Cellular Biophysics

Neuronal Hydrodynamics

Live-cell imaging with a confocal microscope - observing the Quantum dots while they spread along the axon (Photo by Keren Zeevy & Hadas Schori).

Diffusion weighted imaging (DWI) is a central MRI technique with key applications in neurology, both in clinic and in research. Image contrast in DWI is determined by the microscopic displacement of water molecules. This displacement is usually assumed to be governed in vivo by anisotropic random diffusion and is quantified by the apparent diffusion coefficient (ADC).

We study the biophysical basis of changes in the displacement of water molecules that follows neural damage. We stuaddressed a long held view on the important role of cytoplasmic steraming in diffusion imaging of neurons (a view also held by us). We studied different active mechnisms operating in cells, and evaluated their effect on the displacement of water molecules. Our models and NMR experiments predict that, although important from the physioogical point of view, micro-streaming mechanisms were found be insignificant to be detected by Diffusion MRI.

Our hypothesis is that the drop in water displacement that follows neural damage is significantly affected by chnages occurring in the cytoskeleton. We study this using NMR, works on biomimicry polymers and biophysical models.

Brain activity and water displacement

spinal cord

An excised and vital new-born rat spinal, during operation and attachment of a suction electrode for an electrophysiological recording. (Photo by Nitzan Tirosh).

In the last years, changes in ADC were observed during brain stimulation. However it remained unclear whether the observed changes reflect biophysical mechanisms linked to neuronal activity or that the reported variations are related to changes in oxygenation.

We developed an experimental system of an excised and vital new-born rat spinal cord. This experimental model is free of many physiological artifacts and thus allows studying the origins of the diffusion signal changes during brain activation. This research also tests the feasibility of probing neuronal activity in a direct manner, the use of DWI rather than using the BOLD response.

Quantification of water displacement in porous materials

Diffusion weighted NMR experiments can be used to probe the local geometry of pores since the macroscopic signal obtained in the experiment is affected by a geometrical confinement of the diffusing particles.

The single and double Pulsed Field Gradient (SPFG and DPFG) pulse sequences consist a one or two pairs of pulsed magnetic field gradients These pulse sequences were applied to study porous media. Obtaining the theoretical signal for different geometries can be achieved by using the Multiple Correlation Function (MCF) method. The MCF method is based on solving the Bloch-Torrey equation using eigenfunctions of the Laplace operator along with the appropriate boundary conditions which depict what happens when the particles encounter the interface.

We develop methods for characterization of tissue microstructure. For that purpose we characterize the displacement of water molecules within tissues by NMR and model the tissues as porous media.

We developed theory and experiments that allow characterization of complex porous structures such as tissues. In this framework experiments are repeated with gradient pairs that vary in their amplitude, temporal spacing (diffusion time) and relative direction. Experiments performed with phantoms composed of multiple radii and later on with fixed tissues demonstarted that the method allows an accurate reconstruction of pore size distribution.


Microscopy images of ospin al cord white matter and the corresponding segmented masks used for axon counting. The two bottom rows show the resulting distribution of fiber diameters as evaluated by our diffusion MRI method, compared to the histology based evaluation. Solid red lines are the microscopy-based distributions. Blue bins are the MRI-based ADDs. The scale (orange) bars represent 10 μm. (From Benjamini et al. NeuroImage 2016).


Four cross section cryo-fractographs taken from a porous bioresorbable polymer (PDFGA) using the same magnification. Images illustrate why the choice of field of view by the user pre-determines the extracted geometrical properties of the sample (scale bar is 100μm for all four images). An NMR based methods sample the entire volume of the porous polymer, rather than its surface. (Photo by Jonathan J. Elsner and Dan Benjamini).

Cell Studio: a framework for 3D biological and biophysical modeling

Cell Studio is a platform for three dimensional, graphical, interactive simulations of biological and biophysical processes. It features a graphical user interface to generate a simulated experiment. It then facilitates the execution of the experiment and displays an animated graphical representation. The user may control the timeline of the experiment as well as intervene in the experiment itself (e.g. inject molecules). The outcomes of the simulation are both textual statistics on the kinetics of the system, as well as a an animation of the spatio-temporal kinetics.

You can find out more on the Cell Studio website.


Screenshots from the simulation which depict several graphical features. (a): cell division, (b): receptors migrating to the immune synapse in order to bind, (c): a cluster of cells which creates a tissue-like structure, (d): graphs that display real time data from the experiment (on the left, the number of cells in each monoclonal population, on the right, a FACS plot). (From Liberman et al., Submitted for publication



immunology graph

Transplantation of small syngeneic graft from immune-deficient mice results in impairment in graft acceptance and glucose tolerance capacity. After chemical removal of the pancreas WT mice were transplanted with 50 syngeneic pancreatic islets isolated from either WT (n=4) or SCID mice (n=4). (a) Daily Glucose levels, (b) Intravenous glucose tolerance test (Adopted from work of Hauben et al., Transplantation Immunology 2007).

Ecoimmunity is a theory that suggests that the interaction of the immune system with tissue cells (‘self’) is identical to that of the immune system with pathogens: in both cases it is a predator-prey interaction that is continuously active and evolving.

According to Ecoimmunity tolerance to self is not a 'task' of the immune system but is rather a symmetrical balance between the ability of immune cells to predate tissue cells, and the ability of tissue-cells to avoid predation. Moreover, Ecoimmunity suggests that this interaction evolves throughout ontogeny symmetrically: while clonal selection shapes the population of immune clones and their specificities, selection of an expressed phenotype of tissue-cells defines the arsenal of molecular 'defense tools' that will be expressed by tissue-cells. These characteristics of the suggested interaction imply that the immune-tissue interaction is not unique but obeys the common (macroscopic) ecological interactions. Indeed, as in macroscopic ecological systems (in which predators regulate the preys' population and remove infectious individuals) this process serves the tissue: Immune-cells remove tissue-cells that failed to adapt their phenotype or maintain it, in order to resist predation, these cells might have otherwise mediate further damage.

Hauben et al. have already tested the functional manifestation of Ecoimmunity. Ecoimmunity predicts that cells that matured in the absence of an immune system will find difficulty coping with a competent immune system. Indeed, WT mice that were transplanted with pancreatic islets from SCID mice had significantly higher blood-sugar levels, relative to the WT-controls. The result suggests that islets of WT donors, displayed better resistance to the immune system, relative to SCID islets that did not encounter an immune system, prior to the transplantation.

Ochayon et al. deomnstrated molecular changes that appear in a tissue, with relation to its ongoing interaction with the immune system. They Compared mice tissues that develop during ontogeny alongside an active immune system to tissues of cells from immune deficient mice.

They found that the cell from an immune competent host expressed significantly lower levels of molecules that are related to the inteaction with the immune syste (e.g. MHC-I). This result is interpreted as the outcome of an ontogenic pressure towards evasion from the immune system.