Microbial Communities in Biomedical and Environmental Areas, and Systems Biology

Deliverables

Report from Conference on Integrative Metagenomics

Report from Conference on IntegrativeMetagenomics

Organized summer school at BIOCEV
Report from Conference on Microbial Communities: Function, Structure and Complexity

Report from Conference on MicrobialCommunities Function Structure and Complexity

Report on organized courses Computational Genomics
Organized Advanced course in metagenomics and OMICs data integration
Dissemination and Communication strategy document prepared

Dissemination and Communication strategy document prepared

Report on organized courses Methods of Functional Genomics

Report on organized courses Methods of FunctionalGenomics

MiCoBion webpage developed

Publications

Adaptive iron utilization compensates for the lack of an inducible uptake system in Naegleria fowleri and represents a potential target for therapeutic intervention

Author(s): Arbon, D; Zeniskova, K; Mach, J; Grechnikova, M; Malych, R; Talacko, P; Sutak, R
Published in: PLOS NEGLECTED TROPICAL DISEASES, 2020, ISSN 1935-2735
Publisher: Public Library of Science
DOI: 10.1371/journal.pntd.0007759

Cytidine nucleoside analog is an effective antiviral drug against Trichomonasvirus

Author(s): Narayanasamy, RK; Rada, P; Zdrha, A; van Ranst, M; Neyts, J; Tachezy, J
Published in: JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION, 2022, ISSN 1684-1182
Publisher: Elsevier Taiwan
DOI: 10.1016/j.jmii.2021.08.008

Copper Metabolism in Naegleria gruberi and Its Deadly Relative Naegleria fowleri

Author(s): Kateřina Ženíšková; Maria Grechnikova; Robert Sutak
Published in: FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, Issue 9, 2022, ISSN 2296-634X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fcell.2022.853463

Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes

Author(s): Kozyra, K; Zajac, TM; Ansorge, H; Wierzbicki, H; Moska, M; Stanko, M; Stopka, P
Published in: GENES, 2021, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes12050642

Proteomic Analysis of Trichomonas vaginalis Phagolysosome, Lysosomal Targeting, and Unconventional Secretion of Cysteine Peptidases

Author(s): Zimmann, N; Rada, P; Zarsky, V; Smutna, T; Zahonova, K; Dacks, J; Harant, K; Hrdy, I; Tachezy, J
Published in: MOLECULAR & CELLULAR PROTEOMICS, 2022, ISSN 1535-9484
Publisher: American Society for Biochemistry and Molecular Biology
DOI: 10.1016/j.mcpro.2021.100174

Copper detoxification machinery of the brain-eating amoeba Naegleria fowleri involves copper-translocating ATPase and the antioxidant system

Author(s): Grechnikova, M; Zeniskova, K; Malych, R; Mach, J; Sutak, R
Published in: INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE, 2020, ISSN 2211-3207
Publisher: Elsevier BV
DOI: 10.1016/j.ijpddr.2020.10.001

The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista

Author(s): Pyrih, J; Zarsky, V; Fellows, JD; Grosche, C; Wloga, D; Striepen, B; Maier, UG; Tachezy, J
Published in: BMC ECOLOGY AND EVOLUTION, 2021, ISSN 2730-7182
Publisher: BioMed Central
DOI: 10.1186/s12862-021-01777-x

Perspectives: SARS-CoV-2 Spike Convergent Evolution as a Guide to Explore Adaptive Advantage

Author(s): Zahradnik, J; Nunvar, J; Schreiber, G
Published in: FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2022, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2022.748948

The Virome of Healthy Honey Bee Colonies: Ubiquitous Occurrence of Known and New Viruses in Bee Populations

Author(s): Kadleckova, D; Tachezy, R; Erban, T; Deboutte, W; Nunvar, J; Salakova, M; Matthijnssens, J
Published in: MSYSTEMS, 2022, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00072-22

Iron in parasitic protists - from uptake to storage and where we can interfere.

Author(s): Jan Mach; Robert Sutak
Published in: METALLOMICS, Issue 8, 2020, ISSN 1756-5901
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0mt00125b

Biological Roles of Lipocalins in Chemical Communication, Reproduction, and Regulation of Microbiota

Author(s): Stopkova, R; Otcenaskova, T; Matejkova, T; Kuntova, B; Stopka, P
Published in: FRONTIERS IN PHYSIOLOGY, 2021, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2021.740006

Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds.

Author(s): Eleni Voukali; Nithya Kuttiyarthu Veetil; Pavel Němec; Pavel Stopka; Michal Vinkler
Published in: Scientific Reports, Vol 11, Iss 1, Pp 1-16 (2021), Issue 6, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.21203/rs.3.rs-138227/v1

Flow cytometry-based study of model marine microalgal consortia revealed an ecological advantage of siderophore utilization by the dinoflagellate Amphidinium carterae

Author(s): Malych, R; Stopka, P; Mach, J; Kotabova, E; Prasil, O; Sutak, R
Published in: COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2022, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2021.12.023

Orthohantaviruses in Reservoir and Atypical Hosts in the Czech Republic: Spillover Infection and Indication of Virus-Specific Tissue Tropism

Author(s): Václav Hönig; Jan Kamiš; Aneta Maršíková; Tereza Matějková; Pavel Stopka; Anna Mácová; Daniel Růžek; Jana Kvičerová
Published in: MICROBIOLOGY SPECTRUM, Issue 8, 2022, ISSN 2165-0497
Publisher: American Society for Microbiology
DOI: 10.1128/spectrum.01306-22

Do all mice smell the same? Chemosensory cues from inbred and wild mouse strains elicit stereotypic sensory representations in the accessory olfactory bulb.

Author(s): Rohini Bansal; Maximilian Nagel; Romana Stopková; Yizhak Sofer; Tali Kimchi; Pavel Stopka; Marc Spehr; Yoram Ben-Shaul
Published in: BMC biology 19(1), 133 (2021). doi:10.1186/s12915-021-01064-7, Issue 3, 2021, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.18154/rwth-2021-07103

The Mastigamoeba balamuthi genome and the nature of the free-living ancestor of Entamoeba

Author(s): Žárský V., Klimeš V., Pačes J., Vlček Č, Hradilová M., Beneš V., Nývltová E., Hrdý I., Pyrih J, Mach J., Barlow L., Stairs C.W., Eme L., Hall N., Eliáš M., Dacks BJ, Roger A., Tachezy J.
Published in: Mol Biol Evol. 2021 Jun; 38(6): 2240–2259, 2021, ISSN 1537-1719
Publisher: Oxford University Press, Society for Molecular Biology and Evolution
DOI: 10.1093/molbev/msab020

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study

Author(s): Matejkova, T; Hajkova, P; Stopkova, R; Stanko, M; Martin, JF; Kreisinger, J; Stopka, P
Published in: SCIENTIFIC REPORTS, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-70249-x

The response of Naegleria gruberi to oxidative stress

Author(s): Malych, Ronald; Fussy, Zoltan; Zeniskova, Katerina; Arbon, Dominik; Hampl, Vladimir; Hrdy, Ivan; Sutak, Robert
Published in: METALLOMICS, 2022, ISSN 1756-5901
Publisher: Royal Society of Chemistry
DOI: 10.1093/mtomcs/mfac009

Phenotypic and Clonal Stability of Antigen-Inexperienced Memory-like T Cells across the Genetic Background, Hygienic Status, and Aging

Author(s): Moudra, A; Niederlova, V; Novotny, J; Schmiedova, L; Kubovciak, J; Matejkova, T; Drobek, A; Pribikova, M; Stopkova, R; Cizkova, D; Neuwirth, A; Michalik, J; Krizova, K; Hudcovic, T; Kolar, M; Kozakova, H; Kreisinger, J; Stopka, P; Stepanek, O
Published in: JOURNAL OF IMMUNOLOGY, 2021, ISSN 0022-1767
Publisher: American Association of Immunologists
DOI: 10.4049/jimmunol.2001028

Giardia intestinalis mitosomes undergo synchronized fission but not fusion and are constitutively associated with the endoplasmic reticulum

Author(s): Luboš Voleman, Vladimíra Najdrová, Ásgeir Ástvaldsson, Pavla Tůmová, Elin Einarsson, Zdeněk Švindrych, Guy M. Hagen, Jan Tachezy, Staffan G. Svärd, Pavel Doležal
Published in: BMC Biology, Issue 15/1, 2017, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-017-0361-y

High-Throughput Analysis of Human Cytomegalovirus Genome Diversity Highlights the Widespread Occurrence of Gene-Disrupting Mutations and Pervasive Recombination

Author(s): Steven Sijmons, Kim Thys, Mirabeau Mbong Ngwese, Ellen Van Damme, Jan Dvorak, Marnix Van Loock, Guangdi Li, Ruth Tachezy, Laurent Busson, Jeroen Aerssens, Marc Van Ranst, Piet Maes
Published in: Journal of Virology, Issue 89/15, 2015, Page(s) 7673-7695, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.00578-15

A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake

Author(s): Joe Morrissey, Robert Sutak, Javier Paz-Yepes, Atsuko Tanaka, Ahmed Moustafa, Alaguraj Veluchamy, Yann Thomas, Hugo Botebol, François-Yves Bouget, Jeffrey B. McQuaid, Leila Tirichine, Andrew E. Allen, Emmanuel Lesuisse, Chris Bowler
Published in: Current Biology, Issue 25/3, 2015, Page(s) 364-371, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2014.12.004

A Eukaryote without a Mitochondrial Organelle

Author(s): Anna Karnkowska, Vojtěch Vacek, Zuzana Zubáčová, Sebastian C. Treitli, Romana Petrželková, Laura Eme, Lukáš Novák, Vojtěch Žárský, Lael D. Barlow, Emily K. Herman, Petr Soukal, Miluše Hroudová, Pavel Doležal, Courtney W. Stairs, Andrew J. Roger, Marek Eliáš, Joel B. Dacks, Čestmír Vlček, Vladimír Hampl
Published in: Current Biology, Issue 26/10, 2016, Page(s) 1274-1284, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2016.03.053

Understanding the potential of hepatitis C virus internal ribosome entry site domains to modulate translation initiation via their structure and function

Author(s): Anas Khawaja, Vaclav Vopalensky, Martin Pospisek
Published in: Wiley Interdisciplinary Reviews: RNA, Issue 6/2, 2015, Page(s) 211-224, ISSN 1757-7004
Publisher: John Wiley and Sons Inc.
DOI: 10.1002/wrna.1268

Lateral Gene Transfer and Gene Duplication Played a Key Role in the Evolution of Mastigamoeba balamuthi Hydrogenosomes

Author(s): Eva Nývltová, Courtney W. Stairs, Ivan Hrdý, Jakub Rídl, Jan Mach, Jan Pačes, Andrew J. Roger, Jan Tachezy
Published in: Molecular Biology and Evolution, Issue 32/4, 2015, Page(s) 1039-1055, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msu408

Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells

Author(s): Lan-Feng Dong, Jaromira Kovarova, Martina Bajzikova, Ayenachew Bezawork-Geleta, David Svec, Berwini Endaya, Karishma Sachaphibulkij, Ana R Coelho, Natasa Sebkova, Anna Ruzickova, An S Tan, Katarina Kluckova, Kristyna Judasova, Katerina Zamecnikova, Zuzana Rychtarcikova, Vinod Gopalan, Ladislav Andera, Margarita Sobol, Bing Yan, Bijay Pattnaik, Naveen Bhatraju, Jaroslav Truksa, Pavel Stopka, Pavel
Published in: eLife, Issue 6, 2017, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/eLife.22187

Multilevel regulation of an α-arrestin by glucose depletion controls hexose transporter endocytosis

Author(s): Junie Hovsepian, Quentin Defenouillère, Véronique Albanèse, Libuše Váchová, Camille Garcia, Zdena Palková, Sébastien Léon
Published in: The Journal of Cell Biology, Issue 216/6, 2017, Page(s) 1811-1831, ISSN 0021-9525
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.201610094

Yeast cell differentiation: Lessons from pathogenic and non-pathogenic yeasts

Author(s): Zdena Palková, Libuše Váchová
Published in: Seminars in Cell & Developmental Biology, Issue 57, 2016, Page(s) 110-119, ISSN 1084-9521
Publisher: Academic Press
DOI: 10.1016/j.semcdb.2016.04.006

Cyc8p and Tup1p transcription regulators antagonistically regulate Flo11p expression and complexity of yeast colony biofilms

Author(s): Phu Van Nguyen, Otakar Hlaváček, Jana Maršíková, Libuše Váchová, Zdena Palková
Published in: PLOS Genetics, Issue 14/7, 2018, Page(s) e1007495, ISSN 1553-7404
Publisher: PLOS
DOI: 10.1371/journal.pgen.1007495

Messenger RNAs of Yeast Virus-Like Elements Contain Non-templated 5′ Poly(A) Leaders, and Their Expression Is Independent of eIF4E and Pab1

Author(s): Václav Vopálenský, Michal Sýkora, Tomáš Mašek, Martin Pospíšek
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.02366

Copper and iron metabolism in Ostreococcus tauri – the role of phytotransferrin, plastocyanin and a chloroplast copper-transporting ATPase

Author(s): Ivo Florin Scheiber, Jana Pilátová, Ronald Malych, Eva Kotabova, Matyáš Krijt, Daniel Vyoral, Jan Mach, Thibaut Léger, Jean-Michel Camadro, Ondřej Prášil, Emmanuel Lesuisse, Robert Sutak
Published in: Metallomics, Issue 11/10, 2019, Page(s) 1657-1666, ISSN 1756-5901
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9mt00078j

Anaerobic peroxisomes in Mastigamoeba balamuthi

Author(s): Tien Le, Vojtěch Žárský, Eva Nývltová, Petr Rada, Karel Harant, Marie Vancová, Zdeněk Verner, Ivan Hrdý, Jan Tachezy
Published in: Proceedings of the National Academy of Sciences, 2019, Page(s) 201909755, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1909755117

Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol

Author(s): Verner, Z; Zarsky, V; Le, T; Narayanasamy, RK; Rada, P; Rozbesky, D; Makki, A; Belisova, D; Hrdy, I; Vancova, M; Lender, C; Konig, C; Bruchhaus, I; Tachezy, J
Published in: PLOS PATHOGENS, 2021, ISSN 1553-7366
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1010041

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