Genomics of wine yeast: functional analysis of new and variable genes

Projecte de recerca elaborat a partir d’una estada a l’Institut National de la Recherche Agronomique, França, entre 2007 i 2009. Saccharomyces cerevisiae ha estat el llevat utilitzat durant mil.lenis en l'elaboració de vins. Tot i així, es té poc coneixement sobre les pressions de selecció que han actuat en la modelització del genoma dels llevats vínics. S’ha seqüenciat el genoma d'una soca vínica comercial, EC1118, obtenint 31 supercontigs que cobreixen el 97% del genoma de la soca de referència, S288c. S’ha trobat que el genoma de la soca vínica es diferencia bàsicament en la possessió de 3 regions úniques que contenen 34 gens implicats en funcions claus per al procés fermentatiu. A banda, s’han dut a terme estudis de filogènia i synteny (ordre dels gens) que mostren que una d'aquestes tres regions és pròxima a una espècie relacionada amb el gènere Saccharomyces, mentre que les altres dos regions tenen un origen no-Saccharomyces. S’ha identificat mitjançant PCR i seqüenciació a Zygosaccharomyces bailii, una espècie contaminant de les fermentacions víniques, com a espècie donadora d'una de les dues regions. Les hibridacions naturals entre soques de diferents espècies dins del grup Saccharomyces sensu stricto ja han estat descrites. El treball és el primer que presenta hibridacions entre espècies Saccharomyces i no-Saccharomyces (Z. bailii, en aquest cas). També s’assenyala que les noves regions es troben freqüent i diferencialment presents entre els clades de S. cerevisiae, trobant-se de manera gairebé exclusiva en el grup de les soques víniques, suggerint que es tracta d'una adquisició recent de transferència gènica. En general, les dades demostren que el genoma de les soques víniques pateix una constant remodelació mitjançant l'adquisició de gens exògens. Els resultats suggereixen que aquests processos estan afavorits per la proximitat ecològica i estan implicats en l'adaptació molecular de les soques víniques a les condicions d'elevada concentració en sucres, poc nitrogen i elevades concentracions en etanol.

Saccharomyces cerevisiae as a model organism: a comparative study

Background: Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking. Methodology/Principal Findings: In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes. Conclusions/Significance: The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.

On the number of limit cycles bifurcating from a non-global degenerated center

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Creating and using a non-dedicated HPC cluster with ParallelKnoppix

This note describes ParallelKnoppix, a bootable CD that allows econometricians with average knowledge of computers to create and begin using a high performance computing cluster for parallel computing in very little time. The computers used may be heterogeneous machines, and clusters of up to 200 nodes are supported. When the cluster is shut down, all machines are in their original state, so their temporary use in the cluster does not interfere with their normal uses. An example shows how a Monte Carlo study of a bootstrap test procedure may be done in parallel. Using a cluster of 20 nodes, the example runs approximately 20 times faster than it does on a single computer.

ParallelKnoppix - Rapid deployment of a linux cluster for MPI parallel processing using non-dedicated computers

This note describes ParallelKnoppix, a bootable CD that allows creation of a Linux cluster in very little time. An experienced user can create a cluster ready to execute MPI programs in less than 10 minutes. The computers used may be heterogeneous machines, of the IA-32 architecture. When the cluster is shut down, all machines except one are in their original state, and the last can be returned to its original state by deleting a directory. The system thus provides a means of using non-dedicated computers to create a cluster. An example session is documented.

Non compact euclidean cone 3-manifolds with cone angles less than 2∏

We study of noncompact Euclidean cone manifolds with cone angles less than c&2π and singular locus a submanifold. More precisely, we describe its structure outside a compact set. As a corol lary we classify those with cone angles & 2π/3 and those with cone angles = 2π/3.

Tropical varieties for non-archimedean analytic spaces

"Vegeu el resum a l'inici del document del fitxer adjunt."

Cooperative vs. non-cooperative mechanisms in the EU decision making process

According to the account of the European Union (EU) decision making proposed in this paper, this is a bargaining process during which actors shift their policy positions with a view to reaching agreements on controversial issues.

Strongly non-degenerate Lie algebras

Let A be a semiprime 2 and 3-torsion free non-commutative associative algebra. We show that the Lie algebra Der(A) of(associative) derivations of A is strongly non-degenerate, which is a strong form of semiprimeness for Lie algebras, under some additional restrictions on the center of A. This result follows from a description of the quadratic annihilator of a general Lie algebra inside appropriate Lie overalgebras. Similar results are obtained for an associative algebra A with involution and the Lie algebra SDer(A) of involution preserving derivations of A

The EU as a security provider in its neighbourhood: the case of non-proliferation of WMD in the Mediterranean area

As a consequence of the terrorist attacks of 9/11 and the US-led war against Iraq, WMD and their proliferation have become a central element of the EU security agenda. In December 2003, the European Council adopted even a EU Strategy against Proliferation of WMD. The approach adopted in this Strategy can be largely described as a ‘cooperative security provider’ approach and is based on effective multilateralism, the promotion of a stable international and regional environment and the cooperation with key partners. The principal objective of this paper is to examine in how far the EU has actually implemented the ‘cooperative security provider’ approach in the area which the Non-proliferation Strategy identifies as one of its priorities – the Mediterranean. Focusing on the concept of security interdependence, the paper analyses first the various WMD dangers with which the EU is confronted in the Mediterranean area. Afterwards, it examines how the EU has responded to these hazards in the framework of the Barcelona process and, in particular, the new European Neighbourhood Policy. It is argued that despite its relatively powerful rhetoric, the EU has largely failed, for a wide range of reasons, to apply effectively its non-proliferation approach in the Mediterranean area and, thus, to become a successful security provider.