[BiO BB] PhD post in plasmid bioinformatics, genomics and ecology

[Dawn Field]

Dear List,

We recently hired a superb research programmer following a post he made to this list about wanting to move from staight IT into bioinformatics  - so we're making sure to post here for this UK studentship.  For more information about the bioinformatics/genomics aspects of the below studentship please feel free to contact me.


ANNOUNCEMENT
A 3-year NERC funded studentship is available for doctoral research,
starting 1st October 2002, to work on the ecology and functional genomics of plasmids, 
supervised by Professor Mark Bailey, Professor John Fry, and Dr. Dawn Field. 

We are seeking a motivated student able to work at the interface of genomics, 
bioinformatics, evolutionary and ecological genetics, and microbial adaptation to develop 
new approaches and methods of addressing key questions about the role of plasmids 
in short and long-term ecological adaptation.  

To apply, please send a CV and details of two referees (name, address, fax,
and email) to Professor Mark Baily, Microbial Ecology Section, CEH Oxford,
Mansfield Rd, Oxford OX1 3SR. Applications are invited from UK residents.

The closing date for applications is the 31st May 2002.


PROJECT BACKGROUND AND DESCRIPTION
Ecological and functional genomic studies to determine the evolutionary contribution 
of plasmids to the horizontal gene pool of bacteria

The revolution in genomics has already produced 60 + published bacterial genome 
sequences and over 230 plasmid sequences for comparison and study.  The study 
of bacterial genome sequences combined with the introduction of large-scale population 
studies of DNA sequence-level variation has led to a paradigm shift in our thinking about 
how fluid bacterial chromosomes are and the amounts of recombination they are able to 
undergo.  An extremely important aspect of this fluid gene pool that has received far 
less attention is the contribution of plasmids, extrachromosomal genetic elements that 
persist and replicate independently of the host genome.  The significance of 
understanding this horizontal gene pool (HGP) lies in attempting to understand how, 
when and why plasmids contribute to the evolution fitness, persistence, and ecological 
role of a given host in a specific environment.

For the last decade we have studied the microbial genetics of plant associated 
pseudomonads and demonstrated the direct co-operation between host and plasmid 
in local adaptation to the niche.  Current questions we are trying to address include: 
How does plasmid host-range evolve? What selective pressures control plasmid 
persistence or extinction in populations? How different/similar is the genome structure 
and gene content of plasmids taken from the same host? Which plasmid genes/sequences 
are responsible for specific host phenotypes and adaptation? Do rates of recombination 
differ within plasmids when compared to their host chromosome?  To answer these broad 
questions, we need to collect, analyse, and integrate information obtained from a variety 
of experimental and computer-based approaches including:  1) population-level and 
phylogenetic studies of genetic variation found in plasmid and host populations, 2) comparative 
genomics analysis of plasmids and their hosts, 3) transcriptomic studies of plasmid genes 
expressed only in certain hosts/environments, and 4) proteomic studies of host-specific 
and environment-specific protein profiles collected using state-of-the-art proteomic 
technologies.

Students with undergraduate or MRes degrees (or significant research experience) in 
the fields of Ecology, Evolution, Microbiology, or Computational biology (Bioinformatics)
are strongly encouraged to apply.  Students with a background in Computer Science, 
Maths, Statistics, or a related field with a strong desire to learn biological principles will 
also be considered.  The student will be located in the Laboratories of Mark Bailey 
(mbj at ceh.ac.uk) and Dawn Field (Dfield at ceh.ac.uk) at CEH-Oxford and be registered 
for a NERC funded PhD with John Fry (fry at cardiff.ac.uk) at the University of Cardiff.