[alife] Open PhD position in Computational Biology

[Hugues Berry]

Thanks to kindly forward this email to potentially interested students 
and sorry if you received multiple copies.

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Open PhD position in Systems and Computational Biology

**Deciphering the molecular mechanisms of aging in E. coli through 
computer simulations*
**coupled to innovative experimental approaches**
*

at the National Institute for Research in Computer Science and Control 
(INRIA),
Orsay, France,
and the National Institute for Health and Research in Medical Sciences 
(INSERM),
Paris, France
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Contacts :

--Hugues Berry--
Project-Team Alchemy, INRIA Saclay-Île-de-France Research Centre, Orsay, 
France –
hugues.berry at inria.fr - http://www-rocq.inria.fr/~hberry/

--Ariel Lindner--
U571 INSERM, Faculté Necker-Enfants Malades, Paris, France –
lindner at necker.fr - http://www.necker.fr/tamara/pages/ariel.html/

Further information at 
http://www-rocq.inria.fr/~hberry/PhD_proposal_ColAge.html


Summary
----------------

Recent results revealed that E. coli, though a symmetrically dividing 
organism, do age: of the two offsprings of a dividing cell, one is born 
older than the other. Intriguingly, like in multicellular organisms, 
aging in these bacteria is also related to protein aggregation, albeit 
through spatial distribution of protein aggregates within the cells. 
While the molecular mechanisms at play are still to be understood, they 
are likely to be significant for multicellular organisms as well. 
Uncovering the mechanisms of aging in bacteria is thus expected to shed 
new lights on the mechanisms of aging in all life kingdoms.
The general objective of the proposed PhD will be to study the 
mechanisms underlying protein-aggregation-related aging in E. coli. 
Specifically, protein-aggregation-related aging will be addressed 
whereby the student will aim at the identification of the molecular 
mechanisms involved in the observed aggregation patterns: what is the 
intracellular mobility distribution of aggregates that accounts for 
their polar-spatial distribution? Is this phenomenon purely passive or 
active (i.e. requiring ATP-dependent mechanisms, a result of 
interactions, e.g., with the nucleoids or the cell membranes)? Does 
protein unfolding play a role in the observed behaviors? More generally, 
the project may be enlarged to the study of other facets of cellular 
aging (e.g. radical oxygen species, dietary restriction etc.).
To meet this end, the student will undertake a systems biology approach 
and exploit a combination of computer modeling/simulations and recent 
experimental strategies in cell biology (microfluidics, synthetic 
biology). In order to handle these two approaches, the PhD position will 
be co-supervised by two research groups of the Paris area: project-team 
Alchemy at INRIA Saclay (computer simulation) and INSERM U571 at Necker 
Faculty of Medicine, Paris (experimental cell biology).


Required skills
---------------------

We are looking for a student with a high motivation for computational 
approaches of biological systems and their interactions with 
experimental studies. As she/he is expected to carry out both the 
experimental part and the simulation works her-/himself, preferred 
experience would consist of bioinformatics, computer science or 
(bio)physics students with a strong motivation for benchtop experiments 
or, conversely, biology/chemistry students with a strong envy for 
computational and simulation biology.


Scientific environment
------------------------------

This PhD position is part of a bigger research project co-funded by two 
French national institutes (computer science and medical science) whose 
aim is to foster the integration of experimental and modeling/simulation 
approaches in biology. One selected application topics concerns systems 
and synthetic biology studies of growth control and aging in bacteria. 
The PhD student will benefit from this strongly multidisciplinary and 
collaborative environment. Our objective is that he/she will acquire 
enough skills to be equally at ease with experimental and computational 
approaches. More generally, the student will benefit from the 
scientifically inspiring Paris area and its numerous collaboration 
opportunities.


Eligibility
----------------

The funding is part of a geographic mobility PhD program. Candidates 
with a master delivered by a university of Paris area are thus not 
eligible a priori, except if they have previously worked with industry 
or studied abroad or if this PhD represents a drastic thematic change in 
their curriculum. International applications are strongly encouraged. 
Working language will be English, thus French speaking is not necessary.


Miscellaneous
------------------

• Duration: 3 years
• Starting date: September-December 2009.
• Monthly salary: 1890 euros (years 1 & 2) then 1990 euros (year 3)
• Location: Modeling part of the project will be centerd at INRIA, 
Saclay (30 minutes from center Paris); experiments will be carried out 
in A. Lindner’s & F. Taddei’s Lab in Paris Descartes Faculty of Medicine 
(Cochin -Port Royal) in the center of Paris.

-- 
Hugues BERRY
------------------
Project-Team Alchemy
INRIA Saclay-Ile-de-France Research Centre
Parc Club Orsay Universite
3, rue J. Rostand
91893 Orsay Cedex France
tel.: +33 1 72 92 59 22
fax.: +33 1 60 19 66 08
http://www-rocq.inria.fr/~hberry