Selected articles citing the Proteomics Facility

Rahikainen, M., Trotta, A., Alegre, S., Pascual, J., Vuorinen, K., Overmyer, K., Moffatt, B., Ravanel, S., Glawischnig, E. and Kangasjärvi, S. (2016), PP2A-B’γ modulates foliar trans-methylation capacity and formation of 4-methoxy-indol-3-yl-methyl glucosinolate in Arabidopsis leaves. Plant J. Accepted Author Manuscript. doi:10.1111/tpj.13326 [PubMed]

Martinez-Brave MJ, Wahlund CJ, Qazi KR, Moulder R, Lukic A, Rådmark O, Lahesmaa R, Grunewald J, Eklund A, Gabrielsson S. Pulmonary Sarcoidosis is Associated With Exosomal Vitamin D-Binding Protein and Inflammatory Molecules. J Allergy Clin Immunol. 2016 Aug 23. pii: S0091-6749(16)30850-8. [Epub ahead of print] [PubMed]

Soderholm S, Kainov DE, Ohman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA. Phosphoproteomics to characterize host response during influenza A virus infection of human macrophages. Mol Cell Proteomics. 2016 Aug 2. doi: 10.1074/mcp.M116.057984. [Epub ahead of print] [PubMed]

Santio NM, Landor SK, Vahtera L, Ylä-Pelto J, Paloniemi E, Imanishi SY, Corthals G, Varjosalo M, Manoharan GB, Uri A, Lendahl U, Sahlgren C, Koskinen PJ. Phosphorylation of Notch1 by Pim kinases promotes oncogenic signaling in breast and prostate cancer cells. Oncotarget. 2016 May 7. doi: 10.18632/oncotarget.9215. [Epub ahead of print] [PubMed]

Trotta A, Suorsa M, Rantala M, Lundin B, Aro EM. Serine and threonine residues of plant STN7 kinase are differentially phosphorylated upon changing light conditions and specifically influence the activity and stability of the kinase. Plant J. 2016 May 23. doi: 10.1111/tpj.13213. [Epub ahead of print] [PubMed]

Grouneva I, Muth-Pawlak D, Battchikova N, Aro EM. Changes in Relative Thylakoid Protein Abundance Induced by Fluctuating Light in the Diatom Thalassiosira pseudonana. J Proteome Res. 2016 May 6;15(5):1649-58. doi: 10.1021/acs.jproteome.6b00124 Epub 2016 Apr 19. [PubMed]

Mustila H, Paananen P, Battchikova N, Santana-Sánchez A, Muth-Pawlak D, Hagemann M, Aro EM, Allahverdiyeva Y. The Flavodiiron Protein Flv3 Functions as a Homo-Oligomer During Stress Acclimation and is Distinct from the Flv1/Flv3 Hetero-Oligomer Specific to the O2 Photoreduction Pathway. Plant Cell Physiol. 2016 Mar 2. pii:pcw047. [Epub ahead of print] [PubMed]

Landowski CP, Huuskonen A, Wahl R, Westerholm-Parvinen A, Kanerva A, Hänninen AL, Salovuori N, Penttilä M, Natunen J, Ostermeier C, Helk B, Saarinen J, Saloheimo M. Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei. PLoS One. 2015 Aug 26;10(8):e0134723. [PubMed]

Moulder R, Bhosale SD, Erkkilä T, Laajala E, Salmi J, Nguyen EV, Kallionpää H, Mykkänen J, Vähä-Mäkilä M, Hyöty H, Veijola R, Ilonen J, Simell T, Toppari J, Knip M, Goodlett DR, Lähdesmäki H, Simell O, Lahesmaa R. Serum Proteomes Distinguish Children Developing Type 1 Diabetes in a Cohort with HLA-Conferred Susceptibility. Diabetes. 2015 Jun;64(6):2265-78. Epub 2015 Jan 23. [PubMed]

Kanerva M, Vehmas A, Nikinmaa M, Vuori KA. Spatial Variation in Transcript and Protein Abundance of Atlantic Salmon during Feeding Migration in the Baltic Sea. Environ Sci Technol. 2014 Dec 2;48(23):13969-77. [PubMed]

Papakostas S, Vøllestad LA, Bruneaux M, Aykanat T, Vanoverbeke J, Ning M, Primmer CR, Leder EH. Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions. Nat Commun. 2014 Jun 3;5:4071. [PubMed]

Li S, Mhamdi A, Trotta A, Kangasjärvi S, Noctor G. The protein phosphatase subunit PP2A-B’γ is required to suppress day length-dependent pathogenesis responses triggered by intracellular oxidative stress. New Phytol. 2014 Apr;202(1):145-60. Epub 2013 Dec 2. [PubMed]

Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JA, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP. Zebavidin – an avidin-like protein from zebrafish. PLoS One. 2013 Oct 24;8(10):e77207. eCollection 2013. [PubMed]

Lehti MS, Kotaja N, Sironen A. KIF3A is essential for sperm tail formation and manchette function. Mol Cell Endocrinol. 2013 Sep 5;377(1-2):44-55. Epub 2013 Jul 2. [PubMed]

Paino A, Ahlstrand T, Nuutila J, Navickaite I, Lahti M, Tuominen H, Välimaa H, Lamminmäki U, Pöllänen MT, Ihalin R. Identification of a novel bacterial outer membrane interleukin-1Β-binding protein from Aggregatibacter actinomycetemcomitans. PLoS One. 2013 Jul 31;8(7):e70509. Print 2013. [PubMed]

Leskinen PK, Laaksonen T, Ruuskanen S, Primmer CR, Leder EH. The proteomics of feather development in pied flycatchers (Ficedula hypoleuca) with different plumage coloration. Mol Ecol. 2012 Dec;21(23):5762-77. Epub 2012 Oct 30. [PubMed]

Paino A, Lohermaa E, Sormunen R, Tuominen H, Korhonen J, Pöllänen MT, Ihalin R. Interleukin-1β is internalised by viable Aggregatibacter actinomycetemcomitans biofilm and locates to the outer edges of nucleoids. Cytokine. 2012 Nov;60(2):565-74. Epub 2012 Aug 13. [PubMed]

Björkblom B, Padzik A, Mohammad H, Westerlund N, Komulainen E, Hollos P, Parviainen L, Papageorgiou AC, Iljin K, Kallioniemi O, Kallajoki M, Courtney MJ, Mågård M, James P, Coffey ET. c-Jun N-terminal kinase phosphorylation of MARCKSL1 determines actin stability and migration in neurons and in cancer cells. Mol Cell Biol. 2012 Sep;32(17):3513-26. Epub 2012 Jul 2. [PubMed]

Arvas M, Pakula T, Smit B, Rautio J, Koivistoinen H, Jouhten P, Lindfors E, Wiebe M, Penttilä M, Saloheimo M. Correlation of gene expression and protein production rate – a system wide study. BMC Genomics. 2011 Dec 20;12:616. [PubMed]

Kouki A, Haataja S, Loimaranta V, Pulliainen AT, Nilsson UJ, Finne J. Identification of a novel streptococcal adhesin P (SadP) recognizing galactosyl-{alpha}1-4-galactose-containing glycoconjugates: convergent evolution of bacterial pathogens to binding of the same host receptor. J Biol Chem. 2011 Nov 11;286(45):38854-64. Epub 2011 Sep 9. [PubMed]

Battchikova N, Wei L, Du L, Bersanini L, Aro EM, Ma W. Identification of novel Ssl0352 protein (NdhS), essential for efficient operation of cyclic electron transport around photosystem I, in NADPH:plastoquinone oxidoreductase (NDH-1) complexes of Synechocystis sp. PCC 6803. J Biol Chem. 2011 Oct 21;286(42):36992-7001. Epub 2011 Aug 31. [PubMed]

Viitaniemi HM, Leder EH. Sex-biased protein expression in threespine stickleback, Gasterosteus aculeatus. J Proteome Res. 2011 Sep 2;10(9):4033-40. Epub 2011 Jul 21. [PubMed]

Huttunen R, Shweta, Martikkala E, Lahdenranta M, Virta P, Hänninen P, Härmä H. Single-label time-resolved luminescence assay for estrogen receptor-ligand binding. Anal Biochem. 2011 Aug 1;415(1):27-31. Epub 2011 Apr 6. [PubMed]

Trotta A, Wrzaczek M, Scharte J, Tikkanen M, Konert G, Rahikainen M, Holmström M, Hiltunen HM, Rips S, Sipari N, Mulo P, Weis E, von Schaewen A, Aro EM, Kangasjärvi S. Regulatory subunit B’gamma of protein phosphatase 2A prevents unnecessary defense reactions under low light in Arabidopsis. Plant Physiol. 2011 Jul;156(3):1464-80. Epub 2011 May 12. [PubMed]

Soitamo AJ, Jada B, Lehto K. HC-Pro silencing suppressor significantly alters the gene expression profile in tobacco leaves and flowers. BMC Plant Biol. 2011 Apr 20;11:68. [PubMed]

Vähämaa H, Koskinen VR, Hosia W, Moulder R, Nevalainen OS, Lahesmaa R, Aittokallio T, Salmi J. PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use.Int J Proteomics. 2011;2011:450290. Epub 2011 Apr 19. [PubMed]

Paino A, Tuominen H, Jääskeläinen M, Alanko J, Nuutila J, Asikainen SE, Pelliniemi LJ, Pöllänen MT, Chen C, Ihalin R. Trimeric form of intracellular ATP synthase subunit β of Aggregatibacter actinomycetemcomitans binds human interleukin-1β. PLoS One. 2011 Apr 18;6(4):e18929. [PubMed]

Chen Z, Buki K, Vääräniemi J, Gu G, Väänänen HK. The critical role of IL-34 in osteoclastogenesis. PLoS One. 2011 Apr 8;6(4) [PubMed]

Battchikova N, Vainonen JP, Vorontsova N, Keränen M, Carmel D, Aro EM. Dynamic Changes in the Proteome of Synechocystis 6803 in Response to CO(2) Limitation Revealed by Quantitative Proteomics. J Proteome Res. 2010 Sep 20. [PubMed]

Papakostas S, Vøllestad LA, Primmer CR, Leder EH. Proteomic profiling of early life stages of European grayling (Thymallus thymallus).J Proteome Res. 2010 Sep 3;9(9):4790-800. [PubMed]

Meikar O, Da Ros M, Liljenbäck H, Toppari J, Kotaja N. Accumulation of piRNAs in the chromatoid bodies purified by a novel isolation protocol. Exp Cell Res. 2010 May 15;316(9):1567-75. Epub 2010 Feb 26. [PubMed]

Jaspers P, Overmyer K, Wrzaczek M, Vainonen JP, Blomster T, Salojärvi J, Reddy RA, Kangasjärvi J. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. BMC Genomics. 2010 Mar 12;11:170. [PubMed]

Tuomela S, Rautajoki KJ, Moulder R, Nyman TA, Lahesmaa R. Identification of novel Stat6 regulated proteins in IL-4-treated mouse lymphocytes. Proteomics. 2009 Feb;9(4):1087-98. [PubMed]

Mäkinen S, Kelloniemi J, Pihlanto A, Mäkinen K, Korhonen H, Hopia A, Valkonen JP. Inhibition of Angiotensin converting enzyme I caused by autolysis of potato proteins by enzymatic activities confined to different parts of the potato tuber. J Agric Food Chem. 2008 Nov 12;56(21):9875-83. Epub 2008 Oct 9. [PubMed]

Sirpiö S, Allahverdiyeva Y, Holmström M, Khrouchtchova A, Haldrup A, Battchikova N, Aro EM. Novel nuclear-encoded subunits of the chloroplast NAD(P)H dehydrogenase complex. J Biol Chem. 2009 Jan 9;284(2):905-12. Epub 2008 Oct 28. [PubMed]

Vainonen JP, Sakuragi Y, Stael S, Tikkanen M, Allahverdiyeva Y, Paakkarinen V, Aro E, Suorsa M, Scheller HV, Vener AV, Aro EM. Light regulation of CaS, a novel phosphoprotein in the thylakoid membrane of Arabidopsis thaliana. FEBS J. 2008 Apr;275(8):1767-77. Epub 2008 Mar 7. [PubMed]

Hellman J. Polyacrylamide lamination enables mass spectrometry compatible staining and in-gel digestion of proteins separated by agarose IEF.Proteomics. 2007 Oct;7(19):3441-4 [PubMed]

Imanishi SY, Kochin V, Eriksson JE. Optimization of phosphopeptide elution conditions in immobilized Fe(III) affinity chromatography. Proteomics. 2007 Jan;7(2):174-6. [PubMed]

Rautajoki KJ, Marttila EM, Nyman TA, Lahesmaa R. Interleukin-4 inhibits caspase-3 by regulating several proteins in the Fas pathway during initial stages of human T helper 2 cell differentiation. Mol Cell Proteomics. 2007 Feb;6(2):238-51. Epub 2006 Nov 17. [PubMed]

Kochin V, Imanishi SY, Eriksson JE. Fast track to a phosphoprotein sketch – MALDI-TOF characterization of TLC-based tryptic phosphopeptide maps at femtomolar detection sensitivity. Proteomics. 2006 Nov;6(21):5676-82. [PubMed]

Tararuk T, Ostman N, Li W, Björkblom B, Padzik A, Zdrojewska J, Hongisto V, Herdegen T, Konopka W, Courtney MJ, Coffey ET. JNK1 phosphorylation of SCG10 determines microtubule dynamics and axodendritic length. J Cell Biol. 2006 Apr 24;173(2):265-77. Epub 2006 Apr 17. [PubMed]

Papageorgiou AC, Saarinen S, Ramirez-Bartutis R, Kato H, Uchiyama T, Kirikae T, Miyoshi-Akiyama T. Expression, purification and crystallization of Streptococcus dysgalactiae-derived mitogen. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.2006 Mar 1;62(Pt 3):242-4. Epub 2006 Feb 10. [PubMed]

Kurian D, Jansèn T, Mäenpää P. Proteomic analysis of heterotrophy in Synechocystis sp. PCC 6803. Proteomics. 2006 Mar;6(5):1483-94. [PubMed]

Salmi J, Moulder R, Filén JJ, Nevalainen OS, Nyman TA, Lahesmaa R, Aittokallio T. Quality classification of tandem mass spectrometry data. Bioinformatics. 2006 Feb 15;22(4):400-6. Epub 2005 Dec 13. [PubMed]

Björkblom B, Ostman N, Hongisto V, Komarovski V, Filén JJ, Nyman TA, Kallunki T, Courtney MJ, Coffey ET. Constitutively active cytoplasmic c-Jun N-terminal kinase 1 is a dominant regulator of dendritic architecture: role of microtubule-associated protein 2 as an effector. J Neurosci. 2005 Jul 6;25(27):6350-61. [PubMed]

Moulder R, Filén JJ, Salmi J, Katajamaa M, Nevalainen OS, Oresic M, Aittokallio T, Lahesmaa R, Nyman TA. A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics. 2005 Jul;5(11):2748-60. [PubMed]