Thomas Braun | DCI

Thomas Braun

Current Project

Single cell visual proteomics and nanomechanical sensing & imaging

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Short Biography

Thomas Braun received his M.Sc. in biophysical chemistry in 1998, and his Ph.D. 2002 in biophysics from the Biozentrum, University of Basel, Switzerland. During his Ph.D. thesis he applied high-resolution electron microscopy and digital image processing to study the structure and function of membrane proteins. Subsequently, he worked on nanomechanical sensors to characterize the mechanics of membrane proteins at the Institute of Physics, University Basel and the CRANN, Trinity College Dublin, Ireland. Since 2009 he works at C-CINA on new methods for single cell analysis and nanomechanical sensors for biological applications.

Publications
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Grayscale e-beam lithography: Effects of a delayed development for well-controlled 3D patterning

Mortelmans, T., Kazasiz, D., Guzenko, V.A., Padeste, C., Braun, T., Stahlberg, H., Li, X., Ekinci, Y.

Microelectronic Engineering 225, 111272 (2020)

42

‘Differential visual proteomics’: Enabling the proteome-wide comparison of protein structures of single-cells

Syntychaki, A., Rima, L., Schmidli, C., Stohler, T., Bieri, A., Sütterlin, R., Stahlberg, H., Castano-Diez, D., Braun, T.

J. of Proteome Research 18(9), 3521-3531 (2019)

41

Microfluidic protein isolation and sample preparation for high resolution cryo-EM

Schmidli, C., Albiez, S., Rima, L., Righetto, R., , ., Oliva, P., Kovacik, L., Stahlberg, H., Braun, T.

PNAS 116(30), 15007-15012 (2019)

40

Array based real-time measurement of fluid viscosities and mass-densities to monitor biological filament formation

Oliva, P., Bircher, B., Schönenberger, C.-A., Braun, T.

Lab on a Chip 19(7), 1305-1314 (2019)

39

Miniaturized sample preparation for transmission electron microscopy

Schmidli, C., Rima, L., Arnold, S., Stohler, T., Syntychaki, A., Bieri, A., Albiez, S., Goldie, K., Chami, M., Stahlberg, H., Braun, T.

Journal of Visual Experiments (JOVE) (137), (2018)

38

Miniaturizing EM Sample Preparation: Opportunities, Challenges and "Visual Proteomics"

Arnold, S., Müller, S., Schmidli, C., Syntychaki, A., Rima, L., Chami, M., Stahlberg, H., Goldie, K., Braun, T.

Proteomics 18(5-6), e1700176 (2018)

37

Direct protein crystallization on ultrathin membranes for diffraction measurements at X-ray free electron lasers

Opara, N., Martiel, I., Arnold, S., Braun, T., Stahlberg, H., Makita, M., David, C., Padeste, C.

J. of Applied Crystallography 50, 909-918 (2017)

36

Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts

Arnold, S., Albiez, S., Bieri, A., Syntychaki, A., Adaixo, R., McLeod, R., Goldie, K., Stahlberg, H., Braun, T.

J. Struct. Biol. (197), 220-226 (2017)

DOI: 10.1016/j.jsb.2016.11.002

35

Patent: Cryo-electron microscopy from nanoliter sample volumes

Arnold, S., Stahlberg, H., Braun, T.

UniTecTra Technology Opportunity, Ref. No. UA-17/141 (patent application filed), (2016)

34

Total sample conditioning and preparation of nanoliter volumes for electron microscopy

Arnold, S., Albiez, S., Opara, N., Chami, M., Schmidli, C., Bieri, A., Padeste, C., Stahlberg, H., Braun, T.

ACS Nano 10, 4981-4988 (2016)

DOI: 10.1021/acsnano.6b01328

33

Automated high-throughput viscosity and density sensor using nanomechanical resonators

Bircher BA, Krenger R, Braun, T.

Sensor Actuat B-chem 223(C), 784–90 (2016)

DOI: doi:10.1016

32

On-chip lysis of mammalian cells through a handheld corona device

Escobedo, C., Bürgel, S. C., Kemmerling, S., Sauter, N., Braun, T., T. and A. Hierlemann

Lab Chip. 15(14), 2990-7 (2015)

DOI: 10.1039/c5lc00552c

31

Influence of squeeze-film damping on higher-mode microcantilever vibrations in liquid

Bircher, B. A., Krenger, R., Braun, T.

EPJ Techn Instrum 1(1), 10-3 (2014)

DOI: 10.1140/epjti/s40485-014-0010-6

30

openBEB: open biological experiment browser for correlative measurements

Ramakrishnan, C., Bieri, A., Sauter, N., Roizard, S., Ringler, P., Müller, S., Goldie, K., Enimanev, K., Stahlberg, H., Rinn, B., Braun, T.

BMC Bioinformatics 15, 84 (2014)

29

Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy

Giss, D., Kemmerling, S., Dandey, V., Stahlberg, H., Braun, T.

Anal Chem 86(10), 4680-7 (2014)

28

Microfluidics to isolate untagged proteins from cell extracts for visual analysis by electron microscopy

, ., , ., Dandey, V., Stahlberg, H., Braun, T.

17th International Conference on Miniaturized Systems for Chemistry and Life Science Conference proceeding, (2013)

27

Real-time viscosity and mass density sensors requiring microliter sample volume based on nanomechanical resonators

Bircher BA., Duempelmann L., Renggli K., Lang HP., Gerber C.K., Bruns N., Braun, T.

Anal Chem. 85(18), 8676-83 (2013)

DOI: 10.1021/ac4014918

26

Photothermal excitation of microcantilevers in liquid: effect of the excitation laser position on temperature and vibrational amplitude

Bircher B.A., Duempelmann L., Lang H.-P., Gerber C., Braun, T.

Micro & Nano Letters 8(11), 770-4 (2013)

25

Single-cell lysis for visual analysis by electron microscopy

Kemmerling, S., Arnold, S., Bircher, B. A., Sauter, N., Escobedo, C., Dernick, G., Hierlemann, A., Stahlberg, H., Braun, T.

J Struct Biol 183(3), 467-73 (2013)

24

Connecting micro-fluidics to electron microscopy

Kemmerling, Simon, Ziegler, J., Schweighauser, G., Arnold, S., Giss, D., Müller, S., Ringler, P., Goldie, K., Goedecke, N., Hierlemann, A., Stahlberg, H., Engel, A., Braun, T.

J Struct Biol 177(1), 128-134 (2012)

23

Ionic liquids as matrices in microfluidic sample deposition for high-mass matrix- assisted laser desorption/ionization mass spectrometry

Weidmann, S., Kemmerling, S., Madler, S., Stahlberg, H., Braun, T., Zenobi, R.

Eur J Mass Spectrom (Chichester, Eng) 18(3), 279-86 (2012)

22

Sensing surface PEGylation with microcantilevers

Backmann, N., Kappeler, N., Braun, T., Huber, F., Lang, H-P.K, Gerber, Chr., R. Lim

Beilstein Journal of Nanotechnology 1, 3-13 (2010)

DOI: 10.3762/bjnano.1.2

21

Quantitative time-resolved measurement of membrane protein-ligand interactions using microcantilever array sensors.

Braun, T., M. K. Ghatkesar, N. Backmann, W. Grange, P. Boulanger, L. Letellier, H. P. Lang, A. Bietsch, Ch. Gerber, M. Hegner

Nature Nanotechnol 4(3), 179-85 (2009)

DOI: 10.1038/nnano.2008.398

20

Multi-parameter microcantilever sensor for comprehensive characterization of Newtonian fluids

Ghatkesar, M. K., Rakhmatullina, E., Lang, H. P., Gerber, Ch., Hegner, M., Braun, T.

Sensor Actuat B-Chem 135(1), 133-138 (2008)

DOI: 10.1016/j.snb.2008.08.012

19

Comprehensive characterization of molecular interactions based on nanomechanics

Ghatkesar MK, Lang HP, Gerber C, Hegner M, Braun, T.

PLoS ONE 3(11), e3610 (2008)

DOI: 10.1371/journal.pone.0003610

18

Resonating modes of vibrating microcantilevers in liquid

Ghatkesar, M. K., Braun, T., Barwich, V., Ramseyer, J.-P., Gerber, C., Hegner, M., H.P. Lang

Appl Phys Lett 92, 3106 (2008)

DOI: 10.1063/1.2838295

17

Capacitive micromachined ultrasonic transducers for chemical detection in nitrogen

Park, K., Lee, H., Yaralioglu, G., Ergun, A., Oralkan, O., Kupnik, M., Quate, C., Khuri-Yakub, B., Braun, T., Ramseyer, J.P., Lang, H.P., Hegner, M., J.K. Gimzewski

Appl Phys Lett 91(9), 094102 (2007)

16

Digital Processing of Multi-Mode Nano-Mechanical Cantilever Data

Braun, T., Ghatkesar, M. K., Barwich, V., Huber, N., Nugaeva, W., Lang, H.P., Ramseyer, J.P., Gerber, Ch., M. Hegner

Journal of Physics International Conference on Nanoscience and Technology(61), 341-345 (2007)

DOI: 10.1088/1742-6596/61/1/069

15

Functionalization of gold and silicon surfaces by copolymer brushes using surface-initiated ATRP

Rakhmatullina, E., Braun, T., Kaufmann, T., Spillmann, H., Malinova, V., W. Meier.

Macromol Chem Physic 208(12), 1283–1293 (2007)

DOI: 10.1002/macp.200700119

14

Processing of kinetic microarray signals

Braun, T., Huber, F., Ghatkesar, M. K., Backmann, N., Lang, H.-P., Gerber, C., M. Hegner

Sensor Actuat B-Chem 128, 75-82 (2007)

DOI: 10.1016/j.snb.2007.05.031

13

Higher modes of vibration increase mass sensitivity in nanomechanical microcantilevers

Ghatkesar, M. K., Barwich, V., Braun, T., Ramseyer, J.-P., Gerber, C., Hegner, M. et al.

Nanotechnology 18(44), (2007)

12

Self-organization behavior of methacrylate-based amphiphilic di- and triblock copolymers

Rakhmatullina, E., Braun, T., Chami, M., Malinova, V., Meier, W.

Langmuir 23(24), 12371-9 (2007)

11

Conformational change of bacteriorhodopsin quantitatively monitored by microcantilever sensors

Braun, T., Backmann, N., Vögtli, M., Bietsch, A., Engel, A., Lang, H.-P., Gerber, Ch., M. Hegner

Biophysical Journal 90(8), 2970-2977 (2006)

10

Micromechanical mass sensors for biomolecular detection in a physiological environment

Braun, T., Barwich, V., Ghatkesar, M. K., Bredekamp, A. H., Gerber, C., Hegner M., H.P. Lang

Phys Rev E Stat Nonlin Soft Matter Phys. 72(3 PT1), 031907 (2005)

9

The 5 Å structure of heterologously expressed plant aquaporin SoPIP2;1

Kukulski, W., Schenk, A., Johanson, U., Braun, T., de Groot, B., Fotiadis, D., Kjellbom P., A. Engel

J Mol Biol. 350(4), 611-6 (2005)

8

Real-time mass sensing by nanomechanical resonators in fluid

Ghatkesar, M. K., Barwich, V., Braun, T., Bredekamp, A. H., Drechsler, U., Lang, H.-P., Hegner M., Gerber, Ch.

Proceedings of Third IEEE International Conference on Sensors 2, 1060-1063 (2004)

DOI: 10.1109/ICSENS.2004.1426357

7

Two-dimensional crystals: a powerful approach to assess structure, function and dynamics of membrane proteins

Stahlberg, H., Fotiadis, D., Scheuring, S., Remigy, H., Braun, T., Mitsuoka, K., Fujiyoshi, Y., Engel, A.

FEBS Lett 504(3), 166-72 (2001)

6

Myristoylation-dependent N-terminal cleavage of the myristoylated alanine-rich C kinase substrate (MARCKS) by cellular extracts

Braun, T., McIlhinney, R. A., G. Vergères

Biochimi 82(8), 705-15 (2000)

5

Mapping the interface between calmodulin and MARCKS-related protein by fluorescence spectroscopy

Ulrich, A., Schmitz, A. A., Braun, T., Yuan, T., Vogel, H. J., G. Vergères

Proc Natl Acad Sci U S A 97(10), 5191-6 (2000)

4

GlpF: A structural variant of the aquaporin tetramer

Braun, T., Philippsen, A., Wirtz, S., Borgnia, J., Agre, P., Kühlbrandt, W., Engel, A., Stahlberg, H.

In `Molecular biology and physiology of water and solute transport`, Hohmann & S. Nielsen (Eds.) Kluwer Academic, New York. ISBN 0-306-46501-9 , 13-22 (2000)

3

The 3.7 Å projection map of the glycerol facilitator GlpF: a variant of the aquaporin tetramer

Braun, T., Philippsen, A., Wirtz, S., Borgnia, M. J., Agre, P., Kühlbrandt, W., Engel, A., Stahlberg, H.

EMBO Rep 1(2), 183-9 (2000)

2

The 6.9-Å structure of GlpF: a basis for homology modeling of the glycerol channel from Escherichia coli

Stahlberg, H., Braun, T., de Groot, B., Philippsen, A., Borgnia, M. J., Agre, P., Kühlbrandt, W., Engel, A.

J Struct Biol 132(2), 133-41 (2000)

1

Team Leader Visual Proteomics

+41 61 387 32 28

C-CINA, Biozentrum, Uni Basel, Mattenstrasse 26, Room P34, CH-4058 Basel, Switzerland

thomas.braun@unibas.ch Full CV