Syllabus for Functional Genomics
A revised version of the syllabus is available.
- 15 credits
- Course code: 1BG322
- Education cycle: Second cycle
Main field(s) of study and in-depth level:
- Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
- Established: 2007-03-15
- Established by: The Faculty Board of Science and Technology
- Revised: 2007-11-06
- Revised by: The Faculty Board of Science and Technology
- Applies from: Autumn 2008
120 credits including alternative 1) 40 credit points/60 credits biology and 20 credit points/30 credits chemistry; alternative 2) chemistry 40 credit points/60 credits including Biochemistry 10 credit points/15 credits and biology 20 credit points/30 credits including Molecular Genetics 15 credits, and in both cases Microbial Genetics or Molecular Cell Biology or Plant Physiology or Evolutionary Genomics in Natural Populations.
- Responsible department: Biology Education Centre
The overall aim of the course is to provide in-depth knowledge of the structure of organisation and expressions of the genomic information in bacteria, archaea and eukaryotes.
After completion of the course the student shall:
- understand, and be able to describe, all main steps in a genome sequencing project, and be familiar with current large-scale sequencing technologies.
- be able to describe and explain the overall genome structure in microorganisms, plants and animals.
- be able to differentiate between different levels of whole-genome studies and global analyses, including genomics, transcriptomics, proteomics, metabolomics, metagenomics and system biology.
- be familiar with a range of large-scale methods for functional genomics analyses, and with current technical advances within the genomics and functional genomics fields.
- understand, and be able to (describe) provide/suggest, solutions to theoretical and experimental problems related to genomics and functional genomics.
- be able to design and carry out a small functional genomics project, both theoretically and experimentally, using knowledge gained during the course.
- be able to process and analyse large-scale experimental datasets, and to present results and interpretations in a scientifically stringent fashion.
- be able to critically evaluate research reports and scientific publications concerning genomics and functional genomics, and be able to suggest alternative interpretations and relevant follow-up experiments.
- be able to describe and evaluate implications of ongoing developments with the genomics, functional genomics and systems biology fields for society, in terms of consequences for research, commercial aspects and ethical considerations.
- The theoretical part of the course deals with studies of bacteria, archaea and eukaryotes at the whole-genome level. Large-scale methods for DNA sequencing and analysis of complete genomes (genomics) of prokaryotic and eukaryotic model organisms are covered in depth, including different DNA sequencing strategies and technologies, genome structure and organisation, comparative genomics, and evolutionary aspects. Functional genomics constitutes a second main theme, including microarray-based techniques for RNA analysis (transcriptomics), different methods for global protein studies (proteomics) and current attempts at developing similar methodology for studies of metabolites and other small molecules (metabolomics). The course also covers large-scale techniques for studies of protein-protein interaction, metagenomics and systems biology, transgenic organisms, reverse genetics and gene-ethics.
- The experimental part covers practical use of current functional genomics and recombinant DNA techniques, including DNA isolation, PCR, T-vector cloning, automated cycle sequencing of DNA, OLA-based genotyping, isolation of RNA, real-time RT-PCR and reporter gene analysis in transgenic organisms. Two of the exercises are carried out as small research projects, in which the students themselves are responsible for planning, experimental work and data processing and evaluation. The results are presented both as written reports and as presentations together with the rest of the student class. A theoretical analysis of microarray data is also carried out, followed by discussions about data processing, analysis and interpretation of the results.
- The course participants also carry out individual literature projects within current topics related to genomics and functional genomics. The students select topics, search and collect relevant information and literature and then present the project in writing and as a Powerpoint exercise. The literature projects are carried out within the communications training with feedback and self-evaluation for biology students program (Diana).
- Site visits to local biotech companies and functional genomics research laboratories are also carried out during the course, to provide examples of the development and use of functional genomics methods within current biotech industry.
The teaching is carried out as lectures, seminars, practical and computer based (datorövning) experiments and site visits. Participation in seminars and practicals is mandatory. The course is normally taught in English.
To pass the course, the students need an approved theoretical exam (8 credits), as well as approved experimental work (5 credits) and literature project (2 credits).
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Applies from: Autumn 2008
Some titles may be available electronically through the University library.
Lesk, Arthur M.
Introduction to genomics
Oxford ; a New York: Oxford University Press, c2007