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https://www.readbyqxmd.com/read/28650478/a-dna-origami-platform-for-quantifying-protein-copy-number-in-super-resolution
#1
Francesca Cella Zanacchi, Carlo Manzo, Angel S Alvarez, Nathan D Derr, Maria F Garcia-Parajo, Melike Lakadamyali
Single-molecule-based super-resolution microscopy offers researchers a unique opportunity to quantify protein copy number with nanoscale resolution. However, while fluorescent proteins have been characterized for quantitative imaging using calibration standards, similar calibration tools for immunofluorescence with small organic fluorophores are lacking. Here we show that DNA origami, in combination with GFP antibodies, is a versatile platform for calibrating fluorophore and antibody labeling efficiency to quantify protein copy number in cellular contexts using super-resolution microscopy...
June 26, 2017: Nature Methods
https://www.readbyqxmd.com/read/28648678/single-plane-illumination-microscopy-as-a-tool-for-studying-nucleome-dynamics
#2
Jörg Langowski
Single plane illumination microscopy (SPIM) is a new optical method that has become extremely important in recent years. It is based on the formation of a "light slice" in the specimen in which fluorescently tagged molecules are observed. The spatial resolution is close to that of confocal optics, but without the disadvantages inherent to scanning or high laser irradiation doses. A recent development is light sheet fluctuation microscopy, which exploits the dynamic information contained in the fluorescence intensity fluctuations of each image pixel...
June 22, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28646414/dynamic-meso-scale-anchorage-of-gpi-anchored-receptors-in-the-plasma-membrane-prion-protein-vs-thy1
#3
Yuri L Nemoto, Roger J Morris, Hiroko Hijikata, Taka A Tsunoyama, Akihiro C E Shibata, Rinshi S Kasai, Akihiro Kusumi, Takahiro K Fujiwara
The central mechanism for the transmission of the prion protein misfolding is the structural conversion of the normal cellular prion protein to the pathogenic misfolded prion protein, by the interaction with misfolded prion protein. This process might be enhanced due to the homo-dimerization/oligomerization of normal prion protein. However, the behaviors of normal prion protein in the plasma membrane have remained largely unknown. Here, using single fluorescent-molecule imaging, we found that both prion protein and Thy1, a control glycosylphosphatidylinositol-anchored protein, exhibited very similar intermittent transient immobilizations lasting for a few seconds within an area of 24...
June 24, 2017: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28642595/3d-bayesian-cluster-analysis-of-super-resolution-data-reveals-lat-recruitment-to-the-t-cell-synapse
#4
Juliette Griffié, Leigh Shlomovich, David J Williamson, Michael Shannon, Jesse Aaron, Satya Khuon, Garth L Burn, Lies Boelen, Ruby Peters, Andrew P Cope, Edward A K Cohen, Patrick Rubin-Delanchy, Dylan M Owen
Single-molecule localisation microscopy (SMLM) allows the localisation of fluorophores with a precision of 10-30 nm, revealing the cell's nanoscale architecture at the molecular level. Recently, SMLM has been extended to 3D, providing a unique insight into cellular machinery. Although cluster analysis techniques have been developed for 2D SMLM data sets, few have been applied to 3D. This lack of quantification tools can be explained by the relative novelty of imaging techniques such as interferometric photo-activated localisation microscopy (iPALM)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28640821/noise-reduction-in-single-time-frame-optical-dna-maps
#5
Paola C Torche, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes...
2017: PloS One
https://www.readbyqxmd.com/read/28639669/plasmon-enhanced-fluorescence-spectroscopy
#6
REVIEW
Jian-Feng Li, Chao-Yu Li, Ricardo F Aroca
Fluorescence spectroscopy with strong emitters is a remarkable tool with ultra-high sensitivity for detection and imaging down to the single-molecule level. Plasmon-enhanced fluorescence (PEF) not only offers enhanced emissions and decreased lifetimes, but also allows an expansion of the field of fluorescence by incorporating weak quantum emitters, avoiding photobleaching and providing the opportunity of imaging with resolutions significantly better than the diffraction limit. It also opens the window to a new class of photostable probes by combining metal nanostructures and quantum emitters...
June 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28639395/spatiotemporally-controllable-peptide-based-nanoassembly-in-single-living-cells-for-a-biological-self-portrait
#7
Yuanyuan Zhao, Xu Zhang, Zhipeng Li, Shuaidong Huo, Ke Zhang, Juntao Gao, Hao Wang, Xing-Jie Liang
Simultaneous precise localization and activity evaluation of a biomolecule in a single living cell is through an enzyme-specific signal-amplification process, which involves the localized, site-specific self-assembly, and activation of a presignaling molecule. The inactive presignaling tetraphenylethylene (TPE)-peptide derivative, TPE-YpYY, is nondetectable and highly biocompatible and these small molecules rapidly diffuse into living cells. Upon safely arriving at an active site, and accessing the catalytic pocket of an enzyme, TPE-YpYY immediately and quantitatively accumulates in situ in response to enzymatic activity, forms an enzyme anchor TPE-YYY nanoassembly, displays aggregation-induced emission behavior, and finally lights up the active enzyme, indicating its activity, and allowing its status in living cells to be tracked...
June 22, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28637749/cell-cycle-dependent-spatial-segregation-of-telomerase-from-sites-of-dna-damage
#8
Faissal Ouenzar, Maxime Lalonde, Hadrien Laprade, Geneviève Morin, Franck Gallardo, Samuel Tremblay-Belzile, Pascal Chartrand
Telomerase can generate a novel telomere at DNA double-strand breaks (DSBs), an event called de novo telomere addition. How this activity is suppressed remains unclear. Combining single-molecule imaging and deep sequencing, we show that the budding yeast telomerase RNA (TLC1 RNA) is spatially segregated to the nucleolus and excluded from sites of DNA repair in a cell cycle-dependent manner. Although TLC1 RNA accumulates in the nucleoplasm in G1/S, Pif1 activity promotes TLC1 RNA localization in the nucleolus in G2/M...
June 21, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28637186/cpg-and-methylation-dependent-dna-binding-and-dynamics-of-the-methylcytosine-binding-domain-2-protein-at-the-single-molecule-level
#9
Hai Pan, Stephanie M Bilinovich, Parminder Kaur, Robert Riehn, Hong Wang, David C Williams
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28635963/single-molecule-analysis-of-steroid-receptor-and-cofactor-action-in-living-cells
#10
Ville Paakinaho, Diego M Presman, David A Ball, Thomas A Johnson, R Louis Schiltz, Peter Levitt, Davide Mazza, Tatsuya Morisaki, Tatiana S Karpova, Gordon L Hager
Population-based assays have been employed extensively to investigate the interactions of transcription factors (TFs) with chromatin and are often interpreted in terms of static and sequential binding. However, fluorescence microscopy techniques reveal a more dynamic binding behaviour of TFs in live cells. Here we analyse the strengths and limitations of in vivo single-molecule tracking and performed a comprehensive analysis on the intranuclear dwell times of four steroid receptors and a number of known cofactors...
June 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28634335/ordered-hydroxyls-on-ca3ru2o7-001
#11
Daniel Halwidl, Wernfried Mayr-Schmölzer, David Fobes, Jin Peng, Zhiqiang Mao, Michael Schmid, Florian Mittendorfer, Josef Redinger, Ulrike Diebold
As complex ternary perovskite-type oxides are increasingly used in solid oxide fuel cells, electrolysis and catalysis, it is desirable to obtain a better understanding of their surface chemical properties. Here we report a pronounced ordering of hydroxyls on the cleaved (001) surface of the Ruddlesden-Popper perovskite Ca3Ru2O7 upon water adsorption at 105 K and subsequent annealing to room temperature. Density functional theory calculations predict the dissociative adsorption of a single water molecule (E ads = 1...
June 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28633849/effects-of-bovine-serum-albumin-on-a-single-cavitation-bubble
#12
Shuibao Qi, Badreddine Assouar, Weizhong Chen
The dynamics and sonoluminescence (SL) of a single cavitation bubble in bovine serum albumin (BSA) aqueous solutions have been experimentally and theoretically investigated. A phase-locked integral imaging has been used to record the bubble pulsation evolutions. The results show that, under the optimum driving condition, the endurable driving pressure, maximum radius, radius compression ratio and SL intensity of the cavitation bubble increase correspondingly with the increase of BSA concentrations within the critical micelle concentration, which indicates that the addition of BSA increases the power capability of the cavitation bubble...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633825/structural-evolution-growth-mechanism-and-photoluminescence-properties-of-cuwo4-nanocrystals
#13
E L S Souza, J C Sczancoski, I C Nogueira, M A P Almeida, M O Orlandi, M S Li, R A S Luz, M G R Filho, E Longo, L S Cavalcante
Copper tungstate (CuWO4) crystals were synthesized by the sonochemistry (SC) method, and then, heat treated in a conventional furnace at different temperatures for 1h. The structural evolution, growth mechanism and photoluminescence (PL) properties of these crystals were thoroughly investigated. X-ray diffraction patterns, micro-Raman spectra and Fourier transformed infrared spectra indicated that crystals heat treated and 100°C and 200°C have water molecules in their lattice (copper tungstate dihydrate (CuWO4·2H2O) with monoclinic structure), when the crystals are calcinated at 300°C have the presence of two phase (CuWO4·2H2O and CuWO4), while the others heat treated at 400°C and 500°C have a single CuWO4 triclinic structure...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28630286/efficient-switching-of-mcherry-fluorescence-using-chemical-caging
#14
Bas M C Cloin, Elke De Zitter, Desiree Salas, Vincent Gielen, Gert E Folkers, Marina Mikhaylova, Maike Bergeler, Bartosz Krajnik, Jeremy Harvey, Casper C Hoogenraad, Luc Van Meervelt, Peter Dedecker, Lukas C Kapitein
Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME)...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28627118/optical-microresonators-for-sensing-and-transduction-a-materials-perspective
#15
REVIEW
Kevin D Heylman, Kassandra A Knapper, Erik H Horak, Morgan T Rea, Sudheer K Vanga, Randall H Goldsmith
Optical microresonators confine light to a particular microscale trajectory, are exquisitely sensitive to their microenvironment, and offer convenient readout of their optical properties. Taken together, this is an immensely attractive combination that makes optical microresonators highly effective as sensors and transducers. Meanwhile, advances in material science, fabrication techniques, and photonic sensing strategies endow optical microresonators with new functionalities, unique transduction mechanisms, and in some cases, unparalleled sensitivities...
June 19, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28620443/pattern-recognition-for-predictive-preventive-and-personalized-medicine-in-cancer
#16
REVIEW
Tingting Cheng, Xianquan Zhan
Predictive, preventive, and personalized medicine (PPPM) is the hot spot and future direction in the field of cancer. Cancer is a complex, whole-body disease that involved multi-factors, multi-processes, and multi-consequences. A series of molecular alterations at different levels of genes (genome), RNAs (transcriptome), proteins (proteome), peptides (peptidome), metabolites (metabolome), and imaging characteristics (radiome) that resulted from exogenous and endogenous carcinogens are involved in tumorigenesis and mutually associate and function in a network system, thus determines the difficulty in the use of a single molecule as biomarker for personalized prediction, prevention, diagnosis, and treatment for cancer...
March 2017: EPMA Journal
https://www.readbyqxmd.com/read/28618223/covalent-protein-labeling-and-improved-single-molecule-optical-properties-of-aqueous-cdse-cds-quantum-dots
#17
Sara M Wichner, Victor R Mann, Alexander S Powers, Maya A Segal, Mustafa Mir, Jigar N Bandaria, Mark A DeWitt, Xavier Darzacq, Ahmet Yildiz, Bruce E Cohen
Semiconductor quantum dots (QDs) have proven to be superior probes for single-molecule imaging compared to organic or genetically encoded fluorophores, but they are limited by difficulties in protein targeting, their larger size, and on-off blinking. Here, we report compact aqueous CdSe/CdS QDs with significantly improved bioconjugation efficiency and superior single-molecule optical properties. We have synthesized covalent protein labeling ligands (i.e., SNAP tags) that are optimized for nanoparticle use, and QDs functionalized with these ligands label SNAP-tagged proteins ∼10-fold more efficiently than existing SNAP ligands...
June 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28610424/single-molecule-chemistry-with-surface-and-tip-enhanced-raman-spectroscopy
#18
Alyssa B Zrimsek, Naihao Chiang, Michael Mattei, Stephanie Zaleski, Michael O McAnally, Craig T Chapman, Anne-Isabelle Henry, George C Schatz, Richard P Van Duyne
Single-molecule (SM) surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have emerged as analytical techniques for characterizing molecular systems in nanoscale environments. SERS and TERS use plasmonically enhanced Raman scattering to characterize the chemical information on single molecules. Additionally, TERS can image single molecules with subnanometer spatial resolution. In this review, we cover the development and history of SERS and TERS, including the concept of SERS hot spots and the plasmonic nanostructures necessary for SM detection, the past and current methodologies for verifying SMSERS, and investigations into understanding the signal heterogeneities observed with SMSERS...
June 14, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28610423/introduction-super-resolution-and-single-molecule-imaging
#19
Julie Biteen, Katherine A Willets
No abstract text is available yet for this article.
June 14, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28608889/nanoscale-triplet-exciton-diffusion-via-imaging-of-up-conversion-emission-from-single-hybrid-nanoparticles-in-molecular-crystals
#20
Kaishi Narushima, Shuzo Hirata, Martin Vacha
Up-conversion materials composed of donor and acceptor molecules which convert low energy photons into higher energy ones by triplet-triplet annihilation can improve the sensitivity of photocatalysts or the efficiency of solar cells. The use of crystalline materials can lead to a decrease in the up-conversion threshold intensity due to increased diffusion length LT of triplet excitons. Here, we demonstrate direct microscopic imaging of triplet exciton diffusion in polycrystalline films. The generation of high local density of triplet states is achieved by functionalizing alumina nanospheres with donor molecules and dispersing them in the acceptor films...
June 13, 2017: Nanoscale
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