Functionalization of Polymeric Beads as Optical Reporters of Biomembrane Mimicking Cell Substrate Properties

poster abstractNovel biomembrane-mimicking cell substrates based on a polymer-tethered multi-lipid bilayer stack have been recently developed in the Naumann lab. These novel substrates have been shown to induce profound changes in cellular behavior dependent on the number of bilayers in the stack. However, the underlying mechanical substrate properties remain unclear. To overcome this problem, the central goal of my research is the development of a nanoparticle-based optical reporter that provides insight into the dynamic and viscoelastic properties of the multibilayer system. To achieve this goal, fluorescent polystyrene beads and magnetic polystyrene beads were functionalized for use in confocal microscopy and magnetic tweezers (MT) assays, respectively. Both kinds of beads were specifically tailored and functionalized to link the bilayer system to cellular adhesion proteins recognized by plated cells, thus acting as fluorescent cell-substrate linkages. To assure the correct surface functionalization of nanoparticles, Zetasizer assays were run on both kinds of beads to verify expected changes in hydrodynamic radius and zeta potential as reactions progressed. Fluorescent beads were specifically linked to lipid bilayers using maleimide-thiol coupling chemistry, thus allowing subsequent experiments in the presence of plated cells. As confirmed by analysis of cellular nanoparticle uptake, the cellular uptake kinetics of the newly synthesized fluorescent beads could be controlled through adjustment of nanoparticle coating composition. These results are significant because they validate the new nanobead design, which shows enhanced reporter efficiency for confocal microscopy and MT based assays

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Physisorbed Polymer-Tethered Lipid Bilayer with Lipopolymer Gradient

Physisorbed polymer-tethered lipid bilayers consisting of phospholipids and lipopolymers represent an attractive planar model membrane platform, in which bilayer fluidity and membrane elastic properties can be regulated through lipopolymer molar concentration. Herein we report a method for the fabrication of such a planar model membrane system with a lateral gradient of lipopolymer density. In addition, a procedure is described, which leads to a sharp boundary between regions of low and high lipopolymer molar concentrations. Resulting gradients and sharp boundaries are visualized on the basis of membrane buckling structures at elevated lipopolymer concentrations using epifluorescence microscopy and atomic force microscopy. Furthermore, results from spot photobleaching experiments are presented, which provide insight into the lipid lateral fluidity in these model membrane architectures. The presented experimental data highlight a planar, solid-supported membrane characterized by fascinating length scale-dependent dynamics and elastic properties with remarkable parallels to those observed in cellular membranes