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https://www.readbyqxmd.com/read/28530747/bioorthogonal-double-fluorogenic-siliconrhodamine-probes-for-intracellular-super-resolution-microscopy
#1
E Kozma, G Estrada Girona, G Paci, E A Lemke, P Kele
A series of double-fluorogenic siliconrhodamine probes were synthesized. These tetrazine-functionalized, membrane-permeable labels allowed site-specific bioorthogonal tagging of genetically manipulated intracellular proteins and subsequent imaging using super-resolution microscopy.
May 22, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28528641/preserving-the-photoswitching-ability-of-standard-fluorescent-proteins-for-correlative-in-resin-super-resolution-and-electron-microscopy
#2
Errin Johnson, Rainer Kaufmann
There are many different correlative light and electron microscopy (CLEM) techniques available. The use of super-resolution microscopy in CLEM is an emerging application and while offering the obvious advantages of improved resolution in the fluorescence image, and therefore more precise correlation to electron microscopy (EM) ultrastructure, it also presents new challenges. Choice of fluorophore, method of fixation, and timing of the fluorescence imaging are critical to the success of super-resolution CLEM and the relative importance, and technical difficulty, of each of these factors depends on the type of super-resolution microscopy being employed...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28527435/gauge-invariant-theory-for-super-high-resolution-raman-images
#3
Sai Duan, Guangjun Tian, Zhen Xie, Yi Luo
The use of a highly localized plasmonic field has enabled us to achieve sub-nanometer resolution of Raman images for single molecules. The inhomogeneous spatial distribution of plasmonic field has become an important factor that controls the interaction between the light and the molecule. We present here a gauge invariant interaction Hamiltonian (GIIH) to take into account the non-uniformity of the electromagnetic field distribution in the non-relativistic regime. The theory has been implemented for both resonant and nonresonant Raman processes within the sum-over-state framework...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28526726/are-phloem-sieve-tubes-leaky-conduits-supported-by-numerous-aquaporins
#4
Ryan C Stanfield, Uwe G Hacke, Joan Laur
PREMISE OF THE STUDY: Aquaporin membrane water channels have been previously identified in the phloem of angiosperms, but currently their cellular characterization is lacking, especially in tree species. Pinpointing the cellular location will help generate new hypotheses of how membrane water exchange facilitates sugar transport in plants. METHODS: We studied histological sections of balsam poplar (Populus balsamifera L.) in leaf, petiole, and stem organs. Immuno-labeling techniques were used to characterize the distribution of PIP1 and PIP2 subfamilies of aquaporins along the phloem pathway...
May 19, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28518172/super-resolution-microscopy-with-dna-paint
#5
Joerg Schnitzbauer, Maximilian T Strauss, Thomas Schlichthaerle, Florian Schueder, Ralf Jungmann
Super-resolution techniques have begun to transform biological and biomedical research by allowing researchers to observe structures well below the classic diffraction limit of light. DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) offers an easy-to-implement approach to localization-based super-resolution microscopy, owing to the use of DNA probes. In DNA-PAINT, transient binding of short dye-labeled ('imager') oligonucleotides to their complementary target ('docking') strands creates the necessary 'blinking' to enable stochastic super-resolution microscopy...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28515232/the-nuclear-export-factor-crm1-controls-juxta-nuclear-microtubule-dependent-virus-transport
#6
I-Hsuan Wang, Christoph J Burckhardt, Artur Yakimovich, Matthias K Morf, Urs F Greber
Transport of large cargo through the cytoplasm requires motor proteins and polarized filaments. Viruses that replicate in the nucleus of post-mitotic cells use microtubules and the dynein/dynactin motor to traffic to the nuclear membrane, and deliver their genome through nuclear pore complexes (NPCs) into the nucleus. How virus particles (virions) or cellular cargo are transferred from microtubules to the NPC is unknown. Here, we analyzed trafficking of incoming cytoplasmic adenoviruses by single particle tracking and super-resolution microscopy...
May 17, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28515075/pigr-and-pecam-1-bind-to-pneumococcal-adhesins-rrga-and-pspc-mediating-bacterial-brain-invasion
#7
Federico Iovino, Joo-Yeon Engelen-Lee, Matthijs Brouwer, Diederik van de Beek, Arie van der Ende, Merche Valls Seron, Peter Mellroth, Sandra Muschiol, Jan Bergstrand, Jerker Widengren, Birgitta Henriques-Normark
Streptococcus pneumoniae is the main cause of bacterial meningitis, a life-threating disease with a high case fatality rate despite treatment with antibiotics. Pneumococci cause meningitis by invading the blood and penetrating the blood-brain barrier (BBB). Using stimulated emission depletion (STED) super-resolution microscopy of brain biopsies from patients who died of pneumococcal meningitis, we observe that pneumococci colocalize with the two BBB endothelial receptors: polymeric immunoglobulin receptor (pIgR) and platelet endothelial cell adhesion molecule (PECAM-1)...
May 17, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28514494/covalent-protein-labeling-by-spytag-spycatcher-in-fixed-cells-for-super-resolution-microscopy
#8
Veronica Pessino, Yemima Rose Citron, Siyu Feng, Bo Huang
Labeling proteins with high specificity and efficiency is a fundamental prerequisite for microscopic visualization of subcellular protein structures and interactions. While the comparatively small size of epitope tags makes them less perturbative to fusion proteins, they require the use of large antibodies that often limit probe accessibility and effective resolution. Here we use the covalent SpyTag-SpyCatcher system as an epitope-like tag for fluorescent labeling of intracellular proteins in fixed cells for both conventional and super-resolution microscopy...
May 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28513246/molecular-composition-and-distribution-of-gap-junctions-in-the-sensory-epithelium-of-the-human-cochlea-a-super-resolution-structured-illumination-microscopy-sr-sim-study
#9
Wei Liu, Hao Li, Fredrik Edin, Johan Brännström, Rudolf Glueckert, Annelies Schrott-Fischer, Matyas Molnar, Dirk Pacholsky, Kristian Pfaller, Helge Rask-Andersen
BACKGROUND: Mutations in the GJB2 gene, which encodes the Connexin26 (Cx26) protein, are the most common cause of childhood hearing loss in American and European populations. The cochlea contains a gap junction (GJ) network in the sensory epithelium and two connective tissue networks in the lateral wall and spiral limbus. The syncytia contain the GJ proteins beta 2 (GJB2/Cx26) and beta 6 (GJB6/Cx30). Our knowledge of their expression in humans is insufficient due to the limited availability of tissue...
May 17, 2017: Upsala Journal of Medical Sciences
https://www.readbyqxmd.com/read/28512458/a-mitochondrial-autonomously-replicating-sequence-from-pichia-pastoris-for-uniform-high-level-recombinant-protein-production
#10
Jan-Philipp Schwarzhans, Tobias Luttermann, Daniel Wibberg, Anika Winkler, Wolfgang Hübner, Thomas Huser, Jörn Kalinowski, Karl Friehs
Pichia pastoris is a non-conventional methylotrophic yeast that is widely used for recombinant protein production, typically by stably integrating the target gene into the genome as part of an expression cassette. However, the comparatively high clonal variability associated with this approach usually necessitates a time intense screening step in order to find strains with the desired productivity. Some of the factors causing this clonal variability can be overcome using episomal vectors containing an autonomously replicating sequence (ARS)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28508624/temperature-treatment-of-highly-porous-zirconium-containing-metal-organic-frameworks-extends-drug-delivery-release
#11
Michelle H Teplensky, Marcus Fantham, Peng Li, Timothy C Wang, Joshua P Mehta, Laurence J Young, Peyman Z Moghadam, Joseph T Hupp, Omar K Farha, Clemens F Kaminski, David Fairen-Jimenez
Utilizing metal-organic frameworks (MOFs) as a biological carrier can lower the amount of active pharmaceutical ingredient (API) required in cancer treatments to provide a more efficacious therapy. In this work, we have developed a temperature treatment process for delaying the release of a model drug compound from the pores of NU-1000 and NU-901, while taking care to utilize these MOFs' large pore volume and size to achieve exceptional model drug loading percentages over 35 wt.%. Video-rate super-resolution microscopy reveals movement of MOF particles when located outside of the cell boundary, and their subsequent immobilization when taken up by the cell...
May 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28507079/distance-constraints-on-activation-of-trpv4-channels-by-akap150-bound-pkc%C3%AE-in-arterial-myocytes
#12
Sendoa Tajada, Claudia M Moreno, Samantha O'Dwyer, Sean Woods, Daisuke Sato, Manuel F Navedo, L Fernando Santana
TRPV4 (transient receptor potential vanilloid 4) channels are Ca(2+)-permeable channels that play a key role in regulating vascular tone. In arterial myocytes, opening of TRPV4 channels creates local increases in Ca(2+) influx, detectable optically as "TRPV4 sparklets." TRPV4 sparklet activity can be enhanced by the action of the vasoconstrictor angiotensin II (AngII). This modulation depends on the activation of subcellular signaling domains that comprise protein kinase C α (PKCα) bound to the anchoring protein AKAP150...
May 15, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/28499998/scalable-image-coding-based-on-epitomes
#13
Martin Alain, Christine Guillemot, Dominique Thoreau, Philippe Guillotel
In this paper, we propose a novel scheme for scalable image coding based on the concept of epitome. An epitome can be seen as a factorized representation of an image. Focusing on spatial scalability, the enhancement layer of the proposed scheme contains only the epitome of the input image. The pixels of the enhancement layer not contained in the epitome are then restored using two approaches inspired from local learning-based super-resolution methods. In the first method, a locally linear embedding model is learned on base layer patches and then applied to the corresponding epitome patches to reconstruct the enhancement layer...
May 9, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28497957/crimp-accumulation-and-compression-of-billions-of-ions-for-ion-mobility-ms-using-traveling-waves-in-structures-for-lossless-ion-manipulations
#14
Liulin Deng, Sandilya V B Garimella, Ahmed M Hamid, Ian K Webb, Isaac K Attah, Randolph V Norheim, Spencer A Prost, Xueyun Zheng, Jeremy A Sandoval, Erin Shammel Baker, Yehia M Ibrahim, Richard D Smith
We report on the implementation of a traveling wave (TW) based compression ratio ion mobility programming (CRIMP) approach within Structures for Lossless Ion Manipulations (SLIM) that enables both greatly enlarged trapped ion charge capacities and also efficient ion population compression for use in ion mobility (IM) separations. Ion accumulation is conducted in a SLIM serpentine ultra-long path with extended routing (SUPER) region after which CRIMP compression allows the large ion populations to be 'squeezed'...
May 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28497562/different-aggregation-states-of-a-nuclear-localization-signal-tagged-25-kda-c-terminal-fragment-of-tar-rna-dna-binding-protein-43%C3%A2-kda
#15
Akira Kitamura, Sachiko Yuno, Hideki Muto, Masataka Kinjo
The mechanism and cause of motor neuronal cell death in amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disorder, are unknown; gain of function of oligomers and aggregation of misfolded proteins, including carboxyl-terminal fragments (CTFs) of TAR RNA/DNA-binding protein 43 kDa (TDP-43), have been proposed as important causative factors in the onset of ALS. We recently reported that a nuclear localization signal (NLS)-tagged 25-kDa CTF of TDP-43 (TDP25) could decrease the cell-death proportion compared with that promoted by TDP25...
May 12, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28493679/light-induced-fluorescence-modulation-of-quantum-dot-crystal-violet-conjugates-stochastic-off-on-off-cycles-for-multi-color-patterning-and-super-resolution
#16
Sungwook Jung, Joonhyuck Park, Jiwon Bang, Jae-Yeol Kim, Cheolhee Kim, Yongmoon Jeon, Seung Hwan Lee, Ho Jin, Sukyung Choi, Bomi Kim, Woo Jin Lee, Chan-Gi Pack, Jong-Bong Lee, Nam Ki Lee, Sungjee Kim
Photo-switching or modulation of quantum dots (QDs) can be promising for many fields that include display, memory, and super-resolution imaging. However, such modulations have been mostly relied on photo-modulations of conjugated molecules in QD vicinity which typically require high power of high energy photons at UV. We report a visible light-induced facile modulation route for QD-dye conjugates. QD crystal violets conjugates (QD-CVs) were prepared and the crystal violet (CV) molecules on QD quenched the fluorescence efficiently...
May 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28489664/changes-in-mitochondrial-ultrastructure-in-sh-sy5y-cells-during-apoptosis-induced-by-hemin
#17
Jiaxing Dai, Pei Wu, Shancai Xu, Yuchen Li, Yishi Zhu, Ligang Wang, Chunlei Wang, Peiquan Zhou, Huaizhang Shi
Hemorrhagic stroke is associated with high morbidity and mortality. Hemin is a decomposition product of hemoglobin that is related to neuronal apoptosis after hemorrhage, although the molecular basis for this association remains unclear. To address this issue, the present study investigated hemin-induced changes in the apoptotic index and mitochondrial ultrastructure in SH-SY5Y cells. Cell viability was evaluated using Cell Counting Kit-8 and by terminal transferase dUTP nick-end labeling, western blotting, and flow cytometry...
May 5, 2017: Neuroreport
https://www.readbyqxmd.com/read/28489532/video-super-resolution-via-bidirectional-recurrent-convolutional-networks
#18
Yan Huang, Wei Wang, Liang Wang
Super resolving a low-resolution video, namely video super-resolution (SR), is usually handled by either single-image SR or multi-frame SR. Single-Image SR deals with each video frame independently, and ignores intrinsic temporal dependency of video frames which actually plays a very important role in video SR. Multi-Frame SR generally extracts motion information, e.g., optical flow, to model the temporal dependency, but often shows high computational cost. Considering that recurrent neural networks (RNNs) can model long-term temporal dependency of video sequences well, we propose a fully convolutional RNN named bidirectional recurrent convolutional network for efficient multi-frame SR...
May 4, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28489095/metrology-of-dna-arrays-by-super-resolution-microscopy
#19
Christopher M Green, Kelly Schutt, Noah Morris, Reza M Zadegan, William L Hughes, Wan Kuang, Elton Graugnard
Recent results in the assembly of DNA into structures and arrays with nanoscale features and patterns have opened the possibility of using DNA for sub-10 nm lithographic patterning of semiconductor devices. Super-resolution microscopy is being actively developed for DNA-based imaging and is compatible with inline optical metrology techniques for high volume manufacturing. Here, we combine DNA tile assembly with state-dependent super-resolution microscopy to introduce crystal-PAINT as a novel approach for metrology of DNA arrays...
May 10, 2017: Nanoscale
https://www.readbyqxmd.com/read/28486216/ionization-chamber-radial-response-deconvolution-in-megavoltage-photon-beam
#20
Antti Juhani Kulmala, Mikko Tenhunen
The aim of this paper is to study a radial response model as a method, to correct output factor results gathered with ionization chambers of different size and shape in cone collimated RT fields. An enhanced version of a non-parametric super-resolution deconvolution method able to model a radial response function of a small cylinder symmetric ionization chamber is described and demonstrated. The radial response of four ionization chambers with different geometry and radius are estimated using 6 MV photon beam in water at the isocentre plane...
May 9, 2017: Physics in Medicine and Biology
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