Biophysics Seminar

semester, 2017


Thursday, January 19th 2017
11:15 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, January 26th 2017
11:15 am:
Biophysics Seminar in 120 PAN
To be announced.

Thursday, February 2nd 2017
11:15 am:
Biophysics Seminar in 120 PAN
Speaker: David Punihaole, University of Minnesota, Department of Chemistry
Subject: UV Resonance Raman Spectroscopy: A New Tool to Probe Amyloid-like Fibril Structures

There is currently little that is known about the structure of polyglutamine (polyQ) fibrils, which are involved in at least ten neurodegenerative diseases, including Huntington’s. Given their insoluble and non-crystalline nature, new and incisive biophysical methods need to be developed in order to obtain high-resolution structural information of polyQ and other amyloid-like fibrils. Here, we present our recent advances in UV resonance Raman (UVRR) spectroscopy that enable the elucidation of molecular-level structural information of amyloid-like fibrils. We show, for example, how the primary amide UVRR bands report on the local hydrogen bonding and dielectric environment of glutamine side chains. We also discuss a newly discovered spectroscopic marker, the Amide IIIP vibration, which sensitively reports on the side chain structure of glutamine. These and other spectroscopic markers are used to gain insights into the peptide backbone and side chain conformations of polyQ peptides in solution-state and in fibrils. Finally, we demonstrate how the structural information obtained from UVRR can be utilized to guide Molecular Dynamics simulations in order to obtain experimentally validated structural models of polyQ fibrils.


Thursday, February 9th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, February 16th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, February 23rd 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Ragnar Stefansson, University of Minnesota
Subject: To be announced.

Thursday, March 2nd 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, March 9th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Prof. Thomas Gregor, Princeton University
Subject: How the physics of enhancers shapes development

Enhancers are small regulatory pieces of DNA that control the activity of genes, which eventually determine cellular fates during the development of multicellular organisms. They need to measure the concentrations of various input effector molecules, called transcription factors, and then act over often very long distances along the DNA in order to activate a distantly located gene. In this talk I will present my laboratory’s progress on two fundamental physical properties of these enhancers: 1. How do enhancers decode the information of the input transcription factors and then transduce it into a precise output? 2. How do enhancers operate at long distances to instruct gene activity? We use a combination of genome editing, live imaging and statistical mechanics techniques to address these questions in the fruit fly embryo.


Thursday, March 16th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week. Spring Break.

Thursday, March 23rd 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, March 30th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Prof. Peter Kner, University of Georgia
Subject: Wavefront Correction for Superresolution Microscopy

Superresolution microscopy is rapidly becoming an essential tool in the biological sciences allowing imaging biological structure at length scales below 250 nm. Currently, superresolution microscopy has been applied successfully on single cells achieving resolutions of 100nm down to 20nm over a few microns of depth. When superresolution microscopy is applied in thicker samples the resolution rapidly degrades. Optical aberrations and scattering distort and reduce the point spread function causing different superresolution techniques to fail in different ways. I will discuss our work on combining structured illumination microscopy and stochastic optical reconstruction microscopy with adaptive optics to achieve sub-diffraction resolution in thick tissue.


Thursday, April 6th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, April 13th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Prof. Grant W Luxton, University of Minnesota, Dept. of Biochemistry, Molecular Biology and Biophysics
Subject: To be announced.

Thursday, April 20th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, April 27th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Prof. Julius Lucks, Northwestern University
Subject: Uncovering How RNA Molecules ‘Make Decisions’ On the Fly: Towards Understanding and Engineering Cotranscriptional RNA Folding

RNAs are emerging as a powerful substrate for engineering gene expression and cellular behavior since they are now known to control almost all aspects of gene expression. As with all biomolecules, RNA function is intimately related to its structure, since RNA can adopt structures that selectively modulate gene expression. Central questions in biology and bioengineering then are: How do RNAs fold inside cells?; and How can we engineer these folds to control gene expression? In this talk, I will present our work at the interface of these two questions and share results that are beginning to uncover design principles for understanding natural RNAs and engineering RNAs for an array of applications.

I will start by presenting our work on engineering RNA molecular switches that control transcription. The desire to uncover design principles for engineering these RNAs motivates our development of SHAPE-Seq, a technology that couples chemical probing with next-generation sequencing and that helps characterize RNA structures on an ‘omics’ scale. I will then describe our exciting recent developments in using SHAPE-Seq to help break open one of the frontiers of RNA structure-function relationships by uncovering at nucleotide resolution how RNAs fold cotranscriptionally. Specifically I will highlight new data on uncovering the ligand-dependent folding pathways of riboswitches, and how we are beginning to use these datasets to computationally reconstruct cotranscriptional folding pathways. This new ability is allowing us to ask deep questions about how RNA molecules make regulatory decisions ‘on the fly’ during the dynamic process of transcription. By probing the fundamental processes of RNA folding and function, these studies are expected to greatly aid RNA engineering.


Thursday, May 4th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, September 7th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, September 14th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Jared Hennen, University of Minnesota
Subject: Studying Protein Oligomerization in the Nuclear Envelope of Living Cell

Thursday, September 21st 2017
10:10 am:
Speaker: Prof. Bo Huang UCSF, Pharmaceutical Chemistry
Subject: Watching in the inner life of a cell: beyond super-resolution microscopy
Note room change, this week only.

Thursday, September 28th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Dr. Tejas M Gupte, University of Minnesota
Subject: To be announced.

Thursday, October 5th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Ahmed Haikal, University of Minnesota, Duluth
Subject: Macromolecular Crowding Effects on Excited-State Dynamics of Hetero-FRET Probes in Mimetic Environments

Macromolecular crowding is prevalent in all living cells due to the presence of proteins, nucleic acids, and organelles. Cellular crowding is heterogeneous and is known to influence biomolecular transport, biochemical reactions, and protein assembly and folding. Emerging evidence suggests that some cell pathologies may be correlated with compartmentalized crowding. As a result, there is a need for robust biosensors to quantify crowding both spatially and temporally in living cells. Importantly, those biosensors should be compatible with noninvasive and quantitative micro-spectroscopy methods. I will highlight our recent wavelength-dependent excited-state dynamics of new hetero-FRET (mCerulean–linker–mCitrine) biosensors in environments of varying homogeneous and heterogeneous viscosities. Using time-resolved fluorescence and polarization anisotropy measurements, we elucidate the effects of the linker length and flexibility on the energy transfer efficiency as a function of the surrounding environment. Our results represent an important step towards the application of quantitative and non-invasive approaches to investigate macromolecular crowding and protein-protein interactions in living cells using hetero-FRET probes.


Thursday, October 12th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Wendy Gordon, Dept. of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota
Subject: Decoding mechanotransduction mechanisms of cell-surface receptors

Alteration of mechanical forces is an emerging factor in diseases like cancer. Changes in macroscopic stiffness in disease are accompanied by a wealth of changes in a cell’s tensional homeostasis at a molecular level where mechanotransduction signaling pathways are aberrantly activated. Our lab aims to understand molecular mechanisms utilized by cell-surface receptors to sense and respond to physical stimuli in the cellular environment. I will discuss a new bioluminescence resonance energy transfer (BRET)-based molecular tension sensor that we have developed to help identify mechanosensing proteins in the cell. I will also discuss the molecular mechanisms utilized by the extracellular matrix receptor dystroglycan to regulate proteolysis.


Thursday, October 19th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Jose Alejo Amaya, Engelhart/Adamala lab, GCD, University of Minnesota
Subject: The Unexplored Mechanisms and Regularatory Functions of Ribsome Translocation

In every cell, protein synthesis is carried out by the the ribosome, a complex macromolecular RNA-protein assembly. Single-molecule fluorescence methods have been applied to decipher the mechanism and regulatory roles of the multi-step process of translocation that accompanies every round of translation. The elongation factor G(EF-G)-catalyzed movement of substrates through the ribosome was examined from several perspectives or signals reporting on various ribosomal degrees of freedom. Two states interconvert in the presence of EF-G(GDP), displaying novel head domain motions, until translocation is completed. In order to test if the mentioned state fluctuations leading to translocation are correlated to the engagement of the P-site by the incoming peptidyl-tRNA, the translocation of miscoded tRNAs was studied. Severe defects in the late stages of translocation reveal the correlation between this new stage of translocation and P-site tRNA engagement.


Thursday, October 26th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Hao Wu, University of Minnesota
Subject: To be announced.

Thursday, November 2nd 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Daniel Schmidt, University of Minnesota
Subject: To be announced.

Thursday, November 9th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Paul Francois, McGill University
Subject: Untangling the biological hairball of immune recognition networks

Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. I will introduce several models of immune recognition by T cells and will show how a simple procedure can be used to reduce them to functional submodules, using statistical mechanics of complex systems combined with a fitness-based approach inspired by in silico evolution. Our procedure works by putting parameters or combination of parameters to some asymptotic limit, while keeping (or slightly improving) the model performance, and requires parameter symmetry breaking for more complex models. An intractable model of immune recognition with close to a hundred individual transition rates is reduced to a simple two-parameter model, and connected to the ``adaptive sorting" principle that we previously identified and experimentally validated. Our procedure extracts three different mechanisms for early immune recognition, and automatically discovers similar functional modules in different models of the same process allowing for model classification and comparison.


Thursday, November 16th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Bo Huang UCSF, Pharmaceutical Chemistry
Subject: Watching in the inner life of a cell: beyond super-resolution microscopy

Cellular processes are orchestrated by a large number of biomolecules in a spatially and temporally coordinated manner within a tiny volume. To uncover the underlying organizational principles and their functional relevance, we take microscopy visualization as the primary approach to map the spatial localization, temporal dynamics and activity profiles of proteins and nucleic acids. We have used super-resolution microcopy to dissed the molecular organization of the cilium transition zone, revealing its function as a gate of ciliary trafficking. We have also been developing techniques for the mapping of the physical organization of the genome in the nucleus.


Thursday, November 23rd 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week (Thanksgiving Break)

Thursday, November 30th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: David Odde, University of Minnesota
Subject:  Simulating cell migration

David Odde, University of Minnesota Cell migration is key to many biological processes including embryonic development, wound healing, and disease progression. Recent studies have shown that cell migration is sensitive to microenvironmental stiffness, and many cells display a stiffness optimum at which migration is maximal. To create a unified theoretical framework for cell migration, we have now developed and experimentally tested a whole cell migration simulator based on the motor-clutch model of cellular force transmission by imposing coupled force balances and mass balances on molecular motors, adhesion molecules (“clutches”), and actin subunits in a compliant microenvironment. The model predicts a stiffness optimum that can be shifted by altering the number of active molecular motors and clutches. This prediction was tested experimentally using glioma (brain cancer) cells, and we find that the motor-clutch cell migration simulator provides a theoretical framework with which to predict cell adhesion and migration in defined mechanochemical microenvironments in 1D, 2D, and 3D.


Thursday, December 7th 2017
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Renee Frontiera, University of Minnesota
Subject: Towards label-free super-resolution imaging

Super-resolution imaging methods have revolutionized our understanding of biological processes on nanometer length scales, due to their ability to break the optical diffraction limit. These new techniques enable direct visualization of fluorescently-labeled samples on the 10 nm length scale. However, the fluorescent labels required by current super-resolution imaging approaches can be perturbation to structure and function, and fluorophores are prone to significant photobleaching. Thus, we have developed a novel super-resolution imaging technique which does not require the use of fluorescent labels, based on chemically-specific Raman imaging. We combine stimulated Raman microscopy with concepts from stimulated emission depletion microscopy to achieve label-free sub-diffraction imaging. This talk will cover the photophysical principles behind super-resolution Raman imaging, highlight the highest resolution achieved to date, and discuss biological applications of the technique, particularly with respect to imaging nanoscale cellular membrane dynamics.


Thursday, December 14th 2017
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Thursday, December 28th 2017
10:10 am:
Biophysics Seminar in 120 PAN
The seminar is done for the semester.

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