keyword
MENU ▼
Read by QxMD icon Read
search

Single molecule imaging

keyword
https://www.readbyqxmd.com/read/28448050/single-molecule-analysis-of-laser-localized-psoralen-adducts
#1
Jing Huang, Himabindu Gali, Julia Gichimu, Marina A Bellani, Durga Pokharel, Manikandan Paramasivam, Michael M Seidman
The DNA Damage Response (DDR) has been extensively characterized in studies of double strand breaks (DSBs) induced by laser micro beam irradiation in live cells. The DDR to helix distorting covalent DNA modifications, including interstrand DNA crosslinks (ICLs), is not as well defined. We have studied the DDR stimulated by ICLs, localized by laser photoactivation of immunotagged psoralens, in the nuclei of live cells. In order to address fundamental questions about adduct distribution and replication fork encounters, we combined laser localization with two other technologies...
April 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448005/open-source-single-particle-analysis-for-super-resolution-microscopy-with-virusmapper
#2
Robert D M Gray, Jason Mercer, Ricardo Henriques
Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm allows for the routine imaging of nanoscale biological complexes and processes. This increase in resolution also means that methods popular in electron microscopy, such as single-particle analysis, can readily be applied to super-resolution fluorescence microscopy. By combining this analytical approach with super-resolution optical imaging, it becomes possible to take advantage of the molecule-specific labeling capacity of fluorescence microscopy to generate structural maps of molecular elements within a metastable structure...
April 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28446335/quantitative-nano-characterization-of-polymers-using-atomic-force-microscopy
#3
Milad Radiom, Svilen Kozhuharov, Phally Kong, Michela di Giannantonio, Mathieu A Ayer, Plinio Maroni, Andreas F M Kilbinger, Katharina M Fromm, Christoph Weder, Michal Borkovec
The present article offers an overview on the use of atomic force microscopy (AFM) to characterize the nanomechanical properties of polymers. AFM imaging reveals the conformations of polymer molecules at solid- liquid interfaces. In particular, for polyelectrolytes, the effect of ionic strength on the conformations of molecules can be studied. Examination of force versus extension profiles obtained using AFM-based single molecule force spectroscopy gives information on the entropic and enthalpic elasticities in pN to nN force range...
April 26, 2017: Chimia
https://www.readbyqxmd.com/read/28441775/progress-in-the-correlative-atomic-force-microscopy-and-optical-microscopy
#4
REVIEW
Lulu Zhou, Mingjun Cai, Ti Tong, Hongda Wang
Atomic force microscopy (AFM) has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed...
April 24, 2017: Sensors
https://www.readbyqxmd.com/read/28441604/digital-quantitative-analysis-of-microrna-in-single-cell-based-on-ligation-depended-polymerase-colony-polony
#5
Hui Wang, Honghong Wang, Xinrui Duan, Chenghui Liu, Zhengping Li
The ability to dissect cell-to-cell variations of microRNA (miRNA) expression with single-cell resolution has become a powerful tool to investigate the regulatory function of miRNAs in biological processes and the pathogenesis of miRNA-related diseases. Herein, we have developed a novel scheme for digital detection of miRNA in single cell by using the ligation-depended DNA polymerase colony (polony). Firstly, two simply designed target-specific DNA probes were ligated by using individual miRNA as the template...
April 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28440794/se-sad-serial-femtosecond-crystallography-datasets-from-selenobiotinyl-streptavidin
#6
Chun Hong Yoon, Hasan DeMirci, Raymond G Sierra, E Han Dao, Radman Ahmadi, Fulya Aksit, Andrew L Aquila, Alexander Batyuk, Halilibrahim Ciftci, Serge Guillet, Matt J Hayes, Brandon Hayes, Thomas J Lane, Meng Liang, Ulf Lundström, Jason E Koglin, Paul Mgbam, Yashas Rao, Theodore Rendahl, Evan Rodriguez, Lindsey Zhang, Soichi Wakatsuki, Sébastien Boutet, James M Holton, Mark S Hunter
We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C10H16N2O3S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously...
April 25, 2017: Scientific Data
https://www.readbyqxmd.com/read/28437460/an-aggregation-removal-model-for-the-formation-and-size-determination-of-post-synaptic-scaffold-domains
#7
Jonas Ranft, Leandro G Almeida, Pamela C Rodriguez, Antoine Triller, Vincent Hakim
The formation and stability of synapses are key questions in neuroscience. Post-synaptic domains have been classically conceived as resulting from local insertion and turnover of proteins at the synapse. However, insertion is likely to occur outside the post-synaptic domains and advances in single-molecule imaging have shown that proteins diffuse in the plane of the membrane prior to their accumulation at synapses. We quantitatively investigated this scenario using computer simulations and mathematical analysis, taking for definiteness the specific case of inhibitory synapse components, i...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437395/global-survey-of-the-immunomodulatory-potential-of-common-drugs
#8
Gregory I Vladimer, Berend Snijder, Nikolaus Krall, Johannes W Bigenzahn, Kilian V M Huber, Charles-Hugues Lardeau, Kumar Sanjiv, Anna Ringler, Ulrika Warpman Berglund, Monika Sabler, Oscar Lopez de la Fuente, Paul Knöbl, Stefan Kubicek, Thomas Helleday, Ulrich Jäger, Giulio Superti-Furga
Small-molecule drugs may complement antibody-based therapies in an immune-oncology setting, yet systematic methods for the identification and characterization of the immunomodulatory properties of these entities are lacking. We surveyed the immumomodulatory potential of 1,402 small chemical molecules, as defined by their ability to alter the cell-cell interactions among peripheral mononuclear leukocytes ex vivo, using automated microscopy and population-wide single-cell image analysis. Unexpectedly, ∼10% of the agents tested affected these cell-cell interactions differentially...
April 24, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28437075/fluorescent-photoswitchable-diarylethenes-for-biolabeling-and-single-molecule-localization-microscopies-with-optical-superresolution
#9
Benoit Roubinet, Michael Weber, Heydar Shojaei, Mark Bates, Mariano L Bossi, Vladimir N Belov, Masahiro Irie, Stefan W Hell
A modular assembly of water soluble diarylethenes (DAEs), applicable as bio-markers for optical nanoscopy, is reported. Reversibly photoswitchable 1,2-bis(2-alkyl-6-phenyl-1-benzothiophene-1,1-dioxide-3-yl)perfluorocyclopentenes possessing a fluorescent "closed" form were decorated with one or two methoxy group(s) attached to the para-position(s) of phenyl ring(s) and two, four or eight carboxylic acid groups. Antibody conjugates of these DAEs feature low aggregation, efficient photoswitching in aqueous buffers, specific staining of cellular structures and photophysical properties (high emission efficiencies and low cycloreversion quantum yields) enabling their application in superresolution microscopy...
April 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28435961/single-photon-coulomb-explosion-of-methanol-using-broad-bandwidth-ultrafast-euv-pulses
#10
Itamar Luzon, Krishna Jagtap, Ester Livshits, Oleg Lioubashevski, Roi Baer, Daniel Strasser
Single-photon Coulomb explosion of methanol is instigated using the broad bandwidth pulse achieved through high-order harmonics generation. Using 3D coincidence fragment imaging of one molecule at a time, the kinetic energy release (KER) and angular distributions of the products are measured in different Coulomb explosion (CE) channels. Two-body CE channels breaking either the C-O or the C-H bonds are described as well as a proton migration channel forming H2O(+), which is shown to exhibit higher KER. The results are compared to intense-field Coulomb explosion measurements in the literature...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28431428/computational-and-in-vitro-experimental-investigation-of-intrathecal-drug-distribution-parametric-study-of-the-effect-of-injection-volume-cerebrospinal-fluid-pulsatility-and-drug-uptake
#11
Kevin M Tangen, Roxanne Leval, Ankit I Mehta, Andreas A Linninger
BACKGROUND: Intrathecal drug delivery is an attractive option to circumvent the blood-brain barrier for pain management through its increased efficacy of pain relief, reduction in adverse side effects, and cost-effectiveness. Unfortunately, there are limited guidelines for physicians to choose infusion or drug pump settings to administer therapeutic doses to specific regions of the spine or the brain. Although empiric trialing of intrathecal drugs is critical to determine the sustained side effects, currently there is no inexpensive in vitro method to guide the selection of spinal drug delivery parameters...
May 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28426025/modular-low-light-microscope-for-imaging-cellular-bioluminescence-and-radioluminescence
#12
Tae Jin Kim, Silvan Türkcan, Guillem Pratx
Low-light microscopy methods are receiving increased attention as new applications have emerged. One such application is to allow longitudinal imaging of light-sensitive cells with no phototoxicity and no photobleaching of fluorescent biomarkers. Another application is for imaging signals that are inherently dim and undetectable using standard microscopy techniques, such as bioluminescence, chemiluminescence or radioluminescence. In this protocol, we provide instructions on how to build a modular low-light microscope (1-4 d) by coupling two microscope objective lenses, back to back from each other, using standard optomechanical components...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28424742/fret-from-single-to-multiplexed-signaling-events
#13
REVIEW
Gertrude Bunt, Fred S Wouters
Förster resonance energy transfer (FRET) is a powerful tool for the visualization of molecular signaling events such as protein activities and interactions in cells. In its different implementations, FRET microscopy has been mainly used for monitoring single events. Recently, there has been a trend of extending FRET imaging towards the simultaneous detection of multiple events and interactions. The concomitant increase in experimental complexity requires a deeper understanding of the biophysical background of FRET...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28424513/super-multiplex-vibrational-imaging
#14
Lu Wei, Zhixing Chen, Lixue Shi, Rong Long, Andrew V Anzalone, Luyuan Zhang, Fanghao Hu, Rafael Yuste, Virginia W Cornish, Wei Min
The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure-function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28424492/teststorm-versatile-simulator-software-for-multimodal-super-resolution-localization-fluorescence-microscopy
#15
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/28418634/protein-trapping-in-plasmonic-nanoslit-and-nanoledge-cavities-the-behavior-and-sensing
#16
Zheng Zeng, Xiaojun Shi, Taylor Mabe, Shaun Christie, Grant Gilmore, Adam W Smith, Jianjun Wei
A novel plasmonic nanoledge device was presented to explore the geometry-induced trapping of nanoscale biomolecules and examine a generation of surface plasmon resonance (SPR) for plasmonic sensing. To design an optimal plasmonic device, a semi-analytical model was implemented for a quantitative analysis of SPR under plane-wave illumination and a finite-difference time-domain (FDTD) simulation was used to study the optical transmission and refractive index (RI) sensitivity. In addition, total internal reflection fluorescence (TIRF) imaging was used to visualize the migration of fluorescently labeled bovine serum albumin (BSA) into the nanoslits; and fluorescence correlation spectroscopy (FCS) was further used to investigate the diffusion of BSA in the nanoslits...
April 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28416636/p53-dynamically-directs-tfiid-assembly-on-target-gene-promoters
#17
R A Coleman, Z Qiao, S K Singh, C S Peng, M Cianfrocco, Z Zhang, A Piasecka, H Aldeborgh, G Basishvili, W L Liu
p53 is a central regulator that turns on vast gene networks to maintain cellular integrity upon various stimuli. p53 activates transcription initiation in part by aiding recruitment of TFIID to the promoter. However, the precise means by which p53 dynamically interacts with TFIID to facilitate assembly on target gene promoters remains elusive. To address this key question, we have undertaken an integrated approach involving single molecule fluorescence microscopy, single particle cryo-electron microscopy, and biochemistry...
April 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28414097/single-molecule-and-super-resolution-imaging-of-transcription-in-living-bacteria
#18
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/28404480/2d-and-3d-fish-of-expanded-repeat-rnas-in-human-lymphoblasts
#19
Martyna O Urbanek, Michał Michalak, Wlodzimierz J Krzyzosiak
The first methods for visualizing RNAs within cells were designed for simple imaging of specific transcripts in cells or tissues and since then significant technical advances have been made in this field. Today, high-resolution images can be obtained, enabling visualization of single transcript molecules, quantitative analyses of images, and precise localization of RNAs within cells as well as co-localization of transcripts with specific proteins or other molecules. In addition, tracking of RNA dynamics within single cell has become possible...
April 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28402886/three-dimensional-super-resolution-in-eukaryotic-cells-using-the-double-helix-point-spread-function
#20
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
keyword
keyword
32971
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"