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https://www.readbyqxmd.com/read/29907828/super-resolution-three-dimensional-fluorescence-and-optical-diffraction-tomography-of-live-cells-using-structured-illumination-generated-by-a-digital-micromirror-device
#1
Seungwoo Shin, Doyeon Kim, Kyoohyun Kim, YongKeun Park
We present a multimodal approach for measuring the three-dimensional (3D) refractive index (RI) and fluorescence distributions of live cells by combining optical diffraction tomography (ODT) and 3D structured illumination microscopy (SIM). A digital micromirror device is utilized to generate structured illumination patterns for both ODT and SIM, which enables fast and stable measurements. To verify its feasibility and applicability, the proposed method is used to measure the 3D RI distribution and 3D fluorescence image of various samples, including a cluster of fluorescent beads, and the time-lapse 3D RI dynamics of fluorescent beads inside a HeLa cell, from which the trajectory of the beads in the HeLa cell is analyzed using spatiotemporal correlations...
June 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29907794/optical-imaging-featuring-both-long-working-distance-and-high-spatial-resolution-by-correcting-the-aberration-of-a-large-aperture-lens
#2
Changsoon Choi, Kyung-Deok Song, Sungsam Kang, Jin-Sung Park, Wonshik Choi
High-resolution optical imaging within thick objects has been a challenging task due to the short working distance of conventional high numerical aperture (NA) objective lenses. Lenses with a large physical diameter and thus a large aperture, such as microscope condenser lenses, can feature both a large NA and a long working distance. However, such lenses suffer from strong aberrations. To overcome this problem, we present a method to correct the aberrations of a transmission-mode imaging system that is composed of two condensers...
June 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29907748/extracellular-nanovesicles-released-from-the-commensal-yeast-malassezia-sympodialis-are-enriched-in-allergens-and-interact-with-cells-in-human-skin
#3
Henrik J Johansson, Helen Vallhov, Tina Holm, Ulf Gehrmann, Anna Andersson, Catharina Johansson, Hans Blom, Marta Carroni, Janne Lehtiö, Annika Scheynius
Malassezia sympodialis is a dominant commensal fungi in the human skin mycobiome but is also associated with common skin disorders including atopic eczema (AE). M. sympodialis releases extracellular vesicles, designated MalaEx, which are carriers of small RNAs and allergens, and they can induce inflammatory cytokine responses. Here we explored how MalaEx are involved in host-microbe interactions by comparing protein content of MalaEx with that of the parental yeast cells, and by investigating interactions of MalaEx with cells in the skin...
June 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29905697/particle-tracking-by-repetitive-phase-shift-interferometric-super-resolution-microscopy
#4
Itay Gdor, Xiaolei Wang, Matthew Daddysman, Yuval Yifat, Rosemarie Wilton, Mark Hereld, Marie-Françoise Noirot-Gros, Norbert F Scherer
Accurate and rapid particle tracking is essential for addressing many research problems in single molecule and cellular biophysics and colloidal soft condensed matter physics. We developed a novel three-dimensional interferometric fluorescent particle tracking approach that does not require any sample scanning. By periodically shifting the interferometer phase, the information stored in the interference pattern of the emitted light allows localizing particles positions with nanometer resolution. This tracking protocol was demonstrated by measuring a known trajectory of a fluorescent bead with sub-5 nm axial localization error at 5 Hz...
June 15, 2018: Optics Letters
https://www.readbyqxmd.com/read/29905684/channeled-spatio-temporal-stokes-polarimeters
#5
Israel J Vaughn, Andrey S Alenin, J Scott Tyo
We present the analysis and design of spatio-temporal channeled Stokes polarimeters. We extend our recent work on optimal pixelated polarizer arrays by utilizing temporal carrier generation, resulting in polarimeters that achieve super-resolution via the tradeoff between spatial bandwidth and temporal bandwidth. Utilizing the channel space description, we present a linear-Stokes design and two full-Stokes imaging polarimeter designs that have the potential to operate at the full frame rate of the imaging sensor of the system by using hybrid spatio-temporal carriers...
June 15, 2018: Optics Letters
https://www.readbyqxmd.com/read/29900451/selective-suppression-of-cars-signal-with-three-beam-competing-stimulated-raman-scattering-processes
#6
Dae Sik Choi, B Jayachander Rao, Doyeon Kim, Sang-Hee Shim, Hanju Rhee, Minhaeng Cho
Coherent Raman scattering spectroscopy and microscopy are useful methods for studying the chemical and biological structures of molecules with Raman-active modes. In particular, coherent anti-Stokes Raman scattering (CARS) microscopy, which is a label-free method capable of imaging structures by displaying the vibrational contrast of the molecules, has been widely used. However, the lack of a technique for switching-off the CARS signal has prevented the development of the super-resolution Raman imaging method...
June 14, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29899348/super-resolution-network-analysis-defines-the-molecular-architecture-of-caveolae-and-caveolin-1-scaffolds
#7
Ismail M Khater, Fanrui Meng, Timothy H Wong, Ivan Robert Nabi, Ghassan Hamarneh
Quantitative approaches to analyze the large data sets generated by single molecule localization super-resolution microscopy (SMLM) are limited. We developed a computational pipeline and applied it to analyzing 3D point clouds of SMLM localizations (event lists) of the caveolar coat protein, caveolin-1 (Cav1), in prostate cancer cells differentially expressing CAVIN1 (also known as PTRF), that is also required for caveolae formation. High degree (strongly-interacting) points were removed by an iterative blink merging algorithm and Cav1 network properties were compared with randomly generated networks to retain a sub-network of geometric structures (or blobs)...
June 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29893574/nanoscale-spatio-temporal-diffusion-modes-measured-by-simultaneous-confocal-and-sted-imaging
#8
Falk Schneider, Dominic Waithe, Silvia Galiani, Jorge Bernardino de la Serna, Erdinc Sezgin, Christian Eggeling
The diffusion dynamics in the cellular plasma membrane provide crucial insights into molecular interactions, organization and bioactivity. Beam-scanning fluorescence correlation spectroscopy combined with super-resolution stimulated emission depletion nanoscopy (scanning STED-FCS) measures such dynamics with high spatial and temporal resolution. It reveals nanoscale diffusion characteristics by measuring the molecular diffusion in conventional confocal mode and super-resolved STED mode sequentially for each pixel along the scanned line...
June 12, 2018: Nano Letters
https://www.readbyqxmd.com/read/29892068/suppression-of-detyrosinated-microtubules-improves-cardiomyocyte-function-in-human-heart-failure
#9
Christina Yingxian Chen, Matthew A Caporizzo, Kenneth Bedi, Alexia Vite, Alexey I Bogush, Patrick Robison, Julie G Heffler, Alex K Salomon, Neil A Kelly, Apoorva Babu, Michael P Morley, Kenneth B Margulies, Benjamin L Prosser
Detyrosinated microtubules provide mechanical resistance that can impede the motion of contracting cardiomyocytes. However, the functional effects of microtubule detyrosination in heart failure or in human hearts have not previously been studied. Here, we utilize mass spectrometry and single-myocyte mechanical assays to characterize changes to the cardiomyocyte cytoskeleton and their functional consequences in human heart failure. Proteomic analysis of left ventricle tissue reveals a consistent upregulation and stabilization of intermediate filaments and microtubules in failing human hearts...
June 11, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29892029/infrared-spectroscopy-reveals-multi-step-multi-timescale-photoactivation-in-the-photoconvertible-protein-archetype-dronpa
#10
Sergey P Laptenok, Agnieszka A Gil, Christopher R Hall, Andras Lukacs, James N Iuliano, Garth A Jones, Gregory M Greetham, Paul Donaldson, Atsushi Miyawaki, Peter J Tonge, Stephen R Meech
Photochromic fluorescent proteins play key roles in super-resolution microscopy and optogenetics. The light-driven structural changes that modulate the fluorescence involve both trans-to-cis isomerization and proton transfer. The mechanism, timescale and relative contribution of chromophore and protein dynamics are currently not well understood. Here, the mechanism of off-to-on-state switching in dronpa is studied using femtosecond-to-millisecond time-resolved infrared spectroscopy and isotope labelling. Chromophore and protein dynamics are shown to occur on multiple timescales, from picoseconds to hundreds of microseconds...
June 11, 2018: Nature Chemistry
https://www.readbyqxmd.com/read/29892023/super-resolution-ct-image-reconstruction-based-on-dictionary-learning-and-sparse-representation
#11
Changhui Jiang, Qiyang Zhang, Rui Fan, Zhanli Hu
In this paper, a single-computed tomography (CT) image super-resolution (SR) reconstruction scheme is proposed. This SR reconstruction scheme is based on sparse representation theory and dictionary learning of low- and high-resolution image patch pairs to improve the poor quality of low-resolution CT images obtained in clinical practice using low-dose CT technology. The proposed strategy is based on the idea that image patches can be well represented by sparse coding of elements from an overcomplete dictionary...
June 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29889499/ultrashort-carbon-nanotubes-that-fluoresce-brightly-in-the-near-infrared
#12
Noémie Danne, Mijin Kim, Antoine G Godin, Hejin Kwon, Zhenghong Gao, Xiaojian Wu, Nicolai F Hartmann, Stephen K Doorn, Brahim Lounis, YuHuang Wang, Laurent Cognet
The intrinsic near-infrared photoluminescence observed in long single-walled carbon nanotubes is known to be quenched in ultrashort nanotubes due to their tiny size as compared to the exciton diffusion length in these materials (>100 nm). Here we show that intense photoluminescence can be created in ultrashort nanotubes (~40 nm length) upon incorporation of exciton-trapping sp3-defect sites. Using super-resolution photoluminescence imaging at <25 nm resolution, we directly show the preferential localization of excitons at the nanotube ends, which separate by less than 40 nm and behave as independent emitters...
June 11, 2018: ACS Nano
https://www.readbyqxmd.com/read/29888748/acoustical-structured-illumination-for-super-resolution-ultrasound-imaging
#13
Tali Ilovitsh, Asaf Ilovitsh, Josquin Foiret, Brett Z Fite, Katherine W Ferrara
Structured illumination microscopy is an optical method to increase the spatial resolution of wide-field fluorescence imaging beyond the diffraction limit by applying a spatially structured illumination light. Here, we extend this concept to facilitate super-resolution ultrasound imaging by manipulating the transmitted sound field to encode the high spatial frequencies into the observed image through aliasing. Post processing is applied to precisely shift the spectral components to their proper positions in k -space and effectively double the spatial resolution of the reconstructed image compared to one-way focusing...
2018: Communications biology
https://www.readbyqxmd.com/read/29888200/multimodal-light-microscopy-approaches-to-reveal-structural-and-functional-properties-of-promyelocytic-leukemia-nuclear-bodies
#14
REVIEW
Christian Hoischen, Shamci Monajembashi, Klaus Weisshart, Peter Hemmerich
The promyelocytic leukemia ( pml ) gene product PML is a tumor suppressor localized mainly in the nucleus of mammalian cells. In the cell nucleus, PML seeds the formation of macromolecular multiprotein complexes, known as PML nuclear bodies (PML NBs). While PML NBs have been implicated in many cellular functions including cell cycle regulation, survival and apoptosis their role as signaling hubs along major genome maintenance pathways emerged more clearly. However, despite extensive research over the past decades, the precise biochemical function of PML in these pathways is still elusive...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29884886/optimized-protocol-for-combined-palm-dstorm-imaging
#15
O Glushonkov, E Réal, E Boutant, Y Mély, P Didier
Multi-colour super-resolution localization microscopy is an efficient technique to study a variety of intracellular processes, including protein-protein interactions. This technique requires specific labels that display transition between fluorescent and non-fluorescent states under given conditions. For the most commonly used label types, photoactivatable fluorescent proteins and organic fluorophores, these conditions are different, making experiments that combine both labels difficult. Here, we demonstrate that changing the standard imaging buffer of thiols/oxygen scavenging system, used for organic fluorophores, to the commercial mounting medium Vectashield increased the number of photons emitted by the fluorescent protein mEos2 and enhanced the photoconversion rate between its green and red forms...
June 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29884197/super-resolution-fluorescence-microscopy-studies-of-human-immunodeficiency-virus
#16
REVIEW
Jakub Chojnacki, Christian Eggeling
Super-resolution fluorescence microscopy combines the ability to observe biological processes beyond the diffraction limit of conventional light microscopy with all advantages of the fluorescence readout such as labelling specificity and non-invasive live-cell imaging. Due to their subdiffraction size (< 200 nm) viruses are ideal candidates for super-resolution microscopy studies, and Human Immunodeficiency Virus type 1 (HIV-1) is to date the most studied virus by this technique. This review outlines principles of different super-resolution techniques as well as their advantages and disadvantages for virological studies, especially in the context of live-cell imaging applications...
June 8, 2018: Retrovirology
https://www.readbyqxmd.com/read/29883099/malic-acid-carbon-dots-from-super-resolution-live-cell-imaging-to-highly-efficient-separation
#17
Bo Zhi, Yi Cui, Shenyang Wang, Benjamin Frank, Denise N Williams, Richard Patrick Brown, Eric S Melby, Robert J Hamers, Zeev Rosenzweig, D Howard Fairbrother, Galya Orr, Christy L Haynes
As-synthesized malic acid carbon dots are found to possess unique and superior photoblinking properties compared to conventional dyes. Considering their excellent biocompatibility, malic acid carbon dots are suitable for super-resolution fluorescence localization microscopy under a variety of conditions, as we demonstrate in fixed and live trout gill epithelial cells. In addition, during imaging experiments, the so-called "excitation wavelength-dependent" emission was not observed for individual as-made malic acid carbon dots, which motivated us to develop a time-saving and high-throughput separation technique to isolate malic acid carbon dots into fractions of different particle size distributions using C18-reversed phase silica gel column chromatography...
June 8, 2018: ACS Nano
https://www.readbyqxmd.com/read/29878744/role-of-gln222-in-photoswitching-of-aequorea-fluorescent-proteins-a-twisting-and-h-bonding-affair
#18
Barbara Storti, Eleonora Margheritis, Gerardo Abbandonato, Giorgio Domenichini, Jes Dreier, Ilaria Testa, Gianpiero Garau, Riccardo Nifosì, Ranieri Bizzarri
Reversibly photoswitchable fluorescent proteins (RSFPs) admirably combine the genetic encoding of fluorescence with the ability to repeatedly toggle between a bright and dark state, adding a new temporal dimension to the fluorescence signal. Accordingly, in the last years RSFPs have paved the way to novel applications in cell imaging that rely on their reversible photoswitching, including many super-resolution techniques such as F-PALM, RESOLFT, and SOFI that provide nanoscale pictures of the living matter...
June 7, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29877348/two-photon-speckle-illumination-for-super-resolution-microscopy
#19
Awoke Negash, Simon Labouesse, Patrick C Chaumet, Kamal Belkebir, Hugues Giovannini, Marc Allain, Jérôme Idier, Anne Sentenac
We present a numerical study of a microscopy setup in which the sample is illuminated with uncontrolled speckle patterns and the two-photon excitation fluorescence is collected on a camera. We show that, using a simple deconvolution algorithm for processing the speckle low-resolution images, this wide-field imaging technique exhibits resolution significantly better than that of two-photon excitation scanning microscopy or one-photon excitation bright-field microscopy.
June 1, 2018: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/29874548/spectroscopic-analysis-beyond-the-diffraction-limit
#20
Biqin Dong, Janel L Davis, Cheng Sun, Hao F Zhang
The recent surge in spectroscopic Single-Molecule Localization Microscopy (sSMLM) offers exciting new capabilities for combining single molecule imaging and spectroscopic analysis. Through the synergistic integration of super-resolution optical microscopy and single-molecule spectroscopy, sSMLM offers combined strengths from both fields. By capturing the full spectra of single molecule fluorescent emissions, sSMLM can distinguish minute spectroscopic variations from individual fluorescent molecules while preserving nanoscopic spatial localization precision...
June 3, 2018: International Journal of Biochemistry & Cell Biology
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