Inhalt
[ 675BIOLITG13 ] Module Introduction to Genomics
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| Workload |
Mode of examination |
Education level |
Study areas |
Responsible person |
Coordinating university |
| 3 ECTS |
Accumulative module examination |
B1 - Bachelor's programme 1. year |
(*)Bioinformatik |
Alexander W. Bruce |
USB Budweis |
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| Detailed information |
| Original study plan |
Bachelor's programme Bioinformatics 2015W |
| Objectives |
Knowledge of, understanding in, and approaches to topics in Genomics.
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Knowledge of, understanding in, and approaches to following topics:
- Introduction to the ‘Genome’ (definition of the genome/genetic material, types and variety of genome in biology, genome-transcriptome-proteome central dogma, genome structure i.e. concept of genes, regulatory elements and repetitive DNA, genome organisation i.e. chromosomes and histones/ chromatin, DNA replication).
- Historical overview of first ‘Genomic’ methods i.e. chromosome mapping, laborious genetic linkage analyses, chromosome walking, QTLs. Introduction to nucleic acid sequencing from a historical perspective; first organisms – bacteriophages (MS2 PhiX174), bacteria (Haemophilus influenza, E. coli). Individual research group led DNA sequencing of specific loci of more complex organisms. Creation of common databases for this information – need to consolidate and coordinate DNA sequencing efforts
- Scaled-up DNA sequencing to tackle larger genomes (use of human genome project as a case study). – Historical perspective and public versus private initiatives. Techniques used to perform large scale sequencing, Genome sequencing of model organisms – which, how and why? Creation of synthetic organisms (Craig Venter).
- Interpreting the sequenced genome – identifying genes/ transcripts in the sequence and cataloguing them – birth of ‘Bioinformatics’. Databases, Development of more sophisticated genome browsers with increasing amounts of annotation. ‘Gene cards’ and gene specific information features and using BLAST searches to identify experimentally derived sequences against the genome sequence reference datasets (nomenclature definitions).
- Using the genomic sequence and bioinformatics to identify functionally important information e.g. Comparative genomics - phylogenetic analyses of bacteria or viruses (e.g. H5N1 influenza), identification of specific transcription factor binding sites and candidate target genes (e.g. REST and neurogenesis)
- Applying genomics at the bench (development of numerous experimental strategies e.g. originally microarray based now based on novel large scale sequencing technologies) – inclusion of relevant case study examples e.g. the international ENCODE consortium
- Depositing, retrieving and interpreting bench-based genomic experiment data/ results – cross referencing with our experimental databases and web resources
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