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https://www.readbyqxmd.com/read/28428254/a-novel-physiological-role-for-arf1-in-the-formation-of-bi-directional-tubules-from-the-golgi
#1
Francesca Bottanelli, Nicole Kilian, Andreas M Ernst, Felix Rivera-Molina, Lena K Schroeder, Emil B Kromann, Mark D Lessard, Roman S Erdmann, Alanna Schepartz, David Baddeley, Joerg Bewersdorf, Derek Toomre, James E Rothman
Capitalizing on CRISPR/Cas9 gene editing techniques and super-resolution nanoscopy, we have explored the role of the small GTPase ARF1 in mediating transport steps at the Golgi. Surprisingly, beside its well-established role in generating COPI vesicles, we find that ARF1 is additionally involved in the formation of long (∼ 3 μm), thin (∼ 110 nm diameter) tubular carriers. The anterograde and retrograde tubular carriers are both largely free of the classical Golgi coat proteins Coatomer (COPI) and Clathrin...
April 20, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28427029/treatment-of-refractory-and-super-refractory-status-epilepticus-with-brivaracetam-a-cohort-study-from-two-german-university-hospitals
#2
Adam Strzelczyk, Isabel Steinig, Laurent M Willems, Philipp S Reif, Christian Senft, Martin Voss, Bernadette Gaida, Felix von Podewils, Felix Rosenow
PURPOSE: We aimed to ascertain the possible use of brivaracetam (BRV) as an option for treatment of status epilepticus (SE). METHODS: A review of medical records was carried out to detect BRV administration in SE patients treated in Frankfurt and Greifswald during the period February 2016 to January 2017. The primary outcome question concerned SE resolution after BRV initiation. RESULTS: During that period, BRV was started with eleven adult patients with SE...
April 17, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/28425464/metabolic-labelling-of-the-carbohydrate-core-in-bacterial-peptidoglycan-and-its-applications
#3
Hai Liang, Kristen E DeMeester, Ching-Wen Hou, Michelle A Parent, Jeffrey L Caplan, Catherine L Grimes
Bacterial cells are surrounded by a polymer known as peptidoglycan (PG), which protects the cell from changes in osmotic pressure and small molecule insults. A component of this material, N-acetyl-muramic acid (NAM), serves as a core structural element for innate immune recognition of PG fragments. We report the synthesis of modifiable NAM carbohydrate derivatives and the installation of these building blocks into the backbone of Gram-positive and Gram-negative bacterial PG utilizing metabolic cell wall recycling and biosynthetic machineries...
April 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28424492/teststorm-versatile-simulator-software-for-multimodal-super-resolution-localization-fluorescence-microscopy
#4
Tibor Novák, Tamás Gajdos, József Sinkó, Gábor Szabó, Miklós Erdélyi
Optimization of sample, imaging and data processing parameters is an essential task in localization based super-resolution microscopy, where the final image quality strongly depends on the imaging of single isolated fluorescent molecules. A computational solution that uses a simulator software for the generation of test data stacks was proposed, developed and tested. The implemented advanced physical models such as scalar and vector based point spread functions, polarization sensitive detection, drift, spectral crosstalk, structured background etc...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424411/migration-pattern-actin-cytoskeleton-organization-and-response-to-pi3k-mtor-and-hsp90-inhibition-of-glioblastoma-cells-with-different-invasive-capacities
#5
Simon Memmel, Dmitri Sisario, Caren Zöller, Vanessa Fiedler, Astrid Katzer, Robin Heiden, Nicholas Becker, Lorenz Eing, Fábio L R Ferreira, Heiko Zimmermann, Markus Sauer, Michael Flentje, Vladimir L Sukhorukov, Cholpon S Djuzenova
High invasiveness and resistance to chemo- and radiotherapy of glioblastoma multiforme (GBM) make it the most lethal brain tumor. Therefore, new treatment strategies for preventing migration and invasion of GBM cells are needed. Using two different migration assays, Western blotting, conventional and super-resolution (dSTORM) fluorescence microscopy we examine the effects of the dual PI3K/mTOR-inhibitor PI-103 alone and in combination with the Hsp90 inhibitor NVP-AUY922 and/or irradiation on the migration, expression of marker proteins, focal adhesions and F-actin cytoskeleton in two GBM cell lines (DK-MG and SNB19) markedly differing in their invasive capacity...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421321/experimental-investigations-on-fluorescence-excitation-and-depletion-of-carbon-dots
#6
Yunxia Wang, Zhenhua Bai, Qian Wang, Guiren Wang
Carbon dots (CDs) can be readily synthesized and utilized as attractive fluorescent probes for a variety of applications. In this study, we have synthesized CDs using a previously published method and characterized their photo-physical properties. The resultant CDs possess prominent photo-stability and short emission wavelength in the violet region. Our study reveals that CDs, with weak photo-bleaching, enable them to be employed to achieve high spatial resolution in stimulated emission depletion (STED) microscopy...
April 18, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28418639/supermagnetically-tuned-halloysite-nanotubes-functionalized-with-aminosilane-for-covalent-laccase-immobilization
#7
Avinash A Kadam, Jiseon Jang, Dae Sung Lee
Halloysite nanotubes (HNTs) were tuned with supermagnetic Fe3O4 (M-HNTs) and functionalized with γ-aminopropyltriethoxysilane (APTES) (A-M-HNTs). Gluteraldehyde (GTA) was linked to A-M-HNTs (A-M-HNTs-GTA) and explored for the covalent laccase immobilization. The structural characterization of M-HNTs, A-M-HNTs, and A-M-HNTs-GTA immobilized laccase (A-M-HNTs-GTA-Lac) was determined by X-ray photoelectron spectroscopy, field-emission high resolution transmission electron microscopy, magnetic property measurement system, and thermogavimetric analyses...
April 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28416141/multiplexed-engineering-and-analysis-of-combinatorial-enhancer-activity-in-single-cells
#8
Shiqi Xie, Jialei Duan, Boxun Li, Pei Zhou, Gary C Hon
The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28414801/probabilistic-fluorescence-based-synapse-detection
#9
Anish K Simhal, Cecilia Aguerrebere, Forrest Collman, Joshua T Vogelstein, Kristina D Micheva, Richard J Weinberg, Stephen J Smith, Guillermo Sapiro
Deeper exploration of the brain's vast synaptic networks will require new tools for high-throughput structural and molecular profiling of the diverse populations of synapses that compose those networks. Fluorescence microscopy (FM) and electron microscopy (EM) offer complementary advantages and disadvantages for single-synapse analysis. FM combines exquisite molecular discrimination capacities with high speed and low cost, but rigorous discrimination between synaptic and non-synaptic fluorescence signals is challenging...
April 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28414373/superlensing-microscope-objective-lens
#10
Bing Yan, Zengbo Wang, Alan L Parker, Yu-Kun Lai, P John Thomas, Liyang Yue, James N Monks
Conventional microscope objective lenses are diffraction limited; they cannot resolve subdiffraction features of a size smaller than 250-300 nm under white lighting condition. New innovations are required to overcome this limitation. In this paper, we propose and demonstrate a new superlensing objective lens that possesses a resolution of 100 nm, which is a two-times resolution improvement over conventional objectives. This is accomplished by integrating a conventional microscope objective lens with a superlensing microsphere lens using a customized lens adaptor...
April 10, 2017: Applied Optics
https://www.readbyqxmd.com/read/28414216/unraveling-the-thousand-word-picture-an-introduction-to-super-resolution-data-analysis
#11
Antony Lee, Konstantinos Tsekouras, Christopher Calderon, Carlos Bustamante, Steve Pressé
Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light's diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we've termed the interpretation problem...
April 17, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28414097/single-molecule-and-super-resolution-imaging-of-transcription-in-living-bacteria
#12
REVIEW
Mathew Stracy, Achillefs N Kapanidis
In vivo single-molecule and super-resolution techniques are transforming our ability to study transcription as it takes place in its native environment in living cells. This review will detail the methods for imaging single molecules in cells, and the data-analysis tools which can be used to extract quantitative information on the spatial organization, mobility, and kinetics of the transcription machinery from these experiments. Furthermore, we will highlight studies which have applied these techniques to shed new light on bacterial transcription...
April 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28408290/automated-template-based-brain-localization-and-extraction-for-fetal-brain-mri-reconstruction
#13
Sébastien Tourbier, Clemente Velasco-Annis, Vahid Taimouri, Patric Hagmann, Reto Meuli, Simon K Warfield, Meritxell Bach Cuadra, Ali Gholipour
Most fetal brain MRI reconstruction algorithms rely only on brain tissue-relevant voxels of low-resolution (LR) images to enhance the quality of inter-slice motion correction and image reconstruction. Consequently the fetal brain needs to be localized and extracted as a first step, which is usually a laborious and time consuming manual or semi-automatic task. We have proposed in this work to use age-matched template images as prior knowledge to automatize brain localization and extraction. This has been achieved through a novel automatic brain localization and extraction method based on robust template-to-slice block matching and deformable slice-to-template registration...
April 10, 2017: NeuroImage
https://www.readbyqxmd.com/read/28406495/quantitative-3d-structured-illumination-microscopy-of-nuclear-structures
#14
Felix Kraus, Ezequiel Miron, Justin Demmerle, Tsotne Chitiashvili, Alexei Budco, Quentin Alle, Atsushi Matsuda, Heinrich Leonhardt, Lothar Schermelleh, Yolanda Markaki
3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28404912/expression-of-rho-gtpases-family-in-melanoma-cells-and-its-influence-on-cytoskeleton-and-migration
#15
Si-Jian Wen, Wei Zhang, Na-Na Ni, Qiong Wu, Xiao-Po Wang, You-Kun Lin, Jian-Fang Sun
Rho GTPases family members influenced the filopodia, lamellipodia, stress fiber and adhesion plaque of melanoma cells through regulating cytoskeleton recombination. The role of Rho GTPases family in the migration and invasion of melanoma and its molecular mechanism were explored. The morphological difference between three types of melanoma cells (M14, A375 and MV3) and human melanocyte (MC) was observed by the Hoffman microscope. Cells were stained by phalloidin labeled by rhodamine. The differences between 4 types of cells in filopodia, lamellipodia, stress fiber and adhesion plaque (microfilament is the main constituent) were observed under the super-high resolution microscope...
February 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28404749/diffusion-of-lipids-and-gpi-anchored-proteins-in-actin-free-plasma-membrane-vesicles-measured-by-sted-fcs
#16
Falk Schneider, Dominic Waithe, Mathias P Clausen, Silvia Galiani, Thomas Koller, Gunes Ozhan, Christian Eggeling, Erdinc Sezgin
Diffusion and interaction dynamics of molecules at the plasma membrane play an important role in cellular signalling, and they are suggested to be strongly associated with the actin cytoskeleton. Here, we utilise super-resolution STED microscopy combined with fluorescence correlation spectroscopy (STED-FCS) to access and compare the diffusion characteristics of fluorescent lipid analogues and GPI-anchored proteins (GPI-APs) in the live cell plasma membrane and in actin cytoskeleton-free cell-derived giant plasma membrane vesicles (GPMVs)...
April 12, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28402886/three-dimensional-super-resolution-in-eukaryotic-cells-using-the-double-helix-point-spread-function
#17
Alexander R Carr, Aleks Ponjavic, Srinjan Basu, James McColl, Ana Mafalda Santos, Simon Davis, Ernest D Laue, David Klenerman, Steven F Lee
Single-molecule localization microscopy, typically based on total internal reflection illumination, has taken our understanding of protein organization and dynamics in cells beyond the diffraction limit. However, biological systems exist in a complicated three-dimensional environment, which has required the development of new techniques, including the double-helix point spread function (DHPSF), to accurately visualize biological processes. The application of the DHPSF approach has so far been limited to the study of relatively small prokaryotic cells...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28401888/advances-in-pancreatic-islet-monolayer-culture-on-glass-surfaces-enable-super-resolution-microscopy-and-insights-into-beta-cell-ciliogenesis-and-proliferation
#18
Edward A Phelps, Chiara Cianciaruso, Jaime Santo-Domingo, Miriella Pasquier, Gabriele Galliverti, Lorenzo Piemonti, Ekaterine Berishvili, Olivier Burri, Andreas Wiederkehr, Jeffrey A Hubbell, Steinunn Baekkeskov
A robust and reproducible method for culturing monolayers of adherent and well-spread primary islet cells on glass coverslips is required for detailed imaging studies by super-resolution and live-cell microscopy. Guided by an observation that dispersed islet cells spread and adhere well on glass surfaces in neuronal co-culture and form a monolayer of connected cells, we demonstrate that in the absence of neurons, well-defined surface coatings combined with components of neuronal culture media collectively support robust attachment and growth of primary human or rat islet cells as monolayers on glass surfaces...
April 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28401756/gpcr-activation-and-endocytosis-induced-by-a-2d-material-agonist
#19
Wei-Tao Dou, Ya Kong, Xiao-Peng He, Guo-Rong Chen, Yi Zang, Jia Li, He Tian
Agonist-induced activation and endocytosis of G protein-coupled receptors (GPCRs) are crucial for a number of physiological and pathological processes. However, tools that are available for probing GPCR endocytosis have been insufficient. Here, we developed a two-dimensional (2D) material agonist by supramolecular self-assembly between an endogenous agonist of κ-opioid receptor (KOR) and 2D molybdenum disulfide. The 2D material agonist has proven to be amenable for eliciting GPCR activation and endocytosis in cells stably expressing KOR rather than in those without KOR expression...
April 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28398640/fluorescence-microscopy-a-concise-guide-to-current-imaging-methods
#20
Christian A Combs, Hari Shroff
The field of fluorescence microscopy is rapidly growing and offers ever more imaging capabilities for biologists. Over the past decade, many new technologies and techniques have been developed that allow for combinations of deeper, faster, and higher resolution imaging. These have included the commercialization of many super-resolution and light sheet fluorescence microscopy techniques. For the non-expert, it can be difficult to match the best imaging techniques to biological questions. Picking the most appropriate imaging modality requires a basic understanding of the underlying physics governing each of them, as well as information comparing potentially competing imaging properties in the context of the sample to be imaged...
April 10, 2017: Current Protocols in Neuroscience
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