College of Arts and Sciences

DNA Nanotechnology Tools for Single-Molecule Cryo-EM of Membrane Proteins

DNA is a unique polymer. It is the information storage molecule of all known life forms, but can also be used to build up complex, artificial structures that are not found in Biology. Our group is leveraging this programmability to engineer nanoscale architectures and tools for applications in Biophysics and Structural Biology.

I will demonstrate how DNA-lipid nanodiscs1 can be made and used as novel molecular tools to study membrane proteins (MPs) in a native membrane-like environment. MPs are key players in cellular functions such as sensing,

Continue reading… Thorsten Schmidt (Kent State University)

Title: Dynamic DNA Nanotechnology

Sebastian Sensale Rodriguez

Assistant Professor
Department of Physics
Cleveland State University

Abstract: Taking inspiration from macroscopic machines, the last decade has seen a surge of interest in the development of DNA origami devices whose functions heavily rely on conformational changes. These “dynamic” DNA nanodevices have found application in diverse areas of research including drug delivery, molecular computation, nanorobotics and biosensing. While the design, modeling and characterization of macroscopic machines is well determined on the basis of kinematics and continuum mechanics, the intrinsic flexibility and stochastic nature of biological systems at the nanoscale make such tasks be highly challenging. 

Continue reading… Sebastian Sensale (Cleveland State University)

Updated Zoom Link!!!

https://cwru.zoom.us/j/92624627629?pwd=YnNLU2wzL0svRzEzaU9sY24zRklqZz09

Meeting ID: 926 2462 7629
Passcode: biophysics

Title: Synthetic DNA Nanostructures as Platforms for Precise Nanoparticle Organization
 
Assistant Professor
Department of Chemistry
Case Western Reserve University
 
DNA nanotechnology has enabled the ability to build objects and particles at the nanoscale. With the help of a growing repository of DNA self-assembling tools and strategies, it
is possible to create two- and three-dimensional structures, ranging from a few nanometers to micron-scale in size. The cumulative properties of DNA,

Continue reading… Divita Mathur (CWRU)

POSTPONED due to COVID

Continue reading… Thereza Soares (Federal Univ. of Pernambuco)

Biological signals and cell signaling pathways – A computational approach.

Type I interferons are used effectively in the treatment of Hepatitis C by activating a cascade of interferon-stimulated genes with antiviral properties. The signaling cascade involves the binding of IFN to the two subunits of the IFN receptor, IFNAR1 (R1) and IFNAR2 (R2), to form a ternary complex. The kinases – Jak’s and Tyk’s – bound to the cytoplasmic domains of receptor subunits become phosphorylated, which further phosphorylates STAT (p-STAT). Dimers of p-STAT migrate to the nucleus to initiate the transcription of a large number of genes.

Continue reading… Chitra Nayak (Tuskegee University)

Reconstructing cell phenotypic transition dynamics from single cell data

Recent advances in single-cell techniques catalyze an emerging field of studying how cells convert from one phenotype to another, i.e., cell phenotypic transitions (CPTs). Two grand technical challenges, however, impede further development of the field. Fixed cell-based approaches can provide snapshots of high-dimensional expression profiles but have fundamental limits on revealing temporal information, and fluorescence-based live cell imaging approaches provide temporal information but are technically challenging for multiplex long- term imaging. My lab is tackling these grand challenges from two directions, with the ultimate goal of integrating the two directions to reconstruct the spatial-temporal dynamics of CPTs.

Continue reading… Jianhua Xing (University of Pittsburgh)

On the quest of finding the surface of articular cartilage

The primary role of articular cartilage (AC) is to provide a smooth lubricated surface between contacting and moving bones, which allows for ultralow friction as well as wear protection to the sliding epiphysis for almost a century in healthy people. The physical and chemical nature of the topmost surface of AC has intrigued researchers since it was first reported in 1951, called the “lamina splendens”. This layer has been the source of heated and controversial scientific debate since it was first reported. The lamina splendens is important because it forms the interfaces between the cartilage and synovial fluid,

Continue reading… Roberto Carlos Andresen Eguiluz (UC Merced)

Title:  Protein dynamics: Connecting in vitro, in cell, and in vivo

Although biomolecules evolved to function in the cell, most biochemical and biophysical studies have been carried out in vitro. A combination of in vitro, in-cell, and in vivo studies will highlight how steric and non-steric interactions modulate protein folding and protein-RNA interactions. I will introduce a customized pipeline that combines meganuclease mediated transformation with fluorescence-detected temperature-jump microscopy to image fast dynamics of biomolecules in living zebrafish with single-cell resolution. To interpret in vivo and in-cell results, an in vitro systematic series of solvation environments will distinguish contributions from non-steric and steric interactions to stability,

Continue reading… Caitlin Davis (Yale University)

Twenty Years Later: Why No Clinical Quantum Dot Imaging Labels?

Quantum dots (QDs), semiconductor nanoparticles that fluoresce upon light excitation, were first
introduced for biological imaging in 1998. At the time, QDs were heralded as a revolutionary
product that would transform biological imaging. QDs have narrow emission bandwidths and
broad excitation spectra, enabling multiplexed imaging. Their fluorescence is tunable based on
QD size, permitting precise tuning of emission wavelength, and QDs are more resistant to
photobleaching than their molecular dye counterpoints. Yet, despite 20 years of research, there
are no clinically approved QD products and QDs remain a niche item used in specific research
situations.

Continue reading… Jessica Winter (Ohio State University)

Emergence and control in microbial communities:  steering bacterial pathogens through the phenotype space of multidrug resistance
 

Antibiotic resistance is a growing public health threat.  The emergence of resistance far outpaces the development of new drugs, underscoring the need for new strategies aimed at slowing the resistance threat.  In this talk, I’ll discuss our group’s ongoing work to understand the evolution of drug resistance in E. faecalis, an opportunistic bacterial pathogen, using quantitative experiments and theoretical tools from statistical physics and dynamical systems. By combining laboratory evolution with simple mathematical models, we show that unconventional strategies–including aperiodic drug dosing,

Continue reading… Kevin Wood (University of Michigan)