Biology subjects

Raz, O.

Publications and source records attributed to Raz, O..

3 recordsLinked to original sources

bioRxiv2017

Recovery of equilibrium free energy from non-equilibrium thermodynamics with mechanosensitive ion channels in E. coli

Bacterial mechanosensitive channels are major players in cells ability to cope with hypo-osmotic stress. Excess turgor pressure due to fast water influx is reduced as the channels, triggered by membrane tension, open and release osmolytes. However, in vitro measurements of the free energy difference between the open and closed states of ion channels are challenging due to hysteresis effects and inactivation. Exploiting recent developments in statistical physics, we present a general formalism to extract the free energy difference between the closed and open states of mechanosensitive ion channels from non-equilibrium work distributions associated with the channels gating recorded in native patches under ramp stimulation protocols. We show that the work distributions obtained from the gating of MscS channels in E. coli membrane satisfy the strong symmetry relations predicted by the fluctuation theorems and recover the equilibrium free energy difference between the closed and open states of the channel within 1 kB T of its best estimate obtained from an independent experiment.

biophysics↗

bioRxiv2017

A duplex MIPs-based biological-computational cell lineage discovery platform

Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin1. Recently, novel in vivo methods and technologies utilizing genome editing enabled important insights into the cell lineages of animals2-8. In contrast, human cell lineage remains restricted to retrospective approaches, which still lack in resolution and cost-efficient solutions. Here we demonstrate a scalable platform for human cell lineage tracing based on Short Tandem Repeats (STRs) targeted by duplex Molecular Inversion Probes (MIPs). With this platform we accurately reproduced a known lineage of DU145 cell lines cells9 and reconstructed lineages of healthy and metastatic single cells from a melanoma patient. The reconstructed trees matched the anatomical and SNV references while adding further refinements. Our platform allowed to faithfully recapitulate lineages of developmental tissue formation in cells from healthy donors. In summary, our lineage discovery platform can profile informative STR somatic mutations efficiently and we provide a solid, high-resolution lineage reconstruction even in challenging low-mutation-rate healthy single cells.

systems biology↗

bioRxiv2017

Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing

Advances in biochemical technologies have led to a boost in the field of single cell genomics. Observation of the genome at a single cell resolution is currently achieved by pre-amplification using whole genome amplification (WGA) techniques that differ by their biochemical aspects and as a result by biased amplification of the original molecule. Several comparisons between commercially available single cell dedicated WGA kits (scWGA) were performed, however, these comparisons are costly, were only performed on selected scWGA kit and more notably, are limited by the number of analyzed cells, making them limited for reproducibility analysis. We benchmarked an economical assay to compare all commercially available scWGA kits that is based on targeted sequencing of thousands of genomic regions, including highly mutable genomic regions (microsatellites), from a large cohort of human single cells (125 cells in total). Using this approach, we could analyze the genome coverage, the reproducibility of genome coverage and the error rate of each kit. Our experimental design provides an affordable and reliable comparative assay that simulates a real single cell experiment. Results demonstrate the needfor a dedicated kit selection depending on the desired single cell assay.

genomics↗