Biology subjects

Vahid, A.

Publications and source records attributed to Vahid, A..

3 recordsLinked to original sources

bioRxiv2020

Algorithms for the selection of fluorescent reporters

Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition. Selecting an ideal set of fluorophores for a particular measurement technology or vice versa is a multidimensional problem that is difficult to solve with ad hoc methods due to the enormous solution space of possible fluorophore panels. Choosing sub-optimal fluorophore panels can result in unreliable or erroneous measurements of biochemical properties in model systems. Here, we describe a set of algorithms, implemented in an open-source software tool, for solving these problems efficiently to arrive at fluorophore panels optimized for maximal signal and minimal bleed-through.

bioinformatics↗

bioRxiv2018

Unravelling the response of the actin cortex to electric pulses in vesicles

We study the role of a biomimetic actin cortex during the application of electric pulses that induce electroporation or electropermeabilization, using giant unilamellar vesicles (GUVs) as a model system. The actin cortex, a subjacently attached interconnected network of actin filaments, regulates the shape and mechanical properties of the plasma membrane of mammalian cells, and is a major factor influencing the mechanical response of the cell to external physical cues. We demonstrate that the presence of an actin shell inhibits the formation of macropores in the electroporated GUVs. Additionally, experiments on the uptake of dye molecules after electroporation show that the actin network slows down the resealing process of the permeabilized membrane. We further analyze the stability of the actin network inside the GUVs exposed to high electric pulses. We find disruption of the actin layer that is likely due to the electrophoretic forces acting on the actin filaments during the permeabilization of the GUVs. Our findings on the GUVs containing a biomimetic cortex provide a step towards understanding the discrepancies between the electroporation mechanism of a living cell and its simplified model of the empty GUV.

biophysics↗

bioRxiv2018

Interactions between microtubule-driven membrane protrusions induce filament bundling

The plasma membrane and cytoskeleton of living cells are closely coupled dynamical systems. Internal cytoskeletal elements such as actin filaments and microtubules continually exert forces on the membrane, resulting in the formation of membrane protrusions. In this paper we investigate the interplay between the shape of a cell distorted by pushing and pulling forces generated by microtubules and the resulting rearrangement of the microtubule network. From analytical calculations, we find that two microtubules that deform the vesicle can both attract or repel each other, depending on their angular separations and the direction of the imposed forces. We also show how the existence of attractive interactions between multiple microtubules can be deduced analytically, and further explore general interactions through Monte Carlo simulations. Our results suggest that the commonly reported parallel structures of microtubules in both biological and artificial systems can be a natural consequence of membrane mediated interactions.

biophysics↗