Station Biologique de Roscoff
PhD proposals
ESTeam, 9 PhD proposals in Marine Sciences
Station Biologique de Roscoff, France
http://www.sb-roscoff.fr/ESTeam/
- Genetic and genomic analysis of sporophyte/gametophyte alternation
during the life cycle of the brown alga Ectocarpus siliculosus
Supervisors: J. Mark Cock (cock@sb-roscoff.fr) and Susana Coelho (Coelho@sbroscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7139.php
The application of modern genomic methodologies to novel model
organisms is opening new avenues of research in marine biology. The brown
algae are a particularly interesting group because they have evolved complex
multicellular development independently of the classic animal and terrestrial
plant models and because of recent progress towards the establishment of a
complete genome sequence and genetic and genomic tools for a model brown
alga, Ectocarpus siliculosus. The project proposed here will use a combination of
approaches to investigate the genetic control of sporophyte/gametophyte
alternation during the life cycle of Ectocarpus with the aim of identifying
important general mechanisms of developmental control. The project will involve
the use of genomic, genetic and cell biology methodologies to characterise
recently identified mutants with aberrant life cycles and will benefit from tools
such as a dedicated sporophyte/gametophyte microarray that have been
developed within the group.
- Structure and self-assembling of carrageenan. Toward the
biomimetism of the red algal cell walls
Supervisor: W. Helbert ( helbert@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7139.php
Carrageenans are highly sulphated galactans occurring abundantly in the
red algal cell walls. These hydrocolloids are well-known for their gelation
properties which are extensively exploited in industry. In vivo, the gelation is
promoted by the action of enzymes namely the galactose-6-sulfurylases, which
arise at the late step of the biosynthesis the carrageenans. In order to
understand the modalities of self-assembly of carrageenans in the cell wall, the
research program will consist in the characterisation of the biosynthetic
precursors of iota-carrageenan and the analysis of the mode of action of two
classes of galactose-6-sulfurylase.
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Station Biologique de Roscoff
PhD proposals
- From the genome to the structure: Functional and structural
investigation of agarases present in marine bacteria.
Supervisors: M. Czjzek (czjzek@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7139.php
Marine macroalgae synthesize a great diversity of polysaccharides, which
constitute their cell wall and energy storage. These algal polysaccharides
constitute a crucial carbon source for a number of marine bacteria. The recycling
of red algal biomass involves microorganisms which produce (and secrete)
specific glycoside hydrolases, such as diverse agarases. Although most
characterized β-agarases hydrolyze the β-(1,4) linkage in agarose, sequence
analyses indicate that they belong to three unrelated families of glycoside
hydrolases, the families GH16, GH50 and GH86. We have also recently cloned
and sequenced the gene of the -agarase of Alteromonas agaralytica. This
enzyme, which cleaves the -(1,3) linkage of agarose, defines a new structural
family of glycoside hydrolases (GH96). Finally, we have clones corresponding to
-agarases from the family GH50 of Saccharophagus degradans at our
disposition.
Structural and mechanistic data lack for the β-agarases of families GH50 and
GH86 and for family GH96 -agarases. Furthermore, even within family GH16
sequence alignments of new members suggest a large diversity of agarase
functions. In order to investigate agar degradation in further detail we propose to
study the structural determinants of the variation of substrate specificity within
the agarase sub-family of GH16 as well as the structure/function relationship of
agarases from families GH50 and GH96. The objectives of the thesis will be to i)
overexpress different constructs of selected β-agarases and the -agarase in E.
coli; ii) characterize biochemically and enzymatically a selection of soluble gene
products iii) crystallize selected agarases, belonging to families GH16, GH50 or
GH96 and iv) determine the 3D crystallographic structure of selected agarases as
well as that of inactivated mutants in complex with substrate oligosaccharides.
- Abiotic stress in Ectocarpus: a transcriptomic approach
Supervisors: T. Tonon (tonon@sb-roscoff.fr) and C. Boyen (boyen@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7139.php
The remarkable ability of marine brown algae to adapt many different adverse
conditions such as emersion/immersion during tides cycles suggests that these
organisms have evolved specific mechanisms to overcome various environmental
stresses. This PhD project aims at developing a pilot oligo-micro-array,
comprising ca 2000 genes in order to identify the genes networks specifically
involved in abiotic stresses in the filamentous brown alga Ectocarpus siliculosus.
The specific function and activity of a few relevant candidate genes will also be
investigated using more targeted approaches such as RT-PCR experiments and
gene over-expression in heterologous systems.
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Station Biologique de Roscoff
PhD proposals
- Molecular bases of halogenation processes in the brown alga Ectocarpus
siliculosus
Supervisors: P. Potin (potin@sb-roscoff.fr) and C. Leblanc (leblanc@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7139.php
In the research group “Algal Defenses and Halogenation”, a new PhD project
aims at investigating the molecular and biochemical bases of halogen metabolism
in the emerging brown algal model Ectocarpus siluculosus taking advantage of
these new genomic and genetic resources (a large-scale project to sequence the
complete genome of Ectocarpus is underway and will be achieved in 2006 at
Genoscope, France).
The first objective is to mine genes putatively involved in halogenation
processes, such as vanadium haloperoxidases (vHPO) and dehalogenases in the
Ectocarpus genome and EST databases using bioinformatic approaches. The
second objective is to apply proteomics and metabolite profiling methods to
better characterize the biochemistry and chemistry of halogenation in
Ectocarpus. Metabolic profiling of halogenated metabolites will be analysed to
identify the qualitative and quantitative changes in these compounds in control
conditions in Ectocarpus, in response to an elicitor of defence responses and in
the presence of inhibitors of vHPOs. The third objective is to develop new
mutagenesis screens, in order to select mutants: 1) which are impaired in their
halogenation capability in comparison with cultures of wild type gametophytes,
and 2) which present changes in their halogenation properties in response to
different stresses such as defence elicitation. After genetic analyses, in-depth
phenotypic characterization will use transcriptomic, proteomic and metabolite
profiling approaches developed during the previous phases of the project.
Design, functioning and production of trophic networks in the
rocky coastal environment combining stable isotopes (13C, 15N) and
production studies
Supervisor : Pascal Riera (riera@sb-roscoff.fr).
http://www.sb-roscoff.fr/ESTeam/umr7144.php
Design, functioning and production of trophic networks in the rocky coastal
environment combining stable isotopes (gama13C, gama15N) and production
studies
As opposed to most of coastal ecosystems such as mudflats, salt marshes or
estuaries, the food webs associated rocky shores remain poorly studied. The
question of the project is to define trophic groups and relations among them to
unravel the structure and functioning of the food webs of rocky shores. By the
use of stable isotopes and complementary methodological approaches the aim is
(1) to evidence and quantify the major trophic links in coastal rocky shores, (2)
to point out the ecological impact on the biodiversity and the food chains in
different rocky coastal areas submitted to different man-made modifications.
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Station Biologique de Roscoff
PhD proposals
Keywords: Rocky shore, food web, stable isotopes, invertebrates, macromicroalgae, production
- Genomic, transcriptomic and genetic study of photoacclimation
mechanisms and light stress response in the marine picocyanobacteria
Synechococcus spp.”
Supervisors: Laurence Garczarek (garczare@sb-roscoff.fr) and Frédéric Partensky
(partensky@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7144.php
The project we are proposing for Esteam mainly concerns the molecular
study of photophysiology in marine picocyanobacteria. It will require a graduate
student with a strong training in molecular biology. He (or she) will first do some
comparative physiological studies of the effects of visible and UV light under
simulated light:dark cycles for three /Synechococcus/ strains with different
pigmentation (WH7803, WH8102 and M16.17) and one high light-adapted
/Prochlorococcus/ strain (PCC9511). Using a whole genome microarray and a
mutagenesis approach, he (or she) will then make refined studies of the
photoacclimation mechanisms in the WH7803 strain at the transcriptomic level.
This study will be completed by modelling the regulation network(s) involved in
the light stress response in this strain. At last, he (or she) will make some
genome comparisons with other marine picocyanobacteria for all genes identified
as being involved in photoacclimation and light stress responses in WH7803 in
order to draw some considerations about evolution of photosynthesis and
photoacclimation in this ecologically important lineage.
Role of Red-Queen selection, life cycle, and sex in the evolution of
marine pelagic viruses and their hosts
Supervisors: Colomban de Vargas (vargas@sb-roscoff.fr), and Willie Wilson,
(WHW@pml.ac.uk)
http://www.sb-roscoff.fr/ESTeam/umr7144.php
Modern optical and genomic techniques have revealed abundant and diverse
marine planktonic viruses.
Although the influence of viruses on marine
geochemical cycles (via the regulation of host populations), and prokaryote
evolution (via lateral gene transfer), is well recognized, the processes creating
and maintaining such huge oceanic viral diversity, including its rate of evolution,
are largely unknown. Mechanisms of co-evolution between hosts and their
viruses, where both are fighting to respectively decrease and increase virulence,
are certainly playing critical roles. We propose to test two main hypotheses,
using the coccolithophore Emiliania huxleyi as model: (A) virulence in pelagic
host-virus interactions is highly specific, constrained by the boundaries between
species, sub-species, or strains; (B) virulence is not species specific, but lifestages specific, and thus constrained by the sexual alternation between haploid
and diploid populations. Experiments will test if “Red-Queen” processes are
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Station Biologique de Roscoff
PhD proposals
driving ecological/evolutionary diversification in coccolithoviruses and their hosts,
and will address whether host evolution is driven by rapid genomic mutations, or
rather by genomic restructuring through haploidization and/or genetic
recombination associated with sex. Results will enhance our understanding of the
nature and tempo of evolution of planktonic host-virus interactions.
The use of genomic tools to detect molecular adaptation in the
hydrothermal-vent polychaete Alvinella pompejana in response to
thermal and oxidative stresses
Supervisors: Arnaud Tanguy (atanguy@sb-roscoff.fr) and Franck Zal
http://www.sb-roscoff.fr/ESTeam/umr7144.php
Eurythermal eukaryotes associated with deep-sea hydrothermal vents are
one of the most exposed organisms to highly fluctuant thermal regimes over
small spatial scales. The aim of our project is 1) using both transcriptomic and
proteomic approaches, to identify enzymatic system involved the response of
Alvinella pompejana, the "Pompeii worm", to thermal and oxidative stress. 2) to
compare patterns of gene expression between colonists and reproducers in order
to identify a set of genes that could respond to thermal stress adaptive
polymorphims in both stress-regulated genes and to identify over a large set of
genes randomly sampled in the genome of A. pompejana in order to compare
colonists (first young individuals that settle on new ‘hot’ chimneys) and
reproducers (well-established individuals in aged populations from which thermal
conditions are much more cooler).
- Evolution of respiratory adaptations in deep-sea hydrothermal vent
scaleworms
Supervisors Stéphane Hourdez (hourdez@sb-roscoff.fr) and François Lallier
http://www.sb-roscoff.fr/ESTeam/umr7144.php
Polynoids (scaleworms) are annelid worms found in diverse marine
environments, from littoral to abyssal, including hydrothermal vents. Although
hydrothermal vents are oases of life in an otherwise barren background, the
environmental conditions are quite challenging for metazoans: high CO2, heavy
metals and toxic compounds concentrations, low oxygen concentrations and
highly variable temperatures in time and space. Polynoids living there must
therefore exhibit adaptations, in particular respiratory ones. We want to study
the evolution of these adaptations that allowed the colonization of the
hydrothermal vent environment. A primary target for this study is the respiratory
pigment hemoglobin, absent in littoral species, but abundant in vent species. We
are using a molecular approach that aims at sequencing and comparing genes
encoding globins and the genomic regions surrounding them in order to
understand their emergence and evolution within the family Polynoidae. This will
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Station Biologique de Roscoff
PhD proposals
also allow us to understand the regulation of their expression. Time permitting,
this study will be extended to some key metabolic enzymes involved in anaerobic
metabolism, a strategy these worms most likely have to rely on when oxygen
levels are too low.
- Volatile Halogenated Organic Compounds in the marine
environment : Production by macroalgae and phytoplankton.
Exchange fluxes with atmosphere.
Supervisor: Pascal Morin (pmorin@sb-roscoff.fr), P Lecorre
http://www.sb-roscoff.fr/ESTeam/umr7144.php
Macroalgae and different phytoplanktonic species are known to produce different
VHOC : short lifetime polyhalogenated compounds (CH2Br2, CHBr3, CH2I2, …) and
monohalogenated compounds (CH3Br, CH3Cl, CH3I) which have a better
photochemical stability and play a more important role in the chemistry of the
stratosphere. Expanding on previous work in our laboratory, production of
biogenic VHOC by macroalgae will be studied with a particular interest on the
seasonal variations of production and fluxes at the ocean - atmosphere interface
and a budget of the exchange fluxes will be estimated at different time scales
(seasonal, tidal cycles). Studies will be carried out in the Western English
Channel which has one the most important macroalgal beds in the world ocean
and is a key area far from industrial and urban influences to study the production
and fluxes of the biogenic VHOC by macroalgae and in the North Atlantic
subpolar and subtropical gyres for phytoplankton.
- Translational regulation and ions-current modifications during the cell
cycle of marine organisms.
Supervisors: Patrick Cormier (cormier@sb-roscoff.fr) and Stéphane Egée
(egee@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7150.php
The aim of this interdisciplinary project is to study the relationships
between translational control, ions-current modulations and cell cycle following
fertilization in marine organisms. Signal transduction pathways involved in these
different processes will be studied in physiological and evolutionary contexts.
- Evolution, regulation and physiological role of membrane ionics
channels in red blood cells of sea water fishes.
Supervisor : Serge Thomas (thomas@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7150.php
This project, using the electrophysiological technique of extracellular
patch-clamp, is aimed at identification and description of ion movements through
conductive pathways in fish RBC and at addressing the poorly understood
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Station Biologique de Roscoff
PhD proposals
aspects of their regulation and physiological role in different species of fish.
These aspects are considered in the double standpoint i/ of the implication of
ionic channels in upholding the electrolytic and acido-basic steady-state
corresponding to intracellular homeostasis, and ii/ of their participation in the
processes of regulation activated as soon as this steady-state is disrupted
(hypoxia, hypercapnia, pH variations, osmotic shock,...).
- From Sea to Pharmacy: characterization of the intracellular
mechanisms of action of new inhibitors of cell proliferation derived from
marine organisms (variolin B, meridianins, hymenialdisine and
lamellarins)
Supervisor: Laurent Meijer ( meijer@sb-roscoff.fr)
http://www.sb-roscoff.fr/ESTeam/umr7150.php
Marine organisms constitute an original source of enzymes and inhibitors
with great biotechnological potential in the pharmaceutical treatment for several
important human diseases.
Nowadays it is estimated that 30-35 % of drug discovery programs in the
pharmaceutical industry target protein kinases, the enzymes responsible for
protein phosphorylation. Currently about 60 kinase inhibitors are undergoing
clinical evaluation against cancers, inflammation, diabetes, neurodegenerative
diseases. We have focused our efforts on the search for pharmacological
inhibitors of cyclin-dependent kinases (CDKs), a class of enzymes involved in
cancers, Alzheimer’s disease and stroke. The selectivity of such pharmacological
inhibitors and their intracellular mechanism of action remains a matter of debate
and extensive investigation. Using affinity chromatography on immobilized
inhibitor and yeast genetics technology, we will investigate the binding partners
of four inhibitors previously identified in the laboratory. These molecules variolin B, meridianins, hymenialdisine and lamellarins – are all natural products
derived from marine organisms. The synthesis of these molecules and analogs
thereof is on hand, thus circumventing the supply issue generally associated with
natural products. In addition the cellular action of these compounds will be
studied in terms of cell proliferation arrest and cell death induction. The aim of
this study is thus the characterization and optimization of new, marine
organisms-derived leads for the pharmaceutical treatment of cancers, stroke and
Alzheimer’s disease. Training will be provided in [1] biochemistry (enzymology,
affinity chromatography), [2] cell biology (cell proliferation and cell death
analysis), [3] molecular biology (cloning and expression of drug targets, yeast
genetics), [4] pharmacology (molecular screening, drug characterization).
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