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Syllabus 2019-20 - 76712002 - Proteomics, Genomics, Bioinformatics and Systems Biology (Proteómica, genómica, bioinformática y biología de sistemas)

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  • Level 1: Tutorial support sessions, materials and exams in this language
  • Level 2: Tutorial support sessions, materials, exams and seminars in this language
  • Level 3: Tutorial support sessions, materials, exams, seminars and regular lectures in this language
DEGREE: Máster Univ. en Biotecnología y biomedicina (76712002)
FACULTY: Centre for Postgraduate Studies of the University of Jaen

DEGREE: Doble Máster en Biotecnología y Biomedicina y MFPES (Profesorado) (77912004)
FACULTY: Centre for Postgraduate Studies of the University of Jaen

ACADEMIC YEAR: 2019-20
SYLLABUS
1. COURSE BASIC INFORMATION
NAME: Proteomics, Genomics, Bioinformatics and Systems Biology
CODE: 76712002 (*) ACADEMIC YEAR: 2019-20
LANGUAGE: English LEVEL: 2
ECTS CREDITS: 6.0 YEAR: 1 SEMESTER: PC
 
2. LECTURER BASIC INFORMATION
NAME: PERAGÓN SÁNCHEZ, JUAN
DEPARTMENT: U103 - BIOLOGÍA EXPERIMENTAL
FIELD OF STUDY: 060 - BIOQUÍMICA Y BIOLOGÍA MOLECULAR
OFFICE NO.: B3 - 356 E-MAIL: jperagon@ujaen.es P: 953212523
WEBSITE: www4.ujaen.es/~jperagon/
LANGUAGE: - LEVEL: 2
 
NAME: CAÑUELO NAVARRO, ANA ROSA
DEPARTMENT: U103 - BIOLOGÍA EXPERIMENTAL
FIELD OF STUDY: 060 - BIOQUÍMICA Y BIOLOGÍA MOLECULAR
OFFICE NO.: B3 - 302 E-MAIL: acanuelo@ujaen.es P: 2767
WEBSITE: http://www4.ujaen.es/~acanuelo/
LANGUAGE: - LEVEL: 1
 
NAME: ESTEBAN RUIZ, FRANCISCO JOSÉ
DEPARTMENT: U103 - BIOLOGÍA EXPERIMENTAL
FIELD OF STUDY: 050 - BIOLOGÍA CELULAR
OFFICE NO.: B3 - B3-342 E-MAIL: festeban@ujaen.es P: 935212760
WEBSITE: http://www4.ujaen.es/~festeban/
LANGUAGE: - LEVEL: 3
 
3. CONTENT DESCRIPTION

Fundaments of proteomics: Protein folding, sorting, turnover, maturation, degradation and protein-ligand interactions.

Techniques and methods of sample preparation, separation (2-DE, HPLC-MS, other), identification and quantification in proteomics. Protein microarrays. ProteoRed.

Mass espectrometry in proteomics.

Applications of proteomis in the diagnostic, development of drugs, agriculture, industry.

Laboratory Practice: Effects of starvation on rat hepatic proteome by 2D SDS-PAGE. Sample preparation. 2-DE.Staining and analysis of proteins. Introduction to PDQest R (BioRad Laboratories). MS analysis. Identification of proteins and functional proteomics. Introduction to ProteoRed, the Spanish Network for Proteomics. Mass spectrometry equipment in the University of Jaén. Equipment and techniques for protein characterization in the Department of Experimental Biology of the University of Jaén.

An introduction to structural genomics: genome sequencing and phylogenetic structure.

An intoriduction to funtional genomics: tools for high-throughput gene expression and gene annotation.

Data Bases in Molecular Genetics:

  1. Nucleotides: EMBL and Genbank (including dbGSS, dbSTS, dbSNP).
  2. Proteins: NCBI, Expasy, EMBL; NCBI, RELIBASE, 3Dee.
  3. Human gene project (Sanger), and other sequenced genomes (S. cerevisiae, B. subtilis, A. Thaliana, etc).
  4. References (PubMed).
  5. OMIM (On line Mendelian Inheritance in Man).

DNA and protein sequencing and analysis:

Training in automatical DNA sequencing ADN en secuenciados automático. Sequence analysis (BLAST, FASTA, CLUSTAL, seqaid, DNAsis, GCG).

Other Bioinformatic tools in Molecular Genetics:

  1. Gene searching (Genscan, BCM search launcher).
  2. PCR (oligo, Melting).
  3. ARN (Fold).
  4. Proteins and motifs (EMBOSS, Prosite, Expasy).
  5. GWAS tools

Data analysis and modelling:

  1. Microarrays data analysis. (R, NIH DAVID).
  2. Data integration: multivariate analysis and data mining.
  3. Molecular networks.
  4. Systems Biotechnology.
  5. Systems Biology and Systems Dynamics.

4. COURSE DESCRIPTION AND TEACHING METHODOLOGY

General methodology:

1) Academic sessions (20 h in presence of professor),

2) Laboratory sessions (15 h)

3) Practical class with computer adds (23 h)

3) Oral presentations (2 h)

  Course description and teaching methodology for PATIE student:

1) Lecture (Theory): Tutorial session, supply of press material, proposal of activities and exercises in English (in presence of professor or virtual): 1 h per week

2) Lecture (Practice): Tutorial session, supply of press material (in presence of professor or virtual): 1 h per week

c) Seminars: Supply of press material to prepare oral presentation: 1 h per week

d) Homework: 4 h per week

Students with special educational needs should contact the Student Attention Service (Servicio de Atención y Ayudas al Estudiante) in order to receive the appropriate academic support

5. ASSESSMENT METHODOLOGY

Assessment methodology:

Evaluation of attendance, involvement, and academic progress in: 1) theoric activities, 2) laboratory practice, 3) computer practice, 4) other activities.

The sum of the marks obtained in all of these aspects will be the end global mark. If the subject is not passed at Ordinary I  announcement, marks of the parts passed will be considered for Extraordinary II announcement. In this Extraordinary II announcement the mark corresponding to attendance and involving can be substituted by a written evaluation exam.

6. BOOKLIST
MAIN BOOKLIST:
  • Principles of Proteomics. Edition: 2nd ed. Author: Twyman, Richard M. Publisher: New York ; London : Garland Science, cop.2014  (Library)
  • Proteomics in practice: a guide to successful experimental design . Edition: -. Author: -. Publisher: Weinheim : Wiley-VCH &#59; Chichester : John Wiley [distributor], 2008  (Library)
  • Plant proteomics: technologies, strategies, and applications. Edition: -. Author: -. Publisher: Hoboken : John Wiley and Sons, 2008  (Library)
  • Encyclopedia of genetics, genomics, proteomics, and informatics. Edition: 3rd ed.. Author: Rédei, George P.. Publisher: New York : Springer, 2008  (Library)
  • Fundamentals of Data Mining in Genomics and Proteomics [Recurso electrónico] . Edition: -. Author: Dubitzky, Werner. Publisher: Boston, MA : Springer Science+Business Media, LLC, 2007.  (Library)
  • Genomas. Edition: 3a ed.. Author: Brown, Terry A.. Publisher: Buenos Aires ; Madrid : Médica Panamericana, cop. 2008  (Library)
  • Methods of Microarray Data Analysis [Recurso electrónico]. Edition: IV.. Author: Shoemaker, Jennifer S.. Publisher: Boston, MA : Springer Science + Business Media, Inc. Boston, 2005.  (Library)
  • Teoría y ejercicios prácticos de dinámica de sistemas. Edition: [3ª̇ ed. revisada y ampliada]. Author: Martín García, Juan. Publisher: Barcelona : El autor, 2011  (Library)
ADDITIONAL BOOKLIST:
  • Dynamic systems biology modeling and simulation. Edition: -. Author: DiStefano, Joseph J.. Publisher: Amsterdam : Elsevier, Academic Press, [2013]  (Library)
  • Genetics: analysis of genes and genomes. Edition: 7th ed.. Author: Hartl, Daniel L.. Publisher: Sudbury : Jones and Bartlett, 2009.  (Library)
  • Modern multivariate statistical techniques: regression, classification, and manifold learning. Edition: -. Author: Izenman, Alan Julian. Publisher: New York : Springer, cop. 2008  (Library)