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https://www.readbyqxmd.com/read/28654419/affimers-proteins-are-versatile-and-renewable-affinity-reagents
#1
Christian Tiede, Robert Bedford, Sophie J Heseltine, Gina Smith, Imeshi Wijetunga, Rebecca Ross, Danah AlQallaf, Ashley Pe Roberts, Alexander Balls, Alistair Curd, Ruth E Hughes, Heather Martin, Sarah R Needham, Laura C Zanetti-Domingues, Yashar Sadigh, Thomas P Peacock, Anna A Tang, Naomi Gibson, Hannah Kyle, Geoffrey W Platt, Nicola Ingram, Thomas Taylor, Louise P Coletta, Iain Manfield, Margaret Knowles, Sandra Bell, Filomena Esteves, Azhar Maqbool, Raj K Prasad, Mark Drinkhill, Robin S Bon, Vikesh Patel, Sarah A Goodchild, Marisa Martin-Fernandez, Ray J Owens, Joanne E Nettleship, Michael E Webb, Michael Harrison, Jonathan D Lippiat, Sreenivasan Ponnambalam, Michelle Peckham, Alastair Smith, Paul Ko Ferrigno, Matt Johnson, Michael J McPherson, Darren Charles Tomlinson
Molecular recognition reagents are key tools for understanding biological processes and are used universally by scientists to study protein expression, localisation and interactions. Antibodies remain the most widely used of such reagents and many show excellent performance, although some are poorly characterised or have stability or batch variability issues, supporting the use of alternative binding proteins as complementary reagents for many applications. Here we report on the use of Affimer proteins as research reagents...
June 27, 2017: ELife
https://www.readbyqxmd.com/read/28652597/defect-induced-local-variation-of-crystal-phase-transition-temperature-in-metal-halide-perovskites
#2
Alexander Dobrovolsky, Aboma Merdasa, Eva L Unger, Arkady Yartsev, Ivan G Scheblykin
Solution-processed organometal halide perovskites are hybrid crystalline semiconductors highly interesting for low-cost and efficient optoelectronics. Their properties are dependent on the crystal structure. Literature shows a variety of crystal phase transition temperatures and often a spread of the transition over tens of degrees Kelvin. We explain this inconsistency by demonstrating that the temperature of the tetragonal-to-orthorhombic phase transition in methylammonium lead triiodide depends on the concentration and nature of local defects...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28650478/a-dna-origami-platform-for-quantifying-protein-copy-number-in-super-resolution
#3
Francesca Cella Zanacchi, Carlo Manzo, Angel S Alvarez, Nathan D Derr, Maria F Garcia-Parajo, Melike Lakadamyali
Single-molecule-based super-resolution microscopy offers researchers a unique opportunity to quantify protein copy number with nanoscale resolution. However, while fluorescent proteins have been characterized for quantitative imaging using calibration standards, similar calibration tools for immunofluorescence with small organic fluorophores are lacking. Here we show that DNA origami, in combination with GFP antibodies, is a versatile platform for calibrating fluorophore and antibody labeling efficiency to quantify protein copy number in cellular contexts using super-resolution microscopy...
June 26, 2017: Nature Methods
https://www.readbyqxmd.com/read/28642595/3d-bayesian-cluster-analysis-of-super-resolution-data-reveals-lat-recruitment-to-the-t-cell-synapse
#4
Juliette Griffié, Leigh Shlomovich, David J Williamson, Michael Shannon, Jesse Aaron, Satya Khuon, Garth L Burn, Lies Boelen, Ruby Peters, Andrew P Cope, Edward A K Cohen, Patrick Rubin-Delanchy, Dylan M Owen
Single-molecule localisation microscopy (SMLM) allows the localisation of fluorophores with a precision of 10-30 nm, revealing the cell's nanoscale architecture at the molecular level. Recently, SMLM has been extended to 3D, providing a unique insight into cellular machinery. Although cluster analysis techniques have been developed for 2D SMLM data sets, few have been applied to 3D. This lack of quantification tools can be explained by the relative novelty of imaging techniques such as interferometric photo-activated localisation microscopy (iPALM)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641259/face-hallucination-using-linear-models-of-coupled-sparse-support
#5
Reuben A Farrugia, Christine Guillemot
Most face super-resolution methods assume that low- and high-resolution manifolds have similar local geometrical structure, hence learn local models on the low-resolution manifold (e.g. sparse or locally linear embedding models), which are then applied on the high- resolution manifold. However, the low-resolution manifold is distorted by the one-to-many relationship between low- and high- resolution patches. This paper presents the Linear Model of Coupled Sparse Support (LM-CSS) method which learns linear models based on the local geometrical structure on the high-resolution manifold rather than on the low-resolution manifold...
June 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28633193/trictide-a-tricellulin-derived-peptide-to-overcome-cellular-barriers
#6
Jimmi Cording, Basak Arslan, Christian Staat, Sophie Dithmer, Susanne M Krug, Anneliese Krüger, Philipp Berndt, Ramona Günther, Lars Winkler, Ingolf E Blasig, Reiner F Haseloff
The majority of tight junction (TJ) proteins restrict the paracellular permeation of solutes via their extracellular loops (ECLs). Tricellulin tightens tricellular TJs (tTJs) and regulates bicellular TJ (bTJ) proteins. We demonstrate that the addition of recombinantly produced extracellular loop 2 (ECL2) of tricellulin opens cellular barriers. The peptidomimetic trictide, a synthetic peptide derived from tricellulin ECL2, increases the passage of ions, as well as of small and larger molecules up to 10 kDa, between 16 and 30 h after application to human epithelial colorectal adenocarcinoma cell line 2...
June 20, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28628128/adaptive-optics-improves-multiphoton-super-resolution-imaging
#7
Wei Zheng, Yicong Wu, Peter Winter, Robert Fischer, Damian Dalle Nogare, Amy Hong, Chad McCormick, Ryan Christensen, William P Dempsey, Don B Arnold, Joshua Zimmerberg, Ajay Chitnis, James Sellers, Clare Waterman, Hari Shroff
We improve multiphoton structured illumination microscopy using a nonlinear guide star to determine optical aberrations and a deformable mirror to correct them. We demonstrate our method on bead phantoms, cells in collagen gels, nematode larvae and embryos, Drosophila brain, and zebrafish embryos. Peak intensity is increased (up to 40-fold) and resolution recovered (up to 176 ± 10 nm laterally, 729 ± 39 nm axially) at depths ∼250 μm from the coverslip surface.
June 19, 2017: Nature Methods
https://www.readbyqxmd.com/read/28627757/super-resolution-microscopy-and-single-protein-tracking-in-live-bacteria-using-a-genetically-encoded-photostable-fluoromodule
#8
Saumya Saurabh, Adam M Perez, Colin J Comerci, Lucy Shapiro, W E Moerner
Visualization of dynamic protein structures in live cells is crucial for understanding the mechanisms governing biological processes. Fluorescence microscopy is a sensitive tool for this purpose. In order to image proteins in live bacteria using fluorescence microscopy, one typically genetically fuses the protein of interest to a photostable fluorescent tag. Several labeling schemes are available to accomplish this. Particularly, hybrid tags that combine a fluorescent or fluorogenic dye with a genetically encoded protein (such as enzymatic labels) have been used successfully in multiple cell types...
June 19, 2017: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/28627515/lipid-mediated-px-bar-domain-recruitment-couples-local-membrane-constriction-to-endocytic-vesicle-fission
#9
Johannes Schöneberg, Martin Lehmann, Alexander Ullrich, York Posor, Wen-Ting Lo, Gregor Lichtner, Jan Schmoranzer, Volker Haucke, Frank Noé
Clathrin-mediated endocytosis (CME) involves membrane-associated scaffolds of the bin-amphiphysin-rvs (BAR) domain protein family as well as the GTPase dynamin, and is accompanied and perhaps triggered by changes in local lipid composition. How protein recruitment, scaffold assembly and membrane deformation is spatiotemporally controlled and coupled to fission is poorly understood. We show by computational modelling and super-resolution imaging that phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] synthesis within the clathrin-coated area of endocytic intermediates triggers selective recruitment of the PX-BAR domain protein SNX9, as a result of complex interactions of endocytic proteins competing for phospholipids...
June 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28626962/three-dimensional-motion-corrected-sensitivity-encoding-reconstruction-for-multi-shot-multi-slice-mri-application-to-neonatal-brain-imaging
#10
Lucilio Cordero-Grande, Emer J Hughes, Jana Hutter, Anthony N Price, Joseph V Hajnal
PURPOSE: To introduce a methodology for the reconstruction of multi-shot, multi-slice magnetic resonance imaging able to cope with both within-plane and through-plane rigid motion and to describe its application in structural brain imaging. THEORY AND METHODS: The method alternates between motion estimation and reconstruction using a common objective function for both. Estimates of three-dimensional motion states for each shot and slice are gradually refined by improving on the fit of current reconstructions to the partial k-space information from multiple coils...
June 19, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28623362/super-resolution-microscopy-with-very-large-working-distance-by-means-of-distributed-aperture-illumination
#11
Udo Birk, Johann V Hase, Christoph Cremer
The limits of conventional light microscopy ("Abbe-Limit") depend critically on the numerical aperture (NA) of the objective lens. Imaging at large working distances or a large field-of-view typically requires low NA objectives, thereby reducing the optical resolution to the multi micrometer range. Based on numerical simulations of the intensity field distribution, we present an illumination concept for a super-resolution microscope which allows a three dimensional (3D) optical resolution around 150 nm for working distances up to the centimeter regime...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28623289/3d-super-resolution-optical-profiling-using-microsphere-enhanced-mirau-interferometry
#12
Ivan Kassamakov, Sylvain Lecler, Anton Nolvi, Audrey Leong-Hoï, Paul Montgomery, Edward Hæggström
We present quantitative three dimensional images of grooves on a writable Blu-ray Disc based on a single objective Mirau type interferometric microscope, enhanced with a microsphere which is considered as a photonic nanojet source. Along the optical axis the resolution of this microsphere assisted interferometry system is a few nanometers while the lateral resolution is around 112 nm. To understand the physical phenomena involved in this kind of imaging we have modelled the interaction between the photonic jet and the complex disc surface...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28618637/actin-growth-profile-in-clathrin-mediated-endocytosis
#13
D J Tweten, P V Bayly, A E Carlsson
Clathrin-mediated endocytosis in yeast is driven by a protein patch containing close to 100 different types of proteins. Among the proteins are 5000-10000 copies of polymerized actin, and successful endocytosis requires growth of the actin network. Since it is not known exactly how actin network growth drives endocytosis, we calculate the spatial distribution of actin growth required to generate the force that drives the process. First, we establish the force distribution that must be supplied by actin growth, by combining membrane-bending profiles obtained via electron microscopy with established theories of membrane mechanics...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28614327/super-resolution-in-diffractive-imaging-from-hemispherical-elastic-light-scattering-data
#14
Sergiy Lysenko, Valeriy Sterligov, Manuel Gonçalves, Armando Rúa, Iaroslav Gritsayenko, Félix Fernández
Angle-resolved hemispherical elastic light scattering techniques have been used to reconstruct the surface profile of two-dimensional photonic crystals with submicron resolution and metrological precision. Iterative algorithms permit subsequent calculation of a surface autocorrelation function with additional numerical approximation of the power spectrum and then yield final reconstruction of the surface shape. The proposed method enables filtering out unwanted scattering background, precluding the convergence of phase-retrieval algorithms...
June 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28613416/topical-antimicrobial-agents-for-treating-foot-ulcers-in-people-with-diabetes
#15
REVIEW
Jo C Dumville, Benjamin A Lipsky, Christopher Hoey, Mario Cruciani, Marta Fiscon, Jun Xia
BACKGROUND: People with diabetes are at high risk for developing foot ulcers, which often become infected. These wounds, especially when infected, cause substantial morbidity. Wound treatments should aim to alleviate symptoms, promote healing, and avoid adverse outcomes, especially lower extremity amputation. Topical antimicrobial therapy has been used on diabetic foot ulcers, either as a treatment for clinically infected wounds, or to prevent infection in clinically uninfected wounds...
June 14, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28611954/super-resolution-imaging-of-protein-secretion-systems-and-the-cell-surface-of-gram-negative-bacteria
#16
REVIEW
Sachith D Gunasinghe, Chaille T Webb, Kirstin D Elgass, Iain D Hay, Trevor Lithgow
Gram-negative bacteria have a highly evolved cell wall with two membranes composed of complex arrays of integral and peripheral proteins, as well as phospholipids and glycolipids. In order to sense changes in, respond to, and exploit their environmental niches, bacteria rely on structures assembled into or onto the outer membrane. Protein secretion across the cell wall is a key process in virulence and other fundamental aspects of bacterial cell biology. The final stage of protein secretion in Gram-negative bacteria, translocation across the outer membrane, is energetically challenging so sophisticated nanomachines have evolved to meet this challenge...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28611663/epigenetic-modifications-to-h3k9-in-renal-tubulointerstitial-cells-after-unilateral-ureteric-obstruction-and-tgf-%C3%AE-1-stimulation
#17
Timothy D Hewitson, Stephen G Holt, Sven-Jean Tan, Belinda Wigg, Chrishan S Samuel, Edward R Smith
Introduction: Epigenetic regulation of fibrogenesis through post-translational histone modifications (marks) may be a key determinant of progression in renal disease. In this study, we examined the distribution and acquisition of histone 3 Lysine 9 (H3K9) marks after injury and stimulation with the pro-fibrotic cytokine TGF-β1. Our focus was on their presence in activated fibroblasts (myofibroblasts) and epithelial cells (epithelial-mesenchymal transition). Methods and Results: Immunofluorescent microscopy was used to examine global H3K9 acetylation (H3K9Ac) and tri-methylation (H3K9Me3) after unilateral ureteric obstruction (UUO) in mice...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28610423/introduction-super-resolution-and-single-molecule-imaging
#18
Julie Biteen, Katherine A Willets
No abstract text is available yet for this article.
June 14, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28604915/emergence-of-compositionally-tunable-nanoscale-dynamical-heterogeneity-in-model-binary-lipid-biomembranes
#19
Roobala C, Jaydeep K Basu
While the existence of nanoscale dynamical heterogeneity in biological membranes has been suggested to act as an active functional platform for enabling various cellular processes like signal transduction and viral or bacterial entry, it has been extremely difficult to detect the existence of such domains. Model lipid bilayer membranes have been widely used to detect such dynamical heterogeneity in order to avoid complications arising from the compositional heterogeneity of cellular membranes. However, even in model biological membranes the issue of nanoscale lipid dynamics has remained controversial and unresolved due to the difficulty of detecting the existence of such dynamical heterogeneity on the scale of 10-300 nm...
June 12, 2017: Soft Matter
https://www.readbyqxmd.com/read/28604675/identification-of-the-elementary-structural-units-of-the-dna-damage-response
#20
Francesco Natale, Alexander Rapp, Wei Yu, Andreas Maiser, Hartmann Harz, Annina Scholl, Stephan Grulich, Tobias Anton, David Hörl, Wei Chen, Marco Durante, Gisela Taucher-Scholz, Heinrich Leonhardt, M Cristina Cardoso
Histone H2AX phosphorylation is an early signalling event triggered by DNA double-strand breaks (DSBs). To elucidate the elementary units of phospho-H2AX-labelled chromatin, we integrate super-resolution microscopy of phospho-H2AX during DNA repair in human cells with genome-wide sequencing analyses. Here we identify phospho-H2AX chromatin domains in the nanometre range with median length of ∼75 kb. Correlation analysis with over 60 genomic features shows a time-dependent euchromatin-to-heterochromatin repair trend...
June 12, 2017: Nature Communications
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