nireEHU 
Subject
Environmental Toxicogenomics
General details of the subject
- Mode
- Face-to-face degree course
- Language
- English
Description and contextualization of the subject
Environmental genomics, with emphasis on transcriptomic studies in environmentally-relevant non-model organisms. Application of genomic technology to environmental resources management or ecosystem health assessment.Aims
¿ To provide basic notions, with the use of practical examples, that will explain the principal techniques used in environmental genomics, in ecotoxicogenomics and in clinic toxicogenomics.
Objectives
At the end of the Unit, you should:
1. detect/interpret molecularly and mechanistically the adaptation events that living organisms trigger to obtain homeostasis in disease; reproduction; toxicity, feeding regimes and in a changing environment.
2. determine the action mechanisms of different chemical compounds, on different cell functional pathways and structures.
3. understand the usefulness of using transcriptional profiles in the evaluation of the quality of the environment and its application in pollution biomonitoring programs.
4. learn the diagnostic usefulness of the ecotoxicogenomic approach in the determination of the ethiology of diverse pathologies and toxicopathies, in animals.
Key Skills Acquired
At the end of the Unit, you should be able to:
1. master the technology, tools and information required for the planning, development and interpretation of high-throughput genomic and transcriptomic studies.
2. know how to design a research project based upon the study of gene transcription profiles diagnostic of exposure to and/or effect of chemical compounds in laboratory and real field/environmental conditions: selection of sentinel species, sequence information retrieval; traditional and massively parallel sequencing techniques; gene expression analysis techniques; and analysis of gene pathways.
Teaching staff
| Name | Institution | Category | Doctor | Teaching profile | Area | |
|---|---|---|---|---|---|---|
| BILBAO CASTELLANOS, EIDER | University of the Basque Country | Profesorado Adjunto (Ayudante Doctor/A) | Doctor | Bilingual | Cellular Biology | eider.bilbao@ehu.eus |
| CANCIO URIARTE, IBON | University of the Basque Country | Profesorado Pleno | Doctor | Bilingual | Cellular Biology | ibon.cancio@ehu.eus |
| DIAZ DE CERIO ARRUABARRENA, OIHANE | University of the Basque Country | Profesorado Adjunto (Ayudante Doctor/A) | Doctor | Bilingual | Cellular Biology | oihane.diazdecerio@ehu.eus |
Competencies
| Name | Weight |
|---|---|
| Dominar la tecnología, las herramientas y la información requeridas para planificar, desarrollar e interpretar estudios genómicos y transcriptómicos de alto rendimiento. | 25.0 % |
| Detectar/interpretar molecular y mecánicamente los eventos de adaptación desencadenados por los organismos vivos para obtener homeostasis: - En enfermedades (stress, enfermedades infecciosas) - En reproducción - Bajo exposición a compuestos químicos tóxicos - Bajo diferentes regímenes de alimentación (fórmulas alimentarias utilizadas en acuacultura, cambios estacionales en la disponibilidad de alimentos) - En un ambiente cambiante. | 25.0 % |
| Determinar los mecanismos de acción de diferentes compuestos químicos en rutas funcionales y estructura de diferentes células. | 20.0 % |
| Entender la utilidad de usar perfiles transcripcionales en la evaluación de la calidad del ambiente y su aplicación en programas de bioseguimiento de la contaminación = Aprender cómo diseñar un proyecto de investigación basado en el estudio de los perfiles de transcripción génica para el diagnóstico de la exposición a y/o del efecto de compuestos químicos, tanto en el laboratorio como en condiciones ambientales reales de campo: selección de especies centinela, obtención de información de secuencias, técnicas de secuenciación tradicionales y en masa, técnicas de análisis de expresión génica, análisis de rutas génicas. | 20.0 % |
| Que el estudiante reconozca la utilidad diagnóstica de la aproximaciòn toxicogenómica para determinar la etiologia de diverssas patologias y toxicopatias en animales. | 10.0 % |
Study types
| Type | Face-to-face hours | Non face-to-face hours | Total hours |
|---|---|---|---|
| Lecture-based | 24 | 40 | 64 |
| Seminar | 0 | 12 | 12 |
| Applied laboratory-based groups | 2 | 2 | 4 |
| Applied computer-based groups | 8 | 4 | 12 |
| Workshop | 4 | 0 | 4 |
| Industrial workshop | 2 | 2 | 4 |
Training activities
| Name | Hours | Percentage of classroom teaching |
|---|---|---|
| Acquiring basic instrumental skills | 4.0 | 50 % |
| Application Workshops | 4.0 | 50 % |
| Expositive classes | 64.0 | 37 % |
| Groupwork | 4.0 | 100 % |
| Information presentation | 12.0 | 0 % |
| Networking | 12.0 | 60 % |
Assessment systems
| Name | Minimum weighting | Maximum weighting |
|---|---|---|
| Attendance is compulsory. Proactive participation in the activities, practical and oral sessions, will be considered. ¿ Individual report (seminar) including a questionnaire about the course. 3 page abstract (specific subject) that will be made available to lecturers and to all students participating in the course. All students will have to formulate a critical question to each abstract ,that will be also sent to the lecturer. Questions must be answered by all the students/lecturers. Assessment criteria: written report quality, abstract understanding by other students, and rationale at answering the questions raised. | 0.0 % | 50.0 % |
| Essay, Individual work and/or group work | 20.0 % | 0.0 % |
| Practical tasks | 0.0 % | 100.0 % |
| Presentation and public defence of the dissertation | 80.0 % | 0.0 % |
| Questions to discuss | 0.0 % | 100.0 % |
Learning outcomes of the subject
At the end of the Unit, you should be able to:1. master the technology, tools and information required for the planning, development and interpretation of high-throughput genomic and transcriptomic studies.
2. know how to design a research project based upon the study of gene transcription profiles diagnostic of exposure to and/or effect of chemical compounds in laboratory and real field/environmental conditions: selection of sentinel species, sequence information retrieval; traditional and massively parallel sequencing techniques; gene expression analysis techniques; and analysis of gene pathways.
Ordinary 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.
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
1. Environmental genomics and gene sources in the seas, soils, rivers, inside metazoa2. 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, and 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; and 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.
12. 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
Basic bibliography
Relevant papers delivered during the courseWeb resources delivered during the course