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Inicio / Estudios / Máster en Técnicas Avanzadas en Investigación y Desarrollo Agrario y Alimentario / Plan de Estudios

Course Unit Description

GENOMIC TOOLS IN RESEARCH

Course 2022-23

  • On-site

1.Subject data

Name: GENOMIC TOOLS IN RESEARCH

Code: 203301002

Type: Elective

ECTS: 4

Length of subject: Per term

Semester and course: 1st Year - First term

Speciality:

Language: English

Mode of study: On-site class

2. Lecturer data

Lecturer data: EGEA GUTIÉRREZ-CORTINES, MARCOS

Knowledge area: Genética

Department: Ingeniería Agronómica

Telephone: 868071077 - 968325705 - 868071075

Email: marcos.egea@upct.es

Office hours and location:

Qualifications/Degrees:
PhD in Life Sciences from Ben-Gurion University of the Negev (ISRAEL) - 1992

Academic rank in UPCT: Catedrático de Universidad

Number of five-year periods: 6

Number of six-year periods: 4 de investigación y 1 de transferencia

Curriculum Vitae: Full Profile

Lecturer data: WEISS , JULIA ROSL

Knowledge area: Genética

Department: Ingeniería Agronómica

Telephone: 968325777

Email: julia.weiss@upct.es

Office hours and location:

miércoles - 13:00 / 17:00
EDIFICIO DE ETSI AGRONÓMICA, planta 2, Despacho 2.15
Se ruega contactar previamente por correo electrónico indicando emotivo de la tutoría.

Qualifications/Degrees:

Academic rank in UPCT: Catedrática de Universidad

Number of five-year periods: 4

Number of six-year periods: 4 de investigación y 1 de transferencia

Curriculum Vitae: Full Profile

3. Competences and learning outcomes

3.1. Basic curricular competences related to the subject

[CB6 ]. To possess and understand knowledge that provides a basis or opportunity to be original in the development and / or application of ideas, often in a research context.

3.2. General curricular competences related to the subject

[CG1 ]. To learn about the field of study in which agricultural and food research and development are developed and the research skills and methods related to such field.

[CG4 ]. To be able to perform a critical analysis, and an evaluation and synthesis analysis of new and complex ideas in the agri-food sector.

3.3. Specific curricular competences related to the subject

[CE1 ]. To synthesize previous knowledge together with newly acquired knowledge in the matter, so as to be able to cope in agri-food contexts in which there is little specific information.

[CE3 ]. To show a certain degree of scientific and technical training to start a research activity in the field of agri-food.

[CE4 ]. To show a certain degree of understanding of the concepts, principles and theories related to the chosen subjects of the master's program.

Specific topic competences (for elective topics which have them)

Competencias específicas de la asignatura:

1. Describir la estructura de genomas y métodos de análisis.

2. Manejar, a nivel de usuario principiante, programas bioinformáticos para búsqueda de secuencias en bases de datos. Programas Clustal X, BLAST y NJPLOT.

3. Describir los conceptos básicos de filogenética.

Aspectos referidos a la semipresencialidad:

Los estudiantes pueden participar en las actividades formativas de esta asignatura de forma presencial (acudiendo físicamente al espacio en el que se desarrollan) o en línea a través de internet, excepto en "Sesiones Prácticas de laboratorio, campo o planta piloto" en las que solo puede participarse de forma presencial.

3.4. Transversal curricular competences related to the subject

[CT1 ]. Spoken and written effective communication

[CT4 ]. Using information resources responsibly

3.5. Subject learning outcomes

1.- Utilizar el método más adecuado para comunicar ideas, conclusiones o resultados, a una audiencia especializada o no, en contextos nacionales e internacionales.
2.- Localizar, analizar y seleccionar la información precisa para desarrollar su actividad profesional/investigadora.

4. Contents

4.1 Curricular contents related to the subject

1.- Estructura de los genomas. 2.- Genómica física. 3.- Procesos de activación y silenciamiento del genoma. Factores de transcripción y epigenética. 4.- Análisis transcriptómico y genómica funcional. 5.- Técnicas de ganancia y pérdida de función. Abordajes masivos. 6.- Evolución de genomas.

4.2. Theory syllabus

Teaching modules

Units

1. Genome structure 2. DNA and chromosome structure 3. DNA structure 4. Second and third generation sequencing technology 5. Plant and animal genomes 6. Transcription and functional genomics 7. Epigenetics 8. Transcriptomic analysis 9. Genome egimeering technologies

4.3. Practice syllabus

Name

Description

Databases. NCBI, SOLGENOMICS, JGI

Phylogenies

Making constructs of RNAI and CRISPR/Cas

Risks prevention

Promoting the continuous improvement of working and study conditions of the entire university community is one the basic principles and goals of the Universidad Politécnica de Cartagena. Such commitment to prevention and the responsibilities arising from it concern all realms of the university: governing bodies, management team, teaching and research staff, administrative and service staff and students. The UPCT Service of Occupational Hazards (Servicio de Prevención de Riesgos Laborales de la UPCT) has published a "Risk Prevention Manual for new students" (Manual de acogida al estudiante en materia de prevención de riesgos), which may be downloaded from the e-learning platform ("Aula Virtual"), with instructions and recommendations on how to act properly, from the point of view of prevention (safety, ergonomics, etc.), when developing any type of activity at the University. You will also find recommendations on how to proceed in an emergency or if an incident occurs. Particularly when carrying out training practices in laboratories, workshops or field work, you must follow all your teacher's instructions, because he/she is the person responsible for your safety and health during practice performance. Feel free to ask any questions you may have and do not put your safety or that of your classmates at risk.

4.4. Comments

5. Teaching method

Name

Description

Hours

In-class

Name

Class in conventional classroom: theory, problems, case studies, seminars, etc

Description

Lectures in gemonics, transcriptomics and proteomics. Paper research. Bibliographic handling.

Hours

28

In-class

100

Name

Class in laboratory: practical classes / internships

Description

Development of a genomics project

Hours

2

In-class

100

Name

Class in the field or open classroom (technical visits, lectures, etc.). In general, activities that require special resources or planning

Description

Development of a genomics project



Oral presentation and attendance to other presentations

Hours

2

In-class

100

Name

Class in a computer classroom: practical classes / internships

Description

Bioinformatics at user level. USe of standard software for DNA and RNA research

Hours

6

In-class

100

Name

Assessment activities (continuous assessment system)

Description

Completing the tutorials and other aspects related

Hours

2

In-class

100

Name

Assessment activities (final assessment system)

Description

Multiple choice test

Hours

1

In-class

100

Name

Tutorials

Description

Tutorials. Problem and question solving. Online or in the lab/office

Hours

6

In-class

50

Name

Student work: study or individual or group work

Description

preparing oral presentation



Learning subject, reading papers, acquiring Genomics vocabulary

Hours

73

In-class

0

6. Assessment method

6.1. Continous assesment system

Name

Description and criteria

Percentage

Name

Individual test (oral or written)

Description and criteria

Multiple choice test. a minimum of 7 to pass

Percentage

25 %

Name

Evaluation of practical sessions, visits and seminars based on reports and corresponding documents

Description and criteria

depending on year we will do a deliverable of bioinformatics

Percentage

20 %

Name

Solving of cases, theoretical questions, practical exercises or problems given by the teaching staff

Description and criteria

Evaluation redundant with he previous one

Percentage

20 %

Name

Presentation and defence of individual or group assignments (it may include auto-evaluation and peer-evaluation)

Description and criteria

Oral presentation on research in genomics

Percentage

30 %

Name

Attendance to seminars and visits to companies

Description and criteria

Depending on year it will be evaluated

Percentage

0 %

Name

Other evaluation activities

Description and criteria

Short reports of Bioinformatic practicum

Percentage

5 %

6.2. Final assesment system

Name

Description and criteria

Percentage

Name

Individual test (oral or written)

Description and criteria

multiple choice test minimum 7 to pass

Percentage

45 %

Name

Presentation and defence of individual or group assignments (it may include auto-evaluation and peer-evaluation)

Description and criteria

oral presentation of work

Percentage

35 %

Name

Other evaluation activities

Description and criteria

Short reports of Bioinformatic practicum

Percentage

20 %

Information

7. Bibliography and resources

7.1. Basic bibliography

Author: Rashidi, Hooman
Title: Bioinformatics basics applications in biological science and medicine
Editorial: CRC Press
Publication Date: 2000
ISBN: 0849323754

Author: Bergeron, Bryan
Title: Bioinformatics computing
Editorial: Prentice Hall
Publication Date: 2003
ISBN: 0131008250

Author: , Ouellette, B.F. Francis
Title: Bioinformatics a practical guide to the analysis of genes and proteins
Editorial: Joh Wiley & Sons
Publication Date: 2015
ISBN: 9780585240879

Author:
Title: Nature
Editorial: Macmillan Journals ltd., etc.
Publication Date: 1869
ISBN:

Author: Knudsen, Steen
Title: Biologist's guide to analysis of DNA microarray data
Editorial: John Wiley & Sons
Publication Date: 2002
ISBN: 0471224901

Author: Brown, T.A.
Title: Genomes
Editorial: Wiley-Liss
Publication Date: 1999
ISBN: 0471316180

Author: Kahl, Günter
Title: The dictionary of gene technology genomics, transcriptomics, proteomics
Editorial: Wiley-VCH
Publication Date: 2001
ISBN: 3527301003

Author: Graur, Dan
Title: Fundamentals of molecular evolution
Editorial: Sinauer Associates
Publication Date: 2000
ISBN: 0878932666

Author: Page, Roderic D.M.
Title: Molecular evolution a phylogenetic aprroach
Editorial: Blackwell
Publication Date: 2000
ISBN: 0865428891

Author: Schena, Mark
Title: Microarray biochip technology
Editorial: Eaton
Publication Date: 2000
ISBN: 1881299376

7.2. Supplementary bibliography

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