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Single molecule imaging

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https://www.readbyqxmd.com/read/28229174/characterization-of-the-specific-interaction-between-the-dna-aptamer-sgc8c-and-protein-tyrosine-kinase-7-receptors-at-the-surface-of-t-cells-by-biosensing-afm
#1
Michael Leitner, Alexandra Poturnayova, Constanze Lamprecht, Sabine Weich, Maja Snejdarkova, Ivana Karpisova, Tibor Hianik, Andreas Ebner
We studied the interaction of the specific DNA aptamer sgc8c immobilized at the AFM tip with its corresponding receptor, the protein tyrosine kinase-7 (PTK7) embedded in the membrane of acute lymphoblastic leukemia (ALL) cells (Jurkat T-cells). Performing single molecule force spectroscopy (SMFS) experiments, we showed that the aptamer sgc8c bound with high probability (38.3 ± 7.48%) and high specificity to PTK7, as demonstrated by receptor blocking experiments and through comparison with the binding behavior of a nonspecific aptamer...
February 22, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28223507/imaging-mrna-and-protein-interactions-within-neurons
#2
Carolina Eliscovich, Shailesh M Shenoy, Robert H Singer
RNA-protein interactions are essential for proper gene expression regulation, particularly in neurons with unique spatial constraints. Currently, these interactions are defined biochemically, but a method is needed to evaluate them quantitatively within morphological context. Colocalization of two-color labels using wide-field microscopy is a method to infer these interactions. However, because of chromatic aberrations in the objective lens, this approach lacks the resolution to determine whether two molecules are physically in contact or simply nearby by chance...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28217997/in-situ-imaging-of-individual-mrna-mutation-in-single-cells-using-ligation-mediated-branched-hybrization-chain-reaction-ligation-bhcr
#3
Ying Tang, Xiao-Li Zhang, Li-Juan Tang, Ru-Qin Yu, Jian-Hui Jiang
Ultrasensitive and specific in situ imaging of gene expression is essential for molecular medicine and clinical theranostics. We develop a novel fluorescence in situ hybridization (FISH) strategy based on a new branched hybridiza-tion chain reaction (bHCR) for efficient signal amplification in FISH assay and a ligase-mediated discrimination for specific mutation detection. To our knowledge, this is the first time that HCR has been realized for mutation detection in FISH assay. In vitro assay shows that the ligation-bHCR strategy affords high specificity in discriminating single-nucleotide variation in mRNA, and generates a highly branched polymeric product that confers more efficient amplifi-cation or better sensitivity than HCR...
February 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28217990/telomerase-activity-detection-with-amplification-free-single-molecule-stochastic-binding-assay
#4
Xin Su, Zehao Li, Xinzhong Yan, Lei Wang, Xu Zhou, Lin Wei, Lehui Xiao, Changyuan Yu
Since the elongation of telomeres is associated with tumorigenesis, it is of great interest to develop rapid and high-confidence telomerase activity detection methods for disease diagnosis. Currently, amplification based strategies have been extensively explored for telomerase detection in vitro and in vivo. However, amplification typically associated with poor reproducibility and high background which hamper their further applications particularly for real sample assay. Here, we demonstrated a new amplification-free single molecule imaging method for telomerase activity detection in vitro based on nucleic acid stochastic binding with total internal reflection fluorescence microscopy (TIRFM)...
February 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28217720/a-graph-partitioning-approach-to-simultaneous-angular-reconstitution
#5
Gabi Pragier, Ido Greenberg, Xiuyuan Cheng, Yoel Shkolnisky
One of the primary challenges in single particle reconstruction with cryo-electron microscopy is to find a three-dimensional model of a molecule using its noisy two-dimensional projection-images. As the imaging orientations of the projection-images are unknown, we suggest a common-lines-based method to simultaneously estimate the imaging orientations of all images that is independent of the distribution of the orientations. Since the relative orientation of each pair of images may only be estimated up to a two-way handedness ambiguity, we suggest an efficient procedure to consistently assign the same handedness to all relative orientations...
September 2016: IEEE Transactions on Computational Imaging
https://www.readbyqxmd.com/read/28216791/molecular-processes-leading-to-necking-in-extensional-flow-of-polymer-solutions-using-microfluidics-and-single-dna-imaging
#6
Shaurya Sachdev, Aswin Muralidharan, Pouyan E Boukany
We study the necking and pinch-off dynamics of liquid droplets that contain a semidilute polymer solution of polyacrylamide close to overlap concentration by combining microfluidics and single DNA observation. Polymeric droplets are stretched by passing them through the stagnation point of a T-shaped microfluidic junction. In contrast with the sudden breakup of Newtonian droplets, a stable neck is formed between the separating ends of the droplet which delays the breakup process. Initially, polymeric filaments experience exponential thinning by forming a stable neck with extensional flow within the filament...
December 27, 2016: Macromolecules
https://www.readbyqxmd.com/read/28207240/interfaces-in-heterogeneous-catalysts-advancing-mechanistic-understanding-through-atomic-scale-measurements
#7
Wenpei Gao, Zachary D Hood, Miaofang Chi
Developing novel catalysts with high efficiency and selectivity is critical for enabling future clean energy conversion technologies. Interfaces in catalyst systems have long been considered the most critical factor in controlling catalytic reaction mechanisms. Interfaces include not only the catalyst surface but also interfaces within catalyst particles and those formed by constructing heterogeneous catalysts. The atomic and electronic structures of catalytic surfaces govern the kinetics of binding and release of reactant molecules from surface atoms...
February 16, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28202732/atomic-structure-of-granulin-determined-from-native-nanocrystalline-granulovirus-using-an-x-ray-free-electron-laser
#8
Cornelius Gati, Dominik Oberthuer, Oleksandr Yefanov, Richard D Bunker, Francesco Stellato, Elaine Chiu, Shin-Mei Yeh, Andrew Aquila, Shibom Basu, Richard Bean, Kenneth R Beyerlein, Sabine Botha, Sébastien Boutet, Daniel P DePonte, R Bruce Doak, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Daniel R James, Christopher Kupitz, Lukas Lomb, Marc Messerschmidt, Karol Nass, Kimberly Rendek, Robert L Shoeman, Dingjie Wang, Uwe Weierstall, Thomas A White, Garth J Williams, Nadia A Zatsepin, Petra Fromme, John C H Spence, Kenneth N Goldie, Johannes A Jehle, Peter Metcalf, Anton Barty, Henry N Chapman
To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling...
February 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28196307/molecule-counts-in-localization-microscopy-with-organic-fluorophores
#9
Mike Heilemann, Franziska Fricke, Christos Karathanasis, Gerhard Hummer
Single-molecule localization microscopy (SMLM) can be used to count fluorescently labeled molecules even when they are not individually resolved. We demonstrate SMLM molecule counting for nucleic acids labeled with the organic fluorophore Alexa Fluor 647 and imaged under photoswitching conditions. From the observed distributions of the number of fluorophore blinking events, we extracted the number of fluorophores per spot using a statistical model. We validate the molecule counting method for single Alexa Fluor 647 fluorophores, and for trimers of Alexa Fluor 647 constructed on a DNA origami structure...
February 14, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28195693/assembly-domain-based-optogenetic-system-for-the-efficient-control-of-cellular-signaling
#10
Akihiro Furuya, Fuun Kawano, Takahiro Nakajima, Yoshibumi Ueda, Moritoshi Sato
We previously developed the Magnet system, which consists of two distinct Vivid protein variants, one positively and one negatively charged, designated the positive Magnet (pMag) and negative Magnet (nMag), respectively. These two proteins bind to each other through electrostatic interactions, preventing unwanted homodimerization and providing selective light-induced heterodimerization. The Magnet system enables the manipulation of cellular functions such as protein-protein interactions and genome editing, although the system could be improved further...
February 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28195498/quantitative-imaging-of-ozone-vapor-using-photofragmentation-laser-induced-fluorescence-lif
#11
Kajsa Larsson, Dina Hot, Andreas Ehn, Andreas Lantz, Wubin Weng, Marcus Aldén, Joakim Bood
In the present work, the spectral properties of gaseous ozone (O3) have been investigated aiming to perform quantitative concentration imaging of ozone by using a single laser pulse at 248 nm from a KrF excimer laser. The O3 molecule is first photodissociated by the laser pulse into two fragments, O and O2. Then the same laser pulse electronically excites the O2 fragment, which is vibrationally hot, whereupon fluorescence is emitted. The fluorescence intensity is found to be proportional to the concentration of ozone...
January 1, 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28195127/a-novel-application-of-non-destructive-readout-technology-to-localisation-microscopy
#12
Samuel F H Barnett, Mary Snape, C Neil Hunter, Miguel A Juárez, Ashley J Cadby
The fitting precision in localisation microscopy is highly dependent on the signal to noise ratio. To increase the quality of the image it is therefore important to increase the signal to noise ratio of the measurements. We present an imaging system for localisation microscopy based on non-destructive readout camera technology that can increase the signal to noise ratio of localisation based microscopy. This approach allows for much higher frame rates through subsampling a traditional camera frame. By matching the effective exposure to both the start time and duration of a single molecule we diminish the effects of read noise and temporal noise...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194956/direct-imaging-of-single-plasmonic-metal-nanoparticles-in-capillary-with-laser-light-sheet-scattering-imaging
#13
Xuan Cao, Jingjing Feng, Qi Pan, Bin Xiong, Yan He, Edward S Yeung
Understanding the heterogeneous distribution of the physical and chemical properties of plasmonic metal nanoparticles is fundamentally important to their basic and applied research. Traditionally, they are obtained either indirectly via bulk spectroscopic measurements plus electron microscopic characterizations, or through single molecule/particle imaging of nanoparticles immobilized on planar substrates. In this study, by using light-sheet scattering microscopy with a supercontinuum white laser, highly sensitive imaging of individual MNPs flowing inside a capillary, driven by either pressure or electric field, was achieved for the first time...
February 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193035/mitochondria-targeted-ratiometric-fluorescent-nanosensor-for-simultaneous-biosensing-and-imaging-of-o2-%C3%A2-and-ph-in-live-cells
#14
Hong Huang, Fangyuan Dong, Yang Tian
Intracellular pH undertakes critical functions in the formation of a proton gradient and electrochemical potential that drives the adenosine triphosphate synthesis. It is also involved in various metabolic processes occurring in mitochondria, such as the generation of reactive oxygen species, calcium regulation, as well as the triggering of cell proliferation and apoptosis. Meanwhile, the aberrant accumulation of O2(•-) within mitochondria is frequently intertwined with mitochondrial dysfunction and disease development...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28192920/diagnosis-therapy-integrative-systems-based-on-magnetic-rna-nanoflowers-for-co-drug-delivery-and-targeted-therapy
#15
Yingshu Guo, Shuang Li, Yujie Wang, Shusheng Zhang
This study was to develop a codrug delivery system for targeting cancer therapy based on magnetic RNA nanoflowers (RNA NF). Compared with traditional nucleic acid structure, convenient separation can be achieved by introducing magnetic nanoparticle (MNP) into RNA NF. Folic acid (FA) modified MNP/RNA NF (FA/MNP/RNA NF) was used as a targeting nanocarrier with excellent biocompatibility to overcome the nonselectivity of MNP/RNA NF. And then, anticancer drug doxorubicin (DOX) and photosensitizer 5, 10, 15, 20-tetrakis (1-methylpyridinium-4-yl) porphyrin (TMPyP4) binding with RNA NF were used as codrug cargo models...
February 8, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28192299/single-molecule-analysis-of-fluorescent-carbon-dots-towards-localization-based-super-resolution-microscopy
#16
Navneet C Verma, Syamantak Khan, Chayan K Nandi
The advancement of high-resolution bioimaging has always been dependent on the discovery of bright and easily available fluorescent probes. Fluorescent carbon nanodots, an interesting class of relatively new nanomaterials, have emerged as a versatile alternative due to their superior optical properties, non-toxicity, cell penetrability and easy routes to synthesis. Although a plethora of reports is available on bioimaging using carbon dots, single-molecule-based super-resolution imaging is rare in the literature...
October 11, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28191929/stop-frame-filming-and-discovery-of-reactions-at-the-single-molecule-level-by-transmission-electron-microscopy
#17
Thomas W Chamberlain, Johannes Biskupek, Stephen T Skowron, Alexander V Markevich, Simon Kurasch, Oliver Reimer, Kate Walker, Graham A Rance, Xinliang Feng, Klaus Müllen, Andrey Turchanin, Maria A Lebedeva, Alexander Majouga, Valentine Georgievich Nenajdenko, Ute Kaiser, Elena Besley, Andrei N Khlobystov
We report an approach - named chemTEM - to follow chemical transformations at the single-molecule level with the electron beam of a transmission electron microscope (TEM) applied as both a tuneable source of energy and a sub-Angstrom imaging probe. Deposited on graphene, disk-shaped perchlorocoronene molecules are precluded from intermolecular interactions. This allows monomolecular transformations to be studied at the single-molecule level in real time and reveals chlorine elimination and reactive aryne formation as a key initial stage of multi-step reactions initiated by the 80 keV e-beam...
February 13, 2017: ACS Nano
https://www.readbyqxmd.com/read/28187433/doxycycline-directly-targets-par1-to-suppress-tumor-progression
#18
Weilong Zhong, Shuang Chen, Qiang Zhang, Ting Xiao, Yuan Qin, Ju Gu, Bo Sun, Yanrong Liu, Xiangyan Jing, Xuejiao Hu, Peng Zhang, Honggang Zhou, Tao Sun, Cheng Yang
Doxycycline have been reported to exert anti-cancer activity and have been assessed as anti-cancer agents in clinical trials. However, the direct targets of doxycycline in cancer cells remain unclear. In this study, we used a chemical proteomics approach to identify the Protease-activated receptor 1 (PAR1) as a specific target of inhibition of doxycycline. Binding assays and single-molecule imaging assays were performed to confirm the inhibition of doxycycline to PAR1. The effect of doxycycline on multi-omics and cell functions were assessed based on a PAR1/thrombin model...
February 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28185197/multiplex-immunohistochemistry-for-mapping-the-tumor-microenvironment
#19
Jessica Kalra, Jennifer Baker
Multiplex Immunohistochemistry (mIHC) allows for the simultaneous detection of multiple targets of interest in a single tissue section. Using this method it is therefore possible to evaluate several effectors of a signal transduction pathway at one time, co-localization of markers, or distribution of molecules relative to one another within tissues. This method plays an important role in characterizing molecular signaling and the outcome of signal ablation when assessing mechanisms of drug action. Additionally, this approach can be used to characterize: the tumor microenvironment including vascular architecture and hypoxia, cellular proliferation, cell death as well as drug distribution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28181515/erratum-in-vivo-single-molecule-imaging-of-syntaxin1a-reveals-polyphosphoinositide-and-activity-dependent-trapping-in-presynaptic-nanoclusters
#20
Adekunle T Bademosi, Elsa Lauwers, Pranesh Padmanabhan, Lorenzo Odierna, Ye Jin Chai, Andreas Papadopulos, Geoffrey J Goodhill, Patrik Verstreken, Bruno van Swinderen, Frédéric A Meunier
No abstract text is available yet for this article.
February 9, 2017: Nature Communications
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