Thursday, March 31, 2011 at 14h30 in MCD121

Elasticity of motile actin gels
Laurent Kreplak
Department of Physics
Dalhousie University



The comet motility assay, inspired by Listeria locomotion, has been used extensively as an in vitro model to study the structural and motile properties of the actin cytoskeleton. However, there are no quantitative measurements of the mechanical properties of these comets. In this presentation I will show how atomic force microscopy based nano-indentation combined with fluorescence imaging can be used to measure the elastic modulus of comets grown, in an Arp2/3 complex-dependent fashion, on 1µm diameter beads. We use this system to study the mechanical role of human Enabled/Vasodilator-stimulated phosphoprotein protein (Ena/VASP). Recruitment of VASP at the bead surface, has no effect on the initial velocity or morphology of the comets. However it delays the detachment of the comets from the beads for a prolonged period of time and increases the elastic modulus of the comets. Furthermore, we showed that the cross-linking or bundling effect of VASP is concentration and ionic strength dependent. In conclusion, we propose that VASP plays a pivotal role in establishing the mechanical properties in the Arp2/3 complex-dependent motility by amplifying the elastic modulus of the actin network and consequently strengthening its cohesion for enhanced protrusion.


Thusday March 10, 2011 at 14h30, MCD 121

Probing the Mechanical Properties of Individual Bacterial Cells: Physics Meets Biology

John R. Dutcher
Department of Physics
University of Guelph


Bacteria are microorganisms that have evolved over 3.5 billion years and are responsible for a wide range of phenomena in the world around us, ranging from causing diseases to helping to digest food to shaping the surface and sub-surface of the Earth. In response to their environment, bacteria have evolved an amazing set of specialized materials and strategies to ensure their survival. I will describe our AFM-based approach to a simple mechanical experiment: the creep deformation of individual bacterial cells. We interpret the results in terms of a simple viscoelastic model, and we show how the model must be extended to describe the effect of antimicrobial compounds on the mechanical properties.


Thursday March 3, 2011 at 14h30, MCD 121.

Non-equilibrium mechanics of cells and cell models
Christoph F. Schmidt
Fakultät für Physik
Drittes Physikalisches Institut - Biophysik

Mechanical processes, such as cell division and growth or cell locomotion, are essential in cell life and are driven and controlled by the cytoskeleton.  The polymeric components of the cytoskeleton are semiflexible polymers.  The activity of motor proteins drives living cells out of equilibrium.  We study mechanical properties and collective dynamics of cells and of in vitro model systems with microrheology techniques. We use micron-sized probe particles, embedded in the medium to be studied, and laser optical traps to confine the particles, combined with laser interferometry to detect either their Brownian motion or the particles' response to a driving force with sub-nm accuracy and bandwidths up to 100 kHz. We have applied this technology to non-equilibrium systems and have measured, at the same time, the elastic properties and the fluctuations and forces generated by myosin motor proteins interacting with a cross-linked actin network. We have also applied the same type of approach to a mechanosensitive bone cell, MLO-Y4, and have monitored cellular forces transmitted to externally attached probe particles.


Thursday February 17, 2011 at 14h30, MCD121. 

Micromechanical study of DNA-protein interactions and chromosome structure
John F. Marko
Department of Physics and Astronomy
and Department of Molecular Biosciences
Northwestern University, Evanston

The millimeter- to centimeter-long DNA molecules found in cells are made 

manageable and genetically functional by the actions of large numbers of

proteins which bind to the double helix along its length.  I will describe

micromechanical experiments focused on studying protein-DNA interactions

and the folding of DNA into chromosomes.  One type of experiment we carry

is based on micromanipulation of single DNA molecules, where interactions

with proteins can be monitored via changes in mechanical response to

pulling and twisting: I will discuss experiments on proteins that bend and

package DNA, and which change DNA topology.  A second type of experiment

is focused on large-scale chromosome structure: we remove whole

chromosomes from cells for micromechanical study.  I will discuss

experiments which have established a "cross-linked chromatin network"

model for the highly ordered "metaphase" form of chromosomes of animal

cells which occurs during cell division.


Thursday February 10, 2011 at 14h30, MCD121
Novel Cryoprotectants - From Antifreeze Glycoproteins to Potent Inibitors of Ice Recrystallization
Robert Ben
Department of Chemistry
University of Ottawa 


Antifreeze glycoproteins (AFGPs) are peptide-based structures found in many deep sea Teleost fish inhabiting sub-zero environments.  These compounds prevent the seeding of ice crystals in vivo and ultimately protect these organisms against cryoinjury and death. As a result of this ability, these compounds have been investigated as cryoprotectants.  However, the thermal hysteresis exhibited by these proteins precludes their use at temperatures associated with cryopreservation of biological materials.  For the past decade our laboratory has been actively pursuing the rational design and synthesis of functional carbon-linked AFGP analogues possessing custom-tailored antifreeze activity.  These compounds are potent inhibitors of ice recrystallization but do not exhibit thermal hysteresis making them ideally suited for cryopreservation applications.  The design and activity profiles of these analogues and various small molecule inhibitors of ice recrystallization will be presented and the potential to utilize these compounds as cryoprotectants in cell-based systems will be discussed.


Thursday November 25, 2010 in BSC140

The role of lipid membrane in amyloid fibril formation and toxicity
Dr. Zoya Leonenko
Department of Physics and Astronomy,
Department of Biology,
Waterloo Institute for Nanotechnology
University of Waterloo 

Many proteins are known to actively interact with biologically relevant, as well as inorganic and synthetic surfaces that are widely used in nano- and bio-technology. The surfaces interact strongly with proteins and considerably affect their structure and function. Amyloid fibrils are insoluble protein aggregates in beta-sheet conformation that are implicated in at least 20 diseases for which neither the cure nor the diagnostics are currently available. The role of cell membrane surfaces in amyloid fibril formation and toxicity is not well understood. Currently, the experimental data available for amyloid fibril formation both on lipid membrane and inorganic surfaces is limited. The goal of our study is to investigate how the physical properties of the surfaces affect binding of amyloid peptides and affect the fibril formation. We use scanning probe microscopy to study amyloid beta (1-42) binding and fibril formation on model surfaces, which are functionalized with thiol monolayers with negatively, positively or hydrophobic functional groups. We also study interaction of amyloid beta peptide with model lipid membranes of various compositions, which are widely used to mimic cell membrane surfaces. Effect of lipid composition, surface charge, and presence of cholesterol will be discussed.


Thursday, November 18, 2010 at 14h30 in BSC140
Light scattering investigation of soft materials by optical microscopy
Dr. Roberto Cerbino
Università degli Studi di Milano 

Optical microscopy and light scattering are important tools of analysis in soft matter laboratories. Very often they are used in combination, so to take advantage of their complementarity. While microscopy gives access to real space information, its use at the nanoscale in dense, crowded environments is prevented by diffraction. By contrast Dynamic Light Scattering (DLS) techniques operating in reciprocal space have been proven to be well capable of sizing nano-objects in motion. Here we show that the recently demonstrated Differential Dynamic Microscopy (DDM) combines the space-resolving capabilities of microscopy with the advantages of DLS, reconciling thereby these two apparently unrelated worlds. DDM is based on the analysis of real space images to reconstruct the scattering pattern of the samples under study and to monitor its evolution in time. The method can benefit from different contrast enhancement schemes, such as phase-contrast or confocal microscopy. We will present data obtained on a variety of soft systems, ranging from diffusing colloidal suspensions to swimming bacteria


Thursday October 28, 2010 in BSC140

Conformational Sculpting of DNA: Nanofluidics for Single Molecule DNA Analysis and Manipulation"
W. Reisner
Department of Physics, McGill University

My work uses sub micron nanofabrication tools like electron beam lithography to explore the fundamental physics of polymers in confinement and to develop nanotechnology approaches to key problems in biology. When a polymer is confined in a structure with dimension below the polymer’s free solution gyration radius the confining geometry will alter the polymer equilibrium conformation. This fundamental result of statistical physics has a key technological implication: polymer conformation can be manipulated and controlled onchip by design of the nanofludic confining geometry. This talk will consider two implications of this notion of ‘conformational sculpting’ for the field of single molecule DNA analysis. In a nanochannel, self-exclusion interactions within the polymer will create a linear unscrolling of the genome along the channel for analysis. Nanochannel based DNA stretching can serve as a platform for a new optical mapping technique based on measuring the pattern of partial melting along the extended molecules. We believe this melting mapping technology is the first optically based single molecule technique sensitive to genome wide sequence variation that does not require an additional enzymatic labeling or restriction scheme. In addition, by embedding sub micron nanotopographies in a slit-like nanochannel, we can create spatial variation in confinement across the slit. The confinement variation in turns varies a molecule’s configurational freedom, or entropy. Consequently, by controlling device geometry, we can create a user-defined free energy landscape that allows us to ‘sculpt’ the equilibrium configuration of a molecule. Individual square depressions, or nanopits, can be used to trap DNA at specific points in the slit. Arrays of nanopits will lead to complex ‘digitized’ conformations with a single molecule linking a number of pits


Wednesday June 2, 2010 at 11 am. MCD 121

Development and validation of a novel patch-clamp neurochip for interrogation of cultured synaptically connected cells

Marzia Martina1 and Christophe Py2

1Institute for Biological Sciences, National Research Council of Canada, and Adjunct Professor, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa.,
2Institute for Microstructural Sciences, National Research Council of Canada, and Adjunct Professor, Department of Physics, University of Ottawa.

Planar patch-clamp technology has been developed to deliver individual suspended cells to chips incorporating one or more probe sites. In this technique, the standard glass pipette of the technique invented by Neher and Sakmann is replaced by a micron-size orifice in a self-standing film separating the culture medium on the top from the recording solution at the bottom. However, this approach results in lower quality recordings due to low resistance seals, and the relevance of the resulting models is debatable because it relies on suspended cells. The NRC has developed a novel neurochip based on the integration of multiple patch-clamp probes on a chip In our technology, microfluidic channels are integrated below a culture dish surface such that each orifice has a dedicated channel. Surface functionalization promotes the culture of neurons on the probes and the formation of high resistance seals. The NRC neurochip allows interrogating the electrophysiological activity of individual cells at multiple sites within connected cellular networks with resolution at the level of ion channels. A tool with these capabilities has tremendous value in the field of neurophysiology.

In the first part of the talk Dr. Py will discuss the development of the different components of the neurochip. In the second part Dr Martina will present the electrophysiological validation of this technology.

Recently, we have been successful in applying this technology to the field of electrophysiology.  We have obtained, for the first time, whole-cell patch-clamp recordings from neurons cultured on a patch-clamp chip.  We recorded high quality action potentials and currents in current- and voltage-clamp mode, respectively. We also recorded post-synaptic responses from cultured neurons synaptically connected and, importantly, we were able to evoke synaptic potentiation in these neurons.


Wednesday June 24, 2009 in MCD121

Dynamics of Working Memory

David Hansel, Laboratoire de Neurophysique et Physiologie, Université Paris 5-René Descartes


Date: Tuesday, July 14th 2009, 2:00 pm (Note special time)
Location: MCD 120

Conformal and mechanical properties of inhomogeneous semiflexible biopolymers

Zicong Zhou 
Department of Physics, Tamkang University, Taiwan

We study the properties of inhomogeneous semiflexible biopolymers. We show exactly that when free of external force, a semiflexible biopolymer with short range correlations in the sequence-disorder intrinsic curvatures and torsions is equivalent to a biopolymer with well-defined (i.e., without randomness) intrinsic curvature and torsion as well as a renormalized persistence length. We find an exact expression for the distribution function of a two-dimensional inhomogeneous semiflexible biopolymer and use it to evaluate the bending profile. Our results agree well with bending profiles of dsDNA with long-range correlation in base pairs. However, we show that an “equivalent system” does not always exist for the biopolymer under external force. We find that under an external force, the effect of sequence-disorder depends upon the averaging order, the degree of disorder, and the experimental conditions.

Last updated: 2009.12.18