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University of Helsinki Institute of Biotechnology
 
Institute of Biotechnology
DNA Sequencing and Genomics

Research Director:
Petri Auvinen
Tel +358 (0) 2941 58902
e-mail petri.auvinen -at- helsinki.fi

Laboratory Engineer:
Lars Paulin
Tel +358 (0) 2941 58887
e-mail lars.paulin -at- helsinki.fi

Viikinkaari 5D
(Biocenter 2, 4th floor)
P.O.Box 56
FIN-00014 University of Helsinki

Tel +358 (0) 2941 58884

Sequencing service e-mail:
bio-alf -at- helsinki.fi

Institute of Biotechnology
Street address: Viikinkaari 5D (P.O.Box 56)
00014 University of Helsinki
Finland
Tel: +358 (0) 294 1911
Tel: +358 (0) 2941 4482624

Business Identity Code:
FI-03134717
(University of Helsinki)

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Telephone directory
(all contact information included)

E-mail directory

Publications from Users

Short list of some of the publications in which our services have been used. Please inform us of your publications in which you have used our services or machinery (petri.auvinen -at- helsinki.fi).

 

Array hybridizations

Ahlfors R., Brosché M., Kollist H. and Kangasjärvi J. (2009) Nitric oxide modulates ozone-induced cell death, hormone biosynthesis and gene expression in Arabidopsis thaliana. Plant J. 58: 1-12.

Jaspers P., Blomster T., Brosché M., Salojärvi J., Ahlfors R., Vainonen J., Reddy R., Immink R., Angenent G., Turck F., Overmyer K. and Kangasjärvi J. (2009) Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. Plant J. In press

Vahisalu T., Kollist H., Wang Y.-F., Chan W.-Y., Valerio G., Lamminmäki A., Brosché M., Moldau H., Desikan R., Schroeder J.I. and Kangasjärvi J. (2008) SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling. Nature. 452: 487-491

Bogeat-Triboulot M.-B., Brosché M., Renaut J., Jouve L., Le Thiec D., Fayyaz P., Vinocur B., Witters E., Laukens K., Teichmann T., Altman A., Hausman J.-F., Polle A., Kangasjärvi J. and Dreyer E. (2007) Gradual Soil Water Depletion Results in Reversible Changes of Gene Expression, Protein Profiles, Ecophysiology, and Growth Performance in Populus euphratica, a Poplar Growing in Arid Regions. Plant Physiol. 143: 876-892

Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks R, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman AH, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R (2006). An atlas of gene expression from seed to seed through barley development. Funct. Integr. Genomics, 6: 202–211.

Ahlfors R., Lång S., Overmyer K., Jaspers P., Brosché M., Tauriainen A., Kollist H., Tuominen H., Belles-Boix E., Piippo M., Inzé D., Palva E.T. and Kangasjärvi J. (2004) Arabidopsis RADICAL-INDUCED CELL DEATH1 Belongs to the WWE Protein-Protein Interaction Domain Protein Family and Modulates Abscisic Acid, Ethylene, and Methyl Jasmonate Responses. Plant Cell 16: 1925-1937.

 

Characterization of clones obtained from EST library sequencing

Ottow E.A., Polle A, Brosché M., Kangasjärvi J., Dibrov P., Zörb C. and Teichmann T. (2005) Molecular characterization of PeNhaD1: the first member of the NhaD Na+/H+ antiporter family of plant origin. Plant Mol. Biol. 58: 73–86.

 

Membrane arrays manufactured from EST sequencing – amplification:

Ottow E.A., Brinker M., Teichmann T., Fritz E., Kaiser W., Brosché M., Kangasjärvi J., Jiang, X. and Polle A. (2005) Populus euphratica Displays Apoplastic Sodium Accumulation, Osmotic Adjustment by Decreases in Calcium and Soluble Carbohydrates, and Develops Leaf Succulence under Salt Stress. Plant Physiol. 139: 1762-1772.

 

DNA sequencing of clones or PCR fragments

Busche, A.E.L., Aranko, A.S., Talebzadeh-Farooji, M., Bernhard, F., Dötsch, V., and Iwaï,H. (2009). Segmental isotopic labelling of a central domain in a multi-domain protein by protein trans-splicing using only one robust DnaE intein. Angew. Chem. Int. Edit. online.

Oeemig, J.S. Aranko,A. S., Djupsjöbacka, J., Heinämäki, K., and Iwaï H. (2009). Solution structure of DnaE intein from /Nostoc punctiforme: Structural basis for the design of a new split intein suitable for site-specific chemical modification. FEBS lett. 583 1451-1456.

Aranko, A.S., Züger,S., Buchinger, E., and Iwaï, H. (2009). In vivo and in vitro protein ligation by naturally occurring and engineered split DnaE inteins. PLoS ONE 4: e5185.

Heinämäki, K., Oeemig, J.S., Pääkkonen, K., Djupsjöbacka, J. and Iwaï, H. (2009). NMR resonance assignment of DnaE intein from/ Nostoc punctiforme. Biomol. NMR Assign. 3 41-43. Published online

Engelhardt, S., Lee, J., Gäbler, Y., Kemmerling, B., Haapalainen, M., Li, C-M.,Wei, Z.,Keller,H., Joosten, M., Taira, S. and Nurnberger, T. (2009). Separable roles of the Pseudomonas syringae pv.phaseolicola accessory protein HrpZ1 in ion-conducting
pore formation and activation of plant immunity. The Plant Journal 57: 706–717

Ahvenniemi. P., Wolf, M., Mari J. Lehtonen, MJ., Wilson, P., German-Kinnari, M. & Valkonen JPT. (2009). Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani. J. Mol. Evol. DOI 10.1007/s00239-009-9260-3.

Muona, M. Aranko, A.S. and Iwai, H. (2008). Segmental isotopic labelling of a multi-domain protein by protein ligation using protein trans-splicing. ChemBioChem 9, 2958-2961

Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, Schulman AH (2008). Cassandra retrotransposons carry independently transcribed 5S RNA. PNAS, 105(15): 5833-5838.

Chang W, Schulman AH (2008). BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters. The Plant Journal, 56(1): 40 - 50.

Vera, J.C., Wheat, C.W., Fescemyer, H.W., Frilander, M.J., Crawford, D.L., Hanski, I. and Marden, J.H. (2008). Rapid transcriptome characterization for a non-model organism using massively parallel 454 pyrosequencing. Molecular Ecology 17: 1636-1647.

Jakava-Viljanen, M., Murros, A., Palva, A. and Björkroth, J. (2008). Lactobacillus sobrius Konstantinov et al. 2006 is a later synonym of Lactobacillus amylovorus Nakamura 1981. Int. J. Syst. Evol. Microbiol. 58:910-913.

Chen Y, Korkeala H, Aarnikunnas J, Lindström M. (2007). Sequencing the botulinum neurotoxin gene and related genes in Clostridium botulinum type E strains reveals orfx3 and a novel type E neurotoxin subtype. J Bacteriol. 189:8643-50.

Puhka M., Vihinen H., Joensuu M. & Jokitalo E. (2007). Endoplasmic reticulum remains continuous and undergoes sheet-to-tubule transformation during cell division in mammalian cells. J Cell Biol. ;179:895-909.

Tanskanen JA, Sabot F, Vicient CM, Schulman AH (2007). Life without GAG: The BARE-2 retrotransposon as a parasite´s parasite. Gene, 390, 166–174.

Lindholm, P., Voutilainen, M .H., Laurén, J., Peränen, J., Leppänen, V-M., Andressoo, J-O., Lindahl, M., Janhunen, S., Kalkkinen, N., Timmusk, T., Tuominen, RK.. and Saarma, M. (2007). Novel neurotrophic factor CDNF protects and rescues midbrain dopaminergic neurons in vivo. Nature, 448: 73-77.

Yang, J., Runeberg-Roos, P., Leppänen, V.-M. & Saarma, M. (2007). The mouse soluble GFRα4 receptor activates RET independently of its ligand persephin. Oncogene, 26:3892-3898.

Hienonen, E., Romantschuk, M., Fenel, F., Taira, S. (2007). Transcript stabilization by mRNA sequences from hrpA of Pseudomonas syringae J. Biotechnology 128:258-267

Marjamaa K, Hilden, K, Kukkola K, Lehtonen M, Holkeri H, Haapaniemi P, Koutaniemi S, Teeri TH, Fagerstedt K, Lundell T (2006). Cloning, characterization and localisation of three novel class III peroxidases in lignifying xylem of Norway spruce (Picea abies). Plant Molecular Biology 61: 719-732.

Li, C.M., Haapalainen, M., Lee, J., Nurnberger, T., Romantschuk, M., and Taira, S. (2005). Harpin of Pseudomonas syringae pv. phaseolicola harbors a protein-binding site. Mol. Plant-Micr. Interact. 18:60-66.

Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A. Schulman AH (2004). Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics, 166: 1437-1450.

Yu, L.- Y., Jokitalo, E., Sun, F.- S., Mehlen, P., Lindholm, D., Saarma, M. & Arumäe U. (2003). GDNF-deprived sympathetic neurons die via a novel nonmitochondrial pathway. J. Cell Biol., 163: 987-997.

Rivera, C., Hong Li, Thomas-Crusells, J., Lahtinen, H., Viitanen, T., Nanobashvili, A., Kokaia, Z., Airaksinen, M. S., Voipio, J., Kaila, K. & Saarma, M. (2002). BDNF-induced TrkB activation down-regulates the K+–Cl- cotransporter KCC2 and impairs neuronal Cl- extrusion. J. Cell Biol., 159: 747-752.

Hienonen, E., Roine, E., Romantschuk, M., Taira, S. (2002). Secretion signal and mRNA stability of HrpA: a type III secretion dependent pilin of Pseudomonas syringae. Mol. Genetics & Genomics, 266:971-978.

Li, C-M., Brown, I., Mansfield, J., Stevens, C., Boureau, T., Romantschuk, M., Taira, S. (2002). The Hrp pilus of Pseudomonas syringae elongates from its tip and acts as a conduit for translocation of the effector protein HrpZ. Embo J. 21:1909-1915.

Taira, S., Tuimala, J., Roine, E., Nurmiaho-Lassila, E.L., Savilahti, H., Romantschuk, M. (1999). Analysis of the Hrp pilin gene of Pseudomonas syringae pv. tomato DC3000 with scanning mutagenesis. Mol. Microbiol. 34:736-744.

 

QPCR machines

Wrzaczek, M., Brosche, M., Kollist, H. & Kangasjärvi, J. (2009). Arabidopisis GRI is involved in the regulation of cell death induced by extracellular ROS. PNAS www.pnas.org_cgi_doi_10.1073_pnas.0808980106. (also arrays and clone sequencing)

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