CG020 Genomics

Faculty of Science
Autumn 2013
Extent and Intensity
2/0. 2 credit(s) (plus 2 credits for an exam). Type of Completion: zk (examination).
Teacher(s)
doc. RNDr. Jan Hejátko, Ph.D. (lecturer), prof. RNDr. Jiří Fajkus, CSc. (deputy)
RNDr. Roman Hobza, Ph.D. (lecturer), doc. RNDr. Jan Hejátko, Ph.D. (deputy)
RNDr. Hana Konečná (lecturer)
Mgr. Markéta Pernisová, Ph.D. (lecturer)
Mgr. Kamil Růžička, Dr. rer. nat. (lecturer)
Guaranteed by
prof. RNDr. Zdeněk Glatz, CSc.
Department of Biochemistry – Chemistry Section – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Fri 12:00–13:50 B11/205
Prerequisites
Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.
Syllabus
  • Introduction to genomics.
  • Methods of functional genomics.
  • Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analysis of promoter regions of individual genes [ALIBABA], virtual PCR).
  • In silico prediction of gene functions.
  • Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analysis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
  • Fragmental DNA analysis and positional cloning as tools in forward genetics.
  • Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
  • Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
  • Southern blot and DNA molecular hybridization.
  • Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
  • Methods for the gene expression analysis (qualitative and quantitative gene expression profiling, Genevestigator, translational and transcriptional fusions with reporter gene).
  • New approaches: Chemical genetics.
Literature
    recommended literature
  • SAMUELSSON, Tore. Genomics and bioinformatics : an introduction to programming tools for life scientists. Cambridge: Cambridge University Press, 2012, xvii, 338. ISBN 9781107008564. info
  • Genomics. Edited by Isidore Rigoutsos - G. Stephanopoulos. New York: Oxford University Press, 2007, xxi, 314 p. ISBN 9780195300819. info
Teaching methods
The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.
Assessment methods
Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials are available on-line. Type of exam: Written exam. The test consists from 40 questions valued according to their difficulties (1-4 points), the total maximum is 100 points. Evaluation criteria of the examination test are as follows: 100-95 points A, 94-88 points B, 87-80 points C, 79-70 points D, 69-58 points E, <58 points F.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
Listed among pre-requisites of other courses
Teacher's information
http://genpro.sci.muni.cz/
The course is also listed under the following terms Autumn 2010 - only for the accreditation, Autumn 2012, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2013, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2013/CG020