Plenarvorträge - DPG-Tagungen

Arbeitskreis Biologische Physik Freitag
works in Physics and Biology (Springer Verlag Berlin, 1998)
AKB 50.6 Fr 10:30 B
Using Spins to Find Functional Modules of Bio-Molecular Networks
— •Sabine Tornow — Theoretische Physik III, Universitaet
Augsburg, D-86135 Augsburg
Genes and proteins are organized on the basis of their particular mutual
relation, or according to their interaction, in cellular and genetic
networks. These include metabolic or signaling pathways, protein interaction,
regulatory or coexpression networks. Integrating the information
from the different types of networks may lead to the notion of a functional
network and functional modules. To find these modules, we propose
a new technique which is based on collective, multi–body correlations in
a genetic network (a). We calculate the correlation strength of a group of
genes (e.g., in the coexpression network) which were identified as members
of a module in a different network (e.g., in the protein interaction
network) and estimate the probability that this correlation strength was
found by chance. Groups of genes with a significant correlation strength
in different networks have a high probability that they perform the same
function. Here, we propose to evaluate the multi–body correlations applying
the Superparamagnetic approach (b). We compare our method
to the presently applied mean Pearson correlations and show that our
method is more sensitive in revealing functional relationships.
(a)Tornow,S. ,Mewes, H.: Functional modules by relating protein interaction
networks and gene expression, Nucleic Acids Research 31, 6283
(2003)
(b) Blatt, M, Wiseman, M., and Domany, E.: Superparamagnetic clustering
of data. (1996) Phys. Rev. Lett., 76, 3251-5.
AKB 50.7 Fr 10:30 B
Mechanics and Force Generation of a Single Cell in Presence
of Cytoskeleton Structure Modifying Bioactive Lipids. —
•alexandre Micoulet 1 , Joachim P. Spatz 1 , and Thomas Seufferlein
2 — 1 Biophysical Chemistry, University of Heidelberg, 69120
Heidelberg, Germany — 2 Department of Internal Medecin I, University
of Ulm, 89081 Ulm, Germany
In tissues, constantly regulated processes, such as biochemical and mechanical
interactions between a cell and its environment play a major role
in differentiation and gene expression of cells. In contrast, cancer cells
are able to escape to these regulations and migrate through tissues since
their mechanical and adhesion properties change drastically than those
of non-tumor cells. Under physiological conditions, we applied a uniaxial
deformation to a single cell adhering between two parallel glass plates
(microplates). A precise feedback control allowed for measurements at
constant force or constant deformation. Both microplates were functionalized
in order to control cell adhesion. Thus, we manipulated a single
living cell by controlled adhesion and defined external mechanical stress.
We evaluated elasticity and viscosity of different cell types, such as fibroblasts,
human pancreatic cancer cells. In presence of two bioactive lipids,
lysophosphalitidic acid (LPA) and sphingosylphosphorylcholine (SPC),
we analysed the mechanical response of Panc-1 cells. LPA and SPC influenced
the organisation of actin- or keratin-cytoskeleton. E.g., elasticity
of Panc-1 cells decreased in presence of SPC consolidating biological
studies which predicted that SPC could facilitate metastasis.
AKB 50.8 Fr 10:30 B
Fibronectin fiber formation by surface tension on microfabricated
pillar interfaces — •Jens Ulmer, Stefan Graeter,
Wouter Roos, and Joachim Spatz — University of Heidelberg, Institute
for Physical Chemistry, Biophysical Chemistry,
The extracellular matrix (ECM) provides positional and environmental
information for cells which are essential for tissue function. ECM proteins
such as fibronectin (FN), laminin or collagen form distinct protein
networks in vivo that show tissue-specific variation in composition and
architecture. In vivo, FN-matrix assembly is mediated through integrins
which bind FN for forming cell-ECM contacts. FN molecules are then
stretched by cell generated forces. This causes conformational change in
FN molecules and enables FN from solution to bind. Thus, fibrillogenesis
of FN is stimulated and directed by force. We mimicked this force
induced FN assembly into fibers in vitro by stretching surface bound FN
molecules through water surface tension appearing between the surface
of a water drop and the tops of microfabricated pillars. Microfabricated
pillar arrays offer binding points to the ECM molecules which then bridge
the pillars tops by fibre network formation. In addition, micropillar interfaces
are sensitive force sensors which allow quantitative access to
the fiber formation process. The architecture of the resultant structure
showed to depend on concentration of the FN-solution and to be mediated
by forces generated from water surface tensions. Subsequently, the
defined FN-networks offers guiding cues for cell-ECM interactions.
AKB 50.9 Fr 10:30 B
Substrate Dependent Fibronectin Fibrillogenesis of Adherent
Cells — •Tilo Pompe 1,2 , Manfred Bobeth 3 , and Wolfgang
Pompe 3,2 — 1 Institut für Polymerforschung Dresden e.V. — 2 Max-
Bergmann-Zentrum für Biomaterialien Dresden — 3 Institut für
Werkstoffwissenschaft, TU Dresden
Cell-cell and cell-substrate binding is supported by extracellular matrix
proteins like fibronectin. The formation of fibrils from single fibronectin
molecules is a complex process which includes binding of cell
receptors, like integrins, conformational changes of fibronectin by mechanical
forces exerted from the cell, and polymerisation of fibronectin
molecules at newly exposed binding sites. The dependence of fibrillogenesis
on the fibronectin bond strength to the substrate was investigated
on different copolymer surfaces in respect to the characteristic pattern
of the fibronectin fibrils. Additionally, the process of fibrillogenesis was
modelled by Monte-Carlo simulations of the diffusion and aggregation
of integrin-fibronectin complexes, including cytoskeletal forces acting on
the focal adhesions. The resulting pattern was analysed in dependence
on the fibronection-substrate bond strength and compared with the experimental
observations.
AKB 50.10 Fr 10:30 B
Rod-Coil Multiblock Copolymers as a Simple Protein Model:
Some Scaling Arguments — •Christian Nowak and Thomas
Vilgis — MPI f”ur Polymerforschung, Postfach 3148, 55021 Mainz
We consider the behaviour of rod-coil multiblock copolymers by means
of scaling arguments. A rich phase behaviour is found depending on the
quality of the solvent and the strenght of the intermolecular interactions.
The phase behavior is essentially driven by strong attractive interactions
of the rodlike parts which stabilize the rod micelles and the entropy loss
and confinement of the flexible joints. Such systems could serve as a
very simple model for proteins like myoglobin where the helical parts are
modelled by stiff rods which are joined by flexible (chainlike) elements.
AKB 50.11 Fr 10:30 B
First-Passage and Residence Times in a Periodically Driven
Integrate-and-Fire Model — •Michael Schindler, Peter
Talkner, and Peter Hänggi — Institut für Physik, Universität
Augsburg
The stochastic integrate-and-fire model presents a simple model for
the spiking behavior of neurons. In this model a neuron ”fires” if an
Ornstein-Uhlenbeck process crosses a prescibed threshold. After the firing
the process is assumed to be in a refractory state, and from there it
is put back into its initial, active, state.
For short refractory times this process can be characterized by the distribution
of either the first-passage times of the threshold or the residence
times in the active state. We determined the distributions of these times
for the integrate-and-fire model in the presence of a periodic signal. This
is done by solving numerically both the respective Langevin equation
and the equivalent Fokker-Planck equation. The results are compared
with an approximate analytic theory. If the period of the signal is large
compared to the relaxation time of the Ornstein-Uhlenbeck signal and if
the threshold is higher than a few times the noise strength we find theory
and numerics to be in excellent agreement.
AKB 50.12 Fr 10:30 B
Fluorescence intermittency of single CdSe/ZnS quantum
dots: A comparison between organic and water soluble ligand
shells. — •Andrei Yu. Kobitski 1 , Colin D. Heyes 1 , Vladimir
V. Breus 1 , Kirill V. Anikin 1 , and G. Ulrich Nienhaus 1,2 —
1 Department of Biophysics, University of Ulm, D - 89069 Ulm, Germany
— 2 Department of Physics, University of Illinois Urbana-Champaign,
Urbana, IL 61801, USA
Recently, chemically synthesized quantum dots (QDs) are becoming
widely used as fluorescent labels in biophysical and life-science research.
The procedure of preparing organic soluble CdSe/ZnS core/shell QDs
has become well established over the last 10 years and reproducibly
gives monodisperse nanocrystals with high emission quantum yields of
up to 50%. However, the procedure of water solubilization of the particles,
which is needed for bio-related experiments, is not so well deter-