OMICS Proteomics

Ronald Malych, Pavel Stopka, Jan Mach, Eva Kotabová, Ondřej Prášil, Robert Sutak, Flow cytometry-based study of model marine microalgal consortia revealed an ecological advantage of siderophore utilization by the dinoflagellate Amphidinium carterae, Computational and Structural Biotechnology Journal, Volume 20, 2022, Pages 287-295, https://doi.org/10.1016/j.csbj.2021.12.023.

Vondráček O, Mikeš L, Talacko P, Leontovyč R, Bulantová J, Horák P. Differential proteomic analysis of laser-microdissected penetration glands of avian schistosome cercariae with a focus on proteins involved in host invasion. Int J Parasitol. 2022 Feb 23:S0020-7519(22)00017-0. doi: 10.1016/j.ijpara.2021.12.003. Epub ahead of print. PMID: 35218763.

Erban T, Klimov PB, Harant K, Talacko P, Nesvorna M, Hubert J. Label-free proteomic analysis reveals differentially expressed Wolbachia proteins in Tyrophagus putrescentiae: Mite allergens and markers reflecting population-related proteome differences. J Proteomics. 2021 Oct 30;249:104356. doi: 10.1016/j.jprot.2021.104356. Epub 2021 Aug 23. PMID: 34438106.

Vacurova E, Trnovska J, Svoboda P, Skop V, Novosadova V, Reguera DP, Petrezselyová S, Piavaux B, Endaya B, Spoutil F, Zudova D, Stursa J, Melcova M, Bielcikova Z, Werner L, Prochazka J, Sedlacek R, Huttl M, Hubackova SS, Haluzik M, Neuzil J. Mitochondrially targeted tamoxifen alleviates markers of obesity and type 2 diabetes mellitus in mice. Nat Commun. 2022 Apr 6;13(1):1866. doi: 10.1038/s41467-022-29486-z. PMID: 35387987.

Smutná T, Dohnálková A, Sutak R, Narayanasamy RK, Tachezy J, Hrdý I. A cytosolic ferredoxin-independent hydrogenase possibly mediates hydrogen uptake in Trichomonas vaginalis. Curr Biol. 2022 Jan 10;32(1):124-135.e5. doi: 10.1016/j.cub.2021.10.050. Epub 2021 Nov 10. PMID: 34762819.

Bláhová Z, Franěk R, Let M, Bláha M, Pšenička M, Mráz J. Partial fads2 Gene Knockout Diverts LC-PUFA Biosynthesis via an Alternative Δ8 Pathway with an Impact on the Reproduction of Female Zebrafish (Danio rerio). Genes (Basel). 2022 Apr 15;13(4):700. doi: 10.3390/genes13040700. PMID: 35456508; PMCID: PMC9032720.

Magalhaes-Novais S, Blecha J, Naraine R, Mikesova J, Abaffy P, Pecinova A, Milosevic M, Bohuslavova R, Prochazka J, Khan S, Novotna E, Sindelka R, Machan R, Dewerchin M, Vlcak E, Kalucka J, Stemberkova Hubackova S, Benda A, Goveia J, Mracek T, Barinka C, Carmeliet P, Neuzil J, Rohlenova K, Rohlena J. Mitochondrial respiration supports autophagy to provide stress resistance during quiescence. Autophagy. 2022 Oct;18(10):2409-2426. doi: 10.1080/15548627.2022.2038898. Epub 2022 Mar 8. PMID: 35258392; PMCID: PMC9542673.

Erban T, Sopko B, Bodrinova M, Talacko P, Chalupnikova J, Markovic M, Kamler M. Proteomic insight into the interaction of Paenibacillus larvae with honey bee larvae before capping collected from an American foulbrood outbreak: Pathogen proteins within the host, lysis signatures and interaction markers. Proteomics. 2022 Aug 10:e2200146. doi: 10.1002/pmic.202200146. Epub ahead of print. PMID: 35946602.

Volenikova, A., Nguyen, P., Davey, P. et al. Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera. Commun Biol 5, 1281 (2022). https://doi.org/10.1038/s42003-022-04240-9

Wu BC-h, Sauman I, Maaroufi HO, Zaloudikova A, Zurovcova M, Kludkiewicz B, Hradilova M and Zurovec M (2022) Characterization of silk genes in Ephestia kuehniella and Galleria mellonella revealed duplication of sericin genes and highly divergent sequences encoding fibroin heavy chains. Front. Mol. Biosci. 9:1023381. doi: 10.3389/fmolb.2022.1023381

Knizkova, D., Pribikova, M., Draberova, H. et al. CMTM4 is a subunit of the IL-17 receptor and mediates autoimmune pathology. Nat Immunol 23, 1644–1652 (2022). https://doi.org/10.1038/s41590-022-01325-9

Vdovin, A., Jelinek, T., Zihala, D. et al. The deubiquitinase OTUD1 regulates immunoglobulin production and proteasome inhibitor sensitivity in multiple myeloma. Nat Commun 13, 6820 (2022). https://doi.org/10.1038/s41467-022-34654-2

Pacakova L, Harant K, Volf P and Lestinova T (2022) Three types of Leishmania mexicana amastigotes: Proteome comparison by quantitative proteomic analysis. Front. Cell. Infect. Microbiol. 12:1022448. doi: 10.3389/fcimb.2022.1022448

Ujcikova, H.; Roubalova, L.; Lee, Y.S.; Slaninova, J.; Brejchova, J.; Svoboda, P. The Dose-Dependent Effects of Multifunctional Enkephalin Analogs on the Protein Composition of Rat Spleen Lymphocytes, Cortex, and Hippocampus; Comparison with Changes Induced by Morphine. Biomedicines 2022, 10, 1969. https://doi.org/10.3390/biomedicines10081969

Zimmann N, Rada P, Žárský V, Smutná T, Záhonová K, Dacks J, Harant K, Hrdý I, Tachezy J. Proteomic Analysis of Trichomonas vaginalis Phagolysosome, Lysosomal Targeting, and Unconventional Secretion of Cysteine Peptidases. Mol Cell Proteomics. 2022 Jan;21(1):100174. doi: 10.1016/j.mcpro.2021.100174. Epub 2021 Nov 8. PMID: 34763061; PMCID: PMC8717582.

Arbon D, Ženíšková K, Šubrtová K, Mach J, Štursa J, Machado M, Zahedifard F, Leštinová T, Hierro-Yap C, Neuzil J, Volf P, Ganter M, Zoltner M, Zíková A, Werner L, Sutak R. Repurposing of MitoTam: Novel Anti-Cancer Drug Candidate Exhibits Potent Activity against Major Protozoan and Fungal Pathogens. Antimicrob Agents Chemother. 2022 Aug 16;66(8):e0072722. doi: 10.1128/aac.00727-22. Epub 2022 Jul 20. PMID: 35856666; PMCID: PMC9380531.

Fry, M.Y., Najdrová, V., Maggiolo, A.O. et al. Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3. Nat Struct Mol Biol 29, 820–830 (2022). https://doi.org/10.1038/s41594-022-00798-4

Maria Grechnikova, Dominik Arbon, Kateřina Ženíšková, Ronald Malych, Jan Mach, Lucie Krejbichová, Aneta Šimáčková, Robert Sutak,
Elucidation of iron homeostasis in Acanthamoeba castellanii, International Journal for Parasitology, Volume 52, Issue 8, 2022, Pages 497-508, ISSN 0020-7519,
https://doi.org/10.1016/j.ijpara.2022.03.007.

Rada P, Hrdý I, Zdrha A, Narayanasamy RK, Smutná T, Horáčková J, Harant K, Beneš V, Ong S-C, Tsai C-Y, Luo H-W, Chiu C-H, Tang P and Tachezy J (2022) Double-Stranded RNA Viruses Are Released From Trichomonas vaginalis Inside Small Extracellular Vesicles and Modulate the Exosomal Cargo. Front. Microbiol. 13:893692. doi: 10.3389/fmicb.2022.893692

Petrusová, J.; Havalda, R.; Flachs, P.; Venit, T.; Darášová, A.; Hůlková, L.; Sztacho, M.; Hozák, P. Focal Adhesion Protein Vinculin Is Required for Proper Meiotic Progression during Mouse Spermatogenesis. Cells 2022, 11, 2013. https://doi.org/10.3390/cells11132013

Drastichova, Z.; Trubacova, R.; Novotny, J. β-Arrestin2 Is Critically Involved in the Differential Regulation of Phosphosignaling Pathways by Thyrotropin-Releasing Hormone and Taltirelin. Cells 2022, 11, 1473. https://doi.org/10.3390/cells11091473

Ronald Malych, Zoltán Füssy, Kateřina Ženíšková, Dominik Arbon, Vladimír Hampl, Ivan Hrdý, Robert Sutak, The response of Naegleria gruberi to oxidative stress, Metallomics, Volume 14, Issue 3, March 2022, mfac009, https://doi.org/10.1093/mtomcs/mfac009

Ženíšková K, Grechnikova M and Sutak R (2022) Copper Metabolism in Naegleria gruberi and Its Deadly Relative Naegleria fowleri. Front. Cell Dev. Biol. 10:853463. doi: 10.3389/fcell.2022.853463

Stemberkova-Hubackova S, Zobalova R, Dubisova M, Smigova J, Dvorakova S, Korinkova K, Ezrova Z, Endaya B, Blazkova K, Vlcak E, Brisudova P, Le DT, Juhas S, Rosel D, Daniela Kelemen C, Sovilj D, Vacurova E, Cajka T, Filimonenko V, Dong L, Andera L, Hozak P, Brabek J, Bielcikova Z, Stursa J, Werner L, Neuzil J. Simultaneous targeting of mitochondrial metabolism and immune checkpoints as a new strategy for renal cancer therapy. Clin Transl Med. 2022 Mar;12(3):e645. doi: 10.1002/ctm2.645. PMID: 35352502; PMCID: PMC8964933.

Erban, T., Shcherbachenko, E., Talacko, P. et al. Honey proteome of the bumblebee Bombus terrestris: similarities, differences, and exceptionality compared to honey bee honey as signatures of eusociality evolution. Apidologie 53, 16 (2022). https://doi.org/10.1007/s13592-022-00928-3

Jennifer J Tate, Jana Marsikova, Libuse Vachova, Zdena Palkova, Terrance G Cooper, Effects of abolishing Whi2 on the proteome and nitrogen catabolite repression-sensitive protein production, G3 Genes|Genomes|Genetics, Volume 12, Issue 3, March 2022, jkab432, https://doi.org/10.1093/g3journal/jkab432

Horáčková V, Voleman L, Hagen KD, Petrů M, Vinopalová M, Weisz F, Janowicz N, Marková L, Motyčková A, Najdrová V, Tůmová P, Dawson SC, Doležal P. Efficient CRISPR/Cas9-mediated gene disruption in the tetraploid protist Giardia intestinalis. Open Biol. 2022 Apr;12(4):210361. doi: 10.1098/rsob.210361. Epub 2022 Apr 27. PMID: 35472287; PMCID: PMC9042576.

Dienstbier A, Amman F, Petráčková D, Štipl D, Čapek J, Zavadilová J, Fabiánová K, Držmíšek J, Kumar D, Wildung M, Pouchnik D, Večerek B. Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution. Emerg Infect Dis. 2021 Jan;27(1):57-68. doi: 10.3201/eid2701.191541. PMID: 33350934; PMCID: PMC7774529.

Drzmisek, J.; Stipl, D.; Petrackova, D.; Vecerek, B.; Dienstbier, A. Omics Analysis of Blood-Responsive Regulon in Bordetella pertussis Identifies a Novel Essential T3SS Substrate. Int. J. Mol. Sci. 2021, 22, 736.

Sztacho M, Šalovská B, Červenka J, Balaban C, Hoboth P, Hozák P. Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. Cells. 2021 Jan 4;10(1):68. doi: 10.3390/cells10010068. PMID: 33406800; PMCID: PMC7824793.

Čunátová K, Reguera DP, Vrbacký M, Fernández-Vizarra E, Ding S, Fearnley IM, Zeviani M, Houštěk J, Mráček T, Pecina P. Loss of COX4I1 Leads to Combined Respiratory Chain Deficiency and Impaired Mitochondrial Protein Synthesis. Cells. 2021 Feb 10;10(2):369. doi: 10.3390/cells10020369. PMID: 33578848; PMCID: PMC7916595.

Voukali E, Veetil NK, Němec P, Stopka P, Vinkler M. Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. Sci Rep. 2021 Mar 5;11(1):5312. doi: 10.1038/s41598-021-84274-x. PMID: 33674647; PMCID: PMC7935914.

Erban T, Shcherbachenko E, Talacko P, Harant K. A single honey proteome dataset for identifying adulteration by foreign amylases and mining various protein markers natural to honey. J Proteomics. 2021 May 15;239:104157. doi: 10.1016/j.jprot.2021.104157. Epub 2021 Feb 22. PMID: 33631366.

Karel Müller, Petre Ivanov Dobrev, Aleš Pěnčík, Petr Hošek, Zuzana Vondráková, Roberta Filepová, Kateřina Malínská, Federica Brunoni, Lenka Helusová, Tomáš Moravec, Katarzyna Retzer, Karel Harant, Ondřej Novák, Klára Hoyerová, Jan Petrášek, DIOXYGENASE FOR AUXIN OXIDATION 1 catalyzes the oxidation of IAA Amino Acid Conjugates, Plant Physiology, 2021;, kiab242, https://doi.org/10.1093/plphys/kiab242

Lidak T, Baloghova N, Korinek V, Sedlacek R, Balounova J, Kasparek P, Cermak L. CRL4-DCAF12 Ubiquitin Ligase Controls MOV10 RNA Helicase during Spermatogenesis and T Cell Activation. Int J Mol Sci. 2021 May 20;22(10):5394. doi: 10.3390/ijms22105394. PMID: 34065512; PMCID: PMC8161014.

Rouhova L, Kludkiewicz B, Sehadova H, Sery M, Kucerova L, Konik P, Zurovec M. Silk of the common clothes moth, Tineola bisselliella, a cosmopolitan pest belonging to the basal ditrysian moth line. Insect Biochem Mol Biol. 2021 Mar;130:103527. doi: 10.1016/j.ibmb.2021.103527. Epub 2021 Jan 19. PMID: 33476773.

Zabelina V, Takasu Y, Sehadova H, Yonemura N, Nakajima K, Sezutsu H, Sery M, Zurovec M, Sehnal F, Tamura T. Mutation in Bombyx mori fibrohexamerin (P25) gene causes reorganization of rough endoplasmic reticulum in posterior silk gland cells and alters morphology of fibroin secretory globules in the silk gland lumen. Insect Biochem Mol Biol. 2021 Aug;135:103607. doi: 10.1016/j.ibmb.2021.103607. Epub 2021 Jun 5. PMID: 34102294.

Rindos M, Kucerova L, Rouhova L, Sehadova H, Sery M, Hradilova M, Konik P, Zurovec M. Comparison of Silks from Pseudoips prasinana and Bombyx mori Shows Molecular Convergence in Fibroin Heavy Chains but Large Differences in Other Silk Components. Int J Mol Sci. 2021 Jul 31;22(15):8246. doi: 10.3390/ijms22158246. PMID: 34361011; PMCID: PMC8347419.

Makarov M, Meng J, Tretyachenko V, Srb P, Březinová A, Giacobelli VG, Bednárová L, Vondrášek J, Dunker AK, Hlouchová K. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. Protein Sci. 2021 May;30(5):1022-1034. doi: 10.1002/pro.4068. Epub 2021 Mar 26. PMID: 33739538; PMCID: PMC8040869.

Ryabchenko B, Soldatova I, Šroller V, Forstová J, Huérfano S. Immune sensing of mouse polyomavirus DNA by p204 and cGAS DNA sensors. FEBS J. 2021 May 10. doi: 10.1111/febs.15962. Epub ahead of print. PMID: 33969628.

Kučera O, Siahaan V, Janda D, Dijkstra SH, Pilátová E, Zatecka E, Diez S, Braun M, Lansky Z. Anillin propels myosin-independent constriction of actin rings. Nat Commun. 2021 Jul 28;12(1):4595. doi: 10.1038/s41467-021-24474-1. PMID: 34321459; PMCID: PMC8319318.

Vanova KH, Pang Y, Krobova L, Kraus M, Nahacka Z, Boukalova S, Pack SD, Zobalova R, Zhu J, Huynh TT, Jochmanova I, Uher O, Hubackova S, Dvorakova S, Garrett TJ, Ghayee HK, Wu X, Schuster B, Knapp PE, Frysak Z, Hartmann I, Nilubol N, Cerny J, Taieb D, Rohlena J, Neuzil J, Yang C, Pacak K. Germline SUCLG2 Variants in Patients with Pheochromocytoma and Paraganglioma. J Natl Cancer Inst. 2021 Aug 20:djab158. doi: 10.1093/jnci/djab158. Epub ahead of print. PMID: 34415331.

Staňková P, Kučera O, Peterová E, Elkalaf M, Rychtrmoc D, Melek J, Podhola M, Zubáňová V, Červinková Z. Western Diet Decreases the Liver Mitochondrial Oxidative Flux of Succinate: Insight from a Murine NAFLD Model. Int J Mol Sci. 2021 Jun 27;22(13):6908. doi: 10.3390/ijms22136908. PMID: 34199098; PMCID: PMC8268937.

Sistilli G, Kalendova V, Cajka T, Irodenko I, Bardova K, Oseeva M, Zacek P, Kroupova P, Horakova O, Lackner K, Gastaldelli A, Kuda O, Kopecky J, Rossmeisl M. Krill Oil Supplementation Reduces Exacerbated Hepatic Steatosis Induced by Thermoneutral Housing in Mice with Diet-Induced Obesity. Nutrients. 2021 Jan 29;13(2):437. doi: 10.3390/nu13020437. PMID: 33572810; PMCID: PMC7912192.

Kotabova E, Malych R, Pierella Karlusich JJ, Kazamia E, Eichner M, Mach J, Lesuisse E, Bowler C, Prášil O, Sutak R. Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability. mSystems. 2021 Feb 9;6(1):e00738-20. doi: 10.1128/mSystems.00738-20. PMID: 33563784; PMCID: PMC7883536.

Ujcikova H, Hejnova L, Eckhardt A, Roubalova L, Novotny J, Svoboda P. Impact of three-month morphine withdrawal on rat brain cortex, hippocampus, striatum and cerebellum: proteomic and phosphoproteomic studies. Neurochem Int. 2021 Mar;144:104975. doi: 10.1016/j.neuint.2021.104975. Epub 2021 Jan 27. PMID: 33508371.

Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, Srb P, Hexnerova R, Fabry M, Madlikova M, Horejsi M, De Rijck J, Debyser Z, Adelman K, Hodges HC, Veverka V. A ubiquitous disordered protein interaction module orchestrates transcription elongation. Science. 2021 Nov 26;374(6571):1113-1121. doi: 10.1126/science.abe2913. Epub 2021 Nov 25. PMID: 34822292.

Horváthová L, Žárský V, Pánek T, Derelle R, Pyrih J, Motyčková A, Klápšťová V, Vinopalová M, Marková L, Voleman L, Klimeš V, Petrů M, Vaitová Z, Čepička I, Hryzáková K, Harant K, Gray MW, Chami M, Guilvout I, Francetic O, Franz Lang B, Vlček Č, Tsaousis AD, Eliáš M, Doležal P. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat Commun. 2021 May 19;12(1):2947. doi: 10.1038/s41467-021-23046-7. PMID: 34011950; PMCID: PMC8134430.

Aquino Perez C, Burocziova M, Jenikova G, Macurek L. CK1-mediated phosphorylation of FAM110A promotes its interaction with mitotic spindle and controls chromosomal alignment. EMBO Rep. 2021 Jul 5;22(7):e51847. doi: 10.15252/embr.202051847. Epub 2021 May 26. PMID: 34080749; PMCID: PMC8256294.

Storchova R, Burdova K, Palek M, Medema RH, Macurek L. A novel assay for screening WIP1 phosphatase substrates in nuclear extracts. FEBS J. 2021 Oct;288(20):6035-6051. doi: 10.1111/febs.15965. Epub 2021 May 27. PMID: 33982878.

Šimčíková, D., Gardáš, D., Hložková, K. et al. Loss of hexokinase 1 sensitizes ovarian cancer to high-dose metformin. Cancer Metab 9, 41 (2021). https://doi.org/10.1186/s40170-021-00277-2

Cytochrome c Oxidase Subunit 4 Isoform Exchange Results in Modulation of Oxygen Affinity
Cells. 2020 Feb; 9(2): 443. Published online 2020 Feb 14. doi: 10.3390/cells9020443 PMCID: PMC7072730 PMID: 32075102
David Pajuelo Reguera,1 Kristýna Čunátová,1,2 Marek Vrbacký,1 Alena Pecinová,1 Josef Houštěk,1 Tomáš Mráček,1,* and Petr Pecina1,*

Ujcikova, H., Cechova, K., Jagr, M., Roubalova, L., Vosahlikova, M., & Svoboda, P. (2020). Proteomic analysis of protein composition of rat hippocampus exposed to morphine for 10 days; comparison with animals after 20 days of morphine withdrawal. PLOS ONE, 15(4), e0231721. doi:10.1371/journal.pone.0231721 

Ujcikova, H., Cechova, K., Roubalova, L., Brejchova, J., Kaufman, J., Holan, V., & Svoboda, P. (2020). The high-resolution proteomic analysis of protein composition of rat spleen lymphocytes stimulated by Concanavalin A; a comparison with morphine-treated cells. Journal of Neuroimmunology, 341, 577191. doi:10.1016/j.jneuroim.2020.577191

Polanska N, Ishemgulova A, Volfova V,
Flegontov P, Votypka J, Yurchenko V, et al. (2020)
Sergentomyia schwetzi: Salivary gland
transcriptome, proteome and enzymatic activities
in two lineages adapted to different blood sources.
PLoS ONE 15(3): e0230537. https://doi.org/
10.1371/journal.pone.0230537

Jankovska E, Lipcseyova D, Svrdlikova M, Pavelcova M, Kubala Havrdova E, Holada K, Petrak J. Quantitative proteomic analysis of cerebrospinal fluid of women newly diagnosed with multiple sclerosis. Int J Neurosci. 2020 Oct 29:1-11. doi: 10.1080/00207454.2020.1837801. Epub ahead of print. PMID: 33059501.

Kocourek F, Stara J, Sopko B, Talacko P, Harant K, Hovorka T, Erban T. Proteogenomic insight into the basis of the insecticide tolerance/resistance of the pollen beetle Brassicogethes (Meligethes) aeneus. J Proteomics. 2020 Dec 27;233:104086. doi: 10.1016/j.jprot.2020.104086. Epub ahead of print. PMID: 33378720.

Čermák V, Gandalovičová A, Merta L, Harant K, Rösel D, Brábek J. High-throughput transcriptomic and proteomic profiling of mesenchymal-amoeboid transition in 3D collagen. Sci Data. 2020 May 27;7(1):160. doi: 10.1038/s41597-020-0499-2. PMID: 32461585; PMCID: PMC7253430.

Fáberová V, Kalasová I, Krausová A, Hozák P. Super-Resolution Localisation of Nuclear PI(4)P and Identification of Its Interacting Proteome. Cells. 2020 May 11;9(5):1191. doi: 10.3390/cells9051191. PMID: 32403279; PMCID: PMC7291030.

Prikryl P, Satrapova V, Frydlova J, Hruskova Z, Zima T, Tesar V, Vokurka M. Mass spectrometry-based proteomic exploration of the small urinary extracellular vesicles in ANCA-associated vasculitis in comparison with total urine. J Proteomics. 2020 Dec 9;233:104067. doi: 10.1016/j.jprot.2020.104067. Epub ahead of print. PMID: 33307252.

Novák J, Jurnečka D, Linhartová I, Holubová J, Staněk O, Štipl D, Dienstbier A, Večerek B, Azevedo N, Provazník J, Beneš V, Šebo P. A Mutation Upstream of the rplN-rpsD Ribosomal Operon Downregulates Bordetella pertussis Virulence Factor Production without Compromising Bacterial Survival within Human Macrophages. mSystems. 2020 Dec 8;5(6):e00612-20. doi: 10.1128/mSystems.00612-20. PMID: 33293402; PMCID: PMC7742992.

Maršíková J., Pavlíčková M., Wilkinson D., Váchová L., Hlaváček O., Hatáková L., Palková Z. (2020) The Whi2p-Psr1p/Psr2p complex regulates interference competition and expansion of cells with competitive advantage in yeast colonies. PNAS first published June 15, 2020 https://doi.org/10.1073/pnas.1922076117

Langerová H, Lubyová B, Zábranský A, et al. Hepatitis B Core Protein Is Post-Translationally Modified through K29-Linked Ubiquitination. Cells. 2020;9(12):2547. Published 2020 Nov 26. doi:10.3390/cells9122547

Korabecna M, Zinkova A, Brynychova I, Chylikova B, Prikryl P, Sedova L, Neuzil P, Seda O. Cell-free DNA in plasma as an essential immune system regulator. Sci Rep. 2020 Oct 15;10(1):17478. doi: 10.1038/s41598-020-74288-2. PMID: 33060738; PMCID: PMC7566599.

Dibus M, Brábek J, Rösel D. A Screen for PKN3 Substrates Reveals an Activating Phosphorylation of ARHGAP18. Int J Mol Sci. 2020 Oct 20;21(20):7769. doi: 10.3390/ijms21207769. PMID: 33092266; PMCID: PMC7594087.

Makki A., Rada P, Žárský V., Kereiche S., Kovacik L., Novotny M., Jores T., Rapaport D., Tachezy J. 2019 Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. PLoS Biology. 17(1):e3000098. doi: 10.1371/journal.pbio.3000098

Syslova, E., Landa, P., Stuchlikova, L.R., Matouskova, P., Skalova, L., Szotakova, B., Navratilova, M., Vanek, T. and Podlipna, R. (2019) Metabolism of the anthelmintic drug fenbendazole in Arabidopsis thaliana and its effect on transcriptome and proteome. Chemosphere, 218, 662-669.

Palyzová, A., Zahradník, J., Marešová, H., & Řezanka, T. (2019). Characterization of the catabolic pathway of diclofenac in Raoultella sp. KDF8. International Biodeterioration & Biodegradation, 137, 88–94. doi:10.1016/j.ibiod.2018.11.013

Jankovska, E., Svitek, M., Holada, K. and Petrak, J. (2019) Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage. Clin Proteomics, 16, 9.

Vit, O., Harant, K., Klener, P., Man, P. and Petrak, J. (2019) A three-pronged "Pitchfork" strategy enables an extensive description of the human membrane proteome and the identification of missing proteins. J Proteomics, 204, 103411.

Makukhin, N., Havelka, V., Polachova, E., Rampirova, P., Tarallo, V., Strisovsky, K. and Misek, J. (2019) Resolving oxidative damage to methionine by an unexpected membrane-associated stereoselective reductase discovered using chiral fluorescent probes. FEBS J.

Kohutova, J., Elsnicova, B., Holzerova, K., Neckar, J., Sebesta, O., Jezkova, J., Vecka, M., Vebr, P., Hornikova, D., Szeiffova Bacova, B. et al. (2018) Anti-arrhythmic Cardiac Phenotype Elicited by Chronic Intermittent Hypoxia Is Associated With Alterations in Connexin-43 Expression, Phosphorylation, and Distribution. Front Endocrinol (Lausanne), 9, 789.

Sumova, P., Sima, M., Kalouskova, B., Polanska, N., Vanek, O., Oliveira, F., … Volf, P. (2019). Amine-binding properties of salivary yellow-related proteins in phlebotomine sand flies. Insect Biochemistry and Molecular Biology, 103245. doi:10.1016/j.ibmb.2019.103245

Nosek V 1, Míšek J . Enzymatic kinetic resolution of chiral sulfoxides - an enantiocomplementary approach. Chem Commun (Camb). 2019 Aug 27;55(70):10480-10483. doi: 10.1039/c9cc05470g.

Van Nguyen P., Hlavacek O., Marsikova J., Vachova L., Palkova Z. (2018) Cyc8p and Tup1p transcription regulators antagonistically regulate Flo11p expression and complexity. PLoS genetics, https://doi.org/10.1371/journal.pgen.1007495

.Sykora, M., Pospisek, M., Novak, J., Mrvova, S., Krasny, L. and Vopalensky, V. (2018) Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin. PLoS Pathog, 14, e1007377.

Bilkova, B., Swiderska, Z., Zita, L., Laloe, D., Charles, M., Benes, V., Stopka, P. and Vinkler, M. (2018) Domestic Fowl Breed Variation in Egg White Protein Expression: Application of Proteomics and Transcriptomics. J Agric Food Chem, 66, 11854-11863.

Melenovsky, V., Cervenka, L., Viklicky, O., Franekova, J., Havlenova, T., Behounek, M., Chmel, M. and Petrak, J. (2018) Kidney Response to Heart Failure: Proteomic Analysis of Cardiorenal Syndrome. Kidney Blood Press Res, 43, 1437-1450.

Rossmeisl, M., Pavlisova, J., Janovska, P., Kuda, O., Bardova, K., Hansikova, J., Svobodova, M., Oseeva, M., Veleba, J., Kopecky, J., Jr. et al. (2018) Differential modulation of white adipose tissue endocannabinoid levels by n-3 fatty acids in obese mice and type 2 diabetic patients. Biochim Biophys Acta, 1863, 712-725.

Kuda, O., Brezinova, M., Silhavy, J., Landa, V., Zidek, V., Dodia, C., Kreuchwig, F., Vrbacky, M., Balas, L., Durand, T. et al. (2018) Nrf2-Mediated Antioxidant Defense and Peroxiredoxin 6 Are Linked to Biosynthesis of Palmitic Acid Ester of 9-Hydroxystearic Acid. Diabetes, 67, 1190-1199.

Rohde, F., Schusser, B., Hron, T., Farkasova, H., Plachy, J., Hartle, S., Hejnar, J., Elleder, D. and Kaspers, B. (2018) Characterization of Chicken Tumor Necrosis Factor-alpha, a Long Missed Cytokine in Birds. Front Immunol, 9, 605.

Mach, J., Bila, J., Zeniskova, K., Arbon, D., Malych, R., Glavanakovova, M., Nyvltova, E. and Sutak, R. (2018) Iron economy in Naegleria gruberi reflects its metabolic flexibility. Int J Parasitol.

Kuntova, B., Stopkova, R. and Stopka, P. (2018) Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse. Front Genet, 9, 26.

Pyrihová E, Motycková A, Voleman L, Wandyszewska N, Fišer R, Seydlová G, Roger A, Kolísko M, Doležal P. A Single Tim Translocase in the Mitosomes of Giardia intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes. Genome Biol Evol. 2018 Oct 1;10(10):2813-2822. doi: 10.1093/gbe/evy215. PMID: 30265292; PMCID: PMC6200312.

Cerna M, Kuntova B, Talacko P, Stopkova R, and Stopka P. 2017. Differential regulation of vaginal lipocalins (OBP, MUP) during the estrous cycle of the house mouse. Sci Rep 7:11674.

Erban, T., Harant, K., Chalupnikova, J., Kocourek, F. and Stara, J. (2017) Beyond the survival and death of the deltamethrin-threatened pollen beetle Meligethes aeneus: An in-depth proteomic study employing a transcriptome database. J Proteomics, 150, 281-289.

Stopkova R, Klempt P, Kuntova B, and Stopka P. 2017. On the tear proteome of the house mouse (Mus musculus musculus) in relation to chemical signalling. PeerJ 6:e3541.

Valis, K., Grobarova, V., Hernychova, L., Buganova, M., Kavan, D., Kalous, M., Cerny, J., Stodulkova, E., Kuzma, M., Flieger, M. et al. (2017) Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B. Oncotarget, 8, 103137-103153.

Stafkova, J., Rada, P., Meloni, D., Zarsky, V., Smutna, T., Zimmann, N., Harant, K., Pompach, P., Hrdy, I. and Tachezy, J. (2017) Dynamic secretome of Trichomonas vaginalis: Case study of beta-amylases. Mol Cell Proteomics.

Vyklicka, L., Boukalova, S., Macikova, L., Chvojka, S. and Vlachova, V. (2017) The human transient receptor potential vanilloid 3 channel is sensitized via the ERK pathway. J Biol Chem.

Vosahlikova, M., Ujcikova, H., Chernyavskiy, O., Brejchova, J., Roubalova, L., Alda, M. and Svoboda, P. (2017) Effect of therapeutic concentration of lithium on live HEK293 cells; increase of Na+/K+-ATPase, change of overall protein composition and alteration of surface layer of plasma membrane. Biochim Biophys Acta, 1861, 1099-1112.

Laššuthová P, Gregor M, Sarnová L, Machalová E, Sedláček R, Seeman P: Clinical, In Silico, and Experimental Evidence for Pathogenicity of Two Novel Splice Site Mutations in the SH3TC2 Gene. J Neurogenet 2012 26(3-4): 413-20. [pubmed] [doi]

Hartmannova, H., Piherova, L., Tauchmannova, K., Kidd, K., Acott, P.D., Crocker, J.F., Oussedik, Y., Mallet, M., Hodanova, K., Stranecky, V. et al. (2016) Acadian variant of Fanconi syndrome is caused by mitochondrial respiratory chain complex I deficiency due to a non-coding mutation in complex I assembly factor NDUFAF6. Hum Mol Genet, 25, 4062-4079.

Manakov, D., Ujcikova, H., Pravenec, M. and Novotny, J. (2016) Alterations in the cardiac proteome of the spontaneously hypertensive rat induced by transgenic expression of CD36. J Proteomics, 145, 177-186.

Stopka P, Kuntova B, Klempt P, Havrdova L, Cerna M, and Stopkova R. 2016. On the saliva proteome of the Eastern European house mouse (Mus musculus musculus) focusing on sexual signalling and immunity. Sci Rep 6:32481.

Vit, O., Man, P., Kadek, A., Hausner, J., Sklenar, J., Harant, K., Novak, P., Scigelova, M., Woffendin, G. and Petrak, J. (2016) Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments. J Proteomics, 149, 15-22.

Ujcikova, H., Vosahlikova, M., Roubalova, L. and Svoboda, P. (2016) Proteomic analysis of protein composition of rat forebrain cortex exposed to morphine for 10days; comparison with animals exposed to morphine and subsequently nurtured for 20days in the absence of this drug. J Proteomics, 145, 11-23.

Jankovicova J, Frolikova M, Sebkova N, Simon M, Cupperova P, Lipcseyova D, Michalkova K, Horovska L, Sedlacek R, Stopka P, Antalikova J, Dvorakova-Hortova K. Characterization of tetraspanin protein CD81 in mouse spermatozoa and bovine gametes. Reproduction. 2016 Dec;152(6):785-793. doi: 10.1530/REP-16-0304. Epub 2016 Sep 27. PMID: 27679865.