CoE Publications 2015

Allahverdiyeva Y, Battchikova N, Brosché M, Fujii H, Kangasjärvi S, Mulo P, Mähönen AP, Nieminen K, Overmyer K, Salojärvi J and Wrzaczek M (2015) Integration of photosynthesis, development and stress as an opportunity for plant biology. NEW PHYTOLOGIST 208: 647-655 http://dx.doi.org/10.1111/nph.13549   open access

Allahverdiyeva Y, Isojärvi J, Zhang P and Aro EM (2015) Cyanobacterial Oxygenic Photosynthesis is protected by flavodiiron proteins. LIFE 5:716-743 http://dx.doi.org/10.3390/life5010716  open access

Allahverdiyeva Y, Suorsa M, Tikkanen M and Aro EM (2015) Photoprotection of photosystems in fluctuating light intensities. J EXP BOT 66:2427-36 http://dx.doi.org/10.1093/jxb/eru463

Antal TK, Krendeleva TE and Tyystjärvi E (2015) Multiple regulatory mechanisms in the chloroplast of green algae: relation to hydrogen production. PHOTOSYNTH RES 125: 357-381 http://dx.doi.org/10.1007/s11120-015-0157-2

Battchikova N, Angeleri M and Aro EM (2015) Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTH RES 126:47-70 http://dx.doi.org/10.1007/s11120-014-0050-4

Bourdais G, Burdiak P, Gauthier A, Nitsch L, Salojärvi J, Rayapuram C, Idänheimo N, Hunter K, Kimura S, Merilo E, Vaattovaara A, Oracz K, Kaufholdt D, Pallon A, Anggoro DT, Glów D, Lowe J, Zhou J, Mohammadi O, Puukko T, Albert A, Lang H, Ernst D, Kollist H, Brosché M, Durner J, Borst JW, Collinge DB, Karpiński S, Lyngkjær M, Robatzek S, Wrzaczek M and Kangasjärvi J (2015) Large-scale phenomics identifies primary and fine-tuning roles for CRKs in responses related to oxidative stress. PLOS GENETICS 7(11): e1005373. http://dx.doi.org/10.1371/journal.pgen.1005373  open access

Chukhutsina V, Bersanini L, Aro EM and van Amerongen H (2015) Cyanobacterial flv4-2 operon-encoded proteins optimize light harvesting and charge separation in photosystem II. MOLECULAR PLANT 8(5):747-761. http://dx.doi.org/10.1016/j.molp.2014.12.016

Chukhutsina V, Bersanini L, Aro EM and van Amerongen H (2015) Cyanobacterial light-harvesting phycobilisomes uncouple from photosystem I during dark-to-light transitions. SCIENTIFIC REPORTS 5: 14193 http://dx.doi.org/10.1038/srep14193

el-Showk S, Help-Rinta-Rahko H, Blomster T, Siligato R, Marée AF, Mähönen AP and Grieneisen VA (2015) Parsimonious Model of Vascular Patterning Links Transverse Hormone Fluxes to Lateral Root Initiation: Auxin Leads the Way, while Cytokinin Levels Out. PLOS COMPUT BIOL 11: e1004450 http://dx.doi.org/10.1371/journal.pcbi.1004450 open access

Fàbregas N, Formosa-Jordan P, Confraria A, Siligato R, Alonso JM, Swarup R, Bennett MJ, Mähönen AP, Caño-Delgado AI and Ibañes M (2015) Auxin influx carriers control vascular patterning and xylem differentiation in Arabidopsis thaliana. PLOS GENET 11: e1005183 http://dx.doi.org/10.1371/journal.pgen.1005183  open access

Gollan PJ, Tikkanen M and Aro EM (2015) Photosynthetic light reactions: integral to chloroplast retrograde signalling. CURRENT OPINION IN PLANT BIOLOGY 27:180-191 http://dx.doi.org/10.1016/j.pbi.2015.07.006

Grieco M, Suorsa M, Jajoo A, Tikkanen M and Aro EM (2015) Light-harvesting II antenna trimers connect energetically the entire photosynthetic machinery - including both photosystems II and I. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOENERGETICS 1847(6-7):607-619. http://dx.doi.org/10.1016/j.bbabio.2015.03.004

Isojärvi J, Shunmugam S, Sivonen K, Allahverdiyeva Y, Aro EM and Battchikova N (2015) Draft Genome Sequence of Calothrix 336/3, novel H2 Producing Cyanobacterium Isolated from Finnish Lake. GENOME ANNOUNC 3:e01474-14 http://dx.doi.org/10.1128/genomeA.01474-14 open access

Järvi S, Suorsa M and Aro EM (2015) Photosystem II repair in plant chloroplasts-Regulation, assisting proteins and shared components with photosystem II biogenesis. BIOCHIM BIOPHYS ACTA - BIOENERGETICS 847(9):900-9. http://dx.doi.org/10.1016/j.bbabio.2015.01.006 

Jokel M, Kosourov S, Battchikova N, Tsygankov AA, Aro EM and Allahverdiyeva Y (2015) Chlamydomonas Flavodiiron Proteins Facilitate Acclimation to Anoxia During Sulfur Deprivation. PLANT CELL PHYSIOL 56:1598-1607  http://dx.doi.org/10.1093/pcp/pcv085 Open access

Kammonen J, Smolander OP, Sipilä T, Overmyer K, Auvinen P and Paulin L (2015) Increased transcriptome sequencing efficiency with modified Mint-2 digestion-ligation protocol. ANALYTICAL BIOCHEMISTRY 477:38-40, http://dx.doi.org/10.1016/j.ab.2014.12.001

Kaurilind E, Xu E and Brosché M (2015) A genetic framework for H2O2 induced cell death in Arabidopsis thaliana. BMC GENOMICS 16:837 http://dx.doi.org/10.1186/s12864-015-1964-8  Open access

Khorobrykh SA, Karonen M and Tyystjärvi E (2015) Experimental evidence suggesting that H2O2 is produced within the thylakoid membrane in a reaction between plastoquinol and singlet oxygen. FEBS Letters 589: 779-786. http://dx.doi.org/10.1016/j.febslet.2015.02.011

Konert G, Rahikainen M, Trotta A, Durian G, Salojärvi J, Khorobrykh S, Tyystjärvi E and Kangasjärvi S (2015) Subunits B’γ and B’ζ of protein phosphatase 2A regulate photo-oxidative stress responses and growth in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 38:2641-2651 http://dx.doi.org/10.1111/pce.12575 

Konert G, Trotta A, Kouvonen P, Rahikainen M, Durian G, Blokhina O, Fagerstedt K, Muth D, Corthals GL and Kangasjärvi S (2015) Protein phosphatase 2A (PP2A) regulatory subunit B'γ interacts with cytoplasmic ACONITASE 3 and modulates the abundance of AOX1A and AOX1D in Arabidopsis thaliana. NEW PHYTOLOGIST 205:1250-1263 http://dx.doi.org/10.1111/nph.13097  open access

Lambreva MD, Lavecchia T, Tyystjärvi E, Antal TK, Orlanducci S, Margonelli A and Rea G (2015) Potential of carbon nanotubes in algal biotechnology. PHOTOSYNTHESIS RESEARCH 125: 451-471 http://dx.doi.org/10.1007/s11120-015-0168-z

Lehtimäki N, Koskela MM and Mulo P (2015) Post-translational modifications of chloroplast proteins: An emerging field. PLANT PHYSIOLOGY 168: 768-775. http://dx.doi.org/10.1104/pp.15.00117 open access

Lynch F, Santana-Sánchez A, Jämsä M, Sivonen K, Aro EM and Allahverdiyeva Y (2015) Screening native isolates of cyanobacteria and a green alga for integrated wastewater treatment, biomass accumulation and neutral lipid production. ALGAL RESEARCH 11:411-420 http://dx.doi.org/10.1016/j.algal.2015.05.015 [A1]  Open access

Mattila H, Khorobrykh S, Havurinne V and Tyystjärvi E (2015) Reactive oxygen species: Reactions and detection from photosynthetic tissues. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B: BIOLOGY 152: 176-214 http://dx.doi.org/10.1016/j.jphotobiol.2015.10.001

Mekala NR, Suorsa M, Rantala M, Aro EM and Tikkanen M (2015) Plants actively avoid state-transitions upon changes in light intensity - role of light-harvesting complex II protein dephosphorylation in high light.  PLANT PHYSIOLOGY 168(2):721-734. http://dx.doi.org/10.1104/pp.15.00488

Najafpour MM, Fekete M, Sedigh DJ, Aro EM, Carpentier R, Eaton-Rye, JJ, Nishihara H, Shen JR, Allakhverdiev S and Spiccia L (2015) Damage management in water-oxidizing catalysts: From Photosystem II to nano-sized metal oxides. - ACS CATALYSIS 5: 1499-1512. http://dx.doi.org/10.1021/cs5015157

Nath K, Najafpour MM, Voloshin RA, Balaghi SE, Tyystjärvi E, Timilsina R, Eaton-Rye JJ, Tomo T, Nam HG, Nishihara H, Ramakrishna S, Shen J-R and Allakhverdiev SI (2015) Photobiological hydrogen production and artificial photosynthesis for clean energy: From bio to nanotechnologies. PHOTOSYNTHESIS RESEARCH 126: 237-247 http://dx.doi.org/10.1007/s11120-015-0139-4

Nieminen K, Blomster T, Helariutta Y, Mähönen AP (2015) Vascular Cambium Development. Arabidopsis Book. 13: e0177 http://dx.doi.org/10.1199/tab.0177  open access

Ojanen S, Tyystjärvi E, Holmberg H and Ahtila P (2015) Porous membrane as a means of gas and nutrient exchange in a tubular photobioreactor. JOURNAL OF APPLIED PHYCOLOGY 27:1169-1175 http://dx.doi.org/10.1007/s10811-014-0397-0

Pahikkala T, Kari K, Mattila H, Lepistö A, Teuhola J, Nevalainen OS and Tyystjärvi E (2015) Classification of plant species from images of overlapping leaves. COMPUTERS AND ELECTRONICS IN AGRICULTURE 118: 186-192 doi:10.1016/j.compag.2015.09.003

Polishchuk A, Valev D, Tarvainen M, Mishra S, Kinnunen V, Antal T, Yang B, Rintala J and Tyystjärvi E (2015) Cultivation of Nannochloropsis for eicosapentaenoic acid production in wastewaters of pulp and paper industry. BIORESOURCE TECHNOLOGY 193: 469-476 http://dx.doi.org/10.1016/j.biortech.2015.06.135

Randall RS, Miyashima S, Blomster T, Zhang J, Elo A, Karlberg A, Immanen J, Nieminen K, Lee JY, Kakimoto T, Blajecka K, Melnyk CW, Alcasabas A, Forzani C, Matsumoto-Kitano M, Mähönen AP, Bhalerao R, Dewitte W, Helariutta Y and Murray JA (2015) AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins. BIOL OPEN 4:1229-36 http://dx.doi.org/10.1242/bio.013128   open access

Rinne PLH, Paul LK, Vahala J, Ruonala R, Kangasjärvi J and van der Schoot C (2015) Long and short photoperiod buds in hybrid aspen share structural development and expression patterns of marker genes. J. EXP. BOT 66:6745-6760 http://dx.doi.org/10.1093/jxb/erv380

Růžička K, Ursache R, Hejátko J, Helariutta Y (2015) Xylem development – from the cradle to the grave. NEW PHYTOLOGIST 207:519-35 http://dx.doi.org/10.1111/nph.13383  open access

Suorsa M (2015) Cyclic electron flow provides acclimatory plasticity for the photosynthetic machinery under various environmental conditions and developmental stages. FRONTIERS IN PLANT SCIENCE 6(800): 1- 8. http://dx.doi.org/10.3389/fpls.2015.00800

Suorsa M, Rantala M, Mamedov F, Lespinasse M, Trotta A, Grieco M, Vuorio E, Tikkanen M, Järvi S and Aro EM (2015) Light acclimation involves dynamic re-organisation of the pigment-protein megacomplexes in non-appressed thylakoid domains. THE PLANT JOURNAL 84:360-373 http://dx.doi.org/10.1111/tpj.13004

Tikkanen M, Rantala S and Aro EM (2015) Electron flow from PSII to PSI under high light is controlled by PGR5 but not by PSBS. FRONTIERS IN PLANT SCIENCE 6:1-6 http://dx.doi.org/10.3389/fpls.2015.00521

Urbischek M, von Braun SN, Brylok T, Gugel I, Richter A, Koskela M, Grimm B, Mulo P, Bölter B, Soll J, Ankele E and Schwenkert S (2015) The extreme Albino3 C is required for Alb3 stability in Arabidopsis thaliana. PLANTA 242:733-746. http://dx.doi.org/10.1007/s00425-015-2352-y

Vainonen JP and Kangasjärvi J (2015) Plant signaling in acute ozone exposure. PLANT CELL ENVIRON 38:240–252 http://dx.doi.org/10.1111/pce.12273

Wondraczec L, Tyystjärvi E, Méndez-Ramos J, Müller FA and Zhang O (2015) Shifting the Sun: Solar spectral conversion and extrinsic sensitization in natural and artificial photosynthesis. ADVANCED SCIENCE 2: 1500218 (pp. 1-13) http://dx.doi.org/10.1002/advs.201500218

Wrzaczek M, Vainonen JP, Stael S, Tsiatsiani L, Help-Rinta-Rahko H, Gauthier A, Kaufholdt D, Bollhöner B, Lamminmäki A, Staes A, Gevaert K, Tuominen H, Van Breusegem F, Helariutta Y and Kangasjärvi J (2015) GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis. EMBO J 32(1): 55-66 http://dx.doi.org/10.15252/embj.201488582  open access

Xu E, Vaahtera L and Brosché M (2015) Roles of Defense Hormones in the Regulation of Ozone-Induced Changes in Gene Expression and Cell Death. MOLECULAR PLANT 8:1776–1794 http://dx.doi.org/10.1016/j.molp.2015.08.008

Xu E, Vaahtera L, Hõrak H, Hincha DK, Heyer AG and Brosché M (2015) Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana. PLANT, CELL AND ENVIRONMENT 38:1418–1433 http://dx.doi.org/10.1111/pce.12499

Xuan W, Audenaert D, Parizot B, Möller BK, Njo MF, De Rybel B, De Rop G, Van Isterdael G, Mähönen AP, Vanneste S and Beeckman T (2015) Root Cap-Derived Auxin Pre-patterns the Longitudinal Axis of the Arabidopsis Root. CURRENT BIOLOGY 25:1381-1388 http://dx.doi.org/10.1016/j.cub.2015.03.046