Publications

Rahikainen R, Vester SK, Turkki P, Janosko CP, Deiters A, Hytönen VP, Howarth M (2023) Visible Light-Induced Specific Protein Reaction Delineates Early Stages of Cell Adhesion. J. Am. Chem. Soc. 2023, 145, 45, 24459–24465. doi: 10.1021/jacs.3c07827 PMCID: PMC10370186

Jacobs HT, Szibor M, Rathkolb B, da Silva-Buttkus P, Aguilar-Pimentel JA, Amarie OV, Becker L, Calzada-Wack J, Dragano N, Garrett L, Gerlini R, Hölter SM, Klein-Rodewald T, Kraiger M, Leuchtenberger S, Marschall S, Östereicher MA, Pfannes K, Sanz-Moreno A, Seisenberger C, Spielmann N, Stoeger C, Wurst W, Fuchs H, Hrabě de Angelis M, Gailus-Durner V (2023) AOX delays the onset of the lethal phenotype in a mouse model of Uqcrh (complex III) disease. Biochim Biophys. Acta Mol. Basis Dis. Epub ahead of print. doi: 10.1016/j.bbadis.2023.166760 PMID: 37230398

Jacobs HT, Tuomela T, Lillsunde P (2023) Nuclear genetic background influences the phenotype of the Drosophila tko25t mitochondrial protein-synthesis mutant. G3 (Bethesda) 13: jkad078. doi: http://10.1093/g3journal/jkad078, ‘June Featured Article’. PMID: 37017029 PMCID: PMC10234395

Jacobs HT, Ballard JWO (2022) What physiological role(s) does the Alternative Oxidase play in animals? Biochim. Biophys. Acta Bioenerget. 1863, 148556 doi: 10.1016/j.bbabio.2022.148556 PMID: 37230398

Dotsenko V, Oittinen M, Taavela J, Popp A, Peräaho M, Staff S, Sarin J, Leon F, Isola J, Mäki M, Viiri K (2021) Genome-Wide Transcriptomic Analysis of Intestinal Mucosa in Celiac Disease Patients on a Gluten-Free Diet and Postgluten Challenge. Cell Mol Gastroenterol Hepatol. 2021;11(1):13-32. Epub 2020 Jul 31. doi: 10.1016/j.jcmgh.2020.07.010 PMID: 32745639 PMCID: 7593586

George JJ, Oittinen M, Martin-Diaz L, Zapilko V, Iqbal S, Rintakangas T, Arrojo Martins FT, Niskanen H, Katajisto P, Kaikkonen M, Viiri K (2021) Polycomb Repressive Complex 2 regulates genes necessary for intestinal Microfold cell (M cell) development. Cell Mol Gastroenterol Hepatol. 2021 May 28:S2352-345X(21)00103-X. Epub ahead of print. doi: 10.1016/j.jcmgh.2021.05.014 PMID: 34058415

Heazlewood S, Ahmad T, Mohenska M, Guo BB, Gangatirkar P, Josefsson EC, Ellis S, Ratnadiwakara M, Cao H, Cao B, Heazlewood C, Williams B, Fulton M, White J, Ramialison M, Nilsson SK, Anko ML (2021) RNA Binding Protein SRSF3 confers an essential role in megakaryocyte maturation and platelet production. Blood. 2021 Dec 1:blood.2021013826. doi: http://10.1182/blood.2021013826 PMID: 34852174

Pavel A, Del Giudice G, Federico A, Di Lieto A, Kinaret PAS, Serra A, Greco D (2021) Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. Brief Bioinform. 2021 Mar 22;22(2):1430-1441. doi: 10.1093/bib/bbaa417 PMID: 33569598; PMCID: 7929418

Vandestadt C, Vanwalleghem GC, Khabooshan MA, Douek AM, Castillo HA, Li M, Schulze K, Don E, Stamatis SA, Ratnadiwakara M, Änkö ML, Scott EK, Kaslin J (2021) RNA-induced inflammation and migration of precursor neurons initiates neuronal circuit regeneration in zebrafish. Dev Cell. 2021 Aug 23;56(16):2364-2380.e8. doi: http://10.1016/j.devcel.2021.07.021 PMID: 34428400

Barker H, Parkkila S (2020) Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2. PLoS One. 2020 Oct 28;15(10):e0240647. doi: 10.1371/journal.pone.0240647 PMID: 33112891; PMCID: 7592753

Chronopoulos A, Thorpe SD, Cortes E, Lachowski D, Rice AJ, Mykuliak VV, Róg T, Lee DA, Hytönen VP, Del Río Hernández AE (2020) Syndecan-4 tunes cell mechanics by activating the kindlin-integrin-RhoA pathway. Nat Mater. 2020 Jun;19(6):669-678. doi: 10.1038/s41563-019-0567-1 PMID: 31907416

Fedele C, Mäntylä E, Belardi B, Hamkins-Indik T, Cavalli S, Netti PA, Daniel Fletcher DA, Nymark S, Priimagi A & Ihalainen TO (2020) Azobenzene-based sinusoidal surface topography drives focal adhesion confinement and guides collective migration of epithelial cells. Scientific Reports volume 10, Article number: 15329 (2020). doi: 10.1038/s41598-020-71567-w PMID: 32948792; PMCID: 7501301

Kinaret PAS, Del Giudice G, Greco D (2020) Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us. Nano Today. 2020 Dec;35:100945. Epub 2020 Aug 10. doi: 10.1016/j.nantod.2020.100945 PMID: 32834832; PMCID: 7416770

Kinaret PAS, Scala G, Federico A, Sund J, Greco D. Small (2020) Carbon Nanomaterials Promote M1/M2 Macrophage Activation. 2020 May;16(21):e1907609. Epub 2020 Apr 6. PMID: 32250056. doi: 10.1002/smll.201907609 PMID: 32250056

Mykuliak VV, Sikora M, Booth JJ, Cieplak M, Shalashilin DV, Hytönen VP (2020) Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study. Biophys J. 2020 Sep 1;119(5):939-949. doi: 10.1016/j.bpj.2020.07.030 PMID: 32822586

Palma CSD, Kandavalli V, Bahrudeen MNM, Minoia M, Chauhan V, Dash S and Ribeiro AS (2020) Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms, 1863(5), 194515. doi: 10.1016/j.bbagrm.2020.194515 PMID: 32113983

Salminen TS & Vale PF (2020) Drosophila as a model system to investigate the effects of mitochondrial variation on innate immunity. Front. Immunol. 11:521. doi: 10.3389/fimmu.2020.00521 PMID: 32269576/

Szibor M, Gainutdinov T, Fernandez-Vizarra E, Gellerich F, Moore AL (2020) Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: Switch from RET and ROS to FET. Biochimica et Biophysica Acta – Bioenergetics, 2020, 1861(2), 148137. doi: 10.1016/j.bbabio.2019.148137 PMID: 31825809

Urbański LJ, Di Fiore A, Azizi L, Hytönen VP, Kuuslahti M, Buonanno M, Monti SM, Angeli A, Zolfaghari Emameh R, Supuran CT, De Simone G, Parkkila S (2020) Biochemical and structural characterisation of a protozoan beta-carbonic anhydrase from Trichomonas vaginalis. J Enzyme Inhib Med Chem. 2020 Dec;35(1):1292-1299. doi: 10.1080/14756366.2020.1774572 PMID: 32515610; PMCID: 7717681

Alarautalahti V, Ragauskas S, Hakkarainen J, Uusitalo-Järvinen H, Uusitalo H, Hyttinen J, Kalesnykas G, Nymark S. (2019) Viability of Mouse Retinal Explant Cultures Assessed by Preservation of Functionality and Morphology. Investigative Ophthalmology and Visual Science. 60:1914-1927. doi: 10.1167/iovs.18-25156 PMID: 31042799/

Figueirasa E, Silvestrea OF, Ihalainen TO, Niedera JB (2019) Phasor-assisted nanoscopy reveals differences in the spatial organization of major nuclear lamina proteins. Volume 1866, Issue 12, December 2019, 118530. doi: 10.1016/j.bbamcr.2019.118530 PMID: 31415840

Johansson JK, Karema-Jokinen VI, Hakanen S, Jylhä A, Uusitalo H, Vihinen-Ranta M, Skottman H, Ihalainen TO & Nymark S (2019) Sodium channels enable fast electrical signaling and regulate phagocytosis in the retinal pigment epithelium. BMC Biology, 17, Article number: 63. doi: https://doi.org/10.1186/s12915-019-0681-1 PMID: 31412898

Korkka I, Viheriälä T, Juuti-Uusitalo K, Uusitalo-Järvinen H, Skottman H, Hyttinen J, & Nymark S (2019) Functional Voltage-Gated Calcium Channels Are Present in Human Embryonic Stem Cell-Derived Retinal Pigment Epithelium. Stem Cells Translational Medicine. 8(2):179-193. doi: 10.1002/sctm.18-0026 PMID: 30394009; PMCID: 6344904

Rahikainen R, Öhman T, Turkki P, Varjosalo M, Hytönen VP (2019) Talin-mediated force transmission and talin rod domain unfolding independently regulate adhesion signaling. J Cell Sci. 2019 Apr 3;132(7):jcs226514. doi: 10.1242/jcs.226514 PMID: 30837291

Salminen TS, Cannino G, Oliveira MT, Lillsunde P, Jacobs HT, Kaguni LS (2019) Lethal interaction of nuclear and mitochondrial genotypes in Drosophila melanogaster. G3: GENES, GENOMES, GENETICS  9 (7): 2225-2234: doi: 10.1534/g3.119.400315 PMID: 31076384/; PMCID: 6643882

Valanne S*, Salminen TS*, Järvelä-Stölting, M, Vesala, L & Rämet, M (2019) Correction: Immune-inducible non-coding RNA molecule lincRNA-IBIN connects immunity and metabolism in Drosophila melanogaster. PLoS Pathog 15(1): e1007504. doi: 10.1371/journal.ppat.1008088 PMID: 31584999; PMCID: 6777747 *Shared first authorship

Ratnadiwakara M, Archer SK, Dent CI, Ruiz De Los Mozos I, Beilharz TH, Knaupp AS, Nefzger CM, Polo JM, Anko ML (2018) SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program. Elife. 2018 May 9;7:e37419. doi: http://10.7554/eLife.37419 PMID: 29741478

Kinaret P, Marwah V, Fortino V, Ilves M, Wolff H, Ruokolainen L, Auvinen P, Savolainen K, Alenius H, Greco D (2017) Network Analysis Reveals Similar Transcriptomic Responses to Intrinsic Properties of Carbon Nanomaterials in Vitro and in Vivo. ACS Nano. 2017 Apr 25;11(4):3786-3796. Epub 2017 Apr 11. doi: 10.1021/acsnano.6b08650 PMID: 28380293

Oittinen M, Popp A, Kurppa K, Lindfors K, Mäki M, Kaikkonen MU, Viiri K (2017) Polycomb Repressive Complex 2 Enacts Wnt Signaling in Intestinal Homeostasis and Contributes to the Instigation of Stemness in Diseases Entailing Epithelial Hyperplasia or Neoplasia. Stem Cells. 2017 Feb;35(2):445-457. Epub 2016 Sep 13. doi: 10.1002/stem.2479  PMCID: PMID: 27570105/

Patrikainen MS, Tolvanen MEE, Aspatwar A, Barker HR, Ortutay C, Jänis J, Laitaoja M, Hytönen VP, Azizi L, Manandhar P, Jáger E, Vullo D, Kukkurainen S, Hilvo M, Supuran CT, Parkkila S (2017) Identification and characterization of a novel zebrafish (Danio rerio) pentraxin-carbonic anhydrase. PeerJ. 2017 Dec 7;5:e4128. doi: 10.7717/peerj.4128 PMID: 29230365; PMCID: 5723433

Martínez-Reyes I, Diebold LP, Kong H, DeBerardinis RJ, Chandel NS (2016) TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions. Molecular Cell, 2016, 61(2), pp. 199–209. doi: 10.1016/j.molcel.2015.12.002 PMID: 26725009; PMCID: 4724312

Neeli-Venkata R, Startceva S, Annila T, and Ribeiro AS (2016) Polar Localization of the Serine Chemoreceptor of Escherichia coli is Nucleoid Exclusion-Dependent. Biophysical Journal 111(11), 2512–2522. doi: 10.1016/j.bpj.2016.10.024 PMID: 27926852

Ihalainen TO, Aires L, Herzog FA, Schwartlander R, Moeller J & Vogel V (2015) Differential basal-to-apical accessibility of lamin A/C epitopes in the nuclear lamina regulated by changes in cytoskeletal tension. Nature Materials volume 14, pages 1252–1261. doi: 10.1038/nmat4389 PMID: 26301768; PMCID: 4655446

Cannino G, El-Khoury R, Pirinen M, Jacobs HT, Dufour E (2012) Glucose modulates respiratory complex I activity in response to acute mitochondrial dysfunction. Journal of Biological Chemistry, 2012, 287(46), pp. 38729–38740. doi: 10.1074/jbc.M112.386060 PMID: 23007390; PMCID: 3493916

Lloyd-Price J, Gupta A, and Ribeiro AS (2012) SGNS2: A Compartmentalized Stochastic Chemical Kinetics Simulator for Dynamic Cell Populations. Bioinformatics, 28(22):3004-5. doi: 10.1093/bioinformatics/bts556 PMID: 23014631

Kanhere A, Viiri K, Araújo CC, Rasaiyaah J, Bouwman RD, Whyte WA, Pereira CF, Brookes E, Walker K, Bell GW, Pombo A, Fisher AG, Young RA, Jenner RG (2010) Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell. 2010 Jun 11;38(5):675-88. doi: 10.1016/j.molcel.2010.03.019 PMID: 20542000; PMCID: 2886029