Oldenbourg
Rudolf
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Rudolf
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ArticleImage simulation for biological microscopy : microlith(Optical Society, 2014-05-13) Mehta, Shalin B. ; Oldenbourg, RudolfImage simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith (https://code.google.com/p/microlith), which accurately predicts three-dimensional images of a thin specimen observed with any partially coherent imaging system, as well as images of coherently illuminated and self-luminous incoherent specimens. Its accuracy is demonstrated by comparing simulated and experimental bright-field and dark-field images of well-characterized amplitude and phase targets, respectively. The comparison provides new insights about the sensitivity of the dark-field microscope to mass distributions in isolated or periodic specimens at the length-scale of 10nm. Based on predictions using microlith, we propose a novel approach for detecting nanoscale structural changes in a beating axoneme using a dark-field microscope.
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ArticleCytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments(eLife, 2017-11-06) Spira, Felix ; Cuylen-Haering, Sara ; Mehta, Shalin B. ; Samwer, Matthias ; Reversat, Anne ; Verma, Amitabh ; Oldenbourg, Rudolf ; Sixt, Michael ; Gerlich, Daniel W.The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.
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PreprintpH dependent isotropic to nematic phase transitions in graphene oxide dispersions reveal droplet liquid crystalline phases( 2014-05) Tkacz, Rachel ; Oldenbourg, Rudolf ; Mehta, Shalin B. ; Miansari, Morteza ; Verma, Amitabh ; Majumder, MainakSize fractionation, amplified by the surface charge density of graphene oxide (GO) sheets, broadens the pH dependent isotropic (I) to nematic (N) phase transition in aqueous dispersions of graphene oxide (GO). In this biphasic region, a highly organized droplet nematic phase of uniform size (20 ± 2.8 μm diameter) with an isotropic interior is observed.
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PreprintPolarized light microscopy in reproductive and developmental biology( 2013-05) Koike-Tani, Maki ; Tani, Tomomi ; Mehta, Shalin B. ; Verma, Amitabh ; Oldenbourg, RudolfThe polarized light microscope reveals orientational order in native molecular structures inside living cells, tissues, and whole organisms. Therefore, it is a powerful tool to monitor and analyze the early developmental stages of organisms that lend themselves to microscopic observations. In this article we briefly discuss the components specific to a traditional polarizing microscope and some historically important observations on chromosome packing in sperm head, first zygote division of the sea urchin, and differentiation initiated by the first uneven cell division in the sand dollar. We then introduce the LC-PolScope and describe its use for measuring birefringence and polarized fluorescence in living cells and tissues. Applications range from the enucleation of mouse oocytes to analyzing the polarized fluorescence of the water strider acrosome. We end by reporting first results on the birefringence of the developing chick brain, which we analyzed between developmental stages of days 12 through 20.
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ArticleSingle-fluorophore orientation determination with multiview polarized illumination : modeling and microscope design(Optical Society, 2017-12-01) Chandler, Talon ; Mehta, Shalin B. ; Shroff, Hari ; Oldenbourg, Rudolf ; La Riviere, Patrick J.We investigate the use of polarized illumination in multiview microscopes for determining the orientation of single-molecule fluorescence transition dipoles. First, we relate the orientation of single dipoles to measurable intensities in multiview microscopes and develop an information-theoretic metric—the solid-angle uncertainty—to compare the ability of multiview microscopes to estimate the orientation of single dipoles. Next, we compare a broad class of microscopes using this metric—single- and dual-view microscopes with varying illumination polarization, illumination numerical aperture (NA), detection NA, obliquity, asymmetry, and exposure. We find that multi-view microscopes can measure all dipole orientations, while the orientations measurable with single-view microscopes is halved because of symmetries in the detection process. We also find that choosing a small illumination NA and a large detection NA are good design choices, that multiview microscopes can benefit from oblique illumination and detection, and that asymmetric NA microscopes can benefit from exposure asymmetry.
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PreprintPolarized light imaging of birefringence and diattenuation at high resolution and high sensitivity( 2013-07) Mehta, Shalin B. ; Shribak, Michael ; Oldenbourg, RudolfPolarized light microscopy provides unique opportunities for analyzing the molecular order in manmade and natural materials, including biological structures inside living cells, tissues, and whole organisms. 20 years ago, the LC-PolScope was introduced as a modern version of the traditional polarizing microscope enhanced by liquid crystal devices for the control of polarization, and by electronic imaging and digital image processing for fast and comprehensive image acquisition and analysis. The LCPolScope is commonly used for birefringence imaging, analyzing the spatial and temporal variations of the differential phase delay in ordered and transparent materials. Here we describe an alternative use of the LC-PolScope for imaging the polarization dependent transmittance of dichroic materials. We explain the minor changes needed to convert the instrument between the two imaging modes, discuss the relationship between the quantities measured with either instrument, and touch on the physical connection between refractive index, birefringence, transmittance, diattenuation, and dichroism.
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ArticleDirection of actin flow dictates integrin LFA-1 orientation during leukocyte migration(Nature Publishing Group, 2017-12-11) Nordenfelt, Pontus ; Moore, Travis I. ; Mehta, Shalin B. ; Kalappurakkal, Joseph Mathew ; Swaminathan, Vinay ; Koga, Nobuyasu ; Lambert, Talley J. ; Baker, David ; Waters, Jennifer C. ; Oldenbourg, Rudolf ; Tani, Tomomi ; Mayor, Satyajit ; Waterman, Clare M. ; Springer, TimothyIntegrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here, we test whether the integrin, when engaged to an extracellular ligand and the cytoskeleton, adopts a specific orientation dictated by the direction of actin flow on the surface of migrating cells. We insert GFP into the rigid, ligand-binding head of the integrin, model with Rosetta the orientation of GFP and its transition dipole relative to the integrin head, and measure orientation with fluorescence polarization microscopy. Cytoskeleton and ligand-bound integrins orient in the same direction as retrograde actin flow with their cytoskeleton-binding β-subunits tilted by applied force. The measurements demonstrate that intracellular forces can orient cell surface integrins and support a molecular model of integrin activation by cytoskeletal force. Our results place atomic, Å-scale structures of cell surface receptors in the context of functional and cellular, μm-scale measurements.