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Biophysics of Molecules – Uebungsseminar

Michael Nash / Daniel Schiffels

contact: daniel.schiffels@physik.lmu.de ; michael.nash@physik.lmu.de

24.10.2011

Fluorescent DNA-Ag Cluster
talk by Stefan Holler
Literature:

  • Sengupta, B., Ritchie, C. M., Buckman, J. G., Johnsen, K. R., Goodwin, P. M., Petty, J. T., Sengupta, B., et al. (2008). Base-Directed Formation of Fluorescent Silver Clusters Base-Directed Formation of Fluorescent Silver Clusters.

Microscopy, STORM, STED
talk by Lukas Milles
Literature:

  • Rust, M. J., Bates, M., & Zhuang, X. (2006). imaging by stochastic optical reconstruction microscopy ( STORM ). October, 3(10), 793-795. doi:10.1038/NMETH929
  • Klar, T. a, Jakobs, S., Dyba, M., Egner, a, & Hell, S. W. (2000). Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proceedings of the National Academy of Sciences of the United States of America, 97(15), 8206-10.
  • Huang, B., Wang, W., Bates, M., & Zhuang, X. (2008). Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science (New York, N.Y.), 319(5864), 810-3. doi:10.1126/science.1153529

07.11.2011

FRET - protein folding
talk by Andreas Vetter
Literature:

  • Schuler, B., Lipman, E. A., & Eaton, W. A. (2002). Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. October, 743-748. doi:10.1038/nature01062.1.

Paper based biosensors
talk by Matthias Morasch
Literature:

  • Martinez, A. W., Phillips, S. T., Nie, Z., Cheng, C.-M., Carrilho, E., Wiley, B. J., et al. (2010). Programmable diagnostic devices made from paper and tape. Lab on a chip, 10(19), 2499-504. doi: 10.1039/c0lc00021c
  • Posthuma-Trumpie, G. a, Korf, J., & Amerongen, A. van. (2009). Lateral flow (immuno)assay: its strengths, weaknesses, opportunities and threats. A literature survey. Analytical and bioanalytical chemistry, 393(2), 569-82. doi:10.1007/s00216-008-2287-2
  • Reches, M., Mirica, K. a, Dasgupta, R., Dickey, M. D., Butte, M. J., & Whitesides, G. M. (2010). Thread as a matrix for biomedical assays. ACS applied materials & interfaces, 2(6), 1722-8. doi: 10.1021/am1002266


14.11.2011

Protein Structure and Mechanical Triangulation (Karin Burger)
talk by Karin Burger
Literature:

  • Dietz, H., & Rief, M. (2006). Protein structure by mechanical triangulation. Proceedings of the National Academy of Sciences of the United States of America, 103(5), 1244-7. doi:10.1073/pnas.0509217103

Protein Pulling / Force Spectroscopy (Niklas Markwardt)
talk by Niklas Markwardt
Literature:

  • M.Rief, M.Gautel, F.Oesterheld, J.M.Fernandez, H.E.Gaub, Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM, Science 276, 1109-1112 (1997)
  • I.Schwaiger, A.Kardinal, M.Schleicher, A.A.Noegel, M.Rief, A mechanical unfolding intermediate in an actin-crosslinking protein, Nature Struct. Biol. 11, 81-85 (2004)


21.11.2011

Persistence Length of Microtubulus and Actin (Jürgen Stephan)
talk by Jürgen Stephan
Literature:

  • Gittes, F., Mickey, B., Nettleton, J., & Howard, J. (1993). Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. The Journal of cell biology, 120(4), 923-34.

DNA Mechanics (Michael Baumgartl)
talk by Michael Baumgartl
Literature:

  • Smith, S. B., Cui, Y., & Bustamante, C. (1996). Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules. Science, 271, 795-799.
  • Gore, J., Bryant, Z., Nöllmann, M., Le, M. U., Cozzarelli, N. R., & Bustamante, C. (2006). DNA overwinds when stretched. Nature, 442(7104), 836-9. doi:10.1038/nature04974


28.11.2011

Cryo EM (Linda Brützel)
talk by Linda Brützel
Literature:

  • Thomas Heuser, Milen Raytchev, Jeremy Krell, Mary E. Porter, Daniela Nicastro, The dynein regulatory complex is the nexin link and a major regulatory node in cilia and flagella; JCB 2009

05.12.2011

Thermophoresis (Constantin Schöler)
talk by Constantin Schöler
Literatur:

  • Wienken C et al. (2010) “Protein-binding assays in biological liquids using microscale thermophoresis”, Nat. Commun. 1:100 doi: 10.1038/ ncomms1093
  • Mast and Braun (2010) „Thermal Trap for DNA Replication“, Phys. Rev. Lett. 10.1103/PhysRevLett.104.188102
  • Duhr S, Braun D (2006) “Why molecules move along a temperature gradient”, PNAS 103:19678-19682

Lipid Diffusion in 2D (Andreas Meinel)
talk by Andreas Meinel
Literatur:

  • Horton, M. R., Reich, C., Gast, A. P., Rädler, J. O., & Nickel, B. (2007). Structure and dynamics of crystalline protein layers bound to supported lipid bilayers. Langmuir : the ACS journal of surfaces and colloids, 23(11), 6263-9. doi:10.1021/la063690e
  • Dietrich, C., Merkel, R., & Tampe, R. (1997). Diffusion measurement of fluorescence-labeled amphiphilic molecules with a standard fluorescence microscope. Biophysical journal, 72(4), 1701-10. doi:10.1016/S0006-3495(97)78816-7


12.12.2011

Formation of Supported Lipid Bilayers (Mathias Zorn)
talk by Mathias Zorn
Literature:

  • Weirich, K. L., Israelachvili, J. N., & Fygenson, D. K. (2010). Bilayer edges catalyze supported lipid bilayer formation. Biophysical journal, 98(1), 85-92. Biophysical Society. doi:10.1016/j.bpj.2009.09.050

DNA microarrays (Timon Funck)
talk by Timon Funck
Literatur:

  • M. Schena, D Shalon, R. W. Davis, P. 0. Brown; Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray; science 1995
  • D. Shalon, S. J. Smith and P. O. Brown; A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.; Genome Res. 1996
  • P. O. Brown & D. Botstein; Exploring the new world of the genome with DNA microarrays ; nature genetics 1999


19.12.2011

canceled

09.01.2012

Microfluidic T-sensor (Philip Walker)
talk by Philip Walker
Literatur:

  • A. Hatch, A. Kamholz, K. Hawkins, M. Munson, E. Schilling, B. Weigl, P. Yager “A rapid diffusion immunoassay in a T-sensor“, nature biotechnology, 2001, 461-465
  • A. Kamholz, B. Weigl, B. Finlayson, P. Yager, “Quantitative Analysis of Molecular Interaction in a Microfluidic Channel: The T-Sensor”, Anal. Chem. 1999, 71, 5340-5347

Nanohealth Heath (Erik Gawehn)
talk by Erik Gawehn
Literature:

  • J.R.Heath, M.E.Davis. L.Hood, 2009 Nanomedicine targets cancer


16.01.2012

MD simulations (Dario Brack)
talk by Dario Brack
Literature:

  • S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, K. Schulten Molecular dynamics study of unbinding of the avidin-biotin complex Volume 72, Issue 4, April 1997, Pages 1568–158

Tensegrity (Kathrin Mohler)
talk by Kathrin Mohler

  • Ingber, D.E., Cellular mechanotransduction: putting all the pieces together again, FASEB J. 20, 811-827 (2006)
  • Ingber, D.E., Tensegrity II. How structureal networks influence cellular information processing networks, J. of Cell Science 116, 1397-1408 (2003)


23.01.2012

Prestin- Transmembrane proteins (Lorenz Keil)
talk by Lorenz Keil
Literature:

  • Prestin, a new type of motor protein, Peter Dallos and Bernd Fakler, Nature 2002
  • Intracellular Anions as the Voltage Sensor of Prestin, the Outer Hair Cell Motor Protein, Dominik Oliver, Science 2001

Photo-responsive glutamate receptors (Hans Hoeiberg)
talk by Hans Hoeiberg
Literature:

  • Volgraf et al. Allosteric control of an ionotropic glutamate receptor with an optical switch

30.01.2012

Nanopore DNA Sequencing 1 (Susanne Eder)
talk by Susanne Eder
Literature:

  • B.Venkatesan, R. Bashir: Nanopore sensors for nucleic acid analysis, nature vol6 october 2011
  • D. Ranton et al: The potential and challenges of nanopore sequencing, nature vol26 october 2008

Nanopore DNA Sequencing 2 (Jeff Michelmann)
talk by Jeff Michelmann
Literature:

  • J. Eid et al., Real-Time DNA Sequencing from Single Polymerase Molecules, Science Vol. 323, (2009)
  • M. J. Levene et al., Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations, Science Vol. 299, (2003)


03.02.2012

RNA polyerase (Franziska Kriegel)
talk by Franziska Kriegel
Literature:

  • Alberts, Molecular Biology of the Cell

Aquaporin (Josef Hirte)
talk by Josef Hirte
Literature:

  • Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF, Bert L. de Groot and Helmut Grubmüller, 2012

Drug Delivery (Christopher Hitz)
talk by Christopher Hitz
Literature:

  • Tysseling, Vicki M.; Sahni, Vibhu; Pashuck, Eugene T.; Birch, Derin; Hebert, Amy; Czeisler, Catherine et al. (2010): Selfassembling peptide amphiphile promotes plasticity of serotonergic fibers following spinal cord injury. In: J. Neurosci. Res 88 (14), S. 3161–3170
  • Standley, S. M.; Toft, D. J.; Cheng, H.; Soukasene, S.; Chen, J.; Raja, S. M. et al. (2010): Induction of Cancer Cell Death by Self-assembling Nanostructures Incorporating a Cytotoxic Peptide. In: Cancer Research 70 (8), S. 3020–3026.