, Work in progress

Transcription

1 , Work in progress Samuel Blanquart, CR2 INRIA, EPI Bonsai 12 juin 2012

2 Researches, animation and teaching Animation : Phylogeny-days, next week! Teaching : Algorithm and Application for 28 master 1 students (24h). Teaching : Phylogenetics for Ecology and Environment master 1 students (4 hours). Teaching : coaching 3 Individual Projects (PJI), 6 master 1 students (how many hours?). Researches : Invention and conservation of alternative splicings in mammalians (INSERM Lille), Researches : Last answers on the PopPhyl ERC project (ISEM, Montpellier), Researches : The oldest resurrected yet functional enzyme (Regensburg University), Researches : Adaptation to hyper-halophily through enzyme resurrection, still looking for...funding... Other awaiting projects and collaborations.

3 Virtuamium, an eco-info project fossilized since 2002 PJI students, Cyril Capilliez and Clément Boidin. Context : Agent Oriented (AO) logic might be helpful in modeling population genetics, demographics and evolution. Current objective : Implementing a generalized model for arbitrarily complex and evolvable ecological relationships. Perspective : What are tree shapes under realistic ecological models? What about emergence phenomenons? etc.

4 Virtuamium, an eco-info project fossilized since 2002 Separating life-parameters which are specific to species and individuals from a generalized pedator-prey behavior mechanism. Description of a universal pedator-prey automaton executing individuals actions given a species and an individual context. Cloning or sexual reproduction introducing random evolvability over mutable parameter (hunting/hunted-by list, speeds, mass...)

5 Collaboration with Gabriel Bidaux, Laboratory of cell physiology, INSERM U1003 Lille Context : Gabriel has identified many unknown exons in the human TRPM8. Current objective : Determining when those newly identified exons did appear during terrestrial vertebrate evolution. Methods : Full gene region alignment (MAUVE) and alignment analysis.

6 Splicing : Conservation of splice-acceptor sites

7 Splicing : Conservation of splice-donor sites

8 Traduction : Conservation of START codon

9 Traduction : Conservation of STOP codon To be done know : Analyse 3 UTR poly A queues, Validation of prediction in Mus musculus, Writing the paper...

10 ERC PopPhyl, identifying systematic biases in empirical matrices of amino acid replacement 25 empirical replacement matrices were built for 25 metazoan taxonomic levels.

11 ERC PopPhyl, identifying systematic biases in empirical matrices of amino acid replacement How do they differ from each others?

12 ERC PopPhyl, identifying systematic biases in empirical matrices of amino acid replacement First axis of the PCA correlates with replacement rates of amino-acids having codons differing at all 3 positions.

13 Tools for ancestral sequences analysis? PJI, master 1 students : Benoît-Charles Detuncq, Yannick Leroy, Thomas Clément : Viewers for modern and ancestral sequence alignments, and for phylogenetic trees are combined into a same interface, 2012 : introduction of PDB 3D protein models into the interface. Objective : save structural-biologists from madness...

14 a LUCA s Tim barrel resurrected? Computational and Experimental Evidence for the Evolution of a (αβ)8-barrel Protein from an Ancestral Quarter-Barrel Stabilised by Disulfide Bonds. Richter et al JMB.

15 a LUCA s Tim barrel resurrected? In Richter et al 2010, we proposed a scenario of the HisF evolutionary history based on the inferred ancestral sequences, with monomer duplications and gene fusions.

16 a LUCA s Tim barrel resurrected? The ancestral HisF inferred at the bacterial and archaeal MRCA (presumably close to the LUCA) has now been synthesized. It is functional, has the same catalytic activity as modern enzymes, and is stable up to 70 C.

17 Ancestral MalDH of hyperthermophilic Archaea are still waiting for funds! Collaboration with IBS Grenoble, LBBE Lyon, and Ecole Polytechnique Paris. Waiting for ANR acceptance (7 th on waiting list this year...)

18 Other awaiting works and collaborations Many paper to write now. Still need to maintain, hotline, finish, optimize and parallelize a few models of molecular evolution. Pursue the work on genomes rearrangement started with JS, Aïda and GEPV (waiting for Aïda, and for region funds), Evolution of NRPS with Maude, some interesting preliminary results of Aurélien about the domains phylogeny. Beside of my results in the ERC PopPhyl with implication for taxonomic annotation of metagenomes : building a 2000 metazoan mitochondrial genes tree and generalize the taxa-sampling approach for the computation of large but reliable phylogenies.