2012-2013, Work in progress Samuel Blanquart, CR2 INRIA, EPI Bonsai 10 juin 2013
2012 2013 : Researches, animation and teaching Teaching : Algorithm and Application for 20 master 1 students (24h). Teaching : Phylogenetics for Ecology and Environment master 1 students (8 hours). Teaching : coaching 1 Individual Projects (PJI), 2 master 1 students (how many hours?). Researches : Article in preparation for 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... Stand by : Phylogenetic model for heterotachy and heteropecily with Nick Goldman. Stand by : Prediction of new exon and alternative splicing of TRPM8 genes in vertebrate. Perspectives : BnB ANR project and the taxonomic assignation point. Perspectives : Region funds and probabilistic models for genomic arrangement.
Modeling arbitrary complex ecological relationships with PJI students
Modeling arbitrary complex ecological relationships with PJI students
ERC PopPhyl, on the empirical matrices of amino acid replacement A) JTT replacement matrix (Jones et al. 1992), B) Venn diagram of amino-acid properties (Taylor 1986). Exchange between biochemically similar amino-acid are more frequent.
ERC PopPhyl, on the empirical matrices of amino acid replacement 25 empirical replacement matrices were built for 25 metazoan taxonomic levels.
ERC PopPhyl, on the empirical matrices of amino acid replacement Over the elapsed year : Final results found during last spring, Updating my bibliography and start writing during last autumn, Back on my * paper, urgent need to finish!
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 2010. JMB.
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. The ancestral HisF inferred at the bacterial and archaeal MRCA (presumably close to the LUCA) has been synthesized. It is functional, has the same catalytic activity as modern enzymes, is stable up to 70 C, and binds with several modern coeffectors. Rejected by Science (with no comments), rejected by PNAS ( too easy ), submitted to JACS (Journal of American Chemistry Society)...
More results about LUCA s life Collaboration with the LBBE, estimating growth temperatures across cellular life history. Rejected by MBE, submitted to Biology Letters.
Adaptation to halophily in Archaea : MalDH evolution Collaboration with IBS Grenoble, LBBE Lyon, Ecole Polytechnique Paris. Reconstructing trees, species tree, gene tree and reconciliation. New data available last year. Reconstructing ancestral sequences, dependence to the tree topology, to the phylogenetic models. Problem of inferring ancestral sequences and ancestral GAP lengths. Ancestral gene synthesis and characterization, biochemistry, crystallography. The hopeless quest for funds : this year the project was scored A, A, A, by 3 referees, but sadly, we will obtain no fund this year... Beg you 5000 euro Me Lord?
Adaptation to halophily in Archaea : MalDH evolution Brochier-Armanet, Forterre and Gribaldo. Phylogeny and evolution of the Archaea : one hundred genomes later. Current Opinion in Microbiology 2011, 14 :274-281
Adaptation to halophily in Archaea : MalDH evolution
Adaptation to halophily in Archaea : MalDH evolution Enough money to synthesize 4 MalDH ancestors. 3 done yet.
Tools for ancestral sequences analysis? PJI, master 1 students : Benoît-Charles Detuncq, Yannick Leroy, Thomas Clément. 2011 : 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. 2013 : Thank to Thierry for times to debug the code. Objective : save structural-biologists from madness.
Adaptation to halophily in Archaea : MalDH evolution
Adaptation to halophily in Archaea : MalDH evolution
Adaptation to halophily in Archaea : MalDH evolution
Conclusion : other awaiting works and collaborations Still many papers to write right now. Still need to maintain, hotline, finish, optimize and parallelize a few models of molecular evolution. True start of the work on genomes rearrangement started with JS, Aïda and GEPV, Evolving from molecular evolution to ecology : metagenomic data and the taxonomic assignation problem.