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2010-04-12
Funkcijska genomika

Funkcijska genomika (0535)

Nosilci:

  • dr. Radovan Komel (20 ur)
  • dr. Damjana Rozman, docentka (20 ur)
  • dr. Peter Dovč, redni profesor (10 ur)
  • dr. Simon Horvat, docent (10 ur)

Obseg:

60 ur, 20 kreditnih točk

Izobraževalni cilji:

Leta 2000 so objavili grobi osnutek nukleotidnega zaporedja človeškega genoma in napovedali obdobje tako imenovane 'funkcijske genomike', ki bo ob mikroelektroniki in informatiki ter nanotehnologiji ključno področje znanstvenega, gospodarskega in družbenega razvoja v prihodnjih desetletjih. Ob vzporejanju genomov različnih organizmov bodo raziskave usmerjene v ugotavljanje vloge genov oziroma njihovih proteinskih produktov v celici, tkivu in organizmu, uravnavanju njihovega izražanja in medsebojnem komuniciranju nukleinskih kislin in proteinov. Vsebina tega predmeta je pregled nad področji raziskav v funkcijski genomiki in seznanjenje z njenimi metodološkimi pristopi.

Vsebina:

  • Genom (zgradba in vloga človeškega genoma, primerjava z genomi drugih organizmov). Vrste označevalcev DNA (mikrosateliti, RFLP, RAPD, SSCP, SNP). Projekt Človeški genom (zgodovinski pregled, kloniranje in kartiranje genoma - genetske in fizične karte, koncept kvantitativnega lokusa (angl. quantitative trait locus), koncept 'kontigov', STS, EST, določanje nukleotidnega zaporedja, računalniške zbirke podatkov, javnost podatkov - mednarodni konzorcij HGP versus Celera Genomics). Koncept 'bolezenskega gena' (cDNA, kromosomska lokalizacija - citogenetika in somatski celični hibridi, 'reverzna genetika' - polimorfni označevalci, vezano dedovanje, sprehod/skok po kromosomu, mutacijska analiza). Metode preiskave vloge gena (računalniško modeliranje, celične kulture in transgeneza, epifluorescenčna in konfokalna mikroskopija, monoklonska protitelesa, elektronska mikroskopija, transgene poskusne živali, tehnologija utišanja/izničenja genov ('knock-out'), povezava dobljenih podatkov s histologijo, fenotipom in biokemijo). Globalne genomske analize s pomočjo mikromrež (globalno genotipiziranje, re-sekvenciranje, mutacijska analiza, filogenetske študije). Osnovne statistične metode v genomiki (vezava genov, kartiranje, QTL).
  • Transkriptom (načini izražanja genov, mRNA in cDNA, transkriptom; prenos Northern in Western, subtrakcijska hibridizacija, kvantitativni RT-PCR, multipleks PCR, prikaz razlik v izražanju genov (angl. Differential Display); globalne analize izražanja RNA s pomočjo mikromrež - mikromreže oligonukleotidov, genomski in cDNA-čipi).
  • Proteom (proteomika, interakcije protein-protein in protein-DNA; kvasni dvo- in tri-hibridni sistem, dvo-dimenzionalna gelska elektroforeza; sočasna preiskava mutacij in polimorfizmov, sočasno in diferenčno izražanje genov; globalne proteinske analize s pomočjo mikromrež - razvoj mikromrež proteinov (proteinski 'čipi') oziroma mikromrež protiteles, proteomske podatkovne zbirke).
  • Funkcijska genomika - uporaba (odkrivanje genov, genska diagnostika, farmakogenomika, toksikogenomika; odkrivanje celične vloge proteinov in njihove so-odvisnosti; proteini in lastnosti organizmov; gensko zdravljenje, načrtovanje specifičnih / selektivnih zdravil; 'biočipi' in informatika). Funkcijska genomika in družba (varstvo podatkov, pravni in etični vidiki, patentiranje).

Študijski materiali:

Prosojnice iz predavanj:

Študijska literatura:

  1. BEN HUI LIU, 1998. Statistical genomics: Linkage, Mapping and QTL Analysis. CRC Press, Boca raton, New York, 611 s.
  2. BROWN, T.A., 1999. Genomes. BIOS Scientific Publishers Ltd, Oxford, 472 s.
  3. CANTOR, C.R., SMITH, C.L., 1999. Genomics: The Science and Technology behind the Human genome Project. John Wiley and Sons, New York, 596 s.
  4. COOPER, N.G. (Ed.), 1994. The Human genome Project - Dechipering the Blueprint of Heredity. University Science Books, Mill Walley (California).
  5. HUNT, S.P., LIVESEY, F.Y., 2000. Functiona Genomics - A Practical Approach. Oxford University Press, 288 s.
  6. INNIS, M.A., GELFAND, D., SNINSKY, J.J., 1999. PCR Applications - Protocols for Functional Genomics. Academic Press, 566 s.
  7. LOCKHART, D.J., WINZELER, E.A., 2000. Genomics, Gene Expression and DNA Arrays. Nature 405 (6788): 827-836.
  8. MACBEATH, G., SCHREIBER, S.L., 2000. Printing Proteins as Microarrays for High-Throughput Function Determination. Science 289: 1760-1763.
  9. MOSES, V., CAPE, R.E. (eds.) / SPRINGHAM, G.D. (ed., 2nd edition), 1999. Biotechnology - The Science and the Business. Harwood Academic Publishers, Amsterdam, 673 s.
  10. NATURE GENETICS, 1999 Supplement. Special issue: The Chipping Forecast - A collection of 10 reviews on different aspects of microarray analysis.
  11. STRACHAN, T., READ, A.P., 1999. Human Molecular Genetics, 2nd edition. BIOS Scientific Publishers Ltd, Oxford, 576 s.
  12. SUHAI, S., 2000. Genomics and Proteomics - Functional and Computational Aspects. Kluwer Academic Publishers, 258 s.
  13. WILKINS, M.R. (ed.) / WILLIAMS, K.L., HOCHSTRASSER, D.F., 1997. Proteome Research - New Frontiers in Functional Genomics. Springer-Verlag, New York, 243 s.

Obveznosti študenta:

Pisni izpit.

Področje habilitacije:

  • Radovan Komel (biokemija in molekularna biologija)
  • Damjana Rozman (biokemija in molekularna biologija)
  • Peter Dovč (molekularna genetika in animalna biotehnologija, splošna živinoreja)
  • Simon Horvat (molekularna biologija)

Reference nosilcev:

  1. Rossetti, S. / Strmecki, L. / Gamble, V. / Burton, S. / Sneddon, V. / Peral, B. / Roy, S. / Bakkaloglu, A./ Komel, R. / Winearls, C.G. / Harris, P.C., 2001. Mutation analysis of the entire PKD1 gene: genetic and diagnostic implications. Am. J. Hum.Genet. 68 (1): 46-63.
  2. Marc, J. / Preželj, J. / Komel, R. / Kocijančič, A., 1999. VDR genotype and response to etidronate therapy in late postmenopausal women. Osteoporos. Int. 10 (4): 303-306.
  3. Brank, M. / Zajc-Kreft, K. / Kreft, S. / Komel, R. / Grubič, Z., 1998. Biogenesis of acetylcholinesterase is impaired, although its mRNA level remains normal, in the glucocorticoid-treated rat skeletal muscle. Eur. J. Biochem. 251 (1-2): 374-381.
  4. Grubič, Z. / Komel, R. / Walker, W.F. / Miranda, A.F., 1995. Myoblast fusion and innervation with rat motor nerve alter distribution of acetylcholinesterase and its mRNA in cultures of human muscle. Neuron 14 (2): 317-327.
  5. Gasparini, P. / Pignatti, P.F. / Novelli, G. / Dallapiccola, B. / Nunes, V. / Casals, T. / Estivill, X. / Fernandez, E. / Ballasopoulou, A. / Loukopoulos, D. / Lavinha, J. / Simova, M.S. / Komel, R., 1990. Mutation analysis in cystic fibrosis. New Engl. J. Med. 323 (1): 62-63.
  6. Majdič, G. / Parvinen, M. / Bellamine, A. / Harwood, C. / Warren, C. / Waterman, M.R. /Rozman, D., 2000. Expression of lanosterol 14 -demethylase (CYP51), NADPH-cytochrome P450 reductase and squalene synthase proteins during spermatogenseis: step 19 elongating spermatids of the rat can synthesize oocyte-meiosis activating sterols. J. Endocrinol. 166: 463-474.
  7. Debeljak, N. / Horvat, S. / Lee, M. / Rozman, D., 2000. The mouse lanosterol 14 -demethylase (Cyp51) gene: characterization, mapping and evolutionary conservation. Arch. Biochem. Biophys. 379: 37-45.
  8. Rozman, D. / Fink, M. / Fimia G.-M. / Sassone-Corsi, P. / Waterman, M.R., 1999. Lanosterol 14 -demethylase (CYP51): a housekeeping cholesterogenic gene regulated by sterol/SREBP in somatic cells and by cAMP/CREM in spermatids. Mol. Endocrinol. 13: 1951-1962.
  9. Rozman, D. / Waterman, M.R., 1998. Lanosterol 14 -demethylase (CYP51) and spermatogenesis. Drug Metabol. Dispos. 126: 1199-1201.
  10. Rozman, D. / Strömstedt, M. / Tsui L.-C. / Scherer, S.W. / Waterman, M.R., 1996. Structure and mapping of the human lanosterol 14 -demethylase gene (CYP51) encoding the cytochrome P450 involved in cholesterol biosynthesis; comparison of exon/intron organization with other mammalian and fungal CYP genes. Genomics 38: 371-381.
  11. Folch J.M. / Dovč, P. / Medrano, J.F., 1999. Differential expression of bovine beta- lactoglobulin A and B promoter variants in transiently transfected HC11 cells. J. Dairy Res. 66 (4): 537-544.
  12. Kavar, T. / Habe, F. / Brem, G. / Dovč, P., 1999. Mitochondrial D-loop sequence variation among 16 maternal lines of the Lipizzan horse breed. Anim. Genet. 30: 423-430.
  13. Benčina, D. / Narat, M. / Dovč, P. / Drobnič-Valič, M. / Habe, F. / Kleven, S.L., 1999. The characterization of Mycoplasma synoviae EF-Tu protein and proteins involved in hemadherence and their N-terminal amino acid sequences. FEMS Microbiol. Lett. 173: 85-94.
  14. Lum, L.S. / Dovč, P. / Medrano, J.F., 1997. Polymorphism of bovine beta-lactoglobulin promoter and differences in the binding affinity of activator protein-2 transcription factor. J. Dairy Sci. 80: 1389-1397.
  15. Wittmann, W. / von Peschke, W. / Littmann, E. / Behringer, J. / Birkenmaier, St. / Dovč, P., 1993. Mast- und Schlachtleistungen von DL-Kastraten in Abhängigkeit vom MHS-Genotyp. Züchtungskunde 65 (3): 197-205.
  16. Horvat, S. / Medrano, J.F., 2001. Lack of Socs2 expression causes the high-growth phenotype in mice. Genomics - in press.
  17. Horvat, S. / Bünger, L. / Falconer, V.M. / Mackay, P. / Law, A. / Bulfield, G. / Keightley, P.D., 2000. Mapping of obesity QTLs in a cross between mouse lines divergently selected on fat content. Mamm. Genome 11: 2-7.
  18. Smith, J. / Paton, I.R. / Horvat, S. / Medrano, J.F. / Burt, D.W., 2000. Mapping of the RAIDD gene of chicken (Gallus gallus): identification of a region homologous to the mouse high-growth region. Mamm. Genome 11 (8): 706-709.
  19. Horvat, S. / Medrano, J.F., 1998. A 500-kb YAC and BAC conting encompassing the high- grow (hg) deletion in mouse chromosome 10 and identification of murine Raid/Cradd gene in the candidate region. Genomics 54: 159-164.
  20. Horvat, S. / Medrano, J.F. / Behboodi, E. / Anderson, G.B. / Murray, J.D., 1993. Sexing and detection of gene construct in microinjected bovine blastocysts using the polymerase chain reaction. Transgenic Res. 2: 134-140.
2006 - University of Ljubljana, Faculty of Medicine, Center for Functional Genomics and Bio-chips.