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https://www.readbyqxmd.com/read/28346440/endocytic-proteins-are-partitioned-at-the-edge-of-the-clathrin-lattice-in-mammalian-cells
#1
Kem A Sochacki, Andrea M Dickey, Marie-Paule Strub, Justin W Taraska
Dozens of proteins capture, polymerize and reshape the clathrin lattice during clathrin-mediated endocytosis (CME). How or if this ensemble of proteins is organized in relation to the clathrin coat is unknown. Here, we map key molecules involved in CME at the nanoscale using correlative super-resolution light and transmission electron microscopy. We localize 19 different endocytic proteins (amphiphysin1, AP2, β2-arrestin, CALM, clathrin, DAB2, dynamin2, EPS15, epsin1, epsin2, FCHO2, HIP1R, intersectin, NECAP, SNX9, stonin2, syndapin2, transferrin receptor, VAMP2) on thousands of individual clathrin structures, generating a comprehensive molecular architecture of endocytosis with nanoscale precision...
March 27, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28335497/ginsenoside-ppd-s-antitumor-effect-via-down-regulation-of-mtor-revealed-by-super-resolution-imaging
#2
Bo Teng, Junguang Jiang, Lijing Zhao, Jing Gao, Junyu Chen, Zhe Liu, Hongda Wang, Binfeng Lu
Derived from Panax ginseng, the natural product 20(S)-Protopanaxadiol (PPD) has been reported for its cytotoxicity against several cancer cell lines. The molecular mechanism is, however, not well understood. Here we show that PPD significantly inhibits proliferation, induces apoptosis and causes G2/M cell cycle arrest in human laryngeal carcinoma cells (Hep-2 cells). PPD also decreases the levels of proteins related to cell proliferation. Moreover, PPD-induced apoptosis is characterized by a dose-dependent down-regulation of Bcl-2 expression and up-regulation of Bax, and is accompanied by the activation of Caspase-3 as well...
March 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335482/improved-wallis-dodging-algorithm-for-large-scale-super-resolution-reconstruction-remote-sensing-images
#3
Chong Fan, Xushuai Chen, Lei Zhong, Min Zhou, Yun Shi, Yulin Duan
A sub-block algorithm is usually applied in the super-resolution (SR) reconstruction of images because of limitations in computer memory. However, the sub-block SR images can hardly achieve a seamless image mosaicking because of the uneven distribution of brightness and contrast among these sub-blocks. An effectively improved weighted Wallis dodging algorithm is proposed, aiming at the characteristic that SR reconstructed images are gray images with the same size and overlapping region. This algorithm can achieve consistency of image brightness and contrast...
March 18, 2017: Sensors
https://www.readbyqxmd.com/read/28335211/noise-removal-with-maintained-spatial-resolution-in-raman-images-of-cells-exposed-to-submicron-polystyrene-particles
#4
Linnea Ahlinder, Susanne Wiklund Lindström, Christian Lejon, Paul Geladi, Lars Österlund
The biodistribution of 300 nm polystyrene particles in A549 lung epithelial cells has been studied with confocal Raman spectroscopy. This is a label-free method in which particles and cells can be imaged without using dyes or fluorescent labels. The main drawback with Raman imaging is the comparatively low spatial resolution, which is aggravated in heterogeneous systems such as biological samples, which in addition often require long measurement times because of their weak Raman signal. Long measurement times may however induce laser-induced damage...
April 29, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28333635/blind-facial-image-quality-enhancement-using-non-rigid-semantic-patches
#5
Ester Hait, Guy Gilboa
We propose a new way to solve a very general blind inverse problem of multiple simultaneous degradations such as blur, resolution reduction, noise and contrast changes, without explicitly estimating the degradation. The proposed concept is based on combining semantic non-rigid patches, problem-specific high quality prior data and non-rigid registration tools. We show how a significant quality enhancement can be achieved, both visually and quantitatively, in the case of facial images. The method is demonstrated on the problem of cellular photography quality enhancement of dark facial images for different identities, expressions and poses, and is compared to state-of-the-art denoising, deblurring, super-resolution and colorcorrection methods...
March 22, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28333166/effect-of-probe-diffusion-on-the-sofi-imaging-accuracy
#6
Wim Vandenberg, Peter Dedecker
Live-cell super-resolution fluorescence imaging is becoming commonplace for exploring biological systems, though sample dynamics can affect the imaging quality. In this work we evaluate the effect of probe diffusion on super-resolution optical fluctuation imaging (SOFI), using a theoretical model and numerical simulations based on the imaging of live cells labelled with photochromic fluorescent proteins. We find that, over a range of physiological conditions, fluorophore diffusion results in a change in the amplitude of the SOFI signal...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28332832/serpentine-ultra-long-path-with-extended-routing-super-high-resolution-traveling-wave-ion-mobility-ms-using-structures-for-lossless-ion-manipulations
#7
Liulin Deng, Ian K Webb, Sandilya V B Garimella, Ahmed M Hamid, Xueyun Zheng, Randolph V Norheim, Spencer A Prost, Gordon A Anderson, Jeremy A Sandoval, Erin Shammel Baker, Yehia M Ibrahim, Richard D Smith
Ion mobility (IM) separations have a broad range of analytical applications, but insufficient resolution limits many applications. Here we report on ion mobility separations in a Structures for Lossless Ion Manipulations (SLIM) Serpentine Ultra-long Path with Extended Routing (SUPER) traveling wave (TW) ion mobility (IM) module in conjunction with mass spectrometry (MS). Ions were confined in the SLIM by rf fields in conjunction with a DC guard bias, enabling essentially lossless TW transmission over greatly extended paths...
March 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28330620/mad2l2-promotes-open-chromatin-in-embryonic-stem-cells-and%C3%A2-derepresses-the-dppa3-locus
#8
Ali Rahjouei, Mehdi Pirouz, Michela Di Virgilio, Dirk Kamin, Michael Kessel
The chromatin of naive embryonic stem cells (ESCs) has a largely open configuration, as evident by the lack of condensed heterochromatin and the hypomethylation of DNA. Several molecular mechanisms promoting this constellation were previously identified. Here we present evidence for an important epigenetic function of MAD2L2, a protein originally known for its role in DNA damage repair, and for its requirement in germ cell development. We demonstrate using super-resolution microscopy that numerous MAD2L2 microfoci are exclusively associated with euchromatin, similar to other factors of the DNA damage response...
March 10, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28330019/facial-nerve-tractography-a-new-tool-to-detect-perineural-invasion-in-parotid-cancers
#9
René-Charles Rouchy, Arnaud Attyé, Irène Troprès, Maud Medici, Adrian Kastler, Christian Righini, Alexandre Krainik
PURPOSE: To determine whether magnetic resonance (MR) tractography of facial nerve (VIIn) is useful to detect perineural invasion in case of parotid cancers. MATERIALS AND METHODS: Thirty patients, aged 18 or over, were enrolled in this prospective study between December 2013 and March 2016 (IRB 5891), with a diagnosis of parotid tumors (15 malignant, 15 benign). They have undergone preoperative MR scans (3.0-T) before surgical management. The parameters of the diffusion-weighted (DW) sequence were b-value of 1000s/mm(2); 32 directions; voxel size: 2mm isotropic; scan time: 9' The post-processing generates whole-neck constrained spherical deconvolution (CSD)-based tractography data and super-resolution track-weighted imaging (TWI) technique...
March 2017: Journal of Neuroradiology. Journal de Neuroradiologie
https://www.readbyqxmd.com/read/28328539/polarization-sensitive-localization-based-super-resolution-microscopy-with-a-birefringent-wedge
#10
József Sinkó, Tamás Gajdos, Elvira Czvik, Gábor Szabó, Miklós Erdélyi
A practical method has been presented for polarization sensitive localization based super-resolution microscopy using a birefringent dual wedge. The measurement of the polarization degree at the single molecule level can reveal the chemical and physical properties of the local environment of the fluorescent dye molecule and can hence provide information about the sub-diffraction sized structure of biological samples. Polarization sensitive STORM imaging of the F-Actins proved correlation between the orientation of fluorescent dipoles and the axis of the fibril...
March 22, 2017: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28328071/investigation-of-c3-s-hydration-mechanism-by-transmission-electron-microscope-tem-with-integrated-super-x-tm-eds-system
#11
Y Sakalli, R Trettin
Tricalciumsilicate (C3 S, Alite) is the major component of the Portland cement clinker. Hydration of Alite is decisive in influencing the properties of the resulting material. This is due to its high content in cement. The mechanism of the hydration of C3 S is very complicated and not yet fully understood. There are different models describing the hydration of C3 S in various ways. In this work for a better understanding of hydration mechanism, the hydrated C3 S was investigated by using the transmission electron microscope (TEM) and for the first time, the samples for the investigations were prepared by using of focused ion beam from sintered pellets of C3 S...
March 22, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28324607/sted-imaging-in-drosophila-brain-slices
#12
Sandra Fendl, Jesús Pujol-Martí, Joel Ryan, Alexander Borst, Robert Kasper
Super-resolution microscopy is a very powerful tool to investigate fine cellular structures and molecular arrangements in biological systems. For instance, stimulated emission depletion (STED) microscopy has been successfully used in recent years to investigate the arrangement and colocalization of different protein species in cells in culture and on the surface of specimens. However, because of its extreme sensitivity to light scattering, super-resolution imaging deep inside tissues remains a challenge. Here, we describe the preparation of thin slices from the fruit fly (Drosophila melanogaster) brain, subsequent immunolabeling and imaging with STED microscopy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324598/introduction-to-modern-methods-in-light-microscopy
#13
Joel Ryan, Abby R Gerhold, Vincent Boudreau, Lydia Smith, Paul S Maddox
For centuries, light microscopy has been a key method in biological research, from the early work of Robert Hooke describing biological organisms as cells, to the latest in live-cell and single-molecule systems. Here, we introduce some of the key concepts related to the development and implementation of modern microscopy techniques. We briefly discuss the basics of optics in the microscope, super-resolution imaging, quantitative image analysis, live-cell imaging, and provide an outlook on active research areas pertaining to light microscopy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28323277/an-alternative-polysaccharide-uptake-mechanism-of-marine-bacteria
#14
Greta Reintjes, Carol Arnosti, Bernhard M Fuchs, Rudolf Amann
Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered-using super-resolution structured illumination microscopy-that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS)...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28320682/deformable-registration-based-super-resolution-for-isotropic-reconstruction-of-4d-mri-volumes
#15
Geetha Soujanya Chilla, Cher Heng Tan, Chueh Loo Poh
Multi-plane super-resolution (SR) has been widely employed for resolution improvement of MR images. However, this has mostly been limited to MRI acquisitions with rigid motion. In cases of non-rigid motion, volumes are usually pre-registered using deformable registration methods before SR reconstruction. The pre-registered images are then used as input for the SR reconstruction. Since deformable registration involves smoothening of the inputs, using pre-registered inputs could lead to loss in information in SR reconstructions...
March 13, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28319616/dna-probes-for-monitoring-dynamic-and-transient-molecular-encounters-on-live-cell-membranes
#16
Mingxu You, Yifan Lyu, Da Han, Liping Qiu, Qiaoling Liu, Tao Chen, Cuichen Sam Wu, Lu Peng, Liqin Zhang, Gang Bao, Weihong Tan
Cells interact with the extracellular environment through molecules expressed on the membrane. Disruption of these membrane-bound interactions (or encounters) can result in disease progression. Advances in super-resolution microscopy have allowed membrane encounters to be examined, however, these methods cannot image entire membranes and cannot provide information on the dynamic interactions between membrane-bound molecules. Here, we show a novel DNA probe that can transduce transient membrane encounter events into readable cumulative fluorescence signals...
March 20, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28317930/achromatic-light-patterning-and-improved-image-reconstruction-for-parallelized-resolft-nanoscopy
#17
Andriy Chmyrov, Marcel Leutenegger, Tim Grotjohann, Andreas Schönle, Jan Keller-Findeisen, Lars Kastrup, Stefan Jakobs, Gerald Donnert, Steffen J Sahl, Stefan W Hell
Fluorescence microscopy is rapidly turning into nanoscopy. Among the various nanoscopy methods, the STED/RESOLFT super-resolution family has recently been expanded to image even large fields of view within a few seconds. This advance relies on using light patterns featuring substantial arrays of intensity minima for discerning features by switching their fluorophores between 'on' and 'off' states of fluorescence. Here we show that splitting the light with a grating and recombining it in the focal plane of the objective lens renders arrays of minima with wavelength-independent periodicity...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28315485/quantifying-transcription-factor-binding-dynamics-at-the-single-molecule-level-in-live-cells
#18
Diego M Presman, David A Ball, Ville Paakinaho, Jonathan B Grimm, Luke D Lavis, Tatiana S Karpova, Gordon L Hager
Progressive, technological achievements in the quantitative fluorescence microscopy field are allowing researches from many different areas to start unraveling the dynamic intricacies of biological processes inside living cells. From super-resolution microscopy techniques to tracking of individual proteins, fluorescence microscopy is changing our perspective on how the cell works. Fortunately, a growing number of research groups are exploring single-molecule studies in living cells. However, no clear consensus exists on several key aspects of the technique such as image acquisition conditions, or analysis of the obtained data...
March 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28306243/optical-super-resolution-imaging-of-surface-reactions
#19
Tao Chen, Bin Dong, Kuangcai Chen, Fei Zhao, Xiaodong Cheng, Changbei Ma, Seungah Lee, Peng Zhang, Seong Ho Kang, Ji Won Ha, Weilin Xu, Ning Fang
Optical super-resolution imaging has gained momentum in investigations of heterogeneous and homogeneous chemical reactions at the single-molecule level. Thanks to its exceptional spatial resolution and ability to monitor dynamic systems, much detailed information on single-molecule reaction/adsorption processes and single-particle catalytic processes has been revealed, including chemical kinetics and reaction dynamics; active-site distributions on single-particle surfaces; and size-, shape-, and facet-dependent catalytic activities of individual nanocatalysts...
March 17, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28303936/all-passive-pixel-super-resolution-of-time-stretch-imaging
#20
Antony C S Chan, Ho-Cheung Ng, Sharat C V Bogaraju, Hayden K H So, Edmund Y Lam, Kevin K Tsia
Based on image encoding in a serial-temporal format, optical time-stretch imaging entails a stringent requirement of state-of-the-art fast data acquisition unit in order to preserve high image resolution at an ultrahigh frame rate - hampering the widespread utilities of such technology. Here, we propose a pixel super-resolution (pixel-SR) technique tailored for time-stretch imaging that preserves pixel resolution at a relaxed sampling rate. It harnesses the subpixel shifts between image frames inherently introduced by asynchronous digital sampling of the continuous time-stretch imaging process...
March 17, 2017: Scientific Reports
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