C8560 Genetic codes

Faculty of Science
Spring 2014
Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. Ing. Eduard Nikolajevič Trifonov, Ph.D. (lecturer), prof. RNDr. Jiří Fajkus, CSc. (deputy)
Guaranteed by
prof. RNDr. Jiří Fajkus, CSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jiří Fajkus, CSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic knowledge of molecular biology
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30
fields of study / plans the course is directly associated with
Course objectives
Main outcomes of the course include: Students will learn about different kinds of codes carried by DNA sequence; Students will gain understanding principles of different periodical codes hidden in DNA sequence; Special attention will be paid to the understanding of principles of DNA-directed nucleosome positioning
Syllabus
  • In addition to protein-coding message the nucleotide sequences carry instructions for DNA folding, transcription, translation framing, gene splicing, fast adaptation code, and many more (1, 2). Every sequence element belongs simultaneously to several different messages superimposed on one another. The codes of protein sequences are of this nature as well. Most prominent examples of the code overlapping and interaction will be considered. The course is based largely on the most recent publications. This includes the latest developments on the chromatin code and its interactions with other codes (3, 4). Ref. (2) is an extended summary of the course. References: 1. Trifonov, E. N., Sequence codes. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 2324-2326. 2. Trifonov, E. N., Codes of biosequences. In: The Codes of Life. The Rules of Macroevolution. Barbieri, M. (ed.). Springer. New York, in press. 3. Trifonov, E. N., Kogan, S., Cohanim, A. B. Latest on the nucleosome positioning sequence patterns. In "DNA Structure, Chromatin and Gene Expression" (Eds. R. Kiyama, M. Shimizu), Transworld Research Network, Trivandrum (India), pp 43-54 (2006). 4. F. Salih, B. Salih, E. N. Trifonov, Sequence-directed mapping of nucleosome positions, JBSD 26, 1-8 (2008). Outline: Periodical and aperiodical codes in DNA
  • DNA bending versus DNA curvature
  • Nucleosome positioning - DNA sequence patterns
  • Other codes in DNA and RNA sequences
Literature
  • 2. Trifonov, E. N., Codes of biosequences. In: The Codes of Life. The Rules of Macroevolution. Barbieri, M. (ed.). Springer. New York, in press.
  • TRIFONOV, Eduard. Vocabulary of Definitions of Life Suggests a Definition. Journal of Biomolecular Structure & Dynamics. Adenine Press, 2011, vol. 29, No 2, p. 259-266. ISSN 0739-1102. URL info
  • TRIFONOV, Eduard. Nucleosome Positioning by Sequence, State of the Art and Apparent Finale. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. United States: ADENINE PRESS, 2010, vol. 27, No 6, p. 741-746. ISSN 0739-1102. info
  • GABDANK, Idan, Danny BARASH and Eduard TRIFONOV. Single-base Resolution Nucleosome Mapping on DNA Sequences. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. United States: ADENINE PRESS, 2010, vol. 28, No 1, p. 107-121. ISSN 0739-1102. info
  • SALIH, F., B. SALIH and Eduard TRIFONOV. Sequence Structure of Hidden 10.4 base Repeat in the Nucleosomes of C.elegans. Journal of Biomolecular Structure & Dynamics. USA: Adenine Press, 2008, vol. 26, No 3, p. 1-8. ISSN 0739-1102. info
  • FAJKUS, Jiří and Edward N. TRIFONOV. Columnar Packing of Telomeric Nucleosomes. Biochemical and Biophysical Research Communications. California: Academic Press, 2001, roč. 280, No 4, p. 961-963. ISSN 0006-291X. info
Teaching methods
lectures
Assessment methods
Lectures will be given in English within a period of 10 working days (2-4 hours per day). The course will be concluded by colloquium after the last lesson. To pass the colloquium, active participation in concluding discussion and correct answering of >50% questions is required. If preferred by a student, the course may be concluded by final oral exam.
Language of instruction
English
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
The course is taught in blocks.
The course is also listed under the following terms Spring 2013, Spring 2015.
  • Enrolment Statistics (Spring 2014, recent)
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