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June 8, 2016 - The first NewsLetter of SB2!
SB2 NewsLetter #01

8th Bordeaux RNA Club Symposium, June 23-24, 2016

Aptamers Symposium, Bordeaux, June 24-25, 2016

Colloque du GBR BioSynSys, Bordeaux, June 27-29, 2016

Save the dates!

Symposium on Foldamers, Bordeaux, September 26-28, 2016

Workshop Protocells, Bordeaux, October 5, 2016
Poster of the workshop

Past News

Seminar of Philippe Horvath: 11h, Wenesday April 6, 2016
Speaker: Philippe Horvath - DuPont Nutrition
Title: To appear (about CRISPR-Cas)

Seminar of Alain Blanchard: 12h, Tuesday March 15, 2016 - salle TP, Visio 2, Site Carreire, Univ Bordeaux
Speaker: Alain Blanchard - Microbiologie, UMR INRA 1332 Biologie du Fruit et Pathologie, Bordeaux, FRANCE
Title: From the question "what is life?" to the building of minimal cells.
Abstract: Abstract_Blanchard_2016
Context: Ce séminaire a lieu dans le cadre du groupe interdisciplinaire "Philosophie et Biologie" mis en place en janvier 2015 par Thomas Pradeu et Cédric Brun. Pour plus de détails, consultez :

Seminar of Léo Guignard: 14h, Monday January 4, 2016 - IECB, Univ Bordeaux
Speaker: Léo Guignard - INRIA project-team Virtual Plants, joint with CIRAD and INRA, UMR AGAP, Univ. Montpellier 2, FRANCE
Title: A trade off between constraints in embryo geometry and on regulatory genome evolution.
Contact: Denis Dupuis

Call for Projects 2016-2017 by SB2
Deadline: December 9, 2015 - Before 6pm
Go to the Calls for Projects menu

Workshop thématique de l'ATT SB2 : Journée Mitochondrie - Vendredi 4 décembre 2015 - IBGC
Contact: Jean-Pierre Mazat et Jean-Paul di Rago

Assemblée Générale de l'ATT SB2 - Lundi 23 novembre 2015 entre 12h15 et 14h30 - Auditorium de l'IECB
12h15-13h30 : Accueil et déjeuner dans le hall de l'IECB, buffet déjeunatoire
13h30-14h30 : Assemblée Générale de l'ATT SB2, amphi de l'IECB
14h30-15h30 : Séminaire de Fernan Federici (voir ci-dessous)
Diaporama de l'AG : cliquez ici (Ordre du jour provisoire : disponible ici)

Séminaires soutenus par l'Action Thématique Transversale SB2 (Novembre 2015)
Contact: Denis Dupuis

Séminaires soutenus par l'Action Thématique Transversale SB2 (Octobre 2015)
On the occasion of the kick-off meeting and first training course of the Marie Curie ITN network “MetaRNA”, three lectures will be open to the public:
Contact: Valérie Gabelica, Jean-Jacques Toulmé

The Bordeaux IGEM team 2015 got a gold medal in Boston!
All competition results here

News on Bordeaux University web site: news Bordeaux University
Press (Sud-Ouest): Sud-Ouest paper

The Bordeaux IGEM team on internet: facebook - twitter - youtube - web site

BioSynSys 2015 : 1er colloque du GDR "Biologie de Synthèse et des Systèmes", 7-10 septembre 2015 Paris (France)
All the details on the website:

URGENT : financement de thèse à l'Institut de Biologie Systémique et Synthétique dans l'équipe Xénome (campus Génopole, Evry, Région parisienne)
Title: Identification and production of functional xenonucleic acids.
An early-stage researcher position is offered for 3-year structured PhD project with a funding for 2.5 years. The institute of Systems and Synthetic Biology (Genopole campus, Evry, Paris region) has an immediate opening in the Xenome team which ultimate aim is to design and engineer novel cellular components to elaborate safe GMOs. In the multidisciplinary and international collaborative research context of the team (chemistry, molecular biology, microbiology), the successful candidate will focus more precisely on the identification of chemically modified nucleic acids using an in vitro evolution approach in order to implement it in vivo.
Excellent applicants with degrees and/or expertise in biochemistry, biotechnology, molecular biology, microbiology are invited to apply as soon as possible by e-mail to Cécile Gasse:
Applications should include a letter of motivation, curriculum vitae, one or two letters of recommendation, copies of relevant degrees (BSc/MSc). Notably, at the date of recruitment, applicants must be in the first four years of their career and not have a doctoral degree. They can be a national of any country.

The Bordeaux IGEM team 2015 needs financial supports! All the details here
The Bordeaux IGEM team on internet: facebook - twitter - youtube - web site

7th BORDEAUX RNA CLUB workshop, June 25-26, 2015 - European Institute of Chemistry and Biology (IECB) in Bordeaux
More information and the list of invited speakers can be found at:
Registration is free but mandatory. To register please send an email to with your name and contact details.
Extended deadline for registration and abstract submission (talk and poster): June 12th, 2015

Seminar of Eduardo Agosin Trumper: 11h, friday April 3, 2015 - Séminaire de la SFR BIE - Salle de l'IBVM - Campus INRA de Villenave d'Ornon
Title: Modélisation métabolique à l'échelle génomique : applications à la fermentation oenologique.
Speaker: Eduardo Agosin Trumper - Professor - School of EngineeringPontificia Universidad Católica de Chile
Sánchez, B; Pérez-Correa, R; Agosin, E. Construction of robust, dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative reparameterization. Metabolic Engineering 25: 159-173, 2014.
Orellana, M; Aceituno, F; Melo, F, Agosin, E. Metabolic and transcriptomic response of Saccharomyces cerevisiae after an oxygen impulse under carbon sufficient, nitrogen-limited fermentative conditions. FEMS Yeast Research 14: 412-424, 2014.
Aceituno, F.; Orellana, M.; Mendoza, S.; Melo, F.; Agosin, E. Oxygen response of Saccharomyces cerevisiae grown under carbon-sufficient, nitrogen-limited oenological conditions. Applied and Environmental Microbiology 78 (23), 8340-8352, 2012.
Vargas, F; Pizarro, F; Perez R & Agosin, E. Expanding a dynamic flux balance metabolic model of yeast fermentation to genome scale, BMC Systems Biology 5: 75, 2011.
Pizarro, F.; Hewett, M: Nielsen, J.; Agosin, E. Growth temperature exerts a differential physiological and transcriptional response in laboratory and wine strains of Saccharomyces cerevisiae. Applied and Environmental Microbiology 74 (20): 6358-6368, 2008.
Pizarro, F.; Martabit, M; Bruno, C; Perez-Correa, R; Agosin, E. Coupling kinetic expressions and metabolic networks for predicting wine fermentations. Biotechnology and Bioengineering 98 (5): 986-998, 2007.
Pizarro, F; Vargas, F; Agosin, E. A systems biology perspective of wine fermentations. Yeast 24 (11): 977-991, 2007.

Seminar of Jonathan Karr: 11h, Monday March 16, 2015 - Amphitheatre Centre Génomique Fonctionnelle Bordeaux
Title: Toward whole-cell models for engineering.
Abstract: A central challenge in biology is to understand how phenotype arises from genotype. Despite decades of research, a complete understanding of biology remains elusive. Computational techniques are needed to create a unified understanding. Recently, we developed the first comprehensive whole-cell computational model which accounts for the specific function of every annotated gene product and predicts the dynamics of every molecular species over the entire cell cycle. We validated our model by comparing its predictions to a wide range of experimental data. We have used the model to gain new insights into cell cycle regulation and energy usage. We believe that whole-cell models will accelerate bioengineering and medicine by enabling rapid, low cost in silico experimentation, facilitating experimental design and interpretation, and ultimately guiding rational biological design.

15 PhD positions offered by MetaRNA network : Deadline February 7, 2015
All the details on the website:

Seminar of Matias Zurbriggen: 11h, Friday January 23, 2015 - IBVM, INRA, Villenave d'Ornon
Title: Plant and mammalian synthetic biology: from understanding signalling processes to tool development.
Abstract: We pursue a pioneering interdisciplinary research line at the cross-section between plant and mammalian synthetic biology for the development of molecular tools and techniques to control and understand cellular processes and regulatory networks in a quantitatively and spatiotemporally resolved manner. Subsequently, the knowledge-derived on the biological systems is transferred into biotechnological applications. For this, we have developed a versatile mammalian and plant cell platform focusing on synthetic switches, regulatory networks, metabolic pathways and biological sensors. Profiting from this theoretic-experimental platform we derive model-based information on complex biological systems from cellular up to organismic levels by their targeted interrogation with the synthetic biologic tools and platforms.

Seminar of Jean-Christophe Baret: 11h, Friday January 30, 2015 - IECB, Univ Bordeaux
Title: Microfluidic Ultra-High Throughput Screening.
Abstract: Droplet-based microfluidics offers novel tools for the miniaturization and automation of biochemical assays. Over the past years, several platforms have been designed for the analysis and screening of DNA molecules (1), for the analysis of the response of single cells to chemicals (2) or for the selection of improved micro-organisms of practical interest (3). I will present these tools based on emulsion manipulation in microfluidics and present new methods developed for the manipulation and analysis of droplets are rates larger than 100 000 droplets per second (4,5).
(1) Pekin et al. Lab Chip (2011)
(2) Baret et al. Chem. Biol. (2010)
(3) Wang et al. Nat. Biotech (2014)
(4) Lim et al. Lab Chip (2013); Lim et al. Appl. Phys. Letters (2014)
(5) Caen, Lim et al. Submitted (2015)