Publications - Molecular Cell Biology

2011

Publications
- Ali, S, D. L. Champagne, H. P. Spaink, and M. K. Richardson. 2011. Zebrafish embryos and larvae: A new generation of disease models and drug screens. Birth Defects Research Part C: Embryo Today: Reviews 93, no. 2:115-133.

- Alsarraf, H. M. A. B., F. Laroche, H.P. Spaink, S. Thirup and M. Blaise. 2011. Purification, crystallization and preliminary crystallographic studies of the TLDc domain of oxidation resistance protein 2 from zebrafish. Acta Cryst. F67, 1253–1256

- Burgerhout E, Brittijn SA, Kurwie T, Decker P, Dirks RP, Palstra AP, Spaink HP, Van den Thillart GE (2011) First artificial hybrid of the eel species Anguilla australis and Anguilla anguilla. BMC Dev Biol 11:16.

- Carvalho R, de Sonneville J, Stockhammer OW, Savage ND, Veneman W, Dirks RP, Meijer AH, Spaink HP (2011) A high-throughput screen for tuberculosis progression. PlosONE, 6: e16779.

- Harrison MR, Georgiou AS, Spaink HP, Cunliffe VT (2010) The epigenetic regulator Histone Deacetylase 1 promotes transcription of a core neurogenic programme in zebrafish embryos. BMC Genomics 12:24.

- He S, Krens SG, Zhan H, Gong Z, Hogendoorn PC, Spaink HP, Snaar-Jagalska BE (2011) A ΔRaf1-ER-inducible oncogenic zebrafish liver cell model identifies hepatocellular carcinoma signatures. J Pathol. 225:19-28.

- Martens, A. A., N. A. M. Besseling, S. Rueb, E. J. R. Sudholter, H. P. Spaink, and L. C. P. M. De Smet. 2011. Random Scission of Polymers: Numerical Simulations, and Experiments on Hyaluronan Hydrolysis. Macromolecules 44:2559-2567.

- Meckel T, Semrau S, Schaaf MJ, Schmidt T (2011) Robust assessment of protein complex formation in vivo via single-molecule intensity distributions of autofluorescent proteins. J Biomed Opt. 16:076016.

- Meijer AH, Spaink HP (2011) Host-pathogen interactions made transparent with the zebrafish model. Current Drug Targets 12:1000-17.

- Ordas A, Hegedus Z, Henkel CV, Stockhammer OW, Butler D, Jansen HJ, Racz P, Mink M, Spaink HP, Meijer AH (2011) Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection, Fish Shellfish Immunol, Special Issue of the EOFFI symposium, 31:716-724.

- Peng K, Tomatsu I, van den Broek B, Cui C, Korobko AV, van Noort J, Meijer AH, Spaink HP, Kros A (2011) Dextran based photodegradable hydrogels formed via a Michael addition. Soft Matter 7:4881-4887.

- Rotman, J., W. van Gils, D. Butler, H. P. Spaink, and A. H. Meijer. 2011. Rapid screening of innate immune gene expression in zebrafish using reverse transcription - multiplex ligation-dependent probe amplification. BMC Research Notes 4:196

- Sergé A, de Keijzer S, Van Hemert F, Hickman MR, Hereld D, Spaink HP, Schmidt T, Snaar-Jagalska BE (2011) Quantification of GPCR internalization by single-molecule microscopy in living cells. Integr Biol (Camb), 3:675-683.

- van Soest, J.J., O.W. Stockhammer, A. Ordas, G.V. Bloemberg, H.P. Spaink, and A.H. Meijer. 2011. Comparison of static immersion and intravenous injection systems for exposure of zebrafish embryos to the natural pathogen Edwardsiella tarda. BMC Immunology 12:58.

- Zhang Y., E. Stupka, C.V. Henkel, H.J. Jansen,H.P. Spaink, and F.J. Verbeek. 2011. Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data. J Integr Bioinform. 8(2):169.

Book chapters

- Cui C, Benard EL, Kanwal Z, Stockhammer OW, van der Vaart M, Zakrzewska A, Spaink HP, Meijer AH (2011) Infectious disease modeling and innate immune function in zebrafish embryos. Methods Cell Biol, 105: 273-308.

- Ouwerkerk PBF, Meijer AH. (2011) Yeast one-hybrid screens for detection of transcription factor DNA interactions. Methods Molecular Biol. 678:211-27

2010

Publications

- Durston AJ, Jansen HJ, Wacker SA (2010) Time-space translation regulates trunk axial patterning in the early vertebrate embryo. Genomics. 95: 250-5.

- Durston AJ, Jansen HJ, Wacker SA (2010) Time-space translation: a developmental principle. Scientific World Journal. 10: 2207-14.

- de, Jong M., H. Rauwerda, O. Bruning, J. Verkooijen, H. P. Spaink, and T. M. Breit (2010) RNA isolation method for single embryo transcriptome analysis in zebrafish. BMC.Res.Notes 3:73.

- Kabli, S., S. He, H. P. Spaink, A. Hurlstone, E. S. Jagalska, H. J. De Groot, and A. Alia (2010) In vivo magnetic resonance imaging to detect malignant melanoma in adult zebrafish. Zebrafish. 7:143-148.

- Lloret-Vilaspasa F, Jansen HJ, de Roos K, Chandraratna RA, Zile MH, Stern CD, Durston AJ (2010) Retinoid signalling is required for information transfer from mesoderm to neuroectoderm during gastrulation. Int J Dev Biol 54: 599-608.

- Palstra, A. P., D. Schnabel, M. C. Nieveen, H. P. Spaink, and G. E. van den Thillart (2010) Temporal expression of hepatic estrogen receptor 1, vitellogenin1 and vitellogenin2 in European silver eels. Gen.Comp Endocrinol. 166: 1-11.

- Palstra, A. P., D. Schnabel, M. C. Nieveen, H. P. Spaink, and G. Van den Thillart (2010) Swimming suppresses hepatic vitellogenesis in European female silver eels as shown by expression of the estrogen receptor 1, vitellogenin1 and vitellogenin2 in the liver. Reprod.Biol.Endocrinol. 8:27.

- Palstra, A. P., C. Tudorache, M. Rovira, S. A. Brittijn, E. Burgerhout, G. E. van den Thillart, H. P. Spaink, and J. V. Planas. (2010). Establishing zebrafish as a novel exercise model: swimming economy, swimming-enhanced growth and muscle growth marker gene expression. PLoS.One. 5, no. 12:e14483.

- Peng K, Cui C, Tomatsu I, Porta F, Meijer AH, Spaink HP, Kros A (2010) Cyclodextrin/dextran based drug carriers for a controlled release of hydrophobic drugs in zebrafish embryos. Soft matter 6: 3778-3783

- Rauwerda, H., Jong M. de, W. C. de Leeuw, H. P. Spaink, and T. M. Breit (2010) Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example. BMC.Res.Notes 3:192.

- Schoonheim PJ, Chatzopoulou A, Schaaf MJ (2010) The zebrafish as an in vivo model system for glucocorticoid resistance. Steroids 75: 918-25.

- Stockhammer OW, Rauwerda H, Wittink FR, Breit TM, Meijer AH, Spaink HP (2010) Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. Mol Immunol. 48:179-90

- van den Akker, W. M., A. J. Durston, and H. P. Spaink (2010) Identification of hoxb1b downstream genes: hoxb1b as a regulatory factor controlling transcriptional networks and cell movement during zebrafish gastrulation. Int.J.Dev.Biol. 54, no. 1:55-62.

- Van Hemert, F., M.D. Lazova, B.E. Snaar-Jagalska, T. Schmidt (2010) Mobility of G protein is heterogeneous and polarized during chemotaxis. J Cell Science 123, 2922-2930

- Vergunst AC, Meijer AH, Renshaw SA, O’Callaghan D (2010) Burkholderia cenocepacia creates an intra-macrophage replication niche in zebrafish embryos, followed by bacterial dissemination and establishment of systemic infection. Infect Immun. 78:1495-508

- Zakrzewska A, Cui C, Stockhammer OW, Benard EL, Spaink HP, Meijer AH. (2010) Macrophage-specific gene functions in Spi1-directed innate immunity. Blood. 2010, 116:e1-11

Book chapters
- Schaaf MJ and Schmidt TS. In vivo single-molecule microscopy using the zebrafish model system. In: Cell Signaling Reactions: Single-Molecular Kinetic Analysis, Springer 2010

Dissertations

- Shuning He. Cancer and inflammation studies using zebrafish cell lines. 27 May 2010. Promotor: H.P. Spaink; Co-promotor: B.E. Snaar-Jagalska

- Oliver W. Stockhammer. Innate immune signalling of the zebrafish embryo. 19 May 2010. Promotor: H.P. Spaink; Co-promotor: A.H. Meijer

- Anita Ordas. Transcriptome profiling of infectious diseases and cancer in zebrafish. 29 June 2010. Promotor: H.P. Spaink; Co-promotor: A.H. Meijer

- Peter I. Racz. Study of a new member of the myelin protein zero family. 30 June 2010. Promotor: H.P. Spaink; Co-promotor: A.H. Meijer

2009

Publications

-Mione M, Meijer AH, Snaar-Jagalska BE, Spaink HP, Trede NS (2009) Disease modeling in zebrafish: cancer and immune responses-a report on a workshop held in Spoleto, Italy, July 20-22, 2009. Zebrafish 6:445-51

-Bardine N, Donow C, Korte B, Durston AJ, Knöchel W, Wacker SA. (2009) Two Hoxc6 transcripts are differentially expressed and regulate primary neurogenesis in Xenopus laevis.Dev Dyn. 238: 755-65

-Brittijn SA, Duivesteijn SJ, Belmamoune M, Bertens LF, Bitter W, de Bruijn JD, Champagne DL, Cuppen E, Flik G, Vandenbroucke-Grauls CM, Janssen RA, de Jong IM, de Kloet ER, Kros A, Meijer AH, Metz JR, van der Sar AM, Schaaf MJ, Schulte-Merker S, Spaink HP, Tak PP, Verbeek FJ, Vervoordeldonk MJ, Vonk FJ, Witte F, Yuan H, Richardson MK (2009) Zebrafish development and regeneration: new tools for biomedical research. Int J Dev Biol. 53:835-50

-Hegedűs Z, Zakrzewska A, Agoston VC, Ordas A, Rácz P, Mink M, Spaink HP, Meijer AH. (2009) Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol. 46: 2918-30.

-In der Rieden PM, Vilaspasa FL, Durston AJ. (2009) Xwnt8 directly initiates expression of labial Hox genes. Dev Dyn., in press.

-Kabli S, Spaink HP, De Groot HJ, Alia A. (2009) In vivo metabolite profile of adult zebrafish brain obtained by high-resolution localized magnetic resonance spectroscopy.
J Magn Reson Imaging. 29: 275-81.

-Ouwerkerk PBF, Meijer AH. Yeast one-hybrid screens for detection of transcription factor DNA interactions. Methods Molecular Biol., in press

-Palstra AP, Schnabel D, Nieveen MC, Spaink HP, van den Thillart GE. (2009) Temporal expression of hepatic estrogen receptor 1, vitellogenin1 and vitellogenin2 in European silver eels.Gen Comp Endocrinol., in press

-Sarabdjitsingh RA, Meijer OC, Schaaf MJ, de Kloet ER. (2009) Subregion-specific differences in translocation patterns of mineralocorticoid and glucocorticoid receptors in rat hippocampus. Brain Res. 1249: 43-53.

-Schaaf MJ, Chatzopoulou A, Spaink HP. (2009) The zebrafish as a model system for glucocorticoid receptor research.Comp Biochem Physiol A Mol Integr Physiol. 153:75-82

-Schaaf MJ, Koopmans WJ, Meckel T, van Noort J, Snaar-Jagalska BE, Schmidt TS, Spaink HP. (2009) Single-molecule microscopy reveals membrane microdomain organization of cells in a living vertebrate.Biophys J. 97:1206-14.

-Staneloni RJ, Rodriguez-Batiller MJ, Legisa D, Scarpin MR, Agalou A, Cerdán PD, Meijer AH, Ouwerkerk PB, Casal JJ. (2009) Bell-like homeodomain selectively regulates the high-irradiance response of phytochrome A. Proc Natl Acad Sci U S A. 106:13624-9.

-Stockhammer OW, Zakrzewska A, Hegedûs Z, Spaink HP, Meijer AH (2009) Transcriptome profiling and functional analyses of the zebrafish embryonic innate immune response to Salmonella infection. J Immunol. 182: 5641-53.

-van der Sar AM, Spaink HP, Zakrzewska A, Bitter W, Meijer AH (2009) Specificity of the zebrafish host transcriptome response to acute and chronic mycobacterial infection and the role of innate and adaptive immune components. Mol Immunol. 46: 2317-32

-van der Vaart M, Schaaf MJ.(2009) Naturally occurring C-terminal splice variants of nuclear receptors. Nucl Recept Signal. 7:e007.

-Webb KJ, Norton WH, Trümbach D, Meijer AH, Ninkovic J, Topp S, Heck D, Marr C, Wurst W, Theis FJ, Spaink HP, Bally-Cuif L. (2009) Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biol. 10:R81.

-Woltering JM, Vonk FJ, Müller H, Bardine N, Tuduce IL, de Bakker MA, Knöchel W, Sirbu IO, Durston AJ, Richardson MK. (2009) Axial patterning in snakes and caecilians: evidence for an alternative interpretation of the Hox code. Dev Biol. 332: 82-9

Book chapters

-Meijer AH, Zebravissen bij het ontrafelen van het immuunsysteem. (2009) Natuurkundige Voordrachten no. 87, Jaarboek van De Koninklijke Maatschappij voor Natuurkunde ‘Diligentia’.

Dissertations

- F. van Hemert. GPCR and G protein mobility in D. discoideum. 21 December 2009. Promotor: Prof.Dr. T. Schmidt; co-promotor: B.E. Snaar-Jagalska.

-Hans J. Janssen. Anterior-posterior axis formation in Xenopus laevis. 25 March 2009. Promotor: Prof. dr. A.J. Durston.

2008

Publications

-Agalou A, Purwantomo S, Overnäs E, Johannesson H, Zhu X, Estiati A, de Kam RJ, Engström P, Slamet-Loedin IH, Zhu Z, Wang M, Xiong L, Meijer AH, Ouwerkerk PB (2008) A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol Biol 2008 66: 87-103

-de Keijzer S, Sergé A, van Hemert F, Lommerse PH, Lamers GE, Spaink HP, Schmidt T, Snaar-Jagalska BE (2008) A spatially restricted increase in receptor mobility is involved in directional sensing during Dictyostelium discoideum chemotaxis. J Cell Sci 121: 1750-1757.

-Kulzer F, Laurens N, Besser J, Schmidt T, Orrit M, Spaink HP (2008) Photothermal detection of individual gold nanoparticles: perspectives for high-throughput screening.
Chemphyschem. 9:1761-6

-Krens SFG, Corredor-Adámez M, He S, Snaar-Jagalska BE, Spaink HP (2008) ERK1 and ERK2 MAPK are key regulators of distinct gene sets in zebrafish embryogenesis. BMC Genomics 9:196.

-Krens SFG, He S, Lamers GEM, Meijer AH, Bakkers J, Schmidt T,  Herman P. Spaink , B. Ewa Snaar-Jagalska (2008) Distinct functions for ERK1 and ERK2 in cell migration processes during zebrafish gastrulation. Dev Biol,  in press

-Fitzsimons CP, Ahmed S, Wittevrongel C, Schouten TG, Dijkmans TF, Scheenen WJ, Schaaf MJ, de Kloet ER, Vreugdenhil E. (2008) The microtubule associated protein Doublecortin-like regulates the transport of the glucocorticoid receptor in neuronal progenitor cells. Mol Endocrinol., in press (2007 Nov 1; [Epub ahead of print]
PMID: 17975023)

-Marques IJ, Leito JT, Spaink HP, Testerink J, Jaspers RT, Witte F, van den Berg S, Bagowski CP (2008) Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts. J Comp Physiol [B]. , in press (2007 Sep 8; [Epub ahead of print])

-Meijer AH, van der Sar AM, Cunha C, Lamers GEM, Laplante MA, Kikuta H, Bitter W, Becker TS, Spaink HP (2008) Identification and real-time imaging of a myc-expressing neutrophil population during inflammation and mycobacterial granuloma formation in zebrafish. Dev Comp Immunol 32; 36-49

-Palstra AP, Schnabel D, Nieveen MC, Spaink HP, van den Thillart GE (2008) Male silver eels mature by swimming. BMC Physiol. 8:14

-Schaaf MJM, Champagne D, van Laanen IHC, van Wijk DCWA, Meijer AH, Meijer OC, Spaink HP, Richardson MK (2008) Discovery of a functional glucocorticoid receptor β-isoform in zebrafish. Endrocinology

-Schlaman HR, Schmidt K, Ottenhof D, van Es MH, Oosterkamp TH, Spaink HP. (2008) Analysis of interactions of signaling proteins with phage-displayed ligands by fluorescence correlation spectroscopy. J Biomol Screen. 13: 766-76

-van den Akker WM, Brox A, Puelles L, Durston AJ, Medina L (2008) Comparative functional analysis provides evidence for a crucial role for the homeobox gene Nkx2.1/Titf-1 in forebrain evolution. J Comp Neurol. 10: 211-23

-Woltering JM, Durston AJ (2008) MiR-10 Represses HoxB1a and HoxB3a in Zebrafish. PLoS ONE. 3:e1396.

-Zhu Y, Hanna RN, Schaaf MJ, Spaink HP, Thomas P. (2008) Candidates for membrane progestin receptors—past approaches and future challenges. Comp Biochem Physiol C Toxicol Pharmacol. 148:381-9

Books and Book chapters

-De Keijzer S, Snaar-Jagalska BE, Spaink HP, Schmidt T (2008) Single molecule imaging of cellular signaling. In Single molecules in nanotechnology: Springer.

Dissertations
- Nabila Bardine. Hox in frogs: Xenopus reveals novel functions for vertebrate Hox genes. PhD Thesis, Leiden University, 3 December 2008. Promotores: Prof.dr. A. Durston, Prof.dr. W. Knöchel (Ulm Univ. Germany) and Prof.dr. S. Wacker (Ulm Univ. Germany) 

2007

Publications

-Besser J, Bagowski CP, Salas-Vidal E, van Hemert MJ, Bussmann J, Spaink HP (2007) Expression analysis of the family of 14-3-3 proteins in zebrafish development. Gene Expr Patterns7: 511-20

-Besser J, Leito JT, van der Meer DL, Bagowski CP (2007) Tip-1 induces filopodia growth and is important for gastrulation movements during zebrafish development.
Dev Growth Differ 49: 205-14

-Haupt BJ, Osbourn M, Spanhoff R, de Keijzer S, Müller-Taubenberger A, Snaar-Jagalska E, Schmidt T (2007) Asymmetric elastic properties of Dictyostelium discoideum in relation to chemotaxis. Langmuir 23:9352-7

-Henkel CV, Bäck T, Kok JN, Rozenberg G, Spaink HP (2007) DNA computing of solutions to knapsack problems. Biosystems 88: 156-62

-Jansen HJ, Wacker SA, Bardine N, Durston AJ (2007) The role of the Spemann organizer in anterior-posterior patterning of the trunk. Mech Dev 124:668-81

- Mainguy G, Koster J, Woltering J, Jansen H, Durston A (2007) Extensive polycistronism and antisense transcription in the Mammalian Hox clusters. PLoS ONE. 2:e356.

-Rubio MC, Becana M, Sato S, James EK, Tabata S, Spaink HP (2007) Characterization of genomic clones and expression analysis of the three types of superoxide dismutases during nodule development in Lotus japonicus. Mol Plant Microbe Interact 20: 262-75

-Trede N, Meijer AH, Snaar-Jagalska BE, Spaink HP (2007) Model systems for infectious disease and cancer in zebrafish: a report on an EMBO workshop held at the Lorentz Center, Leiden, The Netherlands, 16-18 July 2007. Zebrafish

- Vreugdenhil E, Fitzsimons C, Kolk S, Schaaf MJM, Lucassen P (2007) Doublecortin-Like, a Microtubule Associated Protein Expressed in Radial Glia is Crucial for Neuronal Precursor Division and Radial Process Stability. Eur. J. Neurosci. 25, 635-648

Books and Book chapters

-Purwantomo S, Mulyaningsih ES, Nugroho S, Estiati A, Slamet-Loedin IH, Meijer AH and Ouwerkerk PBF (2007) Transgenic breeding for drought tolerance and blast resistance in rice. Proceedings symposium on application of plant biotechnology for agribusiness. IPB Press, Bogor, Indonesia, ISBN 978-979-493-137-0, Eds. Löffler H, Syamsu K, pp. 11-24.

Dissertations

-S. F. Gabby Krens, The function of mitogen activated protein kinases in zebrafish development. 19 September 2007. Promotores: prof.dr. H.P. Spaink, prof. dr. T. Schmidt, copromoter: dr. B.E. Snaar-Jagalska

-Monique C. M. Welten, Spatio-temporal gene expression analysis from 3D in situ hybridization images. 27 November 2007. Promotores: prof.dr. H.P. Spaink, prof. dr. Verduyn Lunel, copromotor: dr. ir. F.J. Verbeek

-Joost M. Woltering (cum laude), Hox, microRNAs and evolution. Promotor: prof. dr. A.J. Durston

2006

Publications

-Agalou A, Spaink HP, Roussis A (2006) Novel interaction of selenium-binding protein with glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase of Arabidopsis thaliana. Funct Plant Biol 33:847-856.

-Deng X, Phillips J, Brautigam A, Engstrom P, Johannesson H, Ouwerkerk PB, Ruberti I, Salinas J, Vera P, Iannacone R, Meijer AH, Bartels D (2006) A homeodomain leucine zipper gene from Craterostigma plantagineum regulates abscisic acid responsive gene expression and physiological responses Plant Mol Biol 61:469-89.

-He S, E. Salas-Vidal, Rueb S, Krens SFG, Meijer AH, Snaar-Jagalska BE, and Spaink HP (2006) Genetic and transcriptome characterization of model zebrafish cell lines. Zebrafish 3:441-453.

- Kabli, S., A. Alia, H. P. Spaink, F. J. Verbeek, and H. J. M. de Groot. (2006) Magnetic resonance microscopy of the adult zebrafish. Zebrafish 3:431-439.

-Krens SF, Spaink HP, Snaar-Jagalska BE (2006) Functions of the MAPK family in vertebrate development. FEBS Lett 18:4984-4990.

-Krens SF, He S, Spaink HP, Snaar-Jagalska BE (2006) Characterization and expression patterns of the MAPK family in zebrafish. Gene Expr Patterns 6:1019-1026.

-Lommerse PH, Vastenhoud K, Pirinen NJ, Magee AI, Spaink HP, Schmidt T. (2006) Single-molecule diffusion reveals similar mobility for the Lck, H-ras, and K-ras membrane anchors. Biophys J. 91:1090-7.

-Maraschin SDF, Caspers M, Potokina E, Wulfert F, Graner A, Spaink HP, Wang M (2006) cDNA array analysis of stress-induced gene expression in barley androgenesis. Physiol Plantarum 127: 535-550.

-Peres JN, McNulty CL, Durston AJ (2006) Interaction between X-Delta-2 and Hox genes regulates segmentation and patterning of the anteroposterior axis. Mech Dev 123: 321-333.

-Peres JN, Durston AJ (2006) Role of X-Delta-2 in the early neural development of Xenopus laevis. Dev Dyn 235: 802-810.

-Rodrigues-Lima F, Dairou J, Diaz CL, Rubio MC, Sim E, Spaink HP, Dupret JM. (2006) Cloning, functional expression and characterization of Mesorhizobium loti arylamine N-acetyltransferases: rhizobial symbiosis supplies leguminous plants with the xenobiotic N-acetylation pathway. Mol Microbiol. 60:505-12.

-Schlaman HR, Olsthoorn MM, Harteveld M, Dorner L, Djordjevic MA, Thomas-Oates JE, Spaink HP (2006) The production of species-specific highly unsaturated fatty acyl-containing LCOs from Rhizobium leguminosarum bv. trifolii is stringently regulated by nodD and involves the nodRL genes. Mol Plant Microbe Interact. 19: 215-26.

-Schaaf MJ, Willetts L, Hayes BP, Maschera B, Stylianou E, Farrow SN.(2006) The relationship between intranuclear mobility of the NF-kappaB subunit p65 and its DNA binding affinity. J Biol Chem. 281:22409-20.

-Stern CD, Charite J, Deschamps J, Duboule D, Durston AJ, Kmita M, Nicolas JF, Palmeirim I, Smith JC, Wolpert L (2006)  Head-tail patterning of the vertebrate embryo: one, two or many unresolved problems? Int J Dev Biol 50: 3-15.

-van der Meer DLM, Marques IJ, Leito JTD, Besser J, Bakkers J, Schoonheere E, Bagowski CP (2006)  Zebrafish cypher is important for somite formation and heart development. Dev Biol 299: 356-372.

-van der Sar AM, Stockhammer OW, van der Laan C, Spaink HP, Bitter W, Meijer AH (2006) MyD88 innate immune function in a zebrafish embryo infection model Infect Immun 74:2436-2441

-Welten MCM, de Haan SB, Van den Boogert N, Noordermeer JN, Lamers GEM, Spaink HP, Meijer AH, Verbeek FJ (2006) ZebraFISH: Fluorescent in situ hybridization protocol and three-dimensional imaging of gene expression patterns. Zebrafish 3:465-474

-Woltering JM, Durston AJ (2006) The zebrafish hoxDb cluster has been reduced to a single microRNA. Nat Genet. 38:601-2.

Books and Book chapters

-Spaink HP, Snaar-Jagalska BE, Meijer AH (2006) The innate immune system of vertebrates: challenges for future research In: Biology of plant-microbe interactions (Sanchez F, Quinto C, López-Lara IM, Geiger O, eds), pP. 674-680. International Society for Molecular Plant-Microbe Interactions, St.Paul, MN, USA.

Dissertations

-Sandra de Keijzer, Dynamics of a GPCR studied with single-molecule microscopy. 12 april 2006. Promotores: prof.dr.H.P. Spaink, prof. dr. T. Schmidt, copromoter: dr. B.E. Snaar-Jagalska

2005

Publications

-Agalou, A., A. Roussis, and H.P. Spaink (2005). The Arabidopsis selenium binding protein confers tolerance to toxic levels of selenium. Functional Plant Biology 32: 881-890.

-Corredor-Adamez, M., M.C. Welten, H.P. Spaink, J.E. Jeffery, R.T. Schoon, M.A. de Bakker, C.P. Bagowski, A.H. Meijer, F.J. Verbeek, and M.K. Richardson (2005). Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hoxb13a. Evol.Dev. 7: 362-375.

-Canto-Canche, B.B., A.H. Meijer, G. Collu, R. Verpoorte, V.M. Loyola-Vargas (2005). Characterization of a polyclonal antiserum against the monoterpene monooxygenase, geraniol 10-hydroxylase from Catharanthus roseus. J Plant Phys 162: 393-402

-Enckevort, E.J.G. van, G. Droc, P. Piffanelli, R. Greco, C. Gagneur, C. Weber, V.M. González, P. Cabot, F. Fornara, S. Berri, B. Miro, P. Lan, M. Rafel, T. Capell, P. Puigdomènech, P.B.F. Ouwerkerk, A.H. Meijer, E. Pe, L. Colombo, P. Christou, E. Guiderdoni, A. Pereira (2005). EU-OSTID: European Oryza sativa Transposon Insertional Database. Plant Mol Biol 59: 99-110

-Grønlund, M., A. Roussis, E. Flemetakis, N.E.M. Quaedvlieg, H.R.M. Schlaman, Y. Umehara, P. Katinakis, J. Stougaard, and H.P. Spaink (2005). Analysis of promoter activity of the early nodulin Enod40 in Lotus japonicus. Mol.Plant-Microbe Interact. 18: 414-427.

-Henkel, C. V., R. S. Bladergroen, C. I. A. Balog, A. M. Deelder, T. Head, G. Rozenberg, and H. P. Spaink. 2005. Protein output for DNA computing. Natural Computing 4:1-10.

-Henkel, C.V., G. Rozenberg, and H.P. Spaink (2005). Application of mismatch detection methods in DNA computing. DNA Computing 3384: 159-168.

-Lommerse, P.H., B.E. Snaar-Jagalska, H.P. Spaink, and T. Schmidt (2005). Single-molecule diffusion measurements of H-Ras at the plasma membrane of live cells reveal microdomain localization upon activation. J.Cell Sci. 118:1799-1809.

-Maraschin, S. d.F., M. Vennik, G.E. Lamers, H.P. Spaink, and M. Wang (2005). Time-lapse tracking of barley androgenesis reveals position-determined cell death within pro-embryos. Planta 220: 531-540.

-Maraschin, S. d.F., G. Gaussand, A. Pulido, A. Olmedilla, G.E. Lamers, H. Korthout, H.P. Spaink, and M. Wang (2005). Programmed cell death during the transition from multicellular structures to globular embryos in barley androgenesis. Planta 221: 459-470.

-Maraschin, S.F., W. de Priester, H.P. Spaink, and M. Wang (2005). Androgenic switch: an example of plant embryogenesis from the male gametophyte perspective. J.Exp.Bot. 56: 1711-1726.

-Meijer, A.H., F.J. Verbeek, E. Salas-Vidal, M. Corredor-Adamez, J. Bussman, A.M. van der Sar, G.W. Otto, R. Geisler, and H.P. Spaink (2005). Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection. Mol.Immunol. 42: 1185-1203.

-Salas-Vidal, E., A.H. Meijer, X. Cheng, and H.P. Spaink (2005). Genomic annotation and expression analysis of the zebrafish Rho small GTPase family during development and bacterial infection. Genomics 86: 25-37.

-Scarpella, E., E.J. Simons, A.H. Meijer (2005). Multiple regulatory elements contribute to the vascular-specific expression of the rice HD-Zip gene Oshox1 in Arabidopsis. Plant Cell Phys 46: 1400-1410.

-Van der Meer, D.L., G.E. van den Thillart, F. Witte, M.A. de Bakker, J. Besser, M.K. Richardson, H.P. Spaink, J.T. Leito, and C.P. Bagowski. (2005). Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish. Am.J.Physiol Regul.Integr.Comp Physiol 289: 1512-1519.

-Welten, M.C.M., F.J. Verbeek, A.H. Meijer, M.K. Richardson(2005). Gene Expression and Digit Homology in the Chicken Embryo Wing. Evol Dev 7: 18-28.

Books and Book chapters

-Diáz, C.L., H.R.M. Schlaman, and H.P. Spaink (2005). Concurrent visualization of gusA and lacZ reporter gene expression , p. 99-109. In: A. J. Marquez (ed.), Lotus japonicus handbook. Springer, Dordrecht.

-Diáz, C.L., M. Grønlund, H.R.M. Schlaman, and H.P. Spaink (2005). Induction of hairy roots for symbiotic gene expression studies, p. 261-278. In: A. J. Marquez (ed.), Lotus japonicus handbook. Springer, Dordrecht.

-Grønlund, M., A. Agalou, M.C. Rubio, G.E.M. Lamers, A. Roussis, and H.P. Spaink (2005). Embedding root and nodule tissue in plastic (BMM), p. 111-122. In: A. J. Marquez (ed.), Lotus japonicus handbook. Springer, Dordrecht.

Dissertations

-Ch.V. Henkel. Experimental DNA computing. Promotors: Prof. Dr. H.P. Spaink, Prof.Dr. G. Rozenberg, Prof.Dr. Th.H.W. Bäck. 23-02-2005

-S. de Faria Maraschin. Androgenic switch in barley microspores. Promotor: Prof. Dr. H.P. Spaink, co-promotor: Dr. M. Wang. 09-02-2005

-Suzanne J.H. Kuijt. Regulation of Knotted-1 like homebox genes in rice and Arabidopsis. Promotor: Prof.Dr.H.P. Spaink, co-promotores: Dr. A.H. Meijer and Dr. P.B.F. Ouwerkerk. 27-10-2005.

-Adamantia Agalou. Functional analysis of Selenium binding protein in plants and animals. Promotor: Prof. Dr. H.P. Spaink, co-promotor: Dr. A. Roussis. 1-11-2005.

2004

Publications

-Bakkers, J., C. Kramer, J. Pothof, N.E.M. Quaedvlieg , H.P. Spaink, and M. Hammerschmidt  (2004) Has2 is required upstream of Rac1 to govern dorsal migration of lateral cells during zebrafish gastrulation. Development 131: 525-537

-Friml J, Yang X, Michniewicz M, Weijers D, Quint A, Tietz O, Benjamins R, Ouwerkerk PB, Ljung K, Sandberg G, Hooykaas PJ, Palme K, Offringa R. (2004) A PINOID-dependent binary switch in apical-basal PIN polar targeting directs auxin efflux. Science 306:862-865.

-Greco, R., P. B. Ouwerkerk, A. J. Taal, C. Sallaud, E. Guiderdoni, A. H. Meijer, J. H. Hoge, and A. Pereira (2004) Transcription and somatic transposition of the maize En / Spm transposon system in rice. Mol Genet.Genomics 270:514-523.

-Kuijt S.J.H., Lamers G.E.M., Rueb S., Scarpella E., Ouwerkerk P.B.F., Spaink H.P. and A.H. Meijer (2004) Different subcellular localization and trafficking properties. Plant Molecular Biology 55: 781–796.

-Lommerse, P. H., G. A. Blab, L. Cognet, G. S. Harms, B. E. Snaar-Jagalska, H. P. Spaink, and T. Schmidt (2004) Single-molecule imaging of the h-ras membrane-anchor reveals domains in the cytoplasmic leaflet of the cell membrane. Biophys.J 86: 609-616.

-Lommerse PH, Spaink HP, Schmidt T. (2004) In vivo plasma membrane organization: results of biophysical approaches. Biochim Biophys Acta. 1664:119-131.

-Maraschin, S. d. F., M. Vennik, G. E. Lamers, H. P. Spaink, and M. Wang. (2004). Time-lapse tracking of barley androgenesis reveals position-determined cell death within pro-embryos. Planta1432-2048.

-Meijer, A. H., S. F. G. Krens, I. A. Medina Rodriguez, S. He, W. Bitter, B. E. Snaar-Jagalska, and H. P. Spaink. (2004) Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish. Mol Immunol. 40:773-783.

-Scarpella E. and Meijer A.H. (2004) Pattern formation in the vascular system of monocot and dicot plant species. Tansley review, New Phytologist 164: 209–242

-Schmidt KA, Henkel CV, Rozenberg G, Spaink HP. (2004) DNA computing using single-molecule hybridization detection. Nucleic Acids Res. 32: 4962-4968.

-Solheim, B., H. Wiggen, S. Røberg, and H. P. Spaink. 2004. Associations between arctic Cyanobacteria and mosses. Symbiosis  37:169-187.

-Spaink HP (2004) Specific recognition of bacteria by plant LysM domain receptor kinases. Trends Microbiol. 12: 201-204.van Hemert MJ, Niemantsverdriet M, Schmidt T, Backendorf C, Spaink HP. (2004) Isoform-specific differences in rapid nucleocytoplasmic shuttling cause distinct subcellular distributions of 14-3-3 sigma and 14-3-3 zeta. J Cell Sci. 117:1411-1420.

Books and Book chapters

-van der Holst, P. P. G., M. Grønlund, J. Stougaard, and H. P. Spaink. 2004. Symbiosis and defense: two sides of one coin, p. 338-342. In: I. Tikhonovich, B. J. J. Lugtenberg, and N. Provorov (eds.), Proceedings of the XI International Congress on Molecular Plant-Microbe Interactions. International Society for Molecular Plant-Microbe Interactions, St.Paul.

-Verbeek, F. J., D. D. Rodrigues, H. Spaink, and A. Siebes. 2004. Data submission of 3D image sets to a bio-molecular database using active shape models and a 3D reference model for projection, p. 13-23. In: S. Santini and R. Schettini (eds.), Internet Imaging V. SPIE The International Society for Optical Engineering and IS&T The Society for Imaging Science and Technology, San Jose, California.

Dissertations

-P.P.G. van der Holst. Zebrafish Proteins Involved in Chitin Oligosaccharide Signalling. Promotor: Prof.dr. H.P. Spaink, co-promotor: Dr. B.E. Snaar-Jagalska 16-09-2004

-P.H.M. Lommerse. Membrane Organization and Dynamics Investigated by Single-molecule Microscopy. Promotors: Prof.dr. T. Schmidt, Prof.dr. H.P. Spaink, co-promotor Dr. B.E. Snaar-Jagalska  25-03-2004

2003

Publications

-Bladergroen, M.R., K. Badelt and H.P. Spaink. 2003. Infection-blocking genes of a symbiotic Rhizobium leguminosarum strain that are involved in temperature-dependent protein secretion. Mol.Plant Microbe Interact. 16: 53-64.

-Girard, G., A. Roussis, A.P. Gultyaev, C.W.A. Pleij and H.P. Spaink. 2003. Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean. Nucleic Acids Research 31: 5003-5015.

-Greco, R., P.B.F., Ouwerkerk, R.J. De Kam., C. Sallaud, C. Favalli, L. Colombo,  E. Guiderdoni, A.H. Meijer, J.H.C. Hoge and A. Pereira. 2003. Transpositional behaviour of an Ac/Ds system for reverse genetics in rice. Theor. Appl. Genet. 108: 10-24.

-Maraschin, S. F., J. D. Louwerse, G.E. Lamers, H.P. Spaink and M. Wang. 2003. Tissue-specific expression of 14-3-3 isoforms during barley microspore and zygotic embryogenesis. Acta Biologica Cracoviensia 45: 103-106.

-Maraschin, S. F., G.E. Lamers, B.S. de Pater, H.P. Spaink and M. Wang. 2003. 14-3-3 isoforms and pattern formation during barley microspore embryogenesis. J.Exp.Bot. 54: 1033-1043.

-Noreen, S., H.R.M. Schlaman, R.A. Bellogin, A.M. Buendia-Claveria, M.R. Espuny, M. Harteveld, C. Medina, F.J. Ollero, M.M.A. Olsthoorn, M.E. Soria-Diaz, H.P. Spaink, F. Temprano, J. Thomas-Oates, J.M. Vinardell, S.S. Yang, H.Y. Zhang, and J.E. Ruiz-Sainz. 2003. Alfalfa nodulation by Sinorhizobium fredii does not require sulfated Nod-factors. Functional Plant Biology 30:1219-1232.

-Pacios-Bras, C., H.R.M. Schlaman, K. Boot, P. Admiraal, J. Mateos Langerak, J. Stougaard and H.P. Spaink. 2003. Auxin distribution in Lotus japonicus during root nodule development. Plant Mol Biol. 52: 1169-1180.

-Rozenberg, G. and H.P. Spaink. 2003. DNA computing by blocking: Theoretical Computer Science 292: 653-665.

-Sallaud, C., D. Meynard, J. van Boxtel, C. Gay, M. Bes, J.P. Brizard, P. Larmande, D. Ortega, M. Raynal, M. Portefaix, P.B. Ouwerkerk, S. Rueb, M. Delseny and E. Guiderdoni. 2003. Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics. Theor.Appl.Genet.106: 1396-1408.

-Scarpella, E., S. Rueb and A.H. Meijer. 2003. The RADICLELESS1 gene is required for vascular pattern formation in rice. Development 130: 645-658.

-Snaar-Jagalska, B.E., S.F.G. Krens, I. Robina, L.X. Wang and H. P. Spaink. 2003. Specific activation of ERK pathways by chitin oligosaccharides in embryonic zebrafish cell lines. Glycobiology 13: 725-732.

-Thomas-Oates, J., J. Bereszczak, E. Edwards, A. Gill, S. Noreen, J.C. Zhou, M.Z. Chen, L.H. Miao, F.L. Xie, J.K. Yang, Q. Zhou, S.S. Yang, X.H. Li, L. Wang, H.P. Spaink, H.R. Schlaman, M. Harteveld, C.L. Diaz, A.A. van Brussel, M. Camacho, D.N. Rodriguez-Navarro, C. Santamaria, F. Temprano, J.M. Acebes, R.A. Bellogin, A.M. Buendia-Claveria, M.T. Cubo, M.R. Espuny, A.M. Gil, R. Gutierrez, A. Hidalgo, F.J. Lopez-Baena, N. Madinabeitia, C. Medina, F.J. Ollero, J.M. Vinardell and J.E. Ruiz-Sainz. 2003. A catalogue of molecular, physiological and symbiotic properties of soybean-nodulating rhizobial strains from different soybean cropping areas of China. Syst.Appl.Microbiol. 26: 453-465.

-Vinuesa, P., F. Neumann-Silkow, C. Pacios-Bras, H.P. Spaink, E. Martinez-Romero and D. Werner. 2003. Genetic analysis of a pH-regulated operon from Rhizobium tropici CIAT899 involved in acid tolerance and nodulation competitiveness. Mol.Plant Microbe Interact. 16: 159-168.

Books and Book chapters

-Spaink, H.P. 2003. Nieuwe mogelijkheden voor analyse van levensprocessen in cellen, in R. Furth, R. Arlman, P.N.J. Wisse, E. van der Meijden, G.H. Okker-Reitsma, L. van Solkema, R.R.P. de Vries, H. Weijma, and P. Hoogeboom (eds), Natuurkundige voordrachten, Den Haag, Koninklijke Maatschappij voor Natuurkunde, onder de zinspreuk Diligentia: 89-95.
Van der Holst, P.P.G., M. Grønlund, J. Stougaard and H.P. Spaink. 2003. Symbiosis and defence: two sides of one coin, in I Tikhonovich and BJJ Lugtenberg (eds), Proceedings of the XI International Congress on Molecular Plant-Microbe Interactions, Dordrecht, Kluwer Academic Publishers, pp.

Dissertations


-E. Scarpella. Genetic control of vascular tissue development in rice. Promotor: Prof.dr. H.P. Spaink, co-promotor: dr. A.H. Meijer. 19-06-2003

-C. Pacios Bras. The symbiosis between Lotus japonicus and Rhizobia: function of nod factor structural variation. Promotor: Prof.dr. H.P. Spaink. 09-01-2003

Older

Publications 2002

-Deng X, Philips J, Meijer AH, Salamini F, Bartels D (2002) Characterization of five novel dehydration- responsive homeodomain leucine zipper genes from the resurrection plant Craterostigma plantagineum. Plant Mol Biol 49: 601-610.

-Flemetakis, E., A. Agalou, N. Kavroulakis, M. Dimou, A. Martsikovskaya, A. Slater, H. P. Spaink, A. Roussis, and P. Katinakis. (2002). Lotus japonicus gene Ljsbp is highly conserved among plants and animals and encodes a homologue to the mamalian selenium-binding proteins. Mol.Plant-Microbe Interact. 15: 313-322.

-Pacios-Bras, C., Y. E. van der Burgt, A. M. Deelder, P. Vinuesa, D. Werner, and H. P. Spaink. (2002). Novel lipochitin oligosaccharide structures produced by Rhizobium etli KIM5s. Carbohydr.Res. 337: 1191-1200.

-Postma-Haarsma AD,  Rueb S,  Scarpella E, den Besten P,  Hoge JHC, Meijer AH (2002) Developmental regulation and downstream effects of the knox class homeobox genes Oskn2 and Oskn3 from rice. Plant Mol Biol 48: 423-441.

-Robina, I., S. Gomez-Bujedo, J. G. Fernandez-Bolanos, J. Fuentes, and H. P. Spaink. (2002). Synthesis and biological evaluation of oligosaccharides related to the molecule signals in plant defence and the Rhizobium-legume symbiosis. Tetrahedron 58: 521-530.

-Scarpella E, Boot KJM, Rueb S, Meijer AH (2002) The procambium specification gene Oshox1 promotes polar auxin transport capacity and reduces its sensitivity towards inhibition. Plant Physiol 130: 1349-1360.

-Spaink, H. P. (2002). Plant-microbe interactions: a receptor in symbiotic dialogue. Nature 417: 910-911.
Thelander M, Frederiksson D, Schouten J, Hoge JHC, Ronne H (2002) Cloning by pathway activation in yeast: identification of an Arabidopsis thaliana F-box protein that can turn on glucose repression. Plant Mol Biol 49: 69-79.

-Werner, D., J. M. Barea, N. J. Brewin, J. E. Cooper, P. Katinakis, K. Lindström, F. O’Gara, H. P. Spaink, G. Truchet, and P. Müller. (2002). Symbiosis and defence in the interaction of plants with microorganisms. Symbiosis 32: 83-104.

Books and Book chapters

-Bladergroen, M. R. and H. P. Spaink. (2002). Avirulence factors from symbiotic bacteria, p. 164-166. In: S. A. Leong, C. Allen, and E. W. Triplett (eds.), Biology of plant-microbe interactions. International Society for Molecular Plant-Microbe Interactions, St. Paul, MN, USA.

-Breek, C. K. D., F. van Iren, S. E. Wijting, N. Stuurman, and H. P. Spaink. (2002). Expression of multicolor fluorescent fusion proteins in zebrafish cell cultures: a versatile tool in cell biology, p. 373-379. In: Kraayenhof, Visser, and Gerritsen (eds.), Fluorescence Spectroscopy, Imaging and Probes. Springer Verlag, Heidelberg.

-Schmidt, K. A., C. V. Henkel, G. Rozenberg, and H. P. Spaink. (2002). Experimental Aspects of DNA computing by blocking: use of fluorescence techniques for detection, p. 123-128. In: Kraayenhof, Visser, and Gerritsen (eds.), Fluorescence Spectroscopy, Imaging and Probes: New tools in chemical, physical and life sciences. Springer Verlag, Heidelberg.

-Spaink, H. P., C. P. Bras, M. Grønlund, P. van Spronsen, J. W. Kijne, H. R. M. Schlaman, A. Roussis, S. E. Wijting, J. Stougaard, E. Flemetakis, and P. Katinakis. (2002). Responses of Lotus japonicus to Nod Factors, p. 148-152. In: T. M. Finan, M. R. O’Brian, D. B. Layzell, J. K. Vessey, and W. Newton (eds.), Nitrogen fixation: global perspectives. CABI Publishing, Wallingford, UK.

Dissertations

-E.A.D. Postma-Haarsma. Characterization of knox class 1 homeobox genes from rice. Promotor: Prof.dr. H.P. Spaink, co-promotor: dr. A.H. Meijer. 18-06-2002


Publications 2001

-Greco R, Ouwerkerk PB, Taal AJ, Favalli C, Beguiristain T, Puigdomenech P, Colombo L, Hoge JH et al. (2001). Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis. Plant Mol Biol. 46: 215 – 227

-Greco R, Ouwerkerk PB, Sallaud C, Kohli A, Colombo L, Puigdomenech P, Guiderdoni E, Christou P et al. (2001). Transposon insertional mutagenesis in rice. Plant Physiol 125: 1175 - 1177

-Harms GS, Cognet L, Lommerse PH, Blab GA, Kahr H, Gamsjager R, Spaink HP, Soldatov NM et al. (2001). Single-molecule imaging of l-type Ca(2+) channels in live cells. Biophys.J 81: 2639 - 2646

-López-Lara IM, Kafetzopoulos D, Spaink HP, Thomas-Oates JE (2001). Rhizobial NodL O-acetyl transferase and NodS N-methyl transferase functionally interfere in production of modified Nod factors. J.Bacteriol. 183: 3408 - 3416

-Okker RJH, Spaink HP, Lugtenberg BJJ, Schlaman HRM (2001). Mutants in the nodFEL promoter of Rhizobium leguminosarum bv. viciae reveal a role of individual nucleotides in transcriptional activation and protein binding. Arch.Microbiol. 175: 152 - 160

-Ouwerkerk PB, de Kam RJ, Hoge JH, Meijer AH (2001). Glucocorticoid-inducible gene expression in rice. Planta 213: 370 - 378

-Schenk PW, Epskamp SJ, Knetsch ML, Harten V, Lagendijk EL, van Duijn B, Snaar-Jagalska BE (2001). Lysophosphatidic acid- and Gbeta-dependent activation of Dictyostelium MAP kinase ERK2. Biochem.Biophys.Res.Commun. 282: 765 - 772

-van der Holst PP, Schlaman HR, Spaink HP (2001). Proteins involved in the production and perception of oligosaccharides in relation to plant and animal development. Curr.Opin.Struct.Biol. 11: 608 - 616

-van Spronsen PC, Grønlund M, Pacios Bras C, Spaink HP, Kijne JW (2001). Cell biological changes of outer cortical root cells in early determinate nodulation. Mol.Plant-Microbe Interact. 14: 839 - 847

-Yang SS, Bellogin RA, Buendia A, Camacho M, Chen M, Cubo T, Daza A, Diaz CL et al. (2001). Effect of pH and soybean cultivars on the quantitative analyses of soybean rhizobia populations. Journal of Biotechnology 91: 243 - 255

Books and Book chapters 2001

-Greco R, Ouwerkerk PBF, Sallaud C, Kohli A, Favalli C, Beguiristain T, Colombo L, Pe E, Puigdomenech P, Guiderdoni E, Christou P, Hoge JHC, Pereira A (2001) In: Rice Genetics IV (Khush GS, Brar DS, Hardy B, eds.), Science Publishers Inc., Enfield

-Ouwerkerk PBF, Meijer AH (2001) Yeast one-hybrid screening for DNA-Protein Interactions. Current Protocols in Molecular Biology 12.12.1-12.12.22

Dissertations 2001

-M.R. Bladergroen. Rhizobial secretion systems involved in avirulence. Promotor: Prof.dr. H.P. Spaink. 14-11-2001


Publications 2000

-Diaz, C., Spaink, H. P., and Kijne, J. W. (2000). Heterologous rhizobial lipochitin oligosaccharides and chitin oligomers induce cortical cell divisions in red clover roots, transformed with the pea lectin gene. Mol.Plant-Microbe Interact. 13:268-276.

-Flemetakis, E., Kavroulakis, N., Quaedvlieg, N. E., Spaink, H. P., Dimou, M., Roussis, A., and Katinakis, P. (2000). Lotus japonicus contains two distinct ENOD40 genes that are  expressed in symbiotic, nonsymbiotic, and embryonic tissues. Mol.Plant-Microbe Interact. 13:987-994.

-Head, T., Rozenberg, G., Bladergroen, R., Breek, K., Lommerse, PHM., and Spaink, HP. (2000). Computing with DNA by operating on plasmids. Biosystems 57:87-93.

-Kamst, E., Breek, K., and Spaink, H. P. (2000). Functional analysis of chimeric genes derived from the Sinorhizobium meliloti and Mesorhizobium loti nodC genes identifies regions controlling chitin oligosaccharide chain length. Mol.Gen.Genet. 264:75-81.

-Meijer AH, de Kam RJ, d’Erfurth I, Shen W, Hoge JHC (2000b). HD-Zip family I and II proteins from rice: interactions and functional properties. Mol Gen Genet 263: 12-21.

-Olsthoorn, M. M. A., Stokvis, E., Haverkamp, J., Spaink, H. P., and Thomas-Oates, J. E. (2000). Growth temperature regulation of host-specific modifications of rhizobial lipo-chitin oligosaccharides:the function of nodX is temperature regulated. Mol.Plant-Microbe Interact. 13:808-820.

-Ovtsyna, A. O., Schultze, M., Tikhonovich, I., Spaink, H. P., Kondorosi, E., Kondorosi, A., and Staehelin, C. (2000). Nod factors of Rhizobium leguminosarum bv. viciae and their fucosylated derivatives stimulate a Nod factor cleaving activity in pea roots and are hydrolyzed in vitro by plant chitinases at different rates. Mol.Plant-Microbe Interact.13:799-807.

-Pacios Bras, C., Alberich Jordá, M., Wijfjes, A. H. M., Harteveld, M., Stuurman, N., Thomas-Oates, J. E., and Spaink, H. P. (2000). A Lotus japonicus nodulation system based on heterologous expression of the fucosyl transferase NodZ and the acetyl transferase NolL in Rhizobium leguminosarum. Mol.Plant-Microbe Interact. 13:475-479.

-Scarpella E, Rueb S, Boot KJM, Hoge JHC, Meijer AH (2000b). A role for the rice homeobox gene Oshox1 in provascular cell fate commitment. Development 127: 3655-3669.

-Schouten J, de Kam RJ, Fetter K, Hoge JHC (2000). Overexpression of Arabidopsis thaliana SKP1 homologues in yeast inactivates the Mig1 repressor by destabilising the F-box protein Grr1. Mol Gen Genet 263: 309-319.

-Spaink, H. P. (2000). Root nodulation and infection factors produced by rhizobial bacteria. Annu.Rev.Microbiol. 54:257-288.

-Stuurman, N., Pacios Bras, C., Schlaman, H. R. M., Wijfjes, A. H. M., Bloemberg, G., and Spaink, H. P. (2000). Use of green fluorescent protein color variants expressed on stable broad-host-range vectors to visualize rhizobia interacting with plants. Mol.Plant-Microbe 13:1163-1169.

-Van der Fits L, Deakin EA, Hoge JHC, Memelink J (2000). The ternary transformation system: constitutive virG on a compatible plasmid dramatically increases Agrobacterium-mediated plant transformation. Plant Mol Biol 43: 495-502.

Books and Book chapters 2000

-Bladergroen, M. R., Lugtenberg, B. J. J., and Spaink, H. P. (2000). Characterization of a chromosomal NodI homolog, p. 246. In: F. O. Pedrosa, M. Hungria, M. G. Yates, and W. E. Newton (eds.), Nitrogen fixation: from molecules to crop productivity. Kluwer Acad. Pub., Dordrecht.

-Greco R, Ouwerkerk PBF, Sallaud C, Kohli A, Favalli C, Beguiristain T, Colombo L, Pe E, Puigdomenech P, Guiderdoni E, Christou P, Hoge JHC, Pereira A (2000). Transposons and functional genomics in rice. Proceedings of the International Rice Genetics Symposium, in press.

-Meijer AH, Schouten J, Ouwerkerk PBF and Hoge JHC (2000a). Yeast as versatile tool in transcription factor research. In: Gelvin SB, Schilperoort RA (eds) Plant Molecular Biology Manual (2nd edn, suppl IV). Kluwer Academic publishers, Dordrecht, pp E3: 1-28.

-Scarpella E, Hoge JHC, Meijer AH (2000a) Vascular-specific promoters. PCT/EP00/06248.

-Spaink, H. P., Schlaman, H. R. M., Pacios Bras, C., Roussis, A., Stougaard, J., and Stuurman, N. (2000). The use of GFP to study factors involved in the Lotus japonicus symbiosis, p. 219-222. In: F. O. Pedrosa, M. Hungria, M. G. Yates, and W. E. Newton (eds.), Nitrogen fixation: from molecules to crop productivity. Kluwer Acad. Pub., Dordrecht.

-Spaink, H. P., Boot, K. J. M., van Brussel, A. A. N., Pacios Bras, C., and Kijne, J. W. (2000). Responses of the host plant to rhizobial nodulation factors, p. 396-400. In: P. J. G. M. de Wit, T. Bisseling, and W. J. Stiekema (eds.), Biology of plant-microbe interactions. International Society for Molecular Plant-Microbe Interactions, St.Paul.

Dissertations 2000

-J.P.W.M. Bakkers. Chitin oligosaccharides in zebrafish development. Investigations at the molecular cellular level. Promotors: Prof.dr. H.P. Spaink, Prof.dr. J.W. Kijne. 29-06-2000          

-P.W. Schenk. Role of protein kinases in Dyctyostelium discoideum signal transduction. Promotor: Prof.dr. Th.M. Konijn, co-promotor: Dr. B.E. Snaar-Jagalska. 17-02-2000

Publications 1999


-Boone CM, Olsthoorn MMA, Dakora FD, Spaink HP, Thomas-Oates JE (1999). Structural characterisation of lipo-chitin oligosaccharides isolated from Bradyrhizobium aspalati, microsymbionts of commercially important South African legumes. Carbohydr Res 317: 155-163.

-Boot KJM, van Brussel AAN, Tak T, Spaink HP, Kijne JW (1999). Lipochitin oligosaccharides from Rhizobium leguminosarum bv. viciae reduce auxin transport capacity in Vicia sativa subsp. nigra roots. Mol Plant-Microbe Interact 12: 839-844.

-Kamst E, Spaink HP (1999). Functional domains in the chitin oligosaccharide synthase NodC and related ß-polysaccharide synthases. Trends in Glycoscience and Glycotechnol 11: 187-200.

-Kamst E, Zegelaar-Jaarsveld K, van der Marel GA, van Boom JH, Lugtenberg BJJ, Spaink HP (1999). Chemical synthesis of N-acetylglucosamine derivatives and their use as glycosyl-acceptors by the -Mesorhizobium loti chitin oligosaccharide synthase NodC. Carbohydr.Res. 321: 176-189.

-Kamst E, Bakkers J, Quaedvlieg NE, Pilling J, Kijne JW, Lugtenberg BJJ, Spaink HP (1999). Chitin oligosaccharide synthesis by rhizobia and zebrafish embryos starts by glycosyl transfer to O4 of the reducing-terminal residue. Biochemistry 38: 4045-4052.

-Lamrabet Y, Bellogin RA, Cubo T, Espuny R, Gil A, Krishnan HB, Megias M, Ollero FJ, Pueppke SG, Ruiz-Sainz JE, Spaink HP, Tejero-Mateo P, Thomas-Oates J, Vinardell JM (1999). Mutation in GDP-fucose synthesis genes of Sinorhizobium fredii alters nod factors and significantly decreases competitiveness to nodulate soybeans. Mol Plant-Microbe Interact 12: 207-217.

-Meima ME, P Schaap P (1999) Dictyostelium development-socializing through cAMP. Semin.Cell Dev.Biol 10: 567-576

-Meima ME, Schaap P (1999) Fingerprinting of adenylyl cyclase activities during Dictyostelium development indicates a dominant role for adenylyl cyclase B in terminal differentiation. Dev.Biol. 212: 182-190

-Mohanty S, Jermyn KA, Early A, Kawata T, Aubry L, Ceccarelli A, Schaap P, Williams JG, Firtel RA (1999) Evidence that the Dictyostelium Dd-STATa protein is a repressor that regulates commitment to stalk cell differentiation and is also required for efficient chemotaxis: Development, v. 126, p. 3391-3405

-Ouwerkerk PBF, Memelink J (1999) Elicitor-responsive promoter regions in the tryptophan decarboxylase gene from Catharanthus roseus. Plant Mol Biol 39:129-136.

-Ouwerkerk PBF, Hallard D, Verpoorte R, Memelink J (1999). Identification of UV-B light-responsive regions in the promoter of the tryptophan decarboxylase gene from Catharanthus roseus. Plant Mol Biol 41:491-503.

-Ouwerkerk PBF, Memelink J (1999). A G-box element from the Catharanthus roseus strictosidine synthase (Str) gene promoter confers seed-specific expression in transgenic tobacco plants. Mol Gen Genet 261:635-643.

-Ouwerkerk PBF, Trimborn TO, Hilliou F, Memelink J (1999). Nuclear factors GT-1 and 3AF1 interact with multiple sequences within the promoter of the Tdc gene from Madagascar periwinkle: GT-1 is involved in UV light-induced expression. Mol Gen Genet 261:610-622.

-Ovtsyna AO, Rademaker GJ, Esser E, Weinman J, Rolfe BG, Tikhonovich IA, Lugtenberg BJJ, Thomas-Oates JE, Spaink HP (1999). Comparison of characteristics of the nodX genes from various Rhizobium leguminosarum strains. Mol Plant-Microbe Interact 12: 252-258.

-Pasquali G, Erven AS, Ouwerkerk PBF, Menke FL, Memelink J (1999). The promoter of the strictosidine synthase gene from periwinkle confers elicitor-inducible expression in transgenic tobacco and binds nuclear factors GT-1 and GBF. Plant Mol Biol 39:1299-1310.

-Postma-Haarsma AD, Verwoert IIGS, Stronk OP, Koster J, Lamers GEM, Hoge JHC, Meijer AH (1999). Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice embryogenesis. Plant Mol Biol 39:257-271.

-Schenk PW, Nebl T, Fisher PR, Snaar-Jagalska BE  (1999). A serpentine receptor-dependent, G beta- and Ca2+ influx-independent pathway regulates mitogen-activated protein kinase ERK2 in Dictyostelium. Biochem Biophys Res Commun 260: 504-509.

-Schenk PW, Snaar-Jagalska BE  (1999). Signal perception and transduction: the role of protein kinases. Biochim Biophys Acta 1449: 1-24.

-Spaink HP  (1999). Plant genetics-Knocking out nodules. Nature 402: 135-136.

-Stuurman N, Haner M, Sasse B, Hubner W, Suter B, Aebi U  (1999). Interactions between coiled-coil proteins: Drosophila lamin Dm(0) binds to the Bicaudal-D protein. Eur J Cell Biol 78: 278-287.

-Virdy KJ, Sands TW, Kopko SH, van Es S, Meima M, Schaap P, Cotter DA (1999) High cAMP in spores of Dictyostelium discoideum: association with spore dormancy and inhibition of germination. Microbiology 145: 1883-1890.

-Wang M, Hoekstra S, van Bergen S, Lamers GEM, Oppedijk BJ, van der Heijden MW, de Priester W, Schilperoort RA (1999). Apoptosis in developing anthers and the role of ABA in this process during androgenesis in Hordeum vulgare L. Plant Mol Biol 39:489-501.

Publications 1998

-Bladergroen M, Spaink HP (1998). Genes and signal molecules involved in the rhizobia-leguminoseae symbiosis.  Curr. Opinion Plant Biol. 1: 353-359.

-Dekkers L, Bloemendaal CJP, Weger L de, Wijffelman CA, Spaink HP, Lugtenberg BJJ (1998). A two-component system plays an important role in the root-colonizing ability of Pseudomonas fluorescens strain WCS365.  Mol. Plant-Microbe Int. 11: 45-56.

-Canel C, Lopes Cardoso MI, Whitmer S, Fits L van der, Pasquali G, Heijden R van der, Hoge JHC, Verpoorte R (1998). Effects of over-expression of strictosidine synthase and tryptophan decarboxylase on alkaloid production by cell cultures of Catharanthus roseus. Planta 205: 414-419.

-Geiger O, Glushka J, Lugtenberg BJJ, Spaink HP, Thomas-Oates J (1998). Rhizobial NodFE-dependent fatty acids which lack an a-b unsaturation are subject to differential transfer leading to novel phospholipids. Mol. Plant-Microbe Int. 11: 33-44.

-Hallard D, Heijden R van der, Contin A, Tomas Jimenez EM, Snoeijer W, Verpoorte R, Jensen SR, Lopes Cardoso MI, Pasquali G, Memelink J, Hoge JHC (1998). An assay for secologanin in plant tissues based on enzymatic conversion into strictosidine. Phytochem. Anal. 9: 162-167.

-Mathesius U, Schlaman WRM, Spaink HP, Sautter C, Rolfe BG, Djordjevic MA (1998). Auxin transport inhibition precedes root nodule formation in white clover roots and is regulated by flavonoids and derivatives of chitin oligosaccharides.  Plant J. 14: 23-34.

-Meijer AH, Kam RJ de, Qin L, Hoge JHC (1998). Osjab1 (Accession No. AF072849): A rice homolog of the human JAB1 transcriptional coactivator. (PGR98-149) Plant Physiol. 117: 152-153.

-Meijer AH, Ouwerkerk PBF, Hoge JHC (1998). Vectors for transcription factor isolation and target gene identification by means of genetic selection in yeast. Yeast 14: 1407-1416.

-Olsthoorn MMA, López-Lara IM, Petersen BO, Bock K, Haverkamp J, Spaink HP, Thomas-Oates JE (1998). Novel branched Nod factor structure results from a-(1-3) fucosyl transferase activity: the major lipo-chitin oligosaccharides from Mesorhizobium loti strain NZP2213 bear an a-(1-3) fucosyl substituent on a nonterminal backbone residue.  Biochem. 37: 9024-9032.

-Ovtsyna AO, Geurts R, Bisseling T, Lugtenberg BJJ, Tikhonovich IA, Spaink HP (1998). Restriction of host range by the sym2 allele of Afghan pea is non-specific for the type of modification at the reducing terminus of nodulation signals.  Mol. Plant-Microbe Int. 11: 418-422.

-Quaedvlieg NEM, Schlaman HRM, Admiraal PC, Wijting SE, Stougaard J, Spaink HP (1998). Fusions between green fluorescent protein and b-glucuronidase as sensitive and vital bifunctional reporters in plants.  Plant Mol. Biol. 37: 715-727.

-Ritsema T, Gehring AM, Stuitje AR, Drift KMGM van der, Dandal I, Lambalot RH, Walsh CT, Thomas-Oates J, Lugtenberg BJJ, Spaink HP (1998). Functional analyis of an interspecies chimera of acyl carrier proteins indicates a specialized domain for protein recognition.  Mol. Gen. Genet. 257: 641-648.

-Semino C, Allende ML, Bakkers J, Spaink HP, Robbins PW (1998). Expression of Rhizobium oligosaccharide fucosyltransferase in zebrafish embryos disrupts normal development.  Ann. New York Acad. Sciences 842: 49-54.

-Wang M, Oppedijk BJ, Caspers MPM, Lamers GEM, Boot MJ, Geerlings DNG, Bakhuizen B, Meijer AH, Duijn B van (1998). Spatial and temporal regulation of DNA fragmentation in the aleurone of germinating barley. J. Exp. Bot. 49: 1293-1301.

Webredactie Science - Last edited: 02 Nov 2011