Publications in 2006
1)
G. Zacharakis, Helen Shih, Jorge Ripoll, Ralph
Weissleder, and Vasilis Ntziachristos, “Fluorescence normalized
transillumination of fluorescent proteins in small animals”, Molecular Imaging
5, 153 – 159 (2006)
2)
Ripoll J., Ntziachristos V., “From finite to infinite
volumes: Removal of boundaries in diffuse wave imaging”, Phys. Rev. Lett., 96,
art. no. 173903 (2006)
3)
Sikora J., Zacharopoulos A., Douiri A., Schweiger M.,
Horesh L., Arridge S.R., Ripoll J., “Diffuse photon propagation in multilayered
geometries”, Phys Med. Biol., 51, 497-516 (2006)
4)
Gundogdu TF, Tsiapa I, Kostopoulos A, Konstantinidis
G, Katsarakis N, Penciu RS, Kafesaki M, Economou EN, Koschny T, Soukoulis CM,
“Experimental demonstration of negative magnetic permeability in the
far-infrared frequency regime”, Appl. Phys. Lett., 89, art. no. 084103 (2006)
5)
Soukoulis CM, Kafesaki M, Economou EN, “Negative-index
materials: New frontiers in optics”, Advanced Materials, 18 1941-1952 (2006)
6)
Penciu RS, Kafesaki M, Gundogdu TF, Economou EN,
Soukoulis CM, “Theoretical study of left-handed behavior of composite
metamaterials”, Photonics and Nanostructures-Fundamentals and Applications, 4
12-16 (2006)
7)
Fabien
Chauchard, Jenny Svensson, Johan Axelsson, Stefan Andersson-Engels and Sylvie
Roussel “External Parameter Orthogonalisation - Least Squares Support Vector
Machine (EPO-LSSVM) and Partial Least Squares (PLS) for localization of
embedded inclusions using detection of fluorescence”, submitted to Chemometrics
and Intelligent Laboratory systems, (2006)
8) Johan Axelsson, Jenny Svensson,
Stefan Andersson-Engels, “Multispectral prior knowledge used for data
preprocessing in fluorescence molecular tomography”, submitted to Opt. Lett.
(2006)
9) Tomas Svensson, Linda Persson, Mats
Andersson, Sune Svanberg, Stefan Andersson-Engels, Jonas Johansson and Staffan
Folestad, “Non-invasive characterization of pharmaceutical solids using diode
laser oxygen spectroscopy” submitted to J. Pharmaceutical Sci. (2006)
10) Ann Johansson, Jenny Svensson, Niels
Bendsoe, Katarina Svanberg, Eleni Alexandratou, Maria Kyriazi, Dido Yova,
Susanna Gräfe, Tilmann Trebst, Stefan Andersson-Engels, “Fluorescence and
absorption assessment of a lipid mTHPC formulation following topical application
in a skin tumor model”, resubmitted to
J. Biomed. Opt. (2006)
11) Jenny Svensson, Ann Johansson,
Susanna Gräfe, Burkhard Gitter, Tilmann Trebst, Niels Bendsoe, Stefan
Andersson-Engels and Katarina Svanberg, “Tumor Selectivity Using a Systemically
Administered Liposomal mTHPC Formulation and Short Drug-light Interval in a
Murine Tumor Model” Submitted to Photochem Photobiol (2006)
12) Niels Bendsoe, Linda Persson, Ann
Johansson, Johan Axelsson, Jenny Svensson, Susanna Gräfe, Tilmann Trebst,
Stefan Andersson-Engels, Sune Svanberg Katarina Svanberg, “Fluorescence
monitoring of a topically applied liposomal Temoporfin formulationand
photodynamic therapy of non-pigmented skin malignancies”, submitted to J.
Environment. Pathol. Toxicol. Oncol. (2006)
13) A D Zacharopoulos, S R Arridge, O
Dorn, V Kolehmainen and J Sikora, “Three-dimensional reconstruction of shape
and piecewise constant region values for optical tomography using spherical
harmonic parametrization and a boundary element method” Inverse Problems, 22,.
1509-1532. (2006)
14) A D Zacharopoulos, S R Arridge, O
Dorn, V Kolehmainen and J Sikora, “3D Shape Based Reconstruction for Optical
Tomography Using Spherical Harmonics and BEM” JEMWA, vol 20, n 13, 1827-1836,
(2006)
15) S. R. Arridge, O. Dorn, J.P. Kaipio, V. Kolehmainen, M. Schweiger, T. Tarvainen, M. Vauhkonen
and A. Zacharopoulos, “Reconstruction of
subdomain boundaries of piecewise constant coefficients of the Radiative
Transfer Equation from Optical Tomography data.”, Inverse Problems, 22,. 2175-2196. (2006)
16) R Elaloufi,
17) A. von Wallbrunn, C. Höltke, M. Zühlsdorf,
18) R. Pierrat, J.-J. Greffet and R.
Carminati, 2006, "Photon diffusion coefficient in scattering and absorbing
media", J. Opt. Soc. Am. A 23, 1106-1110
19) R. Carminati, J.-J. Greffet, C.
Henkel and J.M. Vigoureux, 2006, "Radiative and non-radiative decay of a
single molecule close to a metallic nanoparticle'', Opt. Comm. 261, 368-375.
20) Y. De Wilde, F. Formanek, R.
Carminati, B. Gralak, P.A. Lemoine, K. Joulain, J.-P. Mulet, Y. Chen and J.-J.
Greffet, 2006, "Thermal radiation scanning tunneling microscopy'",
Nature 444, 740-743.
21) R. Elaloufi,
22) N. Ben Braham, R. Pierrat, L.F.
Rojas-Ochoa, R. Carminati and F. Scheffold, 2006, "The influence of
scattering anisotropy on diffuse reflection of light", Opt. Express,
submitted
23) F.J. García de Abajo, J.J. Sáenz, I Campillo
and J.S. Dolado, (2006), “Site and
Lattice Resonances in Metallic Hole Arrays”, Optics Express, 14, 7-18.
24) Raquel Gómez-Medina, Marine Laroche
and Juan José Sáenz, (2006), “Extraordinary Optical reflection from sub_wave-length
cylinder arrays”, Optics Express, 14, 3730-3737.
25) Gabriel Cwilich, Luis S.
Froufe-Pérez and Juan José Sáenz, (2006), “Spatial wave intensity correlations
in quasi-one-dimensional wires”, Physical Review E, 74, 045603.1-045603.4
(Rapid Communications).
26) P. A. Mello, M. Yepez, L. S.
Froufe-Pérez and J.J. Sáenz, (2006),
“Statistical scattering of waves in disordered waveguides: Universal
properties”, Physica A, 372, 203-209
27) Marine Laroche, Silvia Albaladejo,
Raquel Gómez and Juan José Sáenz, (2006), “Tunning the optical response of
nanocylinder arrays: An analytical study”, Physical Review B, 74,
245422.1-245422.5.
28) G.M. Sacha ,
29) L.S. Froufe-Pérez, M. Yépez, P. A.
Mello, and J.J. Sáenz, (2007), “Statistical Scattering of Waves in Disordered
Waveguides: from Microscopic Potentials to Limiting Macroscopic Statistics “, Physical
Review E, (In Press).
30) E. Sahagún, P. García-Mochales, G.M.
Sacha, and J.J. Sáenz , (2007), “Energy Dissipation due to Capillary
Interactions: Hydrophobicity Maps in Force Microscopy”, Physical Review
Letters, (Submitted).
31) S. Albaladejo, M. Lester, L.S.
Froufe-Pérez, A. García-Martín, and J.J. Sáenz, (2007), “Optical Conductance of
Waveguides Built into Photonic Crystals”, Nature Photonics, (Submitted).
32) L.S. Froufe, R. Carminati and J.J.
Sáenz, (2007), "Fluorescence decay rate statistics of a single molecule in
a disordered cluster of nanoparticles", Physical Review Letters, (Submitted).
33) Braga J, McNally JG and
Carmo-Fonseca M. “A reaction-diffusion model to study RNA motion by
quantitative fluorescence recovery after photobleaching”, submitted
34) C. Dunsby, P.M.P. Lanigan, J. McGinty, D.S.
Elson, J. Requejo-Isidro, I. Munro, N. Galletly, F. McCann, B. Treanor, B.
Onfelt, D.M. Davis, M.A.A. Neil and P.M.W. French “An electronically tunable
ultrafast laser source applied to fluorescence imaging and fluorescence
lifetime imaging microscopy” - J. Phys
D: Appl. Phys. 37 3296-3303 (2004).
35) D. M. Grant, D. S. Elson, D. Schimpf, C.
Dunsby, J. Requejo-Isidro, I. Munro, M. A. A. Neil and P. M. W. French
“Wide-Field Optically-Sectioned Fluorescence Lifetime Imaging using a Nipkow
Disk Microscope and a Tunable Ultrafast Continuum Excitation Source”, E. Nye
and G. Stamp, P. Courtney –Opt. Lett. 30 (2005) 3353-3355.
36) D. M. Owen, P. M. P. Lanigan, C. Dunsby, I.
Munro, D. Grant, M. A. A. Neil, P. M. W. French, and A. I. Magee, “Fluorescence
Lifetime Imaging Provides Enhanced Contrast when Imaging the Phase-Sensitive
Dye di-4-ANEPPDHQ in Model Membranes and Live Cells”, Biophysical Journal 90
(2006) L80-L82.
37) D. M. Owen, P. M. P. Lanigan, C.
Dunsby, I. Munro, D. Grant, M. A. A. Neil, P. M. W. French, and A. I. Magee,
“Fluorescence Lifetime Imaging Provides Enhanced Contrast when Imaging the
Phase-Sensitive Dye di-4-ANEPPDHQ in Model Membranes and Live Cells”,
Biophysical Journal 90 (2006) L80-L82.
38) P. De Beule, D. M. Owen, H. B.
Manning, C. B. Talbot, J. Requejo-Isidro, C. Dunsby, J. McGinty, R. K. P.
Benninger, D. S. Elson, I. Munro, M. J. Lever, P. Anand, M. A. A. Neil and P.
M. W. French “Rapid Hyperspectral Fluorescence Lifetime Imaging”, To be
published in Microscopy Research and Technique
39) Richard K. P. Benninger, Bjorn
Önfelt, Oliver Hofmann, Daniel M. Davis, Mark A. A. Neil, Paul M. W. French and
Andrew J. deMello “Time-resolved Fluorescence Imaging of Microfluidic-based
Binding Interactions”, To be published in Angewande Chemie.
40) Dhonukshe, P., Baluška, F.,
Schlicht, M., Hlavacka, A., Šamaj, J., Friml, J. and Gadella Jr., T.W.J. (2006)
Endocytosis of cell surface material mediates cell plate formation during plant
cytokinesis. Dev. Cell 10: 137-150.
41) Dhonukshe, P., Vischer, N., Gadella
Jr.,, T.W.J. (2006) Contribution of microtubule growth polarity and flux to
spindle assembly and functioning in plant cells, J. Cell Science. 119: 3193-3205.
42) Hoebe, R.A., van Oven, C.H., Gadella
Jr., T.W.J., Dhonukshe, P., van Noorden, C.J.F., Manders, E.M.M. (2007)
Controlled Light Exposure Microscopy (CLEM): Fluorescence Live Cell Imaging
with Strongly Reduced Photobleaching and Photodamage. Nature Biotechnol.
43) Kremers, G.-J., Goedhart, J., van
Munster, E.B. and Gadella Jr., T.W.J. (2006) Cyan and yellow superfluorescent
proteins with improved brightness, protein folding and FRET Förster radius.
Biochemistry 45: 6570-6580.
44) van Munster, E.B., Goedhart, J. And
Gadella Jr., T.W.J. (2006) Combination of spinning disk confocal unit with
frequency domain fluorescence lifetime imaging microscopy (FLIM). Cytometry
accepted
45) Dhonukshe, P., Bargmann, B., Gadella
jr., T.W.J. (2006) Arabidopsis Tubulin Folding Cofactor B interacts with alpha
tubulin in vivo. Plant Cell Physiol. 47:
1406-1411.
46) Adjobo-Hermans, M., Goedhart, J. and
Gadella Jr., T.W.J. (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.
47) Mark C. Coles, Henrique
Veiga-Fernandes, Katie E. Foster, Trisha Norton, Stamatis N. Pagakis, Ben Seddon, Dimitris
Kioussis, “Role of T, NK cells and IL7/IL7r interactions during neonatal
maturation of lymph nodes”, Proc. Natl. Acad. Sci. USA., 103,13457-62, (2006)
48) Henrique Veiga-Fernandes, Mark C.
Coles, Katie E. Foster, Amisha Patel, Adam
Williams, Dipa Natarajan, Amanda Barlow, Vassilis Pachnis & Dimitris
Kioussis, “Tyrosine kinase receptor Ret is a key regulator of Peyer’s Patch
organogenesis”, Nature, In Press, (2007)
None during this
reporting period
49) Wichmann, O., Wittbrodt, J., Schultz, C. A
small molecule FRET probe to monitor PLA2 activity in cells and organisms.
Angew. Chem. Int. Ed. Engl. 45, 508-512 (2006).
50) Brumbaugh, J., Schleifenbaum, A.,
Gasch, A., Sattler, M., Schultz, C. A dual parameter FRET probe for measuring
PKC and PKA activity in living cells. J. Am. Chem. Soc. 128, 24-25 (2006).
51) Piljic, A., Schultz, C. Annexin A4
self-association modulates general membrane protein mobility in living cells.
Mol. Biol. Cell 17, 3318-3328 (2006).
52) Brumbaugh, J., Schleifenbaum, A.,
Stier, G., Sattler, M., Schultz, C. Single and dual parameter FRET kinase
probes based on pleckstrin. Nat. Protocols 1, 1044-1055 (2006).
53) C. Schultz. Lipid-induced
phenotypes. Nat. Chem. Biol. 2, 396-398 (2006).
54) Yudushkin, I. A., Schleifenbaum, A.,
Neel, B. J., Schultz, C., Bastiaens, P. I. H. Imaging the enzyme-substrate
intermediate reveals functional subpopulations of the tyrosine phosphatase
PTP1B in living cells. Science 315, in press (2007).
55) Jost, C., Hoffmann, C., Schultz, C.
Influence of fluorophores on protein kinase C FRET probe performance. Submitted
(2007).
56) Optical detection of very small
nonfluorescent nanoparticles, V. Sandoghdar, E. Klotzsch, V. Jacobsen, A. Renn,
U. Hakanson, M. Agio, I. Gerhardt, J. Seelig, G. Wrigge, Chimia 60, 761 (2006).
57) Enhancement of single molecule
fluorescence using a gold nanoparticle as an optical nano-antenna, S. K?hn, U.
Hakanson, L. Rogobete, V. Sandoghdar, Phys. Rev. Lett. 97, 017402 (2006).
58) Oxygen dependent photochemistry of
fluorescent dyes studied at the single molecule level, A. Renn, J. Seelig, V.
Sandoghdar, Mol. Phys. 104, 409-414 (2006).
59) Interferometric optical detection
and tracking of very small gold nanoparticles at a water-glass interface, V.
Jacobsen, P. Stoller, C. Brunner, V. Vogel and V. Sandoghdar, Optics Express
14, 405-414 (2006).
60) Nanoparticle induced fluorescence
lifetime modification as nanoscopic ruler: demonstration at the single molecule
level, J. Seelig, K. Leslie, A. Renn, S. K?hn, V. Jacobsen, M. van de Corput,
C. Wyman, V. Sandoghdar, Nano Letters, accepted.
61) Label-free Detection of Single
Virions Bound to their Receptor in Supported Membrane Bilayers, H. Ewers, V.
Jacobsen, E. Klotzsch, A. E. Smith, A. Helenius, and V. Sandoghdar, submitted
to Biophysical Journal (January 2007).
62) Bulina ME, Chudakov DM, Britanova OV,
Yanushevich YG, Staroverov DB, Chepurnykh TV, Merzlyak EM, Shkrob MA, Lukyanov
S, Lukyanov KA. (2006) A genetically encoded photosensitizer. Nature
Biotechnol.24, 95-99.
63) Gurskaya NG, Verkhusha VV, Shcheglov AS,
Staroverov DB, Chepurnykh TV, Fradkov AF, Lukyanov S, Lukyanov KA. (2006)
Engineering of a monomeric green-to-red photoactivatable fluorescent protein
induced by blue light. Nature Biotechnol. 24, 461-465.
64) Belousov VV, Fradkov AF, Lukyanov KA,
Staroverov DB, Shakhbazov KS, Terskikh AV, Lukyanov S. (2006) Genetically
encoded fluorescent indicator for intracellular hydrogen peroxide. Nature
Methods. 3, 281-286.
65) Souslova EA, Chudakov DM. (2006)
Photoswitchable cyan fluorescent protein as a FRET donor. Microsc Res Tech. 69,
207-209.
66) Bulina ME, Lukyanov KA, Britanova
OV, Onichtchouk D, Lukyanov S, Chudakov DM. (2006) Chromophore-assisted light
inactivation (CALI) using the phototoxic fluorescent protein KillerRed. Nature
Protocols, 1, 947-953.
67) Chudakov DM, Chepurnykh TV, Belousov
VV, Lukyanov S, Lukyanov KA. (2006) Fast and precise protein tracking using
repeated reversible photoactivation. Traffic. 7, 1304-1310.
68) Evdokimov AG, Pokross ME, Egorov NS,
Zaraisky AG, Yampolsky IV, Merzlyak EM, Shkoporov AN, Sander I, Lukyanov KA,
Chudakov DM. (2006) Structural basis for the fast maturation of Arthropoda
green fluorescent protein. EMBO Rep. 7, 1006-1012.
69) O. Dorn and D. Lesselier, “Level set
methods for inverse scattering”, Topical review, Inverse Problems 22 (2006)
R67-R131
70) O. Dorn and D. Lesselier, “Level set
techniques for structural inversion in medical imaging”, Chapter in book:
"Deformable Models: Theory and
Biomaterial Applications", Editors (Jasjit S. Suri and Aly Farag),
Springer Publishers, ISBN: 978-0-387-31204 8, pp. 61-90, to appear Dec. 2006.
71) S.R. Arridge, O. Dorn, J.P. Kaipio,
V. Kolehmainen, M. Schweiger, T. Tarvainen, M. Vauhkonen and A. Zacharopoulos
“Reconstruction of subdomain boundaries of piecewise constant coefficients of
the Radiative Transfer Equation from Optical Tomography data”, Inverse Problems
22 (2006) pp 2175-2196.
72) Three dimensional reconstruction of
shape and piecewise constant region values for Optical Tomography using
spherical harmonic parameterisation and a Boundary Element Method, A D
Zacharopoulos, S R Arridge, O Dorn, V Kolehmainen and J Sikora, Inverse
Problems 22, pp 1509-1532.
73) M. Schweiger, S.R. Arridge, O. Dorn,
A. Zacharopoulos, V. Kolehmainen, “Reconstructing absorption and diffusion
shape profiles in optical tomography using a level set technique”, Optics
Letters, 31 no. 4, pp. 471-473. (This article was selected by the Optical
Society of America to be published also in the ‘Virtual Journal for Biomedical
Optics’ ISSN 1931-1532, Vol. 1, issue 3, March 7, 2006)
74) Grigoriev I, Splinter D, Keijzer N,
Wulf P, Demmers J, Ohtsuka T, Modesti M, Maly I, Grosveld F, Hoogenraad C,
Akhmanova A. Rab6A regulates transport and targeting of exocytotic carriers.
Submitted.
75) K. Draegenstein, G. Tsibidis, T.
Knoch, A. Akhmanova, G. van Capellen, F. Grosveld and N.Galjart. Novel
mechanism for microtubule plus end binding of mammalian GFP-CLIP170. Submitted
for publication.
76) J. Sellig, K. Leslie, A. Kuhn, V.
Jacobsen, M. van der Corput, C. Wyman and V. Sandghdar. “ Nanoparticle Induced Fluorescence
Lifetime Modification as Nanoscopic Ruler”.
2006 Submitted to Nano Letters.
77) Mohd-Sarip, A., J.A. van der Knaap,
C. Wyman, Roland Kanaar, P. Schedl and C.P. Verrijzer (2006) Architecture of a
Polycomb Nucleoprotein Complex. Molecular Cell, vol. 24, pp. 91-100
78) Wyman, C., and R. Kanaar (2007) DNA
double-strand break repair: All’s well that ends well. Ann. Rev. Genetics, vol. 40, pp. 363-83
79) van Mameren, J., M. Modesti, R.
Kanaar, C. Wyman, G. J. L. Wuite, and E. J. G. Peterman (2006) Dissecting
elastic heterogeneity along DNA molecules coated partly with Rad51 using
concurrent fluorescence microscopy and optical tweezers. Biophys. J. vol. 91,
pp. L78-80.
80) Wyman, C. (2006) Monomer networking
activates recombinases. Structure 14, p. 949-951.
None during this reporting period
81) Plasmon excitation in sets of nanoscale cylinders
and spheres, L. A. Blanco, and M. Nieto-Vesperinas, Phys. Rev. B 73, 035403
(2006)
82) Applied Optics, Vol. 45, Issue 21,
pp. 51 Local field enhancement in an optical force metallic nanotrap:
application to single-molecule spectroscopy, Patrick C. Chaumet,
83) Tunable optical sorting and
manipulation of nanoparticles via plasmon excitation at the single-molecule
level, Anna S. Zelenina, Romain Quidant, Gonçal Badenes, and Manuel
Nieto-Vesperinas, Optics Letters, Vol. 31, Issue 13, pp. 2054-2056
84) Ming Bai,
85) Ming Bai and N. Garcia, Transmission
of light by a single subwavelength cylindrical hole in metallic films, Applied
Physics Letters 89, 141110 (2006).
86) M. Muñoz, Ming Bai, Lu Yonghua, C.
S. Steplecaru and Cheng Hao, Synthesis and Electrostatic Force Microscopy of
Cu-PMMA Nanocomposites thin films, Submitted to Nanotechnology.
87) Lu Yonghua, M. Munoz, C.S.
Steplecaru, Hao Cheng, Bai Ming, N. Garcia, K.Schindler, P. Esquinazi,
Electrostatic force microscopy on oriented graphite surfaces: Coexistence of
insulating and conducting behaviors, Phys. Rev. Lett. 97 (7): Art. No. 076805
AUG 18 2006
88) Arqués, CG1, Doohan, R1, Sharpe, J2
and Torres, M1. Mouse limb mesenchyme is
compartmentalized along the dorso-ventral but not the proximo-distal or
anterior-posterior axes (submitted to Development, 1st round review process).
89) Marit J. Boot1, C. Henrik
Westerberg1, Juanjo Sanz-Ezquerro2, Ronen Schweitzer3, Miguel Torres Sanchez2,
James Sharpe,’ In vitro whole-organ imaging: Quantitative 4D analysis of growth
and dynamic gene expression in mouse limb buds’
90) U. Birk et al. (2006), 'Local
Protein/Gene Density Measurements Using SMI Microscopy' , Proc. SPIE,
6188:212-216
91) D. Baddeley et al. (2006), '4Pi
microscopy deconvolution with variable point-spread function', Applied Optics,
45/27:7056-7064
None
during this reporting period
None during this reporting period
None during this reporting period
None during this reporting period
None during this reporting period
None during this reporting period
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