Publications in 2008
Jorge Ripoll, Vasilis Ntziachristos, Catherine Cannet, Rainer Kneuer, Hans-Ulrich Gremlich, and Nicolau Beckmann, “In Vivo Magnetic Resonance and Optical Imaging in Drug Discovery”, Review for Drugs in Research and Development (2008)
Lasser Tobias; Soubret Antoine; Ripoll Jorge; Ntziachristos Vasilis , “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion”, IEEE transactions on medical imaging, 27(2):188-94. (2008)
Abraham Martin, Juan Aguirre , Ana Sarasa, Anikitos Garofalakis, Heiko Meyer, Clio Mamalaki, Jorge Ripoll and Anna M. Planas, “Non-invasive in vivo assessment of stroke-induced immune depression by three-dimensional fluorescence molecular tomography in transgenic mice expressing GFP in T-lymphocytes”, Mol. Imag. Jul-Aug;7(4):157-67 (2008).
A. Darrell, H. Meyer, K.
George D.Tsibidis and Jorge Ripoll “Investigation of binding mechanisms of nuclear proteins using Confocal Scanning Laser Microscopy and FRAP: a mathematical approach”, J. Theor. Biol 253(4): 755-68 (2008).
Heiko Meyer, Alex Darrell, Athanasios Metaxakis, Charalambos Savakis and Jorge Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster”, Microscopy and Analysis, Sept. (2008)
Athanasios D Zacharopoulos, Pontus Svenmarker, Johan Axelsson, Martin Schweiger, Simon R Arridge, Stefan Andersson-Engels “A matrix-free algorithm for multiple wavelength fluorescence tomography.” Optics Express, Submitted. 2008
Can T. Xu, Niclas Svensson, Johan Axelsson, Pontus Svenmarker, Gabriel Somesfalean, Guanying Chen, Huijuan Liang, Haichun Liu, Zhiguo Zhang and Stefan Andersson-Engels, “Autofluorescence insensitive imaging using upconverting nanocrystals in scattering media”, App. Phys. Letters, 93(1), 2008
Axelsson J., Swartling J. and
Andersson-Engels S., “In vivo photosensitizer tomography inside the humane
prostate”, Opt. Lett. (Manuscript accepted 2008-11-29)
P. Svenmarker, J. Axelsson, M. Schweiger, A. Zacharopoulos, S. R. Arridge, and S. Andersson-Engels, "Multispectral Fluorescence Enhanced Diffuse Optical Tomography Evaluated with Weight Matrix Free Algorithm," in Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2008), paper BMC2.
Soloviev VY, D'Andrea, Valentini G, Cubeddu R, and Arridge SR. Combined reconstruction of fluorescent and optical parameters using time-resolved data. Applied Optics 48, 28-36 (2008).
Soloviev VY, D'Andrea C, Brambilla M, Valentini G, Schulz RB, Cubeddu R, and Arridge SR. An adjoint time domain method for fluorescent imaging in turbid media. Applied Optics 47, 2303-2311, (2008).
Athanasios D Zacharopoulos, Pontus Svenmarker, Johan Axelsson, Martin Schweiger, Simon R Arridge, Stefan Andersson-Engels “A matrix-free algorithm for multiple wavelength fluorescence tomography.” Optics Express, Submitted. 08
A. Corlu, R. Choe, T. Durduran, M. A. Rosen, M. Schweiger, S. R. Arridge, M. D. Schnall, A. G. Yodh, (2007), "Three-dimensional in vivo fluorescence diffuse optical tomography of breast cancer in humans", Optics Express, 15(11) 6696-6716.
A. Bassi, C. D'Andrea, G. Valentini, R. Cubeddu, S.R. Arridge, (2008), "Temporal propagation of spatial information in turbid media", Optics Letters, 33(23).
T. Tarvainen, M. Vaukhonen, S.R.Arridge, (2008), "Image reconstruction in optical tomography using the finite element solution of the frequency domain radiative transfer equation", Journal of Quantitative Spectroscopy and Radiative Transfer, 109, 2767-2778.
J. Waldeck, F. Häger, C. Höltke, C. Lanckohr, A. von Wallbrunn, W. Heindel, G.Theilmeier, M. Schäfers, C.Bremer „Near infrared fluorescence imaging of atheriosclerotic plaques using an alpha(v)beta(3) targeted fluorochrome” J Nucl Med. 2008 Nov;49(11):1845-51
A.
Wall, T. Persigehl, P. Hauff, K. Licha, M. Schirner, S. Müller, A. v.
Wallbrunn, L. Matuszewski, W. Heindel, C. Bremer
Differentiation of
angiogenic burden in human breast cancer xenografts using a new perfusion type
optical contrast agent (NIR96010)
Breast Cancer Res. 2008;10(2):R23
T. Frenzel, J.
Larmann, M. Schmitz, A. Hahnenkamp, C. Lanckohr, A.v. Wallbrunn, J. Waldeck, R.
Hildebrand, W. Heindel, G. Theilmeier, C. Bremer
“Noninvasive in vivo detection of macrophages recruited to sites of vascular injury using planar and tomographic fluorescence imaging technology”, submitted
R. Pierrat, N. Ben Braham, L.F. Rojas-Ochoa, R. Carminati and F. Scheffold, "The influence of the scattering anisotropy factor on diffuse reflection of light", Opt. Commun. 281, 18-22 (2008).
L.S. Froufe-Pérez and R. Carminati, "Lifetime fluctuations of a single emitter in a disordered nanoscopic system: The influence of the transition dipole orientation", Phys. Stat. Sol. (a) 205, 1258-1265 (2008).
L.S. Froufe-Pérez and R. Carminati, "Controlling the fluorescence lifetime of a single emitter on the nanoscale using a plasmonic superlens", Phys. Rev. B 78, 125403 (2008).
M. Boffety, M. Allain, A. Sentenac, M. Massonneau and R. Carminati, "Analysis of the depth resolution limit of luminescence diffuse optical imaging", Opt. Lett. 33, 2290 (2008).
S. Bandiera, D. Jacob, T. Muller, F. Marquier, M. Laroche and J.-J. Greffet, "Enhanced absorption by nanostructured silicon", Appl. Phys. Lett. 93, 193103 (2008)
R. Carminati, M. Donaire and J.J. Saenz, "On the density of states and extinction mean free path of waves in random media: Dispersion relation and sum rules", submitted to Phys. Rev. Lett. (2008)
L.S. Froufe-Pérez,
M. Köber, E.
Sahagún, M. Fuss, F. Briones, M. Luna and J.J. Sáenz
"Adhesion hysteresis in Dynamic Atomic Force Microscopy".
Phys. Stat. Sol. (RRL) 2, 138 (2008).
G.M. Sacha and J.J. Sáenz
"Generalized scattering matrix method for electrostatic calculations of nanoscale systems".
Physical Review B 77, 245423 (2008)
R. Carminati, M.
Donaire and J.J. Saenz,
"On the density
of states and extinction mean free path of waves in random media: Dispersion
relation and sum rules",
Submitted to Phys. Rev. Lett. (2008).
S. Albaladejo, M.I. Marques, M. Laroche and J.J. Saenz,
"Scattering
forces from the curl of the spin angular momentum of a light field",
Submitted to Phys. Rev. Lett. (2008).
M. Donaire and J.J.
Saenz,
"Dipole emission
and coherent transport in random media",
Submitted to Phys. Rev. Lett. (2008).
M. Fuss,
"Phase contrast
in Simultaneous Topography and Recognition Imaging",
Submitted to Ultramicroscopy (2008)
J. Rino, J.M.P. Desterro, T. R. Pacheco, T.W.J. Gadella Jr, M.
Carmo-Fonseca M. “Splicing Factors SF1 and U2AF associate in extra-spliceosomal
complexes”. Mol Cell Biol, 28(9):3045-57 (2008)
E. Auksorius, B. R. Boruah, C. Dunsby, P. M. P.
Lanigan, G. Kennedy, M. A. A. Neil and P. M. W. French, Stimulated emission
depletion microscopy with a supercontinuum source and fluorescence lifetime
imaging, Optics Letters 33 (2008) 113-115
James McGinty, Khadija B. Tahir, Romain Laine,
Clifford B. Talbot, Christopher Dunsby, Mark A. A. Neil, Laura Quintana Rio,
James Swoger, James Sharpe and Paul M.
W. French, Fluorescence Lifetime Optical Projection Tomography, Journal of
Biophotonics 1 (2008) 390-394
D. M. Grant, W. Zhang, E. J. McGhee, T. D.
Bunney, C. B. Talbot, S. Kumar, I Munro, C. Dunsby, M. A. A. Neil, M. Katan and
P. M. W. French, Multiplexed FRET to monitor multiple signalling events in live
cells, Biophysical Journal: Biophysical Letters 95 (2008) L69-L71
Clifford B. Talbot, James McGinty, David M.
Grant, Ewan J. McGhee, Dylan M. Owen, Wei Zhang, Tom D. Bunney, Ian Munro,
Beverly Isherwood, Rob Eagle, Andre Hargreaves, Chris Dunsby, Mark A. A. Neil,
Paul M. W. French, High speed unsupervised fluorescence lifetime imaging
confocal multiwell plate reader for high content analysis, Journal of
Biophotonics 1 (2008) 514–521
J. McGinty, J. Requejo-Isidro, I. Munro, C.B.
Talbot, C. Dunsby, P. Kellett, J. D. Hares, M.A.A. Neil and P.M.W. French,
Signal-to-Noise Characterisation of Time-Gated Intensifiers used for Wide-field
Time-Domain FLIM, To be submitted.
D. Shcherbo, E.A. Souslova, J. Goedhart, T.V. Chepurnykh, A. Gaintzeva, I.X. Shemiakina, T.W.J. Gadella Jr., S. Lukyanov and D. Chudakov (2009) Convenient and reliable FRET/FLIM apoptosis reporter, BMC Biotech, Accepted
J. Goedhart and T.W.J. Gadella Jr (2008) Fluorescence resonance energy transfer imaging of PKC signalling in living cells using genetically encoded fluorescent probes. J. R. Soc. Interface, Epub Oct 28.
J.E. Vermeer, J.M. Thole, J. Goedhart, E. Nielsen, T. Munnik and T.W.J. Gadella Jr. (2008) Plant J. Epub, Oct 25.
M.J.W.
Adjobo-Hermans, J. Goedhart, T.W.J. Gadella Jr. (2008) Regulation of PLC beta
1a membrane anchoring by its substrate phosphatidylinositol (4,5)-bisphosphate,
J. of Cell Science 121, 3770-3777
M. Schenning, J. Goedhart, T.W.J. Gadella Jr., D. Avram, K.W.A. Wirtz, G.T. Snoek (2008) The anti-apoptotic activity associated with phosphatidylinositol transfer protein alpha activates the MAPK and Akt/PKB pathway, Biochim. Biophys. Acta 1783, 1700-1706.
G.-J. Kremers, E.B. van Munster, J. Goedhart, T.W.J. Gadella (2008) Quantitative lifetime unmixing of multiexponentially decaying fluorophores using single-frequency fluorescence lifetime imaging microscopy. Biophys. J., 95, 378-389.
J. Rino, J.M.P. Desterro, T.R. Pacheco, T.W.J. Gadella Jr., M. Carmo-Fonseca (2008) Splicing factors SF1 and U2AF associate in extraspliceosomal complexes. Mol. Cell. Biol. 28, 3045-3057.
W. van
Leeuwen, J.E.M. Vermeer, Gadella, T.W.J., Munnik, T. (2008) 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.
Katie Foster, Julie
Sheridan, Henrique Veiga-Fernandes, Kathleen Roderick, Vassilis Pachnis, Ralf
Adams, Clare Blackburn, Dimitris Kioussis, Mark Coles.
Contribution of Neural Crest derived cells in
the embryonic and adult thymus
J.
Immunol., 2008, 180: 3183 – 3189
Black, S. L., Stanley, W. A., Filipp, F. V., Bhairo, M., Verma, A., Wichmann, O., Sattler, M., Wilmanns, M., Schultz, C. (2008) Probing lipid and drug binding domains with fluorescent dyes. Bioorg. Med. Chem. 16, 1162-1173 (2008).
Jost, C., Reither, G., Hoffmann, C., Schultz, C. Influence of fluorophores on protein kinase C FRET probe performance. ChemBioChem 9, 1379-1384 (2008).
Skrahina, T., Piljic, A., Schultz, C. (2008) Heterogeneity and timing of aggregate formation by different annexin isoforms. Exp. Cell Res. 314, 1039-1047 (2008).
Prinz, A., Reither, G., Diskar, M., Schultz, C. (2008) Fluorescence and Bioluminescence Procedures for Functional Proteomics. Proteomics 8, 1179-1203 (2008).
Piljic, A., Schultz, C. (2008a) Simultaneous recording of multiple cellular events by FRET. ACS Chem. Biol. 3, 156-160.
Alen Piljić, A., Schultz,
C. (2008b) Analysis of protein
complex hierarchy in living cells. ACS
Chemical Biology 3, 749-755.
Neef, A., Schultz, C. (2009)
Selective fluorescent labeling of lipids in living cells. Angew. Chem. Int. Ed., in press.
Cobos-Correa, A., Trojanek, J.,
Diemer, S., Mall, M. A., Schultz, C. (2009) MMP12 activity in pulmonary
inflammation visualized by a membrane-targeted fluorescent reporter. Nat. Chem. Biol., under review.
P. Kukura, M. Celebrano, A. Renn,
V. Sandoghdar, Imaging a Single Quantum Dot When It Is Dark, Nano Lett.
(on line Aug. 2008; cover of the print issue March 2009).
P. Kukura, H. Ewers, A. Renn, C.
Müller, A. Helenius, V. Sandoghdar, Rocking, tumbling, and sliding: Real-time
nanomotion of a membrane-bound virus, Science (submitted, Jan. 2009).
A. Walser, A. Renn, S. Götzinger, V.
Sandoghdar, Lifetime-limited zero-phonon spectra of single molecules in methyl
methacrylate, Chem. Phys. Lett. (accepted Jan. 2009).
Cox LJ, Hengst U, Gurskaya NG, Lukyanov KA, Jaffrey SR. Intra-axonal translation and retrograde trafficking of CREB promotes neuronal survival. Nature Cell Biol. 2008, 10, 149-159.
Mishin AS, Subach FV, Yampolsky
IV, King W, Lukyanov KA, Verkhusha VV. The first mutant of the Aequorea
victoria green fluorescent protein that forms a red chromophore. Biochemistry.
2008, 47, 4666-4673.
Subach OM, Gundorov IS, Yoshimura M, Subach FV, Zhang J, Grüenwald D, Souslova EA, Chudakov DM, Verkhusha VV. Conversion of red fluorescent protein into a bright blue probe. Chem. Biol. 2008, 15, 1116-1124.
Shcherbo D, Murphy CS, Ermakova
GV, Solovieva EA, Chepurnykh TV, Shcheglov AS, Verkhusha VV, Pletnev VZ,
Hazelwood KL, Roche PM, Lukyanov S, Zaraisky AG, Davidson MW, Chudakov DM.
Far-red fluorescent tags for protein imaging in living tissues. Biochem. J.
O. Dorn, M. Moscoso, D. Álvarez, R. Villegas,
N. Irishina, P. Medina, (2008) “Structural inversion with level sets”, Springer
Lecture Notes, CIME summer school on ‘Level Set and PDE based Reconstruction
Methods: Applications to Inverse Problems and Image Processing’, Cetraro
(Cosenza) - September 8 - September 13, 2008, (invited Springer lecture notes,
to be submitted in Jan 2009)
P. Medina, D Álvarez, M. Moscoso, “Estimating
lifetime and fluorophore distributions in optical molecular imaging using a
shape-based approach”, (to be submitted in Jan 09 to a refereed journal).
M Schweiger, O Dorn and S R Arridge, “3-D shape
and contrast reconstruction in optical tomography with level sets, AIP 2007
First International Congress of IPIA and Conference on Applied Inverse Problems
2007: Theoretical and Computational Aspects, June 25-29, 2007, Vancouver,
Canada, 2008 J. Phys.: Conf. Ser. 124 012043 (11pp) doi: 10.1088/1742-6596/124/1/012043
Smal I, Draegestein K, Galjart N, Niessen W, Meijering E. Particle filtering for multiple object
tracking in dynamic fluorescence microscopy images: application to microtubule
growth analysis. IEEE Trans Med Imaging.
2008 Jun;27(6):789-804.
Tanenbaum ME, Macůrek L, Galjart N, Medema
RH. Dynein, Lis1 and CLIP-170 counteract Eg5-dependent centrosome separation
during bipolar spindle assembly. EMBO J. 2008 Dec 17;27(24):3235-45.
Gontan C, de Munck A, Vermeij M, Grosveld F,
Tibboel D, Rottier R Sox2 is important for two crucial processes in lung
development: branching morphogenesis and epithelial cell differentiation.. Dev
Biol. 2008;317(1):296-309.
de Laat W, Klous P, Kooren J, Noordermeer D,
Palstra RJ, Simonis M, Splinter E, Grosveld F. Three-dimensional organization
of gene expression in erythroid cells. Curr Top Dev Biol. 2008;82:117-39
Jhunjhunwala S, van Zelm MC, Peak MM, Cutchin
S, Riblet R, van Dongen JJ, Grosveld FG, Knoch TA, Murre C. The 3D structure of
the immunoglobulin heavy-chain locus: implications for long-range genomic
interactions. Cell. 2008;133(2):265-79
Smal I, Meijering E, Draegestein K, Galjart N,
Grigoriev I, Akhmanova A, van Royen ME, Houtsmuller AB, Niessen W. Multiple
object tracking in molecular bioimaging by Rao-Blackwellized marginal particle
filtering. Med Image Anal. 2008 Dec;12(6):764-77.
Dragestein KA, van Cappellen WA, van Haren J,
Tsibidis GD, Akhmanova A, Knoch TA, Grosveld F, Galjart N. Dynamic behavior of
GFP-CLIP-170 reveals fast protein turnover on microtubule plus ends. J Cell
Biol. 2008;180(4):729-37
Grigoriev I, Gouveia SM, van der Vaart B,
Demmers J, Smyth JT, Honnappa S, Splinter D,
van der Heijden,
T., Modesti, M., Hage, S., Kanaar, R., Wyman, C., Dekker, C., 2008,
Homologous recombination in real time: DNA strand exchange by RecA
Mol Cell.,30(4):530-538
Kanaar R, Wyman C, Rothstein R., 2008, Quality control of DNA break metabolism: in the 'end', it's a good thing. EMBO J., 27(4):581-588
Kanaar R, Wyman C., 2008, DNA repair by the MRN complex: break it to make it.
Cell, 135(1):14-16.
Yann Roche,
Dianwen Zhang, Gezina Maria J. Segers-Nolten, Wim Vermeulen,
Claire Wyman, Kaoru Sugasawa, Jan Hoeijmakers, Cees Otto., 2008, Fluorescence Correlation Spectroscopy of the binding of nucleotide excision repair protein XPC- hHr23B with DNA substrates. J. Fluoresc., 18(5):987-95. Epub 2008 Jun 24.
Joost van Mameren, Mauro Modesti, Roland Kanaar, Claire Wyman,
Erwin J. G. Peterman, and Gijs J. L. Wuite., 2008, Counting RAD51 proteins disassembling from nucleoprotein filaments under tension”. Nature, online publication 7 December 2008 | doi:10.1038/nature07581.
Y.M. Mochkine, Mohd-Sarip A, Demmers JA, and Verrijzer CP.
Histone Chaperone ASF1 Cooperates with a LID/KDM5-containing Complex to Mediate Gene-Selective Silencing.
Submitted to Mol. Cell, 2008
M. Mellado
and Y. Carrasco. 2008
Imaging
techniques: new insights into chemokine/chemokine receptor biology at the
immune system
Pharmacol.
& Therap. 119:24-32
M. Mellado,
A.M. Martín de Ana, L. Gómez, C. Martínez-A and J.M. Rodríguez-Frade. 2008
Chemokine
receptor 2 blockade prevents asthma in a cynomolgus monkey model
J. Pharm.
& Exp Therap. 324:769-775
O.M. Pello,
L. Martínez-Muñoz, V. Parrillas, A. Serrano, J.M. Rodríguez-Frade, M.J. Toro,
P. Lucas, M Monterrubio, C. Martínez-A and M. Mellado. 2008
Ligand
stabilization of CXCR4/d-opioid receptor heterodimers reveals a mechanism for
immune response regulation
Eur. J.
Immunol. 38:537-549
J.L. Garcia-Pomar, A. Cortijo y M. Nieto-Vesperinas,
Fully Valley-Polarized Electron Beams in
Graphene,
P. Chaumet, M. Nieto-Vesperinas y A. Rahmani, Photonic Forces at the Nanoscale, Chapter 2 of Nano-Optics and Near-Field Optical Microscopy, (editors: A. Zayats y D. Richards). Artech House, London 2009. 376 pags., ISBN 978-1-59693-283-8.
Ming Bai, Chaonan Wang and
Marit J
Boot, C Henrik Westerberg, Juanjo Sanz-Ezquerro, James Cotterell, Ronen
Schweitzer, Miguel Torres & James Sharpe (2008) “In vitro whole-organ
imaging: 4D quantification of growing mouse limb buds”. Nature Methods
5:609-612
Burn SF, Boot MJ, de Angelis C, Doohan R, Arques CG, Torres M, Hill RE (2008) “The dynamics of spleen morphogenesis” Dev Biol. 2008 Jun 15;318(2):303-11. Epub 2008 Mar 28
Mercader N, Selleri L, Criado LM, Pallares P, Parras C, Cleary ML and Torres M (2008) Ectopic Meis1 expression in the mouse limb bud alters P-D patterning in a Pbx1-independent manner. Int J Dev Biol , (doi: 10.1387/ijdb.072430nm)
P.Lemmer, M.Gunkel, D.Baddeley, R. Kaufmann, A.
Urich, Y. Weiland, J.Reymann, P. Müller, M. Hausmann, C. Cremer (2008) SPDM –
Light Microscopy with Single Molecule Resolution at the Nanoscale. Applied
Physics B 93: 1-12.
J. Reymann, D. Baddeley, P. Lemmer, W. Stadter, T. Jegou, K. Rippe, C.
Cremer, U. Birk (2008) High precision structural analysis of subnuclear
complexes in fixed and live cells via Spatially Modulated Illumination (SMI)
microscopy. Chromosome Research 16: 367 –382.
I. Weidenfeld, M. Gossen, R. Löw, D. Kentner, S. Berger, H. Bujard, Dirk Görlich, Dusan Bartsch, Kai Schönig “Inducible expression of coding and inhibitory RNAs from retargetable genomic loci” Nucleic Acids Research (submission NAR-02588-Met-G-2008)
S. Berger, B. Pesold; S. Reber, K. Schönig, I. Weidenfeld, J. Miao, O. Gruss, D. Bartsch “Quantitative analysis of conditional gene inactivation using rationally designed, tet-controlled miRNAs” Nucleic Acids Research (submission NAR-02497-2008)
None
None
None
Mira
E., B. León, D. F. Barber, S. Jiménez-Baranda, I. Goya, L. Almonacid, G.
Márquez, A. Zaballos, C. Martínez-A., J. V. Stein, C. Ardavín and S.
Mañes. 2008. Statins induce regulatory T cell
recruitment via a CCL1 dependent pathway. J
Immunol. 181(5):3524-34
Pfeiffer
F., V. Kumar, S. Butz, D. Vestweber, B. A. Imhof, J. V. Stein and B.
Engelhardt. 2008. Distinct molecular
composition of blood and lymphatic vascular endothelial cell junctions
establishes specific functional barriers within the peripheral lymph node. Eur J Immunol. 38(8):2142-55
Thelen
M. and J. V. Stein. 2008. How
chemokines invite leukocytes to dance. Nat
Immunol. 9(9):953-9
Marit J Boot, C Henrik Westerberg, Juanjo Sanz-Ezquerro,
James Cotterell, Ronen Schweitzer, Miguel Torres & James Sharpe (2008) “In vitro whole-organ imaging: 4D
quantification of growing mouse limb buds”. Nature Methods 5:609-612
James McGinty, Khadija B. Tahir, Romain Laine, Clifford B. Talbot, Christopher Dunsby, Mark A. A. Neil, Laura Quintana, James Swoger, James Sharpe, Paul M. W. French (2008) “Fluorescence lifetime optical projection tomography”. Journal of Biophotonics. 1(5):390-394.