Publications

2017

Reinhard NR, Mastop M, Yin T, Wu Y, Bosma EK, Gadella TWJ Jr, Goedhart J, Hordijk PL. The balance between Gα(i)-Cdc42/Rac and Gα(12)/(13)-RhoA pathways determines endothelial barrier regulation by Sphingosine-1-Phosphate. Mol Biol Cell. 2017 Sep 27. pii: mbc.E17-03-0136. doi: 10.1091/mbc.E17-03-0136.

Mastop M, Bindels DS, Shaner NC, Postma M, Gadella TWJ Jr, Goedhart J. Characterization of a spectrally diverse set of fluorescent proteins as FRET acceptors for mTurquoise2. Sci Rep. 2017 Sep 20;7(1):11999. doi:10.1038/s41598-017-12212-x

Yuchen Long, Yvonne Stahl, Stefanie Weidtkamp-Peters, Marten Postma, Wenkun Zhou, Joachim Goedhart, María-Isabel Sánchez-Pérez, Theodorus W. J. Gadella, Rüdiger Simon, Ben Scheres & Ikram Blilou: ‘In vivo FRET–FLIM reveals cell-type-specific protein interactions in Arabidopsis roots’, in Nature (26 July 2017).

van de Moosdijk AA, Fu NY, Rios AC, Visvader JE, van Amerongen R (2017), ‘Lineage Tracing of Mammary Stem and Progenitor Cells’, Methods Mol Biol. 2017;1501:291-308

Goedhart J, van Unen J. Molecular perturbation strategies to examine spatiotemporal features of Rho GEF and Rho GTPase activity in living cells. Small GTPases. 2017 May 19:1-9.

Zuidscherwoude M, Dunlock VE, van den Bogaart G, van Deventer SJ, van der Schaaf A, van Oostrum J, Goedhart J, In ‘t Hout J, Hämmerling GJ, Tanaka S, Nadler A, Schultz C, Wright MD, Adjobo-Hermans MJW, van Spriel AB. Tetraspanin microdomains control localized protein kinase C signaling in B cells. Sci Signal. 2017 May 9;10(478).

Vermeer JEM, van Wijk R, Goedhart J, Geldner N, Chory J, Gadella TWJ Jr, Munnik T. In Vivo Imaging of Diacylglycerol at the Cytoplasmic Leaflet of Plant Membranes. Plant Cell Physiol. 2017 Jan 31. doi: 10.1093/pcp/pcx012. [Epub ahead of print]

Bindels DS, Haarbosch L, van Weeren L, Postma M, Wiese KE, Mastop M, Aumonier S, Gotthard G, Royant A, Hink MA, Gadella TWJ Jr. (2017) mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat Methods. Jan 2017. doi: 10.1038/nmeth.4074. [Epub ahead of print]

2016

Jacobsen A, Heijmans N, Verkaar F, Smit MJ, Heringa J, van Amerongen R, Feenstra KA. (2016) Construction and experimental validation of a Petri net model of Wnt/β-Catenin signaling. PLoS One 11, e0155743.  doi: 10.1371/journal.pone.0155743

Heemskerk N, Schimmel L, Oort C, van Rijssel J, Yin T, Ma B, van Unen J, Pitter B, Huveneers S, Goedhart J, Wu Y, Montanez E, Woodfin A, van Buul JD. F-actin-rich contractile endothelial pores prevent vascular leakage during leukocyte diapedesis through local RhoA signalling. Nat Commun. 2016 Jan 27;7:10493. doi: 10.1038/ncomms10493

Raspe M, Kedziora KM, van den Broek B, Zhao Q, de Jong S, Herz J, Mastop M, Goedhart J, Gadella TW, Young IT, Jalink K. (2016) siFLIM: single-image frequency-domain FLIM provides fast and photon-efficient lifetime data. Nat Methods 13, 501-504. doi: 10.1038/nmeth.3836

Reinhard NR, van Helden SF, Anthony EC, Yin T, Wu YI, Goedhart J, Gadella TW, Hordijk PL. (2016) Spatiotemporal analysis of RhoA/B/C activation in primary human endothelial cells. Sci Rep. 6, 25502. doi: 10.1038/srep25502

van Unen J, Stumpf AD, Schmid B, Reinhard NR, Hordijk PL, Hoffmann C, Gadella TW Jr, Goedhart J. (2016) A new generation of FRET Sensors for robust measurement of Gαi1, Gαi2 and Gαi3 activation kinetics in single cells. PLoS One 11, e0146789. doi: 10.1371/journal.pone.0146789

van Unen J, Rashidfarrokhi A, Hoogendoorn E, Postma M, Gadella TW Jr, Goedhart J. (2016) Quantitative single-cell analysis of signaling pathways activated immediately downstream of Histamine receptor subtypes. Mol Pharmacol. 90, 162-176. doi: 10.1124/mol.116.104505

Marten Postma and Peter J.M. van Haastert. Mathematics of experimentally generated chemoattractant gradients. Chemotaxis: Methods and Protocols. Series: Methods in Molecular Biology. Springer New York (2016)

MC Boelens, M Nethe, S Klarenbeek, JR de Ruiter, E Schut, N Bonzanni, AL Zeeman, E Wientjens, E van der Burg, L Wessels, R van Amerongen, J Jonkers (2016), ‘PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma’, Cell Reports 16(8): 2087–2101

Loh KM, van Amerongen R, Nusse R (2016), ‘Generating cellular diversity and spatial form: Wnt Signaling and the Evolution of Multicellular Animals’, Developmental Cell 38(6): p643–655

van de Moosdijk AAA, van Amerongen R (2016), ‘Identification of reliable reference genes for qRT-PCR studies of the developing mouse mammary gland’, Scientific Reports 6:35595 DOI: 10.1038/srep35595

Lloyd-Lewis B, van de Moosdijk AAA, Bentires-Alj M, Clarke RB, van Amerongen R (2016), ‘Complexity galore: 3D cultures, biomechanics and systems medicine at the eighth ENBDC workshop “Methods in Mammary Gland Development and Cancer”’, Breast Cancer Res (2016) 18: 115.

2015

Amerongen, R. van (2015). Lineage Tracing in the Mammary Gland Using Cre/lox Technology and Fluorescent Reporter Alleles. In M. Vivanco del Mar (Ed.), Mammary Stem Cells: methods and protocols (Methods in Molecular Biology, 1293) (pp. 187-211). New York: Humana Press.

Boer, R. de, Smith, R.L., De Vos, W.H., Manders, E.M.M., Brul, S. & Spek, H. van der (2015). Caenorhabditis elegans as a Model System for Studying Drug Induced Mitochondrial Toxicity. PLoS One, 10 (5):e0126220. doi: 10.1371/journal.pone.0126220

Dattoli, A.A., Hink, M.A., DuBuc, T.Q., Teunisse, B.J., Goedhart, J., Röttinger, E. & Postma, M. (2015). Domain analysis of the Nematostella vectensis SNAIL ortholog reveals unique nucleolar localization that depends on the zinc-finger domains. Scientific Reports, 5:12147. doi: 10.1038/srep12147

Dattoli, A.A. (2015, December 02). Structural and functional analysis of the development of the translucent sea anemone, Nematostella vectensis. Universiteit van Amsterdam (183 pag.). Prom./coprom.: prof. dr. Th.W.J. Gadella & dr. M. Postma.

Glukhova, M.A., Hynes, N., Vivanco, dM, Amerongen, R. van, Clarke, R.B. & Bentires-Alj, M. (2015). The seventh ENBDC workshop on methods in mammary gland development and cancer. Breast Cancer Research, 17 (9):119. doi: 10.1186/s13058-015-0629-5

Haarbosch, L., Goedhart, J., Hink M.A., van Weeren, L., Bindels, D.S. & T.W.J. Gadella. Engineering of optimized fluorescent proteins: an overview from a cyan & FRET perspective. In Optical Probes in Biology (2015). J. Zhang, S. Mehta & C. Schultz ed., CRC Press

Hink, M.A. (2015). Fluorescence correlation spectroscopy. In P.J. Verveer (Ed.), Advanced Fluorescence Microscopy: Methods and Protocols (Methods in Molecular Biology, 1251) (pp. 135-150). New York: Humana Press.

Huveneers, S., Daemen, M.J.A.P. & Hordijk, P.L. (2015). Between Rho(k) and a hard place: the relation between vessel wall stiffness, endothelial contractility, and cardiovascular disease. Circulation Research, 116 (5), 895-908. doi: 10.1161/CIRCRESAHA.116.305720

Klarenbeek, J., Goedhart, J., Batenburg, A. van, Groenewald, D. & Jalink, K. (2015). Fourth-generation epac-based FRET sensors for cAMP feature exceptional brightness, photostability and dynamic range: characterization of dedicated sensors for FLIM, for ratiometry and with high affinity. PLoS One, 10 (4), e0122513. doi: 10.1371/journal.pone.0122513

Long, Y., Goedhart, J., Schneijderberg, M., Terpestra, I., Shimotohno, A., Bouchet, B.P., Akhmanova, A., Gadella (jr.), Th.W.J., Heidstra, R., Scheres, B. & Blilou, I. (2015). SCARECROW-LIKE23 and SCARECROW jointly specify endodermal cell fate but distinctly control SHORT-ROOT movement. Plant Journal, 84 (4), 773-784. doi: 10.1111/tpj.13038

Nahidiazar, L., Kreft, M., Broek, B. van den, Secades, P., Manders, E.M.M., Sonnenberg, A. & Jalink, K. (2015). The molecular architecture of hemidesmosomes, as revealed with super-resolution microscopy. Journal of Cell Science, 128 (20), 3714-3719. doi: 10.1242/jcs.171892

Nieuwenhuizen, R.P.J., Nahidiazar, L., Manders, E.M.M., Jalink, K., Stallinga, S. & Rieger, B. (2015). Co-Orientation: Quantifying Simultaneous Co-Localization and Orientational Alignment of Filaments in Light Microscopy. PLoS One, 10 (7), e0131756. doi: 10.1371/journal.pone.0131756

Pandey, R., Pieper, G.H., Beek, A. ter, Vischer, N.O.E., Smelt, J.P.P.M., Manders, E.M.M. & Brul, S. (2015). Quantifying the effect of sorbic acid, heat and combination of both on germination and outgrowth of Bacillus subtilis spores at single cell resolution. Food Microbiology, 52, 88-96. doi: 10.1016/j.fm.2015.06.007

Pandey, R., Beek, A. van de, Vischer, N.O., Smelt, J.P.P.M., Kemperman, R., Manders, E.M.M. & Brul, S. (2015). Quantitative analysis of the effect of specific tea compounds on germination and outgrowth of Bacillus subtilis spores at single cell resolution. Food Microbiology, 45 (Pt A), 63-70. doi: 10.1016/j.fm.2014.03.006

Schaefer, A. & Hordijk, P.L. (2015). Cell-stiffness-induced mechanosignaling – a key driver of leukocyte transendothelial migration. Journal of Cell Science, 128 (13), 2221-2230. doi: 10.1242/jcs.163055

Shahi, S., Beerens, B., Manders, E.M.M. & Rep, M. (2015). Dynamics of the establishment of multinucleate compartments in Fusarium oxysporum. Eukaryotic Cell, 14 (1), 78-85. doi: 10.1128/EC.00200-14

Smith, R.L., De Vos, W.H., Boer, R. de, Manders, E.M.M. & Spek, H. van der (2015). In vivo visualization and quantification of mitochondrial morphology in C. elegans. In V. Weissig & M. Edeas (Eds.), Mitochondrial medicine. – Vol. 2: Manipulating mitochondrial function (Methods in molecular biology, 1265) (pp. 367-377). New York: Humana Press.

Timmerman, I., Heemskerk, N., Kroon, J., Schaefer, A., Rijssel, J. van, Hoogenboezem, M., Unen, J. van, Goedhart, J., Gadella, T.W.J., Yin, T., Wu, Y., Huveneers, S. & Buul, J.D. van (2015). A local VE-cadherin and Trio-based signaling complex stabilizes endothelial junctions through Rac1. Journal of Cell Science, 128, 3041-3054. doi: 10.1242/jcs.168674

Unen, J. van, Woolard, J., Rinken, A., Hoffmann, C., Hill, S.J., Goedhart, J., Bruchas, M.R., Bouvier, M. & Adjobo-Hermans, M.J.W. (2015). A Perspective on Studying G-Protein-Coupled Receptor Signaling with Resonance Energy Transfer Biosensors in Living Organisms. Molecular Pharmacology, 88 (3), 589-595. doi: 10.1124/mol.115.098897

Unen, J. van, Reinhard, N.R., Yin, T., Wu, Y.I., Postma, M., Gadella, Th.W.J. & Goedhart, J. (2015). Plasma membrane restricted RhoGEF activity is sufficient for RhoA-mediated actin polymerization. Scientific Reports 5, 14693.  doi: 10.1038/srep14693

Vischer, N.O.E., Verheul, J., Postma, M., Berg van Saparoea, B. van den, Galli, E., Natale, P., Gerdes, K., Luirink, J., Vollmer, W., Vicente, M & Blaauwen, T. den (2015). Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ. Frontiers in Microbiology, 6, 586. doi: 10.3389/fmicb.2015.00586

Hink MA. Fluorescence correlation spectroscopy. Methods Mol Biol. (2015) 1251, 135-50. doi: 10.1007/978-1-4939-2080-8_8.

van Unen J., Woolard J., Rinken A., Hoffmann C., Hill S., Goedhart J., Bruchas M., Bouvier M., Adjobo-Hermans M. A perspective on studying GPCR signaling with RET Biosensors in living organisms.Mol Pharmacol.  Epub (2015)

 

2014

Amerongen, R. van (2014). Bipotent mammary stem cells: now in amazing 3D. Breast Cancer Research, 2014 (16):480. doi: 10.1186/s13058-014-0480-0

Bindels D.S., Goedhart J., Hink M.A., van Weeren L., Joosen L., Gadella T.W.J. Jr. Optimization of fluorescent proteins. Methods Mol Biol. (2014) 1076, 371. doi: 10.1007/978-1-62703-649-8_16. View PubMed

DuBuc, T.Q., Dattoli, A., Babonis, L.S., Salinas-Saavedra, M., Rottinger, E., Martindale, M.Q. & Postma, M. (2014). In vivo imaging of Nematostella vectensis embryogenesis and late development using fluorescent probes. BMC Cell Biology, 15 (1), 44. doi: 10.1186/s12860-014-0044-2

Goedhart J, Hink MA, Jalink K. An introduction to fluorescence imaging techniques geared towards biosensor applications. Methods Mol Biol. (2014) 1071, 17 doi: 10.1007/978-1-62703-622-1_2. View PubMed

Green J, Nusse R, van Amerongen R. The role of ryk and ror receptor tyrosine kinases in wnt signal transduction., Cold Spring Harb Perspect Biol. (2014) 6(2). pii: a009175. View PubMed

Hamers D, van Voorst Vader L, Borst JW, Goedhart J. Development of FRET biosensors for mammalian and plant systems. Protoplasma (2014) 251:333. doi: 10.1007/s00709-013-0590-z. View PubMed

Hink MA. Quantifying intracellular dynamics using fluorescence fluctuation  spectroscopy. Protoplasma. (2014) 251, 307 doi: 10.1007/s00709-013-0602-z. View PubMed

Hoogendoorn E, Crosby KC, Leyton-Puig D, Breedijk RM, Jalink K, Gadella TW,Postma M. The fidelity of stochastic single-molecule super-resolution reconstructions critically depends upon robust background estimation. Sci Rep. (2014) 4, 3854. doi: 10.1038/srep03854. View PubMed

Ingaramo M, York AG, Hoogendoorn E, Postma M, Shroff H, Patterson GH. Richardson-lucy deconvolution as a general tool for combining images with complementary strengths. Chemphyschem. (2014) 15, 794 doi:10.1002/cphc.201300831. View PubMed 

Jezierska J, Goedhart J, Kampinga HH, Reits EA, Verbeek DS. SCA14 mutation V138E leads to partly unfolded PKCγ associated with an exposed C-terminus, altered kinetics, phosphorylation and enhanced insolubilization.J Neurochem. (2014) 128:741 doi: 10.1111/jnc.12491. View PubMed

Joosen, L., Hink, M.A., Gadella, T.W.J. & Goedhart, J. (2014). Effect of fixation procedures on the fluorescence lifetimes of Aequorea victoria derived fluorescent proteins. Journal of Microscopy, 256 (3), 166-176. doi: 10.1111/jmi.12168

Kemper, K., Goeje, P.L. de, Peeper, D.S. & Amerongen, R. van (2014). Phenotype switching: tumor cell plasticity as a resistance mechanism and target for therapy. Cancer Research, 74 (21), 5937-41. doi: 10.1158/0008-5472.CAN-14-1174

Moling, S., Pietraszewska-Bogiel, A., Postma, M., Fedorova, E., Hink, M.A., Limpens, E., Gadella, T.W. & Bisseling, T. (2014). Nod factor receptors form heteromeric complexes and are essential for intracellular infection in medicago nodules. The Plant Cell, 26 (10), 4188-99. doi: 10.1105/tpc.114.129502

Noam, Y., Ehrengruber, M.U., Koh, A., Feyen, P., Manders, E.M.M., Abbott, G.W., Wadman, W.J. & Baram, T.Z. (2014). Filamin A promotes dynamin-dependent internalization of hyperpolarization-activated cyclic nucleotide-gated type 1 (HCN1) channels and restricts /h in hippocampal neurons. The Journal of Biological Chemistry, 289 (9), 5889-5903. doi: 10.1074/jbc.M113.522060

Rinkevich, Y., Montoro, D.T., Contreras-Trujillo, H., Harari-Steinberg, O., Newman, A.M., Tsai, J.M., Lim, X., Van-Amerongen, R., Bowman, A., Januszyk, M., Pleniceanu, O., Nusse, R., Longaker, M.T., Weissman, I.L. & Dekel, B. (2014). In vivo clonal analysis reveals lineage-restricted progenitor characteristics in mammalian kidney development, maintenance, and regeneration. Cell Reports, 7 (4), 1270-83. doi: 10.1016/j.celrep.2014.04.018

Schipper-Krom S, Juenemann K, Jansen AH, Wiemhoefer A, van den Nieuwendijk R, Smith DL, Hink MA, Bates GP, Overkleeft H, Ovaa H, Reits E. Dynamic recruitment of active proteasomes into polyglutamine initiated inclusion bodies. FEBS Lett. (2014) 588:151. doi: 10.1016/j.febslet.2013.11.023. View PubMed 

Schouten, M., De Luca, G.M.R., Alatriste González, D.K., Jong, B.E. de, Timmermans, W., Xiong, H., Krugers, H., Manders, E.M.M. & Fitzsimons, C.P. (2014). Imaging dendritic spines of rat primary hippocampal neurons using structured illumination microscopy. Journal of Visualized Experiments, 87, e51276. doi: 10.3791/51276

Shehata, M., Amerongen, R. van, Zeeman, A.L., Giraddi, R.R. & Stingl, J. (2014). The influence of tamoxifen on normal mouse mammary gland homeostasis. Breast Cancer Research, 16 (4), 411. doi: 10.1186/s13058-014-0411-0

Tark-Dame, M., Jerabek, H., Manders, E.M.M., Heermann, D.W. & Driel, R. van (2014). Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling. PLoS Computational Biology, 10 (10), e1003877. doi: 10.1371/journal.pcbi.1003877

Verbruggen, P., Heinemann, T., Manders, E., Bornstaedt, G. von, Driel, R. van & Höfer, T. (2014). Robustness of DNA Repair through Collective Rate Control. PLoS Computational Biology, 10 (1), e1003438. doi: 10.1371/journal.pcbi.1003438

2013

Adjobo-Hermans, M.J.W., Crosby, K.C., Putyrski, M., Bhageloe, A., Weeren, L. van, Schultz, C., Goedhart, J. & Gadella (jr.), T.W.J. (2013). PLCbeta isoforms differ in their subcellular location and their CT-domain dependent interaction with Galphaq. CELL SIGNAL, 25(1), 255-263. View PubMed

Bilan, D.S., Pase, L., Joosen, L., Gorokhovatsky, A.Y., Ermakova, Y.G., Gadella (jr), T.W.J., Grabher, C., Schultz, C., Lukyanov, S. & Belousov, V.V. (2013). HyPer-3: A Genetically Encoded H(2)O(2) Probe with Improved Performance for Ratiometric and Fluorescence Lifetime Imaging. ACS Chem Biol, 8(3), 535-542. View PubMed

Chu, B., Postma,M. Hardie, R.C. Fractional Ca2+ Currents through TRP and TRPL Channels in Drosophila Photoreceptors. Biophys J. 104:1905-1916 (2013). View PubMed

Crosby K.C., Postma M., Hink M.A., Zeelenberg C.H., Adjobo-Hermans M.J.W., Gadella T.W.J. Quantitative analysis of self-association and mobility of annexin A4 at the plasma membrane. Biophys J. 104: 1875-85 (2013) View PubMed

De Luca, G.M.R., Breedijk, R.M.P., Brandt, R.A.J., Zeelenberg, C.H.C., de Jong, B.E., Timmermans, W., Azar, L.N., Hoebe, R.A., Stallinga, S., Manders, E.M.M.  Re-scan confocal microscopy: scanning twice for better resolution (2013) BIOMEDICAL OPTICS EXPRESS  Vol.4 (11), 2644-2656. View PubMed

Gillis J., Schipper-Krom S., Juenemann K., Gruber A., Coolen S., van den Nieuwendijk R., van Veen H., Overkleeft H., Goedhart J., Kampinga H.H., Reits E.A.J. (2013) The DNAJB6 and DNAJB8 protein chaperones prevent intracellular aggregation of polyglutamine peptides. J. Biol. Chem. 288(24):17225-37. View PubMed

Goedhart, J., van Unen, J., Adjobo-Hermans, M. J. W. and Gadella Jr., T.W.J. Signaling efficiency of G alpha q through its effectors p63RhoGEF and GEFT depends on their subcellular location. SCIENTIFIC REPORTS 3, 2284 (2013). View PubMed

Hink M.A, Postma M. Monitoring receptor oligomerization by line-scan fluorescence cross-correlation spectroscopy. Methods Cell Biol. 117, 197-212 (2013). View PubMed

Lestini R., Laptenok S.P., Kuhn J., Hink M.A., Schanne-Klein M.-C., Liebl U. and Myllykallio H. Intracellular dynamics of archaeal FANCM homologue Hef in response to halted DNA replication. Nucleic Acid Research 41, 10358-10370 (2013). View PubMed

Lim, X. Tan, S.H., Koh, W.L.C., Chau, R.M.W., Yan, K.S., Kuo, C.J. van Amerongen, R., Klein, A.M., Nusse, R. (2013) Interfollicular Epidermal Stem Cells Self-Renew via Autocrine Wnt Signaling. Science 342 (6163), 1226-1230. View PubMed

Pandey, R., Beek, A. ter, Vischer, N.O., Smelt, J.P., Brul, S. & Manders, E.M. (2013). Live cell imaging of germination and outgrowth of individual bacillus subtilis spores; the effect of heat stress quantitatively analyzed with SporeTracker. PLoS One, 8(3), e58972. View PubMed

Pietraszewska, A., Lefebvre, B., Koini, A.M., Klaus-Heisen, D., Takken, F.L., Geurts, R., Cullimore, J.V. & Gadella, T.W. (2013). Interaction of Medicago truncatula Lysin Motif Receptor-Like Kinases, NFP and LYK3, Produced in Nicotiana benthamiana Induces Defence-Like Responses. PLoS One, 8(6), e65055. View PubMed

van der Ploeg R., Verheul J., Vischer N.O., Alexeeva S., Hoogendoorn E., Postma M., Banzhaf M., Vollmer W., den Blaauwen T. Colocalization and interaction between elongasome and divisome during a preparative cell division phase in Escherichia coli. Mol Microbiol. 87:1074-1087 (2013). View PubMed

Verhoeven, G.S., Dogterom, M. & Blaauwen, T. den (2013). Absence of long-range diffusion of OmpA in E. coli is not caused by its peptidoglycan binding domain. BMC Microbiology, 13(1), 66. View PubMed

 

2012

Banzhaf, M., Berg van Saparoea, B. van den, Terrak, M, Fraipont, C., Egan, A., Philippe, J., Zapun, A., Breukink, E., Nguyen-Distèche, M., Blaauwen, T. den & Vollmer, W. (2012). Cooperativity of peptidoglycan synthases active in bacterial cell elongation. Molecular Microbiology, 85(1), 179-194.

Bilan, D.M., Pase, L., Joosen, L., Gorokhovatsky, A.Y., Ermakova, Y.G., Gadella, T.W.J., Jr., Grabher, C. , Schultz, C., Lukyanov, S. and Belousov, V.V. (2012) HyPer-3: A Genetically Encoded H2O2 Probe with Improved Performance for Ratiometric and Fluorescence Lifetime Imaging. ACS Chem. Biol., DOI: 10.1021/cb300625g, EPubl. December 20, 2012.

Goedhart, J., Stetten, D. von, Noirclerc-Savoye, M., Lelimousin, M., Joosen, L., Hink, M.A., Weeren, L. van, Gadella, Th.W.J. & Royant, A. (2012). Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%. Nat Commun, 3, 751.

Hink, M.A. (2012) Single-molecule microscopy using silicone oil immersion objective lenses. Biomedical Scientist, Feb12, 83-85.

Lefebvre, B., Klaus-Heisen, D., Pietraszewska-Bogiel, A., Hervé, M., Camut, S., Auriac, M.C., Gasciolli, V., Nurisso, A., Gadella, T.W. & Cullimore, J. (2012). Role of N-glycosylation sites and CXC motifs in trafficking of Medicago trunculata Nod Factor Perception protein to the plasma membrane. The Journal of Biological Chemistry, 287(14), 10812-10823.

Leisch, N., Verheul, J., Heindl, N.R., Gruber-Vodicka, H.R., Pende, N., Blaauwen, T. den & Bulgheresi, S. (2012). Growth in width and FtsZ ring longitudinal positioning in a gammaproteobacterial symbiont. CURR BIOL, 22(19), R831-R832.

Noam, Y., Phan, L., McClelland, S., Manders, E.M., Ehrengruber, M.U., Wadman, W.J., Baram, T.Z. & Chen, Y. (2012). Distinct regional and subcellular localization of the actin-binding protein filamin A in the mature rat brain. J. Comp. Neurol., 520(13), 3013-3034.

Shcherbakova, D.M., Hink, M.A., Joosen, L., Gadella, Th.W.J. & Verkhusha, V.V. (2012). An orange fluorescent protein with a large Stokes shift for single-excitation multicolor FCCS and FRET imaging. Journal of the American Chemical Society, 134(18), 7913-7923.

Song, Z., Postma, M., Billings, S.A., Coca, D., Hardie, R.C. & Juusola, M. (2012). Stochastic, adaptive sampling of information by microvilli in fly photoreceptors. Curr. Biol., 22(15), 1371-1380.

Stetten, D. von, Noirclerc-Savoye, M., Goedhart, J., Gadella, T.W.J. & Royant, A. (2012). Structure of a fluorescent protein from Aequorea victoria bearing the obligate-monomer mutation A206K. Acta Crystallogr Sect F Struct Biol Cryst Commun, 68(Pt 8), 878-882.

bookchapters:

Ploeg, R. van der & Blaauwen, T. den (2012). In vivo bacterial morphogenetic protein interactions. In A. Meghea (Ed.), In Molecular Interactions (pp. 239-262). INTECH.

 

2011

Adjobo-Hermans, M.J.W., Goedhart, J., Weeren, L. van, Nijmeijer, S., Manders, E.M.M., Offermanns, S. & Gadella, T.W.J. (2011). Real-time visualization of heterotrimeric G protein Gq activation in living cells. BMC Biology, 9, 32.

Beek, A. ter, Hornstra, L.M., Pandey, R., Kallemeijn, W.W., Smelt, J.P.P.M., Manders, E.M.M. & Brul, S. (2011). Models of the behaviour of (thermally stressed) microbial spores in foods: Tools to study mechanisms of damage and repair. Food Microbiology, 28(4), 678-684.

Crosby, K.C., Pietraszewska-Bogiel, A., Gadella, T.W.J. & Winkel, B.S.J. (2011). Förster resonance energy transfer demonstrates a flavonoid metabolon in living plant cells that displays competitive interactions between enzymes. FEBS Letters, 585(14), 2193-2198.

De Vos, W.H., Houben, F., Kamps, M., Malhas, A., Verheyen, F., Cox, J., Manders, E.M.M., Verstraeten, V.L.R.M., Steensel, M.A.M. van, Marcelis, C.L.M., Wijngaard, A. van den, Vaux, D.J., Ramaekers, F.C.S. & Broers, J.L.V. (2011). Repetitive disruptions of the nuclear envelope invoke temporary loss of cellular compartmentalization in laminopathies. Human molecular genetics.

De Vylder, J., De Vos, W.H., Manders, E.M. & Philips, W. (2011). 2D mapping of strongly deformable cell nuclei, based on contour matching. Cytometry. Part A, 79A(7), 580-588.

Fraipont, C., Alexeeva, S., Wolf, B., Ploeg, R. van der, Schloesser, M., Blaauwen, T. den & Nguyen-Distèche, M. (2011). The integral membrane FtsW protein and peptidoglycan synthase PBP3 form a subcomplex in Escherichia coli. Microbiology, 157(1), 251-259.

Goedhart, J. & Gadella, T.W.J. (2011). Bypassing GPCRs with chemical dimerizers. Chemistry & Biology, 18(9), 1067-1068.

Goedhart, J., Weeren, L. van, Adjobo-Hermans, M. J., Elzenaar, I., Hink, M.A. & Gadella, T. W. J. (2011). Quantitative Co-Expression of Proteins at the Single Cell Level – Application to a Multimeric FRET Sensor. PLoS One, 6(11), e27321.

Hink, M.A., Vries, S.C. de & Visser, A.J. (2011). Fluorescence fluctuation analysis of receptor kinase dimerization. Methods in Molecular Biology, 779, 199-215.

Klarenbeek, J.B., Goedhart, J., Hink, M.A., Gadella, T.W.J. & Jalink, K. (2011). A mTurquoise-based cAMP sensor for both FLIM and ratiometric read-out has improved dynamic range. PLoS One, 6(4), e19170.

Klaus-Heisen, D., Nurisso, A., Pietraszewska, A., Mbengue, M., Camut, S., Timmers, T., Pichereaux, C., Rossignol, M., Gadella, T.W.J., Imberty, A., Lefebvre, B. & Cullimore, J.V. (2011). Structure-function similarities between a plant receptor-like kinase and the human interleukin-1 receptor-associated kinase-4. The Journal of Biological Chemistry, 286(13), 11202-11210.

Kleinschmidt, J.H., Bulieris, P.V., Qu, J., Dogterom, M. & Blaauwen, T. den (2011). Association of neighboring β-strands of outer membrane protein A in lipid bilayers revealed by site-directed fluorescence quenching. Journal of Molecular Biology, 407(2), 316-332.

Marlatt, M.W., Philippens, I., Manders, E.M.M., Czeh, B., Joels, M., Krugers, H. & Lucassen, P.J. (2011) Distinct structural plasticity in the hippocampus and amygdala of the middle-aged common marmoset (Callithrix jacchus) Experimental Neurology, 230(2), 291-301

Olrichs, N.K., Aarsman, M.E.G., Verheul, J., Arnusch, C.J., Martin, N.I., Hervé, M., Vollmer, W., Kruijff, B. de, Breukink, E. & Blaauwen, T. den (2011). A novel in vivo cell-wall labeling approach sheds new light on peptidoglycan synthesis in Escherichia coli. ChemBioChem, 12(7), 1124-1133.

Oomen, C.A., Soeters, H., Audureau, N., Vermunt, L., Hasselt, F.N. van, Manders, E.M.M., Joëls, M., Krugers, H. & Lucassen, P.J. (2011). Early maternal deprivation affects dentate gyrus structure and emotional learning in adult female rats. Psychopharmacology, 214(1), 249-260.

Pietraszewska-Bogiel, A. & Gadella, T.W.J. (2011). FRET microscopy: from principle to routine technology in cell biology. Journal of Microscopy, 241(2), 111-118.

Sosinska, G.J., Koning, L.J. de, Groot, P.W.J. de, Manders, E.M.M., Dekker, H.L., Hellingwerf, K.J., Koster, C.G. de & Klis, F.M. (2011). Mass spectrometric quantification of the adaptations in the wall proteome of Candida albicans in response to ambient pH. Microbiology, 157(1), 136-146.

Tamulonis, C., Postma, M., Marlow, H.Q., Magie, C.R., Jong, J. de & Kaandorp, J. (2011). A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering. Developmental Biology, 351(1), 217-228.

Tamulonis, C.V.T., Postma, M. & Kaandorp, J.A. (2011). Modeling Filamentous Cyanobacteria Reveals the Advantages of Long and Fast Trichomes for Optimizing Light Exposure. PLoS One, 6(7).

Ter Beek, A., Hornstra, L.M., Pandey, R., Kallemeijn, W.W., Smelt, J.P.P.M., Manders, E.M.M. & Brul, S. (2011) Models of the behaviour of (thermally stressed) microbial spores in foods: Tools to study mechanisms of damage and repair   Food Microbiology, 28(4), 678-684

Weerman, E.J., van der Geest, H.G., van der Meulen, M.D., Manders, E.M.M., van de Koppel, J., Herman, P.M.J. & Admiraal, W. (2011)Ciliates as engineers of phototrophic biofilms. Freshwater Biology, 56(7), 1358-1369

bookchapters:

Hink, M.A., Vries, S.C. de & Visser, A.J.W.G. (2011). Fluorescence fluctuation analysis of receptor kinase dimerization. In N. Dissmeyer & A. Schnittger (Eds.), Plant kinases: Methods and protocols (Methods in molecular biology, 779-3) (pp. 199-215). New York: Humana Press.

Kwaaitaal, M., Schor, M., Hink, M.A., Visser, A.J.W.G. & Vries, S.C. de (2011). Fluorescence correlation spectroscopy and fluorescence recovery after photobleaching to study receptor kinase mobility in planta. In N. Dissmeyer & A. Schnittger (Eds.), Plant kinases: Methods and protocols (Methods in molecular biology, 779-3) (pp. 225-242). New York: Humana Press.

 

2010

Alexeeva,S., T.W.J. Gadella Jr, J. Verheul, G.S. Verhoeven and T. den Blaauwen (2010) Direct interactions of early and late assembling division proteins in Escherichia coli cells resolved by FRET. Mol. Microbiol. 77, 384–398.

Goedhart, J., van Weeren, L., Hink, M.A., Vischer, N.O., Jalink, K., and Gadella, T.W.J., Jr. (2010) Bright cyan fluorescent protein variants identified by fluorescence lifetime screening. Nat. Methods 7, 737-139

Luijsterburg M.S., von Bornstaedt G., Gourdin A.M., Politi A.Z., Moné M.J., Warmerdam D.O., Goedhart J., Vermeulen W., van Driel R. and Höfer T. (2010) Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair. J. Cell Biol. 189, 445-463

Potluri, L., A. Karczmarek, J. Verheul, A. Piette, J. Wilkin, N. Werth, M. Banzhaf, W. Vollmer, K.D. Young, M. Nguyen-Distèche and T. den Blaauwen (2010) Septal and lateral wall localization of PBP5, the major D,D-carboxypeptidase of Escherichia coli, requires substrate recognition and membrane attachment. Mol. Microbiol. 77, 300–323

Schaffner-Barbero C., Gil-Redondo R., Ruiz-Avila L.B., Huecas S., Läppchen T., den Blaauwen T., Diaz J.F., Morreale A., Andreu J.M. (2010) Insights into nucleotide recognition by cell division protein FtsZ from a mant-GTP competition assay and molecular dynamics. Biochemistry 49, 10458-10472

Schultz C, Neef A.B., Gadella T.W. Jr. and Goedhart J. (2010) Imaging lipids in living cells. Cold Spring Harb Protoc. 2010 (8), pdb.top83

Soprova Z., Sauri A., van Ulsen P., Tame J.R., den Blaauwen T., Jong W.S., Luirink J. (2010) A conserved aromatic residue in the autochaperone domain of the autotransporter Hbp is critical for initiation of outer membrane translocation. J. Biol. Chem. 285, 38224-38233

Typas A., Banzhaf M., van den Berg van Saparoea B., Verheul J., Biboy J., Nichols R.J., Zietek M., Beilharz K., Kannenberg K., von Rechenberg M., Breukink E., den Blaauwen T., Gross C.A., Vollmer W. (2010) Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell 143, 1097-1109

 

2009

Alfarez, D.N., De Simoni, A., Velzing, E.H., Bracey, E., Joëls, M., Edwards, F.A. & Krugers, H.J. (2009). Corticosterone reduces dendritic complexity in developing hippocampal CA1 neurons. Hippocampus  19, 828-836.

Bagot, R.C.,  Hasselt , F.N. van,  Champagne   , D.L., Meaney, M., Krugers, H. & Joels, M. (2009). Maternal care determines rapid effects of stress mediators on synaptic plasticity in adult rat hippocampal dentate gyrus. Neurobiol. Learning Mem. 92, 292-300.

Bellou, S., M.A. Hink, E. Bagli, E. Panopoulou, P.I.H. Bastiaens, C. Murphy and T. Fotsis. (2009) VEGF auto-regulates its proliferative and migratory ERK1/2 and p38 MAPK cascades by enhancing the expression of DUSP1 and DUSP5 phosphatases in endothelial cells. Am. J. Physiol. Cell. Physiol. 297, C1477-89.

Chameau, P., Inta, D., Vitalis, T., Monyer, H., Wadman, W.J. & Hooft, J.A. van (2009). The N-terminal region of reelin regulates postnatal dendritic maturation of cortical pyramidal neurons. Proc Natl Acad Sci USA  106, 7227-7232.

Deng, D.M., Hoogenkamp, M.A., Cate, J.M. ten & Crielaard, W. (2009). Novel metabolic activity indicator in Streptococcus mutans biofilms. J. Microbiol. Meth. 77, 67-71.

Deng, D.M., Urch, J.E., Cate, J.M. ten, Rao, V.A., Aalten, D.M.F. van & Crielaard, W. (2009). Streptococcus mutans SMU.623c codes for a functional, metal-dependent polysaccharide deacetylase that modulates interactions with salivary agglutinin. J. Bacteriol. 191, 394-402.

Dinant, C., Luijsterburg, S.M., Höfer, T., Bornstaedt, G. von, Vermeulen, W., Houtsmuller, A.B. & Driel, R. van (2009). Assembly of multiprotein complexes that control genome function. J. Cell Biol. 185, 21-26.

Goedhart, J., and Gadella Jr., T.W.J. (2009) Fluorescence resonance energy transfert imaging of PKC signaling in living cells using genetically encoded fluorescent probes. J.R. Soc. Interface 6: S27-S34.

Hornstra, L.M., Beek, A.S. ter, Smelt, J.P.P.M., Kallemeijn, W.W. & Brul, S. (2009). On the origin of heterogeneity in (preservation) resistance of Bacillus spores: Input for a ‘systems’ analysis approach of bacterial spore outgrowth. Int. J. Food Microbiol. 134, 9-15.

Klis, F.M., Sosinska, G.J., Groot, P.W.J. de & Brul, S. (2009). Covalently linked cell wall proteins of Candida albicans and their role in fitness and virulence. FEMS Yeast Res. 9, 1013-1028.

Luijsterburg, M.S., Dinant, C., Lans, H., Stap, J., Wiernasz, E.S., Lagerwerf, S., Warmerdam, D.O., Lindh, M., Brink, M.C., Dobrucki, J.W., Aten, J.A., Fousteri, M., Jansen, G., Dantuma, N.P., Vermeulen, W., Mullenders, L.H.F., Houtsmuller, A.B., Verschure, P.J. & Driel, R. van (2009). Heterochromatin protein 1 is recruited to various types of DNA damage. J. Cell Biol. 185, 577-586.

Marlatt, M.W., Hoozemans, J.J.M., Veerhuis, R. & Lucassen, P.J. (2009). Alzheimer’s disease and adult neurogenesis: Are endogenous stem cells part of the solution? US Neurol. 5, 12-14.

Mateos-Langerak, J., Bohn, M., de Leeuw, W., Giromus, O., Manders, E.M., Verschure, P.J., Indemans, M.H., Gierman, H.J., Heermann, D.W., van Driel, R., and Goetze, S. (2009) Spatially confined folding of chromatin in the interphase nucleus. Proc Natl Acad Sci U S A 106, 3812-3817.

Michielse, C.B., Wijk, R. van, Reijnen, L., Manders, E.M.M., Boas, S., Olivain, C., Alabouvette, C. & Rep, M. (2009). The nuclear protein Sge1 of Fusarium oxysporum is required for parasitic growth. PLOS Pathogens 5, e1000637.

Mishkind, M., Vermeer, J.E.M., Darwish, E. & Munnik, T. (2009). Heat stress activates phospholipase D and triggers PIP2 accumulation at the plasma membrane and nucleus. Plant J. 60, 10-21.

Mohammadi,T., Ploeger, G.E.J., Verheul,J., Comvalius, A.D., Martos, A., Alfonso, C., van Marle, J., Rivas, G. and den Blaauwen, T. (2009) The GTPase activity of Escherichia coli FtsZ determines the magnitude of the FtsZ polymer bundling by ZapA in vitro. Biochemistry 48, 11056–11066

Oomen  ,   C.A.    , Girardi, C.E.N., Cahyadi, R., Verbeek, E.C., Krugers, H., Joëls, M. & Lucassen, P.J. (2009). Opposite effects of early maternal deprivation on neurogenesis in male versus female rats. PLoS One 4, e3675.

Rzeznicka, I.I., Wurpel, G.W.H.,  Bonn   , M., Horst, M.A. van der, Hellingwerf, K.J., Matsunaga, S., Yamada, T. & Kawai, M. (2009). Observation of photoactive yellow protein anchored to a modified Au(111) surface by scanning tunneling microscopy. Chem. Phys. Lett. 472, 113-117.

Schafer, D., Muller, M., Bonn, M., Marr, D.W., van Maarseveen, J., and Squier, J. (2009) Coherent anti-Stokes Raman scattering microscopy for quantitative characterization of mixing and flow in microfluidics. Opt Lett 34, 211-213.

Shcherbo, D., Souslova, E.A., Goedhart, J., Chepurnykh, T.V., Gaintzeva, A., Shemiakina, II, Gadella, T.W., Lukyanov, S., and Chudakov, D.M. (2009) Practical and reliable FRET/FLIM pair of fluorescent proteins. BMC Biotechnol 9, 24.

Tessadori, F.G., Zanten, M. van, Pavlova, P., Clifton, R., Pontvianne, F., Basten Snoek, L., Millenaar, F.F., Schulkes, R.K., Driel, R. van, Voesenek, L.A.C.J., Spillane, C., Pikaard, C.S., Fransz, P.F. & Peeters, A.J.M. (2009). PHYTOCHROME B and HISTONE DEACETYLASE 6 Control Light-Induced Chromatin Compaction in Arabidopsis thaliana. PLOS Genetics 5, e1000638.

Van Moerkercke, A., Schauvinhold,  I. , Pichersky, E., Haring, M.A. & Schuurink, R.C. (2009). A plant thiolase involved in benzoic acid biosynthesis and volatile benzenoid production. Plant J. 60, 292-302.

Verhoeven, G.S., Alexeeva, S., Dogterom, M., and den Blaauwen, T. Differential bacterial surface display of peptides by the transmembrane domain of OmpA. PLOS One 4, e6739

Vermeer, J.E., Thole, J.M., Goedhart, J., Nielsen, E., Munnik, T., and Gadella, T.W., Jr. (2009) Imaging phosphatidylinositol 4-phosphate dynamics in living plant cells. Plant J 57, 356-372.

De Vos, W.H., Hoebe, R.A., Joss, G.H., Haffmans, W., Baatout, S., Van Oostveldt, P., and Manders, E.M. (2009) Controlled light exposure microscopy reveals dynamic telomere microterritories throughout the cell cycle. Cytometry A 75, 428-439.

Zhou, M., Conboy, L., Sandi, C., Joëls, M. & Krugers, H.J. (2009). Fear conditioning enhances spontaneous AMPA receptor-mediated synaptic transmission in mouse hippocampal CA1 area. Eur. J. Neurosci. 30, 1559-1564.

Zonia, L. & Munnik, T. (2009). Uncovering hidden treasures in pollen tube growth mechanics. Tr. Plant Sci. 14, 318-327.

bookchapters:

Fransz, P. (2009). Chromatin domains and function. In I. Meier (Ed.), Functional organization of the plant nucleus (Plant cell monographs, 14) (pp. 131-155).  Berlin   : Springer.

T.W.J. Gadella (Ed.), FRET and FLIM Techniques (2009). Laboratory techniques in biochemistry and molecular biology 33,  Elsevier Science, Amsterdam. T.W.J. Gadella Jr., Total internal reflection fluorescence lifetime imaging microscopy. (2009) In “FRET and FLIM imaging techniques” (ed. Gadella). Laboratory Techniques in Biochemistry and Molecular Biology (ser. Ed. P.C. Van der Vliet) Burlington: Academic Press. pp. 395-412.

G.-J. Kremers and J. Goedhart. Visible fluorescent proteins for FRET. (2009) In “FRET and FLIM imaging techniques” (ed. Gadella). Laboratory Techniques in Biochemistry and Molecular Biology (ser. Ed. P.C. Van der Vliet) Burlington: Academic Press. pp. 171-224.  Vos, W.H. de, Hoebe, R.A., Joss, G., Manders, E.M.M. & Oostveldt, P. van (2009). Controlled light exposure microscopy reveals telomeric microterritories throughout the cell cycle. In A. Aretz, B. Hermanns-Sachweh & J. Mayer (Eds.), EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany (pp. 169). Berlin Heidelberg: Springer.

Willems, P.H.G.M., Swarts, H.G., Hink, M.A. & Koopman, W.J.H. (2009). The Use of Fluorescence Correlation Spectroscopy to Probe Mitochondrial Mobility and Intramatrix Protein Diffusion. In W.S. Allison & I.E. Scheffler (Eds.), Mitochondrial Function, Part A: Mitochondrial Electron Transport Complexes and Reactive Oxygen Species (Methods in Enzymology, 456) (pp. 287-302-chapter 16). Elsevier Inc.

 

2008

Adjobo-Hermans, M.J., Goedhart, J., and Gadella, T.W., Jr. (2008) Regulation of PLCbeta1a membrane anchoring by its substrate phosphatidylinositol (4,5)-bisphosphate. J Cell Sci 121, 3770-3777.

den Blaauwen, T., de Pedro, M.A., Nguyen-Disteche, M., and Ayala, J.A. (2008) Morphogenesis of rod-shaped sacculi. FEMS Microbiol Rev 32, 321-344.

Deng, D.M. & Crielaard, W. (2008). Microbiële genetica: Nieuwe mogelijkheden voor preventie en behandeling van (orale) infecties. Nederlands Tijdschrift voor Tandheelkunde 115, 93-99.

Dhonukshe, P., Grigoriev, I., Fischer, R., Tominaga, M., Robinson, D.G., Hasek, J., Paciorek, T., Petrasek, J., Seifertova, D., Tejos, R., Meisel, L.A., Zazimalova, E., Gadella, T.W., Jr., Stierhof, Y.D., Ueda, T., Oiwa, K., Akhmanova, A., Brock, R., Spang, A., and Friml, J. (2008) Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes. Proc Natl Acad Sci U S A 105, 4489-4494.

Does, H.C. van der, Lievens, B., Claes, L., Houterman, P.M., Cornelissen, B.J.C. & Rep, M. (2008). The presence of a virulence locus discriminates Fusarium oxysporum isolates causing tomato wilt from other isolates. Envir. Microbiol., 10, 1475-1485.

Gladilin, E., Goetze, S., Mateos-Langerak, J., Driel, R. van, Eils, R. & Rohr, K. (2008). Shape normalization of 3D cell nuclei using elastic spherical mapping. J. Microsc. 231, 105-114.

Hoebe, R.A., Van der Voort, H.T., Stap, J., Van Noorden, C.J., and Manders, E.M. (2008) Quantitative determination of the reduction of phototoxicity and photobleaching by controlled light exposure microscopy. J Microsc 231, 9-20.

Hoogstraten, D., Bergink, S., Ng, J.M.Y., Verbiest, V.H.M., Luijsterburg, M.S., Geverts, B., Raams, A., Dinant, C., Hoeijmakers, J.H.J., Vermeulen, W. & Houtsmuller, A.B. (2008). Versatile DNA damage detection by the global genome nucleotide excision repair protein XPC. J. Cell Sci. 121, 2850-2859.

Kanger, J.S., Subramaniam, V. & Driel, R. van (2008). Intracellular manipulation of chromatin using magnetic nanoparticles. Chromos. Res. 16, 511-522.

Kremers, G.J., van Munster, E.B., Goedhart, J., and Gadella, T.W., Jr. (2008) Quantitative lifetime unmixing of multiexponentially decaying fluorophores using single-frequency fluorescence lifetime imaging microscopy. Biophys J 95, 378-389.

Lappchen, T., Pinas, V.A., Hartog, A.F., Koomen, G.J., Schaffner-Barbero, C., Andreu, J.M., Trambaiolo, D., Lowe, J., Juhem, A., Popov, A.V., and den Blaauwen, T. (2008) Probing FtsZ and tubulin with C8-substituted GTP analogs reveals differences in their nucleotide binding sites. Chem Biol 15, 189-199.

Luijsterburg, M.S., White, M.F., Driel, R. van & Dame, R.T. (2008). The major architects of chromatin: Architectural proteins in bacteria, archaea and eukaryotes. Crit. Rev. Biochem. Mol. Biol. 43, 393-418.

Molly, L., Nackaerts, O., Vandewiele, K., Manders, E., van Steenberghe, D., and Jacobs, R. (2008) Speech adaptation after treatment of full edentulism through immediate-loaded implant protocols. Clin Oral Implants Res 19, 86-90.

Oomen, L.C.J.M., Sacher, R., Brocks, H.H.J., Zwier, J.M., Brakenhoff, G.J. & Jalink, K. (2008). Immersion oil for high-resolution live-cell imaging at 37°C: Optical and physical characteristics. J. Microsc. 232, 353-361.

Pereira-Cenci, T., Del Bel Cury, A.A., Crielaard, W. & Cate, J.M. ten (2008). Development of Candida-associated denture stomatitis: New insights. J. Appl. Oral Sci. 16, 86-94.

Pereira-Cenci, T., Deng, D.M., Kraneveld, E.A., Manders, E.M., Del Bel Cury, A.A., Ten Cate, J.M., and Crielaard, W. (2008) The effect of Streptococcus mutans and Candida glabrata on Candida albicans biofilms formed on different surfaces. Arch Oral Biol 53, 755-764.

Rinia, H.A., Burger, K.N., Bonn, M., and Muller, M. (2008) Quantitative label-free imaging of lipid composition and packing of individual cellular lipid droplets using multiplex CARS microscopy. Biophys J 95, 4908-4914.

Rino, J., Desterro, J.M., Pacheco, T.R., Gadella, T.W., Jr., and Carmo-Fonseca, M. (2008) Splicing factors SF1 and U2AF associate in extraspliceosomal complexes. Mol Cell Biol 28, 3045-3057.

Schafer, D., Squier, J.A., van Maarseveen, J., Bonn, D., Bonn, M., and Muller, M. (2008) In situ quantitative measurement of concentration profiles in a microreactor with submicron resolution using multiplex CARS microscopy. J Am Chem Soc 130, 11592-11593.

Schenning, M., Goedhart, J., Gadella, T.W., Jr., Avram, D., Wirtz, K.W., and Snoek, G.T. (2008) The anti-apoptotic activity associated with phosphatidylinositol transfer protein alpha activates the MAPK and Akt/PKB pathway. Biochim Biophys Acta 1783, 1700-1706.

Sosinska, G.J., Groot, P.W.J. de, Teixeira De Mattos, M.J., Dekker, H.L., Koster, C.G. de, Hellingwerf, K.J. & Klis, F.M. (2008). Hypoxic conditions and iron restriction affect the cell-wall proteome of Candida albicans grown under vagina-simulative conditions. Microbiol. 154, 510-520.

Sovago, M., Campen, R.K., Wurpel, G.W., Muller, M., Bakker, H.J., and Bonn, M. (2008) Vibrational response of hydrogen-bonded interfacial water is dominated by intramolecular coupling. Phys Rev Lett 100, 173901.

Thole, J.M., Vermeer, J.E., Zhang, Y., Gadella, T.W., Jr., and Nielsen, E. (2008) Root hair defective4 encodes a phosphatidylinositol-4-phosphate phosphatase required for proper root hair development in Arabidopsis thaliana. Plant Cell 20, 381-395.

van den Ent, F., Vinkenvleugel, T.M., Ind, A., West, P., Veprintsev, D., Nanninga, N., den Blaauwen, T., and Lowe, J. (2008) Structural and mutational analysis of the cell division protein FtsQ. Mol Microbiol 68, 110-123.

van der Does, H.C., Duyvesteijn, R.G., Goltstein, P.M., van Schie, C.C., Manders, E.M., Cornelissen, B.J., and Rep, M. (2008) Expression of effector gene SIX1 of Fusarium oxysporum requires living plant cells. Fungal Genet Biol 45, 1257-1264.

Verbeek, D.S., Goedhart, J., Bruinsma, L., Sinke, R.J., and Reits, E.A. (2008) PKC gamma mutations in spinocerebellar ataxia type 14 affect C1 domain accessibility and kinase activity leading to aberrant MAPK signaling. J Cell Sci 121, 2339-2349.

Verweij, W., Spelt, C., Di Sansebastiano, G.P., Vermeer, J., Reale, L., Ferranti, F., Koes, R., and Quattrocchio, F. (2008) An H+ P-ATPase on the tonoplast determines vacuolar pH and flower colour. Nat Cell Biol 10, 1456-1462.

book chapters:

Brakenhoff, F. & Zwier, J. (2008). Characterization and calibration in wide field and sectioned fluorescence microscopy SIPcharts. In U. Resch-Genger (Ed.), Standardization and quality assurance in fluorescence measurements II: Bioanalytical and biomedical applications (Springer series on fluorescence, 6) (pp. 25-54). Berlin: Springer (ISBN 978-3-540-70570-3).

 

2007

Chameau, P.J.P., Qin, Y.J., Smit, G. & Joëls, M. (2007). Glucocorticoids specifically enhance L-type calcium current amplitude and affect calcium channel subunit expression in the mouse hippocampus. J. Neurophys. 97, 5-14.

Fakan, S. & Driel, R. van (2007). The perichromatin region: A functional compartment in the nucleus that determines large-scale chromatin folding. Semin. Cell Dev. Biol. 18, 676-681.

Goedhart, J., Vermeer, J.E., Adjobo-Hermans, M.J., van Weeren, L., and Gadella, T.W., Jr. (2007) Sensitive detection of p65 homodimers using red-shifted and fluorescent protein-based FRET couples. PLoS One 2, e1011.

Goetze, S., Mateos Langerak, J., Gierman, H.J., Leeuw, W. de, Giromus, O., Indemans, M.H., Koster, J., Ondrej, V., Versteeg, R. & Driel, R. van (2007). The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol. Cell. Biol. 27, 4475-4487

Goetze, S., Mateos Langerak, J. & Driel, R. van (2007). Three-dimensional genome organization in interphase and its relation to genome function. Semin. Cell Dev. Biol. 18, 707-714

Hoebe, R.A., Van Oven, C.H., Gadella, T.W., Jr., Dhonukshe, P.B., Van Noorden, C.J., and Manders, E.M. (2007) Controlled light-exposure microscopy reduces photobleaching and phototoxicity in fluorescence live-cell imaging. Nat Biotechnol 25, 249-253.

Jong, W.S., ten Hagen-Jongman, C.M., den Blaauwen, T., Slotboom, D.J., Tame, J.R., Wickstrom, D., de Gier, J.W., Otto, B.R., and Luirink, J. (2007) Limited tolerance towards folded elements during secretion of the autotransporter Hbp. Mol Microbiol 63, 1524-1536.

Karczmarek, A., Martinez-Arteaga, R., Alexeeva, S., Hansen, F.G., Vicente, M., Nanninga, N., and den Blaauwen, T. (2007) DNA and origin region segregation are not affected by the transition from rod to sphere after inhibition of Escherichia coli MreB by A22. Mol Microbiol 65, 51-63.

Kremers, G.J., Goedhart, J., van den Heuvel, D.J., Gerritsen, H.C., and Gadella, T.W., Jr. (2007) Improved green and blue fluorescent proteins for expression in bacteria and mammalian cells. Biochemistry 46, 3775-3783.

Lange, M.J.L. de, Bonn, M. &  Müller, M. (2007). Direct measurement of  phase coexistence in DPPC/Cholesterol vesicles using Raman spectroscopy. CHEM PHYS LIPIDS, 146(2),  76-84

Luijsterburg, M.S., Goedhart, J., Moser, J., Kool, H., Geverts, B., Houtsmuller, A.B., Mullenders, L.H., Vermeulen, W., and van Driel, R. (2007) Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC. J Cell Sci 120, 2706-2716.

Mateos Langerak, J., Goetze, S., Leonhardt, H., Cremer, T., Driel, R. van & Lanctôt, C. (2007). Nuclear architecture: Is it important for genome function and can we prove it? J. Cell. Biochem.102, 1067-1075

Mateos Langerak, J., Brink, M.C., Luijsterburg, M.S., Kraan, I. van der, Driel, R. van & Verschure, P.J. (2007). Pericentromeric heterochromatin domains are maintained without accumulation of HP1. Mol. Biol. Cell 18, 14 64-1471

Merzlyak, E.M., Goedhart, J., Shcherbo, D., Bulina, M.E., Shcheglov, A.S., Fradkov, A.F., Gaintzeva, A., Lukyanov, K.A., Lukyanov, S., Gadella, T.W., and Chudakov, D.M. (2007) Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat Methods 4, 555-557.

Mohammadi, T., Karczmarek, A., Crouvoisier, M., Bouhss, A., Mengin-Lecreulx, D., and den Blaauwen, T. (2007) The essential peptidoglycan glycosyltransferase MurG forms a complex with proteins involved in lateral envelope growth as well as with proteins involved in cell division in Escherichia coli. Mol Microbiol 65, 1106-1121.

Muller, M., and Zumbusch, A. (2007) Coherent anti-Stokes Raman Scattering Microscopy. Chemphyschem 8, 2156-2170.

Norris, V., den Blaauwen, T., Cabin-Flaman, A., Doi, R.H., Harshey, R., Janniere, L., Jimenez-Sanchez, A., Jin, D.J., Levin, P.A., Mileykovskaya, E., Minsky, A., Saier, M., Jr., and Skarstad, K. (2007) Functional taxonomy of bacterial hyperstructures. Microbiol Mol Biol Rev 71, 230-253.

Norris, V., den Blaauwen, T., Doi, R.H., Harshey, R.M., Janniere, L., Jimenez-Sanchez, A., Jin, D.J., Levin, P.A., Mileykovskaya, E., Minsky, A., Misevic, G., Ripoll, C., Saier, M., Jr., Skarstad, K., and Thellier, M. (2007) Toward a hyperstructure taxonomy. Annu Rev Microbiol 61, 309-329.

Rinia, H.A., Bonn, M., Muller, M., and Vartiainen, E.M. (2007) Quantitative CARS spectroscopy using the maximum entropy method: the main lipid phase transition. Chemphyschem 8, 279-287.

Rinia, H.A., Wurpel, G.W., and Muller, M. (2007) Measuring molecular order and orientation using coherent anti-stokes Raman scattering microscopy. Methods Mol Biol 400, 45-61.

Royen, M.E. van, Cunha, S.M., Brink, M.C., Mattern, K.A., Nigg, A.L., Dubbink, H.J., Verschure, P.J., Trapman, J. & Houtsmuller, A.B. (2007). Compartmentalization of androgen receptor protein-protein interactions in living cells. J. Cell Biol. 177, 63-72

Scheffers, D.J., Robichon, C., Haan, G.J., den Blaauwen, T., Koningstein, G., van Bloois, E., Beckwith, J., and Luirink, J. (2007) Contribution of the FtsQ transmembrane segment to localization to the cell division site. J Bacteriol 189, 7273-7280.

Smits, M., Ghosh, A., Sterrer, M., Muller, M., and Bonn, M. (2007) Ultrafast vibrational energy transfer between surface and bulk water at the air-water interface. Phys Rev Lett 98, 098302.

Smits, M., Sovago, M., Wurpel, G.W.H., Kim, D.,  Müller

Smits, M., Ghosh, A., Bredenbeck, J., Yamamoto, S., Müller, M. & Bonn, M. (2007). Ultrafast energy flow in model biological membranes. New J. Phys., 9, 390.

Sovago, M., Wurpel, G.W., Smits, M., Muller, M., and Bonn, M. (2007) Calcium-induced phospholipid ordering depends on surface pressure. J Am Chem Soc 129, 11079-11084.

Tessadori, F., Chupeau, M.C., Chupeau, Y., Knip, M., Germann, S., Driel, R. van, Fransz, P.F. & Gaudin, V. (2007). Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. J. Cell Science 120, 1200-1208.

Tessadori, F., Schulkes, R.K., Driel, R. van & Fransz, P.F. (2007). Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis. Plant J. 50, 848-857.

van Leeuwen, W., Vermeer, J.E., Gadella, T.W., Jr., and Munnik, T. (2007) Visualization of phosphatidylinositol 4,5-bisphosphate in the plasma membrane of suspension-cultured tobacco BY-2 cells and whole Arabidopsis seedlings. Plant J 52, 1014-1026.

van Munster, E.B., Goedhart, J., Kremers, G.J., Manders, E.M., and Gadella, T.W., Jr. (2007) Combination of a spinning disc confocal unit with frequency-domain fluorescence lifetime imaging microscopy. Cytometry A 71, 207-214.

Wiegert, O., Joëls, M. & Krugers, H. (2007). Corticosteroid hormones, synaptic strength and emotional memories: corticosteroid modulation of memory — a cellular and molecular perspective. Prog. Brain. Res., 167, 269-271.

bookchapters:

Müller, M., Rinia, H.A., Bonn, M., Vartiainen, E.M., Lisker, M. & Bel, A. (2007). Quantitative multiplex CARS spectroscopy in congested spectral regions. In A. Periasamy & P.T.C. So (Eds.), Multiphoton Microscopy in the Biomedical Sciences VII Vol. 6442. SPIE. The International Society for Optical Engineering.

Pillai, R.S., Brakenhoff, G.J. & Müller, M. (2007). Third harmonic generation: anomalous behavior in the THG z-response and microscopy applications. In A. Periasamy & P.T.C. So (Eds.), Multiphoton Microscopy in the Biomedical Sciences VII Vol. 6442. SPIE.

Rinia, H.A., Burger, K.N.J., Bonn, M. & Müller, M. (2007). Multiplex coherent anti-Stokes Raman scattering microscopy on lipid droplets in HeLa cells. In T. Wilson & A. Periasamy (Eds.), Confocal, Multiphoton, and Nonlinear Microscopic Imaging III Vol. 6630. SPIE. The International Society for Optical Engineering.

Rinia, H.A., Wurpel, G.W.H. & Müller, M. (2007). Measuring molecular order and orientation using coherent anti-Stokes Raman scattering microscopy. In A.M. Dopico (Ed.), Methods in Membrane Lipids (pp. 45-61). Totowa (NJ), USA: Humana Press Inc., 2007.

Verhoeven, G., Dogterom, M., Alexeeva, S.V. & Blaauwen, T. den (2007). Studying bacterial cell division using optical tweezers. In biophysical society annual meeting abstracts issues Vol. Jan. 2007. Biophys. J. (pp. 306A-360A).

 

2006

Adjobo-Hermans, M.J., Goedhart, J., and Gadella, T.W., Jr. (2006) Plant G protein heterotrimers require dual lipidation motifs of Galpha and Ggamma and do not dissociate upon activation. J Cell Sci 119, 5087-5097.

Alfarez,  D.N., Wiegert, O. & Krugers, H. (2006). Stress,    corticosteroid hormones and hippocampal synaptic function. CNS    & Neurol. Disorders Drug Targets 5, 521-529.

Amir, W., Planchon, T.A., Durfee, C.G., Squier, J., Gabolde, P., Trebino, R., & Müller

Bertsche, U., Kast, T., Wolf, B., Fraipont, C., Aarsman, M.E., Kannenberg, K., von Rechenberg, M., Nguyen-Disteche, M., den Blaauwen, T., Holtje, J.V., and Vollmer, W. (2006) Interaction between two murein (peptidoglycan) synthases, PBP3 and PBP1B, in Escherichia coli. Mol Microbiol 61, 675-690.

Brink, M.C., Velden, Y. van der, Leeuw, W. de, Mateos Langerak, J., Belmont, A.S., Driel, R. van & Verschure, P.J. (2006). Truncated HP1 lacking a functional chromodomain induces heterochromatinization upon in vivo targeting. Histochem. Cell. Biol. 125, 53-61.

Chameau, P.J.P. & Hooft, J.A. van (2006). Serotonin 5-HT(3) receptors in the central nervous system. Cell Tissue Res. 326, 573-581.

den Blaauwen, T., Aarsman, M.E., Wheeler, L.J., and Nanninga, N. (2006) Pre-replication assembly of E. coli replisome components. Mol Microbiol 62, 695-708.

Dhonukshe, P., Baluska, F., Schlicht, M., Hlavacka, A., Samaj, J., Friml, J., and Gadella, T.W., Jr. (2006) Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Dev Cell 10, 137-150.

Dhonukshe, P., Bargmann, B.O., and Gadella, T.W., Jr. (2006) Arabidopsis tubulin folding cofactor B interacts with alpha-tubulin in vivo. Plant Cell Physiol 47, 1406-1411.

Dhonukshe, P., Vischer, N., and Gadella, T.W., Jr. (2006) Contribution of microtubule growth polarity and flux to spindle assembly and functioning in plant cells. J Cell Sci 119, 3193-3205.

Fransz, P.F., Hoopen, R. ten & Tessadori, F. (2006). Composition and formation of heterochromatin in Arabidopsis thaliana. Chromos. Res. 14, 71-82.

Kantardzhieva, A., Alexeeva, S.V., Versteeg,  I., & Wijnholds, J. (2006). MPP3 is recruited to the MPP5 protein scaffold at  the retinal outer limiting membrane. FEBS J., 273, 1152-1165.

Kremers, G.J., Goedhart, J., van Munster, E.B., and Gadella, T.W., Jr. (2006) Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET Forster radius. Biochemistry 45, 6570-6580.

Leeuw, W. de, Verschure, P.J. & Liere, R. van (2006). Visualization and analysis of large data collections: a case study applied to confocal microscopy data. IEEE Transactions on visualization and computer graphics 12 (5).

Mylne, J.S., Barrett, L., Tessadori, F., Mesnage, S., Johnson, L., Bernatavichute, Y.V., Jacobsen, S.E., Fransz, P.F. & Dean, C. (2006). LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1 is required for epigenetic silencing of FLC. Proc. Nat. Acad. Sci. USA 103, 5012-5017.

Pillai, R.S., Brakenhoff, G.J., and Muller, M. (2006) Analysis of the influence of spherical aberration from focusing through a dielectric slab in quantitative nonlinear optical susceptibility measurements using third-harmonic generation. Opt Express 14, 260-269.

Pillai, R.S., Brakenhoff, G.J., & Müller, M.  (2006). Anomalous behavior in the third harmonic generation z response through  dispersion induced shape changes and matching X(3). Appl. Phys. Lett., 89, 111123-1-111123-3.

Pillai, R.S., Oh, E.M., Yokoyama, H., Brakenhoff, G.J., and Muller, M. (2006) Imaging colloidal particle induced topological defects in a nematic liquid crystal using third harmonic generation microscopy. Opt Express 14, 12976-12983.

Rinia, H.A., Bonn, M., and Muller, M. (2006) Quantitative multiplex CARS spectroscopy in congested spectral regions. J Phys Chem B 110, 4472-4479.

Rinia, H.A., Bonn, M., Vartiainen, E.M., Schaffer, C.B., and Muller, M. (2006) Spectroscopic analysis of the oxygenation state of hemoglobin using coherent anti-Stokes Raman scattering. J Biomed Opt 11, 050502.

Vardi, A., Formiggini, F., Casotti, R., De Martino, A., Ribalet, F., Miralto, A., and Bowler, C. (2006) A stress surveillance system based on calcium and nitric oxide in marine diatoms. PLoS Biol 4, e60.

Vartiainen, E.M., Rinia, H.A., Muller, M., and Bonn, M. (2006) Direct extraction of Raman line-shapes from congested CARS spectra. Opt Express 14, 3622-3630.

Verschure, P.J. (2006). Chromosome organization and gene control: It is difficult to see the picture when you are inside the frame. J. Cell. Biochem. 99, 23-34.

Verschure, P.J., Visser, A.E. & Rots, M.G. (2006). Step out of the groove: epigenetic gene control systems and engineered transcription factors.  Advances in Genetics Incorporating   Mol. Gen. Medicine 56, 163-204.

Vermeer, J.E., van Leeuwen, W., Tobena-Santamaria, R., Laxalt, A.M., Jones, D.R., Divecha, N., Gadella, T.W., Jr., and Munnik, T. (2006) Visualization of PtdIns3P dynamics in living plant cells. Plant J 47, 687-700.

Wurpel, G.W.H., & Müller, M. (2006). Water confined by lipid bilayers: A multiplex CARS study. Chem. Phys. Lett., 425, 336-341.

Zaritsky, A., Woldringh, C.L., Einav, M., & Alexeeva, S.V. (2006). Use of thymine limitation and thymine starvation to study bacterial physiology and cytology. J. Bacteriol., 188, 1667-1679.

Zonia, L.E., Müller, M., & Munnik, T. (2006). Hydrodynamics and Cell Volume Oscillations in the Pollen Tube Apical Region are Integral Components of the Biomechanics of Nicotiana tabacum Pollen Tube Growth. Cell Biochem. Bioph., 46, 209-232.

Zotter, A., Luijsterburg, S.M., Warmerdam, D.O., Ibrahim, S., Nigg, A.L., Cappellen, W.A. van, Hoeijmakers, J.H.J., Driel, R. van, Vermeulen, W. & Houtsmuller, A. (2006). Recruitment of the nucleotide excision repair endonuclease XPG to sites of UV-induced DNA damage depends on functional TFIIH. Mol. Cell. Biol. 26, 8868-8879.

bookchapters:

Manders, E.M.M., Soll, D.R., Terasaki, M., & Dailey, M.E. (2006). Confocal microscopy of living cells. In J. Pawley (Ed.), Handbook of confocal microscopy, third edition. New York, USA: Springer Science and Business Media.

Rinia, H.A., Wurpel, G.W.H., & Müller, M. (2006). Measuring molecular order and orientation using CARS microscopy. In A. Dopico (Ed.), Protocols in Biophysics to Study Membrame Lipids. Totowa, NY, USA: Humana Press Inc..

Rinia, H.A., Wurpel, G.W.H., & Müller, M. (2006). Visualization and characterization of domains in model membranes. In A. Ottova-Tien (Ed.), Advances in Planar Lipid Bilayers and Liposomes 3. Elsevier.