Elixir projects

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ELIXIR - Projects

list of projects running on ELIXIR node

Actual projects

Cobitis transcriptome

Introduction of next-generation sequencing technologies has opened a new era in population genetics, allowing for rapid and inexpensive collection of genome-wide sequence data even for non-model species. Here, we propose to use 454 sequencing to study history of speciation and patterns of hybridization in two non-model organisms: hybrid complex of spined loaches and two hybridizing species of nightingales. Both groups lay on opposite extremes of potential hybridization outcomes: while in nightingales the Mendelian hybrids mediate gene flow between the species, hybridization in spined loaches leads to asexuality. We will sequence cDNA from multiple somatic and germinal tissues from several individuals of each species. The obtained data will help us to understand several fundamental questions about speciation, including the role of sex chromosomes in reproductive isolation or the origin of sexual species from asexual hybrid lineages. Moreover, our data will enable us to identify candidate speciation genes, which can provide new insights into the genetic underpinnings of speciation.

Mastigamoeba balamuthi genome

Mitochondrion is a central organelle for formation of cellular FeS clusters. This function is mediated by iron-sulfur cluster (ISC) assembly machinery that was inherited from α-proteobacterial ancestor of mitochondria. Surprisingly, in Entamoeba histolytica and its free- living relative Mastigamoeba balamuthi, the ISC machinery was replaced by ε-proteobacterial NIF-like system. In M. balamuthi genome, we identified two paralogues of NifS (cysteine desulfurase) and NifU (scaffold protein). One paralogue of each protein was equipped with amino-terminal extension that targeted the protein to mitochondria (MbNifS-M, MbNifU-M), while the second paralogue was found in the cytosol (MbNifS-C, MbNifU-C). Accordingly, cysteine desulfurase activity was detected in both cytosol and organellar fractions of M. balamuthi. Dual localization of NIF system corresponded to the dual localization of FeS proteins (hydrogenase, pyruvate:ferredoxin oxidoreductase). Entamoeba possessed only single EhNifS and EhNifU that we identified in cytosol, but not in mitosomes, reduced forms of mitochondria. Our results suggest that M. balamuthi acquired the genes for NifS and NifU from the bacterial donor. Both genes were duplicated and destined to function in the cytosol and in mitochondria, where they replaced the original eukaryotic ISC machinery. The mitochondrial form of NIF machinery was most likely lost in Entamoeba.

Lamprey RNA-Seq

  • RNDr. Petr Bartůněk, Ph.D., Institute of Molecular Genetics, AS CR
  • Mgr. Jan Paces, Ph.D., Institute of Molecular Genetics, AS CR

Genomes of the eukaryotic superphylum Discoba

  • Mgr. Marek Eliáš Ph.D., University of Ostrava, Faculty of Science, Department of Biology and Ecology
  • Mgr. Vladimír Hampl Ph.D., Charles University in Prague
  • Mgr. Jan Paces, Ph.D., Institute of Molecular Genetics, AS CR

We propose a project to more systematically explore the genomes of different discoban groups and of a malawimonad with the aim to substantially improve the understanding of the evolution and biology of these organisms and to solve the question about their actual position in the phylogeny of eukaryotes as a whole. The proposal builds on some preliminary results that attest to the feasibility of the project and our competence to undertake such an endeavour.

ChIP-Seq on Pax6 and methylation

  • RNDr. Zbyněk Kozmik, Ph.D., Institute of Molecular Genetics, AS CR
  • Mgr. Jan Paces, Ph.D., Institute of Molecular Genetics, AS CR
  • Grant no: GAČR P305-11-2198

Genetics and development of mammal eye.

Abstract in czech: Zrak je pro člověka možná nejdůležitějším smyslem. Morfogeneze oka u savců je sice předmětem studia již dlouho, ale teprve v posledních dvou dekádách začala být objasnována úloha jednotlivých genů během embryonálního vývoje. Cílem projektu je kombinovat myší genetiku (kondicionální myší knockouty) s analýzou molekulárních mechanismů zodpovědných za embryonální vývoj oka.Projekt se zaměří především na úlohu genu Pax6 a kanonické signální dráhy Wnt. V projektu budeme : (1) testovat genetickou závislost vývoje oka a Pax6 genu na homeodoménových transkripčních faktorech rodiny Meis, (2) studovat genetickou interakci mezi genem Pax6 a kanonickou signální dráhou Wnt, (3) hledat geny regulované transkripčním faktorem Pax6. Detailní analýza molekulárních sítí a jejich genetických komponent umožní pochopit zákonitosti, kterými se řídí embryonální vývoj oka. Projekt tak přispěje k lepšímu porozumění vrozených vad u člověka a jejich kvalitnější diagnostice.

ChIP-Seq on TCF

  • Mgr. Ondřej Machoň, CSc., Institute of Molecular Genetics, AS CR
  • Mgr. Jan Paces, Ph.D., Institute of Molecular Genetics, AS CR
  • Grant no: GAČR 305/12/2042

Role of transcription factor Tcf in cell pluripotenzy and during neurogenesis.

Abstract (in czech): Indukovane pluripotentni buňky (iPS) jsou svymi vlastnostmi podobne zarode nym kmenovym buňkam, zejmena tim, že se neomezeně množi v kultuře a jsou schopny diferencovat do všech typů tělnich buněk. Jednou z popsanych strategii, ktere vedou k vyvolani buněčne pluripotence, je geneticke reprogramovani pomoci transkripčnich faktorů Oct4, Sox2, c-myc a Klf4. Tyto faktory jsou nezbytne v tomto procesu, ale přesny mechanismus noveho uspořadani kontroly genomu neni zdaleka pochopen. Faktory Tcf, jaderne přenašeče buněčne signalizace Wnt, se mohou v procesu vyvolane pluripotence učastnit noveho nastaveni genove kontroly. Pomoci aktivace genů jako je Oct4 budeme v nervovych kmenovych buňkach z kondicionalnich knock-out myši zkoumat ulohu faktorů Tcf3 a Tcf4 při vzniku buněk iPS. Vedle toho budeme pracovat na ziskani lidskych buněk iPS aktivaci genu Oct4 v primarnich buňkach očni sitnice, ktere jsou v mnohem podobne nervovym kmenovym buňkam. Tyto experimenty mohou přispět k nalezeni vhodneho a bezpečneho zdroje buněk k lečebnym učelům pomoci buněk iPS.

The use of metagenomics and metatranscriptomics to reveal soil microbial biodiversity in human affected areas

  • RNDr. Miloslav Devetter, Ph.D., Institute of soil Biology, Biology centre, AS CR
  • Mgr. Jan Paces, Ph.D., Institute of Molecular Genetics, AS CR
  • Grant no: MSMT, VSMSMTPMS12, METAGEN-13

Abstract: We aim to assess soil microbial diversity across various ecosystems impacted by human activities (intensive agricultural practice associated with animal excrement amendments and drainage, de-glaciation and cryoturbation associated with global warming) using 454 pyrosequencing. Both amplicon and shot-gun sequencing as well as bioinformatics tools and data analysis workflows will be developed in cooperation with international partners. Our main goals will be to i) develop RNA extraction method for soils and subsoils as well as for manure-amended soils and perform metatrascriptomic study of the active microbial communities in situ or in soil microcosms and ii) develop tools for sequencing and annotation of plasmids recovered from soil. Effort will be put into encouraging scientists and students to use metagenomic and metatranscriptomic approaches in our laboratories and developing sustainable international cooperation in this field.

Old projects

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