Frank Brown, University of California - Santa Barbara
Hosted by Garegin Papoian
Title: Mechanics and dynamics of simulated membranes: extracting bending moduli and difficulty in the extraction of diffusion coefficients
Time: 4:00PM - 5:00PM
Date: Monday, September 11, 2017
Abstract
Detailed molecular simulations are increasingly used in membrane biophysics to assist in the interpretation of experiments. However, many of the most fundamental physical properties prove difficult to accurately measure in silico due to small system sizes. The membrane bending modulus and lateral diffusion coefficient for proteins/lipids are two such properties. Two different stories will be presented related to the inference (or attempted inference) of these properties from simulation.
Colenso Speer, University of Maryland College Park
Hosted by Sergei Sukharev
Title: Reconstructing Visual Circuits with Volumetric Super-resolution Fluorescence Microscopy
Time: 4:00PM - 5:00PM
Date: Monday, September 18, 2017
Abstract
Light microscopy enables multi-color imaging, analysis, and live tracking of diverse cellular and molecular processes and is a vital tool for neuroscience. In the last decade, super-resolution microscopy techniques have extended the spatial resolution of optical imaging to the nanoscale and enabled new investigations of the molecular organization and structural properties of synapses in the nervous system. In this talk I will introduce our laboratory’s efforts to apply STochastic Optical Reconstruction Microscopy (STORM), a localization-based super-resolution imaging approach, to the analysis of synaptic structure and connectivity in the brain. I will present an overview of STORM technology for neural circuit imaging including considerations for optimizing sample preparation, super-resolution image quality, and automated data analysis. I will present data demonstrating the imaging and analysis of synaptic inputs to morphologically identified neurons and introduce future directions for cell type-specific super-resolution imaging of functionally characterized circuits. Our group is developing and applying these tools to investigate the activity-dependent and molecular mechanisms that regulate circuit assembly and plasticity in the central nervous system, using the mammalian visual system as a model. We anticipate that volumetric super-resolution microscopy will provide important new structural and molecular imaging data that will complement the connectomic reconstruction of visual circuits by electron microscopy.
Kandice Tanner, National Institute of Health/National Cancer Institute
Hosted by Wolfgang Losert
Title: Engineering the physical properties of the tumor microenvironment
Time: 4:00PM - 5:00PM
Date: Monday, October 2, 2017
Abstract
Transformation of the physical microenvironment including changes in mechanical stiffness of the extracellular matrix (ECM) may be one of the crucial factors that drives cancer progression. In addition to tissue mechanics, the surface topography of the ECM microenvironment has been shown to modulate gene expression. Simply put, how do changes in the physical microenvironment drive cancer progression? 3D culture models can approximate in vivo architecture and signaling cues, allowing for real time characterization of cell-ECM dynamics. We developed tissue mimetics that recreate the complex in vivo geometries while independently controlling bulk stiffness and ECM ligand density. We also developed tools that allow us to resolve and quantitate minute forces that cells sense in the local environment (on the order of microns) within thick tissue (in mm). Using these methods, we are able to dissect the contributions of the physical properties from those due to chemical properties on cell fate as it relates to malignancy and normal tissue homeostasis. Finally, we validated our in vitro findings in an in vivo model using zebrafish as our model for metastasis.
Abhishek Kumar, Center for Nanoscale Science and Technology/National Institute of Standards and Technology
Hosted by Sergei Sukharev/Daniel Serrano
Title: Light sheet fluorescence microscopy for fast, gentle, and high resolution imaging
Time: 4:00PM - 5:00PM
Date: Monday, October 9, 2017
Abstract
Light Sheet Fluorescence Microscopy (LSFM) has emerged as a powerful fluorescence microscopy tool for cell and developmental biology. LSFM is very well suited for long term imaging as it offers optical sectioning, high-speed imaging, and low photobleaching and phototoxicity. I will give a brief overview of this field and then discuss our implementation of LSFM: a fiber coupled dual-view inverted Selective Plane Illumination Microscope (diSPIM). DiSPIM provides an isotropic resolution of 350 nm by computationally fusing two volumetric views acquired by switching illumination and detection between two perpendicular objectives in an alternating duty cycle. Isotropic resolution is advantageous for many biological applications and I will discuss few examples. I will also discuss our latest improvements to the diSPIM - increasing contrast, resolution and optical sectioning. Finally, I will conclude by discussing functional imaging of C. elegans nervous system during embryogenesis using diSPIM.
Pratyush Tiwary, University of Maryland College Park
Hosted by Christopher Jarzynski
Title: How, when and why does a drug leave the binding pocket of a host protein?
Time: 4:00PM - 5:00PM
Date: Monday, October 23, 2017
Abstract
Using molecular dynamics (MD) simulations to study the kinetics of drug unbinding is a desirable but difficult task primarily due to the extremely long timescales involved. Recent progress in enhanced sampling methods, including the development of new sampling approaches, makes it possible to address this and a range of related problems with full atomistic resolution, reaching timescales previously unattainable in MD simulations. In this talk, I will discuss the key principles behind these approaches. I will then highlight some applications calculating pathways, timescales and rate-determining steps of ligand unbinding in various systems including an FDA-approved anti-cancer drug as it unbinds from host kinase.
Daniel Larson, National Institute of Health/National Cancer Institute
Hosted by Sergei Sukharev
Title: Understanding transcription and splicing heterogeneity in gene expression
Time: 4:00PM - 5:00PM
Date: Monday, October 30, 2017
Abstract
Transcriptional regulation in metazoans occurs through long range genomic contacts between enhancers and promoters, and most genes are transcribed at irregular intervals in episodic ‘bursts’ of RNA synthesis. The relationship between these two phenomena and the dynamic regulation of genes in human cells in response to upstream signals is unknown. Here, we describe the use of single-molecule live-cell RNA imaging to dissect the regulation of the estrogen-responsive TFF1 gene under endogenous regulation. Although this gene is highly induced, we observe short active periods and variable inactive periods ranging from minutes to days. The heterogeneity in inactive times gives rise to the widely-observed ‘noise’ in human gene expression. We also observed that alleles in the same cell have similar activity, but the activity ranges among the cell population. Surprisingly, alleles are not independent but rather show correlated dynamics in the same nucleus, leading to a regime of ‘coupled intrinsic noise’ which dominates expression variability. We derive a mathematical model of regulation which relates the frequency and stability of gene loops to the ability of a cell to ‘sense’ changes in estrogen.
Arthur Palmer, Columbia University
Hosted by David Fushman
Title: Protein conformational dynamics in recognition and catalysis: AlkB, GCN4, and Ribonuclease H
Time: 2:00PM - 3:00PM
Date: Monday, November 13, 2017
Abstract
NMR spectroscopy and molecular dynamics (MD) simulations are powerful approaches for probing aspects of conformational dynamics in biological macromolecules. Methods that can be utilized to characterize dynamics on picosecond-nanosecond and on microsecond-millisecond time scales will be illustrated by applications to the DNA-repair enzyme AlkB [1], the enzyme ribonuclease H [2], and the yeast transcription factor GCN4 [3]. In the first example, NMR spin-relaxation measurements establish that the equilibrium distribution of ordered and disordered conformations of the nucleotide recognition element controls order of addition of substrates. In the second example, spin-relaxation measurements and MD simulations as a function of temperature for proteins from psychrotrophic, mesophilic, and thermophilic bacterial species characterize the coupling between conformational dynamics, stability, and function. In the third example, spin-relaxation measurements at five static magnetic fields and MD simulations lead to a two-step selected- and induced-fit mechanism of binding to DNA. Taken together, these cases illustrate the importance of rare, sparsely populated, conformational states in protein function.
Bryan Spring, Northeastern University
Hosted by Giuliano Scarcelli
Title: Selective treatment and imaging of cancer micrometastases using biophysical approaches
Time: 4:00PM - 5:00PM
Date: Monday, December 4, 2017
Abstract
Molecular-targeted, activatable probes are emerging for optical biopsy of cancer. An unexplored potential clinical use of this approach is to monitor and treat residual cancer micrometastases that escape surgery and chemotherapy. This talk will introduce a new platform for activatable phototherapy and in vivo imaging of residual metastases that enables high-fidelity imaging and treatment of cancer cells. Optically active nanomaterials—that use light as both a drug release mechanism and as a cytotoxic modality—are an emerging component of this approach and will also be introduced. These developments stem from the cross-fertilization of biophysical imaging and quantum photophysics with cancer research.
Jonathan Sachs, University of Minnesota
Hosted by Jeffery Klauda
Title: Alpha-Synuclein biophysics: membranes, fibrils and disease
Time: 4:00PM - 5:00PM
Date: Monday, December 11, 2017
Abstract
In this seminar, I will provide an overview of our work on alpha-Synuclein biophysics. Our work combines computational modeling with experimental studies to understand aspects of the protein that are thought to underlie its role in Parkinson’s disease. In particular, I will describe our findings regarding the impact of the protein on membrane curvature and vesicle mechanics, as well as the phase behavior of membranes. I will also discuss our findings regarding Synuclein’s interaction with curvature inducing lipids in the mitochondria. Then, I will present our most recent study of Synuclein fibrils, a computational analysis of the thermodynamic stability of the first Synuclein fibril structure, which was published last year.