupled receptors, with
which it will be possible to trace evolving cell type complexity. In this, I will develop automated
pipelines to exploit all available data sets for relevant taxa, including preliminary genome data,
transcriptome sets (in-house and from public databases) etc.
To distinguish orthologs and paralogs, we will use modifications of algorithms within the POPE
software pipeline (Juliusdottir et al. 2008). This pipeline involves the use of BLAST to gather
homologous (i.e. paralogous and orthologous) sequences from all species. These sequences are aligned
and used to reconstruct a phylogeny using probabilistic models e.g. (Guindon and Gascuel, 2003). In
brief, the software interprets these gene trees by rerooting the subtree around the gene of interest using
an externally defined paralogous gene or (more generally) an outgroup to the species of interest.
Sequences outside of the subtree are paralogs of the gene of interest. Genes within the sub-tree
represent a set of orthologs. We will apply this pipeline, developed in my group, to protein based
datasets including representatives from the deuterostomes (Strongylocentrotus, Saccoglossus, Ciona &
chordates), and Xenacoelomorpha. For outgroups we will use the protostomes (with genomes from
ecdysozoans and lophotrochozoans) and basal metazoans (Nematostella, Hydra, Amphimedon, Clytia).
This procedure will allow us to build up gene sets from the taxa of interest and identify genes
orthologous across different subsets of taxa.
An obvious concern with analysis of gene loss is that we are looking for an absence in fragmentary
data sets. We think this unlikely to be a serious issue however, in particular for well-conserved genes,
as new genome projects are likely to generate extremely high coverage relative to classical sequencing
techniques and even relatively discontiguous assemblies are likely to yield DNA sequences of
sufficient length to reveal homology to target genes. It is encouraging, for instance, that our
Xenoturbella genomic data shows an extra Hox gene and several miRNA genes compared to PCR
based and small-RNA sequencing approaches.
3. Identification of lineage specific protein motifs
A major point of debate in the evo-devo field is the relative importance of protein-coding vs. noncoding (i.e. DNA regulatory element) evolutionary change (Hoekstra and Coyne, 2007). The apparent
stasis in the evolution of key developmental genes has given rise to the metaphor of a shared ‘toolkit’
underlying all metazoan development, and the widely held opinion that the most interesting
differences between species are primarily those of regulatory DNA, affecting gene expression patterns
rather than protein coding change (Davidson, 2006).
The extent of functional, lineage specific evolution within protein-coding genes has not been properly
explored. In part this has been due to a lack of subtlety in dealing with gene products as structural
entities with various interacting components, and in part a lack of deep sequence sampling both within
and between phyla. I am undertaking detailed analyses of the evolution of protein coding genes, with a
particular emphasis on transcription factors, with the aim of identifying non-domain regions exhibiting
regimes of lineage specific purifying selection. I propose that such regions are likely to be functional
molecular synapomorphies and are likely to play a role in lineage specific biology.
For instance, deuterostome orthologs of FOXG contain an engrailed homology 1 (EH1) motif Cterminal to the Forkhead domain, a motif that is absent in protostomes and outgroups. The additional
EH1 motif is likely to be involved in the recruitment of chromatin modifying enzymes, and so to have
lineage specific effects on EH1 function.
126
Genomic perspectives on Deuterostome Evolution
Figure 1. Snail-like Zn Finger transcription factors contain different N-terminal protein interaction motifs in
different phyla. The motifs all interact with the chromatin histone modification machinery, but different
components of this machinery. In some ‘derived’ taxa such as tunicates and platyhelminthes, Snail-like
transcription factors appear to lack such motifs entirely.
In general, transcription factors often contain short regions of conservation outside of their DNA
binding domains. In many cases, these are known to interact with chromatin modifying enzymes
(Figure 1), which generally do not have site-specific DNA recognition domains of their own, or are
subject to post-translational modifications regulating the activity of the factor. As these motifs are
often lineage specific they represent an important source of protein side (as opposed to DNA)
modification of developmental pathways.
The potentially small size of these regions can make their identification challenging. In order to
perform such analyses on a large scale, I am working on modifying bioinformatics methods previously
used to define amino acid residues responsible for functional differences between paralogs, such a
relative entropy based approaches (Hannehalli and Russel, 2000). The basic idea is that instead of
using paralogous groups to define sub-types, we can investigate combinations of species groups to
search for taxa in which conserved regions are found. When these conserved regions differ between
groups they are good candidates for being responsible for lineage specific functions. In order to apply
this method on a large scale, I will additionally need to develop statistics to assess the significance of
such patterns. This will enable a proper assessment of whether particular gene classes are likely to
have undergone protein coding change that may be responsible for species specific functional
differences, and whether this is a mode of evolution that significantly affects orthologs as well as
paralogs.
4. Finding genomic correlates of phenotypic change.
I am interested in particular in genomic changes (novelties) associated with specific clades. The
previous sections describe how I will identify four major potential sources of clade-specific novelty: i)
novel genes (i.e. unique to a clade), ii) gene losses, iii) gene duplications, iv) instances of lineage
specific gene evolution (see motifs section above and (Studer and Robinson-Revachi, 2010). These
genes and features will be mapped onto a phylogenetic tree of the animals themselves, allowing the
quantification of the relative contribution of gene duplication, gene loss and accelerated rates of
evolution to genome evolution and the assignment of specific instances of these processes to the
clades we have identified. These node specific genetic novelties will allow the identification of
plausible sources of evolutionary novelty associated with each node of the tree.
127
Genomic perspectives on Deuterostome Evolution
A particular focus here will be on correlated losses. Whereas gene gains can occur only once on a
phylogeny, gene losses can occur multiple times independently, raising the possibility that functional
linkages can be detected by the common absence of particular genes (or genes and protein interaction
motifs). This kind of analysis will become increasingly important as more genomes are sequenced
leading to a ‘higher resolution’ understanding of the frequency of loss events. An obvious application
of this analysis is studying parallel changes in secondarily simple taxa, such as platyhelminthes and
acoelomorphs.
The final step is to associate these novelties (gained, lost, duplicated or changed genes) with a
function, a genetic process/pathway or a phenotype in order to give insights into the functional
correlates of the novelties. I will interrogate Gene Ontology databases and biological pathways data
(e.g. KEGG, Reactome) to associate each gene novelty with a putative function. I will use these data
(and any other suitable for inferring gene function including expression pattern data) to assign putative
gene functions and associate these with the known biology/morphology of the groups they are
associated with.
The ultimate goal is to discover genetic elements associated with the evolution of specific
morphological and physiological innovations. Particular emphasis will be placed on processes and
structures that are associated with differently ranked groupings within the deuterostomes or that have
been lost within the Xenacoelomorpha.
5. Conserved non-coding regions: understanding conserved patterns of gene expression.
A central long term aim of my research program is the development of techniques for cross-species
comparison of gene regulatory networks controlling developmental processes over large (e.g. interphylum) taxanomic distances. Understanding the linkages between developmental regulatory genes
and their targets (which may potentially be lineage specific) will aid in the understanding of the
evolution of cell types responsible for particular biological functions (Arendt, 2008). For instance,
transcription factors tend to be older than the functions with which they are typically associated e.g.
(Sebe-Pedros et al., 2011). As an example Interferon Regulatory Factors (IRFs) in vertebrates are
named after their role in regulating interferon production, crucial molecules of the immune response.
IRFs are also found in invertebrates, but interferons themselves are a vertebrate novelty. If we fully
understood the roles of IRFs in invertebrates, we might be better placed to understand from where
(e.g. what sorts of cells) the vertebrate immune response evolved. In general, if it is possible to
develop a robust predictive framework, we will be able to track the acquisition of target genes by
transcription factors over time, and better understand their ancestral functions.
In the absence of direct experimental data, a necessary first step is being able to extract information on
pathway structure from genomic sequence alone. For regulatory networks, this means the ability to
predict protein-DNA interactions, and thus to establish whether orthologous genes are regulated in the
same way in different species. Although Transcription Factor Binding Sites (TFBS) are often not
conserved between species, I and others have shown that some sites can be well conserved (Copley et
al., 2007). It is possible that such well conserved sites correspond to likely locations for the assembly
of multi-transcription factor complexes, with such complexes performing the signal integration that
defines the properties of a regulatory network (structural studies performed by a summer intern, Tim
Hele, provide support for this). Good progress in this area will be possible with broader datasets of
closely related genomes, of the kind currently available for drosophilids, nematodes and vertebrates.
In addition to direct conservation of TFBSs, of the kind observable in sequence alignments, it is likely
that rapid turnover of sites will lead to situations where enhancer regions of sequence conserve a
particular composition of sites, without individual sites being directly homologous. I am examining
the predictive power of particular TFBS profiles to identify genes associated with particular functional
classes across long phylogenetic distances. Orthologous transcription factors typically show
conservation of DNA binding specificities throughout the species in which they are present – the
amino acid residues involved in specific base recognition are completely conserved. Building on my
prior work on the NF-NB system in drosophilids (Copley et al., 2007), I have been investigating its
conservation in other animals. Initial results screening upstream genomic regions from sea urchin and
Nematostella with NF-NB binding site profiles reveal that the most highly scoring regions tend to be
128
Genomic perspectives on Deuterostome Evolution
upstream of genes belonging to families implicated in immune responses. These results are crude, and
to explore them more fully it will be necessary to a) better define groups of orthologs, in order to be
sure that the same genes are being considered in different species (thus there is a dependency on
earlier parts of this document) and b) consider combinations of transcription factors. In the case of NFNB, for example, obvious candidates include members of the IRF (Interferon Regulatory Factor)
family, which are known to have a synergistic role with NF-NB in vertebrates (Panne et al., 2007).
More generally, the richly detailed sets of TFBS binding data coming from human ChIP-Seq
experimental data sets (Birney et al., 2007) will provide many examples of transcription factor / target
gene associations that can be explored for evolutionary conservation in non-vertebrate systems, thus
shedding light on the evolution of regulatory pathways.
Cited literature (other than recent group publications in reference list)
Webster BL, Copley RR, Jenner RA, Mackenzie-Dodds JA, Bourlat SJ, Rota-Stabelli O, Littlewood DT, Telford MJ:
Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan. Evol Dev 2006,
8(6):502-510.
Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L et al: TreeFam: a curated
database of phylogenetic trees of animal gene families. Nucleic acids research 2006, 34(Database issue):D572-580.
Juliusdottir T, Pettersson F, Copley RR: POPE--a tool to aid high-throughput phylogenetic analysis. Bioinformatics 2008,
24(23):2778-2779.
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst
Biol 2003, 52(5):696-704.
Hoekstra HE, Coyne JA: The locus of evolution: evo devo and the genetics of adaptation. Evolution 2007, 61(5):995-1016.
Davidson EH: The Regulatory Genome: Academic Press; 2006.
Hannenhalli SS, Russell RB: Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol
2000, 303(1):61-76.
Studer RA, Robinson-Rechavi M: Large-scale analysis of orthologs and paralogs under covarion-like and constant-butdifferent models of amino acid evolution. Mol Biol Evol 2010, 27(11):2618-2627.
Arendt D: The evolution of cell types in animals: emerging principles from molecular studies. Nat Rev Genet 2008,
9(11):868-882.
Sebe-Pedros A, de Mendoza A, Lang BF, Degnan BM, Ruiz-Trillo I: Unexpected repertoire of metazoan transcription factors
in the unicellular holozoan Capsaspora owczarzaki. Mol Biol Evol 2011, 28(3):1241-1254.
Copley RR, Totrov M, Linnell J, Field S, Ragoussis J, Udalova IA: Functional conservation of Rel binding sites in
drosophilid genomes. Genome research 2007, 17(9):1327-1335.
Panne D, Maniatis T, Harrison SC: An Atomic Model of the Interferon-beta Enhanceosome. Cell 2007, 129(6):1111-1123.
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET,
Thurman RE et al: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot
project. Nature 2007, 447(7146):799-816
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Mitosis and Spindle checkpoints
Group 7: “Mitotic control and spindle checkpoints”
Group leader : Stefania Castagnetti
Additional projected members in January 2014 : Lydia Besnardeau (AI CNRS, 50%).
The eukaryotic cell cycle comprises an ordered set of events leading from chromosome duplication
during S-phase to chromosome segregation during mitosis. The correct and unidirectional progression
of these events is fundamental to the generation at each cell division of viable daughter cells with an
identical set of chromosomes. Genome integrity is safeguarded by checkpoint mechanisms, which
prevent progression through the cell cycle until each stage is successfully completed, ensuring
dependence of initiation of each stage upon successful completion of others (Elledge, 1996). In
eukaryotic cells, a highly conserved checkpoint operates at metaphase. Evidence that progression
through mitosis is carefully monitored was first obtained with the use of drugs that depolymerise
microtubules and promote a prolonged mitotic arrest in vertebrate cells (Brues and Cohen, 1936). It is
now widely accepted that the spindle checkpoint is a feedback control system that monitors the state
of kinetochore-microtubule attachment and prolongs metaphase, increasing the time available for
correct microtubule capture (Musacchio). Kinetochore integrity is essential for proper checkpoint
activation. Unattached kinetochores recruit checkpoint components and produce an effector, named
checkpoint complex (MCC) (Hardwick et al., 2000), which prevents advancement to anaphase by
inhibiting APC/C, a multisubunit E3 ubiquitin ligase, ultimately responsible for allowing anaphase
onset and mitotic exit (Fang et al.). Laser ablation studies (Rieder et al.,1995) and micromanipulation
of chromosomes (Li and Nicklas, 1995) also showed that as little as one unattached kinetochore is
sufficient to activate the checkpoint and halt anaphase onset. Correct bipolar attachment leads to
tension across kinetochores, which satisfies the checkpoint allowing mitotic progression (Nicklas et
al., 1995).
Following sister chromatid separation,
tension across kinetochores is lost but the
checkpoint remains silenced, suggesting
that anaphase cells are no longer
competent to activate the spindle
checkpoint. At anaphase onset, Aurora B
kinase, the catalytic subunit of the
chromosome passenger complex (CPC),
which acts as a sensor for attachment at
kinetochores, leaves the centromeres and
relocalizes to the spindle midzone (Liu and
Lampson, 2009). It has been suggested that
this
relocalization
might
prevent
reactivation of the mitotic checkpoint in
anaphase. Preventing CPC translocation to
the midzone indeed causes recruitment of
checkpoint proteins to kinetochores in
anaphase, but does not delay mitotic exit
(Vazquez-Novelle et al., 2010). These
results suggest that relocalization of CPC
to the spindle midzone is not sufficient to
Figure 1: Unattached kinetochores activate the checkpoint. explain checkpoint inactivation during
Binding of kinetochores to microtubules from opposite poles anaphase.
(bipolar attachment) generates tension across kinetochores,
which satisfies the checkpoint. What stops checkpoint Part of the work I carried out more
recently and which is described below
activation after anaphase onset?
indicates an important contribution of
SPB/centrosomes
in
making
cells
competent for spindle checkpoint activation (my unpublished data). The results reported below
suggest a novel level of regulation never described before, which we intend to analyze in our shortterm goal. Upon anaphase onset, loss of sister chromatid cohesion is followed by the fast movement of
sister chromatids to the spindle poles (SPB/centrosome), driven by depolymerization of kinetochore
microtubules. The working model proposed here (Fig. 1) suggests that kinetochores, the platforms for
130
Mitosis and Spindle checkpoints
spindle checkpoint signaling, are available for checkpoint signaling exclusively from mitotic
commitment to the metaphase to anaphase transition. Association with SPB/centrosomes after
anaphase masks kinetochores, preventing spindle checkpoint activation. The single cell fission yeast
Schizosaccharomyces pombe provides an ideal model system to test this hypothesis, as its
kinetochores remain associated with the SPB past anaphase, during interphase (kinetochore clustering)
and interfering with kinetochore or SPB structure/function affects kinetochore clustering.
Relying on our expertise with yeast genetics and cell biology we set as short term objective to
highlight and dissect the role played by the spindle pole bodies, the yeast centrosome equivalent, and
its associated protein pool in mitotic progression and spindle checkpoint control and to identify novel
factors required for control of mitotic progression.
Short term Objectives (2-3 years)
1. Screen for new factors required for control of mitotic progression and spindle checkpoint
control.
2. Characterization of the role of the SPB-kinetochore interaction in mitotic progression.
Objective 1: Screen for new factors required for control of mitotic progression and spindle
checkpoint control.
The project described in this
objective builds on my
previous work demonstrating
microtubule
independent
mitotic progression and mitotic
exit in S. pombe and aims at
the identification of new
factors involved in regulating
mitotic progression. As in
other organisms, a spindle
checkpoint in S. pombe delays
mitotic progression in the
presence
of
microtubule
defects, which disrupt the
spindle. I have shown,
Figure 2: Nuclear fission in the absence of spindle microtubules. A) Cells
however, that when cytokinesis
treated with 50μg/ml MBC for 6 hours. B) Nuclei undergoing mitosis
is impaired, fission yeast cells
(+DMSO) or nuclear fission (+MBC). C) Schematic of nuclear fission.
Scale bar 10μm.
do not arrest in mitosis in the
absence
of
spindle
microtubules. Instead these cells exit mitosis and undergo subsequent rounds of DNA replication
(Castagnetti et al.). About 50% of these cells also undergo an unusual spindle independent nuclear
division (Fig. 2a,b), which was termed “nuclear fission” (Castagnetti et al.). Under this conditions,
sister chromatids are probably pulled apart not by microtubules but by the SPBs they are associated
with (Fig.2c). Nuclear fission is blocked if SPB maturation and/or sister chromatid separation are
prevented genetically (Castagnetti et al.). This observation prompted the use of this experimental set
up to screen for genes whose deletion would cause a change in nuclear division pattern/dynamics as
well as changes in the pattern of DNA replication. Deletion of these genes is expected to result in loss
of nuclear fission and should be easily identifiable by visual screening. Changes in the dynamics of
mitosis would also affect progression through S-phase resulting in a change in the pattern of DNA
accumulation, which can be monitored by flow cytometry. To test the feasibility of this approach I
carried out a preliminary screen. I generated double mutants of all deletions already available in our
lab with the temperature sensitive mutant cdc11-119 (which blocks cytokinesis at the restrictive
temperature), and screened the resulting double mutants by flow cytometry (sampling every 2 hours)
and microscopically, using dapi staining. This analysis allowed the isolation of a partial deletion in the
SPAC11E3.05 ORF (Hiraoka et al., 2011) which causes a significant reduction in nuclear fission and
blocks DNA replication. SPAC11E3.05 encodes a WD repeats containing protein, highly conserved
across eukaryotes. A further characterization of the function of the SPACC11E3.05 encoded protein
will be carried out as described in Objective 2.
131
Mitosis and Spindle checkpoints
Due to the availability of the complete collection of S.pombe single gene deletions (commercially
available from Bioneer, Korea (Kim et al., 2010)), the reproducibility of the nuclear fission phenotype
and the success of the preliminary screen, we intend to extend the screen to cover the entire genome.
In more details, the deletion collection will be crossed to the temperature sensitive mutant cdc11-119
which blocks cytokinesis at the restrictive temperature, and the nucleus will be labelled with cut11GFP (a nuclear envelope protein) to allow visual screening in live cells. To facilitate the generation of
labeled double mutants we will generate a background strain containing the tagged nuclear marker
cut11-GFP (marked with nourseothricin, NAT) in close proximity to the cytokinesis mutation cdc11119, so that the mutation and the marker will co-segregate at high frequency, allowing rapid
identification of the temperature sensitive mutation through the NAT resistence. The background
strain will also contain the pem1 mutation, a recessive cyclohexamide resistence mutation, which will
allow to select against residual diploids carried over after sporulation. The background strain cdc11119 cut11-GFP: pem1 will be crossed to ordered arrays of viable haploids each bearing a deletion of a
single non-essential S.pombe gene (about 3500 strains), marked with the kanamycin (G418) resistence
gene (Kim et al.). The obtained diploids will be sporulated and selected on G418-plates, to select for
the presence of the deletion, then replica plated to cyclohexamide to eliminate residual diploids and
finally to NAT-plates to obtain double mutants. The selected double mutants will be grown in glass
bottom 96-wells plates overnight and then screened visually after 6 hours at the restrictive
temperature, for changes in patterns of nuclear division in the absence (+MBC) of spindle
microtubules. This screen will allow the identification of factors involved in mitotic progression, exit
from mitosis and control of the SAC, particularly those which were not uncovered in previous screen
due to the overpowering presence of spindle microtubules or because their function was required after
the metaphase-to-anaphase transition, when the spindle checkpoint is inactivated. Interesting
candidates will be further characterized to define their role in mitosis. Initially we will focus
particularly on those genes whose encoded proteins either localize at SPB/kinetochores or are required
for kinetochore clustering.
Objective 2: Characterization of the role of SPB-kinetochore interaction in mitotic progression
and during anaphase
In fission yeast, centromeres cluster at the nuclear envelope in the vicinity of the SPBs (Funabiki et
al.) in a microtubule independent fashion (Funabiki et al., 1993). This clustering is normally lost upon
entry into mitosis (Funabiki et al., 1993). I showed that MBC treated cells, which proceed through Mphase without delay, do not show any declustering of kinetochores upon mitotic commitment
(Castagnetti et al.). On the contrary, partial deletion of the SPAC11E3.05 ORF, identified in the
preliminary screen described in Objective 1, causes declustering of centromeres from the SPB (King et
al., 2008) and blocks DNA replication irrespectively of the presence of spindle microtubules (Fig. 4a).
Taken together these observations suggest that clustering of kinetochores at SPBs alleviate a cell cycle
block, allowing cells to proceed through S-phase and replicate their DNA, in the absence of spindle
microtubules.
A further characterization of the phenotype of SPAC11E3.05 deleted cells showed that these cells
present with slow growth, with a doubling time twice longer than wild type cells, and are sensitive to
MBC (Fig.3b). Unexpectedly, both phenotypes are suppressed by deletion of mad2 (Fig.3b). These
observations suggest that these cells cannot proceed normally through mitosis due to spindle
checkpoint activation.
Figure 3: a) facs analysis of cdc11-119
SPACC11(¨ FHOOV LQ WKH SUHVHQFH RU
absence (-) of MBC, taken every hour after shift to
restrictive temperature. b) Dilution series of fission
\HDVW FHOOV ZLOG W\SH PDG¨ 63$&&(¨ 63$&&(¨PDG¨
Combining the data reported above, one could
envisage a model whereby SPB binding to
kinetochores masks them (in much the same way
as microtubule binding in metaphase) making
132
Mitosis and Spindle checkpoints
them unavailable for recruiting checkpoint proteins and therefore for checkpoint activation.
In anaphase clustering of kinetochores at SPB would then block checkpoint reactivation until
kinetochores decluster from SPB and become visible to the checkpoint again, upon mitotic
commitment in the following cell cycle.
By a combination of genetic, biochemical and cell biological approaches, I aim at testing the
hypothesis described above while analyzing the role of SPACC11E3.05 encoded protein in mitotic
progression. I will analyze the effect of kinetochores clustering at SPB on mitotic progression and the
dynamic behavior of checkpoint proteins in the presence and absence of kinetochore clustering
(imaging of live cells bearing fluorescently tagged SPB components and checkpoint proteins) to
determine whether clustering and checkpoint activation are related and specifically mutually
exclusive. In parallel I will analyze checkpoint activation in synchronous population when
declustering is induced/inhibited at different stages of mitosis, in the presence or absence of
microtubule depolymerizing drugs, using a collection of temperature sensitive mutants, which affect
mitotic progression and kinetochore clustering.
Mid-term objectives (3-5 years)
To characterize the spindle checkpoint in Paracentrotus lividus embryos
Studies in mouse, frog, sea urchin and ascidian embryos have shown that spindle checkpoint control is
relaxed during early embryogenesis and in embryonic stem cells, despite the enrichment of a large
number of mitotic spindle checkpoint proteins. This contrasts with the situation in adult somatic cells,
but is similar to what I have observed in fission yeast cells. Understanding the differences between
somatic and embryonic cells could improve our understanding of both general cell cycle control as
well as the developmental programme of early embryos. Available data on the checkpoint response
during embryogenesis are quite sparse, come from a variety of model systems and mostly predate the
molecular era. My first aim will thus be to characterize in detail the spindle checkpoint response in P.
lividus embryos.
I plan initially to establish at what stage in embryogenesis cells begin to activate a canonical spindle
checkpoint response in response to microtubule depolymerization, and how, prior to that moment, they
respond to different degrees of mitotic insult. I will analyze cellular behavior, including nuclear
envelope breakdown, chromosome disjunction and mitotic exit as well as biochemical changes like
levels of cyclin dependent kinase activity and DNA replication in eggs, zygotes and different stage
embryos. I will compare the abundance and localization pattern of checkpoint proteins in embryonic
stages before and after checkpoint onset by using cross-reacting antibodies to conserved cell cycle
regulators generated for close related organisms such as the starfish (Hara et al.), or injecting transcript
coding for tagged checkpoint factors. This will lead to a better understanding of checkpoint activation
during early embryogenesis and will provide the basis of using sea urchin as a model system for
understanding mitotic control.
Long-term objectives
Understanding the evolutionary origins of mitosis
Although a great deal of work and speculation has gone into the evolution of many biological events,
hypothesis on the origin of mitosis remain vague. Central to mitosis, as we know it today, is the
formation of the microtubule-based spindle. Such a spindle is not found in prokaryotic cells such as
bacteria and is generally thought to have evolved when eukaryotes arose, probably 1.5 billion years
ago. No intermediates are known. The nuclear fission I have described in fission yeast might represent
one such evolutionary intermediate mechanism between prokaryotes and eukaryotes whereby
chromosomes separate attached to the nuclear membrane, rather than to a mitotic spindle. Later in
evolution the appearance of microtubule-based spindle generated mitosis, which led to greater
segregation accuracy superseding the older more primitive form of nuclear fission. Testing such
hypothesis would be difficult. However learning about mitosis in organisms more distantly related to
the usually studied model organisms, will provide useful information about the evolution of mitosis in
eukaryotes. Initially I will characterize mitosis in unicellular organisms like the haploid unicellular
photosynthetic alga, Chlamydomonas reinhardiand the soil-living amoeba Dictyostelium discoideum,
which show kinetochore tethering to the nuclear envelope, the unicellular marine green alga
Ostreococcus tauri, which has more kinetochores than spindle microtubules and in dinoflagellates,
where spindle microtubules are cytoplasmic while chromosomes are intranuclear and mitosis occurs
with an intact nuclear envelope. Following this analysis I intend to extendt the analysis to other more
133
Mitosis and Spindle checkpoints
distantly related organisms. EM and light microscopy analysis where possible will allow to define
common elements required for chromosome segregation in the absence and presence of spindle
microtubules. In the long term using biochemical purifications and genome analysis I will try to define
the minimal molecular machinery required for chromosome segregation in the primordial eukaryotic
cell.
Cited literature (other than recent group publications in reference list)
Brues, A. M. and Cohen, A. (1936). Effects of colchicine and related substances on cell division. Biochem J 30, 1363-1368 1.
Elledge, S. J. (1996). Cell cycle checkpoints: preventing an identity crisis. Science 274, 1664-72.
Fang, G., Yu, H. and Kirschner, M. W. (1998). The checkpoint protein MAD2 and the mitotic regulator CDC20 form a
ternary complex with the anaphase-promoting complex to control anaphase initiation. Genes Dev 12, 1871-83.
Funabiki, H., Hagan, I., Uzawa, S. and Yanagida, M. (1993). Cell cycle-dependent specific positioning and clustering of
centromeres and telomeres in fission yeast. J Cell Biol 121, 961-76.
Hara, M., Mori, M., Wada, T., Tachibana, K. and Kishimoto, T. (2009). Start of the embryonic cell cycle is dually locked in
unfertilized starfish eggs. Development 136, 1687-96.
Hardwick, K. G., Johnston, R. C., Smith, D. L. and Murray, A. W. (2000). MAD3 encodes a novel component of the spindle
checkpoint which interacts with Bub3p, Cdc20p, and Mad2p. J Cell Biol 148, 871-82.
Hiraoka, Y., Maekawa, H., Asakawa, H., Chikashige, Y., Kojidani, T., Osakada, H., Matsuda, A. and Haraguchi, T. (2011).
Inner nuclear membrane protein Ima1 is dispensable for intranuclear positioning of centromeres. Genes Cells 16, 100011.
Kim, D. U., Hayles, J., Kim, D., Wood, V., Park, H. O., Won, M., Yoo, H. S., Duhig, T., Nam, M., Palmer, G. et al. (2010).
Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol 28,
617-23.
King, M. C., Drivas, T. G. and Blobel, G. (2008). A network of nuclear envelope membrane proteins linking centromeres to
microtubules. Cell 134, 427-38.
Li, X. and Nicklas, R. B. (1995). Mitotic forces control a cell-cycle checkpoint. Nature 373, 630-2.
Liu, D. and Lampson, M. A. (2009). Regulation of kinetochore-microtubule attachments by Aurora B kinase. Biochem Soc
Trans 37, 976-80.
Musacchio, A. Spindle assembly checkpoint: the third decade. Philos Trans R Soc Lond B Biol Sci 366, 3595-604.
Nicklas, R. B., Ward, S. C. and Gorbsky, G. J. (1995). Kinetochore chemistry is sensitive to tension and may link mitotic
forces to a cell cycle checkpoint. J Cell Biol 130, 929-39.
Rieder, C. L., Cole, R. W., Khodjakov, A. and Sluder, G. (1995). The checkpoint delaying anaphase in response to
chromosome monoorientation is mediated by an inhibitory signal produced by unattached kinetochores. J Cell Biol 130,
941-8.
Vazquez-Novelle, M. D., Mirchenko, L., Uhlmann, F. and Petronczki, M. (2010). The 'anaphase problem': how to disable the
mitotic checkpoint when sisters split. Biochem Soc Trans 38, 1660-6.
134
Fiches individuelles
Barreau, C., Castagnetti, S., Chenevert, J., Copley, R., Croce, J., Dumollard, R., Houliston, E., Hudson, C.,
McDougall, A., Momose, T., Prulière, G., Rouvière, C., Sardet, C., Schubert, M., Tiozzo, S., Yasuo, H.
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
ingénieurs de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie
de la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour
attester l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule
unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement
destinées à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal,
responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : BARREAU
Prénom : Carine
Date de naissance : 02/12/1976
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : UPMC
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
_
Maître de Conférences (classe normale)
Thèse soutenue _
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU : section 65
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme :
1)
Points forts des activités de recherche et résultats marquants :
By studying of a set of conserved germ cell markers during Clytia development: Vasa, Nanos1, Nanos2,
Piwi and PL10, we found that:
-
Maternal mRNAs for all these genes are concentrated in a germ plasm-like region in the egg.
-
Those mRNAs are inherited by the i-cell lineage (multipotent stem cell population) in the embryo.
-
i-cells can be generated in the absence of this germ plasm.
-
Relationship between germ plasm, germ line and stem cells should be reconsidered.
This work has been done in collaboration with M. Manuel’s group in Paris (UMR 7138, UPMC).
2)
Production scientifique :
1) Leclère L, Jager M, Barreau C, Chang P, Le Guyader H, Manuel M, Houliston E (2012). Maternally
localized germ plasm mRNAs and germ cell/stem cell formation in the cnidarian Clytia. Dev. Biol.
364:236-48.
Before my entry in the unit:
2) Barreau C, Benson E, Gudmannsdottir E, Newton F, White-Cooper H (2008). Post-meiotic transcription
in Drosophila testes. Development. 135:1897-902.
3) Barreau C, Benson E, White-Cooper H (2008). Comet and cup genes in Drosophila spermatogenesis: the
first demonstration of post-meiotic transcription. Biochem. Soc. Trans. 36:540-2.
4) Keryer-Bibens C, Barreau C, Osborne HB (2008). Tethering of proteins to RNAs by bacteriophage
proteins. Biol. Cell. 100:125-38.
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
3)
Points forts des activités ne relevant pas de la production scientifique :
Teaching:
Since 2008, 192 hours of TD/TP done per year:
In Villefranche:
1. UE « Développement des organismes marins » (6 ECTS)
Master 2 Biologie Moléculaire et Cellulaire, spécialité Biologie Cellulaire, Développement et
Cellules Souches.
I am responsible for this UE, which is entirely carried out in Villefranche.
2. UE « Analyse scientifique » (6 ECTS)
Master 2 Biologie Moléculaire et Cellulaire, spécialité Biologie Cellulaire, Développement et
Cellules Souches.
This UE is carried out in Villefranche for most of the students.
3. UE « Développement et évolution des organismes pluricellulaires » (6 ECTS)
Master 1 Biologie Intégrative et Physiologie.
I am co-responsible for this UE, half carried out in Villefranche, since 2009-2010.
On Jussieu campus:
4. UE « Méthodologies en biologie moléculaire et cellulaire » (12 ECTS)
Master 1 Biologie Moléculaire et Cellulaire.
5. UE « Biologie cellulaire et moléculaire des eucaryotes » (6 ECTS)
Licence 3 Sciences du Vivant.
6. UE « Unicité du vivant » (6 ECTS)
Licence 1 Sciences du Vivant. In 2008-2009 only.
7. Participation in examination juries of master 1 and 2 viva (Biologie Intégrative et Physiologie,
spécialité Biologie et Physiologie des Organismes) since 2010-2011.
Supervision of post-doc/PhD/Master:
PhD (x1)
Master (x1)
Administrative and scientific responsibilities:
1. André Picard Network: I am a local representative of this network, structuring the UPMC
developmental biology, since its inception in 2009.
2. OOV Conseil d’Administration: college B elected representative (2012-2016)
3. OOV Conseil d’Etablissement: college B elected representative (2012-2016)
4. OOV Conseil Des Enseignements: participation to the meetings aiming at implementing OOV
teaching (twice a year).
5. Scientific equipments: responsible for purchase and maintenance of molecular biology big
equipments pooled between the 2 OOV units.
Public diffusion:
Annual participation to the “fête de la science” (organisation and stand holding).
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
10/09/2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
12-09-2012
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de recherche ou cadre scientifique,
autres personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
(label et n°, intitulé, établissement principal,
responsable)
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : Stefania
Prénom : Castagnetti
Date de naissance : 11/07/1973
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
_
Corps-grade : CR1
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1)
Points forts des activités de recherche et résultats marquants :
Throughout my scientific career I have been interested in the role of the microtubule cytoskeleton during the cell
cycle. Lately my interest has focused mainly on the mechanism underlying chromosome segregation during mitosis and
its control by the spindle checkpoint. Historically, the genetically amenable fission yeast Schizosaccharomyces pombe,
has proven an ideal system to study cell cycle progression and so far I have used it as an elective model system for my
studies, taking advantage of its powerful genetics. Recently, I focused on the role of structural cellular components,
such as centrosomes and kinetochores in controlling mitotic progression and have identified a novel role for the SPB,
the yeast centrosome equivalent, in modulating spindle checkpoint response. I observed that SPB-kinetochore
interaction blocks spindle checkpoint signalling and is also necessary for maintenance of nuclear integrity. I am
currently dissecting the molecular basis of the SPB-kinetochore interaction and characterizing in more details the
phenotype of mutants causing SPB-kinetochore declustering. In collaboration with Professor Svetina at the University
of Ljubjliana, we are modelling yeast mitosis incorporating these observations, to generate a testable hypothesis. As
many mitotic regulators are localized on centrosomes, it is likely that the function we have uncovered in fission yeast
is conserved in metazoans. Given the pioneering work on mitosis carried out using the sea urchin embryo, I intend to
use Paracentrotus lividus as a metazoan system to complement the fission yeast studies, once my group will be
established.
My recent work also led to the identification of a nuclear division process, we called nuclear fission, which takes place
in the absence of spindle microtubules, but requires SPB-kinetochore association and actin. I suggested that nuclear
fission represents an ancestral mechanism for chromosome segregation, which predates spindle-based mitosis. Nuclear
tethering, at SPBs, or through simpler molecular anchors would have been central to this ancestral segregation.
Testing this hypothesis will be hard but would open new avenues to the way we think about evolution of mitosis. I
intend to follow up on this issue and carry out a comparative analysis of mitosis in unicellular organisms
(dynoflagellates, protists, amebae, algae) both at the cellular and molecular level.
So far my work has been supported by a Royal Society Dorothy Hodgkin fellowship (2006-2010) and by start-up funds
from the University of Exeter (2012-2013).
2) Production scientifique :
1) Sofueva S, Osman F, Lorenz A, Steinacher R, Castagnetti S, Ledesma J, Whitby MC. (2011) Ultrafine anaphase
bridges, broken DNA and illegitimate recombination induced by a replication fork barrier. Nucleic Acids Res.
39(15):6568-84
2) Castagnetti S., Oliferencko S. and Nurse P. (2010) Fission Yeast Cells Undergo Nuclear Division in the Absence of
Spindle Microtubules. PLoS Biol 8 (10)
3) Castagnetti S, Novák B, Nurse P. (2007) Microtubules offset growth site from the cell centre in fission yeast. J Cell
Sci. 120:2205-13
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
3)
Points forts des activités ne relevant pas de la production scientifique :
Invited presentations at conferences:
1. 5th international fission yeast meeting. (Tokyo, 2009)
Invited seminars and workshops:
1. Department of Biophysics (University of Ljubjliana/Slovenia 2012)
2. UCL (London/England, 2010).
3. Department of Biochemistry (Oxford University/UK, 2009).
4. Department of Pathology (Oxford University/UK, 2009),
5. Pombe club (CRUK, London/UK, 2008).
Teaching:
1. Currently lecturing a module on “cytoskeleton and human diseases” for 3rd year undergraduates at
University of Exeter and leading practical classes in cell biology for 1st year undergraduate at University
of Exeter.
Scientific evaluations:
1. Refereeing for research grants: BBSRC (x1)
Member of professor/lecturer selection juries:
Lecturer at University of Exeter since 2012
Administrative responsibilities:
Lecturer since 2012.
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
10/09/12
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
(label et n°, intitulé, établissement principal,
responsable)
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : CHENEVERT
Prénom : Janet
Date de naissance : 26/01/1963
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
†
Corps-grade :CR1
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1)
Points forts des activités de recherche et résultats marquants :
My research focuses on cell polarity and the spatial control of cell divisions, using primarily the early embryos of
ascidians. The ascidian egg is famous for its contribution to the discovery of mosaic development (Conklin 1905,
Gilbert 2010) and the local model Phallusia mammillata is highly favorable for studying cytoskeletal mechanisms
which generate polarity and establish axes (Sardet et al 2007). To complement our summaries of embryological and
molecular methods for ascidians (Sardet et al 2011; Paix et al 2011) I have recently submitted a paper detailing
protein biochemistry methods (Chenevert et al: “Biochemical purification of mitochondrial HSP60 and ATPsynthase
from ascidian eggs: Implications for antibody specificity”).
We have characterized the centrosome attracting body (CAB) which is a large cortical structure controlling
asymmetric divisions of the ascidian germ line. The CAB assembles under a membranous patch of polarity proteins
aPKC/PAR6/PAR3 and concentrates during mitosis (Patalano et al 2006). The CAB appears to have no influence over
spindles during interphase but at prometaphase it captures the nearest centrosome leading to unequal cleavage
(Prodon et al 2010). We are now trying to determine the molecular connection between the cell cycle machinery and
CAB components and function. ARC funding 2012-2014 “Regulation of oriented and asymmetric cell division by the
cell cycle machinery during embryonic development” Dumollard, McDougall, Pruliere, Chenevert.
We have recently found that during meiotic asymmetric divisions, the polarity kinase aPKC localizes to the meiotic
spindle and after fertilization migrates to the nearby cortex in a microtubule-dependent manner. Inhibitor treatment
and expression of dominant-negative constructs indicate that this dramatic change in aPKC localization controls
spindle rotation leading to polar body formation. Project funded by ARC 2012-2014, coordinator R Dumollard.
I have also collaborated with G Pruliere to examine the role of aPKC in the sea urchin embryo. In the swimming
blastula, aPKC forms a ring structure between the basal body and the axoneme where it controls the length and
activity of motile cilia (Pruliere et al 2011). During early embryonic divisions the kinase is associated with mitotic
spindles and enriched on apical membranes, but excluded from the vegetal cortex which forms micromeres. Inhibition
at this stage leads to defective multipolar spindles and failure of cell division.
We have begun functional studies on selected motor proteins in ascidians. We find that myosin 2 plays a role in
positioning of the first mitotic spindle with respect to localized mRNAs, but is dispensable for a flow of cytoplasmic
actin induced by fertilization. We are also collaborating with J Sobszak-Thepot (“Cell cycle and differentiation” UMR
7622 UPMC, Paris) to examine the mitotic functions of the kinesin MKLP2 and the kinase aPKC in both invertebrate and
mammalian systems. (Travel funding: Picard network exploratory mobility grant, coordinator J Chenevert, first visit
May 2012). With K Inaba (Shimoda Marine Station Japan) we are creating tools for determining the localization and
role of cytoplasmic dynein during cell polarizations and division. Funding PICS travel grant 2010-2012, “Structure and
function of the cortex and cytoskeleton of the ascidian egg and embryo : proteomic and imaging approaches”
coordinator C Sardet, visits in April 2010 and October 2012.
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
We have undertaken a comparative genomics analysis of the composition and expression of the motor protein families
(myosins, dyneins, kinesins) via an international network “Ascidian motor toolkit” composed of J Chenevert and G
Pruliere (Villefranche), bioinformatician M Kollmar (Gottingen Germany, Max Planck Institute) and microarray
specialist L Yamada (Sugashima Marine Station Japan, Nagoya University). Travel funding: EU Assemble grant for
preparation of samples at the Stazione Zoologica Anton Dohrn in Naples, visit Feb 2011; PICS travel grant for FranceJapan collaboration 2010-2012.
These projects were supported by the following
Research grants (coordinator C Sardet):
-ANR (JJ,PSDFWî
-AFM )URP(JJWR(PEU\Rî
-ARC &RUWLFDO51$VDQGSURWHLQVî
Travel grants :
-PICS CNRS (USA) collaboration on localized RNAs (2005-2007)
-PICS CNRS (Japan) collaboration on the Cortex (2010-2012)
-Assemble EU (Naples) on Motor protein gene expression, coordinator J Chenevert (2011)
-Picard UPMC (Paris) on Motor proteins and mitotic kinases, coordinator J Chenevert (2012)
2)
Production scientifique :
1)
2)
3)
4)
5)
6)
7)
8)
9)
3)
Sardet, C, Paix, A, Prodon, F, Dru P, and Chenevert, J. (2007). From oocyte to 16 cell stage: the cytoplasmic
and cortical reorganizations which pattern the ascidian embryo. Developmental Dynamics 236: 1716-31.
Paix A, Yamada L, Dru P, Lecordier H, Pruliere G, Chenevert J, Satoh N, Sardet C. (2009). Cortical anchorages
and cell type segregations of maternal postplasmic/PEM RNAs in ascidians. Developmental Biology 336:96111.
Prodon F, Chenevert J, Hébras C, Dumollard R, Faure E, Gonzalez-Garcia J, Nishida H, Sardet C, McDougall A.
(2010). Dual mechanism controls asymmetric spindle position in ascidian germ cell precursors. Development.
137:2011-21.
Paix A, Chenevert J, Sardet C. (2011). Localization and anchorage of maternal mRNAs to cortical structures
of ascidian eggs and embryos using high resolution in situ hybridization. Methods in Molecular Biology 714:4970.
McDougall A, Chenevert J, Lee KW, Hebras C, Dumollard R. (2011). Cell cycle in ascidian eggs and embryos.
Results and Problems in Cell Differentiation 53:153-69.
Sardet C, McDougall A, Yasuo H, Chenevert J, Pruliere G, Dumollard R, Hudson C, Hebras C, Le Nguyen N,
Paix A. (2011). Embryological methods in ascidians: the Villefranche-sur-Mer protocols. Methods in Molecular
Biology 770:365-400.
Pruliere G, Cosson J, Chevalier S, Sardet C, Chenevert J. (2011). Atypical protein kinase C controls sea urchin
ciliogenesis. Molecular Biology of the Cell 22:2042-3.
McDougall A, Chenevert J, and Dumollard R. (2012). Cell cycle control in oocytes and during early embryonic
cleavage cycles in ascidians. International Review of Cell and Molecular Biology 297: 235-264.
Database creation www.mtocdb.org/(2011). Annotation of Ciona centriole micrographs and translation of key
literature from French for “Microtubule Organizing Center Database” which aims to trace the evolutionary
organization, composition, and function of the centrosome using all species for which the genome is known.
Points forts des activités ne relevant pas de la production scientifique :
Invited seminars and workshops:
1. International Tunicate Database meeting (Nice, 2010)
2. EFOR meeting (Paris, 2011)
3. EFOR meeting (Paris, 2012)
Teaching:
1. Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology
course at Villefranche-sur-Mer.
2. Coordination of demonstrations for visiting Masters “Morphology and Evolution of Animals” Philipps
University of Marburg Germany
Co-supervision of post-doc/PhD/master:
3 student interns
2 technicians
2 PhD students
1 post-doc
Scientific evaluations:
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
1. Refereeing for journals: Current Biology (x1), Molecular Biology of the Cell (x1), Developmental Biology
(x2)
2. member Editorial board, journal “Invertebrate Reproduction and Development”
Member of professor/lecturer selection jury:
Jurist for Maitre de conference/lecturer position for University Aix-Marseille/IBDML poste 4020 (2012)
Administrative responsibilities:
1. Assistant teamleader Biomarcell group with Christian Sardet since 2007
2. Communication liason: coordinate outreach activities and media presentations: represent UMR7009
in OOV public relations committee
3. Elected member Conseil d’Administration OOV, college B 2009-2010
Organisation of conferences/workshops:
1. Fourth International Tunicate Meeting, local organizing committee (St Jean Cap Ferrat, June 2007)
2. International Tunicate Database meeting, co-organizer of Protein session (Nice, November 2010)
3. EFOR meeting, co-organizer of Tunicate session (Paris, January 2012)
Public science education diffusions:
1. Communication liason, coordinate outreach activities and media presentations
2. Create stands and demonstrations for the general public (“ Fete de la Science” 1 week, “Celebration
125 ans de l'OOV”, “ Portes ouvertes de la Darse”, “Journée de la Mer” etc
3. Conduct tours for local and international schools (www.isn-nice.com)
4. Give presentations of our research to schools, politicians and the press (radio, tv, newspaper)
5. Organize “Bain en Entreprise” 1 week internships for middle school level students
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
10/09/12
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
10/09/12
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
4
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres personnels
ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal, responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : Copley
Prénom : Richard
Date de naissance : 25/11/1970
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
†
Corps-grade :
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1) Points forts des activités de recherche et résultats marquants :
My expertise is in the application of computational methods to study proteins and genomes, with a main focus on the
evolution of the animals. The overall goal is to understand the evolution of the animals in terms of evolving genome
content.
In the last few years, I have been deeply involved in the application of Next Generation Sequencing methods to de
novo sequence animal genomes and transcriptomes, and, in a more applied manner, the study of population level
variation and its relation to organismal phenotypes (pathogenic phenotypes in humans).
Continuing a long-standing collaboration with Max Telford (University College London), we have sequenced the
genome of Xenoturbella bocki, These data were instrumental in identifying miRNAs that supported the case that
Xenoturbella is a deuterostome (Phillippe et al, Nature 2011). Analysis of the Xenoturbella data is ongoing (in
collaboration with Albert Poustka, Berlin). We are applying methods developed by my D.Phil student Yang Li to
improve the quality of protein predictions on fragmentary genome assemblies (manuscript submitted), identify
orthologous genes and molecular synapomorphies of deuterostomes. I am also collaborating with Adam ClaridgeChang (Singapore) on genome sequence of the hydrothermal vent worm Paralvinella sulfincola, and am a member of
the international Priapulus caudatus genome sequencing project. A goal of all my genome analyses is to understand
the extent of functional shifts within orthologous protein-coding genes, as evidenced by the gain and loss of proteinprotein interaction motifs, in order to understand the evolution of protein interaction networks.
A second major area of research activity has involved the analysis of conservation of transcription factor binding sites
regulating gene expression (refs. 5,7,12). With collaborators I have shown that strong transcription factor binding
sites are more likely to be evolutionarily conserved, and genes regulated by particular transcription factors be
associated with more binding sites, whatever the level of binding site conservation (ref. 12). These results (and those
of many others) demonstrate that cross-species comparisons of binding site conservation are likely to yield functional
insights into the conservation of developmental regulatory pathways. Integrating my studies of genome protein
coding content and regulatory sequence evolution over large (i.e. inter-phylum) evolutionary distances will be a major
future direction.
2)
Production scientifique :
1. Shanks ME, Downes SM, Copley RR, Lise S, Broxholme J, Hudspith KAZ, Kwasniewska A, Davies WIL, Hankins
MW, Packham E, Clouston P, Seller A, Wilkie AOM, Taylor JC, Ragoussis J, Nemeth AH (2012) Eur. J.
Hum. Genet. in press. Next Generation Sequencing (NGS) as a diagnostic tool for retinal degeneration
reveals a much higher detection rate in early onset disease
2. Davies IL, Downes SM, Fu JK, Shanks ME, Copley RR, Lise S, Ramsden S, Black GCM, Gibson K, Foster RG,
Hankins MW, Nemeth AH. (2012) Genet. Med., in press, Next Generation Sequencing (NGS) in healthcare
delivery: lessons from the functional analysis of rhodopsin
3. Telford MJ and Copley RR, (2011) Trends Genet 27:186-95, Improving animal phylogeneis with genomic data.
4. Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ.
(2011) Nature 470:255-8. Acoelomorph flatworms are deuterostomes related to Xenoturbella.
5. Goh FG, Thomson SJP, Krausgruber T, Lanfrancoti A, Copley RR, Udalova IA (2010) Blood, 116:5580-8. Beyond
the enhanceosome: cluster of novel NB sites downstream of the human IFN-E is essential for LPS-induced
gene activation.
6. Taylor JM, Street TL, Hao L, Copley R, Taylor MS, Hayden PJ, Stolper G, Mott R, Hein J, Moffatt MF, Cookson
WO. (2009) PLoS One. 4:e7651. Dynamic and physical clustering of gene expression during epidermal
barrier formation in differentiating keratinocytes.
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
7.
8.
9.
10.
11.
12.
13.
3)
Mole DR, Blancher C, Copley RR, Pollard P, Gleadle JM, Ragoussis J, Ratcliffe PJ (2009) J Biol Chem 284:1676716775 Genome-wide chromatin-immunoprecipitation by the HIF-1a and HIF-2a transcription factors and
its correlation with gene regulation
Johannesson M, Lopez-Aumatell R, Diez M, Tuncel J, Blazquez G, Martinez E, Canete A, Vicens-Costa E,
Graham D, Copley RR, Hernandez-Pliego P, Beyeen A, Stridh P, Ockinger J, Fernandez C, Percio S. Gulko
PS, Brenner M, Tobena A, Guitart-Masip M, Gimenez-Llort L, Dominiczak A, Holmdahl R, Gauguier D,
Olsson T, Mott R, Valdar W, Redei E, Fernandez-Teruel A, and Flint J (2009) Genome Res 19:150-158. A
resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: The NIH
heterogeneous stock
Juliusdottir T, Pettersson F, Copley RR (2008) Bioinformatics 24:2778-2779 POPE - a tool to aid highthroughput phylogenetic analysis.
Copley RR. (2008) Phil Trans Roy Soc B 363:1453-1461 The animal in the genome: comparative genomics and
evolution.
Fullerton JM, Willis-Owen SA, Shifman S, Copley RR, Miller SR, Bhomra A, Davidson S, Oliver PL, Mott R, Flint
J. (2008) Biol Psychiatry 63:874-883 Human-Mouse Quantitative Trait Locus Concordance and the
Dissection of a Human Neuroticism Locus.
Copley RR, Totrov M, Linnell J, Field S, Ragoussis J, Udalova IA (2007) Genome Res, 17:1327-1335. Functional
conservation of Rel binding sites in drosophilid genomes,
Hull J, Campino S, Rowlands K, M-S, Copley RR, Taylor MS, Rockett K, Elvidge G, Keating B, Knight J,
Kwiatkowski D. (2007) PLoS Genet 3:e99. Identification of common genetic variation which modulates
alternative splicing.
Points forts des activités ne relevant pas de la production scientifique :
Invited seminars and workshops:
1.
2.
3.
4.
5.
6.
7.
EMBRC International Workshop on Marine E-Infrastructure, “Large scale sequencing to better
understand animal evolution”, 29 March 2012
The Natural History Museum, London, “Using genomes to understand animal evolution, with examples
from next gen sequencing of Xenoturbella”, 22 May 2011
University of Oxford, Zoology Dept. Evo-Devo Meeting, “The Ancestry and Evolution of Developmental
Genes”, 8th May 2009
University of Bristol, UK, “The evolution of animal proteins”, 16th March, 2009.
University of Birmingham, UK, “The Animal in the Genome: Comparative Genomics and Evolution”,
30th October 2008
The Natural History Museum, London, Museomics meeting, “Phylogenomics and the handling of large
datasets”, 29th February 2008.
Novartis Foundation Symposium on Animal Evolution, London, “The Animal in the Genome:
Comparative Genomics and Evolution”, 20th June 2007
Teaching:
1.
Sequence analysis course for Oxford Doctoral Training Centre (D.Phil.) students 2010/2011
2.
EMBO practical course. ‘Molecular approaches to Evolution and Development’, Kristineberg Marine
Station, Sweden 29th June – 11th July, 2008
Supervision of post-doc/PhD/master:
PhD (x2)
Summer student projects (x2)
Scientific evaluations:
1. Refereeing for journals: including Nature, Genome Research etc.
2. Refereeing for research grants: MRC Biomedical Informatics Training and Career Development Panel,
2009 onging; MRC Doctoral Training Grant Panel, 2011
Member of PhD steering committees:
1. Felix Bemm (ongoing, Jörg Schultz group, Würzburg, Germany)
Member of PhD examination juries:
1. Thomas Butts (University of Oxford, David Ferrier/Peter Holland, 2009
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
10/09/12
Signature :
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
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Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie
de la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour
attester l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule
unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement
destinées à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal,
responsable)
(intitulé, établissement support, responsable)
UMR7009 Biologie du Développement CNRS UPMC
Evelyn Houliston
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV) CNRS UPMC
Evelyn Houliston
Nom : Croce
Prénom : Jenifer
Date de naissance : 05/08/1977
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
CR2
_
Thèse soutenue _
HDR
†
Corps-grade :
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : CNRS New Section 22
1)
Points forts des activités de recherche et résultats marquants :
After a post-doc at Duke University (Durham, NC, USA) in the laboratory of Dr. David McClay, I joined the CNRS
unit UMR7009 in 2009 in the team named “Régionalisation et Morphogénèse de l’embryon d’oursin” and
directed by Dr. Christian Gache. My main research activity between 2009 and 2012 has been first to achieve
some of the work started during my post-doc and second to launch new projects that I wanted to develop in
the lab. Therefore my three main results over the 2009-2012 period concern (1) a post-doctoral study realized
in Dr. McClay’s lab, (2) a collaborative work carried out between Dr. McClay’s and Dr. Gache’s laboratories,
and (3) a project that I developed in Dr. Gache’s lab before and after he retired in August 2010.
1. Delta/Notch dynamics. During this study I characterized at a molecular level the segregation of the
endoderm and non-skeletogenic mesoderm identities over the course of the sea urchin embryogenesis
performing a careful analysis of the expression patterns of three key genes of these identities with a cellular
resolution both in time and space.
2. Wnt6. Through the combination of microsurgeries and microinjections I determined over this analysis the
presence at the vegetal cortex of the sea urchin egg of maternal determinants required for the development of
all the vegetal tissues. I established also the key role of canonical Wnt signaling and the Wnt6 ligand in all or
part of this process.
3. Frizzled7. In this project Guy Lhomond (IE1, CNRS) and I have identified Frizzled7 as the membrane receptor
of the Wnt6 ligand. We showed that this couple is responsible for the activation of the canonical Wnt pathway
at the onset of sea urchin embryogenesis and that its action is necessary for endoderm specification.
In parallel of these three main projects, which have all been published in the peer-reviewed journal
Development, I have also initiated three additional studies in the lab carried out by Guy Lhomond, myself and
a couple of master and BTS students that I have supervised : (i) role of Frizzled9 in the specification of the sea
urchin vegetal tissues, (ii) conjoint or separate involvement of the Delta/Notch pathway and canonical Wnt
signaling in the specification of the vegetal tissues, and (iii) spatiotemporal dynamics of the endoderm and
non-skeletogenic mesoderm gene regulatory circuits during Paracentrotus lividus embryogenesis.
i. Frizzled9. Our preliminary data show that Frizzled9 is controlling the activation of canonical Wnt signaling
starting 9 hours post-fertilization, thereby after the action of Frizzled7, and that its action is required for the
maintenance of both endoderm and non-skeletogenic mesoderm gene expression. We are currently
investigating in more depth the link between these two phenomena and researching the Wnt ligand(s) that
initiate Frizzled9 signaling.
Vague D : campagne d’évaluation 2012-2013
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
ii. Delta/Notch vs. canonical Wnt. Over the course of the sea urchin embryogenesis Delta (the ligand of the
'HOWD1RWFKSDWKZD\DQGş-catenin (the main nuclear effector of canonical Wnt signaling) are detected first
in the precursors of the skeletogenic mesoderm (the micromeres) and then in the common progenitors of the
endoderm and the non-skeletogenic mesoderm (the macromeres). Through the combination of microsurgeries
and microinjections we have identified that in the micromeres canonical Wnt signaling is required for the
development of the adjacent non-skeletogenic mesoderm lineage but solely through the control of the
expression of Delta in the former cells, whereas in the macromeres it appears required in parallel to the
presence of the Delta ligand for the specification of that same lineage. This ongoing work involved the
participation of Dr. David McClay (Duke University, Durham, NC, USA) who did and will teach me how to
perform microsurgeries on sea urchin embryos.
iii. Spatiotemporal dynamics. After studying the spatiotemporal dynamics of three key genes of the endoderm
and the non-skeletogenic mesoderm lineages throughout Lytechinus variegatus embryogenesis during my postdoc, I realized how important it is to reposition molecular knowledge in the context of the embryo with a
cellular resolution both in time and space. For this reason I have begun a collaborative work with Dr. Nadine
Peyrieras (Gif-sur-Yvette, CNRS, UPR3294) which aims to determine the spatiotemporal dynamics of about 10
endoderm and non-skeletogenic mesoderm genes from the 60-cell stage to the onset of gastrulation. That work
has been started and our preliminary data provides the first cues about the segregation of the endoderm and
the non-skeletogenic mesoderm lineages in Paracentrotus lividus, which seems to occur differently than in L.
variegatus.
Former and current projects were supported by the following research grants : ARC (2007-2009)
coordinated by Christian Gache and Emergence-UPMC program (2009-2010) coordinated by Jenifer Croce.
2)
Production scientifique :
Before joining the UMR7009 (2007-2008)
1. Croce, J. C., McClay, D. R., 2008. Evolution of the Wnt pathways. Methods Mol Biol. 469, 3-18. [On
invitation]
Since joining the UMR7009 (2009-2012)
1. Croce JC and McClay DR (2010) Dynamics of the Delta/Notch Signaling on Endomesoderm
Segregation in the Sea Urchin Embryo. Development 137(1): 83-91. [Editorial comment]
2. Croce JC, Range R, Wu SY, Miranda E, Lhomond G, Peng CF, Lepage T and McClay DR (2011).
Wnt 6 activates endoderm in the sea urchin gene regulatory network. Development 138(15), 32973306. [Editorial comment]
3. /KRPRQG * 0F&OD\ '5 *DFKH & DQG &URFH -& )UL]]OHG VLJQDOLQJ GLUHFWV şcatenin nuclearisation and initiates endoderm specification in macromeres during sea urchin
embryogenesis. Development 139(4):816-25. [Exposed in cover]
4. Croce, JC and Holstein TW (book chapter in preparation). The evolution of Wnt signaling in Wnt
signaling in Development and Disease: Molecular Mechanisms and Biological Functions (Wiley
publisher). [On invitation]
3)
Points forts des activités ne relevant pas de la production scientifique :
Invited presentations at conferences:
1. Invitation at Imperial College London (London, 2008)
2. Invitation at University of Chicago (Chicago, 2008)
3. The XVIIIth Sea Urchin meeting (Woods Hole, 2008)
4. The XIXth Sea Urchin meeting (Woods Hole, 2009)
5. The XXth Sea Urchin meeting (Woods Hole, 2011)
Invited seminars and workshops:
1. Journées André Picard (Paris, 2012).
2. EFOR meeting (Paris, 2012).
Scientific evaluations:
1. Refereeing for journals: Development (x2), Mech. Dev. (x2), Dev. Biol. (x2), CMLS (x1)
2. Refereeing for research grants: United States-Israel Binational Science Foundation (x1),
Emergence-UPMC (x1)
3. Refereeing as an external expert for the Assemble Remote Access Calls (x12)
Vague D : campagne d’évaluation 2012-2013
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Member of lecturer selection juries:
Lecturer position at Université Paul Sabatier (Toulouse, 2012)
Lecturer position at IBV (Nice, 2012)
Administrative responsibilities:
1. Group leader (2010-2013)
2. Vice-president of the “conseil scientifique” of the Observatoire Océanologique de Villefranchesur-Mer (since 2010)
3. Member of the bureau of the André Picard scientific network (since 2010)
4. Responsible of the annual evaluation of the engineer working in the group (since 2010)
Organizing conferences/workshops:
In organizing committee of “The Developmental Biology of the Sea Urchin XIX” meeting (2009)
Teaching:
1. Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology
course at Villefranche-sur-Mer.
2. Teaching assistant at the summer embryology course in Woods Hole, MA, USA (in 2009 and 2010).
Supervision of post-doc/PhD/master/BTS:
Master (x3)
BTS (x4)
Public diffusion:
Annual participation in Open Days.
Annual tutoring in the laboratory of college and secondary school students.
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date : 9-9-2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
10th September 2012
Vague D : campagne d’évaluation 2012-2013
Février 2012
Signature :
4
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres personnels
ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
(intitulé, établissement support, responsable)
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom :DUMOLLARDl
Prénom :Rémi
Date de naissance :22/08/1974
Courriel :[email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
†
Corps-grade : CR1
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
DR20
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_
3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : Commission 22 CNRS
1)
Points forts des activités de recherche et résultats marquants :
Since 2007 I have been working on metabolism of mouse eggs in collaboration and on ascidian development in
Villefranche
Work on mouse oocytes
I have been studying the activity of mitochondria in ascidian and mammalian eggs and early embryos for
some years (see Dumollard et al., 2003; 2004a, 2004b, 2006, 2007a, 2007b, in collaboration with Prof John Carroll and
Prof Michael Duchen from University College London and with Prof Karl Swann from Cardiff University) and I have
maintained a collaboration only with Prof Karl Swann from Cardiff University (funded by an ACS CNRS/Royal Society
grant for 2008 and 2009) and Elisabeth Christians (CIC Toulouse). My collaboration with Karl Swann led to 3 papers
(Dumollard et al., 2008 and 2009; Yu et al., 2010). My collaboration with Elisabeth Christians led to the publication of
one paper in 2010 (see Bierkamp et al 2010).
I am now working on these topics only in collaboration, as a consultant.
Work in Villefranche
Understanding how cell cycle mechanisms have been adapted to carry out specific tasks related to reproductive
biology and developmental biology.
Specific Aims
1. Cell cycle control during the meiotic cell cycle
We are interested in how the meiotic cell cycle of oocytes has become specialized so that chromosomes segregate
twice: first during meiosis I then again during meiosis II
Identification of the mechanism controlling the egg-to-embryo transition
We discovered that preventing the inactivation of the Mos/ MAPK pathway prevented the egg-to-embryo transition
and in doing so extended the duration of meiosis such that fertilized eggs extruded up to five polar bodies rather than
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
just two (Dumollard et al., 2011). Our working model is that, in the ascidian, the number of rounds of meiosis is
limited to precisely two by the duration of activity of the Mos/MAPK pathway. We also discovered that by maintaining
the Mos/MAPK pathway active that sperm-triggered calcium oscillations persisted indefinitely. Previously we had
shown that maintaining MPF active also prevents cessation of the sperm-triggered calcium oscillations (Levasseur and
McDougall, 2000). Our working model is that a positive negative feedback cycle exists such that MPF and MAPK
activities provide positive feedback maintaining the calcium oscillations and that the calcium increases provide
negative feedback by favoring the loss of both MPF and MAPK activities, thus ensuring that the calcium oscillations
stop at the appropriate time (when both MPF and MAPK activities fall to basal levels at meiotic exit).
2. Cell cycle control during development in ascidian embryos
We are interested in how the cell cycle has been co-opted by developmental mechanisms to generate embryo
morphology. In ascidians as in other embryos the cell cycle is remodeled in two ways. 1) Spindles are re-oriented so
that blastomeres divide in specific directions or to give cells that differ in size (unequal cleavage), and 2) cell cycle is
remodeled leading to the establishment of cell cycle asynchrony which in the ascidian embryo begins at the 16-22 cell
stage. These two phenomena, together with cell adhesion, are the only mechanisms used to create the distinctive
form of the 112 cell gastrula in ascidians since no cell displacement occurs up to the gastrula stage. In addition to cell
cycle asynchrony, the orientation of every cell division plane is predictable in ascidian embryos up to the gastrula
stage (this underlies the fate map). The ascidian model is therefore well-adapted to understand how core cell cycledependent phenomena such as spindle re-orientation and cell cycle duration are controlled during development in a
chordate embryo. We initially focused on the process of unequal cleavage that generates small two germ cell
precursors at the 64 cell stage, and discovered a mechanism that causes the spindle to position asymmetrically near
the cortex during prometaphase (Prodon et al., 2010). Our more recent unpublished observations reveal that spindles
re-orient during embryonic development in the ascidian embryo at precise developmental stages (notably at the 32
cell stage). This work is in preparation. We also addressed how cell cycle asynchrony is established in ascidian
embryos. Briefly, cell cycle asynchrony first occurs at the 16 cell stage and then again at the 64 cell stage leading to
the formation of a 76 cell stage and 112 cell stage embryo. Our data will show how S phase length is controlled by
signaling pathways activated at the 16 and 64 cell stages.
2)
1)
Production scientifique :
Dumollard R, Duchen M. and Carroll J. (2007a). The role of mitochondrial function in the oocyte and embryo.
Curr. Top. Dev. Biol. 2007;77:21-49
2)
Dumollard R, Ward Z, Carroll J. and Duchen M. (2007b). Regulation of redox metabolism in the mouse oocyte
and early embryo. Development 134(3):455-65.
3)
Dumollard R, Campbell K, Halet G, Carroll J, and Swann K. (2008). Regulation of cytosolic and mitochondrial
ATP levels in mouse eggs and zygotes. Developmental Biology.;316(2):431-40.
4)
Dumollard R, Carroll J, Duchen MR, Campbell K, Swann K. (2009) Mitochondrial function and redox state in
mammalian embryos. Semin Cell Dev Biol.;20(3):346-53.
5)
Bierkamp C, Luxey M, Metchat A, Audouard C, Dumollard R, Christians E. (2010) Lack of maternal Heat Shock
Factor 1 results in multiple cellular and developmental defects, including mitochondrial damage and altered
redox homeostasis, and leads to reduced survival of mammalian oocytes and embryos. Dev Biol. Mar
15;339(2):338-53.
6)
Prodon F, Chenevert J, Hébras C, Dumollard R, Faure E, Gonzalez-Garcia J, Nishida H, Sardet C, McDougall A.
(2010) Dual mechanism controls asymmetric spindle position in ascidian germ cell precursors. Development.
Jun;137(12):2011-21
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
7)
Yu Y, Dumollard R, Rossbach A, Lai FA, Swann K. (2010) Redistribution of mitochondria leads to bursts of ATP
production during spontaneous mouse oocyte maturation. J Cell Physiol. Sep;224(3):672-80.
8)
Dumollard R, Levasseur M, Hebras C, Huitorel P, Carroll M, Chambon JP, McDougall A. (2011) Mos limits the
number of meiotic divisions in urochordate eggs. Development. Mar;138(5):885-95
9)
McDougall A, Chenevert J, Lee KW, Hebras C, Dumollard R. (2011) Cell cycle in ascidian eggs and embryos.
Results Probl Cell Differ. ;53:153-69.
10) Sardet C, McDougall A, Yasuo H, Chenevert J, Pruliere G, Dumollard R, Hudson C, Hebras C, Le Nguyen N, Paix
A. (2011) Embryological methods in ascidians: the Villefranche-sur-Mer protocols. Methods Mol Biol. ;770:365400.
11) McDougall, A., Chenevert, J. and Dumollard, R. (2012). Cell Cycle Control in Oocytes and during Embryonic
Cleavage Cycles in Ascidians. Int Rev Cell Mol Biol. 297, 237-266.
12) Collado-Fernandez E, Picton HM, and Dumollard, R. (2012). Metabolism throughout follicle and oocyte
development in mammals. Int. J. Dev. Biol. (in press)
3)
Points forts des activités ne relevant pas de la production scientifique :
Conference/Workshop Organization:
1. Co-organizer. 2007 International Tunicate Meeting. Villefranche/Cap Ferrat, France.
2. Co-organizer. 2010 International Marine Organism Microscopy Workshop , Villefranche, France.
Invited presentations at conferences:
1. Bi-annual Tunicate meetings (Montreal 2011).
Invited seminars and workshops:
1. International meeting 2008. Conférence Jacques Monod in Roscoff, France. Speaker
2. International workshop.2010. ESF theme school. Heidelberg, Germany.. Speaker & Session Chair
3. International workshop 2010. “Mitochondria and Reproduction”– IBIR, Bulgarian Academy of Science,
Sofia, Bulgaria. Speaker & Session Chair.
4. International meeting 2010. SSIF Annual Conference. Istanbul, Turkey. Speaker.
5. International meeting 2011; 1st Meeting of the Ovarian Club, Barcelona,Spain. Speaker.
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
11/09/2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
11/09/2012
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
4
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
ingénieurs de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie
de la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour
attester l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule
unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement
destinées à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal,
responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : HOULISTON
Prénom : Evelyn
Date de naissance : 12/01/1963
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Thèse soutenue †
HDR
†
Corps-grade :
_
Thèse soutenue _
HDR
_
Corps-grade:
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Enseignant-chercheur
†
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
DR1
Ingénieur
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière : Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : CNRS section26
1) Points forts des activités de recherche et résultats marquants :
Most significant scientific contributions, achieved together with other members of the ‘Maternal Determinants’
group:
-
Establishment of a new experimental model species for cellular and molecular studies in developmental
biology and evolution : the cnidarian Clytia hemisphaerica (see refs 9,10)
-
Demonstration that maternal mRNAs coding for Wnt pathway regulators become differentially localised
during oogenesis and oocyte maturation in Clytia, and are responsible for setting up embryonic polarity.
(refs 1 -3)
-
Demonstration that the kinase Mos is an animal innovation regulating specific aspects of oocyte meiotic
divisions, notably polar body formation and egg cytostatic arrest. (ref. 4)
-
Contribution to a highly-cited collaborative international study of the phylogenetic relationships
between the metazoan animal groups (ref. 5)
-
Discovery through bioinformatics analyses that Clyia mRNAS often contain trans-spiced 5’ leaders, and
that this type of mRNA modification probably evolved convergently many times during eukaryote
evolution (ref. 8)
-
Demonstration that Clytia has localised germ plasm that is inherited by a multipotent stem cell
population (i-cells) in the embryo, but that i-cells can form in the absence of this germ plasm. This
unexpected finding fuels reconsideration of the relationship between germ plasm, germ line and stem
cells (ref. 15)
-
Contribution to a collaborative international study of showing convergent evolution of striated muscle in
bilaterians and cnidarians, published in Nature (ref. 16)
-
Characterisation of Planar Cell Polarity development in the Clytia larva, and demonstration that it is
regulated by the Fz-PCP pathway through a highly conserved role for a Clytia Strabismus gene (ref 17).
2)
Production scientifique :
Publications :
1. Momose, T. and Houliston, E. (2007) Two Oppositely Localised Frizzled RNAs as Axis Determinants in a
Cnidarian Embryo PloS Biology 5(4), e70
2. Momose, T., Derelle, R. and Houliston, E. (2008) A maternally localised Wnt ligand required for axial
patterning in the cnidarian Clytia hemisphærica. Development 135 2105-2113.
3. Amiel, A. and Houliston, E. (2009) Three distinct RNA localization mechanisms contribute to oocyte
polarity establishment in the cnidarian Clytia hemisphærica. Dev. Biol 327, 191-203.
Vague D : campagne d’évaluation 2012-2013
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
Amiel, A., Leclère, L., Robert, L., Chevalier, S. and Houliston, E. (2009) Conserved functions for Mos
in eumetazoan oocyte maturation revealed by studies in a cnidarian. Curr. Biol. 19, 305-311.
Philippe, H., Derelle, R., Lopez,P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Deniel, E,
Houliston, E. Quéinnec, E., Da Silva, C., Wincker, P., Le Guyader, H., Leys, S., Jackson, D.J.,
Degnan, B.M., Schreiber, F., Erpenbeck, D., Morgenstern, B., Wörheide, G. and Manuel, M. (2009)
Phylogenomics restores traditional views on deep animal relationships. Curr. Biol. 19, 706-12
Git, A., Allison, R., Perdiguero, E., Nebreda, A.R., Houliston, E. and Standart, N. (2009) Vg1RBP
phosphorylation by Erk2 MAP kinase correlates with the cortical release of Vg1 mRNA during meiotic
maturation of Xenopus oocytes. RNA 15, 1121-33
Lapébie, P., Gazave, E., Ereskovsky, A., Derelle, R., Bézac, C., Renard, E., Houliston, E. &
Borchiellini, C. (2009). WNT/ß-catenin signalling and epithelial patterning in the homoscleromorph
sponge Oscarella. PLoS One 4, e5823.
Derelle, R. Momose, T., Manuel, M. Winker P., Da Silva C. and Houliston, E. (2010) Evolution of spliced
leaders in Meatazoa : insights from ctenophores and Hydrozoa. RNA 16 696–707
Amiel, A., Chang, P., Momose, T. and Houliston, E. (2010) "Clytia hemisphaerica: A cnidarian model
for studying oogenesis" In “The Universal Process of Oogenesis” ed M.-H. Verlhac. Wiley. In press
Houliston, E., Momose, T. and Manuel, M. (2010) Clytia hemispherica : A jellyfish cousin joins the
laboratory. Trends in Genetics. 26 , 159-167
Forêt, S., Knack, B., Houliston, E., Momose, T., Manuel, M., Queinnec, E., Hayward, DC., Ball, E.E.
and Miller, D.J. (2010) New tricks with old genes: The genetic bases of novel cnidarian traits. Trends
in Genetics. 26 , 154-158
Fourrage C, Chevalier S, and Houliston E. (2010) A highly conserved Poc1 protein characterized in
embryos of the hydrozoan Clytia hemisphaerica: localization and functional studies. PLoS One.
5(11):e13994.
Lapébie P, Borchiellini C, Houliston E. (2011) Dissecting the PCP pathway: one or more pathways?:
Does a separate Wnt-Fz-Rho pathway drive morphogenesis? Bioessays 33, 759-68.
Gaffré M, Martoriati A, Belhachemi N, Chambon JP, Houliston E, Jessus C, Karaiskou A. (2011) A
critical balance between Cyclin B synthesis and Myt1 activity controls meiosis entry in Xenopus
oocytes. Development. 138, 3735-44.
Leclère , L., Jager, M., Barreau, C., Chang, P.. Le Guyader, H., Manuel, M and Houliston, E. (2012)
Maternally localized germ plasm mRNAs and germ cell/stem cell formation in the cnidarian Clytia. Dev
Biol, 364, 236–248
Steinmetz, P.R.H., Kraus, J.E.M. Larroux, C., Hammel, J.U., Amon-Hassenzahl, A., Houliston, E.,
Wörheide,G., Nickel, M., Degnan, B.M. & Technau, U (2012) Independent evolution of striated muscle
in cnidarians and bilaterians. Nature 487, 231-234.
Momose, T., Kraus, Y. & Houliston, E. (2012) A highly conserved function for Strabismus in
establishing planar cell polarity in the ciliated ectoderm during larval development in the cnidarian
Clytia hemisphaerica. Development. In press
3) Points forts des activités ne relevant pas de la production scientifique :
Main Invitations to speak at International conferences:
2007
FASEB/ EMBO workshop on RNA localisation (La Ciocca, Italie)
2009
Treilles foundation symposium (Tourtour): Meiotic divisions in Oocytes
2009
FASEB/ EMBO workshop on RNA localisation (Virginia, USA)
2010
Euro-EvoDevo 2010 (Paris)
2011
Treilles foundation symposium (Tourtour): Future of EvoDevo
2012
The 9th Okazaki Biology Conference "Marine Biology II (Okasaki/ Okinawa, Japan)
2013
Gordon conference on Fertilisation and the activation of Development (New Hampshire, USA)
Teaching :
Yearly Participation in teaching the UPMC Masters level (BMC programme) Developmental Biology course at
Villefranche
2008- 2010: 2hr Presentation in the UPMC Masters level (BMC programme) Developmental Biology in Paris
2010 2hr Presentation in a graduate school programme in the University of Vienna programme de formation de
2011 : Presentation and discussion session (4h) in a graduate school programme Lausanne
Graduate student supervision :
2004-8 : Aldine AMIEL (PhD Université Pierre et Marie Curie)
2006-10 : Cécile FOURRAGE (PhD Université Pierre et Marie Curie)
2011- present Antonella RUGGIERO (PhD Université Pierre et Marie Curie- co-supervision)
Post-doc supervision :
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
2006-08 : Romain DERELLE
2008- present : Pascal LAPEBIE
Scientific Evaluations :
Regular refereeing for journals ( Development, Dev. Biol., Int . J. Dev Biol., J. Cell Science…), and research
grants (ANR, Wellcome, Fondation, Suisses and German science foundations, UPMC..)
Member of PhD/HDR examination juries for Michael Saina, SARs Institute, Bergen, Norway (2008) .Manon
Quiquand, University of Geneva, Swizerland (2009); Eve Corot -Morel, Université Pierre et Marie Curie, Paris
(2012).
Administrative Responsabilities
Director of the “maternal determinant” group since 2005.
Director of the UMR 7009 “Biologie du Développement” since January 2009.
Participation as UMR7009 director in numerous OOV committees and working groups (Conseil D’Administration,
Comité de Direction, Conseil D’Etablissement, Conseil Scientifique, Library Commission, Health and Safety
Commission ; Teaching council; Consultation groups on renovation work, sea water pumping aquarium
installations….
2009-2010: Scientific Coordinator of the Clytia hemisphaerica full Genome sequencing and annotation project
in partnership with the Genoscope (collaboration with M. Manuel ‘s group , UMR 7138, UPMC Jussieu)
2009-2011 Major actor for the OOV in the preparation of the ESFRI European Infrastructure project EMBRC”
(European Marine Biology Ressource Center), federating 12 marine stations across Europe. Currently in the
“Preparatory Phase”. OOV contact for Work Packages 2 (Scientific Activity), 3 (e-infrastructure ) and 10
(stakeholders) .
2010-2011 Major participant for the OOV in the preparation of the “EMBRC-Fr” Grande Emprunt Infrastructure
project, federating the 3 UPMC marine stations. Financed (16 M€ TOTAL, 2012-2020) and currently being
implemented
2009 and 2010: Coordination of the ”DEVONET “‘Labex” project involving 9 Laboratory and private partners
from the 3 UPMC Marines stations, The Jussieu campus, Université Paris IV and the Musée National de Histoire
Naturelle.
2010: President of a CNRS selection commitee for recruitment of an ‘Ingénieur de Recherche” at the Roscoff
Biological Station.
Public diffusion
Annual Participation in the ‘Fête de la Science » at the OOV.
Many interviews for TV and written media, including participation in a Documentary on Plankton made for
ARTE by Jean-Yves Collet.
Regular presentation of the laboratories’ activities to representatives of local and National political and
strategic bodies (Regional Council, Departmental Council, ‘Pole Mer PACA”, European Commission …)
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date : 12th September 2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
12th September 2012
Signature :
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres personnels
ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
(label et n°, intitulé, établissement principal, responsable)
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : HUDSON
Prénom : CLARE
Date de naissance : 21/02/1973
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance :
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
†
Corps-grade : CR1
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1)
Points forts des activités de recherche et résultats marquants :
In the laboratory of Hitoyoshi YASUO, we are studying how embryonic precursors are specified during development.
We chose to study the embryos of the invertebrate chordate, Ciona intestinalis because they develop with a fixed
cell-cleavage, well-described cell-lineage and their embryos are relatively simple. In particular, the laboratory is
focused on the early developmental fate choices that lead, step-by-step to the formation of the notochord and the
neural lineages and how the neural lineages are subsequently patterned.
I have made significant contributions to several projects. In the last four years, I have contributed to a study
revealing that the b-catenin signalling pathway acts during early cleavage stages in two successive binary cell fate
choices to generate the three embryonic germ layers. The first step involves the segregation of ectoderm from
mesendoderm, whereby b-catenin specifies the mesendoderm. The second step involves the segregation of mesoderm
and endoderm whereby b-catenin specifies the endoderm. Thus, a simple b-catenin code over two cell divisions is
sufficient to generate the three germ layers of Ciona: b-catenin OFF-OFF specifies ectoderm, ON-ON endoderm and
ON-OFF mesdoderm (Hudson/Kawai/Negishi/Yasuo, in preperation). Following on from our work revealing the
antagonistic relationship between ephrin and FGF signalling during the fate choice between neural and notochord
fates (Picco et al, 2007, Development), I have contributed to a project revealing that this antagonistic relationship is
also operating during the fate choice between neural and epidermal fates (Haupaix/Picco/Hudson/Sirour/Yasuo,
unpublished). Our previous work analysed in detail the patterning of the ascidian neural plate. We found that the
posterior part of the neural plate, which consists of two rows of 8 cells is patterned by 3 signalling pathways, Nodal,
Delta/Notch and FGF/ERK (Hudson and Yasuo, 2005, Development; Hudson et al, 2007 Development). Nodal divides
the cells into medial and lateral fates whereby Nodal specifies lateral fates. One of the earliest transcriptional targets
of Nodal is Snail, encoding a transcription factor repressor. I have analysed in detail the role of Snail during
patterning of the ascidian neural plate. Using both gain and loss of function experiments I have revealed that a
surprisingly large part of neural plate patterning is mediated by Snail function (Hudson et al, unpublished). Finally,
our previously published work revealed the role of Nodal and Delta/Notch signalling during patterning across the
medial-lateral axis (future ventral-dorsal) of the ascidian neural plate. This seemed surprisingly at odds with the
mechanisms used to pattern the dorsal-ventral axis of the vertebrate neural tube, where BMP and SHH signalling are
pivotal players. Focusing on the specification of motoneurons that form in a ventral-lateral portion on the neural
tube, in a similar position to those in vertebrates, we investigated the role of these signalling pathways in specifying
ascidian motoneurons (Hudson et al, 2011, Development). We found that, despite the well conserved expression of a
SHH ortholog in the ventral neural tube and of BMP2/4 in the dorsal neural tube, we could find no evidence that these
factors were critical players in ascidians motoneuron specification. Thus, we revealed that, despite similar gene
expression profiles and morphological outcomes in ascidians and vertebrates, there are significant differences in the
mechanisms used to specify motoneuron fate in these different groups of chordate embryos.
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer
2)
Production scientifique :
1) Hitoyoshi Yasuo and Clare Hudson. (2007). FGF8/17/18 functions together with FGF9/16/20 during formation of the
notochord in Ciona embryos. Dev. Biol. 302:92-103.
2) Vincent Picco, Clare Hudson, and Hitoyoshi Yasuo. (2007). Ephrin/Eph signalling drives the asymmetric division of
notochord/neural precursors in Ciona embryos. Development 134, 1491-1497. Editorial highlight 'Asymmetric cell
division: fateful FGF antagonism' in same issue. Cited in Faculty 1000.
3) Clare Hudson, Sonia Lotito and Hitoyoshi Yasuo. (2007). Sequential and combinatorial inputs from Nodal,
Delta2/Notch and FGF/MEK/ERK signalling pathways establish a grid like organisation of distinct cell identities in the
ascidian neural plate. Development 134, 3527-3537. Editorial highlight 'Neural patterning grid unlocked' in same
issue.
4) Clare Hudson and Hitoyoshi Yasuo. (2008). Similarity and diversity in mechanisms of muscle fate induction between
ascidian species. Biol. Cell, 100, 265-277. Review. With cover image, same issue.
5) O. Tassy, D. Dauga, F. Daian, D. Sobral, F. Robin, P. Khoueiry, D. Salgado, V. Fox, D. Caillol, R. Schiappa, B.
Laporte, A. Rios, G. Luxardi, T. Kusakabe, J. S. Joly, S. Darras, L. Christiaen, M. Contensin, H. Auger, C. Lamy, C.
Hudson, U. Rothbächer, M. Gilchrist, K. W. Makabe, K. Hotta, S. Fujiwara, N. Satoh, Y. Satou and P. Lemaire (2010).
The ANISEED database: digital representation, formalization and elucidation of a chordate developmental program.
Genome Research, 20, 1459-68.
6) Clare Hudson, Moly Ba, Christian Rouvière and Hitoyoshi Yasuo (2011). Divergent mechanisms specify chordate
motoneurons: evidence from ascidians. Development 138, 1643-1652. With cover image, same issue. Cited in Faculty
1000.
7) Christian Sardet, Alex McDougall, Hitoyoshi Yasuo, Janet Chenevert, Gérard Pruliere, Rémi Dumollard, Clare
Hudson, Celine Hebras, Ngan Le Nguyen and Alexandre Paix. (2011). Embryological methods in ascidians: the
Villefranche-sur-Mer protocols. Methods Mol Biol. 770, 365-400.
3)
Points forts des activités ne relevant pas de la production scientifique :
Awards:
1. Médaille du Bronze CNRS 2008 (Section 26).
Invited seminars and workshops:
1. Sars International Centre for Marine Molecular Biology. (Bergen/Norway, 2007).
2. SDB 71st Annual Meeting (Montreal/Canada, 2012)
Scientific evaluations:
1. Refereeing for journals: Development (x1), Dev. Biol. (x4), Biol. Cell (x1)
Member of PhD steering committees:
1. Mathieu Gineste (on-going, Patrick Lemaire's group, Montpellier)
Member of PhD examination juries:
1. Anne-Mette Soviknes (PhD/2007, Joel. C. Glover's group, University of Bergen/Sars International Centre
for Marine Molecular Biology, Norway)
2. Pierre Khoueiry (PhD/2008, Patrick Lemaire's group, Marseille)
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
14/9/12
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
14/09/2012 Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
ingénieurs de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie
de la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour
attester l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule
unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement
destinées à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal,
responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom :McDougall
Prénom :Alexander
Date de naissance :17/01/1966
Courriel :[email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
CR1
_
Thèse soutenue _
HDR
†
Corps-grade :
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
DR20
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1) Points forts des activités de recherche et résultats marquants :
Overall Aim
Understanding how cell cycle mechanisms have been adapted to carry out specific tasks related to
reproductive biology and developmental biology.
Specific Aims
1. Cell cycle control during the meiotic cell cycle
We are interested in how the meiotic cell cycle of oocytes has become specialized so that chromosomes
segregate twice: first during meiosis I then again during meiosis II.
(i) Identification of new proteins involved in meiotic chromosome segregation
We employed two approaches to identify new proteins involved in meiotic chromosome segregation. Yeast two
hybrid and proteomic analysis (this latter approach exploited the advantages of the ascidian model for
biochemistry). We discovered a shugoshin-interacting protein (Set/I2PP2A) following a yeast two hybrid screen
using ascidian oocytes. In collaboration with the Wassmann laboratory (Jussieu) we have extended our
analysis of Set/I2PP2A to the mouse oocyte. This work is in preparation for publication. We also performed a
proteomic screen of metaphase I proteins in collaboration with the Verlhac laboratory (College de France). By
creating Venus-tagged fusion proteins of selected candidates we have so far identified around 10 new proteins
that are localized to chromosomes in the unfertilized ascidian egg. This work is ongoing.
(ii) Identification of the mechanism controlling the egg-to-embryo transition
We discovered that preventing the inactivation of the Mos/ MAPK pathway prevented the egg-to-embryo
transition and in doing so extended the duration of meiosis such that fertilized eggs extruded up to five polar
bodies rather than just two (Dumollard et al., 2011). Our working model is that in the ascidian the number of
rounds of meiosis is limited to precisely two by the duration of activity of the Mos/MAPK pathway. We also
discovered that by maintaining the Mos/MAPK pathway active that sperm-triggered calcium oscillations
persisted indefinitely. Previously we had shown that maintaining MPF active also prevents cessation of the
sperm-triggered calcium oscillations (Levasseur and McDougall, 2000). Our working model is that a positive
negative feedback cycle exists such that MPF and MAPK activities provide positive feedback maintaining the
calcium oscillations and that the calcium increases provide negative feedback by favoring the loss of both MPF
and MAPK activities, thus ensuring that the calcium oscillations stop at the appropriate time (when both MPF
and MAPK activities fall to basal levels at meiotic exit).
2. Cell cycle control during development in ascidian embryos
We are interested in how the cell cycle has been co-opted by developmental mechanisms to generate embryo
morphology. In ascidians as in other embryos the cell cycle is remodeled in two ways. 1) Spindles are reoriented so that blastomeres divide in specific directions or to give cells that differ in size (unequal cleavage),
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
and 2) cell cycle duration is remodeled leading to the establishment of cell cycle asynchrony which in the
ascidian embryo begins at the 16-24 cell stage. These two phenomena, together with cell adhesion, are the
only mechanisms used to create the distinctive form of the 112 cell gastrula in ascidians since no cell
displacement occurs up to the gastrula stage. In addition to cell cycle asynchrony, the orientation of every cell
division plane is predictable in ascidian embryos up to the gastrula stage (this underlies the fate map). The
ascidian model is therefore well-adapted to understand how core cell cycle-dependent phenomena such as
spindle re-orientation and cell cycle duration are controlled during development in a chordate embryo. We
initially focused on the process of unequal cleavage that generates small two germ cell precursors at the 64
cell stage, and discovered a mechanism that causes the spindle to position asymmetrically near the cortex
during prometaphase (Prodon et al., 2010). Our more recent unpublished observations reveal that spindles reorient during embryonic development in the ascidian embryo at precise developmental stages (notably at the
32 cell stage). This work is in preparation. We also addressed how cell cycle asynchrony is established in
ascidian embryos. Briefly, cell cycle asynchrony first occurs at the 16 cell stage and then again at the 64 cell
stage leading to the formation of a 76 cell stage and 112 cell stage embryo. Our data will show how S phase
length is controlled by signaling pathways activated at the 16 and 64 cell stages.
2) Production scientifique :
1. Chambon, J.P., Nakayama, A., Takamura, K., McDougall, A, and Satoh N. (2007). ERK- and JNK-signalling
regulate gene networks that stimulate metamorphosis and apoptosis in tail tissues of ascidian tadpoles.
Development. 134,1203-19.
2. Levasseur, M., Carroll, M. Jones, K. T. and McDougall, A. (2007). A novel mechanism controls the Ca2+
oscillations triggered by activation of ascidian eggs and has an absolute requirement for CDK1 activity. J. Cell
Sci. 120, 1763-1771.
3. Prodon, F., Chenevert, J., Hébras, C., Dumollard, R., Faure, E., Gonzalez-Garcia,F., Nishida, H., Sardet, C
and McDougall, A. (2010). Dual mechanism controls asymmetric spindle position in ascidian germ cell
precursors. Development, 137, 211-221.
4. Dumollard ,R., Levasseur ,M., Hebras, C., Huitorel, P., Carroll, M., Chambon, J-P. and McDougall,. A. (2011).
Mos limits the number of meiotic divisions in urochordate eggs. Development, 138, 885-895.
5. McDougall, A., Chenevert, J., Lee, K. W., Hebras, C. and Dumollard, R. (2011). Cell Cycle in Ascidian Eggs
and Embryos. Results Probl Cell Differ.53,153-69.
6. Sardet,C., McDougall, A., Yasuo,H., Chenevert, J., Pruliere, G., Dumollard, R., Hudson, C., Hebras, C.,
Nguyen, N. and Paix, A. (2011). Embryological Methods in Ascidians: the Villefranche-sur-Mer Protocols.
Methods Mol Biol,. 770, 365-400.
7. McDougall, A., Chenevert, J. and Dumollard, R. (2012). Cell Cycle Control in Oocytes and during Embryonic
Cleavage Cycles in Ascidians. Int Rev Cell Mol Biol. 297, 237-266.
3)
Points forts des activités ne relevant pas de la production scientifique :
Conference/Workshop Organization:
1. Co-organizer. 2007 International Tunicate Meeting. Villefranche/Cap Ferrat, France.
2. Co-organizer. 2010 International Marine Organism Microscopy Workshop , Villefranche, France.
Invited presentations at conferences:
1. Bi-annual Tunicate meetings (Session chair Okinawa, 2009, Session chair Montreal 2011).
Invited seminars and workshops:
1. International workshop.2008. Oocytes. Kyoto, Japan. Speaker
2. International workshop 2009. Oocytes. Fondation des Treilles meeting, France. Speaker.
3. International workshop 2010. Oocytes. Friday Harbor, San Juan Island, USA. Session chair.
4. International workshop 2010 Tunicate Information Systems. Nice, France. Session chair.
5. EFOR meeting 2011. Paris, France. Session chair.
6. Journées André Picard 2011. Banyuls, France. Speaker.
7. EFOR meeting 2012. Paris, France. Session chair
Teaching:
1. Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology
course at Villefranche-sur-Mer.
2. Yearly participation in teaching the Nice Sophia Antipolis University (UNSA) Masters course in
Nice (Pathologies: Meiotic Aneuploidy course).
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer
3. Yearly participation in teaching the University of Paris VII Masters course (Reproduction:
Fertilization course)
4. Member of the Master Steering committee (University of Nice).
Supervision of post-doc/PhD/master:
post-doc (x3)
Master (x3)
Scientific evaluations:
1. Refereeing for journals: Trends in Cell Biology (1), Nature Chemical Biology (1), Seminars in Cell
and Developmental Biology (1), Developmental Biology (2), Nature Communications (1), Plos One
(1), Cell Calcium (1).
2. Refereeing for research grants: BBSRC (1), MRC (1)
Member of PhD examination juries:
1. Sarah Pace (Mary Herbert's group, ICFL, Newcastle University, UK, 2009)
2. Jessica Azoury (Marie-Helene Verlhac's group, Jussieu, UPMC, 2010)
3. Asheleigh Herriott (Junyong Huang's group, Newcastle University, UK, 2011)
Member of HDR examination juries:
1. Christiane Bierkamp (Centre
de Biologie du Développement, Toulouse, 2010)
2. Isabelle Gillot (IBDML, Nice, 2012)
3. Jean-Pierre Tassan (School of Medicine, University of Rennes, 2012)
Administrative responsibilities:
Group leader since 2003
IBISA labelled Platform Villefranche Scientific Representative
Group Finances UMR7009
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
10/09/2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date : 12-09-2012
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
4
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
ingénieurs de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie
de la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour
attester l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule
unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement
destinées à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal,
responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : MOMOSE
Prénom : Tsuyoshi
Date de naissance : 24/03/1971
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
CR1
_
Thèse soutenue †
HDR
†
Corps-grade :
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1)
Points forts des activités de recherche et résultats marquants :
My research activity takes advantages of the laboratory animal Clytia hemisphaerica, which is developed as a
model animal mainly in our research group. This hydrozoan jellyfish has ideal characteristics for developmental
and cell biology research such as transparent eggs and embryos for microscopy, daily production of eggs and
etc. In addition, we established highly reproducible gene manipulation techniques of microinjecting Morpholino
antisense oligonucleotide and mRNA. Using Clytia is highly advantageous over other cnidarian model animal
and we are leading studies for molecular mechanisms of cnidarian embryonic body axis development.
Furthermore, its simple body structure with relatively small numbers of cell types provides highly competitive
and unique research model for certain domains of developmental biology research such as Wnt/TGF-şVLJQDOLQJ
or Planar Cell Polarity (PCP) development even in comparison to the dominant models such as Drosophila and
vertebrates. In terms of PCP research for example, I am studying PCP development in live embryo under
microscope, which is not feasible in most of other PCP models. With its evolutionary old divergence from
bilaterians Clytia provides unique view for PCP research. We also were able to thoroughly screen target genes
for Wnt signaling with Digital Gene Expression (DGE) analysis using next-generation sequencing technologies,
fully taking advantages of homogeneous cell population and uniform genetic background of Clytia embryos.
These projects were/are being supported by the following research grants: subventions ARC (Tsuyoshi Momose
2008-2010) and ANR Programme ‘Blanc’ (Co-founding to our group and Michael Manuel’s group in UMR7138,
2007-2009; 2009-2012). I am in charge of sample/data management in our group for the Clytia hemisphaerica
whole genome sequencing project in partnership with the Genoscope (2009).
2)
Production scientifique :
1) Momose, T, Houliston, E (2007) Two oppositely localised frizzled RNAs as axis determinants in a
cnidarian embryo. PLoS Biol. 5:e70
2) Momose, T, Derelle R, Houliston E (2008) A maternally localised Wnt ligand required for axial
patterning in the cnidarian Clytia hemisphaerica. Development. 135:2105-2113.
3) Derelle, R, Momose, T, Manuel, M, Da Silva, C, Wincker, P, and Houliston, E (2010). Convergent
origins and rapid evolution of spliced leader trans-splicing in metazoa: insights from the ctenophora
and hydrozoa. RNA 16:696–707.
4) Forêt, S, Knack, B, Houliston, E, Momose, T, Manuel, M, Quéinnec, E, Hayward, DC, Ball, EE, and
Miller, DJ (2010). New tricks with old genes: the genetic bases of novel cnidarian traits. Trends
Genet 26:154–158.
Vague D : campagne d’évaluation 2012-2013
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
5) Houliston, E, Momose, T, and Manuel, M (2010) Clytia hemisphaerica: a jellyfish cousin joins the
laboratory. Trends Genet 26:159–167.
6) Hwang, JS, Takaku, Y, Momose, T, Adamczyk, P, Özbek, S, Ikeo, K, Khalturin, K, Hemmrich, G,
Bosch, TCG, Holstein, TW, et al. (2010). Nematogalectin, a nematocyst protein with GlyXY and
galectin domains, demonstrates nematocyte-specific alternative splicing in Hydra. Proc Natl Acad
Sci USA 107:18539–18544.
7) Amiel, A, Chang, P, Momose, T, and Houliston, E (2010). Clytia hemisphaerica: A cnidarian model for
studying oogenesis. In Oogenesis: the Universal Process, M-H Verlhac, and A Villeneuve, eds.
(Oxford: John Wiley & Sons Ltd.), pp. 81–101.
8) Momose, T, Kraus, Y and Houliston, E (2012)
3)
Points forts des activités ne relevant pas de la production scientifique :
Invited presentations at conferences:
1. Invited talk in GCOE symposium, Nara Institute of Science and Technology. (Nara/Japan, 2008)
2. Invited talk in Gordon Research Conference. Fertilization & Activation of Development.
(Holderness, NH/ USA, 2009)
3. EFOR meeting (Paris, 2012).
Invited seminars and workshops:
1. Seminar in Biozentrum, Universität Basel. (Basel/Switzerland, 2009) (Communication: Walter
Gehring)
2. Seminar in͒Universitat de Barcelona, Departamento de Genética, (Barcelona/Spain, 2009)
(Communication: Hiroshi Suga)
3. Seminar in SARS Center (Bergen/Norway, 2010) (Communication: Fabian Rentzsch)
4. Invited keynote talk in 7thWorkshop for Hydrozoan Society. ͒
(Porto Cesareo/Italy, 2010)
(Communication: Stefano Piraino)
5. Invited talk and practical course for ASSEMBLE Workshop, (Napoli/Italy, 2012)
Teaching:
1. Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology
course at Villefranche-sur-Mer.
Supervision of post-doc/PhD/master:
post-doc (x1)
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date : 10 sept, 2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
11th September, 2012
Vague D : campagne d’évaluation 2012-2013
Février 2012
Signature :
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres personnels
ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal, responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : Prulière
Prénom : Gérard
Date de naissance : 28/07/1956
Courriel :[email protected]
Établissement d’affectation ou organisme d’appartenance : INSERM
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
†
Corps-grade :CR1
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
†
†
_
1 Sciences de l’homme et de la société
2 Sciences et technologies
3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : INSERM, CSS3
1)
Points forts des activités de recherche et résultats marquants :
My work focuses on the establishment of early polarities which control the early development of the ascidians Phallusia
mammillata and Ciona intestinalis and the sea urchin Paracentrotus lividus. My background in Biochemistry and Cell
biology has allowed me to contribute to the analysis of the cytoskeleton behaviour during early development of these
species. I am currently the primary resource for sea urchin cell biology in our unit as well as for methods and
mechanisms concerning actin and tubulin cytoskeleton, methods and mechanisms. This is important for our laboratory
and I am often consulted by students, post-docs and scientists for assistance.
One strength of my work has been to show through several examples that aPKC, member of the polarity complex
aPKC/Par3/Par6 generally considered associated to the plasma membrane and thought to regulate the actin skeleton, is
also a regulator of the microtubule cytoskeleton:
-I have shown with my collegues that the aPKC/Par3/Par6 polarity complex is present in the CAB of the ascidian embryo
to regulate asymmetric divisions (Patalano et al 2006, Coll J. Chenevet and C. Sardet).
- More recently, I have find that the polarity complex must also control asymmetric divisions corresponding to meiosis.
We find aPKC and Par3 associated to the meiotic spindle of Phallusia mammillata unfertilized oocytes. After
fertilization, aPKC migrates to the nearby cortex in a microtubule-dependent manner to induce the spindle rotation
necessary for polar body extrusion. Treating the oocytes with in an inhibitor specific for aPKC or with a « kinase dead »
dominant negative form of aPKC inhibits meiosis (Pruliere et al, manuscript in preparation, coll J.Chenevert, R.
Dumollard et A. McDougall, project founded by ARC).
-My last published article shows a role for sea urchin aPKC during embryo ciliogenesis (Prulière et al 2011, coll
J.Chenevert and C Sardet).The analysis of the localization of aPKC in the swimming blastula revealed that it
concentrates in a ring structure at the basis of each motile cilium, in between the transition zone and the basal body.
Inhibition of aPKC by its pseudo-substrate leads to aPKC mislocalisation and cilia growth inhibition. We postulate that
aPKC may regulate cilia intraflagellar transport.
- This work also shows that aPKC associates to mitotic spindle microtubules and travels towards their (+) end, which
suggests an association to a kinesin. This seems to be confirmed by the inhibition of aPKC in sea urchin and ascidian
early embryos which leads to centrosomes segregation defaults. We are currently analyzing the possibility of an
association between aPKC and MKLP2, a mitotic kinesin, which when inhibited gives a similar phenotype (collaboration
J.Chenevert, J.Sobszak, UPMC).
B) I have begun a functional studies on motor proteins associated to actin in ascidians (coll J.Chenevert, M.Kollmar,
Max Planck Institute, Gottingen, Allemagne; L.Yamada, Sugashima Marine Station Japan, Nagoya University; Travel
funding: PICS travel grant for France-Japan collaboration 2010-2012).
. - Using blebbistatin inhibition, I have shown that the cortical contraction and mRNA determinant concentration at the
vegetal pole do not depend on myosin II. Moreover, we find that myosin 2 plays a role in positioning of the first mitotic
spindle (Pruliere and Chenevert, in preparation)
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
2)
Production scientifique :
-Atypical protein kinase C controls sea urchin ciliogenesis. Pruliere G, Cosson J, Chevalier S, Sardet C, Chenevert
J. Molecular Biology of the Cell. 2011 Jun 15;22(12):2042-53.
-Cortical anchorages and cell type segregations of maternal postplasmic/PEM RNAs in ascidians. Paix A, Yamada
L, Dru P, Lecordier H, Pruliere G, Chenevert J, Satoh N, Sardet C. Developmental Biology 2009 Dec 1;336(1):96111
-McDougall A, Yasuo H, Chenevert J, Pruliere G, Dumollard R, Hudson C, Hebras C, Le Nguyen N, Paix A.
Methods in Molecular Biology. 2011;770:365-400.
3)
Points forts des activités ne relevant pas de la production scientifique :
1-Organisation of conferences/workshops:
Co-organizer. 2007 International Tunicate Meeting. Villefranche/Cap Ferrat, France.
reviewer
2-Public science education diffusions:
Many presentations to the public:
« fête de la science » (UNSA, Valrose, OOV,Villefranche)
« Célébration des 125ans de l'observatoire »
« Journées de la Mer », Villefranche
Conduct tours for local and international schools
presentations of our research to schools, politicians and the press (Contes, Nice)
presentations at « la Maison pour tous », Contes, during "Arts et Culture" seminars
2-Teaching
-
Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology course at
Villefranche-sur-Mer.
-Supervision of:
-Mehdi Inglebert : L3, Université de Corte (2010 et 2011)
-Romain Bachot : Elève Ingénieur en Génie Biologique, Université de Nice Polytech, 2011
-Marjory Chassier : L3 Université de Rennes, 2012
co-supervision of:
-Hélène Le Cordier, assistant ingénieur, groupe de Christian Sardet
-Lydia Besnardeau, assistant ingénieur, groupe de C. Sardet
-François Prodon, thèse puis stage post-doctoral
-Alexandre Paix, thésard de 3ème cycle
Scientific evaluations:
Refereeing for journals: "Developmental Biology", "Molecular biology of the cell", Current Biology.
Administrative responsabilities.
Correspondant UMR7009 pour la bibliothèque
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
21/06/2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
14/09/2012
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
ingénieurs de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie
de la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour
attester l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule
unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement
destinées à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
(label et n°, intitulé, établissement principal,
responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Nom : Rouvière
Prénom : Christian
Date de naissance : 28/02/1961
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Enseignant-chercheur
†
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Thèse soutenue †
HDR
†
Corps-grade :
Chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Ingénieur
_
Thèse soutenue _
HDR
†
Corps-Grade : IR HC
HDR
†
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Corps grade :
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
†
†
_
1 Sciences de l’homme et de la société
2 Sciences et technologies
3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme :
1)
Production scientifique :
1) Hudson, C., Ba, M., Rouviere C. & Yasuo, H. (2011). "Divergent mechanisms specify chordate
motoneurons: evidence from ascidians." Development 138: 1643-1652.
2) Cattaneo, Raffaela; Rouvière, Christian; Rassoulzadegan, Fereidoun; Weinbauer, Marcus (2010).
Association of marine viral and bacterial communities with reference black carbon particles under
experimental conditions: An analysis with scanning electron, epifluorescence and confocal laser
scanning microscopy. FEMS Microbiology Ecology volume 74(2), 382-396.
2)
Points forts des activités ne relevant pas de la production scientifique :
Training and Education :
1. Microscopie à fluorescence
-Centre Commun de microscopie de Nice
14-17 Mai 2009
19-22 Avril 2010
14-16 mars 2011
17-19 oct 2011
2-4 avril 2012
-Microscopie à fluorescence (Institut de Pharmacologie et de Biologie Structurale Toulouse)
16-19 avril 2007
CNRS Greg Clermont-Ferrand
4-7 décembre 2007
-CNRS Marseille Luminy
14-17 juin 2011
2. Bases conceptuelles et pratiques du traitement de l'image
-CEPAM Sophia Antipolis
21-23 septembre 2009
-INSERM Marseille (3+2 jours)
17-19 mars 2010 et 6-7 mai 2010
7_9 nov 2011 et 14-15 dec 2011
13-15 mars 2012 et 12-13 mai 2012
-CNRS Sophia Antipolis
14-16 juin 2010
4-6 mai 2011
21-23 mai 2012
-CNRS Entreprise Marseille Luminy
24-27 mai 2011
-CECIL Lyon
9-10 juin 2011
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
-INSERM Toulouse
14-16 mai 2012
26-28 novembre 2012
3. ImageJ Niveau II
-INSERM Toulouse
21-23 novembre 2012
4. Traitement de l’image acquise en biologie
-CNRS Sophia Antipolis
11-13 juin 2007
2 au 4 juin 2008
12-14 mai 2009
-Sté SCC-CNRS Toulouse
6-8 février 2007
2-4 octobre 2007
-INSERM Clermont Ferrand
24-26 mars 2009
-INSERM Marseille La Timone 2008
5. Analyse morphomathématique des images
-Lyon- université de médecine de Rockfeller
15-19 octobre 2007
10-14 Mars 2008
5. Pilotage de périphériques et prototypes pour la biologie
-Ateliers pour l’Ecole thématique MiFoBio 2008
22-27 septembre 2008
Teaching :
1. licence professionnelle de Biotechnologies (L3): responsible of UV 06 : traitement d’images (since
2003).
2. Enseignement en médecine : Imagerie en clinique et en recherche : les bio marqueurs (2006,
2007)
3. Ecole doctorale de Nice 22 février 2012 : Traitement d’image.
Organisation of conferences/workshops :
1. Co-Organisation for formation TechCo « Métrologie » action nationale de formation du CNRS from
14 to 16 mai 2007 à Villefranche/mer and from 28 to 30 mai 2008
2. Workshop Co-organisation « Marine Cell Biology Live Cell Imaging Workshop/Conference » 31
janvier au 4 fevrier 2011 (http://biodev.obs-vlfr.fr/workshop/)
3. GDR 2588 member « microscopie fonctionnelle du vivant »
4. Member of the steering committee of the technical network : « microscopie photonique de
fluorescence multidimensionnelle » RT mfm.
5. Member of the steering committee of the Network :’école thématique Mifobio 2008, 2010 et 2012
(http://www.mifobio.fr/)
Scientific evaluations:
1. research between public/companies (x1)
2. allocation of funding for projects oriented "microscopy": cooperation contract (x1)
Member of selection juries:
1. IR Hc
2. IR université
3. T graphiste
Administrative responsibilities:
Coordinator of a research service
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date : 9/09/12
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres personnels
ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal, responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : SARDET
Prénom : Christian
Date de naissance : 25/08/1946
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Thèse soutenue †
HDR
†
Corps-grade :
X
Thèse soutenue X
HDR
†
Corps-grade: DR1
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Enseignant-chercheur
†
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
Emerite
Ingénieur
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière : Chercheur Emerite (depuis 08/2011)
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
X 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU : 65
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme :
1) Points forts des activités de recherche et résultats marquants :
Structure and function of the cortex of eggs and embryos / ascidian cortical maternal determinant RNAs
PICS collaboration with Japan: K Inaba (Tsukuba Univ.), L Yamada (Nagoya Univ. ) H Nishida (Osaka Univ.)
Significant Results using the ascidian model: 1) First démonstration that cortical maternal RNAs segregate in
blastomeres with different cell fates depending on their oocyte cortex localization and binding to the cortical
endoplasmic réticulum network (cER) or to germinal granules (See REF 4). 2) Demonstration that the localized
translation of a maternal determinant RNA in the oocyte cortex is triggered by fertilizaton and calcium activation.
Translation is bi-polarized occuring first in the vegetal cortex and then in the posterior pole where the determinant
RNA is relocalized (see REF 9).
This work was funded by the following research grants (coordinator C Sardet):
-ANR (JJ,PSDFWî with Houliston and McDougall groups
-AFM )URP(JJWR(PEU\Rî
-ARC &RUWLFDO51$VDQGSURWHLQVî
-PICS CNRS (USA) collaboration on localized RNAs (2005-2007)
-PICS CNRS (Japan) collaboration on the Cortex (2010-2012)
2) Production scientifique :
- 1) Sardet, C , Paix, A., Prodon, F., Dru, P. and Chenevert, J. (2007) From oocyte to 16 cell stage: the cytoplasmic
and cortical reorganizations which pattern the ascidian embryo. Developmental Dynamics. 236: 1716-31.
- 2) Sardet C, Swalla BJ, Satoh N, Sasakura Y, Branno M, Thompson EM, Levine M, Nishida H. (2008). Euro chordates:
Ascidian community swims ahead. The 4th International Tunicate meeting in Villefranche sur Mer. Dev Dyn.
î
- 3) Prodon F, Sardet C, Nishida H. (2008). Cortical and cytoplasmic flows driven by actin microfilaments polarize the
FRUWLFDO(5îP51$GRPDLQDORQJWKHDîYD[LVLQDVFLGLDQRRF\WHV'HYHORSPHQWDO%LRORJ\î
- 4) Paix A, Yamada L, Dru P, Lecordier L, Pruliere G, Chenevert J, Satoh N, Sardet C. (2009) Cortical anchorages and
FHOOW\SHVHJUHJDWLRQVRIPDWHUQDOSRVWSODVPLF3(051$VLQDVFLGLDQV'HYHORSPHQWDO%LRORJ\î
- 5) Harzsh S, Muller C.H.G., Rieger V., Perez Y, Sintoni S., Sardet C.; Hansson B.. (2009). Fine structure of ventral
nerve center and interspecific identification of individual neurons in the enigmatic Chaetognatha. Zoomorphology,
î
- 6) Prodon F, Chenevert J, Hébras C, Dumollard R, Faure E, Gonzalez-Garcia J, Nishida H, Sardet C, McDougall
A.(2010) Dual mechanism controls asymmetric spindle position in ascidian germ cell precursors. 137, 2011-2021
- 7) Paix A, Chenevert J, Sardet C (2011) Localization and anchorage of maternal mRNAs to cortical structures of
ascidian eggs and embryos using high resolution in situ hybridization Dans “Messages on the move: “Techniques in RNA
visualization” Methods in Molecular Biology, 714, 49-70
- 8) Sardet C, McDougall A, Yasuo H, Dumollard R, Hudson C, Pruliere G, Le Nguyen N, Chenevert J, Paix A. (2011)
Embryological methods in ascidians: the Villefranche protocols, Dans “Vertebrate Embryogenesis: Methods and
Protocols” Methods in Molecular Biology, 770, 365- 400
- 9) Paix A, Le Nguyen PN, Sardet C.(2011) Bi-polarized translation of ascidian maternal mRNA determinant pem-1
associated with regulators of the translation machinery on cortical Endoplasmic Reticulum (cER). Developmental
Biology, 357, 211- 226
- 10) Prulière, G., Cosson, J., Chevalier, S., Sardet, C., & Chenevert, J. (2011). Atypical protein kinase C controls sea
urchin ciliogenesis. Mol Biol Cell 22, 2042-2053.
-11) Karsenti, E., Acinas, S.G.., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F.,
Claverie, J.M., Follows, M., Gorsky, G., Hingamp. P., Ludicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F.,
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Ogata, H., Pesant, S., Reynaud, E.G., Sardet,C., Sieracki, M. E., Speich, S., Velayoudon, D., Weissenbach, J., Wincker, P.
(2011). A Holistic Approach to Marine Eco-Systems Biology. Plos Biology 9, 1-5.
3)
Points forts des activités ne relevant pas de la production scientifique :
Invited seminars and workshops:
1. 2011, Intern. tunicate meeting, 06 / 2011, speaker “Cellular and molecular structure of the cortex and its
role in ascidian development" - Montreal (Canada),
2. 2011, Gordon Conférence on Fertilization and Development, 07/11, speaker « Structure and function of the
egg cortex » Plymouth, New Hampshire ( USA)
3. 2009, Gordon Conférence on Fertilization , 07/09, Organizer an speaker session "Polarity of eggs and
embryos" Plymouth, New Hampshire ( USA)
4. 2009 , 2008, 2007- The Volker Schmid Training Course, mai 2009, Instructor, Roscoff ( France )
5. 2009 – International Meeting "Modelling complex biological systems in the context of genomics” 04/09, La
Colle sur Loup, (France)
6. 2009 JAMBIO Symposium Japon, 03/09 , speaker »Marine models for development » Shimoda (Japan)
7. 2007 – International Meeting« Fédération Réaumur des Sciences du Vivant », 11/07, Speaker and final
remarks. Grenoble (France) 2007,
8. 2007 - Okazaki Biology Conferences: 6th Conference “Evolution and development”, 12/07, Speaker Okazaki
and Ise (Japan)
Teaching:
Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology course at
Villefranche-sur-Mer.
2. Instructor The Volker Schmid Training Course, mai 2009, Roscoff ( France )
1.
Supervision of post-doc/PhD/master:
1. Alexandre Paix PhD 2010 (UNS)
2. Ngan Le Nguyen PhD 2011 (UPMC)
3. Jean-Baptiste Romagnon PhD expected 2012 (UPMC Euromed) co-supervision with Lars Stemman, LOV
4. Post-doc François Prodon, co-supervise with A McDougall
Scientific evaluations:
1. Refereeing for journals: Current Biology (x1), Development (x2), Developmental Biology (x3)
Member of PhD examination juries:
1. Nathalie Oulhen Roscoff 2008
2. Sandrine Tyteca Toulouse 2008
1.
2.
Administrative responsibilities:
Teamleader Biomarcell group
Elected member Conseil d’Administration OOV, college A
Organisation of conferences/workshops:
Workshop “Marine Genomics Europe: Marine Genomics: An Ocean of Techniques, October 2007, Orthodox
Academy of Crete, Greece,
2. 4th International Tunicate Meeting St Jean Cap Ferrat) organizer and chair of session Fertilization
3. Gordon Conférence on Fertilization , July 2009, organizer and chair of session "Polarity of eggs and embryos"
Plymouth (USA)
4. Tara Oceanexpédition. Workshops 2008-2012 : Villefranche sur Mer, Paris, Naples, Roscoff, Lorient.
1.
Public science education diffusions:
1. European award for « Communication in the life sciences » (EMBO 2007)
2. Co-Founder and coordinator of the Tara Oceans Expédition (2009 - 2012)
3. Encyclopedia of Life Fellow (Rubinstein fellow: 2012)
4. Founder « Plankton Chronicles project » www.planktonchronicles.org (2009 – present)
5. Conférences for the général public, exhibits, book post face.
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
07 /08 / 2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
14/09/2012
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres personnels
ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
ingénieurs de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de
la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées
à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal, responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : SCHUBERT
Prénom : Michael
Date de naissance : 20/02/1974
Courriel :
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
_
Corps-grade : CR1
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1)
Points forts des activités de recherche et résultats marquants :
The principal investigator, Michael SCHUBERT, has a long-standing scientific record in the field of evolution
and development. For well over a decade, the principal investigator has been at the forefront of research using the
cephalochordate amphioxus as a model organism, both as far as scientific discoveries are concerned and for the
development of amphioxus as a laboratory model. For example, the principle investigator has participated in the
genome sequencing consortium of the Florida amphioxus (Branchiostoma floridae) and is currently very actively
involved in the coordination of the consortium accompanying the sequencing of the genome of the European
amphioxus (Branchiostoma lanceolatum). Moreover, in a collaborative effort involving the principal investigator,
the first amphioxus facilities run on artificial seawater have been established in Gif-sur-Yvette and in Lyon, where
amphioxus adults can be kept, spawned and the spawned eggs injected without any limitations. In addition to this
involvement in the advancement of non-standard animal model systems, the principal investigator has also farreaching knowledge of the signaling cascade controlled by vitamin A derivatives (also called retinoids) and of the
biological functions played by this signaling network in various different animal systems. As a matter of fact, the
principal investigator was the first to discover evidence that retinoid-dependent signaling has originated much
earlier in animal evolution than previously thought and that this morphogen-dependent signaling cascade was
already present in the last common bilaterian ancestor of both protostomes and deuterostomes. Finally, the
principle investigator also has a very elaborate list of past and ongoing collaborations that have yielded significant
discoveries published in high impact journals. Since the beginning of his PhD thesis in 1997, the principle
investigator has published 43 research and 10 review articles, which, together with 2 book chapters, have been
cited more than 1400 times (h-index: 22 – as of 30/07/2012).
The past and ongoing research projects were/are being supported by the following research grants accorded to
Michael SCHUBERT: French ACI-BCMS grant “Evolution des Voies de Signalisation des Rétinoids chez les Chordés”
(2004-2007, co-investigator) worth €90.000, European Integrated Project “CRESCENDO” (2006-2011, coinvestigator) worth €164.500, French ANR Blanc grant “RAnteriorHox” (2007-2011, principle investigator) worth
€300.000, US-French FACCTS project “Evolution of Retinoic Acid Signaling in Deuterostomes” (2009-2010, coinvestigator) worth €5.000, French ANR Blanc grant “EvolAx” (2009-2012, co-investigator) worth €78.000, French
CNRS-PEPS grant (2010, co-investigator) worth €15.000, Portugal-French FCT grant (2011, co-investigator) worth
€12.150, French ANR Jeune Chercheur grant “RAvolution” (2011-2014, principle investigator) worth €250.000.
2) Production scientifique :
Research articles
1) Beaster-Jones L, Schubert M and Holland LZ (2007). Cis-regulation of the amphioxus engrailed gene: insights
into evolution of a muscle-specific enhancer. Mech. Dev. 124:532-542.
2) Fuentes M, Benito E, Bertrand S, Paris M, Mignardot A, Godoy L, Jimenez Delgado S, Oliveri D, Candiani S,
Hirsinger E, D’Aniello S, Pascual-Anaya J, Maeso I, Pestarino M, Vernier P, Nicolas JF, Schubert M, Laudet V,
Geneviere AM, Albalat R, Garcia Fernandez J, Holland ND and Escriva H (2007). Insights into spawning behavior
and development of the European amphioxus (Branchiostoma lanceolatum). J. Exp. Zool. B 308:484-493.
3) Kozmik Z, Holland ND, Kreslova J, Oliveri D, Schubert M, Jonasova K, Holland LZ, Pestarino M, Benes V and
Candiani S (2007). Pax-Six-Eya-Dach network during amphioxus development: conservation in vitro but contextspecificity in vivo. Dev. Biol. 306:143-159.
4) Rasmussen SLK, Holland LZ, Schubert M, Beaster-Jones L and Holland ND (2007). Amphioxus AmphiDelta:
evolution of Delta protein structure, segmentation, and neurogenesis. Genesis 45:113-122.
5) Holland LZ, Albalat R, Azumi K, Benito-Gutierrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S,
Dishaw LJ, Ferrier DEK, Garcia-Fernandez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallbook F, Hirose D,
Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z,
Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA,
Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert
M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK,
Vague D : campagne d’évaluation 2012-2013
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Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N and Holland PWH (2008). The
amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 18:1100-1111.
6) Paris M, Brunet F, Markov GV, Schubert M and Laudet V (2008). The amphioxus genome enlightens the evolution
of the thyroid hormone signaling pathway. Dev. Genes Evol. 218:667-680.
7) Paris M, Escriva H, Schubert M, Brunet F, Brtko J, Ciesielski F, Roecklin D, Vivat-Hannah V, Jamin EL, Cravedi
JP, Scanlan TS, Renaud JP, Holland ND and Laudet V (2008). Amphioxus postembryonic development reveals the
homology of chordate metamorphosis. Curr. Biol. 18:825-830.
8) Paris M, Pettersson K, Schubert M, Bertrand S, Pongratz I, Escriva H and Laudet V (2008). An amphioxus
orthologue of the estrogen receptor that does not bind estradiol: insights into estrogen receptor evolution. BMC
Evol. Biol. 8:219.
9) Schubert M*, Brunet F*, Paris M, Bertrand S, Benoit G and Laudet V (2008). Nuclear hormone receptor signaling
in amphioxus. Dev. Genes Evol. 218:651-665. *These authors contributed equally to this work.
10) Kucera T, Strilic B, Regener K, Schubert M, Laudet V and Lammert E (2009). Ancestral vascular lumen formation
via basal cell surfaces. PLoS ONE 4, e4132.
11) Onai T, Lin HC, Schubert M, Koop D, Osborne PW, Alvarez S, Alvarez R, Holland ND and Holland LZ (2009).
Retinoic acLG DQG :QWş-catenin have complementary roles in anterior/posterior patterning embryos of the
basal chordate amphioxus. Dev. Biol. 332, 223-233.
12) Osborne PW, Benoit G, Laudet V, Schubert M* and Ferrier DEK* (2009). Differential regulation of ParaHox genes
by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae). Dev. Biol. 327:252-262.
*
These authors contributed equally to this work.
13) Zhong J, Zhang QJ, Xu QS, Schubert M, Laudet V and Wang YQ (2009). Complete mitochondrial genomes
defining two distinct lancelet species in the West Pacific Ocean. Mar. Biol. Res. 5:278-285.
14) Koop D, Holland ND, Semon M, Alvarez S, de Lera AR, Laudet V, Holland LZ and Schubert M (2010). Retinoic acid
signaling targets Hox genes during the amphioxus gastrula stage: insights into early anterior-posterior patterning
of the chordate body plan. Dev. Biol. 338:98-106.
15) Albalat R*, Brunet F*, Laudet V and Schubert M (2011). Evolution of retinoid and steroid signaling: vertebrate
diversification from an amphioxus perspective. Genome Biol. Evol. 3:985-1005. *These authors contributed
equally to this work.
16) Campo-Paysaa F*, Semon M*, Cameron RA, Peterson KJ and Schubert M (2011). microRNA complements in
deuterostomes: origin and evolution of microRNAs. Evol. Dev. 13:15-27. *These authors contributed equally to
this work.
17) Koop D, Holland LZ, Setiamarga D, Schubert M and Holland ND (2011). Tail regression induced by elevated
retinoic acid signaling in amphioxus larvae occurs by tissue remodeling, not cell death. Evol. Dev. 13:427-435.
18) Sobreira TJP*, Marletaz F*, Simoes-Costa M*, Schechtman D, Pereira AC, Brunet F, Sweeney S, Pani A, Aronowicz
J, Lowe CJ, Davidson B, Laudet V, Bronner-Fraser M, de Oliveira PSL, Schubert M* and Xavier-Neto J* (2011).
Structural shifts of aldehyde dehydrogenase enzymes were instrumental for the early evolution of retinoiddependent axial patterning in metazoans. Proc. Natl. Acad. Sci. U.S.A. 108:226-231. *These authors
contributed equally to this work.
19) Theodosiou M, Colin A, Schulz J, Laudet V, Peyrieras N, Nicolas JF, Schubert M and Hirsinger E (2011).
Amphioxus spawning behavior in an artificial seawater facility. J. Exp. Zool. B 316:63-275.
20) Candiani S, Moronti L, Ramoino P, Schubert M and Pestarino M (2012). A neurochemical map of the developing
amphioxus nervous system. BMC Neurosci. 13:59.
Review articles and book chapters
1) Campo-Paysaa F, Marletaz F, Laudet V and Schubert M (2008). Retinoic acid signaling in development: tissuespecific functions and evolutionary origins. Genesis 46:640-656.
2) Theodosiou M, Laudet V and Schubert M (2010). From carrot to clinic: an overview of the retinoic acid signaling
pathway. Cell. Mol. Life Sci. 67:1423-1445.
3) Gutierrez-Mazariegos J*, Theodosiou M*, Campo-Paysaa F* and Schubert M (2011). Vitamin A: a multifunctional
tool for development. Semin. Cell Dev. Biol. 22:603-610. *These authors contributed equally to this work.
4) Carvalho, JE and Schubert M (2012). Retinoic acid: metabolism, developmental functions and evolution.
Vitamin-Binding Proteins – Their Functional Consequences (K. Dakshinamurti and S. Dakshinamurti, Editors).
CRC Press/Taylor & Francis Group, in press.
5) Lecroisey C, Laudet V and Schubert M (2012). The cephalochordate amphioxus: a key to reveal the secrets of
nuclear receptor evolution. Brief. Funct. Genomics 11:156-166.
6) Semon M, Schubert M and Laudet V (2012). Programmed genome rearrangements: in lampreys, all cells are not
equal. Curr. Biol. 22, R641-R643.
7) Xavier-Neto J, Trueba SS, Stolfi A, Souza HM, Sobreira TJP, Schubert M and Castillo HA (2012). An unauthorized
biography of the second heart field and a pioneer/scaffold model for cardiac development. Curr. Top. Dev.
Biol. 100:67-105.
3) Points forts des activités ne relevant pas de la production scientifique :
Invited presentations at conferences:
1. 1st Annual Meeting of the EU Integrated Project CRESCENDO (Paris/France, 2007)
2. 2nd Meeting of the European Society for Evolutionary Developmental Biology (Ghent/Belgium, 2008)
3. 3rd Meeting of the European Society for Evolutionary Developmental Biology, (Paris/France, 2010)
4. 15th Evolutionary Biology Meeting (Marseille/France, 2011)
5. 4th Meeting of the European Society for Evolutionary Developmental Biology (Lisbon/Portugal, 2012)
Vague D : campagne d’évaluation 2012-2013
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3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
6. 10th International Congress on Cell Biology and 16th Meeting of the Brazilian Society for Cell Biology (Rio de
Janeiro/Brazil, 2012)
Invited seminars and workshops:
1. Unité de Biologie Moléculaire du Développement, Institut Pasteur (Paris/France, 2008)
2. Unité de Biologie du Développement, Observatoire Océanologique (Villefranche-sur-Mer/France, 2009)
3. Unité Mer et Santé, Station Biologique (Roscoff/France, 2009)
4. Institut de Neurobiologie Alfred Fessard, CNRS (Gif-sur-Yvette/France, 2010)
5. Biology Department, Universität Konstanz (Konstanz/Germany, 2010)
6. Developmental Biology Unit, EMBL (Heidelberg/Germany, 2010)
7. Centre de Génétique et de Physiologie Moléculaire et Cellulaire, UCBL (Lyon/France, 2011)
8. 3rd Meeting of the Réseau d’Etudes Fonctionnelles chez les Organismes Modèles (Paris/France, 2012)
9. Unité de Biologie du Développement, Observatoire Océanologique (Villefranche-sur-Mer/France, 2012)
10. Centre de Génétique et de Physiologie Moléculaire et Cellulaire, UCBL (Lyon/France, 2012)
11. 2nd Unione Zoologica Italiana Spring School (Venice/Italy, 2012)
12. Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais (Campinas/Brazil,
2012)
Teaching:
1. Reviewer for Master “Biosciences” at University of Lyon (Lyon/France, 2008/2009 and 2009/2010)
2. Thesis defense committee member for Master “Biosciences” at University of Lyon (Lyon/France, 2010/2011)
Supervision of Post-doc/PhD/Master:
1. Post-doc (x2)// PhD (x3) //Master (x4)
Scientific evaluation:
1. Editorial Board Member and Academic Editor of PLoS ONE
2. Editorial Board Member of The Open Evolution Journal, TheScientificWorldJournal, Developmental Biology
Journal, Dataset Papers in Biology
3. Refereeing for journals: Biochimica et Biophysica Acta - Gene Structure and Expression, BMC Evolutionary
Biology, Current Biology, Evolution & Development, Gene, Genesis, Indian Journal of Marine Sciences,
International Journal of Biological Sciences, Italian Journal of Zoology, Journal of Experimental Zoology Part
B: Molecular and Developmental Evolution, Journal of Molecular Biology, Journal of Molecular Endocrinology,
Marine Biology, Marine Ecology, Molecular Biology and Evolution, Nature Communications, Nutrients, PLoS
ONE, Proceedings of the Royal Society B: Biological Sciences
4. Refereeing for research grants: ANR
Member of PhD/Master examination juries:
1. Chen Jie (PhD student in my group, Lyon/France, 2011)
2. Florent Campo-Paysaa (PhD student in my group, Lyon/France, 2011)
3. Mohamed Rabie Belgacem (PhD student in Hector Escriva’s group, Banyuls-sur-Mer/France, 2011)
4. João Emanuel Marques Carvalho (Master student in my group, Lisbon/Portugal, 2012)
Member of HDR examination juries:
1. Andrea Pasini (Marseille/France, 2011)
2. Sébastien Darras (Marseille/France, 2012)
Administrative responsibilities:
1. Member of council and executive committee (as treasurer) of the “European Society for Evolutionary
Developmental Biology” (since 2006)
2. Member of scientific committee and organizer of the biannual meetings of the “European Society for
Evolutionary Developmental Biology” (since 2006)
3. Sub-group leader (since 2007)
4. Member of the “comité national de la recherche scientifique”, section 24 (“interactions cellulaires”) (20082012)
5. Person in charge of the amphioxus animal facility at the Ecole Normale Supérieure (Lyon/France, 2008-2012)
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date : 10/09/2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
10th September 2012
Vague D : campagne d’évaluation 2012-2013
Février 2012
Signature :
4
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres
personnels ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les
ingénieurs de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie
de la future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour
attester l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule
unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement
destinées à l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(label et n°, intitulé, établissement principal,
responsable)
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : TIOZZO
Prénom : STEFANO
Date de naissance : 18-11-1974
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance : CNRS
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
CR1
_
Thèse soutenue †
HDR
†
Corps-grade :
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_
3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1)
Points forts des activités de recherche et résultats marquants :
My appointment at the UMR7009 begun on April 1st 2010 as CDD, until October 2010 when I have obtained a
CNRS-CR1 position. The projects, related to the main line of research of the laboratory, have been for the first
year a follow up of the research done as post-doc at UCSB (De Tomaso lab).
-
Data related to the expression and function of HCN channels in colonial ascidians heart were previously
collected have been analyzed in the latter months. A manuscript has been written and successfully
published (Hellenbach and Tiozzo et al. 2011, J. Exp. Biol. Part A).
A review on germ cells formation and gonad regeneration in ascidians has been completed and published
(Tiozzo et al. 2011 Dev. Dyn).
In the first half of 2011 literature has been gathered and a review on asexual propagation and regeneration
in colonial ascidians has been written and accepted in Biological Bulletin (Kuern et al. 2011).
Data collected in the last two years have been analyzed in the last months and a manuscript on
“Phagocyte dynamics during colonial propagation of a basal chordate: implications for development and
host defense” will be ready for submission by the middle of the summer; the later study have been done in
collaboration with Prof. Robert Lauzon (Union College, Albany NY, USA).
Entirely new projects started during the first years of lab activity and currently ongoing:
-
A series of experiments aimed to identify the temporal and spatial pattern of expression of germ layers
markers in the asexual development of B.schlosseri were started: a battery of gene markers have been
cloned, RNA probes synthetized and whole mount in situ hybridizations are currently being performed.
TEM analyses of whole body regeneration are in progress as well as immunohistochemical analyses of
epigenetic markers during the early phase of budding. This study has been used also to improve the
technique of in situ hybridization on paraffin section of Botryllus schlosseri colonies and juveniles. This is
currently an ongoing project, part of it in collaboration with De Tomaso lab (UCSB, USA).
-
A series of transciptomic data from Botryllus schlosseri, obtained during my postdoc from different stages
of asexual development, have been analyzed and assembled in collaboration with Philippe Dru
(Bioinformatician at UMR7009). A web based database has been generated, and different types of
assembling are now available and commonly used as main source of gene screening in this model.
-
A study on whole body regeneration on Botryllus schlosseri have been funded and started with a
morphological characterization and description of proliferative and apoptotic pattern during first step of
Vague D : campagne d’évaluation 2012-2013
Février 2012
2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
the regeneration. Quantification and analyses of pattern of expression of candidate genes involved on
maintenance of the pluripotency, tumorogenesis and endomesoderm differentiation is ongoing. At the
same time the development of technique of microscurgery and RNA linear amplification are under assay.
The latter will allow to precisely isolate tissue in order to perfom RNAseq and eventually transcriptomic
analysed of the first step of the whole body regeneration.
-
The model Macrostomum lignano (Plathelminthes) has been introduced in the lab. Preliminary studies
allowed developing a microsurgery technique to induce central nervous system regeneration. A simple and
reliable description of the latter have been done. We also identified orthologous of pro-neural genes in
Macrostomun and preliminary data showed their presence/activity in a context of adult homeostasis and
CNS regeneration.
-
Through collaboration with Prof. Roger Croll (Dalhausie University), who spent 8 months on sabbatical in
our laboratory, we provide the first anatomical description of olfactory sensory bulbs in a species of
cephalopods and a species of terrestrial snail. This represents the first detailed description of
lophotrochozoan olfactory system, and it will be followed by a screening of olfactory receptors possibly
trough tissue isolation and RNAseq.
2)
Production scientifique :
Before joining the UMR7009 (from 2007)
1. Stefano Tiozzo, Federico D. Brown, Anthony W. De Tomaso. Regeneration and Stem Cell in Ascidians.
In “Stem Cells: From Hydra to Man”. 2008. Springer eds.
2. Stefano Tiozzo, Ayelet Voskoboynik, Federico D. Brown, Anthony W. De Tomaso. A conserved role of
the VEGF pathway in angiogenesis of an ectodermally-derived vasculature. Dev. Bio. 2008 315(1):24355.
3. Stefano Tiozzo, Anthony W. De Tomaso. Functional analysis of Pitx during asexual regeneration in a
primitive chordate. Evol. Dev . 2009 11(2):152-62.
4. Stefano Tiozzo, Maureen Murray, Bernard M. Degnan, Anthony W. De Tomaso, Roger P. Croll.
Development of the neuromuscular system during asexual propagation in an invertebrate chordate.
Dev. Dyn. 2009 238(8):2081-94.
5. Stefano Tiozzo*, Federico D. Brown*, Michelle Roux*, Billie J. Swalla, Anthony W. De Tomaso. Early
lineage specification of long-lived germline precursors in the colonial ascidian, Botryllus schlosseri.
Development. 2009 136(20):3485-94. *equal contribution.
After joining the UMR7009
1. Stefano Tiozzo*, Kaz Kawamura*, Lucia Manni*, Takeshi Sunanaga*, Paolo Burighel*, Anthony W. De
Tomaso*. Gemline cell formation and gonad regeneration in solitary and colonial ascidians. Dev. Dyn.
2011 240(2):299-308. *equal contribution.
2. Stefano Tiozzo*, Ulrich Kuern*, Snjezana Rendulic*, Robert Lauzon. Asexual propagation and
regeneration in colonial ascidians. Biol. Bull. 2011 221(1):43-61 *equal contribution.
3. Annette Hellbach, Stefano Tiozzo, Jungho Ohn, Michael Liebling, Anthony W. De Tomaso.
Characterization of HCN2 and its cardiac function in the protochordate B. schlosseri. In press J.Exp.
Zool. A Ecol Genet Physiol 2011 315(8):476-86.
In preparation
Robert Lauzon, Catherine Castagna, Louis Kerr, Stefano Tiozzo. Phagocyte dynamics during colonial
propagation of a basal chordate: implications for development and host defense
3)
Points forts des activités ne relevant pas de la production scientifique :
1) Establishment of the laboratory.
With the help of the part-time technician assigned by the UMR7009 we planned the overall experiments for the
following months and consequently placed orders for consumable (plasticware, glassware, kits for molecular
biology, etc.) and basic equipment (centrifuges, set of pipettes, agitators, etc.). The laboratory space was
planned accordingly to the needs and the missing benches and furniture have been ordered and put on place.
The animal facility was designed and then built by a private company. Several modifications have been
successively added to this facility in order to optimize it and make it operative. Then specimens of Botryllus
schlosseri (ascidiacea) have been collected in situ and along the coast of south of France, plus ordered from
other French marine facilities. The marine culture has then been established.
2) Grant writing.
In order to provide financial support to the new established laboratory, several national and international grant
proposals have been written and submitted (Marie Curie, ARC, AFM, UPMC-EMERGENCE, ATIP-AVENIR, ANR
Blanc II). All the proposals concerned topics related to the line of research presented at the CNRS Section 21.
At the current time, the laboratory received financial support from the European Community through the Marie
Vague D : campagne d’évaluation 2012-2013
Février 2012
3
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Curie Reintegration Grant – IRG (100.000 Euro in four years) and from the UPMC via an UPMC-EMERGENCE grant
(90.000 Euro). Whereas the first is devoted to provide consumables and small equipment, the latter will be
entirely used to cover a three year salary for a PhD student. In this sense, a public search has been done and a
candidate has been selected and joined the laboratory starting from October 1st 2011.
3)
Invited presentations at conferences:
x Annuel meeting SFBD (Dourdan, 2007).
x Joint meeting SEBD-SFBD (Toulouse, 2009).
4)
Invited seminars and workshops:
x Journées André Picard (Banyuls, 2011).
x EFOR meeting (Paris, 2011).
x EFOR meeting (Paris, 2012).
5)
Teaching:
x Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology
course at Villefranche-sur-Mer.
6)
Supervision of post-doc/PhD/master:
x PhD (x1)
x Master (x2)
7)
Scientific evaluations:
x Refereeing for journals: Dev Biol (x1), Zootaxa. (x1), MBE (x1), Cell. Tissue Res. (x1),
x Refereeing for research grants: Israel Science Foundation (x1)
8)
Member of PhD steering committees:
x Julien Laurent (PhD/2011-2014, Centre Scientifique de Monaco, Monaco).
x Quentin Schenkelaars (PhD/2012-2015, UMR7263 IMBE, Marseille).
9) Administrative responsibilities: Group leader since 2010.
10) Other activities.
During the last years I attended three international (Sesimbra, Montreal , Nice) and two national
conferences/meetings (Paris, Banyuls) where the lab was present either with talks and poster, and one
workshop (Villefranche); established two new international collaborations: De Tomaso lab (UCSB, US) and Croll
lab (Dalhousie University, Nova Scotia - Canada).I am part of an Organizing Committee with Jean-Stephane Joly
(UPR3294 CNRS) and Xavier Beilly (Station Biologique de Roscoff) addressed to organize a workshop on
“EMERGING AQUATIC MODEL SPECIES FOR BIOMEDICAL RESEARCH”, funded by EMBRC.
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date :
12-09-2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
12-09-2012
Signature :
Vague D : campagne d’évaluation 2012-2013
Février 2012
4
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Vague D :
campagne d’évaluation 2012 - 2013
Unité de recherche
2.3. Fiche individuelle d’activité
(à joindre à la partie « projet »)
Enseignant-chercheur, chercheur, ingénieur de
recherche ou cadre scientifique, autres personnels
ayant une activité de recherche
(la fiche ne devra pas dépasser 4 pages)
Fiche à remplir obligatoirement par tous les enseignants-chercheurs et chercheurs, ainsi que par les ingénieurs
de recherche, les cadres scientifiques et les autres personnels ayant une activité de recherche.
Elle doit être jointe à la partie « Projet » du dossier : elle concerne les personnels appelés à faire partie de la
future unité au 1er janvier 2014.
La signature de ces fiches par la personne concernée et le directeur de l’unité est obligatoire pour attester
l’appartenance de cette personne à l’unité de recherche. On ne peut être rattaché qu’à une seule unité.
Il convient de rappeler que ces fiches complètent la présentation de l’unité et ne sont nullement destinées à
l’évaluation individuelle des personnes, qui ne relève pas des missions de l’AERES.
Unité de recherche d’appartenance en 2012 :
(label et n°, intitulé, établissement principal, responsable)
Unité soumise à une reconnaissance
prenant effet 1er janvier 2014 :
(intitulé, établissement support, responsable)
UMR7009, Biologie du Développement, CNRS
Evelyn HOULISTON
Laboratoire de Biologie du Développement de
Villefranche-sur-Mer (LBDV), CNRS, UPMC
Evelyn HOULISTON
Nom : YASUO
Prénom : Hitoyoshi
Date de naissance : 08/12/1967
Courriel : [email protected]
Établissement d’affectation ou organisme d’appartenance :
Vague D : campagne d’évaluation 2012-2013
Février 2012
1
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
Enseignant-chercheur
†
Thèse soutenue †
HDR
†
Corps-grade :
Bénéficiaire de la PES :
†
Membre IUF junior
senior
†
†
Chercheur
_
Thèse soutenue _
HDR
_
Corps-grade : DR2
Ingénieur
†
Thèse soutenue †
HDR
†
Corps-Grade :
HDR
†
Corps grade :
Cadre scientifique ou autre personnel ayant une activité de recherche :
Préciser :
Thèse soutenue †
Situation particulière :
(délégation, détachement, mise à disposition, etc.)
Domaine scientifique principal :
† 1 Sciences de l’homme et de la société
† 2 Sciences et technologies
_ 3 Sciences de la vie et de l’environnement
Rattachement scientifique :
Section du CNU :
ou
Département(s) scientifique(s) et/ou commissions
spécialisées d’un organisme : 22 (new section)
1)
Points forts des activités de recherche et résultats marquants :
Our group has been studying how embryonic precursors are generated during development with a particular interest in
dissecting a sequence of specification events leading to acquisition of specific fates. We chose to study ascidian
embryogenesis as a model system because it proceeds with a fixed cell division pattern, a small number of cells and
well-described cell lineage. The strength of our research group resides in our rigorous experimental approach
exploring these advantageous features of the ascidian model to describe fate specification events at the level of
individual cells. We have so far focused on cell fate choice events that lead to formation of the notochord and caudal
neural lineage and how the caudal neural lineage is subsequently patterned. In these lineages, we were able to
dissect every cell fate choices starting from the 16-cell stage to the neural plate stage, thus covering four successive
rounds of cell divisions. We have identified the molecular natures of the signalling events controlling these cell fate
choices. Importantly, our findings show that most of these cell fate choices operate in a binary mode. In addition to
these projects, we have initiated projects addressing cell biological bases of ascidian embryogenesis, namely oriented
cell divisions. Cell division patterns during ascidian embryogenesis are extremely conserved among solitary ascidian
species belonging to different orders and are most likely to be an issue of developmental constraint. We are focusing
on two sister cells which are part of the notochord/neural lineage since they divide in the same direction as their
mother do to generate them. Our results show that these sister cells exhibits distinct modes of spindle orientation? In
one of these cells, the duplicated centrosomes exhibit an asymmetrical behaviour whereby one centrosome with
extensive astral microtubules remains immotile while the other with fewer astral microtubules moves 180° around the
nucleus. Interestingly, we have found that this asymmetric centrosome movement depends on the cell shape which is
slightly tapered on the side where the immotile centrosome resides.
These projects were/are being supported by the following research grants written by Clare HUDSON and
Hitoyoshi YASUO; subventions ARC (2005-2007; 2008-2010) and ANR Programme ‘Blanc’ (2005-2007; 2009-
2013). I was also the coordinator of the Phallusia mammillata EST project in partnership with the Genoscope
(2009).
2)
Production scientifique :
1) Yasuo H and Hudson C (2007). FGF8/17/18 functions together with FGF9/16/20 during formation of the
notochord in Ciona embryos. Dev. Biol. 302:92-103.
2) Meedel TH, Chang P and Yasuo H (2007). Muscle development in Ciona intestinalis requires the b-HLH
myogenic regulatory factor gene Ci-MRF. Dev. Biol. 302:333-344.
3) Picco V, Hudson C, and Yasuo H (2007). ephrin/Eph signalling drives the asymmetric division of
notochord/neural precursors in Ciona embryos. Development 134:1491-1497. *Cited in Faculty 1000.
4) Hudson C, Lotito S and Yasuo H (2007). Sequential and combinatorial inputs from Nodal, Delta2/Notch and
FGF/MEK/ERK signalling pathways establish a grid like organisation of distinct cell identities in the ascidian
neural plate. Development 134:3527-3537.
5) Hudson C and Yasuo H (2008). Similarity and diversity in mechanisms of muscle fate induction between
ascidian species. Biol. Cell. 100:265-77. Review.
6) Sardet C, McDougall A, Yasuo H, Chenevert J, Pruliere G, Dumollard R, Hudson C, Hebras C, Le Nguyen N
and Paix A (2011). Embryological methods in ascidians: the Villefranche-sur-Mer protocols. Methods Mol.
Biol. 770:365-400.
Vague D : campagne d’évaluation 2012-2013
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2
Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV)
7) Hudson C, Ba M, Rouvière C and Yasuo H (2011). Divergent mechanisms specify chordate motoneurons:
evidence from ascidians. Development 138:1643-52. *Cited in Faculty 1000.
8) Nishitsuji K, Horie T, Ichinose A, Sasakura Y, Yasuo H and Kusakabe TG (2012). Cell lineage and cisregulation for a unique GABAergic/glycinergic neuron type in the larval nerve cord of the ascidian Ciona
intestinalis. Dev. Growth Differ. 54(2):177-86.
3)
Points forts des activités ne relevant pas de la production scientifique :
Invited presentations at conferences:
1. Annuel meeting SFBD (Dourdan, 2007).
2. Joint meeting SEBD-SFBD (Toulouse, 2009).
Invited seminars and workshops:
1. National Institute for Medical Research (Mill Hill/England, 2007).
2. Institute of Toxicology and Genetics (Karlsruhe/Germany, 2007).
3. Journées André Picard (Paris, 2010).
4. EFOR meeting (Paris, 2011).
5. EFOR meeting (Paris, 2012).
Teaching:
1. Yearly participation in teaching the UPMC Masters level (BMC programme) Developmental Biology course
at Villefranche-sur-Mer.
2. Yearly participation in teaching the Nice Sophia Antipolis University (UNSA) Masters level Developmental
Biology course in Nice.
Supervision of post-doc/PhD/master:
post-doc (x2)
PhD (x2)
Master (x3)
Scientific evaluations:
1. Refereeing for journals: Development (x4), Mech. Dev. (x2), Curr. Biol. (x1), PLoS One (x1), Dev. Gene
Evo. (x1)
2. Refereeing for research grants: ANR (x4)
Member of PhD steering committees:
1. Leslie Marchal (PhD/2008, Laurent Kodjabachian’s group, Marseille)
2. François Robin (PhD/2009, Patrick Lemaire’s group, Marseille)
3. Ngan Le Nguyen Phuong (PhD/2012, Christian Sardet’s group, Villefranche-sur-Mer)
4. Agnès Roure (on-going, Sebastion Darras’s group, Marseille)
Member of PhD examination juries:
1. Vincent Picco (PhD student in my group, 2008)
2. François Robin (Patrick Lemaire’s group, Marseille, 2009)
3. Daniel Sobral (Patrick Lemaire’s group, Marseille, 2009)
4. Aurélie Quillien (Patrick Blader/Elise Cau group, Toulouse, 2010)
Member of HDR examination juries:
1. Andrea Pascini (IBDML, Marseille, 2008)
2. Sebastien Darras (IBDML, Marseille, 2012)
3. Vincent Bertrand (IBDML, Marseille, 2012)
Member of professor/lecturer selection juries:
Professor position in the IBDML (Marseille, 2011)
Administrative responsibilities:
Group leader since 2001.
Signature de la personne concernée par cette fiche d'activité
Je certifie n’avoir demandé mon rattachement qu’à une seule unité de recherche.
Date : le 11 septembre 2012
Signature :
Signature du responsable de l'unité de recherche d’appartenance en 2012
Date :
11 septembre 2012
Vague D : campagne d’évaluation 2012-2013
Février 2012
Signature :
3
Annexes 13 à 17
Sommaire Annexes Projet
Annexe 13
Organigramme prévisionnel 2014
Annexe 14
Règlement intérieur
Annexe 15
Protocoles d’accueil et de départ
Annexe 16
Maquette Master BBMa
Annexe 17
Plan de formation 2013
BioDev 2008
ANNEXE 14
Règlement Intérieur et ARTT
UMR 7009 CNRS UPMC, Biologie du Développement
1. Plusieurs décrets et la lettre de cadrage de la Direction du CNRS définissent les conditions de mise
en place de l'ARTT dans les Unités. Tout le personnel de l'Unité est concerné.
La lettre de cadrage du CNRS et un extrait de la présentation du Délégué Régional ont été
communiqués à l’ensemble de l’Unité par mail.
2. Le Conseil d'Etablissement de l'Observatoire Océanologique a voté la répartition suivante :
38h30 par semaine et 45 jours de repos par an.
De plus, deux jours de congés supplémentaires peuvent être accordés au titre du "fractionnement".
3. Organisation annuelle, hebdomadaire et journalière du travail (personnel à temps plein) :
Durée annuelle 1600 h.
Durée et cycle hebdomadaires : 38 h 30, sur 5 jours, du lundi au vendredi.
Durée journalière : 7 h 42
Plage horaire journalière : de 8h à 20 h.
Horaire de début : entre 8h et 9h 30.
Pause méridienne : entre 12h et 14 h
4. Congés et absences
Durée des absences de service : l'absence de service ne peut excéder 31 jours consécutifs (sans
déduction des samedis, dimanches et jours fériés).
Jours de fermeture : alignement sur l’Observatoire (fermeture non encore décidée).
Déclaration : les absences et congés doivent être annoncés le plus tôt possible aux responsables du
groupe, du service et de l'Unité pour concertation. Une fois décidés, ils doivent être déclarés par mail
pour pouvoir être gérés dans l'Unité et la Délégation.
Les absences pour motif de service (missions, cours, comités etc…) font l'objet de formalités
spécifiques.
5. Dérogations. Les dérogations récurrentes aux règles d'organisation doivent être autorisées par écrit
par le responsable de l'Unité.
6. Les agents qui pourraient faire l'objet de sujétions ou d'astreintes pour l'entretien ou la collecte des
animaux ou pour des missions embarquées à bord de navires du CNRS recevraient une indemnisation
à ce titre.
7. Règles d'Hygiène et Sécurité.
Il est strictement interdit de fumer dans les locaux de l'UMR comme dans tout l'Observatoire.
Les règles propres à notre activité sont présentées dans un document spécifique rédigé par l'ACMO
("Règlement Hygiène et Sécurité").
Commentaires.
Ce texte fournit un cadre général et une référence pour l'organisation du travail dans l'Unité. Il
s'applique avec toute la souplesse nécessaire pour concilier au mieux et dans la transparence les
impératifs du travail scientifique de chacun et les nécessités des services communs, et les contraintes
personnelles. La quantité globale de travail fourni et sa qualité restent les exigeances premières.
ANNEXE 14
BioDev 2008
Des contraintes ont été définies au niveau de l'Unité pour des raisons de sécurité et de bon
fonctionnement. La plage horaire journalière - ne pas confondre avec l'horaire de plage journalier – est
la période dans laquelle devrait se situer la quasi totalité du temps de travail. La présence simultanée
de tous favorise les interactions et permet un meilleur fonctionnement de l'Unité. Pour des raisons de
sécurité le travail solitaire hors plage horaire et hors jours ouvrables doit être limité au strict nécessaire
(voir règles d'Hygiène et Sécurité).
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PRESENTATION DU LABORATOIRE
Septembre 2012
Laboratoire de Biologie du Développement
UMR7009
- 
- 
- 
- 
- 
Institut de rattachement : INSB
Directrice : Evelyn Houliston
Tutelles : CNRS/UPMC
Plan de formation : OUI
Correspondante Formation : Jenifer Croce
UMR7009
38 personnes
24 CNRS
-  11 CR/DR
-  12 ITA
4 UPMC
-  1 MC
-  1 AI
-  2 T
10 Autres
-  1 CR INSERM
-  4 Post Doc/CDD
-  5 Thésards
Liste personnels de l'UMR7009 au 01/01/2013 et situation
NOM
Prénom
BA
BARREAU
BEKKOUCHE
BESNARDEAU
Moly
Carine
Faisal
Lydia
CARVALHO
Joao
CHANG
CHENEVERT
CHEVALIER
CROCE
DRU
DUMOLLARD
GILLETTA
GOMEZ
HAUPAIX
HEBRAS
HOULISTON
HUDSON
KHAMLA
Patrick
Janet
Sandra
Jenifer
Philippe
Rémi
Laurent
Anne-Marie
Nicolas
Céline
Evelyn
Clare
Mohamed
LAHAYE
François
LEPAGE
LHOMOND
LOTITO
MCDOUGALL
MOMOSE
PRULIERE
Thierry
Guy
Sonia
Alexander
Tsuyoshi
Gérard
RICCI
Lorenzo
ROMAGNAN
ROUVIERE
Jean Baptiste
Christian
RUGGIERRO
Antonella
SARDET
Christian
SCHUBERT
SIROUR
TIOZZO
Michael
Cathy
Stéfano
YASUO
Hitoyoshi
Grade
TCN
MCAS
IE2
AI
Date naissance
18/02/1982
02/12/1976
24/10/1973
03/07/1970
THESARD 12/11/1988
IR1
15/03/1949
CR1
26/01/1963
AI
24/07/1977
CR2
05/08/1977
AI
22/03/1964
CR1
22/08/1974
ATP2
28/05/1978
AI
21/10/1968
THESARD
26/03/1984
TCN
11/12/1978
DR1
12/01/1963
CR1
21/02/1973
T
17/10/1967
AI
29/12/1976
DR2
23/06/1962
IE1C
17/01/1960
TCN
23/07/1973
CR1
17/01/1966
CR1
24/03/1971
CR1
28/07/1956
THESARD 07/08/1981
THESARD
06/04/1982
IRHC
28/02/1961
THESARD 29/06/86
DR1
25/08/1946
CR1
20/02/1974
ASI
26/10/1976
CR1
18/11/1974
DR2
08/12/1967
Appartenance
CNRS
UPMC
CNRS
CNRS
Situation
Détachement
Permanent
Permanent
Permanent
Non permanent
CNRS
CNRS
CNRS
CNRS
CNRS
CNRS
CNRS
CNRS
UNS
CNRS
CNRS
CNRS
UPMC
CNRS
Permanent
Permanent
Permanent
Permanent
Permanent
Permanent
Permanent
Permanent
Non permanent
Permanent
Permanent
Permanent
Permanent
Permanent
CNRS
CNRS
CNRS
CNRS
CNRS
INSERM
Permanent
Permanent
Permanent
Permanent
Permanent
Permanent
UPMC
UNS
Non permanent
CNRS
UPMC
CNRS
CNRS
UPMC
CNRS
CNRS
Non permanent
Permanent
Non permanent
Emérite
Permanent
Permanent
Permanent
Permanent
Plan de Formation
UMR7009 Biologie Développement
Présentation scientifique :
Les membres de l'Unité ont exprimé leurs besoins en formation dans 5 domaines principaux.
1) Hygiène et Sécurité. Nous nous efforçons d'actualiser les compétences spécifiques des responsables
(ACMO, PCR…) et de généraliser les formations de base à l'ensemble du personnel.
2) Management / Gestion. Un renouvellement des équipes de l’UMR est en cours. Notre objectif est que
tout nouveau chef d’équipe suive les modules de base de la formation « Management ». Un besoin pour
certaines formations plus spécifiques a été exprimé par certains chercheurs, notamment pour la gestion
des contrats et l’encadrement des étudiants en thèses.
3) Bureautique et Informatique. Plusieurs agents, notamment ceux affectés au service commun « I4 »
(informatique, imagerie, bioinformatique et infographie) , ainsi que ceux du service administratif, ont
exprimé des besoins en formation sur des logiciels d'infographie et de bureautique spécifiques qu'ils
utilisent au quotidien mais dont les mises à jour augmentent régulièrement leur complexité d'utilisation.
4) BioInformatique. Suivre les rapides évolutions du secteur de la bioinformatique est un des grands défis
du moment dans notre domaine. La génération de grands volumes de séquences génomiques et
transcriptomiques est de plus en plus routinier dans notre champ de recherche grâce au développement
rapide de nouvelles méthodes de séquençage nucléotidique. Pour chacune des espèces modèles utilisées
par nos équipes de recherche, le génome est de plus connu ou en cours d’assemblage ou d’annotation,
avec une forte implication des membres de l'UMR dans chacune de ces étapes et dans la transmission des
données. Le séquençage « haut débit », en permettant l’analyse en parallèle de plusieurs milliers de gènes,
rend aussi possible l’étude de l’expression d’un ensemble de gènes au cours du développement
(transcriptome) ou après des perturbations génétiques spécifiques, et donc l'établissement de réseaux de
gènes. Une bonne maîtrise des techniques de bioinformatique devient donc incontournable pour analyser
et comparer les séquences, interroger les banques de données, construire les réseaux d'interaction, etc.
Des apprentissages dans ce domaine sont ainsi indispensables pour un grand nombre des membres de
notre unité, en particulier au niveau des analyses de données transcriptomiques et de phylogénie
moléculaire. Plusieurs agents ont suivi et/ou demandent à suivre des formations individuelles adaptées à
leurs besoins spécifiques. L'AI responsable du service commun de bioinformatique (Philippe Dru) a
également besoin de formations particulières supplémentaires sur des techniques précises.
5) Techniques spécifiques de recherche expérimentale. Plusieurs techniciens de recherche ont besoin de
formations spécifiques afin de suivre les évolutions des techniques qu'ils emploient dans leur métier,
notamment en biologie moléculaire (QPCR) et en biochimie.
6) Langue. Nous recrutons de plus en plus de personnels de tout niveau (statutaires, doctorants et postdoctorants) dont le français n’est pas la première langue. Pour permettre leur intégration rapide et leur
pleine participation à la vie du laboratoire, une formation en français est souvent indispensable.
Inversement il devient de plus en plus important pour les agents français du laboratoire de pouvoir
communiquer en anglais, pour les collaborations dans les réseaux internationaux et pour l’accueil de
collaborateurs étrangers.
Vision globale des formations demandées:
Un des objectifs principaux du plan actuel de formation est d’apporter à tout le personnel de l’unité une
formation théorique et pratique sur les technologies les plus récentes (à citer par exemple un besoin
important de formation en PCR quantitative). Les autres besoins les plus exprimés sont pour les
formations en Français pour les étrangers, en bureautique, en management et en secourisme.
Satisfaire le besoin croissant de formation en bioinformatique est prioritaire. Les formations de base en
bioinformatique, ainsi que pour le traitement d’images, sont assurées en interne par notre service
« Informatique-BioInformatique-Imagerie-Infographie ».
Cependant,
certains
techniques
en
bioinformatique plus spécifiques sont importantes à maitriser par les agents de l’UMR et necessitent des
formations externes:
1- Analyse de données génomiques, transcriptomiques, protéomiques
2- Comparaison de séquences ; phylogénie moléculaire ; modélisation.
3- Traitement de séquences en Blast simple et en batch.
4- Introduction et formations avancées au logiciel R.
5- Outils pour la reconstruction de réseaux biologiques.
Pour les points 1 et 2 nous prévoyons dans la période 2013-2014 d’organiser sur le site de l'UMR deux
journées de formation thématiques pointues, en invitant des formateurs spécialisés dans les domaines
(notamment des experts du séquence à haut débit et de la phylogénie moléculaire).
Offres de formation et de compétences de l’unité
Certaines technologies sont très bien maîtrisées au sein de notre unité. Plusieurs formations sont déjà
dispensées par certains de nos agents tant au niveau national (microscopie à fluorescence, confocale ou à
déconvolution et traitement d’images) qu’au niveau local (hybridation in situ ; micro-injection et
manipulation des oeufs de nos espèces modèles ; bioinformatique).
Le premier domaine de compétence de l'unité concerne la microscopie et l’imagerie. Nous possédons un
équipement remarquable et nous avons des personnels très compétents. Tous les nouveaux entrants
profitent déjà des formations en interne sur l’utilisation des microscopes et le traitement d’images. Le
second domaine de formation concerne la biologie (biologie cellulaire, biologie moléculaire,
développement embryonnaire…). Plusieurs chercheurs et ITA maîtrisent parfaitement certaines
techniques de pointe, et transmettent régulièrement leur savoir faire.
Microscopie :
- Traitement des images numériques
- Microscopie confocale
- Microscopie électronique : Méthodes de congélation rapide et cryo-décapage
Biologie:
- Hybridation in situ sur des embryons d’oursins, d’ascidies, de méduses...
- Injection d’ARN messager dans des ovocytes de xénopes, méduses, ascidies, oursins.
- Elevage de méduses : maintien des adultes et maîtrise du cycle de vie
Bioinformatique :
- Initiation à la manipulation de séquences, comparaisons.
- Initiation à Bioedit, un logiciel de manipulation de séquences
Des formations dans ces domaines pour être dispensées dans nos locaux par les personnes compétentes.
Elles pourraient concerner de petits groupes (1 à 3 personnes) pouvant facilement s’intégrer dans nos
laboratoires.
1
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Type T1 : adaptation immédiate au poste de travail « ici et maintenant ».
Objectif : apporter à la personne des compétences qui sont nécessaires et directement utilisables dans le cadre des fonctions qu’elle occupe (adaptation à son poste de travail).
(en termes
DOMAINE
1
CONTEXTE
2
de compétences attendues)
ECHEANCE
SOUHAITEE 4
Bureautique
Utilisation quotidienne Gestion des documents longs,
du logiciel Word
mises en pages..
2013
Bureautique
Augmentation du
nombre de
document/dossiers à
traiter sous Excel
Savoir utiliser les
fonctionnalités d’excel
2013
Logiciels
Web: cms, Photoshop,
Illustrator, 3ds Max
2013
Bureautique
Finances
Finances
Informatique
Informatique
Informatique
Informatique
Informatique
Bioinformatique
Bioinformatique
Bioinformatique
Bioinformatique
Montage de projet
nationaux type ANR,
ARC Ligue
2013
1
6
A.M. Gomez (CNRS)
E. Houliston (CNRS)
A.M Gomez (CNRS)
M. Khamla (UPMC)
A. Ruggiero (thèse)
A.M. Gomez (CNRS)
1
J. Croce (CNRS)
2
Multiples besoins de La maitrise des bases déjà
mis en place de Base existantes sous Mysql ,CMS
de données au sein de (joomla, etc …) , Openldap
l’unité
2013
Introduction à la
virtualisation
Faire fonctionner des serveurs
privés virtuels sous XEN et
VMWARE
2013
Web
Communication orale et écrite
pour le web et les
manifestations "grand public"
2013
Le développement de nouvelles
fonctionnalités d’analyse
adaptées étroitement aux
recherches du laboratoire se
fait en JAVA
2013
F. Bekkouche (CNRS)
1
F. Bekkouche (CNRS)
2
M. Khamla (UPMC)
1
C. Rouvière (CNRS)
1
Formation à l'utilisation Formation aux outils IMARIS,
d'un logiciel spécifique 3D studio max, Avizo et
MATLAB pour modélisation en
3D
2013
Utilisation des outils et
logiciels
bioinformatique au
quotidien
2013
Faire des alignements et Blasts
en Batch, traiter des séquences
génomiques et
transcriptomiques (EST)
PUBLIC CONCERNE
2
2013
Programmation en
Java.
POUR L’UNITE 5
1
De plus en plus de
Savoir monter un dossier
dossiers de demandes financier calcul couts complets,
de financement
personnels (ANR...)
extérieurs
Apprendre les bases utiles d'un
montage de dossier type ANR,
ARC ligue
PRESTATAIRE
EVENTUEL
PRIORITE
OBJECTIF 3
F. Bekkouche (CNRS)
2
1
Formation à l'utilisation Introduction au logiciel R pour
d'un logiciel spécifique le traitement des données
transcriptomiques
2013
Des modèles de
réseaux d’interactions
géniques sont définis
au labo. Il faut les
modéliser..
Projets en cours
d’Annotation des
génomes de méduse,
ascidie, oursins.
Intégration de leurs
transcriptomes.
Définition de modèles de
réseaux intergéniques :
application aux nouveaux
modèles de protéines.
2013
Mise en place d’outils
permettant l’annotation de
génome
2013
S. Chevalier (CNRS)
C. Sirour (UPMC)
S. Lolito (CNRS)
F. Lahaye (CNRS)
A.
Ruggerio (thèse)
S. Tiozzo (CNRS)
2
Ph. Dru (CNRS)
2
Ph. Dru (CNRS)
1
REPONSE
FORMATION
ENVISAGEE
(+ coût)
Bioinformatique
Bioinformatique
Bioinformatique
Volumes croissants de Analyse des données de
données de sequence transcriptome et de genome
à traiter
2013
1
Evolution du sujet de
recherche vers
l’Evolution et
Développement
Comprendre et savoir faire un
2013
arbre phylogénétique à partir
de données moléculaires.
Acquérir des bases théoriques
en évolution
Arrivée de 3 génomes Traitement des données
Avant fin de l’année
et de 3 transcriptomes génomiques avec un langage
2012
au laboratoire :
objet.
Traitement automatisé.
Mise à Jour.
Scientifique
Analyses Statistiqies
Traitement statistique des petits
échantillons
2013
Scientifique
Evolution des
techniques de
Microscopie
Savoir utiliser les nouveaux
outils de microscopie (SPIM,
Spinning disc etc...)
2013
Scientifique
Scientifique
Scientifique
Evolution des
Pouvoir analyser des données
techniques d’ analyse issues des images de
d’images
microscopie (3D,
Modelisation…)
2013
Devenir autonome pour les
Besoin de renforcer
ses connaissances "de techniques de BM et pour les
base" en biologie
manipulations de séquences
moléculaire et sur les nucléotiques
principales de diverses
techniques utilisées au
laboratoire
Biochimie
Apprendre la mise en œuvre de
la technique d'interaction
protéine-protéine par GST pulldown et criblage par double
hybride dans la levure
2013
1
2
S. Tiozzo (CNRS)
Barreau (UPMC)
1
G. Lhomond (CNRS)
R. Lara-Ramirez (CNRS)
J. Carvalho (thèse)
E. Zieger (thèse)
L. Besnardeau (CNRS)
1
2013
Scientifique
Expérimentation :
QPCR
Utilisation LightCycler 480,
initiation aux applications et
conception de manipulations de
quantification QPCR
2013
Besoin d’aquerir une
nouvelle technique, en
relation avec des
projets en cours
Apprendre les bases des
techniques de protéomique
dont la production de protéines
recombinantes
2013
Langue
Cours de Français
2013
2
1
Besoin Spécifique
Evolution du sujet de
recherche vers
l’Evolution et
Développement
L. Besnardeau (CNRS)
S. Lotito (CNRS)
F. Lahaye (CNRS)
G. Lhomond (CNRS)
E. Zieger (thèse)
J. Carvalho (thèse)
R.Lara-Ramirez (CNRS)
F. Lahaye (CNRS)
1
1
Evolution des ita
J. Croce (CNRS)
M. Schubert (CNRS)
C. Sirour (UPMC)
S. Lolito (CNRS)
F. Lahaye (CNRS)
2013
Migration de protéines sur gel
en 2D, isoelectric focusing
Communication
C.
1
Biochimie
Communication
E. Houliston (CNRS)
S. Chevalier (CNRS)
C. Barreau (UPMC)
Ph. Dru (CNRS)
Ph. Dru (CNRS)
1
Scientifique
Scientifique
1
G. Lhomond (CNRS)
P. Dru (CNRS)
J. Croce (CNRS)
J. Carvalho (thèse)
R.
Lara-Ramirez (CNRS) E.
Zieger (thèse)
Préparation orale, amélioration
de l’expression écrite, pour
concours internes et sélection
professionnelle
2013
Cours en Evo-Devo
2013
S. Lotito (CNRS)
E. Zieger (thèse)
J. Carvalho (thèse)
R.Lara-Ramirez (CNRS)
Plusieurs ITA
1
A. Ruggerio (thèse)
2
Interne BioDev
Besoin Spécifique
Besoin Spécifique
Management
Management
Evolution de
l’animalerie
Visite d'animaleries élevant des
ciones et/ou des amphioxus
2013
Fonctionnement et utilisation de
lasers
candidate potentiel de Apprendre les Bases du
devenir responsable management
d’ équipe
2013
Laser
Encadrant d'étudiants Apprendre les bases du
en thèse
management d'étudiants en
thèse
L. Gilletta (CNRS)
1
2
2013
1
2013
1
C. Rouvière (CNRS)
J. Croce (CNRS)
S. Tiozzo (CNRS)
T.
Momose (CNRS)
H.
Yasuo (CNRS)
A.
McDougall (CNRS) M.
Schubert (CNRS)
C. Barreau (UPMC)
Type T2 :
adaptation à l’évolution prévisible des métiers « ici et demain ».
Objectif : Apporter à la personne des compétences au regard de l’évolution prévisible de son emploi (adaptation à son métier)
DOMAINE 1
CONTEXTE 2
Formation Anglais Besoin dans le
cadre du travail
d’anglais écrit et
OBJECTIF 3
(en termes
de compétences
attendues)
Perfectionnement
de la langue
PRIORITé
POUR L’UNITé 5
éCHEANCE
SOUHAITé 4
2013
PUBLIC CONCERNé
6
L. Gilletta (CNRS)
RéPONSE
FORMATION
ENVISAGéE
PRESTATAIRE
éVENTUEL
(+ coût)
Type T3 : développement des qualifications ou acquisition de nouvelles qualifications« ailleurs et demain ».
Objectif : Permettre à la personne d’acquérir des compétences s’inscrivant dans un projet professionnel et allant au-delà de celles exigées dans la fonction occupée
DOMAINE 1
Hygiène et sécurité
CONTEXTE 2
OBJECTIF 3
(en termes
de compétences
attendues)
Formation initiale
ACMO
PRIORITé
POUR L’UNITé 5
éCHEANCE
SOUHAITé 4
2013
PUBLIC CONCERNé 6
S. Chevalier (CNRS)
RéPONSE
FORMATION
ENVISAGéE
PRESTATAIRE
éVENTUEL
(+ coût)

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