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Super resolution

Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Christophe Leterrier, Jason Mercer, Ricardo Henriques
Super-resolution microscopy depends on steps that can contribute to the formation of image artifacts, leading to misinterpretation of biological information. We present NanoJ-SQUIRREL, an ImageJ-based analytical approach that provides quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolution equivalents of the same acquisition volume, this approach generates a quantitative map of super-resolution defects and can guide researchers in optimizing imaging parameters...
February 19, 2018: Nature Methods
Haifeng Yuan, Elke Debroye, Eva Bladt, Gang Lu, Masoumeh Keshavarz, Kris P F Janssen, Maarten B J Roeffaers, Sara Bals, Edward H Sargent, Johan Hofkens
Organic-inorganic halide perovskites (OIHPs) have demonstrated outstanding energy conversion efficiency in solar cells and light-emitting devices. In spite of intensive developments in both materials and devices, electronic traps and defects that significantly affect their device properties remain under-investigated. Particularly, it remains challenging to identify and to resolve traps individually at the nanoscopic scale. Here, photo-active traps (PATs) are mapped over OIHP nanocrystal morphology of different crystallinity by means of correlative optical differential super-resolution localization microscopy (Δ-SRLM) and electron microscopy...
February 19, 2018: Advanced Materials
Elvis Pandžić, Asmahan Abu-Arish, Renee W Whan, John W Hanrahan, Paul W Wiseman
Molecular, vesicular and organellar flows are of fundamental importance for the delivery of nutrients and essential components used in cellular functions such as motility and division. With recent advances in fluorescence/super-resolution microscopy modalities we can resolve the movements of these objects at higher spatio-temporal resolutions and with better sensitivity. Previously, spatio-temporal image correlation spectroscopy has been applied to map molecular flows by correlation analysis of fluorescence fluctuations in image series...
February 15, 2018: Methods: a Companion to Methods in Enzymology
Joshua S Titlow, Lu Yang, Richard M Parton, Ana Palanca, Ilan Davis
No abstract text is available yet for this article.
2018: Methods in Molecular Biology
Juan Carlos Polanco, Chuanzhou Li, Nela Durisic, Robert Sullivan, Jürgen Götz
In Alzheimer disease and related disorders, the microtubule-associated protein tau aggregates and forms cytoplasmic lesions that impair neuronal physiology at many levels. In addition to affecting the host neuron, tau aggregates also spread to neighboring, recipient cells where the misfolded tau aggregates, in a manner similar to prions, actively corrupt the proper folding of soluble tau, and thereby impair cellular functions. One vehicle for the transmission of tau aggregates are secretory nanovesicles known as exosomes...
February 15, 2018: Acta Neuropathologica Communications
Duc Nguyen, Joshua J Goings, Huy A Nguyen, Joseph Lyding, Xiaosong Li, Martin Gruebele
We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x 0 , y 0 ) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x 0 , y 0 ) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density φ i x 0 ,y 0 2 of the excited orbital in the tunneling region...
February 14, 2018: Journal of Chemical Physics
Guang Yang, Chao Liu, Shih-Hsun Chen, Muzaffer A Kassab, J Damon Hoff, Nils G Walter, Xiaochun Yu
DNA double-strand breaks (DSBs) are fatal DNA lesions and activate a rapid DNA damage response. However, the earliest stage of DSB sensing remains elusive. Here, we report that PARP1 and the Ku70/80 complex localize to DNA lesions considerably earlier than other DSB sensors. Using super-resolved fluorescent particle tracking, we further examine the relocation kinetics of PARP1 and the Ku70/80 complex to a single DSB, and find that PARP1 and the Ku70/80 complex are recruited to the DSB almost at the same time...
February 13, 2018: Nucleic Acids Research
Dane Taylor, Rajmonda S Caceres, Peter J Mucha
Applied network science often involves preprocessing network data before applying a network-analysis method, and there is typically a theoretical disconnect between these steps. For example, it is common to aggregate time-varying network data into windows prior to analysis, and the trade-offs of this preprocessing are not well understood. Focusing on the problem of detecting small communities in multilayer networks, we study the effects of layer aggregation by developing random-matrix theory for modularity matrices associated with layer-aggregated networks with N nodes and L layers, which are drawn from an ensemble of Erdős-Rényi networks with communities planted in subsets of layers...
July 2017: Physical Review. X
Nicolas Unsain, Martin D Bordenave, Gaby F Martinez, Jalil Sami, Catalina von Bilderling, Federico M Barabas, Luciano A Masullo, Aaron D Johnstone, Philip A Barker, Bisbal Mariano, Fernando D Stefani, Alfredo O Cáceres
Axonal degeneration occurs in the developing nervous system for the appropriate establishment of mature circuits, and is also a hallmark of diverse neurodegenerative diseases. Despite recent interest in the field, little is known about the changes (and possible role) of the cytoskeleton during axonal degeneration. We studied the actin cytoskeleton in an in vitro model of developmental pruning induced by trophic factor withdrawal (TFW). We found that F-actin decrease and growth cone collapse (GCC) occur early after TFW; however, treatments that prevent axonal fragmentation failed to prevent GCC, suggesting independent pathways...
February 14, 2018: Scientific Reports
Travis I Moore, Jesse Aaron, Teng-Leong Chew, Timothy A Springer
We use super-resolution interferometric photoactivation and localization microscopy (iPALM) and a constrained photoactivatable fluorescent protein integrin fusion to measure the displacement of the head of integrin lymphocyte function-associated 1 (LFA-1) resulting from integrin conformational change on the cell surface. We demonstrate that the distance of the LFA-1 head increases substantially between basal and ligand-engaged conformations, which can only be explained at the molecular level by integrin extension...
February 13, 2018: Cell Reports
Limin Zou, Su Zhang, Baokai Wang, Jiubin Tan
A new scheme of super-resolution optical fluctuation imaging (SOFI) is proposed to broaden its application in the high-order case by separating the elimination of shot noise from the computation of cumulant, applying the low-pass denoising (LPD) operator to SOFI. The high-order cumulants are derived from a basic recursion of moments with the suppression of shot noise by the LPD on raw data. SOFI based on LPD (LPD-SOFI) demonstrates a 10.6-fold lateral resolution enhancement with the cumulant order of the 16th and a seven-fold three-dimensional resolution enhancement with the cumulant order of the 10th in experiments performed on a sparse sample of quantum dots...
February 15, 2018: Optics Letters
Taehwang Son, Changhun Lee, Jinwon Seo, In-Hong Choi, Donghyun Kim
In this Letter, we describe spatially switched surface plasmon microscopy (ssSPM) based on two-channel momentum sampling. The performance evaluated with periodic nanowires in comparison with conventional SPM and bright-field microscopy shows that the resolution of ssSPM is enhanced by almost 15 times over conventional SPM. ssSPM provides an extremely simple way to attain diffraction limit in SPM and to go beyond for super-resolution in label-free microscopy techniques.
February 15, 2018: Optics Letters
Rui Yan, Seonah Moon, Samuel J Kenny, Ke Xu
As an elegant integration of the spatial and temporal dimensions of single-molecule fluorescence, single-molecule localization microscopy (SMLM) overcomes the diffraction-limited resolution barrier of optical microscopy by localizing single molecules that stochastically switch between fluorescent and dark states over time. While this type of super-resolution microscopy (SRM) technique readily achieves remarkable spatial resolutions of ∼10 nm, it typically provides no spectral information. Meanwhile, current scanning-based single-location approaches for mapping the positions and spectra of single molecules are limited by low throughput and are difficult to apply to densely labeled (bio)samples...
February 14, 2018: Accounts of Chemical Research
Michael Hausmann, Emma Wagner, Jin-Ho Lee, Gerrit Schrock, Wladimir Schaufler, Matthias Krufczik, Franziska Papenfuß, Matthias Port, Felix Bestvater, Harry Scherthan
Ionizing radiation (IR)-induced damage confers functional and conformational changes to nuclear chromatin associated with DNA single and double strand breaks. This leads to the activation of complex DNA repair machineries that aim to preserve the integrity of the DNA molecule. Since hetero- and euchromatin are differentially accessible to DNA repair pathways, local chromatin re-arrangements and structural changes are among the consequences of an activated DNA damage response. Using super-resolution localization microscopy (SRLM), we investigated the X-ray-induced repositioning of γ-H2AX and histone H3K9me3 heterochromatin marks in the nuclei of HeLa cells...
February 14, 2018: Nanoscale
Sascha Conic, Dominique Desplancq, Alexia Ferrand, Veronique Fischer, Vincent Heyer, Bernardo Reina San Martin, Julien Pontabry, Mustapha Oulad-Abdelghani, Kishore Babu N, Graham D Wright, Nacho Molina, Etienne Weiss, László Tora
Fluorescent labeling of endogenous proteins for live-cell imaging without exogenous expression of tagged proteins or genetic manipulations has not been routinely possible. We describe a simple versatile antibody-based imaging approach (VANIMA) for the precise localization and tracking of endogenous nuclear factors. Our protocol can be implemented in every laboratory allowing the efficient and nonharmful delivery of organic dye-conjugated antibodies, or antibody fragments, into different metazoan cell types...
February 12, 2018: Journal of Cell Biology
Jesse S Aaron, Aaron B Taylor, Teng-Leong Chew
Fluorescence image co-localization analysis is widely utilized to suggest biomolecular interaction. However, there exists some confusion as to its correct implementation and interpretation. In reality, co-localization analysis consists of at least two distinct sets of methods, termed co-occurrence and correlation. Each approach has inherent and often contrasting strengths and weaknesses. Yet, neither one can be considered to always be preferable for any given application. Rather, each method is most appropriate for answering different types of biological question...
February 8, 2018: Journal of Cell Science
Gergely Knorr, Eszter Kozma, Judith Schaart, Krisztina Németh, György Török, Peter Kele
The synthesis, fluorogenic characterization and labeling application of four tetrazine-quenched cyanine probes with emission maxima in the red - far red range is reported. Fluorescence of the cyanine-cores is quenched via through-bond-energy-transfer (TBET) exerted by a bioorthogonal tetrazine unit. Upon bioorthogonal labeling reaction with cyclooctyne tagged proteins, the quenching effect ceases, thus the fluorescence reinstates, resulting in an increase in fluorescence intensity. As a rare example amongst indocyanines, one of our new probes was found suitable in STED-based super-resolution imaging...
February 12, 2018: Bioconjugate Chemistry
Adam Taylor, René Verhoef, Michael Beuwer, Yuyang Wang, Peter Zijlstra
We demonstrate the all-optical reconstruction of gold nanoparticle geometry using super-resolution microscopy. We employ DNA-PAINT to get exquisite control over the (un)binding kinetics by the number of complementary bases and salt concentration, leading to localization accuracies of ∼5 nm. We employ a dye with an emission spectrum strongly blue-shifted from the plasmon resonance to minimize mislocalization due to plasmon-fluorophore coupling. We correlate the all-optical reconstructions with atomic force microscopy images and find that reconstructed dimensions deviate by no more than ∼10%...
February 1, 2018: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Jeroen Vangindertael, Rafael Camacho, Wouter Sempels, Hideaki Mizuno, Peter Dedecker, Kris Pieter Frans P F Janssen
Ever since the inception of light microscopy, the laws of physics have seemingly thwarted every attempt to visualize the processes of life at its most fundamental, sub- cellular, level. The diffraction limit has restricted our view to length scales well above 250 nm and in doing so, severely compromised our ability to gain true insights into many biological systems. Fortunately, continuous advancements in optics, electronics and mathematics have since provided the means to once again make physics work to our advantage...
February 9, 2018: Methods and Applications in Fluorescence
Ana Agostinho, Anna Kouznetsova, Abrahan Hernández-Hernández, Kristoffer Bernhem, Hans Blom, Hjalmar Brismar, Christer Höög
Sexual dimorphism has been used to describe morphological differences between the sexes, but can be extended to any biologically-related process that varies between males and females. The synaptonemal complex (SC) is a tripartite structure that connects homologous chromosomes in meiosis. Here, aided by super-resolution microscopy techniques, we show that the SC is subject to sexual dimorphism, in mouse germ cells. We have identified a significantly narrower SC width in oocytes and have established that this difference does not arise from a different organization of the lateral elements nor from a different isoform of transverse filament protein SYCP1...
February 2, 2018: Journal of Cell Science
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