CICLO DE CONFERENCIAS BIOTECNOLOGÍA para todo(s)

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- Jueves, 12 de noviembre

Transgénicos para todos… ¿o para nadie?

José Antonio López Guerrero

Profesor Titular de Microbiología. Universidad Autónoma

de Madrid.

- Jueves, 19 de noviembre

Aplicaciones de la biotecnología en la investigación biomédica

Fernando Peláez Pérez

Director Programa de Biotecnología. Centro Nacional de Investigaciones Oncológicas (CNIO).

- Jueves, 26 de noviembre

Mesa Redonda

Biocombustibles de segunda generación

Antonio Fernández Medarde

Consejero Delegado. Instituto Biomar S.A., León.

Fernando Gómez de Liaño Aparicio

Director de Nuevos Proyectos. Sniace S.A., Madrid

Gabriel Moncalián Montes

Investigador del Departamento de Biología Molecular. Universidad de Cantabria

Lugar: Paraninfo UC, C/ Sevilla 6. Hora: 20:00 h

X Jornada de Investigación del Departamento de Biología Molecular

SynBioNT: A Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions

The field of synthetic biology holds a great promise for the design, construction and development of artificial (i.e. man-made) biological (sub)systems thus offering viable new routes to genetically modified organisms, smart drugs as well as model systems to examine artificial genomes and proteomes. The informed manipulation of such biological (sub)systems could have an enormous positive impact on our societies, with its effects being felt across a range of activities such as the provision of healthcare, environmental protection and remediation, etc.
The basic premise of synthetic biology is that methods commonly used to design and construct non-biological systems, such as those employed in the computational sciences and the engineering disciplines, could also be used to model and program novel synthetic biosystems. Synthetic biology thus lies at the interface of a variety of disciplines ranging from biology through chemistry, physics, computer science, mathematics and engineering.
The overarching aim of this network is to generate new vigorous interactions between the disciplines that impinge (and contribute to) Synthetic Biology by supporting a range of community building activities. These activities will be centred on the specific technical goal of achieving programmable interactions between biological and artificial cells.

By focusing on this specific technical challenge we hope to contribute to bridging the gap between synthetic biology from the top-down (i.e. knocking out or modifying functions of existing cells) and bottom-up synthetic biology, that is, from first principles. We believe that both approaches are important and will have a role to play in the future of synthetic biology, hence a challenge that calls for the interaction between top-down systems (modified cells) and bottom-up systems (chells, protocells) provides the ideal background against which a new research community can be built and sustained.
This network is funded by BBSRC (BB/F01855X/1) with co-funding from EPSRC and ESRC.

http://psiren.cs.nott.ac.uk/projects/synbiont/wiki/WikiStart#WelcometoSynBioNT

Invited Seminar: Directed Evolution of Enzymes

Friday 19th of June

"Iterative saturation mutagenesis as a method for accelerated directed evolution"
Dr. Pankaj Soni.
Prof. Manfred T. Reetz Group. Max Planck Institut fur Kohlenforschung. Muelheim an der Ruhr. Germany.

"Directed Evolution of enantioselective Hybrid Catalysts"
Dr. Jerome J.-P. Peyralans.
Prof. Manfred T. Reetz Group. Max Planck Institut fur Kohlenforschung. Muelheim an der Ruhr. Germany.

Combating Resistance to Antibiotics (CRAB) Meeting

http://www.unican.es/fltq/eventos/20090511d.htm

CRAB meeting
Santander 11-12 May 2009
Scientific and Social Program
Site of scientific sessions: Escuela Superior de Telecomunicaciones. Universidad de Cantabria (located in Avda. de los Castros), about 15 min walking from the hotel.

Monday 11

9h00 - Fernando de la Cruz / Didier Mazel:
Introductory comments and organization details

WP1: Integrons
9h30 D. Mazel: Integrons here and now
10h00 Z. Baharoglu: SOS induction of integrón-integrase expression by conjugation
10h30 C. Loot: Folding of hairpin attC sites: consequences on integrón recombination
11h00 E. Zechner: Conjugative biofilms in a catheter-associated UTI model.
11h30 Coffee break

WP3: Conjugation
12h00 E. Zechner: Regulation at the relaxosome – T4CP interface.
12h30 G. Moncalián: The R388 relaxase and relaxosome.
12h45 M.P. Garcillán: Plasmid classification by relaxases.
13h00 E. Cabezón: Biochemistry of conjugative coupling proteins.
13h15 I. Aréchaga: Biochemostry of type IV secretion systems ATPases
13.30 F. de la Cruz: Inhibition of conjugation
14h15 Lunch at Restaurante (about 15 min walking from the meeting site)
16h30: CRAB administration meeting and discussion about final report (only for IPs; the other participants have free afternoon and evening)

Tuesday 12
WP2: Transposons
9h30 M. Chandler I
10h00 M. Chandler II
10h30 M. Chandler III
11h00 F. Olatz
11h30 Coffee break

WP4: Stability
12h00 L. Van Melderen: Toxin-antitoxin systems: a lot more than we thought…
12h30 J. Guglielmini : Resurrecting old killers: reconstruction of ancestral toxins from toxin-antitoxin systems.
13h00 P. Gabant : How to Make Antibiotics Obsolete: Use of Bacterial Selection Modules for Efficient Protein Production in E. coli
13h30 F Hayes
14h15 Lunch
16h30: CRAB administration meeting and discussion about final report (only for IPs; the other participants have free afternoon and evening)
18 – 20 h: Guided tour to the city of Santander
21 h: CRAB diner. Restaurante “El Peñón” (San Juan de la Canal)

Plasmids and plasmid modules as orthogonal devices in Synthetic Biology

ESF-UB Conference in Biomedicine

EUROPEAN CONFERENCE ON SYNTHETIC BIOLOGY (ECSB) II: DESIGN, PROGRAMMING AND OPTIMISATION OF BIOLOGICAL SYSTEMS

The field of synthetic biology holds a great promise for the design, construction and development of biological systems (artificial or modified), by offering viable new routes to ‘genetically modified’ organisms, smart drugs and hybrid computational-biological devices. The informed manipulation of such biological systems could have an enormous positive impact on our societies, with its effects being felt across a range of activities such as the provision of healthcare, environmental protection and remediation to the construction of smarter more ubiquitous bio-integrated computing systems, etc.
The basic premise of synthetic biology is that methods commonly used to build non-biological systems, such as those employed in the computational sciences and the engineering disciplines that can deal with large and complex systems, could also be used to specify, design, implement, test and deploy novel synthetic biosystems. Synthetic biology lies at the interface of a variety of disciplines ranging from biology through chemistry, physics, computer science, mathematics and engineering.
Two communities are emerging within synthetic biology, namely top-down - i.e. knocking out or modifying functions of existing cells, and bottom-up - that is construction of artificial systems from first principles, protocells, etc. The aim of this conference is to generate new vigorous interactions between the disciplines that impinge on (and contribute to) Synthetic Biology, and to bring together in the same context top-down and bottom-up researchers.
ECSB 2009 is the second conference in the series. It will comprise invited talks by internationally known scientists who are leaders in their fields, tutorials to introduce young researchers to Synthetic Biology, contributed talks and posters. We expect this to be a major international and multi-disciplinary scientific and educational event. The conference will be limited to just over 100 participants, in a venue whose environment is highly conducive to networking and scientific interactions.
Some, but not all, of the topics to be presented in the conference include: DNA sequencing and synthesis, chemical and biological networks, computational techniques (modelling, data mining, optimisation) for synthetic biology, minimal genomes, evolution (natural, directed and simulated), origins of life, biological systems, cell cycles and circuits, and infrastructures for synthetic biology, minimal cells.

Conference title: Plasmids and plasmid modules as orthogonal devices in Synthetic Biology
Prof. Fernando de la Cruz. Universidad de Cantabria.

http://www.esf.org/activities/esf-conferences/details/2009/confdetail294.html?conf=294&year=2009

The diversity of conjugative relaxases and its application in plasmid classification

The diversity of conjugative relaxases and its application in plasmid classification
María Pilar Garcillán-Barcia 1 , María Victoria Francia 2 & Fernando de la Cruz 1
1 Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, Santander, Spain; and 2 Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla e Instituto de Formación e Investigación Marqués de Valdecilla (IFIMAV), Santander, Spain
Correspondence: Fernando de la Cruz, Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, C. Herrera Oria s/n, 39011 Santander, Spain. Tel.: +34 942201942; fax: +34 942201945; e-mail: delacruz@unican.es
Editor: Eduardo Rocha
Copyright © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
KEYWORDS
plasmid classification • relaxase • bacterial conjugation • type IV secretion system • coupling protein
ABSTRACT
Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids encode a complete set of transfer genes (MOB+T4SS). The only essential ingredient of the MOB machinery is the relaxase, the protein that initiates and terminates conjugative DNA processing. In this review we compared the sequences and properties of the relaxase proteins contained in gene sequence databases. Proteins were arranged in families and phylogenetic trees constructed from the family alignments. This allowed the classification of conjugative transfer systems in six MOB families: MOBF, MOBH, MOBQ, MOBC, MOBP and MOBV . The main characteristics of each family were reviewed. The phylogenetic relationships of the coupling proteins were also analysed and resulted in phylogenies congruent to those of the cognate relaxases. We propose that the sequences of plasmid relaxases can be used for plasmid classification. We hope our effort will provide researchers with a useful tool for further mining and analysing the plasmid universe both experimentally and in silico.

Darwin 200

The 200th anniversary of the birth of Charles Robert Darwin falls on 12 February 2009. No single researcher has since matched his collective impact on the natural and social sciences; on politics, religions, and philosophy; on art and cultural relations. In this landmark year, our Nature news special provides continuously updated news, research and analysis on Darwin's life, his science and his legacy.

http://www.nature.com/news/specials/darwin/index.html

Toward minimal bacterial cells: evolution vs. design.

Andrés Moya 1,2,3 , Rosario Gil 1,2,3 , Amparo Latorre 1,2,3 , Juli Peretó 1,2,4 , Maria Pilar Garcillán-Barcia 5 & Fernando de la Cruz 5
1 Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain; 2 CIBER de Epidemiología y Salud Pública, Madrid, Spain; 3 Departament de Genètica, Universitat de València, València, Spain; 4 Departament de Bioquímica i Biologia Molecular, Universitat de València, València, Spain; and 5 Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain

Recent technical and conceptual advances in the biological sciences opened the possibility of the construction of newly designed cells. In this paper we review the state of the art of cell engineering in the context of genome research, paying particular attention to what we can learn on naturally reduced genomes from either symbiotic or free living bacteria. Different minimal hypothetically viable cells can be defined on the basis of several computational and experimental approaches. Projects aiming at simplifying living cells converge with efforts to make synthetic genomes for minimal cells. The panorama of this particular view of synthetic biology lead us to consider the use of defined minimal cells to be applied in biomedical, bioremediation, or bioenergy application by taking advantage of existing naturally minimized cells.

http://dx.doi.org/10.1111/j.1574-6976.2008.00151.x

Coprinus cinereus rad50 Mutants Reveal an Essential Structural Role for Rad50 in Axial Element and Synaptonemal Complex Formation, Homolog Pairing and

Sonia N. Acharya*,1, Alexander M. Many*,1,2, Andrew P. Schroeder*, Felicia M. Kennedy*, Oleksandr P. Savytskyy*, Jennifer T. Grubb*, Jack A. Vincent*, Elizabeth A. Friedle*, Martina Celerin*, Daniel S. Maillet*, Heather J. Palmerini*, Megan A. Greischar*, Gabriel Moncalian,3, R. Scott Williams, John A. Tainer and Miriam E. Zolan*,4
* Department of Biology, Indiana University, Bloomington, Indiana 47405 and The Scripps Research Institute, La Jolla, California 92037

The Mre11/Rad50/Nbs1 (MRN) complex is required for eukaryotic DNA double-strand break (DSB) repair and meiotic recombination. We cloned the Coprinus cinereus rad50 gene and showed that it corresponds to the complementation group previously named rad12, identified mutations in 15 rad50 alleles, and mapped two of the mutations onto molecular models of Rad50 structure. We found that C. cinereus rad50 and mre11 mutants arrest in meiosis and that this arrest is Spo11 dependent. In addition, some rad50 alleles form inducible, Spo11-dependent Rad51 foci and therefore must be forming meiotic DSBs. Thus, we think it likely that arrest in both mre11-1 and the collection of rad50 mutants is the result of unrepaired or improperly processed DSBs in the genome and that Rad50 and Mre11 are dispensable in C. cinereus for DSB formation, but required for appropriate DSB processing. We found that the ability of rad50 mutant strains to form Rad51 foci correlates with their ability to promote synaptonemal complex formation and with levels of stable meiotic pairing and that partial pairing, recombination initiation, and synapsis occur in the absence of wild-type Rad50 catalytic domains. Examination of single- and double-mutant strains showed that a spo11 mutation that prevents DSB formation enhances axial element (AE) formation for rad50-4, an allele predicted to encode a protein with intact hook region and hook-proximal coiled coils, but not for rad50-1, an allele predicted to encode a severely truncated protein, or for rad50-5, which encodes a protein whose hook-proximal coiled-coil region is disrupted. Therefore, Rad50 has an essential structural role in the formation of AEs, separate from the DSB-processing activity of the MRN complex.

http://dx.doi.org/10.1534/genetics.108.092775%20

Analysis of ColE1 MbeC unveils an extended ribbon-helix-helix family of nicking-accessory proteins

Athanasia Varsaki, Gabriel Moncalián, Maria del Pilar Garcillán-Barcia, Constantin Drainas, and Fernando de la Cruz*
MbeC is a 13 kDa ColE1-encoded protein required for efficient mobilization of ColE1, a plasmid widely used in cloning vector technology. MbeC protein was purified and used for in vitro DNA-binding, which showed that it binds specifically dsDNA containing the ColE1 oriT. Amino-acid sequence comparison and secondary structure prediction imply that MbeC is related to the ribbon-helix-helix (RHH) protein family. Alignment with RHH members pointed a conserved arginine (R13 in MbeC) which was mutated to alanine. The mutant MbeC(R13A) was unable to bind either ssDNA or dsDNA. Limited proteolysis fragmented MbeC in two stable folding domains: the N-terminal domain, which contains the RHH motif and the C-terminal domain, which comprises a signature shared by nicking-accessory proteins. Results indicate that MbeC plays a similar role in conjugation as TraY and TrwA of plasmids F and R388, respectively. Thus, it appears that an extended, possibly universal mechanism of DNA conjugative processing exists, in which oriT-processing is carried out by relaxases assisted by homologous nicking-accessory proteins. This mechanism seems to be shared by all major conjugative systems analyzed so far.
http://dx.doi.org/10.1128/JB.01342-08

Reply to The binding stoichiometry of CIN85 SH3 domain A and Cbl-b

Daniela Jozic, Nayra Cardenes, Yonathan Lissanu Deribe, Gabriel Moncalian, Daniela Hoeller, Yvonne Groemping, Ivan Dikic, Katrin Rittinger, Jeronimo Bravo
Nature Structural & Molecular Biology 15, 891 - 892 (01 Sep 2008), doi: http://dx.doi.org/10.1038/nsmb0908-891, Correspondence