The TAU biological and soft matter seminar gathers
researchers from physics, chemistry, biology, and medicine, who are interested
in the behavior of biomaterials and complex fluids. The aim is to get
acquainted with the work and research interests of colleagues across the
different disciplines. The seminar is very informal and student-oriented.
Meetings take about two hours, allowing for many questions and lively
discussions.
Time and Location
Unless otherwise noted, the seminar takes place on Wednesdays,
14:00-16:00, at Shenkar-Physics Building , Room #105.
E-Mail List
If you wish to join the seminar e-mail list, please send a message to biosoft@post.tau.ac.il.
November 16th 2011: Oren Regev (BGU)
Carbon nanotube-liposome conjugate for efficient drug transportation
Carbon nanotubes (CNT) are widely explored as carriers for drug delivery due to their facile transport through cellular membranes. However, the amount of loaded drug on a CNT is rather small. Liposomes on the other hand are employed as carrier of a large amount of drug. We developed a new drug delivery system, in which drug-loaded liposomes are covalently attached to CNT to form a CNT-liposomes conjugate (CLC). The advantage of this novel approach is the large amount of drug that can be delivered into cells by the CLC system, thus preventing potential adverse systemic effects of CNT when administered at high doses. This system is expected to provide versatile and controlled means for enhanced delivery of one or more agents stably associated with the liposomes.
November 30th 2011: Dan Ben-Yaakov (TAU)
Non-Electrostatic Interactions and Ion-Specific Effects in Ionic Solutions
Franz Hofmeister and co-workers reported already during the 1880's and 1890's on monovalent ionic species (such as fluoride and chloride) that are more effective at precipitating proteins ("salting out") than others (such as bromide and iodide). This pioneering observation of ion-specific effects was followed by a huge amount of experimental studies, reporting on ion-specific interactions emerging in various experimental systems. Examples include bulk properties such as activity and viscosity of ionic solutions, as well as interfacial properties such as air/water surface tension and interaction of surfactant micelles, lipid-bilayer membranes, proteins, DNA molecules and more.
Although being an old observation, the theoretical origin for these effects is still not fully formulated. Dispersion forces, solvation, ionic size and polarizability are several examples of the mechanisms suggested during the recent decades as possible candidates to explain the specificity, and to interpret a large body of experimental evidence. However, the complexity of the inter-constituents interactions is a major difficulty of constructing a complete theoretical model.
By using a simplified phenomenological approach we try to obtain a more intuitive understanding of non-electrostatic and ion-specific effects. Several such models will be discussed in the seminar. In particular, I will elaborate on the preferential solvation of ions in a binary mixture, and the ionic hydration shell, as sources of an ion-solvent interaction. The influence of these additional effects on the density profiles and the inter-surface force will be discussed. For inter-surface separations at the nanometers range a significant effect on the force is found. The change of the force (relative to the prediction of the standard Poisson-Boltzmann model) may be either positive or negative, depending on the nature of the non-electrostatic interactions. I will discuss the results and their consequences to the interpretation of experimental data.
December 14th 2011: Anne Bernheim (BGU)
Releasing the brakes: how cortactin enhances actin-based motility
The polymerization of actin is directed to the surface of the cell membrane or vesicles, by localizing to the surface nucleating molecules which then activates the branching of the filaments using the Arp2/3 complex. The actin network that forms at the surface produces an elastic pushing force on the surface. However, the same nucleating molecules that initiates actin polymerization, also inherently inhibits the translation of the protrusive force into motion, by binding to the same actin network. This is an inherent problem, as in order to localize the branching process to the membrane, the nucleating factor has to make contact with the network during the formation of the new branch. In order to address this problem we have used a bottom-up approach in which beads coated with actin nucleators are pushed by the polymerization of an actin network at their surface. We found that cortactin (known to play an important role in cell movement), plays a critical role in translating actin polymerization at a bead surface into motion by releasing the network-bound nucleaor from the new branching site. This enhanced release has two major effects: it increases the turnover rate of branching per nucleator molecule, and it decreases the friction-like force caused by the binding of the moving surface with respect to the growing actin network.
December 28th 2011: Lia Addadi (WIS)
Structural Organization and Localization of Mixed Cholesterol: Lipid Domains in Cell Membranes
Lipid microdomains, or rafts, consisting of sphingolipids and cholesterol, play important roles in membrane trafficking and in signaling. Despite years of study on these domains, many open questions remain about their precise characteristics. To address the combined issues of composition, structure and location of these domains, we have developed new experimental approaches, based on the use of specific monoclonal antibodies as recognition tools, combined with direct structure determinations on single hydrated lipid bilayers by X-ray diffraction. One such 'structural' antibody was raised against a mixed phase of cholesterol and ceramide of known structure, and has been used to demonstrate the existence and location of ceramide/cholesterol domains in cultured cells. I'll discuss the possible implications of these findings, and in particular the relevance of understanding the role of lipid lateral organization in biological membranes.
January 11th 2012: Mario Feingold (BGU)
Towards Single Cell Optical Tomography
Using a single-beam, oscillating Optical Tweezers we demonstrate trapping and rotation of rod-shaped bacterial cells with respect to the optical axis. The angle of rotation is determined by the amplitude of the oscillation. This technique allows imaging fluorescently labeled 3D sub-cellular structures from different, optimized viewpoints. To illustrate our method we analyze the Z-ring of E. coli. We use cells that express FtsZ-GFP and have their cytoplasmic membrane stained with FM4-64. In a vertically oriented cell, both the Z-ring and the cytoplasmic membrane images appear as symmetric circular structures that lend themselves to quantitative analysis.
Scanning the cell alignment and using 3D image reconstruction from the corresponding images of a fluorescently labeled 3D sub-cellular structure, would make our approach analogous to that of cryo-electron tomography.
January 25th 2012: Diego Krapf (CSU)
Anomalous diffusion and ergodicity breaking in the plasma membrane: the role of endocytosis
Kv2.1 is unusual among voltage-gated K+ channels in that it localizes to micron-sized clusters on the cell surface of neurons. Within these clusters, Kv2.1 is non-conducting. I will discuss single-molecule tracking experimental results showing that these surface structures are specialized platforms involved in the trafficking of membrane proteins to and from the cell surface. This study is the first to identify stable cell surface platforms dedicated to ion channel trafficking. Multi-color TIRF-based studies indicate that fluorescently labeled K+ channel containing vesicles directly tether to and deliver cargo in a discrete fashion to the Kv2.1 surface clusters. We find that retrieval of Kv2.1 from the membrane occurs also at the cluster perimeter, via a clathrin-mediated endocytic pathway.
The internalization of channels is often aborted because the channel escapes from the endocytic pit. However, when a channel is captured by a clathrin-coated pit it is temporarily immobilized. These stalling events introduce an anomalous subdiffusion process that can be modeled by a continuous time random walk (CTRW). Transient immobilization not only induces anomalous subdiffusion but also weak ergodicity breaking, that is, the ensemble and time averages do not coincide. We find evidence showing that the ensemble and temporal distributions are different. Interestingly, ergodicity is recovered in the presence of actin inhibitors. By performing simultaneous TIRF imaging of quantum-dot-tagged Kv2.1 and RFP-tagged clathrin light chain, we find that stalling events mainly take place when the channel is captured within a forming clathrin coated pit. These results show that abortive endocytic events are responsible for the maintenance of a CTRW with a power law distribution of stalling times.
March 7th 2012: Uri Nevo (TAU)
Neuronal Hydrodynamics
In the last two decades it was discovered by Diffusion weighted MRI (DWI) that changes in the magnitude of water displacement in cells, and specifically in brain tissue, are a 'real time' marker of ischemia and of other types of tissue damage. Displacement of water molecules inside cells is usually studied with respect to diffusion, a process hard to model in the complex and crowded cellular environment. Not much is known about an additional component of displacement: active cellular mechanisms contributing to displacement of water molecules inside cells.
Our research hypothesis is that a significant component of water displacement in cells and specifically in neurons is that of actively induced micro-streaming. We currently focus on two mechanisms, neuronal activity and axonal transport, and study their effect on the cytoplasmic fluid. In the coming lecture I will review the least known mechanical dimension of neuronal activity and will describe our theoretical and experimental work aiming to quantify micro-streaming inside neurons. These include analytical and numerical modeling, DWI and optical microscopy and interferometry. I will end by speculating on the possible implications of the work on the study of brain function.
March 21st 2012: Rudi Podgornik (University of Ljubljana)
Protein-DNA interactions determine the shapes of DNA toroids condensed in virus capsids
I will present recent experimental results and their theoretical framework on DNA packing in viro, i.e. inside virus capsids. Nematic nano drop theory of confined DNA packing provides a suitable framework to describe the effects of osmotic pressure as well as interaction of DNA with the internal capsid wall - the hypotope. It seems that sometimes DNA can interact with the capsid wall with attractive and sometimes with repulsive interactions. I will present arguments that allow us to solve this problem and explain some features of experiments.
March 28th 2012: Ajay Gopal (UCLA)
Visualizing Large RNA Molecules in Solution
Single-stranded (ss) RNAs longer than a few hundred nucleotides are branched polyelectrolytes that do not have a unique structure in solution. The equilibrium properties therefore reflect the average of an ensemble of structures. I will describe how cryo-electron microscopy is used to image projections of individual long ssRNA molecules and characterize the anisotropy of their ensembles in solution. A flattened prolate volume is found to best represent the shapes of these ensembles.
The measured sizes and anisotropies are in good agreement with complementary determinations using small-angle X-ray scattering and coarse-grained molecular dynamics simulations. A long viral ssRNA is compared with shorter non-coding transcripts to demonstrate that prolate geometry and flatness are generic properties independent of sequence length and origin. The anisotropy persists under physiological as well as low-ionic-strength conditions, revealing a direct correlation between secondary structure asymmetry and 3D shape and size. I will discuss the physical origin of the generic anisotropy and illustrate its implications for viral self-assembly by comparing branching propensities in viral and non-viral RNAs.
April 4th 2012: Tim Salditt (Universität Göttingen)
Membrane fusion by x-rays: from model membranes to organelles
Understanding the physical mechanisms underlying membrane fusion requires a
multi winged approach, involving model systems as well as biological membranes.
We study fusion intermediates occurring in form of ordered passages or stalks
connecting neighbouring bilayers in multilamellar model membrane stacks. The
stalks exhibit long range crystalline order with rhombohedral symmetry in a fluid ‘host’
membrane stack, which is studied by high resolution x-ray diffraction under grazing
incidence angles. Information on membrane curvature, and hydration interaction can
be revealed by analyzing the quantitative electron density maps, collected for
controlled environmental parameters and membrane composition. Phase
diagrams can be analyzed in view of stabilizing or destabilizing agents for stalk
formation.
While in these equilibrium phase, dehydration forces bring bilayers together favoring
at some point the formation of stalks, it is specific membrane proteins and their
interaction which set the local boundary conditions for membrane apposition in
biological membrane fusion. In view of studying fusion in the presence of SNARE
proteins, we have started a x-ray structural characterization of synaptic vesicles (SV)
by small-angle x-ray scattering, and currently extent this work towards studies of SV
dockled to and interaction with model bilayers.
Finally we present a novel high resolution x-ray imaging scheme capable of yielding a
magnified hologram of a freely suspended lipid membrane illuminated by highly
divergent and coherent x-ray beams. We propose this setup to image fusion
trajectories at high resolution in future experiments.
April 18th 2012: Nathalie Q. Balaban (HUJI)
Generation of Variability by a Threshold-based Molecular Mechanism
In the face of antibiotics, bacterial populations avoid extinction by harboring a subpopulation of dormant cells that are largely drug-insensitive. This phenomenon, termed 'persistence', is a major obstacle for the treatment of a number of infectious diseases. The biophysical mechanism responsible for variability, despite uniform conditions, which generates both actively growing as well as dormant cells within a genetically identical population was unknown. We present a detailed quantitative study of the genetic module implicated in antibiotic persistence of E.coli. We find that the differentiation of bacteria, into either dormant or not, occurs through threshold amplification of molecular noise in toxin-antitoxin modules.
Fluctuations in toxin protein levels above and below the threshold result in the co-existence of dormant and growing cells. Stochastic modeling of protein-protein interactions offers predictions for the molecular mechanism behind the threshold noise amplification, which were further confirmed by single-cell measurements. We conclude that toxin-antitoxin modules in general represent a mixed network motif that can serve to produce a subpopulation of dormant cells and to supply a mechanism for regulating the frequency and duration of growth arrest. Toxin-antitoxin modules thus provide a natural molecular design for implementing a bet-hedging strategy.
May 2nd 2012: Nir Gov (WIS)
Modeling random active forces in biology
Biologically driven (active) non-equilibrium
fluctuations are often characterized by their non-Gaussianity or by an
"effective temperature", which is frequency dependent and higher than
the ambient temperature. We address these two measures theoretically
by examining a randomly kicked particle, with a variable number of kicking
motors, and show how these two indicators of non-equilibrium behavior
can contradict. Our results are compared with new experiments on
shape fluctuations of red-blood cell membranes, and demonstrate how
the physical nature of the motors in this system can be revealed using
these global measures of non-equilibrium.
The concept of the effective temperature is extended to active particles
trapped in a potential well. We calculated the average escape time and
find that Kramers' reaction-rate theory holds in this
system. Using the calculated escape time
we attempt to describe the observed anomalous motion of
tracer particles in the active actin-myosin gel.
May 16th 2012: Daniel Harries (HUJI)
Mechanism of peptide stabilization by crowders, osmolytes, and salts
The interior of living cells is a highly complex environment crowded not only by many macromolecules such as DNA and proteins, but also by molecularly small osmolytes. These two ubiquitous cosolute classes non-specifically interact with many biomacromolecules, and their concentrations are constantly regulated to allow proper biological function. While the role of osmolytes and crowders has been extensively studied, their thermodynamic mechanisms of action are still debated. We have been experimentally and computationally studying the folding of a model peptide and its aggregation into amyloid fibers, and following the perturbations to its stability upon cosolute addition. Our findings have also allowed us to dissect peptide stability into enthalpic and entropic contributions. We find that cosolutes may act by different mechanisms that correlate with their concentration and molecular size. Surprisingly, however, we found that cosolute action is not governed by crowding alone, but may also depend on chemical identity that goes beyond excluded volume interactions. These results also imply that water is involved in the stabilizing action of many osmolytes. Our findings suggest that different cosolutes may act through disparate mechanisms, but because of similar dependence on concentration and size may still appear to be mechanistically related.
May 30th 2012: Naomi Oppenheimer (TAU)
Dynamics in a membrane with immobile inclusions
Cell membranes are anchored to the cytoskeleton via immobile inclusions. We investigate the effect of such anchors on the in-plane dynamics of a fluid membrane and mobile inclusions embedded in it. The immobile particles lead to a decreased diffusion coefficient of mobile ones and suppress the correlated diffusion of particle pairs. Due to the long-range, quasi-two-dimensional nature of membrane flows, these effects become significant at a low area fraction (below one percent) of immobile inclusions.
