Biology subjects

Shaw, T. R.

Publications and source records attributed to Shaw, T. R..

5 recordsLinked to original sources

bioRxiv2023

TorsinA is essential for the timing and localization of neuronal nuclear pore complex biogenesis

Nuclear pore complexes (NPCs) regulate information transfer between the nucleus and cytoplasm. NPC defects are linked to several neurological diseases, but the processes governing NPC biogenesis and spatial organization are poorly understood. Here, we identify a temporal window of strongly upregulated NPC biogenesis during neuronal maturation. We demonstrate that the AAA+ protein torsinA, whose loss of function causes the neurodevelopmental movement disorder DYT-TOR1A (DYT1) dystonia, coordinates NPC spatial organization during this period without impacting total NPC density. Using a new mouse line in which endogenous Nup107 is Halo-Tagged, we find that torsinA is essential for correct localization of NPC formation. In the absence of torsinA, the inner nuclear membrane buds excessively at sites of mislocalized, nascent NPCs, and NPC assembly completion is delayed. Our work implies that NPC spatial organization and number are independently regulated and suggests that torsinA is critical for the normal localization and assembly kinetics of NPCs.

cell biology↗

bioRxiv2022

Measuring the co-localization and dynamics of mobile proteins in live cells undergoing signaling responses

ii.Summary/AbstractSingle molecule imaging in live cells enables the study of protein interactions and dynamics as they participate in signaling processes. When combined with fluorophores that stochastically transition between fluorescent and reversible dark states, as in super-resolution localization imaging, labeled molecules can be visualized in single cells over time. This improvement in sampling enables the study of extended cellular responses at the resolution of single molecule localization. This chapter provides optimized experimental and analytical methods used to quantify protein interactions and dynamics within the membranes of adhered live cells. Importantly, the use of pair-correlation functions resolved in both space and time allows researchers to probe interactions between proteins on biologically relevant distance and time-scales, even though fluorescence localization methods typically require long times to assemble well-sampled reconstructed images. We describe an application of this approach to measure protein interactions in B cell receptor signaling and include sample analysis code for post-processing of imaging data. These methods are quantitative, sensitive, and broadly applicable to a range of signaling systems.

biophysics↗

bioRxiv2022

Chemical potential measurements constrain models of cholesterol-phosphatidylcholine interactions

Bilayer membranes composed of cholesterol and phospholipids exhibit diverse forms of non-ideal mixing. In particular, many previous studies document macroscopic liquid-liquid phase separation as well as nanometer-scale heterogeneity in membranes of phosphatidylcholine (PC) lipids and cholesterol. Here, we present experimental measurements of cholesterol chemical potential (c) in binary membranes containing dioleoyl PC (DOPC), 1-palmitoyl-2-oleoyl PC (POPC), or dipalmitoyl PC (DPPC), and in ternary membranes of DOPC and DPPC, adapting a calibrated experimental protocol developed to measure c in cells (Ayuyan and Cohen, Biophys. J. 114:904-918). c is the thermodynamic quantity that dictates the availability of cholesterol to bind other factors, and notably must be equal between coexisting phases of a phase-separated mixture. It is simply related to concentration under conditions of ideal mixing but is found to be far from ideal for the majority of lipid mixtures investigated. Here we perform experimental measurements of c, constraining thermodynamic models of membrane interactions. Our measurements are consistent with models involving cholesterol-phospholipid complexes, but only if complexes are more weakly bound than has been assumed in previous reports. Experimental measurements are also well described by regular solution theory and lattice models with pairwise interactions between components. We find that c can vary by ~1.5 kBT at constant cholesterol mole-fraction implying a more than five-fold change in its availability for binding receptors and other reactions. These findings reinforce that c depends on membrane composition overall, suggesting avenues for cells to alter the availability of cholesterol without varying cholesterol concentration. SIGNIFICANCEThe chemical potential of cholesterol (c) reflects its availability to interact with other molecules. In a complex mixtures this chemical potential can vary dramatically even at fixed cholesterol concentration. In this report, we present measurements of c in bilayer membranes composed of mixtures of cholesterol with one or two phospholipids. We find that c in these mixtures depends strongly on the phospholipids that are present, with activity varying by a factor of more than five at fixed cholesterol concentration. This suggests that the availability of cholesterol in biological membranes could be tuned without altering cholesterol concentration directly, by adjusting the concentration of other lipid or protein components.

biophysics↗

bioRxiv2022

A method to estimate the effective point spread function of static single molecule localization microscopy images

Single molecule localization microscopy (SMLM) permits the visualization of cellular structures an order of magnitude smaller than the diffraction limit of visible light, and an accurate, objective evaluation of the resolution of an SMLM dataset is an essential aspect of the image processing and analysis pipeline. Here we present a simple method that uses the pair autocorrelation function evaluated both in space and time to measure the time-interval dependent effective point spread function of SMLM images of static samples. Using this approach, we demonstrate that experimentally obtained images typically have effective point spread functions that are broader than expected from the localization precision alone, due to additional uncertainty arising from factors such as drift and drift correction algorithms. The method is demonstrated on simulated localizations, DNA origami rulers, and cellular structures labelled by dye-conjugated antibodies, DNA-PAINT, or fluorescent fusion proteins. STATEMENT OF SIGNIFICANCESingle molecule localization microscopy (SMLM) is a class of imaging methods that resolve fluorescently labeled structures beyond the optical resolution limit of visible light. SMLM detects stochastically blinking labels over time, and localizes each blink with precision of order 10 nm. The effective resolution depends on factors such as signal-to-noise ratio, localization algorithm, and several post-processing steps such as stage drift correction. We present a method to evaluate this effective resolution by taking advantage of temporal correlations of fluorophore blinking to separate the distribution of pairs of localizations from the same molecule from those from different molecules. The method is robust on useful timescales for a range of SMLM probes.

biophysics↗

bioRxiv2021

A Mean Shift Algorithm for Drift Correction in Localization Microscopy

Single molecule localization microscopy (SMLM) techniques transcend the diffraction limit of visible light by localizing isolated emitters sampled stochastically. This time-lapse imaging necessitates long acquisition times, over which sample drift can become large relative to the localization precision. Here we present a novel, efficient, and robust method for estimating drift using a simple peak-finding algorithm based on mean shifts that is effective for SMLM in 2 or 3 dimensions.

biophysics↗