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Scientific Output Nanobiophysics Group |
2012 |
Hunting the Chameleon: Structural Conformations of the Intrinsically Disordered Protein Alpha-Synuclein. Drescher M, Huber M, Subramaniam V. Chembiochem. 2012 Mar 21. [Epub ahead of print] PMID: 22438319 [PubMed - as supplied by publisher] |
Locally resolved membrane binding affinity of the α-Synuclein N-terminus. Robotta M, Hintze C, Schildknecht S, Zijlstra N, Jüngst C, Karreman C, Huber M, Leist M, Subramaniam V, Drescher M. Biochemistry. 2012 Apr 12. [Epub ahead of print] PMID: 22494024 [PubMed - as supplied by publisher] |
Lateral mobility of individual integrin nanoclusters orchestrates the onset for leukocyte adhesion. Gert Jan Bakker, Christina Eich, Juan Torreno-Pina, Ruth Diez-Ahedo, Gemma Perez-Samper, Thomas S. van Zanten, Carl G. Figdor, Alessandra Cambi, and Maria F. Garcia-Parajo Proc Natl Acad Sci USA vol. 109 no. 13, 4869-4874. |
Kinetic measurements give new insights into lipid membrane permeabilization by ɑ-synuclein oligomers Stöckl M, Claessens MMAE, Subramaniam V Mol. BioSyst., 8 (1), 338 - 345 (2012) |
2011 |
Integrin-Dependent Activation of the JNK Signaling Pathway by Mechanical Stress Pereira AM, Tudor C, Kanger JS, Subramaniam V, Martin-Blanco E PLoS ONE 6(12): e26182 (2011) |
The structural basis for increased toxicity of pathological Abeta42:Abeta40 ratios in Alzheimer's disease Kris Pauwels, Thomas L. Williams, Kyle L. Morris, Wim Jonckheere, Annelies Vandersteen, Geoff Kelly, Joost Schymkowitz, Frederic Rousseau, Annalisa Pastore, Louise C. Serpell, Kerensa Broersen. JBC December (2011) |
Wafer-scale thin encapsulated two-dimensional nanochannels and its application toward visualization of single molecules Hoang, H.T., Tong, H.D., Segers-Nolten, I.M., Tas, N.R., Subramaniam, V. and Elwenspoek, M.C. J. Colloid & Interface Sci. (2011) |
Biophysical Analysis of Amyloid Formation Segers-Nolten I., van Raaij M., and Subramaniam V. P. Ducheyne, K.E. Healy, D.W. Hutmacher, D.W. Grainger, C.J. Kirkpatrick (eds.) Comprehensive Biomaterials, vol. 2, pp. 347-359 Elsevier. |
Room temperature excitation spectroscopy of single quantum dots Christian Blum, Frank Schleifenbaum, Martijn Stopel, Sébastien Peter, Marcus Sackrow, Vinod Subramaniam, Alfred J. Meixner Beilstein Journal of Nanotechnology 2011, 2, 516-524 |
Femtomolar DNA detection by parallel colorimetric darkfield microscopy of functionalized gold nanoparticles Verdoold, R., Gill, R., Ungureanu, F., Molenaar, R., Kooyman, R.P.H. Biosensors and Bioelectronics 27 (2011) 77– 81 |
Dark proteins disturb multichromophore coupling in tetrameric fluorescent proteins Blum, C., A.J. Meixner, and V. Subramaniam Journal of Biophotonics, 2011. 4(1-2): p. 114-12 |
Interactions of Perylene Bisimide in the One-Dimensional Channels of Zeolite L Busby, M., A. Devaux, C. Blum, V. Subramaniam, G. Calzaferri, and L. De Cola J. Phys. Chem. C 2011, 115, 5974–5988 |
Microspectroscopic analysis of green fluorescent proteins infiltrated into mesoporous silica nanochannels Ma, Y.J., P. Rajendran, C. Blum, Y. Cesa, N. Gartmann, D. Bruhwiler, and V. Subramaniam Journal of Colloid and Interface Science, 2011. 356(1): p. 123-130; |
Spectral versatility of Fluorescent Proteins observed on the single molecule Blum, C., and V. Subramaniam Springer Series on Fluorescence, ed. G. Jung: Springer, 2012, Volume 11, 217-240 |
Analysis of single quantum-dot mobility inside 1D nanochannel devices |
Hoang, H.T., Segers-Nolten, I.M., Tas, N.R., van Honschoten, J.W., Subramaniam, V. and Elwenspoek, M.C. |
Nanotechnology, 22, 275201-275209 |
Acousto-optic-assisted diffuse optical tomography Aliaksandr Bratchenia, Robert Molenaar, Ton G. van Leeuwen, and Rob P.H. Kooyman Optics Letters, Vol. 36, Issue 9, pp. 1539-1541 (2011) |
A standardized and biocompatible preparation of aggregate-free amyloid beta peptide for biophysical and biological studies of Alzheimer’s disease |
Broersen K, Jonckheere W, Rozenski J, Vandersteen A, Pauwels K, Pastore A, Rousseau F, Schymkowitz J. |
Protein Engineering, Design & Selection pp. 1–8, 2011 |
Amyloid Precursor Protein mutation E682K at the alternative beta-secretase cleavage beta’- site increases Abeta generation |
Zhou L, Brouwers N, Benilova I, Vandersteen A, Mercken M, Van Laere K, Van Damme P, Demedts D, Van Leuven F, Sleegers K, Broersen K, Van Broeckhoven C, Vandenberghe R, De Strooper B. |
EMBO Mol Med 3, 1–12 (2011) |
2010 |
Long-range energy propagation in nanometer arrays of light harvesting antenna complexes |
Escalante, M., A. Lenferink, Y. Zhao, N. Tas, J. Huskens, C. N. Hunter, V. Subramaniam, and C. Otto |
Nano Letters, 10: 1450–1457 |
Microbioreactors for Raman microscopy of stromal cell differentiation |
Pully, V. V., A. T. M. Lenferink, H. W. J. van Manen, V. Subramaniam, C. A. van Blitterswijk, and C. Otto |
Analytical Chemistry 82: 1844–1850 |
Evidence of Coexisting Horseshoe and Extended Helix Conformations of Membrane-Bound Alpha-Synuclein |
Robotta, M., P. Braun, B. van Rooijen, V. Subramaniam, Huber M., Drescher M. |
ChemPhysChem, in press. |
Membrane Permeabilization by Oligomeric α-Synuclein: In Search of the Mechanism |
Van Rooijen, B. D., Claessens M. M. A. E., Subramaniam V. |
PLoS ONE 5(12): e14292. |
Strategies for Patterning Biomolecules with Dip-Pen Nanolithography |
Wu, C.-C., Reinhoudt D. N. , Otto C. , Subramaniam V., Velders A. H. |
Volume 7, Issue 8, pages 989–1002 (2011) |
Dendritic Ruthenium(II)-based Dyes Tunable for Diagnostic or Therapeutic Applications |
Ruggi, A., Beekman C. , Wasserberg D., Subramaniam V., Reinhoudt D. N., van Leeuwen F. W. B., Velders A. H. |
Chem. Eur. J. 2011, 17, 464 – 467 (2011) |
Visualizing Resonance Energy Transfer in Supramolecular Surface Patterns of β-CD Functionalized QD Hosts and Organic Dye Guests by Fluorescence Lifetime Imaging |
Dorokhin, D. Hsu S.-H. , Tomczak N. , Blum C. , Subramaniam V. , Huskens J. , Reinhoudt D. N. , Velders A.H., Vancso G.J. |
Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, small 2010, 6, No. 24, 2870–2876 |
Patterning of Peptide Nucleic Acids using Reactive Microcontact Printing |
Calabretta, A., Wasserberg D. , Posthuma T. , Subramaniam V. , Van Amerongen A. , Corradini R. , Tedeschi T. , Sforza S. , Reinhoudt D.N. , Marchelli R. , Huskens J. , Jonkheijm P. |
Langmuir 2011, 27(4), 1536–1542 |
Neurotoxicity of Alzheimer disease Aβ-peptides is induced by small changes in the Aβ42 to Aβ40 ratio |
Kuperstein, I., K. Broersen, I. Benilova, Iryna, J. Rozenski, W. Jonckheere, M. Debulpaep, A. Vandersteen, I. Segers-Nolten, K. van der Werf, V. Subramaniam, D. Braeken, G. Callewaert, C. Bartic, R. D’Hooge, I. C. Martins, F. Rousseau, J. Schymkowitz, and B. de Strooper |
The EMBO Journal, 29: 3408 - 3420 |
Studies of Interaction Between Cyanine Dye T-284 and Fibrillar Alpha-Synuclein |
Volkova K. D., V. B. Kovalska, M. Yu Losytskyy, G. Veldhuis, G. M. J. Segers-Nolten, O. I. Tolmachev, V. Subramaniam, and S. M. Yarmoluk |
J Fluoresc (2010) 20:1267–1274 |
Pyrylium monolayers as amino-reactive platform |
Scaramuzzo, F. A., A. González-Campo, C-C. Wu, A. H. Velders, V. Subramaniam, G. Doddi, P. Mencarelli, M. Barteri, P. Jonkheijm and J. Huskens |
Chem. Commun. 46: 4193-4195 |
Simultaneous time-resolved measurement of the reaction rates and the refractive index of photopolymerisation processes |
Bak, T. M., J. B. Beusink, V. Subramaniam, and J. S. Kanger |
Applied Optics, 49: 3316-3322 |
Spatially resolved local intracellular chemical sensing using magnetic particles |
Shekhar, S., A. Klaver, C. Figdor, V. Subramaniam, and J. S. Kanger |
Sensors and Actuators: B, 148: 531-538 |
Membrane Interactions of Oligomeric Alpha-Synuclein: Potential Role in Parkinson's Disease |
van Rooijen BD, Claessens MM, Subramaniam V |
Curr Protein Pept Sci. 2010, 11(5), pp. 334-342(9) |
A Stable Lipid-Induced Aggregate of alpha-Synuclein |
Drescher M, Rooijen BD, Veldhuis G, Subrmaniam V, Huber M |
J Am Chem Soc. 2010, 132 (12), pp 4080–4082 |
Force spectroscopy and fluorescence microscopy of dsDNA–YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region |
Murade CU, Subramaniam V, Otto C, Bennink ML |
Nucleic Acids Res. 2010, 38(10):3423-3431 |
Protein Immobilization on Ni(II) Ion Patterns Prepared by Microcontact Printing and Dip-Pen Nanolithography |
Wu CC, Reinhoudt DN, Otto C, Velders AH, Subramaniam V |
ACS Nano 2010, 4 (2), pp 1083–1091 |
The use of fluorescent dyes and probes in surgical oncology |
te Velde, E.A, Veerman, Th, Subramaniam, V, Ruers, Th |
European Journal of Surgical Oncology 36 (1), pp. 6-15 doi:10.1016/j.ejso.2009.10.014 |
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2009 |
Tryptophan Fluorescence Reveals Structural Features of α-Synuclein Oligomers |
van Rooijen, B.D., van Leijenhorst-Groener, K.A., Claessens, M.M.A.E., Subramaniam, V. |
Journal of Molecular Biology 394 (5), pp. 826-833 |
Single Molecule Spectral Dynamics at Room Temperature Schleifenbaum, F., C. Blum, V. Subramaniam, and A.J. Meixner Molecular Physics, 2009. 107(18): p. 1923-1942; |
Multiparameter Single Molecule Spectroscopy gives insight into the complex Photophysics of Fluorescence Energy Transfer (FRET) coupled Biosystems. Schleifenbaum, F., C. Blum, K. Elgass, S. Peter, V. Subramaniam, and A.J. Meixner. Proc. of SPIE Vol. 7190 71900U-1 (2009) |
Method to deterministically study photonic nanostructures in different experimental instruments. Husken, B.H., L.A. Woldering, C. Blum, and W.L. Vos, Journal of Microscopy-Oxford, 2009. 233(1): p. 18-23; |
Expression of sensitized Eu3+ luminescence at a multivalent interface. Hsu, S.H., M.D. Yilmaz, C. Blum, V. Subramaniam, D.N. Reinhoudt, A.H. Velders, and J. Huskens Journal of the American Chemical Society, 2009. 131(35): p. 12567-12569; |
Interaction of oxazole yellow dyes with DNA studied with hybrid optical tweezers and fluorescence microscopy |
Murade, C.U., Subramaniam, V., Otto, C., Bennink, M.L. |
Biophysical Journal 97 (3), pp. 835-843 |
Modulation of protein dimerization by a supramolecular host-guest system |
Uhlenheuer, D.A., Wasserberg, D., Nguyen, H., Zhang, L., Blum, C., Subramaniam, V., Brunsveld, L. |
Chemistry - A European Journal 15 (35), pp. 8779-8790 |
Manipulation of the local density of photonic states to elucidate fluorescent protein emission rates |
Cesa, Y., Blum, C., Van Den Broek, J.M., Mosk, A.P., Vos, W.L., Subramaniam, V. |
Physical Chemistry Chemical Physics 11 (14), pp. 2525-2531 |
Spectral emission imaging to map photonic properties below the crystal surface of 3D photonic crystals. Blum, C., A.P. Mosk, W.L. Vos, and V. Subramaniam, Journal of the Optical Society of America B, 2009. 26(11): p. 2101–2108; |
Controlling fluorescent proteins by manipulating the local density of photonic states. Blum, C., Y. Cesa, J.M. van den Broek, A.P. Mosk, W.L. Vos, and V. Subramaniam. Proc. of SPIE. 2009. Munich, Germany: SPIE. |
Temperature-modulated quenching of quantum dots covalently coupled to chain ends of poly(N-isopropyl acrylamide) brushes on gold |
Tagit, O., Tomczak, N., Benetti, E.M., Cesa, Y., Blum, C., Subramaniam, V., Herek, J.L., Julius Vancso, G. |
Nanotechnology 20 (18), art. no. 185501 |
Gold nanoparticle assays: Towards single molecule unamplified DNA detection |
Verdoold, R., Ungureanu, F., Wasserberg, D., Kooyman, R.P.H. |
Proceedings of SPIE - The International Society for Optical Engineering 7312, art. no. 73120N |
The use of a colour camera for quantitative detection of proteinbinding nanoparticles |
Ungureanu, F., Halamek, J., Verdoold, R., Kooyman, R.P.H. |
Progress in Biomedical Optics and Imaging - Proceedings of SPIE 7192, art. no. 71920O |
Sequence-specific physical properties of African green monkey alpha-satellite DNA contribute to centromeric heterochromatin formation |
Bussiek, M., Hoischen, C., Diekmann, S., Bennink, M.L. |
Journal of Structural Biology 167 (1), pp. 36-46 |
Fabrication of nano structures in thin membranes with focused ion beam technology |
Gadgil, V.J., Tong, H.D., Cesa, Y., Bennink, M.L. |
Surface and Coatings Technology 203 (17-18), pp. 2436-2441 |
Single-molecule FRET reveals structural heterogeneity of SDS-bound α-synuclein |
Veldhuis, G., Segers-Nolten, I., Ferlemann, E., Subramaniam, V. |
ChemBioChem 10 (3), pp. 436-439 |
Multimode microscopy: Spectral and lifetime imaging |
Blum, C., Cesa, Y., Escalante, M., Subramaniam, V. |
Journal of the Royal Society Interface 6 (SUPPL. 1), pp. S35-S43 |
Single-molecule spectroscopy of fluorescent proteins. Blum, C. and V. Subramaniam Analytical and Bioanalytical Chemistry, 2009. 393(2): p. 527-541; |
FRET Pair Printing of Fluorescent Proteins. Escalante, M., C. Blum, Y. Cesa, C. Otto, and V. Subramaniam, Langmuir, 2009. 25(12): p. 7019-7024; |
A hybrid total internal reflection fluorescence and optical tweezers microscope to study cell adhesion and membrane protein dynamics of single living cells |
Snijder-Van As, M.I., Rieger, B., Joosten, B., Subramaniam, V., Figdor, C.G., Kanger, J.S. |
Journal of Microscopy 233 (1), pp. 84-92 |
Rapid, ultrasensitive detection of microorganisms based on interferometry and lab-on-a-chip nanotechnology |
Ymeti, A., Nederkoorn, P.H.J., Dudia, A., Subramaniam, V., Kanger, J.S. |
Proceedings of SPIE - The International Society for Optical Engineering 7306, art. no. 73060J |
Porous multilayer-coated AFM tips for dip-pen nanolithography of proteins |
Wu, C.-C., Xu, H., Otto, C., Reinhoudt, D.N., Lammertink, R.G.H., Huskens, J., Subramaniam, V., Velders, A.H. |
Journal of the American Chemical Society 131 (22), pp. 7526-7527 |
Explorations of the application of cyanine dyes for quantitative aα-synuclein detection |
Volkova, K.D., Kovalska, V.B., Segers-Nolten, G.M., Veldhuis, G., Subramaniam, V., Yarmoluk, S.M. |
Biotechnic and Histochemistry 84 (2), pp. 55-61 |
2008 |
Intracellular manipulation of chromatin using magnetic nanoparticles |
Kanger, J.S., Subramaniam, V., Van Driel, R. |
Chromosome Research 16 (3), pp. 511-522 |
Biofunctionalized lipid-polymer hybrid nanocontainers with controlled permeability |
Dudia, A., Koçer, A., Subramaniam, V., Kanger, J.S. |
Nano Letters 8 (4), pp. 1105-1109 |
Lipid bilayer disruption by oligomeric α-synuclein depends on bilayer charge and accessibility of the hydrophobic core |
van Rooijen, B.D., Claessens, M.M.A.E., Subramaniam, V. |
Biochimica et Biophysica Acta - Biomembranes 1788 (6), pp. 1271-1278 |
Membrane binding of oligomeric α-synuclein depends on bilayer charge and packing |
van Rooijen, B.D., Claessens, M.M.A.E., Subramaniam, V. |
FEBS Letters 582 (27), pp. 3788-3792 |
Concentration dependence of α-synuclein fibril length assessed by quantitative atomic force microscopy and statistical-mechanical theory |
Van Raaij, M.E., Van Gestel, J., Segers-Nolten, I.M.J., De Leeuw, S.W., Subramaniam, V. |
Biophysical Journal 95 (10), pp. 4871-4878 |
Tissue transglutaminase modulates α-synuclein oligomerization |
Segers-Nolten, I.M.J., Wilhelmus, M.M.M., Veldhuis, G., Van Rooijen, B.D., Drukarch, B., Subramaniam, V. |
Protein Science 17 (8), pp. 1395-1402 |
PhD Theses |
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Marieke Snijder - van As Controlled initiation and quantitative visualization of cell interaction dynamics - a novel hybrid microscopy method- doi:org/10.3990/1.9789036531252 2 December, 2010 |
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Chien-Ching Wu Novel Dip-Pen Nanolithography Strategies for Nanopatterning 18 June, 2010 |
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Chandrashekhar Murade Insights into DNA intercalation using combined optical tweezers and fluorescence microscopy 11 June, 2010 |
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Tomasz Bak Two photon microstereolithography of polymers for tissue engineering 16 December, 2009 |
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Maryana Escalante Marun Nanofabrication of bio-inspired architectures with light harvesting proteins 11 December, 2009 |
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Bart van Rooijen Structural and functional insights into interactions of oligomeric α-synuclein with lipid membranes 26 November, 2009 |
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Martijn van Raaij Biophysical characterization of alpha-synuclein aggregates: Parkinson's disease at the nanoscale 10 December, 2008 |
Inaugural Lecture |
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Prof. Dr. Vinod Subramaniam Biophysics of Protein Misfolding 21 June, 2007 |
