Description and contextualization of the subject

Environmental genomics, with emphasis in transcriptomic studies in environmentally relevant non-model organisms. Application of genomic technology to environmental resources management or ecosystem health assessment.

Ordinary call: orientations and renunciation

Las condiciones de renuncia a la convocatoria ordinaria se rigen por la Normativa de permanencia del alumnado de los másteres universitarios aprobada por el acuerdo de consejo social de la UPV/EHU el 22 de Julio de 2015. En todo caso habrá que comunicar por escrito al profesor(a) responsable de la asignatura la renuncia a la convocatoria, antes de la primera prueba de evaluación de la asignatura.



El método de evaluación incluido en esta guía puede sufrir cambios si las directrices de las autoridades sanitarias así lo estableciesen. Las modificaciones a adoptar se anunciarían oportunamente, contando con las estrategias y herramientas necesarias para garantizar el derecho del alumnado a ser evaluado con equidad y justicia.

Extraordinary call: orientations and renunciation

Condiciones de evaluación a discutir con el profesorado.



Las condiciones de renuncia a la convocatoria ordinaria se rigen por la Normativa de permanencia del alumnado de los másteres universitarios aprobada por el acuerdo de consejo social de la UPV/EHU el 22 de Julio de 2015. En todo caso habrá que comunicar por escrito al profesor(a) responsable de la asignatura la renuncia a la convocatoria, antes de la primera prueba de evaluación de la asignatura.



El método de evaluación incluido en esta guía puede sufrir cambios si las directrices de las autoridades sanitarias así lo estableciesen. Las modificaciones a adoptar se anunciarían oportunamente, contando con las estrategias y herramientas necesarias para garantizar el derecho del alumnado a ser evaluado con equidad y justicia.

Temary

Sinopsis (Lectures)

1. Environmental genomics and gene sources in the seas, soils, rivers, inside metazoa (a sea of genes!!).

2. Environmental metagenomics and gene discovery

3. Genomic services for aquaculture, fisheries research, study of fish stock dynamics, agriculture, food supply, comparative physiology...

4. Genomics and environmental model organisms.

5. Marine genomics and patents.

6. Basic concepts in toxicogenomics: ecotoxicogenomics, functional genomics, transcriptomics, proteomics, metabolomics, analysis of gene expression, gene ontology.

7. Molecular mechanisms in cell toxicity: effects on gene transcription levels. Gene families with predictive capacity in toxicology: inflammation, peroxisome proliferation, mutagenesis, carcinogenesis, teratogenesis, agonists of AhR and other nuclear receptors, metal scavengers, detoxification metabolism, cytotoxicity, apoptosis, immunosuppression¿

8. How to address the lack of basic gene sequence information about the species of interest. Cloning, expressed sequence tags (ESTs). Suppression subtractive hybridisation-PCR. Gene sequencing, Genome vs transcriptome sequencing. Massively parallel sequencing techniques. Sequence/Gene annotation (Gene ontology).

9. Basic techniques for the qualitative and quantitative study of differential gene expression (effects of chemical compounds). Toxicological fingerprinting. RT-PCR, Q-RT-PCR. Northern-blot, dot-blot, in situ hybridisation. Differential display PCR. Suppression subtractive hybridisation-PCR. Microarrays (microchips) and transcriptomics

10. Toxicogenomics vs proteomics vs metabolomics. Systems biology.

11. Knock-down and transgenic technology and the gene dissection of relevant molecular pathways.



Practicals: Navigating through the web in search of gene/genome/metagenome data bases. Gene sequence repositories, Genome sequence repositories (NCBI, ENSEMBL, GOLD). Gene expression repositories (GEO, Arrayexpress). Pathway analysis based on Gene ontology (GoFact, KEGG pathways). Microarray data interpretation and analysis tools.





Bibliography



Aleström P, Holter JL, Nourizadeh-Lillabadi R. (2006). Zebrafish in functional genomics and aquatic biomedicine. Trends Biotechnol. 24: 15-21.

Ankley GT, Daston GP, Degitz SJ, Denslow ND, Hoke RA, Kennedy SW, Miracle AL, Perkins EJ, Snape J, Tillitt DE, Tyler CR, Versteeg D (2006). Toxicogenomics in regulatory ecotoxicology. Environ. Sci. Technol. 40, 4055-4065.

Boutet I; Tanguy A; Moraga D (2004). Response of the Pacific oyster Crassostrea gigas to hydrocarbon contamination under experimental conditions. Gene 329: 147-157.

Cossins AR, Crawford DL (2005). Fish as models for environmental genomics. Nat. Rev. Genet. 6, 324-333.

Cossins A, Fraser J, Hughes M, Gracey A (2006). Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity. J. Exp. Biol. 209, 2328-2336.

Denslow ND, Garcia-Reyero N, Barber DS (2007). Fish 'n' chips: the use of microarrays for aquatic toxicology. Mol. Biosyst. 3, 172-177.

Diatchencko et al. (1996). Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93: 6025-6030.

Neumann NF, Galvez F (2002) DNA microarrays and toxicogenomics: applications for ecotoxicology? Biotech. Advan. 20: 391-419.

Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D. (2009). Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol. 18: 3128-3150.

Pennie WD, Woodyatt NJ; Aldridge TC; Orphanides G (2001) Application of genomics to the definition of the molecular basis for toxicity. Toxicol. Lett. 120: 353-358.

Roest Crollius H, Weissenbach J. (2005). Fish genomics and biology. Genome Res. 15: 1675-1682.

Rusch DB, Halpern AL, Sutton G et al. (2007). The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5(3):e77.

Snape JS, Maund SJ; Pickford DB, Hutchinson TH (2004) Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. Aquat. Toxicol. 67:143-154.

Thomas et al., (2001) Identification of toxicologically predictive gene sets using cDNA microarrays. Mol. Pharmacol. 60: 1189-1194.

Yooseph S, Sutton G, Rusch DB, (2007). The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5(3):e16.





Web resources



.- Gene/genome sequence repositories

http://www.ncbi.nlm.nih.gov/

http://www.ensembl.org/index.html

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi



.- Genome projects

http://www.genomesonline.org/



.- Clustal

http://www.ebi.ac.uk/Tools/clustalw2/



.- Primer design: Primer 3 (v. 0.4.0)

http://frodo.wi.mit.edu/primer3/



.- Proteomic tools: translation etc¿

http://www.expasy.ch/tools/



.- Reverse complementary

http://www.bioinformatics.org/sms/rev_comp.html



.- Promoter motif search

http://motif.genome.jp/

http://jaspar.genereg.net/



.- Gene ontology database

http://www.geneontology.org/



.- Blast2Go

http://www.blast2go.org/



.- GenMapp

http://www.genmapp.org/



.- Pathways, gene functional classification: KEGG, Biosystems, Panther, Biocarta, AB

http://www.genome.jp/kegg/pathway.html

http://www.ncbi.nlm.nih.gov/sites/biosystems

http://www.pantherdb.org/

http://www.biocarta.com/genes/index.asp

http://www5.appliedbiosystems.com/tools/pathway/



.- Microarray data analysis

http://www.tm4.org/mev/ (multiexperiment viewer)



.= Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, et al. TM4: a free, open-source system for microarray data management and analysis. . Vol 34.; 2003.



.- Functional analysis of gene expression profiles

http://babelomics.bioinfo.cipf.es/

http://david.abcc.ncifcrf.gov/



.- Gene expression repositories

http://www.ncbi.nlm.nih.gov/geo/ (Gene expression omnibus)

http://www.ebi.ac.uk/microarray-as/ae/ (Arrayexpress)

http://www.ebi.ac.uk/gxa/ (Arrayexpress atlas)



.- eArray Custom Agilent microarray design

https://earray.chem.agilent.com/earray/ <br /><br />

Bibliography

Basic bibliography

Aleström P, Holter JL, Nourizadeh-Lillabadi R. (2006). Zebrafish in functional genomics and aquatic biomedicine. Trends Biotechnol. 24: 15-21.

Ankley GT, Daston GP, Degitz SJ, Denslow ND, Hoke RA, Kennedy SW, Miracle AL, Perkins EJ, Snape J, Tillitt DE, Tyler CR, Versteeg D (2006). Toxicogenomics in regulatory ecotoxicology. Environ. Sci. Technol. 40, 4055-4065.

Boutet I; Tanguy A; Moraga D (2004). Response of the Pacific oyster Crassostrea gigas to hydrocarbon contamination under experimental conditions. Gene 329: 147-157.

Cossins AR, Crawford DL (2005). Fish as models for environmental genomics. Nat. Rev. Genet. 6, 324-333.

Cossins A, Fraser J, Hughes M, Gracey A (2006). Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity. J. Exp. Biol. 209, 2328-2336.

Denslow ND, Garcia-Reyero N, Barber DS (2007). Fish 'n' chips: the use of microarrays for aquatic toxicology. Mol. Biosyst. 3, 172-177.

Diatchencko et al. (1996). Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93: 6025-6030.

Neumann NF, Galvez F (2002) DNA microarrays and toxicogenomics: applications for ecotoxicology? Biotech. Advan. 20: 391-419.

Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D. (2009). Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol. 18: 3128-3150.

Pennie WD, Woodyatt NJ; Aldridge TC; Orphanides G (2001) Application of genomics to the definition of the molecular basis for toxicity. Toxicol. Lett. 120: 353-358.

Roest Crollius H, Weissenbach J. (2005). Fish genomics and biology. Genome Res. 15: 1675-1682.

Rusch DB, Halpern AL, Sutton G et al. (2007). The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5(3):e77.

Snape JS, Maund SJ; Pickford DB, Hutchinson TH (2004) Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. Aquat. Toxicol. 67:143-154.

Thomas et al., (2001) Identification of toxicologically predictive gene sets using cDNA microarrays. Mol. Pharmacol. 60: 1189-1194.

Yooseph S, Sutton G, Rusch DB, (2007). The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5(3):e16.

Links

.- Gene/genome sequence repositories



http://www.ncbi.nlm.nih.gov/



http://www.ensembl.org/index.html



http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi







.- Genome projects



http://www.genomesonline.org/







.- Clustal



http://www.ebi.a