Genomics and BioInformatics
Members
Čestmír Vlček
Václav Pačes
Jan Pačes
Lenka Drábková
Hynek Strnad
Michal Kolář
Miluše Hroudová
Zdeněk Krejčík
Jana Šáchová
Markéta Urbanová
Jakub Rídl
Petr Vojta
Daniel Panchártek
Šárka Pinkasová
Petr Savický
Research program
Genomics and bioinformatics belong to the most vigorously developing disciplines of contemporary life sciences. The Department of Genomics and Bioinformatics was amongst the first laboratories to complete a genome project. It was in the mid eighties when the complete nucleotide sequence of the bacteriophage PZA DNA was determined. Since then the laboratory has been developing new approaches and strategies to the large-scale DNA sequencing and was involved in several international genome projects such as the Pseudorabies virus and bovine herpesvirus genome projects, Saccharomyces cerevisiae genome project and Rhodobacter capsulatus genome project. Information generated in these projects was used in evolutionary studies and recently also in biotechnological applications. In collaboration with other groups of the Institute individual members of the Department became involved in characterization of several developmental genes and in studies on transcriptional profiles of expression of several mouse genes. With the advances in the human genome project and mouse genome project we now analyze these genomes especially as it concerns foreign elements present in these and other (e.g. bacterial) genomes.
The tools of bioinformatics were developed in order to analyze nucleotide sequences generated in these projects as well as those available in the international databases.
In collaboration with the laboratory of Zbyněk Kozmík two developmental genes of different chordate organisms were characterized. We found mammalian orthologues of osa, a gene of Drosophila melanogaster that encodes a nuclear protein. The mouse orhologue Osa1 is expressed during development. The cDNA nucleotide sequences derived from mouse and human genes revealed three developmentally conserved domains.
The structure has been described for the amphioxus AmphiVent gene, a homologue of vertebrate Vent genes. We found that AmphiVent encodes a protein distinguished by an unusual homeodomain in which the forty-seventh amino acid is a threonine instead of the canonical isoleucine. Only the mammalian Vent and ladybird-like proteins are similar enough in the flanking regions of the homeodomain. This suggests that in spite of the evolutionary distance these genes are close relatives with analogous functions. The phylogenetic tree confirmed this suggestion.
The international genome project of Rhodobacter capsulatus has been completed. Several genes with possible biotechnology applications are now being characterized.
A special attention was given to human genome analysis, namely to the isochore structures of individual human chromosomes. In addition, distribution of Alu and LINE repetitive sequences was characterized. HERVd, the database of human endogenous retroviruses was assembled. This database is now available at http://herv.img.cas.cz/ It is being used for detailed characterization of HERVs, their integration, stability, and distribution.
In collaboration with botanists phylogenetic analyses based on chloroplast, rRNA, and nuclear DNA sequences were performed for several plant types.
TopFuture plans
The Oncogene is a project directed towards identification of specific markers in cancer tissue with potential applications in medical diagnosis. We use Affymetrix microarray chip analysis for detection of appropriate gene sets.
The Center for Applied Genomics was established in 2005 with a five-year grant from the Ministry of Education, Youth and Sports. The aim of the project is to establish in the Czech Republic a base for the complex study of genomes, and thereby create conditions for utilizing genomics in basic as well as applied biomedical research, in pharmaceutical applications and in biotechnology. To achieve this several leading laboratories have combined their efforts and experience with a variety of relevant methods. The project "Center for Applied Genomics" has its own web-page.
To understand the evolution of higher metazoan genomes and the developmental processes that they regulate, it is necessary to make comparisons with an appropriate outgroup. The Cnidaria, a group of lower Metazoa, are the natural outgroup for comparative genomics and developmental studies. An extra germ layer and a second axis of body symmetry are the features that distinguish higher Metazoa from lower animals such as cnidarians. The availability of the model animal genomic sequences will allow inferences to be made about the gene complement of the common bilaterian ancestor. Cnidarian genomes are potentially a key to understanding many aspects of animal evolution. We plan to trial our genomic potential and begin characterize genomes and genes of at least two different cnidarian species, Cracpedacusta sowerbyi and Tripedalia cystophora.
TopPublications
- 2007
- Drábková L, Vlček Č. The phylogenetic position of Oxychloë (Juncaceae): evidence from one nuclear, three plastid regions and morphology Taxon 56 (1): 95-102
- Fujimura N, Vacík T, Machoň O, Vlček Č, Scalabrin S, Speth M, Diep D, Krauss S, Kozmik Z. Wnt-mediated down-regulation of Sp1 target genes by a transcriptional repressor Sp5 Journal of Biological Chemistry 282 (2): 1225-1237 Jan 12 2007
- 2006
- Pavlicek A, Gentles AJ, Paces J, et al. Retroposition of processed pseudogenes: the impact of RNA stability and translational control Trends in Genetics 22 (2): 69-73 Feb 2006
- Bukovska G, Klucar L, Vlcek C, et al. Complete nucleotide sequence and genome analysis of bacteriophage BFK20 - A lytic phage of the industrial producer Brevibacterium flavum Virology 348 (1): 57-71 Apr 25 2006
- Drabkova L, Kirschner J, Vlcek C Phylogenetic relationships within Luzula DC. and Juncus L. (Juncaceae): A comparison of phylogenetic signals of trnL-trnF intergenic spacer, trnL intron and rbcL plastome sequence data Cladistics 22 (2): 132-143 Apr 2006
- 2005
- Flachs P, Horakova O, Brauner P, et al. Polyunsaturated fatty acids of marine origin upregulate mitochondrial biogenesis and induce beta-oxidation in white fat Diabetologia 48 (11): 2365-2375 Nov 2005
- Urbanek P, Paces J, Paces V An approach towards experimental cDNA sequence determination of predicted genes: An example from Arabidopsis U3-55k homologues Gene 358: 67-72 Sep 26 2005
- Belshaw R, Katzourakis A, Paces J, et al. High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection Molecular Biology and Evolution 22 (4): 814-817 Apr 2005
- Divina P, Vlcek C, Strnad P, et al. Global transcriptome analysis of the C57BL/6J mouse testis by SAGE: evidence for nonrandom gene order BMC Genomics 6: Art. No. 29 Mar 5 2005
- Trachtulec Z, Mihola O, Vlcek C, et al. Positional cloning of the Hybrid sterility 1 gene: fine genetic mapping and evaluation of two candidate genes Biological Journal of the Linnean Society 84 (3): 637-641 Mar 2005
- 2004
- Pačes J., Pavlíček A., Zíka R., Kapitonov V. V., Jurka J., Pačes V. : HERVd: the Human Endogenous Retrovirus Database: update. Nucleic Acids Res. 32: 50, 2004.
- Zíka R., Pačes J., Pavlíček A., Pačes V.: WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences. Nucleic Acids Res. 32: W48-W49 Suppl. 2, 2004.
- Pačes J., Zíka R., Pačes V., Pavlíček A., Clay O., Bernardi G.: Representing GC variation along eukaryotic chromosomes. Gene 333: 135-141, 2004.
- Belshaw R., Pereira V., Katzourakis A., Talbot G., Pačes J., Burt A., Tristem M.: Long-term reinfection of the human genome by endogenous retroviruses. Proc. Natl. Acads. Sci. 101: 4894-4899, 2004.
- Jenčová V., Strnad H., Chodora Z., Ulbrich P., Hickey W. J., Pačes V.: Chlorocatechol catabolic enzymes from Achromobacter xylosoxidans A8. International biodeterioration & biodegradation 54: 175-181, 2004.
- Drábková L., Kirschner J., Vlček Č., Pačes V.: TrnL-trnF intergenic spacer and trnL intron define clades within Luzula and Juncus (Juncaceae): Importance of structural mutations . J. Mol. Evolution 59: 1-10, 2004.
- Trachtulec Z., Vlček Č., Mihola O., Forejt J.: Comparative analysis of the PDCD2-TBP-PSMB1 region in vertebrates. Gene 335: 151-157, 2004.
- 2003
- Drábková L., Kirschner J., Seberg O., Petersen G., Vlček Č.: Phylogeny of the Juncaceae based on rbcL sequences, with special emphasis on Luzula DC. and Juncus L. Plant Systematics and Evolution 240, 133-147, 2003.
- Brdičková N., Brdička T., Angelisová P., Horvath O., Spička J., Hilgert I., Pačes J., Simeoni L., Kliche S., Merten C., Schraven B., Hořejší V.: Lime: A new membrane raft-associated adaptor protein involved in CD4 and CD8 coreceptor signaling. J. Exp. Med. 198: 1453-62, 2003.
- Ryšlavá E., Krejčík Z., Macek T., Nováková H., Demnerová K., Macková M.: Study of PCB degradation in real contaminated soil. Fresenius Enviromental Bulletin 12: 296-301, 2003.
- Drábková L., Kirschner J., Vlček Č., Seberg O., Petersen G.: A phylogeny of Luzula and Juncus (Juncaceae) based on rbcL, trnL intron, and trnL-trnF plastid DNA sequences. Cladistics 19, 151-151, 2003.
- 2002
- Pavlíček, A., Pačes J., Clay, O., Bernardi, G.: A compact view of isochores in the draft human genome sequence. FEBS Letters 511: 165-169, 2002.
- Pavlíček, A., Pačes J., Elleder, D., Hejnar, J.: Processed pseudogenes of human endogenous retroviruses generated by LINEs: their integration, stability, and distribution. Genome Res. 12: 391-399, 2002.
- Pavlíček, A., Clay, O., Jabbari, K., Pačes J., Bernardi, G.: Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17. FEBS Letters 511: 175-177, 2002.
- Ulbrich P., Strnad H., Hejkalová V., Pačes J.and Pačes V.: Genetic determination of polyhydroxyalkanoate metabolism in Rhodobacter capsulatus SB1003. Folia Biol. 48: 157-159,2002.
- Pačes J., Pavlíček, A., Pačes V.: HERVd: database of human endogenous retroviruses. Nucleic Acids Res. 30: 205-206, 2002.
- Pačes J., Pačes V.: DicodonUse: The programme for dicodon bias visualization in prokaryotes. Folia Biol. 48: 246-249, 2002.
- Pavlíček A.,Pačes J., Zíka R. , Hejnar J: Length distribution of long interspersed nuclear elements (LINEs) and processed pseudogenes of human endogenous retroviruses: implications for retrotransposition and pseudogene detection. Gene 300: 189-194, 2002.
- Urbánek P., Pačes J., Králová J., Dvořák M., Pačes V. Cloning and expression of PARP-3 (Adprt3) and U3-55k, two genes closely linked on mouse chromosome 9. Folia Biol. 48: 182-191, 2002.
- Elleder D., Pavlíček A., Pačes J., Hejnar J.: Preferential integration of human immunodeficiency virus type 1 into genes, cytogenetic R bands and GC-rich DNA regions: insight from the human genome sequence. FEBS Letters 517: 285-286, 2002.
- Pavlíček A., Pačes J., Elleder D., Hejnar J.: Processed Pseudogenes of human endogenous retroviruses generated by LINEs: Their integration, stability, and distribution. Genome Res. 12: 391-399, 2002.
- Pavlíček A., Pačes J., Clay O., Bernardi G.: A compact view of isochores in the draft human genome sequence. FEBS Letters 511: 165-169, 2002.
- Drábková L., Kirschner J., Vlček Č.: Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. Plant Mol. Biol. Rep. 20: 161-175, 2002.