Kristiina Himanen

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  1. Histone 2B monoubiquitination complex integrates transcript elongation with RNA processing at circadian clock and flowering regulators

    General information

    Publication statusPublished
    MoE publication typeA1 Journal article-refereed
    OrganisationsCSIC, Consejo Superior de Investigaciones Cientificas (CSIC), EEAD, Ghent University, Ghent University, University of Regensburg, University of Calabria, Autonomous University of Barcelona
    ContributorsWoloszynska, M., Le Gall, S., Neyt, P., Boccardi, T. M., Grasser, M., Laengst, G., Aesaert, S., Coussens, G., Dhondt, S., Van De Slijke, E., Bruno, L., Fung-Uceda, J., Mas, P., Van Montagu, M., Inze, D., Himanen, K., De Jaeger, G., Grasser, K. D., Van Lijsebettens, M.
    Number of pages10
    Pages8060-8069
    Publication date16 Apr 2019
    Peer-reviewedYes

    Publication information

    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume116
    Issue number16
    ISSN (Print)0027-8424
    Original languageEnglish
    Fields of ScienceH2Bub, HUB1 interactome, RNA-binding protein, RRM domain, KH domain, PRE-MESSENGER-RNA, H2B MONOUBIQUITINATION, LOCUS-C, ANTISENSE TRANSCRIPTS, CHROMATIN STATES, BINDING PROTEINS, SPEN PROTEINS, ARABIDOPSIS, FLC, REPRESSION, 1184 Genetics, developmental biology, physiology, 1182 Biochemistry, cell and molecular biology
    DOIs
    SourceWOS
    Source-ID000464767500068

    Research output: Contribution to journalArticleScientificpeer-review

  2. A transnational and holistic breeding approach is needed for sustainable wheat production in the Baltic Sea region

    General information

    Publication statusPublished
    MoE publication typeA2 Review article in a scientific journal
    OrganisationsViikki Plant Science Centre (ViPS), Plant Phenomics, Plant Production Sciences, Department of Agricultural Sciences, Organismal and Evolutionary Biology Research Programme, Helsinki Institute of Sustainability Science (HELSUS), Crop Science Research Group, Swedish University of Agricultural Sciences, Lantmannen Lantbruk, Aarhus University, University of Copenhagen, Lithuanian Research Centre for Agriculture and Forestry, Swedish Board of Agriculture, Yara Crop Nutrition, Estonian Crop Research Institute, Institute of Plant Breeding and Acclimatization, Poland, Nordic Genetic Resource Center
    ContributorsChawade, A., Armoniene, R., Berg, G., Brazauskas, G., Frostgard, G., Geleta, M., Gorash, A., Henriksson, T., Himanen, K., Ingver, A., Johansson, E., Jorgensen, L. N., Koppel, M., Koppel, R., Makela, P., Ortiz, R., Podyma, W., Roitsch, T., Ronis, A., Svensson, J. T., Vallenback, P., Weih, M.
    Number of pages10
    Pages442-451
    Publication dateDec 2018
    Peer-reviewedYes

    Publication information

    JournalPhysiologia Plantarum
    Volume164
    Issue number4
    ISSN (Print)0031-9317
    Ratings
    • Scopus rating (2018): SJR 1.23 SNIP 1.016
    Original languageEnglish
    Fields of ScienceFIELD CROPS, FREEZING TOLERANCE, GENOMIC SELECTION, NITROGEN, EFFICIENCY, IMPACT, MODEL, PREDICTION, PHENOMICS, GENOTYPE, 1184 Genetics, developmental biology, physiology, 1182 Biochemistry, cell and molecular biology, 1183 Plant biology, microbiology, virology
    Electronic versions
    DOIs
    SourceWOS
    Source-ID000453411500009

    Research output: Contribution to journalReview ArticleScientificpeer-review

  3. Nordic research infrastructures for plant phenotyping

    General information

    Publication statusPublished
    MoE publication typeA2 Review article in a scientific journal
    OrganisationsViikki Plant Science Centre (ViPS), Plant Phenomics, Department of Agricultural Sciences, Plant Production Sciences, PlantLink, University of Eastern Finland (UEF), Swedish University of Agricultural Sciences, Swedish University of Agricultural Sciences, National Plant Phenotyping Infrastructure
    ContributorsAlexandersson, E., Keinanen, M., Chawade, A., Himanen, K.
    Number of pages10
    Pages7-16
    Publication date2018
    Peer-reviewedYes

    Publication information

    JournalAgricultural and Food Science
    Volume27
    Issue number1
    ISSN (Print)1459-6067
    Ratings
    • Scopus rating (2018): SJR 0.423 SNIP 0.847
    Original languageEnglish
    Fields of Scienceplant phenomics, climate control, imaging sensors, growth facilities, networking, QUANTITATIVE TRAIT LOCI, THROUGHPUT, ARABIDOPSIS, PLATFORM, 1183 Plant biology, microbiology, virology
    Electronic versions
    URLs
    SourceWOS
    Source-ID000428950900002

    Research output: Contribution to journalReview ArticleScientificpeer-review

  4. Functional Analysis of the Arabidopsis TETRASPANIN Gene Family in Plant Growth and Development

    General information

    Publication statusPublished
    MoE publication typeA1 Journal article-refereed
    OrganisationsDepartment of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Arcavacata of Rende, Italy, Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium, Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium, Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium, Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
    ContributorsWang, F., Muto, A., Van de Velde, J., Neyt, P., Himanen, K., Vandepoele, K., Van Lijsebettens, M.
    Publication date2015
    Peer-reviewedYes

    Publication information

    JournalPlant Physiology
    ISSN (Print)0032-0889
    Ratings
    • Scopus rating (2015): SJR 3.597 SNIP 1.786
    Original languageEnglish

    Research output: Contribution to journalArticleScientificpeer-review

  5. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

    General information

    Publication statusPublished
    MoE publication typeA1 Journal article-refereed
    OrganisationsBiosciences, Viikki Plant Science Centre (ViPS), Institute of Biotechnology, Bioinformatics for Molecular Biology and Genomics (BMBG), Plant-Fungal Interactions Group, Plant ROS-Signalling, Department of Forest Sciences, Department of Agricultural Sciences, Plant stress and natural variation, Ecosystem processes/ Jaana Bäck, Asteraceae developmental biology and secondary metabolism, Plant Production Sciences, Tapio Palva Research Group, Environmental Sciences, Terrestrial Interactions Research Group, Finnish Museum of Natural History, Botany, Embryophylo, Receptor-Ligand Signaling Group, DNA Sequencing and Genomics, Forest Ecology and Management, University of Eastern Finland (UEF), Tartu University, USDA ARS, United States Department of Agriculture (USDA), University of Turku, Norwegian University of Life Sciences, University of Oulu, Oulu, Uppsala University, University of Buffalo, University of Eastern Finland, Kuopio, Umeå University, Russian Academy of Sciences,, Natural Resources Institute Finland (LUKE), University of Cambridge, University of Eastern Finland, National Botanic Gardens of Ireland, Glasnevin, King’s College London (KCL), University of Tartu, University of Buffalo, Estonian University of Life sciences
    ContributorsSalojärvi, J., Smolander, O., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., Lamminmäki, A., Immanen, J., Lan, T., Tanskanen, J., Rastas, P., Amiryousefi, A., Jayaprakash, B., Kammonen, J. I., Hagqvist, R., Eswaran, G., Ahonen, V. H., Serra, J. A., Asiegbu, F. O., Barajas-Lopez, J. D. D., Blande, D., Blokhina, O., Blomster, T., Broholm, S., Brosche, M., Cui, F., Dardick, C., Ehonen, S. E., Elomaa, P., Escamez, S., Fagerstedt, K. V., Fujii, H., Gauthier, A., Gollan, P. J., Halimaa, P., Heino, P. I., Himanen, K., Hollender, C., Kangasjarvi, S., Kauppinen, L., Kelleher, C. T., Kontunen-Soppela, S., Koskinen, J. P., Kovalchuk, A., Karenlampi, S. O., Kärkönen, A. K., Lim, K., Leppälä, J., Macpherson, L., Mikola, J., Mouhu, K., Mähönen, A. P., Niinemets, U., Oksanen, E., Overmyer, K., Palva, E. T., Pazouki, L., Pennanen, V., Puhakainen, T., Poczai, P., Possen, B. J. H. M., Punkkinen, M., Rahikainen, M. M., Rousi, M., Ruonala, R., van der Schoot, C., Shapiguzov, A., Sierla, M., Sipilä, T. P., Sutela, S., Teeri, T. H., Tervahauta, A. I., Vaattovaara, A., Vahala, J., Vetchinnikova, L., Welling, A., Wrzaczek, M., Xu, E., Paulin, L. G., Schulman, A. H., Lascoux, M., Albert, V. A., Auvinen, P., Helariutta, Y., Kangasjarvi, J.
    Number of pages12
    Pages904-912
    Publication date8 May 2017
    Peer-reviewedYes

    Publication information

    JournalNature Genetics
    Volume49
    Issue number6
    ISSN (Print)1061-4036
    Ratings
    • Scopus rating (2017): SJR 22.243 SNIP 5.972
    Original languageEnglish
    Fields of ScienceARABIDOPSIS-THALIANA, TRANSCRIPTION FACTOR, BETULA-PUBESCENS, CAMBIAL ACTIVITY, FLOWERING TIME, PHYTOCHROME-C, CYTOKININ, SIZE, EVOLUTION, PLANTS, 1184 Genetics, developmental biology, physiology
    Electronic versions
    DOIs
    SourceWOS
    Source-ID000402062300015

    Research output: Contribution to journalArticleScientificpeer-review

  6. Genomic and phenomic screens for flower related RING type ubiquitin E3 ligases in Arabidopsis

    Flowering time control integrates endogenous as well as environmental signals to promote flower
    development. The pathways and molecular networks involved are complex and integrate many
    modes of signal transduction. In plants ubiquitin mediated protein degradation pathway has been
    proposed to be as important mode of signaling as phosphorylation and transcription. To
    systematically study the role of ubiquitin signaling in the molecular regulation of flowering we
    have taken a genomic approach to identify flower related Ubiquitin Proteasome System
    components. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosen
    as targets of the genomic screen. To this end the complete list of Arabidopsis RING E3 ligases
    were retrieved and verified in the Arabidopsis genome v11. Their differential expression was used
    for their categorization into flower organs or developmental stages. Known regulators of flowering
    time or floral organ development were identified in these categories through literature search and
    representative mutants for each category were purchased for functional characterization by growth
    and morphological phenotyping. To this end, a workflow was developed for high throughput
    phenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsis
    plants in one experimental round.

    General information

    Publication statusPublished
    MoE publication typeA1 Journal article-refereed
    OrganisationsDepartment of Agricultural Sciences, Plant Phenomics, Biosciences, Viikki Plant Science Centre (ViPS), Asteraceae developmental biology and secondary metabolism, Plant Production Sciences
    ContributorsPavicic, M., Mouhu, K., Wang, F., Bilicka, M. M., Chovanček, E., Himanen, K. I. H.
    Number of pages17
    Publication date28 Mar 2017
    Peer-reviewedYes

    Publication information

    JournalFrontiers in plant science
    Volume8
    Article number in E-publication (not DOI)416
    ISSN (Print)1664-462X
    Ratings
    • Scopus rating (2017): SJR 1.731 SNIP 1.232
    Original languageEnglish
    Fields of Science414 Agricultural biotechnology (Arabidopsis, flower, RING E3 ligase, ubiquitin, high throughput, image based phenotyping, phenomics data analysis, ZINC-FINGER PROTEIN, PROTEASOME SYSTEM, GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, CONSTANS EXPRESSION, GENE-EXPRESSION, GABI-KAT, THALIANA, plant, time, information)
    Electronic versions
    DOIs

    Research output: Contribution to journalArticleScientificpeer-review

  7. Haastattelututkimus molekyylibiotieteellisiltä aloilta valmistuneiden tohtoreiden kokemuksista koulutuksen ja työelämän vastaavuuksista.

    Employment of PhDs from the biological fields appears to be facing challenges outside academia. This interview study was conducted to analyze the experiences of PhD graduates from the fields of molecular biosciences on how the research education prepared them to the working life outside academia, and how well the studies did match with the expectations and demands in the working life. In this interview study the working life skills were categorized as 1) research skills, 2) generic skills and 3) application of biological world view. In general, the research training gave good background to work as a well-respected experts in different fields. However, the lack of direct match between the fields of research training and the job description had demanded additional training from each PhD who had moved outside the academia.

    General information

    Publication statusPublished
    MoE publication typeD2 Article in professional manuals or guides or professional information systems or text book material
    OrganisationsDepartment of Agricultural Sciences, Biosciences, Viikki Plant Science Centre (ViPS), Plant Production Sciences
    ContributorsHimanen, K. I. H.
    Number of pages19
    Pages33-51
    Publication date2016

    Host publication information

    Title of host publicationTeaching in Life Sciences: Current practices and development
    Volume2

    Publication series

    NameTeaching in Life Sciences: Current practices and development
    Volume2
    ISSN (Electronic)2343-1822

    Research output: Chapter in Book/Report/Conference proceedingChapterProfessional

  8. Didaktinen essee biotekniikan yliopisto-opetuksesta

    Tässä esseessä pohditaan biotekniikan alan yliopisto-opetuksen didaktiikkaa. Määritelmän mukaan didaktiikka käsittää oppiaineiden opetussuunnitelmia, käytettävissä olevia opetusmenetelmiä ja oppiainekohtaista opetusta ja sen kehittämistä (Uusikylä & Atjonen, 2005). Yliopisto-opetuksen didaktiikassa erityispiirteenä on tutkimuksellisuuden korostuminen ja kunkin tieteenalan vaikutus oppiaineeseen (Neumann 2002). Johtuen juuri näistä tieteenalojen rakenteiden ja suuntauksien eroista, ei voidakaan puhua yhtenäisestä yliopistodidaktiikasta. Tässä esseessä keskitytään biotieteellisen biotekniikan didaktiikkaan ja tarkastellaan erityisesti laboratoriokurssien merkitystä biotekniikan yliopisto-opetuksessa. Biotieteiden alojen tiedon kertyminen on nopeatempoista ja uutta tutkimustietoa julkaistaan kuukausittain useissa molekyylibiologian alan julkaisusarjoissa. On arvioitu, että biotieteellinen tietomäärä kaksinkertaistuu noin viiden vuoden välein (Efferth, 2001). Tämä jatkuva uuden tiedon kertyminen asettaa erityisiä haasteita tieteellisen tutkimustiedon seuraamiselle ja kyvylle reagoida uusiutuvaan tietoon. Alan aktiivisuuden ja tutkimuksen intensiivisyyden vuoksi biotieteiden opetuksessa tutkimuksellisuus on erityisen korostunutta osittain ehkä opetuksen kehittämisen kustannuksella. Tämän suuntauksen puolesta puhuu myös se, että opetuksessa käytetään erityisen paljon uusimpia tieteellisiä julkaisuja eikä niinkään kirjoja, joiden tiedot vanhentuvatkin nopeasti. Tieto sinänsä ei vanhene tai muutu mutta täydentyy ja syvenee nopeassa tahdissa. Mielestäni tärkeä pohdinnan kohde on opettajan didaktinen moraali; se kuvastanee panostusta opetukseen ja siten myös opetuksen arvostusta. Halutaanko yliopisto-opiskelijoille tarjota parasta mahdollista tutkijakoulutusta, onko käytössä riittävästi resursseja opetuksen uudistamiseen samassa tahdissa tutkimuksen uusiutumisen kanssa. Olisi toivottavaa, että myös luento ja kurssi opetuksessa pystyttäisiin reagoimaan alan nopeaan kehitykseen. Kehitysehdotuksena pohdin, miten tutkimusperusteinen opetus voisi auttaa tässä ja mahdollisesti vielä motivoida opetuksen molempia osapuolia.

    General information

    Publication statusPublished
    MoE publication typeD2 Article in professional manuals or guides or professional information systems or text book material
    OrganisationsDepartment of Agricultural Sciences, Plant Phenomics, Viikki Plant Science Centre (ViPS), Plant Production Sciences, Yliopistopedagogiikan tutkimus- ja kehittämisyksikkö
    ContributorsHimanen, K. I. H.
    Number of pages7
    Pages2-8
    Publication date22 Dec 2015

    Host publication information

    Title of host publicationEsseitä tieteenalakohtaisesta opetuksesta lukuvuosilta 2013-2015
    Place of publicationHelsinki
    PublisherHelsingin yliopisto, Yliopistopedagogiikan tutkimus- ja kehittämisyksikkö
    EditorsLahtinen, A., Lindfors, B.
    Fields of Science414 Agricultural biotechnology
    URLs

    Research output: Chapter in Book/Report/Conference proceedingChapterProfessional

  9. Kasvibiotekniikka täyttää tänä vuonna 30 vuotta (mutta ei juhli)

    General information

    Publication statusPublished
    MoE publication typeE1 Popularised article, newspaper article
    OrganisationsDepartment of Agricultural Sciences, Plant Phenomics, Viikki Plant Science Centre (ViPS), Asteraceae developmental biology and secondary metabolism, Plant Production Sciences
    ContributorsHimanen, K., Pietiäinen, M. I.
    Publication date9 Jan 2014

    Host publication information

    Title of host publicationmaataloustieteen päivät
    Fields of Science4111 Agronomy
    URLs

    Research output: Chapter in Book/Report/Conference proceedingChapterGeneral public

  10. Histone H2B monoubiquitination is required to reach maximal transcript levels of circadian clock genes in Arabidopsis

    General information

    Publication statusPublished
    MoE publication typeA1 Journal article-refereed
    OrganisationsDepartment of Plant Systems Biology, Ghent, Ghent University
    ContributorsHimanen, K., Woloszynska, M., Boccardi, T. M., Groeve, S. D., Nelissen, H., Bruno, L., Vuylsteke, M., Lijsebettens, M. V.
    Number of pages12
    Pages249-260
    Publication date2012
    Peer-reviewedYes

    Publication information

    JournalPlant Journal
    Volume72
    Issue number2
    ISSN (Print)0960-7412
    Ratings
    • Scopus rating (2012): SJR 4.385 SNIP 1.684
    Original languageEnglish
    Fields of Sciencemicroarrays, flowering date, degradation, mutations, flowering, genes, effects, cell cycle, ubiquitin, dormancy, mutants, ligases, anthesis, acetylation, embryos, phenotypes, gene expression, synergists, chromatin, 1184 Genetics, developmental biology, physiology, 414 Agricultural biotechnology
    DOIs
    Sourceovid.caba
    Source-ID20123362716

    Research output: Contribution to journalArticleScientificpeer-review

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