C8560 Genetic codes

Přírodovědecká fakulta
jaro 2014
Rozsah
2/0. 2 kr. (příf plus uk plus > 4). Doporučované ukončení: k. Jiná možná ukončení: zk.
Vyučující
prof. Ing. Eduard Nikolajevič Trifonov, Ph.D. (přednášející), prof. RNDr. Jiří Fajkus, CSc. (zástupce)
Garance
prof. RNDr. Jiří Fajkus, CSc.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Kontaktní osoba: prof. RNDr. Jiří Fajkus, CSc.
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Předpoklady
Basic knowledge of molecular biology.
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Předmět si smí zapsat nejvýše 30 stud.
Momentální stav registrace a zápisu: zapsáno: 0/30, pouze zareg.: 0/30, pouze zareg. s předností (mateřské obory): 0/30
Mateřské obory/plány
Cíle předmětu
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
Osnova
  • 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
Literatura
  • 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, roč. 29, č. 2, s. 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, roč. 27, č. 6, s. 741-746. ISSN 0739-1102. info
  • GABDANK, Idan, Danny BARASH a Eduard TRIFONOV. Single-base Resolution Nucleosome Mapping on DNA Sequences. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. United States: ADENINE PRESS, 2010, roč. 28, č. 1, s. 107-121. ISSN 0739-1102. info
  • SALIH, F., B. SALIH a 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, roč. 26, č. 3, s. 1-8. ISSN 0739-1102. info
  • FAJKUS, Jiří a Edward N. TRIFONOV. Columnar Packing of Telomeric Nucleosomes. Biochemical and Biophysical Research Communications. California: Academic Press, 2001, roč. 280, č. 4, s. 961-963. ISSN 0006-291X. info
Výukové metody
přednášky
Metody hodnocení
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.
Vyučovací jazyk
Angličtina
Navazující předměty
Informace učitele
Lectures will be given in English within a period of two weeks (2-4 lessons per day). In spring term 2014 this will be held in February 17-25. The course will be concluded by colloquium after the last lesson.
Další komentáře
Studijní materiály
Předmět je vyučován každoročně.
Výuka probíhá blokově.
Předmět je zařazen také v obdobích jaro 2013, jaro 2015.