Diversity, Ecology and Evolution of Microbes group
Ecology, systematics and evolution Unit
Work & Related Experience:
- 2020 – Present: Post-Doctoral Researcher, Ecology, systematics and evolution Unit, Université Paris-Saclay.
- 2020: Initiated and co-organized the Online Poster Session on Protists (link).
- 2021: Teaching – “Genomics of Microbial Eukaryotes a.k.a. Protists”, Course on Genomics of Microorganisms, Moscow Institute of Physics and Technology, 18/5/2021, Online.
- 2013 – 2020: Researcher, Faculty of Science, Charles University in Prague.
Education & Related Experience:
- 2013 – 2020: PhD study of Parasitology, Faculty of Science, Charles University in Prague. Thesis: Genomics of Preaxostyla flagellates (link)
- 2019: Whole Transcriptome Data Analysis Course, EMBL Heidelberg.
- 2019: Workshop on single DNA molecule sequencing, Vestec.
- 2018 – 2020: Supervision of a BSc student on the cell biology of Paratrimastix pyriformis.
- 2017 – 2018, 2018 – 2019: Teaching – Molecular phylogenetics and systematics, practical course.
- 2017: Invited seminar talk “Genomics and cell biology of Paratrimastix pyriformis“, University of Warsaw.
- 2017: Co-supervision of a visiting MSc student on the cell biology of Preaxostyla.
- 2017: Workshop on Genomics, Český Krumlov.
- 2016: Opponent for a BSc thesis “Biogenesis and function of peroxisomes, particularly in parasitic protists”.
- 2014: Research stay at the Dalhousie University in Halifax, NS, Canada.
- 2011 – 2013: MSc study of Parasitology, Faculty of Science, Charles University in Prague. Thesis: Mitochondrion of Trimastix pyriformis (link).
- 2013: Course of Methods of Functional Genomics, České Budějovice.
- 2008 – 2011: BSc study of Biology, Faculty of Science, Charles University in Prague. Thesis: Lateral gene transfer and its utilization in the phylogeny of eukaryotes (link).
Funding & Awards:
- 2019: Živa Magazine Award for the best popular science article by authors 26 – 30 years old (Losers Finders: Life without Semiautonomous Organelles), Živa, Czech Academy of Sciences.
- 2017: Bedřich Hrozný Award for creative work (A Eukaryote without a Mitochondrial Organelle), Charles University.
- 2016: Josef Lux Award for ethically significant media act (Scientists against fear and indifference), The Josef Lux Foundation.
- 2014, 2015: Holz-Conner Travel Award, International Society of Protistologists.
- 2013 – 2017: STARS – Supporting Talented PhD Research Students, Charles University.
- Since 2018: International Society for Evolutionary Protistology.
- 2020 – Present: Media director (elected).
- 2018 – 2020: Newsletter editor (elected).
- Since 2014: International Society of Protistologists.
- 2016 – Present: Community manager.
- 2016 – 2017: Nominating committee (elected).
- Since 2011: Czech Parasitological Society.
- ESE New Arrivals Day, Orsay, France (Online), 5/5/2021.
Talk: Genomics of Proteorhodophytina Red Algae.
- Online Poster Session on Protists, 10-14/8/2020.
- VIII European Congress of Protistology, Rome, Italy, 28/7–2/8/2019.
Talk: Path towards amitochondriality: Comparative genomics of Preaxostyla.
- 49th Jírovec’s Protozoological Days, Kostelec nad Černými lesy, Czech Republic, 22–26/4/2019.
Talk: Comparative genomics of Preaxostyla flagellates: insights into the evolution of amitochondriality.
- 5th joint meeting of the Phycological Society of America & International Society of Protistologists, Vancouver, BC, Canada, 29/7–2/8/2018.
Talk: How to lose a mitochondrion: Comparative genomics of Preaxostyla.
- Weekend with Science 2018, Břežany, Czech Republic, 14–17/6/2018.
Talk: Path towards amitochondriality: Introduction to our projects on Preaxostyla.
- XXII meeting of the International Society for Evolutionary Protistology, Droushia, Cyprus, 18–27/5/2018.
Talk: A comparative genomic study on metabolism and cell biology of Preaxostyla flagellates.
- 48th Jírovec’s Protozoological Days, Kunčice pod Ondřejníkem, Czech Republic, 30/4–4/5/2018.
Talk: Metabolism and Cell Biology of Preaxostyla Flagellates: A Comparative Genomic Study.
- 15th International Congress of Protistology, Prague, 30/7–4/8/2017.
Talk: Genomics and cell biology of the free living preaxostylan flagellate Paratrimastix pyriformis.
Co-organizer of social events.
- 46th Jírovec’s Protozoological Days, Bítov, Czech Republic, 2–6/5/2016.
Talk: Preaxostyla: the evolution of anaerobic protists.
- VII European Congress of Protistology (ECOP-ISOP), Seville, Spain, 5-10/9 2015
Talk: Evolutionary History of the Arginine Deiminase Pathway among Eukaryotes.
- 45th Jírovec’s Protozoological Days, Dubovice, Czech Republic, 11–15/05, 2015.
Talk: Evolutionary History of the Arginine Deiminase Pathway among Eukaryotes
- Protist 2014, Banff, Alberta, Canada, 3–8/08, 2014
Talk: Mitochondrial organelle of Trimastix pyriformis.
- 44th Jírovec’s Protozoological Days, Krásná, Czech Republic, 12–16/05, 2014.
Talk: Hydrogenosome-Like Organelle of Trimastix pyriformis.
- 43rd Jírovec’s Protozoological Days, Nový Dvůr, Czech Republic, 6–10/05, 2013.
Talk: Mitochondrion-like Organelle of Trimastix pyriformis.
- 42nd Jírovec’s Protozoological Days, Kletečná, Czech Republic, 7-11/05, 2012.
Talk: SUF system for synthesis of Fe-S clusters in Monocercomonoides and Trimastix.
- VI European Congress of Protistology (ECOP), Berlin, Germany, 25-29/7, 2011.
- 41st Jírovec’s Protozoological Days, Benecko v Krkonoších, Czech Republic, 2011.
- Karnkowska A et al.: The oxymonad genome displays canonical eukaryotic complexity in the absence of a mitochondrion. Molecular Biology and Evolution 2019, msz147.
- Vacek V, Novák LVF, Treitli SC, Táborský P, Čepička I, Kolísko M, Keeling PJ, Hampl V: Fe-S Cluster Assembly in Oxymonads and Related Protists. Molecular Biology and Evolution 2018, msy168.
- Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AGB, Keeling PJ, Roger AJ, Čepička I, Hampl V: Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol Biol 2016, 16:197.
- Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V: A Eukaryote without a Mitochondrial Organelle. Curr Biol 2016, 26:1274–1284.
- Zubáčová Z, Novák L, Bublíková J, Vacek V, Fousek J, Rídl J, Tachezy J, Doležal P, Vlček Č, Hampl V: The Mitochondrion-Like Organelle of Trimastix pyriformis Contains the Complete Glycine Cleavage System. PLoS One 2013, 8:e55417.
- 2015 – 2018: Initiated and co-organized a civic campaign “Scientists against fear and indifference” aimed at countering xenophobia and supporting evidence-based policy in immigration and integration of foreigners in the Czech Republic. Read more here.
- Since 2011: Published popular science articles covering parasitology, protistology, and microbiology. Mostly in Czech. Full list here.
- 2007 – 2017: Observatory guide at Prague’s Štefánik Observatory. Amateur and semi-professional astronomical work, public science outreach activities in astronomy and related fields. Observatory page.
- 2017: lecture “The first three billions: chapters from the evolution of microorganisms”.