75 - Paris

Recent developments in Metagenomic Research

Type: 
Colloque
Date: 
21/10/2016
Ville: 
75 - Paris
Pays: 
France
Courte description: 
The program includes the latest experimental advances and technical developments in the fields of metagenomics to decipher the functional processes and interactions carried out by complex microbial communities, i.e., those residing in soil, the ocean, and the human gut. The goal is to cover this broad area of investigation thanks to inclusion of multidisciplinary talks discussing overlapping subjects.

Summer School in Metagenomics

Type: 
Formation
Date: 
12/09/2016 - 16/09/2016
Ville: 
75 - Paris
Pays: 
France
Courte description: 
Metagenomics, the sequencing of DNA directly from a sample without first culturing and isolating the organisms, has become the principal tool of “meta-omic” analysis. It can be used to explore the diversity, function, and ecology of microbial communities. The aim of these 4 days workshop will be to give researchers and students an overview of the tools and bioinformatics techniques available for the analysis of next generation sequence data from microbial communities. Its content will focus on the taxonomic assignment and the functional analysis of metatranscriptomic and metagenomic data. The format will comprise a mixture of lectures and hands-on practical tutorials where students will process example data sets in real-time.

M3

Acronyme ou nom de la structure: 
Nom complet (en toutes lettres): 
Modélisation Moléculaire Mésoscopique
Adresse: 
Laboratoire Jean Perrin Université Paris 6 CNRS UMR 8237 4 place Jussieu T32-33 4e, Case Courrier 114 75252 PARIS Cedex 05, France
Téléphone: 
+33 (0)1 44 27 47 12
Fax: 
+33 (0)1 44 27 47 16
Description (English): 

Mesoscopic modelling of biopolymers

Our objective is to develop a tool of modelling and simulation of nucleic acids (NA). The proposed approach consists in describing the conformation as a flexible beam, represented by a ribbon, by means of the theory of non-linear elasticity of beams.

The determination of the conformation of NA (DNA or RNA) is a challenge as great as that put by the conformation of proteins. Indeed, the current knowledge of the detailed conformations of NA is very low (5-10 % of the Protein Data Bank, PDB, the bank of all the known conformations of biological macromolecules). Nevertheless since 2000, we admit that the conformation of NA could be as rich and varied as that of the proteins, and that the part of the genome transcribed in ARN is of an order of magnitude greater than that of the proteins. Therefore, the conformational wealth of NA and the low level of current knowledge make difficult the bioinformatic approach, which consists in deducing a conformation from those already known. That is why the physical modelling of biomolecules is very important for NA and one of the major objectives of research in molecular modelling is the treatment of the various scales, atomic and mesoscopic (residues, several nucléotides) in a coherent and physical way.

We developed an approach of molecular modelling called Biopolymer Chain Elasticity (BCE). It is based on the observation that the sugar-phosphate chain of NA behaves at mesoscopic scales as a flexible beam. We recently finalized a protocol for the resolution of the conformation of DNA hairpins [1] (cf. banner above), with which we solved the structure of an aptamer anti-MUC1 [2] (cf. figure 1). The results are remarkable because the conformations correspond at the same time to a minimum at different scales : global, intermediate, and local, i.e. an energy minimum on the scale of the loop of several nucleotides, of the individual nucleotides in the loop, and atomic bonds [1, 2]. Our objective is to generalize this methodology for the hierarchical modelling of NA chains by using the theory of the non-linear elasticity of beams. We approach the problem on two scales: (I) that of the skeleton treated as a geometrical and mechanical object, and (II) that of the side chains, considered as stiff objects articulated around their attachment point onto the skeleton. From then on, a tool of simulation containing real active ribbons for the resolution of macromolecules is possible.

 

English keywords: 
Mesoscopic modelling of biopolymers
Plate-forme: 
0
SFBI: 
Membre de la SFBI
Adhésion morale: 
0

BIS

Acronyme ou nom de la structure: 
Nom complet (en toutes lettres): 
Unité de Bioinformatique Structurale
Adresse: 
Unité de Bioinformatique Structurale 25-28 Rue du Docteur Roux 75724 Paris cedex 15
SFBI: 
Membre de la SFBI

Colloque du GDR 3699 "Biologie de Synthèse et des Systèmes

Type: 
Colloque
Date: 
07/09/2015 - 10/09/2015
Ville: 
75 - Paris
Pays: 
France
Courte description: 
Ce premier colloque du GDR BioSynSys réunira les équipes participantes autour des thématiques suivantes : • Ingénierie des réseaux biologiques et de leur régulation • Ingénierie des protéines et des biocatalyseurs • Ingénierie métabolique • Ingénierie des génomes • Biologie orthogonale • Biologie intégrative et prédictive • Modélisation de phénomènes biologiques • Conception d'organismes synthétiques • Ethique et enjeux sociétaux de la Biologie de synthèse • Développement d'outils / méthodologie pour la Biologie de synthèse • Développement vers l'industrie • Nanotechnologies et automatisation pour la Biologie de synthèse.
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