Research topics
Genomics, evolutionary biology, expression profiling in oncology
Genomics and bioinformatics belong to the most vigorously developing disciplines of contemporary life sciences. The Laboratory 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 bovine herpesvirus genome project, 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 Laboratory became involved in characterization of several developmental genes and in studies on transcriptional profiles of expression of several mouse genes. 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 we begin to characterize genes expressed in the rhopalium, a special multifunctional organ of the cubozoan jellyfish Tripedalia cystophora. The genome project of Rhodobacter capsulatus has been completed. Several genes with possible biotechnology applications are now being characterized. Since 2008, the group is equipped with the 454 next-generation sequencing technology.
Current grant support
Ministry of Education, Youth and Sports of the Czech Republic (Center for Applied Genomics, grant No.: 1M6837805002)
Ministry of Education, Youth and Sports of the Czech Republic (NPV II, grant ONKOGEN)
Ministry of Education, Youth and Sports of the Czech Republic (NPV II, grant METAGENOM)
Grant Agency of the Czech Republic (P305/10/J052)
Grant Agency of the Czech Republic (P506/11/1320)
Grant Agency of the Czech Republic (P506/11/1317)
Grant Agency of the Czech Republic (P305/11/1061)
Most important recent papers
(2008-present; names of the lab members underlined)Hoyerova K, Perry L, Hand P, Lankova M, Kocabek T, May S, Kottova J, Paces J, Napier R, Zazimalova E. Functional characterization of PaLAX1, a putative auxin permease, in heterologous plant systems. Plant Physiol 146(3): 1128-41, 2008. (Pubmed) (DOI)
Kozmik Z, Swamynathan SK, Ruzickova J, Jonasova K, Paces V, Vlcek C, Piatigorsky J. Cubozoan crystallins: evidence for convergent evolution of pax regulatory sequences. Evol Dev 10(1): 52-61, 2008. (Pubmed) (DOI)
Trachtulec Z, Vlcek C, Mihola O, Gregorova S, Fotopulosova V, Forejt J. Fine haplotype structure of a chromosome 17 region in the laboratory and wild mouse. Genetics 178(3): 1777-84, 2008. (Pubmed) (DOI)
Jencova V, Strnad H, Chodora Z, Ulbrich P, Vlcek C, Hickey WJ, Paces V. Nucleotide sequence, organization and characterization of the (halo)aromatic acid catabolic plasmid pA81 from Achromobacter xylosoxidans A8. Res Microbiol 159(2): 118-27, 2008. (Pubmed) (DOI)
Kozmik Z, Ruzickova J, Jonasova K, Matsumoto Y, Vopalensky P, Kozmikova I, Strnad H, Kawamura S, Piatigorsky J, Paces V, Vlcek C. Assembly of the cnidarian camera-type eye from vertebrate-like components. Proc Natl Acad Sci U S A 105(26): 8989-93, 2008. (Pubmed) (DOI)
Kolar M, Lassig M, Berg J. From protein interactions to functional annotation: graph alignment in Herpes. BMC Syst Biol 2: 90, 2008. (Pubmed) (DOI)
Mihola O, Trachtulec Z, Vlcek C, Schimenti JC, Forejt J. A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323(5912): 373-5, 2009. (Pubmed) (DOI)
Uhlik O, Jecna K, Mackova M, Vlcek C, Hroudova M, Demnerova K, Paces V, Macek T. Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing. Appl Environ Microbiol 75(20): 6471-7, 2009. (Pubmed) (DOI)
Strnad H, Lacina L, Kolar M, Cada Z, Vlcek C, Dvorankova B, Betka J, Plzak J, Chovanec M, Sachova J, Valach J, Urbanova M, Smetana K Jr. Head and neck squamous cancer stromal fibroblasts produce growth factors influencing phenotype of normal human keratinocytes. Histochem Cell Biol 133(2): 201-11, 2010. (Pubmed) (DOI)
Strnad H, Lapidus A, Paces J, Ulbrich P, Vlcek C, Paces V, Haselkorn R. Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol 192(13): 3545-6, 2010. (Pubmed) (DOI)
Mercer RG, Callister SJ, Lipton MS, Pasa-Tolic L, Strnad H, Paces V, Beatty JT, Lang AS. Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus. J Bacteriol 192(11): 2701-10, 2010. (Pubmed) (DOI)
Zaveska Drabkova L, Vlcek C. Molecular phylogeny of the genus Luzula DC. (Juncaceae, Monocotyledones) based on plastome and nuclear ribosomal regions: a case of incongruence, incomplete lineage sorting and hybridisation. Mol Phylogenet Evol 57(2): 536-51, 2010. (Pubmed) (DOI)
Strnad H, Ridl J, Paces J, Kolar M, Vlcek C, Paces V. Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8. J Bacteriol 193(3): 791-2, 2011. (Pubmed) (DOI)
Vlcek C, Marande W, Teijeiro S, Lukes J, Burger G. Systematically fragmented genes in a multipartite mitochondrial genome. Nucleic Acids Res 39(3): 979-88, 2011. (Pubmed) (DOI)
Melenovsky V, Benes J, Skaroupkova P, Sedmera D, Strnad H, Kolar M, Vlcek C, Petrak J, Benes J Jr, Papousek F, Oliyarnyk O, Kazdova L, Cervenka L. Metabolic characterization of volume overload heart failure due to aorto-caval fistula in rats. Mol Cell Biochem 354(1-2): 83-96, 2011. (Pubmed) (DOI)
Szabo P, Kolar M, Dvorankova B, Lacina L, Stork J, Vlcek C, Strnad H, Tvrdek M, Smetana K Jr. Mouse 3T3 fibroblasts under the influence of fibroblasts isolated from stroma of human basal cell carcinoma acquire properties of multipotent stem cells. Biol Cell 103(5): 233-48, 2011. (Pubmed) (DOI)
Kozmikova I, Smolikova J, Vlcek C, Kozmik Z. Conservation and diversification of an ancestral chordate gene regulatory network for dorsoventral patterning. PLoS One 6(2): e14650, 2011. (Pubmed) (DOI)
Future plans
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.
Since 2006, the "Oncogene" is a project directed towards identification of specific markers in cancer tissue with potential applications in medical diagnosis. We are going to use Affymetrix and Illumina microarray chip analyses for detection of appropriate gene sets.
To understand the evolution of eukaryote genomes and the developmental processes that they regulate, new genome drafts will be produced using 454 pyrosequencing. Namely they are two protozoan genomes, Mastigamoeba balamuthi and Diplonema palillatum.
The new aim of the group is to apply methods of metagenomics for estimation of the genetical potencial of microorganism present in contaminated underground water and soil samples, with special respect to degradative pathways, performebioinformatic analysis, prepare and test conditions and new microbial consorcia well suited for bioremediation purposes.