Scientific Output Nanobiophysics Group

2015

Two distinct β-sheet structures in Italian-mutant amyloid-beta fibrils: a potential link to different clinical phenotypes

Hubin E, Deroo S, Schierle GK, Kaminski C, Serpell L, Subramaniam V, van Nuland N, Broersen K, Raussens V, Sarroukh R.

Cell Mol Life Sci. 2015 Jul 21. http://www.ncbi.nlm.nih.gov/pubmed/26190022

Using magnetic probes to study receptor clustering in live cells

Celikkol Bu, Cambi A, Figdor CG, Subramaniam V, Kanger JS

Biophysical Journal, 106(2, Suppl. 1), 20a. 10.1016/j.bpj.2013.11.164

How do lipids localize in Lewy Bodies?

Chaudhary H, Subramaniam V Claessens M

Biophysical Journal, 106(2, suppl. 1), 301a. 10.1016/j.bpj.2013.11.1749

MicroRNA levels as prognostic markers for the differentiation potential of human mesenchymal stromal cell donors

Georgi N, Taipaleenmaeki H, Raiss CC, Groen N, Portalska KK, Blitterswijk CA van, Boer J de, Post JN, Wijnen A van, Karperien HBJ

Stem Cells and Development. In press. 10.1089/scd.2014.0534

Spatiotemporal proliferation of human stromal cells adjusts to nutrient availability and leads to stanniocalcin-1 expression in vitro and in vivo

Higuera G, Fernandes H, Spitters TWGM, Peppel J van de, Auffermann N, Truckenmuller RK, Escalante M, Stoop R, Leeuwen JP van, Boer J de, Subramaniam V, Karperien HBJ, Blitterswijk CA van, Boxtel A van, Moroni L

Biomaterials, 61, pp. 190-202. 10.1016/j.biomaterials.2015.05.017

Microcantilever based distance control between a probe and a surface

Molenaar R, Prangsma JC, Werf KO van der, Bennink ML, Blum C, Subramaniam V

Review of Scientific Instruments, 86, 1-8. 10.1063/1.4922885

The formation of higher order structures by the neuronal protein alpha-synuclein: self-assembly over multiple length scales

Semerdzhiev S, Claessens M, Subramaniam V

Biophysical Journal, 106(2, suppl. 1), 683a-684a. 10.1016/j.bpj.2013.11.3783

Long-range distance constraints for the fibril fold of Parkinson's protein alpha-synuclein

Shabestari, MH, Kumar P, Segers-Nolten IMJ, Claessens MMAE, Rooijen BD van, Subramaniam V, Huber M

Biophysical Journal, 106(2, suppl. 1), 269a. 10.1016/j.bpj.2013.11.1576

Repeats in the α-synuclein sequence determine its conformation on membranes and influence aggregation properties

Shvadchak VV, Subramaniam V

Biophysical Journal, 106(2, suppl. 1), 268a. 10.1016/j.bpj.2013.11.1574

Alpha-synuclein amyloid oligomers act as multivalent nanoparticles to cause hemifusion in negatively charged vesicles

Stefanovic A, Claessens MMAE, Blum C, Subramaniam V

Small, 11(19), pp. 2257-2262. 10.1002/smll.201402674

Functional optical coherence tomography of pigmented lesions

Wessels R, Bruin DM de, Relyveld GN, Faber DJ, Vincent AD, Sanders J, Leeuwen TG van, Ruers TJM

Journal of the European Academy of Dermatology and Venereology, 29(4), pp. 738-744. 10.1111/jdv.12673

 

2014

 

Mechanistic insights in glycation-induced protein aggregation

Adrover M, Marino L, Sanchis P, Pauwels K, Kraan YM, Lebrun P, Vilanova B, Munoz F, Broersen K, Donoso J

Biomacromolecules, 15(9), pp. 3449-3462. 10.1021/bm501077j

Nanoparticle aggregate-based fluorescence enhancement for highly sensitive and reproducible detection of DNA

Annink C, Gill R

Particle & Particle Systems Characterization, 31(9), pp. 943-947. 10.1002/ppsc.201400061

Podosomes of dendritic cells facilitate antigen sampling

Baranov MV, Beest M ter, Reinieren-Beeren I, Cambi A, Figdor CG, Bogaart G van den

Journal of Cell Science, 127(5), pp. 1052-1064. 10.1242/jcs.141226

Priming by chemokines restricts lateral mobility of the adhesion receptor LFA-1 and restores adhesion to ICAM-1 nano-aggregates on human mature dendritic dells

Borgman KJ, Zanten TS van, Manzo C, Cabezon R, Cambi A, Benitez-Ribas D, Garcia Parajo MF

PLOS One, 9:e99589(6). 10.1371/journal.pone.0099589

Classification of dynamical diffusion states in single molecule tracking microscopy

Bosch PJ, Kanger JS, Subramaniam V

Biophysical Journal, 107(3), pp. 588-598. 10.1016/j.bpj.2014.05.049

Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single molecule tracking microscopy in live cells

Bosch PJ, Correa IR, Sonntag MH, Brunsveld L, Kanger JS, Subramaniam V

Biophysical Journal, 107, pp. 803-814. 10.1016/j.bpj.2014.06.040

Membrane interactions and fibrillization of alpha-synuclein play an essential role in membrane disruption

Chaudhary H, Stefanovic A, Subramaniam V, Claessens MMAE

FEBS Letters, 588, pp. 4457-4463. 10.1016/j.febslet.2014.10.016

Characterization of Sierpinski carpet optical antenna at visible and near-infrared wavelengths

Chen TL, Dikken DJW, Prangsma JC, Segerink FB, Herek JL

New Journal of Physics, 16:093024. 10.1088/1367-2630/16/9/093024

Spatiotemporal organization and mechanosensory function of podosomes

Dries K van den, Bolomini-Vittori M, Cambi A

Cell Adhesion & Migration, 8(3), pp. 268-272. 10.4161/cam.28182

Transient dynamics of Abeta contribute to toxicity in Alzheimer's disease

Hubin E, Nuland N van, Broersen K, Pauwels K

Cellular and Molecular Life Sciences, 71(18), pp. 3507-3521. 10.1007/s00018-014-1634-z

Amyloids of alpha-synuclein affect the structure and dynamics of supported lipid bilayers

Iyer AS, Petersen NO, Claessens MMAE, Subramaniam V

Biophysical Journal, 106, pp. 2585-2594. 10.1016/j.bpj.2014.05.001

Detection of melanoma metastases in resected human lymph nodes by noninvasive multispectral photoacoustic imaging

Langhout GC, Grootendorst DJ, Nieweg OE, Wilhelmus M, Wouters JM, Hage JA van der, Jose J, Boven H van, Steenbergen W, Manohar S, Ruers TJM

International Journal of Biomedical Imaging, 163652. 10.1155/2014/163652

Plasticity of the MAPK signaling network in response to mechanical stress

Pereira A, Tudor C, Pouille P-A, Shekhar S, Kanger JS, Subramaniam V, Martin-Blanco E

PLOS One, 9:e101963(7). 10.1371/journal.pone.0101963

Dynamic coupling of ALCAM to the actin cortex strengthens cell adhesion to CD6

Riet J te, Helenius J, Strohmeyer N, Cambi A, Figdor CG, Muller DJ

Journal of Cell Science, 127(7), pp. 1595-1606. 10.1242/jcs.141077

Predicting the loading of virus-like particles with fluorescent proteins

Rurup WF, Verbij F, Koay MST, Blum C, Subramaniam V, Cornelissen JJLM

Biomacromolecules, 15(2), pp. 558-563. 10.1021/bm4015792

Self-assembly of protein fibrils into suprafibrillar aggregates: bridging the nano- and mesoscale

Semerdzhiev SA, Dekker DR, Subramaniam V, Claessens MMAE

ACS Nano, 8(6), pp. 5543-5551. 10.1021/nn406309c

Application of MALDI-TOF mass spectrometry for study on fibrillar and oligomeric aggregates of alpha-synuclein

Severinovskaya OV, Kovalska VB, Losytskyy MY, Cherepanov VV, Subramaniam V, Yarmoluk SM

Biopolymers and Cell, 30(3), pp. 190-196. 10.7124/bc.000895

A four-amino acid linker between repeats in the α-synuclein sequence is important for fibril formation

Shvadchak VV, Subramaniam V

Biochemistry, 53(2), pp. 279-281. 10.1021/bi401427t

Solution conditions define morphological homogeneity of alpha-synuclein fibrils

Sidhu A, Segers-Nolten GMJ, Subramaniam V

Biochimica et Biophysica Acta: Proteins and Proteomics, 1844, pp. 2127-2134. 10.1016/j.bbapap.2014.09.007

Monitoring of tumor radio frequency ablation using derivative spectroscopy

Spliethoff JW, Tanis E, Evers DJ, Hendriks BH, Prevoo W, Ruers TJM

Journal of Biomedical Optics, 19:97004(9). 10.1117/1.JBO.19.9.097004

Monitoring of tumor response to Cisplatin using optical spectroscopy

Spliethoff JW, Evers DJ, Jaspers JE, Hendriks BH, Rottenberg S, Ruers TJM

Translational Oncology, 7(2), pp. 230-239. 10.1016/j.tranon.2014.02.009

α-Synuclein oligomers distinctively permeabilize complex model membranes

Stefanovic A, Stockl MT, Claessens MMAE, Subramaniam V

FEBS Journal, 281(12), pp. 2838-2850. 10.1111/febs.12824

Excitation spectra and stokes shift measurements of single organic dyes at room temperature

Stopel MHW, Blum C, Subramaniam V

Journal of Physical Chemistry Letters, 5(18), pp. 3259-3264. 10.1021/jz501536a

Local recurrence rates after radiofrequency ablation or resection of colorectal liver metastases. Analysis of the European Organisation for Research and Treatment of Cancer

Tanis E, Nordlinger B, Mauer M, Sorbye H, Coevorden F van, Gruenberger TM, Schlag PM, Punt CJA, Ledermann J, Ruers TJM

European Journal of Cancer, 50(5), pp. 912-919. 10.1016/j.ejca.2013.12.008

Syntenin-1 and ezrin proteins link activated leukocyte cell adhesion molecule to the actin cytoskeleton

Tudor C, Riet J te, Eich C, Harkes R, Smisdom N, Bouhuijzen Wenger J, Ameloot M, Holt M, Kanger JS, Figdor CG, Cambi A, Subramaniam V

Journal of Biological Chemistry, 289(19), pp. 13445-13460. 10.1074/jbc.M113.546754

Optical biopsy of epithelial cancers by optical coherence tomography

Wessels R, Bruin DM de, Faber DJ, Leeuwen TG van, Beurden MFB van, Ruers TJM

Lasers in Medical Science, 29(3), pp. 1297-1305. 10.1007/s10103-013-1291-8

The value of optical coherence tomography in determining surgical margins in squamous cell carcinoma of the vulva: a single-center prospective study

Wessels R, Beurden MFB van, Bruin DM de, Faber DJ, Vincent AD, Sanders J, Leeuwen AGJM van, Ruers TJM

International Journal of Gynecological Cancer, 25(1), pp. 112-118. 10.1097/IGC.0000000000000310

Elucidating the aggregation number of dopamine-induced alpha-synuclein oligomeric assemblies

Zijlstra N, Claessens MMAE, Blum C, Subramaniam V

Biophysical Journal, 106, pp. 440-446. 10.1016/j.bpj.2013.12.009

Microdomains in the membrane landscape shape antigen-presenting cell function

Zuidscherwoude M, Winde CM de Cambi A, Spriel AB van

Journal of Leukocyte Biology, 95(2), pp. 251-263. 10.1189/jlb.0813440

2013

 

Intra-laser-cavity microparticle sensing with a dual-wavelength distributed-feedback laser

Bernhardi EH, Werf KO van der, Hollink AJF, Worhoff K, Ridder RM de, Subramaniam V, Pollnau M

Laser & photonics Reviews 7(4), pp. 589-595. eemcs-eprint-23493

Magnetic Nanoparticles as Mediators of Ligand-Free Activation of EGFR Signaling

Bharde AA, Palankar R, Fritsch C, Klaver A, Kanger JS, Jovin TM, Arndt-jovin DJ

PLOS one 8(7), pp. 1-11. 10.1371/journal.pone.0068879

Selection of patients for hepatic surgery of colorectal cancer liver metastasis based on genomic aberrations

Bruin SC, Ronde JJ de, Wiering B, Braaf LM, Wilt JH de, Vincent AD, Velthuysen ML van, Ruers TJM, Wessels LF, Veer LJ van 't

Annals of surgical oncology 20(3, suppl), pp. 560-569. 10.1245/s10434-013-2985-7

Visualizing signaling nanoplatforms at a higher spatiotemporal resolution

Cambi A, Lakadamyali M, Lidke DS, Garcia-Parajo MF

Journal of Cell Science 126, pp. 3817-3821. 10.1242/jcs.137901

Dual-color superresolution microscopy reveals nanoscale organization of mechanosensory podosomes

Dries K van den, Schwartz SL, Byars J, Meddens MBM, Bolomini-Vittori M, Lidke DS, Figdor CG, Lidke KA, Cambi A

Molecular Biology of the Cell 24(13), pp. 2112-2123. 10.1091/mbc.E12-12-0856

Diffuse reflectance spectroscopy: towards clinical application in breast cancer

Evers DJ, Nachabe R, Vrancken Peeters MJ, Hage JA van der, Oldenburg HS, Rutgers EJ, Lucassen GW, Hendriks BH, Wesseling J, Ruers TJM

Breast Cancer Research and Treatment 137(1), pp. 155-165. 10.1007/s10549-012-2350-8

Optical sensing for tumor detection in the liver

Evers DJ, Nachabe R, Hompes D, Coevorden F van, Lucassen GW, Hendriks BH, Velthuysen ML van, Wesseling J, Ruers TJM

European Journal of Surgical Oncology 39(1), pp. 68-75. 10.1016/j.ejso.2012.08.005

Emission enhancement and lifetime modification of phosphorescence on silver nanoparticle aggregates

Gill R, Tian L, Amerongen H, Subramaniam V

Physical Chemistry Chemical Physics (PCCP), 15(38), pp. 15734-15739. 10.1039/C3CP50407G

Fast, single-step, and surfactant-free oligonucleotide modification of gold nanoparticles using DNA with a positively charged tail

Gill R, Goeken KL, Subramaniam V

Chemical Communications, 49(97), pp. 11400-11402. 10.1039/c3cc47138a

Evaluation of superparamagnetic iron oxide nanoparticles (Endorem) as a photoacoustic contrast agent for intra-operative nodal staging

Grootendorst DJ, Jose J, Fratila RM, Visscher M, Velders AH, Haken B ten, Leeuwen AGJM van, Steenbergen W, Manohar S, Ruers TJM

Contrast Media & Molecular Imaging, 8(1), pp. 83-91. 10.1002/cmmi.1498

Intra-operative ex vivo photoacoustic nodal staging in a rat model using a clinical superparamagnetic iron oxide nanoparticle dispersion

Grootendorst DJ, Fratila RM, Visscher M, Haken B ten, Wezel RJA van, Rottenberg S, Steenbergen W, Manohar S, Ruers TJM

Journal of Biophotonics, 6(6-7), pp. 493-504. eemcs-eprint-23397

Optical techniques for the intraoperative assessment of nodal status

Grootendorst DJ, Steenbergen W, Manohar S, Ruers TJM

Future Oncology, 9(11), 1741-1755. 10.2217/fon.13.125

Automated podosome identification and characterization in fluorescence microscopy images

Meddens MBM, Rieger B, Figdor CG, Cambi A, Dries K van den

Microscopy and Microanalysis, 19(1), pp. 180-189. 10.1017/S1431927612014018

Surface modification of electrospun fibre meshes by oxygen plasma for bone regeneration

Nandakumar A, Tahmasebi Birgani Z, Reis Santos D, Mentink A, Auffermann N, Werf KO van der, Bennink ML, Moroni L, Blitterswijk CA van, Habibovic P

Biofabrication, 5:015006(1). 10.1088/1758-5082/5/1/015006

Au coated Ni nanowires with tuneable dimensions for biomedical applications

Pondman KM, Maijenburg AW, Celikkol FB, Pathan AA, Kishore UD, Haken B ten, Elshof JE ten

Journal of Materials Chemistry. B: Materials for Biology and Medicine, 1(44), pp. 6129-6136. 10.1039/C3TB20808G

Hepatic resection for metastatic melanoma in The Netherlands: survival and prognostic factors

Ridder J de, Walsum M van, Nagtegaal ID, Wilt J de, Ruers TJM

Melanoma Research, 23(1), pp. 27-32. 10.1097/CMR.0b013e32835b70c8

Single-molecule imaging technique to study the dynamic regulation of GPCR function at the plasma membrane.

Snaar-Jagalska, B.E., Cambi, A., Schmidt, T. & Keijzer, S. de

Methods in Enzymology 2013, 521, 47-67. 10.1016/B978-0-12-391862-8.00003-X

Improved identification of peripheral lung tumors by using diffuse reflectance and fluorescence spectroscopy

Spliethoff JW, Evers DJ, Klomp HM, Sandick JW van, Wouters MWJM, Nachabe R, Lucassen GW, Hendriks BHW, Wesseling J, Ruers TJM

Lung Cancer, 80(2), pp. 165-171. 10.1016/j.lungcan.2013.01.016

Alpha-Synuclein Oligomers: an Amyloid Pore? Insights into Mechanisms of alpha-Synuclein Oligomer-Lipid Interactions

Stockl MT, Zijlstra N, Subramaniam V

Molecular Neurobiology, 47(2), pp. 613-621. 10.1007/s12035-012-8331-4

Toward fast and quantitative modification of large gold nanoparticles by thiolated DNA: scaling of nanoscale forces, kinetics, and the need for thiol reduction

Zhang X, Gouriye T, Goeken KL, Servos MR, Gill R

Journal of Physical Chemistry C, 117(30), pp. 15677-15684. 10.1021/jp403946x

Shining light on amyloid protein aggregates: Single-molecule photobleaching of sub-stoichiometrically labeled alpha-synuclein oligomers reveals molecular composition

Zijlstra N, Segers-Nolten I, Claessens MMAE, Blum C & Subramaniam V

Microscopy and Analysis (E EMEA edition), pp. 24-24.

The Multiple Faces of Prostaglandin E2 G-Protein Coupled Receptor Signaling during the Dendritic Cell Life Cycle

de Keijzer S, Meddens MBM, Torensma R, Cambi A

International Journal of Molecular Sciences, 14(4), pp. 6542-6555. 10.3390/ijms14046542

Modulation of the gelation efficiency of fibrillar and spherical aggregates by means of thiolation

Munialo CD, Martin AH, Broersen K, Van Der Linden E, de Jongh HH.

J Agric Food Chem,61(47), pp. 11628-11635. doi:10.1021/ja3102133

Blinking statistics of colloidal quantum dots at different excitation wavelengths

Stopel MWH, Prangsma JC, Blum C, Subramaniam V

RSC Advances, 3, pp. 17440-17445. doi:10.1039/C3RA43637C

Oriented Protein Immobilization using Covalent and Noncovalent Chemistry on a Thiol-Reactive Self-Reporting Surface

Wasserberg D, Nicosia C, Tromp EE, Subramaniam V, Huskens J, Jonkheijm P

Journal of the American Chemical Society 135, pp. 3104-3111. doi:10.1021/ja3102133

Imaging the static dielectric constant in vitro and in living cells by a bioconjugable GFP chromophore analog

Signore G, Abbandonato G, Storti B, Stöckl M, Subramaniam V, Bizzarri R

Chem Commun 49, pp. 1723-1725. doi:10.1039/C3CC38071H

Interplay between myosin IIA-mediated contractility and actin network integrity orchestrates podosome composition and oscillations

van den Dries K, Meddens M, de Keijzer S, Shekhar S, Subramaniam V, Figdor CG, Cambi A

Nature Communications 4: 1412. doi:10.1038/ncomms2402

What’s in a name? Why these proteins are intrinsically disordered?

Dunker AK, Babu M, Barbar E, Blackledge M, Bondos SE, Dosztányi Z, Dyson HJ, Forman-Kay J, Fuxreiter M, Gsponer J, Han K-H, Jones DT, Longhi S, Metallo SJ, Nishikawa K, Nussinov R, Obradovic Z, Pappu R, Rost B, Selenko P, Subramaniam V, Sussman JL, Tompa P, Uversky VN

Intrinsically Disordered Proteins, 1 (1) e24157

 

2012

α-Synuclein Oligomers: an Amyloid Pore? Insights into Mechanisms of α-Synuclein Oligomer–Lipid Interactions

Stöckl MT, Zijlstra N, Subramaniam V

Molecular Neurobiology 47, pp. 613-621. doi:10.1007/s12035-012-8331-4

Nanophotonic Control of the Foerster Resonance Energy Transfer Efficiency

Blum C, Zijlstra N, Lagendijk A, Wubs M, Mosk AP, Subramaniam V, Vos WL

Physical Review Letters, 109, 203601. doi:10.1103/PhysRevLett.109.203601

Non-invasive imaging through opaque scattering layers

Bertolotti J, Putten EG van, Blum C, Lagendijk A, Vos WL, Mosk, AP

Nature, 491, pp. 232-234. doi:10.1038/nature11578

Patterning perylenes on surfaces using thiol–ene chemistry

Wasserberg D, Steentjes T, Stopel MWH, Huskens J, Blum C, Subramaniam V, Jonkheijm P

Journal of Materials Chemistry, 22, pp. 16606-16610. doi:10.1039/c2jm32610h

A comparative analysis of the aggregation behavior of amyloid-β peptide variants

Vandersteen A, Hubin ES, Sarroukh R, De Baets G, Schymkowitz J, Rousseau F, Subramaniam V, Raussens V, Wenschuh H, Wildemann D, Broersen K

FEBS Lett. 2012 Nov 30;586(23), pp. 4088-93. doi:10.1016/j.febslet.2012.10.022

Molecular plasticity regulates oligomerization and cytotoxicity of the multi-peptide length Abeta pool

Vandersteen A, Masman MF, De Baets G, Jonckheere W, van der Werf K, Marrink SJ,

Rozenski J, Benilova I, De Strooper B, Subramaniam V, Schymkowitz J, Rousseau F, Broersen K

J Biol Chem, 287 (44), pp. 36732-36743. doi:10.1074/jbc.M112.394635

Size-selective detection in integrated optical interferometric biosensors

Mulder HKP, Ymeti A, Subramaniam V, Kanger JS

Optics Express, 20 (19), pp: 20934–20950. doi: 10.1364/OE.20.020934

Alpha-galactosidase aggregation is a determinant of pharmacological chaperone efficacy on Fabry disease mutants

Siekierska A, De Baets G, Reumers J, Gallardo R, Rudyak S, Broersen K, Couceiro J, Van Durme J, Schymkowitz J, Rousseau F

Journal of Biological Chemistry, 287 (34), pp. 28386-28397. doi: 10.1074/jbc.M112.351056

A method for spatially resolved local intracellular mechanochemical sensing and organelle manipulation

Shekhar S, Cambi A, Figdor CG, Subramaniam V, Kanger JS.

Biophysical Journal, 103 (3), pp. 395-404. doi:10.1016/j.bpj.2012.06.010

Molecular composition of sub-stoichiometrically labeled α-synuclein oligomers determined by single-molecule photobleaching

Zijlstra N, Blum C, Segers-Nolten IMJ, Claessens MMAE, Subramaniam V

Angewandte Chemie International Edition, 51 (35), pp. 8821–8824. doi: 10.1002/anie.201200813

Structural model for α-synuclein fibrils derived from high resolution imaging and nanomechanical studies using atomic force microscopy

Sweers KKM, Segers-Nolten IMJ, Bennink ML, Subramaniam V.

Soft Matter, 8, pp. 7215-7222. doi:10.1039/c2sm25426c

Nanomechanical properties of single amyloid fibrils

Sweers KKM, Bennink ML, Subramaniam V

J Phys: Condens Matter, 24 243101. doi:10.1088/0953-8984/24/24/243101

Hunting the chameleon: structural conformations of the intrinsically disordered protein alpha-synuclein

Drescher M, Huber M, Subramaniam V

Chembiochem. 13 (6), pp. 761-768. doi: 10.1002/cbic.201200059

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, 51 (19), pp. 3960-3962. doi:10.1021/bi300357a

Lateral mobility of individual integrin nanoclusters orchestrates the onset for leukocyte adhesion

Bakker GJ, Eich C, Torreno-Pina J, Diez-Ahedo R, Perez-Samper G, van Zanten TS, Figdor CG, Cambi A, Garcia-Parajo MF

Proc Natl Acad Sci USA, vol. 109 no. 13, pp. 4869-4874. doi: 10.1073/pnas.1116425109

Kinetic measurements give new insights into lipid membrane permeabilization by ɑ-synuclein oligomers

Stöckl M, Claessens MMAE, Subramaniam V

Mol BioSyst, 8 (1), pp. 338 – 345. doi:10.1039/C1MB05293D

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. doi:10.1371/journal.pone.0026182

The structural basis for increased toxicity of pathological Abeta42:Abeta40 ratios in Alzheimer's disease

Pauwels K, Williams TL, Morris KL, Jonckheere W, Vandersteen A, Kelly G, Schymkowitz J, Rousseau F, Pastore A, Serpell LC, Broersen K

J Biol Chem, 287, pp. 5650-5660. doi:/10.1074/jbc.M111.264473

Wafer-scale thin encapsulated two-dimensional nanochannels and its application toward visualization of single molecules

Hoang HT, Tong HD, Segers-Nolten IM, Tas NR, Subramaniam V, Elwenspoek MC

J Colloid & Interface Sci, 367 (1), pp. 455-459. doi:10.1016/j.jcis.2011.10.001

Biophysical analysis of amyloid formation

Segers-Nolten I, van Raaij M, 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

Blum C, Schleifenbaum F, Stopel M, Peter S, Sackrow M, Subramaniam V, Meixner AJ   

Beilstein Journal of Nanotechnology, 2, 516-524. doi:10.3762/bjnano.2.56

Femtomolar DNA detection by parallel colorimetric darkfield microscopy of functionalized gold nanoparticles

Verdoold R, Gill R, Ungureanu F, Molenaar R, Kooyman RPH

Biosensors and Bioelectronics, 27, pp. 77– 81. doi:10.1016/j.bios.2011.06.019 

Dark proteins disturb multichromophore coupling in tetrameric fluorescent proteins

Blum C, Meixner AJ, Subramaniam V

Journal of Biophotonics, 4(1-2): pp. 114-112. doi:0.1002/jbio.201000075

Interactions of perylene bisimide in the one-dimensional channels of zeolite L

Busby M, Devaux A, Blum C, Subramaniam V, Calzaferri G, De Cola L

J Phys Chem C 115, pp. 5974–5988. doi:10.1021/jp1108625

Microspectroscopic analysis of green fluorescent proteins infiltrated into mesoporous silica nanochannels

Ma YJ, Rajendran P, Blum C, Cesa Y, Gartmann N, Bruhwiler D, Subramaniam V

Journal of Colloid and Interface Science, 356(1): pp. 123-130. doi:10.1016/j.jcis.2010.12.082

Spectral versatility of fluorescent proteins observed on the single molecule

Blum C, Subramaniam V

Springer Series on Fluorescence, ed. G. Jung: Springer, 11, pp. 217-240. doi:10.1007/4243_2011_22

Analysis of single quantum-dot mobility inside 1D nanochannel devices

Hoang HT, Segers-Nolten IM, Tas NR, van Honschoten JW, Subramaniam V, Elwenspoek MC

Nanotechnology, 22, pp. 275201-275209. doi:10.1088/0957-4484/22/27/275201

Acousto-optic-assisted diffuse optical tomography

Bratchenia A, Molenaar R, Leeuwen TG, Kooyman RPH

Optics Letters, 36 (9), pp. 1539-1541. doi:10.1364/OL.36.001539

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, 24 (9), pp. 743-750. doi:10.1093/protein/gzr020

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. doi:10.1002/emmm.201100138

2010

Long-range energy propagation in nanometer arrays of light harvesting antenna complexes

Escalante M, Lenferink A, Zhao Y, Tas N, Huskens J, Hunter CN, Subramaniam V, Otto C

Nano Letters, 10: pp. 1450–1457. doi:10.1021/nl1003569

Microbioreactors for Raman microscopy of stromal cell differentiation

Pully VV, Lenferink ATM, van Manen HMJ, Subramaniam V, van Blitterswijk CA, Otto C

Analytical Chemistry 82, pp. 1844–1850. doi:10.1021/ac902515c

Direct evidence of coexisting horseshoe and extended helix conformations of membrane-bound alpha-synuclein

Robotta M, Braun P, van Rooijen B, Subramaniam V, Huber M, Drescher M

ChemPhysChem, 12 (2), pp. 267-269.

Membrane permeabilization by oligomeric α-synuclein: in search of the mechanism

Van Rooijen BD, Claessens MMAE, Subramaniam V

PLoS ONE 5(12): e14292. doi:10.1371/journal.pone.0014292

Strategies for patterning biomolecules with dip-pen nanolithography

Wu C-C, Reinhoudt DN, Otto C, Subramaniam V, Velders AH

Small, 7 (8), pp. 989–1002. doi:10.1002/smll.201001749

Dendritic ruthenium(II)-based dyes tunable for diagnostic or therapeutic applications

Ruggi A, Beekman C, Wasserberg D, Subramaniam V, Reinhoudt DN, van Leeuwen FWB, Velders AH

Chem Eur J 17, 464 – 467. doi:10.1002/chem.201002514

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 DN, Velders AH, Vancso GJ

Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, small 2010, 6 ( 24), pp. 2870–2876.

doi:10.1002/smll.201000713

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 DN, Marchelli R, Huskens J, Jonkheijm P

Langmuir, 27(4), pp. 1536–1542. doi:10.1021/la102756k

Neurotoxicity of Alzheimer disease Aβ-peptides is induced by small changes in the Aβ42 to Aβ40 ratio

Kuperstein I, Broersen K, Benilova I, Rozenski J, Jonckheere W, Debulpaep M, Vandersteen A, Segers-Nolten I, van der Werf K, Subramaniam V, Braeken D, Callewaert G, Bartic C, D’Hooge R, Martins IC, Rousseau F, Schymkowitz J, De Strooper B

EMBO Journal, 29, pp. 3408 – 3420. doi:10.1038/emboj.2010.211

Studies of interaction between cyanine dye T-284 and fibrillar alpha-synuclein

Volkova KD, Kovalska VB, Yu Losytskyy M, Veldhuis G, Segers-Nolten GMJ, Tolmachev OI, Subramaniam V, Yarmoluk SM

J Fluoresc 20, pp. 1267–1274. doi:10.1007/s10895-010-0678-1

Pyrylium monolayers as amino-reactive platform

Scaramuzzo FA, González-Campo A, Wu C-C, Velders AH, Subramaniam V, Doddi G, Mencarelli P, Barteri M, Jonkheijm P, Huskens J

Chem. Commun. 46, pp. 4193-4195. doi:10.1039/c002203a

Simultaneous time-resolved measurement of the reaction rates and the refractive index of photopolymerisation processes

Bak TM, Beusink JB, Subramaniam V, Kanger JS

Applied Optics, 49, pp. 3316-3322. doi:10.1364/AO.49.003316

Spatially resolved local intracellular chemical sensing using magnetic particles

Shekhar S, Klaver A, Figdor C, Subramaniam V, Kanger JS

Sensors and Actuators: B, 148, pp. 531-538. doi:10.1016/j.snb.2010.05.006

Membrane interactions of oligomeric alpha-synuclein: potential role in Parkinson's disease

van Rooijen BD, Claessens MM, Subramaniam V

Curr Protein Pept Sci. 11(5), pp. 334-342(9). doi:10.2174/138920310791330659

A stable lipid-induced aggregate of alpha-synuclein

Drescher M, Rooijen BD, Veldhuis G, Subrmaniam V, Huber M

J Am Chem Soc. 132 (12), pp. 4080–4082. doi:10.1021/ja909247j

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. 38(10), pp. 3423-3431. doi:10.1093/nar/gkq034

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 4 (2), pp. 1083–1091. doi:10.1021/nn901270c

The use of fluorescent dyes and probes in surgical oncology

te Velde EA, Veerman Th, Subramaniam V, Ruers Th

European Journal of Surgical Oncology 36 (1), pp. 6-15. doi:10.1016/j.ejso.2009.10.014

 

 

2009

Tryptophan fluorescence reveals structural features of α-synuclein oligomers

van Rooijen BD, van Leijenhorst-Groener KA, Claessens MMAE, Subramaniam V

Journal of Molecular Biology 394 (5), pp. 826-833. doi:10.1016/j.jmb.2009.10.021

Single molecule spectral dynamics at room temperature

Schleifenbaum F, Blum C, Subramaniam V, Meixner AJ

Molecular Physics, 107(18), pp. 1923-1942. doi:10.1080/00268970802635004

Multiparameter single molecule spectroscopy gives insight into the complex photophysics of fluorescence energy transfer (FRET) coupled biosystems

Schleifenbaum F, Blum C, Elgass K, Peter S, Subramaniam V, Meixner AJ

Proc. of SPIE Vol. 7190 71900U-1. doi:10.1117/12.809298

Method to deterministically study photonic nanostructures in different experimental instruments

Husken BH, Woldering LA, Blum C, Vos WL

Journal of Microscopy-Oxford, 233(1), pp. 18-23. doi:10.1111/j.1365-2818.2008.03091.x

Expression of sensitized Eu3+ luminescence at a multivalent interface

Hsu SH, Yilmaz MD, Blum C, Subramaniam V, Reinhoudt DN, Velders AH, Huskens J

Journal of the American Chemical Society, 131(35), pp. 12567-12569. doi:10.1021/ja904747p

Interaction of oxazole yellow dyes with DNA studied with hybrid optical tweezers and fluorescence microscopy

Murade CU, Subramaniam V, Otto C, Bennink ML

Biophysical Journal 97 (3), pp. 835-843. doi:10.1016/j.bpj.2009.05.024

Modulation of protein dimerization by a supramolecular host-guest system

Uhlenheuer DA, Wasserberg D, Nguyen H, Zhang L, Blum C, Subramaniam V, Brunsveld L

Chemistry - A European Journal 15 (35), pp. 8779-8790. doi:10.1002/chem.200900462

Manipulation of the local density of photonic states to elucidate fluorescent protein emission rates

Cesa Y, Blum C, Van Den Broek JM, Mosk AP, Vos WL, Subramaniam V

Physical Chemistry Chemical Physics 11 (14), pp. 2525-2531. doi:10.1039/b817902f

Spectral emission imaging to map photonic properties below the crystal surface of 3D photonic crystals

Blum C, Mosk AP, Vos WL, Subramaniam V

Journal of the Optical Society of America B, 26(11), pp. 2101–2108. doi:10.1364/JOSAB.26.002101

Controlling fluorescent proteins by manipulating the local density of photonic states.

Blum C, Cesa , van den Broek JM, Mosk AP, Vos WL, Subramaniam V

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 EM, Cesa Y, Blum C, Subramaniam V, Herek JL, Vancso G

Nanotechnology 20 (18), art. no. 185501. doi:10.1088/0957-4484/20/18/185501

Gold nanoparticle assays: Towards single molecule unamplified DNA detection

Verdoold R, Ungureanu F, Wasserberg D, Kooyman RPH

Proceedings of SPIE - The International Society for Optical Engineering 7312, art. no. 73120N.

doi:10.1117/12.818120

The use of a colour camera for quantitative detection of proteinbinding nanoparticles

Ungureanu F, Halamek J, Verdoold R, Kooyman RPH

Progress in Biomedical Optics and Imaging - Proceedings of SPIE 7192, art. no. 71920O

doi:10.1117/12.806522

Sequence-specific physical properties of African green monkey alpha-satellite DNA contribute to centromeric heterochromatin formation

Bussiek M, Hoischen C, Diekmann S, Bennink ML

Journal of Structural Biology 167 (1), pp. 36-46. doi:10.1016/j.jsb.2009.03.010

Fabrication of nano structures in thin membranes with focused ion beam technology

Gadgil VJ, Tong HD, Cesa Y, Bennink ML

Surface and Coatings Technology 203 (17-18), pp. 2436-2441. doi:10.1016/j.surfcoat.2009.02.036

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. doi:10.1002/cbic.200800644

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. doi:10.1098/rsif.2008.0356.focus

Single-molecule spectroscopy of fluorescent proteins

Blum C, Subramaniam V

Analytical and Bioanalytical Chemistry 393(2), pp. 527-541. doi:10.1007/s00216-008-2425-x

FRET pair printing of fluorescent proteins

Escalante M, Blum C Cesa Y, Otto C, Subramaniam V

Langmuir 25(12). pp. 7019-7024. doi:10.1021/la900223f

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 MI, Rieger B, Joosten B, Subramaniam V, Figdor CG, Kanger JS

Journal of Microscopy 233 (1), pp. 84-92. doi:10.1111/j.1365-2818.2008.03099.x

Rapid, ultrasensitive detection of microorganisms based on interferometry and lab-on-a-chip nanotechnology

Ymeti A, Nederkoorn PHJ, Dudia A, Subramaniam V, Kanger JS

Proceedings of SPIE - The International Society for Optical Engineering 7306, art. no. 73060J. doi:10.1117/12.818466

Porous multilayer-coated AFM tips for dip-pen nanolithography of proteins

Wu C-C, Xu H, Otto C, Reinhoudt DN, Lammertink RGH, Huskens J, Subramaniam V, Velders AH

Journal of the American Chemical Society 131 (22), pp. 7526-7527. doi:10.1021/ja901756a

Explorations of the application of cyanine dyes for quantitative α-synuclein detection

Volkova KD, Kovalska VB, Segers-Nolten GM, Veldhuis G, Subramaniam V, Yarmoluk SM

Biotechnic and Histochemistry 84 (2), pp. 55-61. doi:10.1080/10520290902798799

2008

Intracellular manipulation of chromatin using magnetic nanoparticles

Kanger JS, Subramaniam V, Van Driel R

Chromosome Research 16 (3), pp. 511-522. doi:10.1007/s10577-008-1239-1

Biofunctionalized lipid-polymer hybrid nanocontainers with controlled permeability

Dudia A, Koçer A, Subramaniam V, Kanger JS

Nano Letters 8 (4), pp. 1105-1109. doi:10.1021/nl073211b

Lipid bilayer disruption by oligomeric α-synuclein depends on bilayer charge and accessibility of the hydrophobic core

van Rooijen BD, Claessens MMAE, Subramaniam V

Biochimica et Biophysica Acta - Biomembranes 1788 (6), pp. 1271-1278. doi:10.1016/j.bbamem.2009.03.010

Membrane binding of oligomeric α-synuclein depends on bilayer charge and packing

van Rooijen BD, Claessens MMAE, Subramaniam V

FEBS Letters 582 (27), pp. 3788-3792. doi:10.1016/j.febslet.2008.10.009

Concentration dependence of α-synuclein fibril length assessed by quantitative atomic force microscopy and statistical-mechanical theory

Van Raaij ME, Van Gestel J, Segers-Nolten IMJ, De Leeuw SW, Subramaniam V

Biophysical Journal 95 (10), pp. 4871-4878. doi:10.1529/biophysj.107.127464

Tissue transglutaminase modulates α-synuclein oligomerization

Segers-Nolten IMJ, Wilhelmus, MMM, Veldhuis,G, Van Rooijen BD, Drukarch B, Subramaniam V

Protein Science 17 (8), pp. 1395-1402. doi: 10.1110/ps.036103.108

PhD Theses

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

Chien-Ching Wu

Novel Dip-Pen Nanolithography Strategies for Nanopatterning

doi:10.3990/1.9789036530170

18 June, 2010

Chandrashekhar Murade

Insights into DNA intercalation using combined optical tweezers and fluorescence microscopy

doi:10.3990/1.9789036530460

11 June, 2010

Tomasz Bak

Two photon microstereolithography of polymers for tissue engineering

doi:10.3990/1.9789036528471

16 December, 2009

Maryana Escalante Marun

Nanofabrication of bio-inspired architectures with light harvesting proteins

doi:10.3990/1.9789036529198

11 December, 2009

Bart van Rooijen

Structural and functional insights into interactions of oligomeric α-synuclein with lipid membranes

doi:10.3990/1.9789036529310

26 November, 2009

Martijn van Raaij

Biophysical characterization of alpha-synuclein aggregates: Parkinson's disease at the nanoscale

doi:10.3990/1.9789036527477

10 December, 2008

Inaugural Lecture

Prof. Dr. Vinod Subramaniam

Biophysics of Protein Misfolding

21 June, 2007