Archive for December, 2009

In Vino Veritas

December 25th, 2009

cpfChristmas is a great time to try new wines with some of your favorite recipes. For Christmas eve dinner, I enjoyed an excellent Saint Emilion Grand Cru, a Pontet Fumet 2004 — a concentrated, hearty wine consisting of Merlot Noir, Cabernet Franc and Cabernet Sauvignon. Philippe Bardet, the winegrower of this family estate has done a great job in producing a wine with a dense, garnet colour and with a powerful, complex nose revealing very ripe dark and red berry aromas and an elegant oakiness. But this delicacy is also the outcome of entangled metabolic activities of a cortege of yeasts, including the well-known Saccharomyces cerevisiae. This yeast has been used for millennia in winemaking, but did you know that natural genetic engineering plays a key role in the evolution of this microbial winemaker? In a recent study published in PNAS, Novo et al. analyzed the selective forces acting on the wine yeast genome.

They sequenced the complete genome of the diploid commercial wine yeast EC1118 using a Sanger/454 pyrosequencing hybrid approach, resulting in an assembly covering 97% of the S. cerevisiae S288c reference genome. The wine yeast EC1118 differed strikingly from the other S. cerevisiae isolates in possessing several unique large regions encompassing 34 genes involved in key wine fermentation functions. Phylogeny and synteny analyses suggest that one of these genomic regions originated from a species closely related to the Saccharomyces genus, whereas another region was acquired by a eukaryote-eukaryote transfer event from Zygosaccharomyces bailii, a major contaminant of wine fermentations. These data suggest that constant remodeling of fungal genome, through the contribution of exogenous genes, may be favored by ecologic proximity.   These processes led to the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations found in the must.

This study and previous studies published earlier this year (Liti et al. 2009, Schacherer et al., 2009) highlight population genomics of domestic and wild yeasts. In their survey of seventy domestic and wild yeasts (S. cerevisiae, S. paradoxus), Liti et al. revealed extensive differences in genomic (variation in gene content, SNPs, indels, copy numbers and transposable elements) and phenotypic variation despite ecological similarities. Their results could be interpreted in two ways. One is as a domestication of one or two groups of yeasts, the Wine/European and Sake strains, with selection for improved fermentation properties. These domesticated groups then gave rise to feral and clinical derivatives and were involved in the generation of out-crossed derivatives found in all sources. The alternative interpretation is that human activity simply may have used existing strains from populations that had appropriate fermentation properties providing the opportunity to out-breed through movement of strains and supplying a novel disturbed environment.

Liti et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337-341.

Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras J-L, Wincker P, Casaregola S, Dequin S. (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci U S A. 22: 16333-16338.

Postdoctoral Position in Microbial Metagenomics

December 24th, 2009

POST DOC POSITION

Microbial Metagenomics in Forest Soils

The Martin lab (INRA Nancy) is hiring 1 motivated postdoc scientist in the computational analysis of metagenomics data, with a particular emphasis on forest-associated microbial communities.

Bacteria and fungi play fundamental roles in the ecology of forest ecosystems. A powerful new tool in microbial ecology studies is metagenomics wherein one uses next generation sequencing methods on DNA or RNA isolated directly from environmental samples. Metagenomics involves sampling and sequencing the genome sequences of a community of organisms that inhabit a common environment, such as the ocean, the soil or the human gut. Metagenomics provides an unbiased picture of the community structure (species richness and distribution) and its functional potential. It is rapidly moving from being a description tool to an experimental tool as a result of comparisons now being made of metagenomes submitted to environmental perturbations.

We are seeking a post-doctoral bioinformatician to work on methodology for analysis of metagenomic data as part of a new series of projects aiming to describe the spatiotemporal dynamics of bacteria and fungi in forest soils. The proposed research projects focus on bioinformatics tool development for comparative metagenomics of next-generation sequencing data [Buée et al. (2009) New Phytologist, Uroz et al. (2009) Environmental Microbiology, Martin & Martin (2010) New Phytologist] as well as further development and/or application of multivariate analysis methods towards forest ecosystems.

The Tree-Microbe Interactions Department is an exciting, interdisciplinary research group with excellent facilities and research groups in fungal genomics, bacteriology, microbial ecology and molecular biology. The Martin lab is located on the campus of INRA in Nancy, a vibrant, international city in Northeastern France.

Qualifications

We are looking for people with a demonstrated interest in working at the interface between bioinformatics, microbial ecology, and fungal biology.

Applicants should have a PhD in a microbial genomics or computational field. Applicants should have substantial experience with database programming (e.g. SQL), scripting (e.g. Perl or Python), and bioinformatics tools.

Term: Appointments will last 1 year beginning in February-March 2010.

Interested candidates are encouraged to send their CV, along with a letter stating their interest and contact details of two references to Francis Martin (fmartin@nancy.inra.fr). Informal enquiries can also be addressed to the same email address.

Applications close: 31 January 2010

IMC9: The Biology of Fungi

December 24th, 2009

edinb

With the surge of fungal genome release, studying the biology of the Mycota has never been as exciting as it is today. The International Mycological Congress represents one of the largest scientific forum to provide an up-to-date perspective of mycology in all its guises. The 9th International Mycological Congress (IMC9: the Biology of Fungi) will be held in August 2010 in Edinburgh, Scotland. The conference themes will include:

  • Cell biology, biochemistry and physiology
  • Environment, ecology and interactions
  • Evolution, biodiversity and systematics
  • Fungal pathogenesis and disease control
  • Genomics, genetics and molecular biology

Register at: http://www.imc9.info/index.htm.