- Fecha: 20 de Marzo 2012
- Lugar: Aula del Instituto del Agua, C/ Ramón y Cajal, 4
- Horario: 12,00h
- Descripción: Seminario abierto impartido por el Dr. Ramiro Vilchez Vargas (Centro Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Alemania)
Resumen de la conferencia: Since decades, microarrays approaches have been applied for gene expresion pattern in pure culture using RNA as template. However, in the last five years, microarrays have been applied also for gene detection in environmental samples, using DNA as template, without a strict optimization and validation of experimental procedures. The challenge of transforming one tecnique, originally developed for expression pattern into detecting profile became not a tribial issue. Developed of novel internal positive controls, optimization of hybridization and washing temperatures and amplification, digestion and labelling methods were carefully optimized. The optimization was performed using the genome DNA of four complete sequenced type strains previous the application of the microarray approach to the environmental samples. Once that an acceptable correlation between the intesity of the signals and its reliability was stablished, microarray approach offered the screening tool to apply on a huge number of environmental samples and design new primers to obtain new genes sequences involved in catabolic pathways. These sequences can be retrieved by Sanger sequencing, after ligation, transformation and PCR reaction using primers inserted in the correspondent vector. However, new tecniques have been develope recently that allow to obtain thousand of 100-mers nucleotides in a single run and reasonable price. Furthermore, a modification of the experimental procedure prior the hybridization on the microarray, allows to obtain the pattern of abundance versus expression in the environmental samples.
A considerable improvements have been done in a short period of time regarding to nucleic acids sequencing. DNA double helix was discovered in 1953. First DNA sequence (24 nucleotides) was obtained by Gilbert and Maxan in 1973. And making a small jump into the history, here we are sequencing seven millions of nucleotides in less than 35 hours (MiSeq System, Illumina). Many companies are offering on the market several equipments and technologies: Roche (454), HiSeq 2000 and MiSeq (Illumina), SOLiD 5500 xl (Applied Biosystems), Heliscope (Helicos), Life Tech Ion torrent PGM (Life Technologies), Oxford Nanopore GridION (Oxford Nanopore Technologies). The possible applications of this potential is a breakthrough in the experimental design, taking into consideration the time and cost: sequencing of strains with improved characteristics, real time PCR of the complete sets of genes of one bacteria (two conditions), sequencing of environmental PCR products, metagenomics and metatranscriptomic of environmental samples and some other dreams are possible, although handling 3.7–4.6 Gb of information requires strong
bioinformatic programs and interfaces, some of them free available on the net.
Curriculum Vitae: Dr. Ramiro Vilchez Vargas studied Chemistry at the University of Granada, Sciences Faculty (1993-98), defended his Master Thesis under the supervision of Prof. Dr. D. Alejandro Fernández Barrero and Prof. Dr. D. Eduardo Cabrera Torres (1997-99) and defended his PhD in the Water Research Institute under the supervision of Dr. Prof. D. Jesús González López and Dr. Da Belén Rodelas González (2000-05), during this period of time eight publications in international journals and four book chapters were published and some collaborations with companies (EMASA, EMASAGRA among others). His first Postdoctoral position was in the Research Group of Prof. Dr. Irene Wagner-Döbler (Helmholtz Centre for Infection Research -HZI-) studying the molecules involved in Quorum Sensing using the opportunistic oral pathogens Streptococcus mutans as model. During this period of time four publications were published in international journals. His second Postdoctoral position, also in HZI centre, is taken currently place in the Research Group of Prof. Dr. D. Dietmar Pieper in the Group of Microbial Interaction and Processes and until now with four publications published in international journals and one under reviewing process.
He is involved in two European Projects, BACSIN (http://www.unil.ch/bacsin) and MAGICPAH (http://www.magicpah.org/) developing and applying techniques in molecular biology such a microarrays for catabolic genes detection and high throughput sequencing. BACSIN is a macro European Project, form by fourteen partners distributed mainly across Europe (one of them located in California). On the frame of BACSIN project (2008-2012) the studied of catabolic potential in the environment was assessed using the catabolic array which was printed, optimized, validated and applied at HZI centre. On the frame of MAGICPAH project (2000-2014) high throughput sequencing approaches are been applying to environmental DNA and RNA to discover new genes with catabolic potentials.
Organiza: Programa de Actividades Innovación Docente. Instituto del Agua.
Más información: Dra. Belen Juarez (PDI)
Instituto del Agua / Fac. Farmacia
email: belenjj@ugr.es