Articles, book chapters and dissertations

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.

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. [PubMed]

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. [PubMed]

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 [PubMed]

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. [PubMed]

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. [PubMed]

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 [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

Smits, M., Sovago, M., Wurpel, G.W.H., Kim, D., Müller, M. & Bonn, M. (2007). Polarization-Resolved Broad-Bandwidth Sum-Frequency Generation Spectroscopy of Monolayer Relaxation. J. Phys. Chem. C, 111(25), 8878-8883.

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. [PubMed]

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. [PubMed]

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. [PubMed]

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.

Läppchen, T. (2007, januari 17). Synthesis of GTP Analogues and Evaluation of their Effect on the Antibiotic Target FtsZ and its Eurkaryotic Homologue Tubulin. UvA Universiteit van Amsterdam (167 pag.) (Amsterdam). Prom./coprom.: G.J. Koomen & dr T. den Blaauwen.

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. [PubMed]

Amir, W., Planchon, T.A., Durfee, C.G., Squier, J., Gabolde, P., Trebino, R., & Müller, M. (2006). Simultaneous visualization of spatial and chromatic aberrations by two-dimensional Fourier transform spectral interferometry. Opt. Lett., 31, 2927-2929.

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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

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. [PubMed]

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. [PubMed]

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. [PubMed]

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. [PubMed]

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.

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..