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https://www.readbyqxmd.com/read/28527435/gauge-invariant-theory-for-super-high-resolution-raman-images
#1
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/28525955/imaging-and-manipulating-energy-transfer-among-quantum-dots-at-individual-dot-resolution
#2
Duc A Nguyen, Huy A Nguyen, Joseph W Lyding, Martin Gruebele
Many processes of interest in quantum dots involve charge or energy transfer from one dot to another. Energy transfer in films of quantum dots as well as between linked quantum dots has been demonstrated by luminescence shift, and the ultrafast time-dependence of energy transfer processes has been resolved. Bandgap variation among dots (energy disorder) and dot separation are known to play an important role in how energy diffuses. Thus it would be very useful if energy transfer could be visualized directly on a dot-by-dot basis among small clusters or within films of quantum dots...
May 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28524357/double-caging-linker-for-and-type-fluorogenic-construction-of-protein-antibody-bioconjugates-and-in-situ-quantification
#3
Shiyong Liu, Guhuan Liu, Guohai Shi, Haoyue Sheng, Yanyan Jiang, Haojun Liang
We report on in situ fluorescent quantification of the conjugation efficiency between azide-terminated synthetic polymers/ imaging probes and thiol-functionalized antibodies/proteins/peptides, by utilizing a doubly caged profluorescent and heterodifunctional core molecule (C1) as the self-sorting bridging unit. Orthogonal dual 'click' coupling of C1 with azide- and thiol-functionalized precursors leads to highly fluorescent bioconjugates, whereas single click products of C1 remain essentially nonfluorescent...
May 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28523559/techniques-for-single-molecule-mrna-imaging-in-living-cells
#4
Kevin Czaplinski
Typical measurement of macromolecules in a biological sample typically averages the result over all the cells or molecules within the sample, and while these types of measurements provide very useful information, they completely miss heterogeneity among the components within the sample that could be a very important aspect of the sample's function. These techniques are also limited in their ability to examine intracellular spatial orientation of molecular activity, which is often a critical component to the regulation of biological processes, particularly in cells with unique spatial relationships, such as neurons...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28522808/plasmonics-enhanced-smartphone-fluorescence-microscopy
#5
Qingshan Wei, Guillermo Acuna, Seungkyeum Kim, Carolin Vietz, Derek Tseng, Jongjae Chae, Daniel Shir, Wei Luo, Philip Tinnefeld, Aydogan Ozcan
Smartphone fluorescence microscopy has various applications in point-of-care (POC) testing and diagnostics, ranging from e.g., quantification of immunoassays, detection of microorganisms, to sensing of viruses. An important need in smartphone-based microscopy and sensing techniques is to improve the detection sensitivity to enable quantification of extremely low concentrations of target molecules. Here, we demonstrate a general strategy to enhance the detection sensitivity of a smartphone-based fluorescence microscope by using surface-enhanced fluorescence (SEF) created by a thin metal-film...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522739/imaging-macrophage-accumulation-in-a-murine-model-of-chronic-pancreatitis-with-125-i-iododpa-spect-ct
#6
Catherine A Foss, Liansheng Liu, Ronnie C Mease, Haofan Wang, Pankaj Pasricha, Martin G Pomper
Background and Aims: Pancreatitis remains a diagnostic challenge in patients with mild to moderate disease, with current imaging modalities inadequate. Given the prominent macrophage infiltrate in chronic pancreatitis, we hypothesized that (125)I-iodo-DPA-713 (iodoDPA), a small-molecule radiotracer that specifically targets macrophages, could be used with single photon emission computed tomography-computed tomography (SPECT-CT) to image pancreatic inflammation in a relevant experimental model. Methods: Chronic pancreatitis was induced in C57BL/6 mice with cerulein and were contrasted with vehicle-injected controls...
May 18, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28521053/compaction-and-condensation-of-dna-mediated-by-the-c-terminal-domain-of-hfq
#7
Antoine Malabirade, Kai Jiang, Krzysztof Kubiak, Alvaro Diaz-Mendoza, Fan Liu, Jeroen A van Kan, Jean-François Berret, Véronique Arluison, Johan R C van der Maarel
Hfq is a bacterial protein that is involved in several aspects of nucleic acids metabolism. It has been described as one of the nucleoid associated proteins shaping the bacterial chromosome, although it is better known to influence translation and turnover of cellular RNAs. Here, we explore the role of Escherichia coli Hfq's C-terminal domain in the compaction of double stranded DNA. Various experimental methodologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy, isothermal titration microcalorimetry and electrophoretic mobility assays have been used to follow the assembly of the C-terminal and N-terminal regions of Hfq on DNA...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28518172/super-resolution-microscopy-with-dna-paint
#8
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/28514955/label-free-biosensing-of-salmonella-enterica-serovars-at-single-cell-level
#9
Bin Wang, Bosoon Park, Bingqian Xu, Yongkuk Kwon
BACKGROUND: The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. The atomic force microscopy (AFM) has been used to study the molecular mechanism of the reactions for protein and aptamers. The surface plasmon resonance (SPR) have been used in fast detections of various pathogens such as bacteria. This study used both AFM and SPR to investigate the complex reactions between aptamers and outer membrane proteins (OMPs) on the surface of S. typhimurium...
May 17, 2017: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/28512753/serum-neurofilament-light-a-biomarker-of-neuronal-damage-in-multiple-sclerosis
#10
Giulio Disanto, Christian Barro, Pascal Benkert, Yvonne Naegelin, Sabine Schädelin, Antonella Giardiello, Chiara Zecca, Kaj Blennow, Henrik Zetterberg, David Leppert, Ludwig Kappos, Claudio Gobbi, Jens Kuhle
OBJECTIVE: Neurofilament light chains (NfL) are unique to neuronal cells, are shed to the CSF and are detectable at low concentrations in peripheral blood. Various diseases causing neuronal damage have resulted in elevated CSF concentrations. We explored the value of an ultrasensitive single-molecule array (Simoa) serum NfL (sNfL) assay in MS. METHODS: sNfL levels were measured in healthy controls (HC, n=254) and two independent MS cohorts: (1) cross-sectional with paired serum and CSF samples (n=142); (2) longitudinal with repeated serum sampling (n=246, median (IQR) follow-up 3...
May 16, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28512623/ca-2-microdomains-in-t-lymphocytes
#11
REVIEW
Insa M A Wolf, Andreas H Guse
Early Ca(2+) signaling is characterized by occurrence of Ca(2+) microdomains formed by opening of single or clusters of Ca(2+) channels, thereby initiating first signaling and subsequently activating global Ca(2+) signaling mechanisms. However, only few data are available focusing on the first seconds and minutes of Ca(2+) microdomain formation and related signaling pathways in activated T-lymphocytes. In this review, we condense current knowledge on Ca(2+) microdomain formation in T-lymphocytes and early Ca(2+) signaling, function of Ca(2+) microdomains, and microdomain organization...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28508356/progress-and-potential-of-imaging-mass-spectrometry-applied-to-biomarker-discovery
#12
Jusal Quanico, Julien Franck, Maxence Wisztorski, Michel Salzet, Isabelle Fournier
Mapping provides a direct means to assess the impact of protein biomarkers and puts into context their relevance in the type of cancer being examined. To this end, mass spectrometry imaging (MSI) was developed to provide the needed spatial information which is missing in traditional liquid-based mass spectrometric proteomics approaches. Aptly described as a "molecular histology" technique, MSI gives an additional dimension in characterizing tumor biopsies, allowing for mapping of hundreds of molecules in a single analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507703/advanced-electroanalytical-chemistry-at-nanoelectrodes
#13
Yi-Lun Ying, Zhifeng Ding, Dongping Zhan, Yi-Tao Long
Nanoelectrodes, with dimensions below 100 nm, have the advantages of high sensitivity and high spatial resolution. These electrodes have attracted increasing attention in various fields such as single cell analysis, single-molecule detection, single particle characterization and high-resolution imaging. The rapid growth of novel nanoelectrodes and nanoelectrochemical methods brings enormous new opportunities in the field. In this perspective, we discuss the challenges, advances, and opportunities for nanoelectrode fabrication, real-time characterizations and high-performance electrochemical instrumentation...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28507695/ani-1-an-extensible-neural-network-potential-with-dft-accuracy-at-force-field-computational-cost
#14
J S Smith, O Isayev, A E Roitberg
Deep learning is revolutionizing many areas of science and technology, especially image, text, and speech recognition. In this paper, we demonstrate how a deep neural network (NN) trained on quantum mechanical (QM) DFT calculations can learn an accurate and transferable potential for organic molecules. We introduce ANAKIN-ME (Accurate NeurAl networK engINe for Molecular Energies) or ANI for short. ANI is a new method designed with the intent of developing transferable neural network potentials that utilize a highly-modified version of the Behler and Parrinello symmetry functions to build single-atom atomic environment vectors (AEV) as a molecular representation...
April 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28505422/oxygen-sensing-with-perfluorocarbon-loaded-ultraporous-mesostructured-silica-nanoparticles
#15
Amani L Lee, Clifford T Gee, Bradley P Weegman, Samuel A Einstein, Adam R Juelfs, Hattie L Ring, Katie R Hurley, Sam M Egger, Garrett Swindlehurst, Michael G Garwood, William C K Pomerantz, Christy L Haynes
Oxygen homeostasis is important in the regulation of biological function. Disease progression can be monitored by measur-ing oxygen levels, thus producing information for the design of therapeutic treatments. Non-invasive measurements of tissue oxygenation require the development of tools with minimal adverse effects and facile detection of features of interest. Fluo-rine magnetic resonance imaging (19F-MRI) exploits the intrinsic properties of perfluorocarbon (PFC) liquids for anatomical imaging, cell tracking, and oxygen sensing...
May 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/28505270/htsvis-a-web-app-for-exploratory-data-analysis-and-visualization-of-arrayed-high-throughput-screens
#16
Christian Scheeder, Florian Heigwer, Michael Boutros
Summary: Arrayed high-throughput screens (HTS) cover a broad range of applications using RNAi or small molecules as perturbations and specialized software packages for statistical analysis have become available. However, exploratory data analysis and integration of screening results has remained challenging due to the size of the data sets and the lack of user-friendly tools for interpretation and visualization of screening results. Here we present HTSvis, a web application to interactively visualize raw data, perform quality control and assess screening results from single to multi-channel measurements such as image-based screens...
May 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28497688/defocused-imaging-of-uv-driven-surface-bound-molecular-motors
#17
Bartosz Krajnik, Jiawen Chen, Matthew A Watson, Scott L Cockroft, Ben L Feringa, Johan Hofkens
Synthetic molecular motors continue to attract great interest due to their ability to transduce energy into nanomechanical motion, the potential to do work and drive systems out-of-equilibrium. Of particular interest are unidirectional rotary molecular motors driven by chemical fuel or light. Probing the mechanistic details of their operation at the single-molecule level is hampered by the diffraction limit, which prevents the collection of dynamic posi-tional information by traditional optical methods. Here we use defocused wide-field imaging to examine the unidirectional rotation of individual molecular rotary motors on a quartz surface in unprecedented detail...
May 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28495969/fold-change-detection-and-scale-invariance-of-cell-cell-signaling-in-social-amoeba
#18
Keita Kamino, Yohei Kondo, Akihiko Nakajima, Mai Honda-Kitahara, Kunihiko Kaneko, Satoshi Sawai
Cell-cell signaling is subject to variability in the extracellular volume, cell number, and dilution that potentially increase uncertainty in the absolute concentrations of the extracellular signaling molecules. To direct cell aggregation, the social amoebae Dictyostelium discoideum collectively give rise to oscillations and waves of cyclic adenosine 3',5'-monophosphate (cAMP) under a wide range of cell density. To date, the systems-level mechanism underlying the robustness is unclear. By using quantitative live-cell imaging, here we show that the magnitude of the cAMP relay response of individual cells is determined by fold change in the extracellular cAMP concentrations...
May 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28494964/near-membrane-refractometry-using-supercritical-angle-fluorescence
#19
Maia Brunstein, Lopamudra Roy, Martin Oheim
Total internal reflection fluorescence (TIRF) microscopy and its variants are key technologies for visualizing the dynamics of single molecules or organelles in live cells. Yet truly quantitative TIRF remains problematic. One unknown hampering the interpretation of evanescent-wave excited fluorescence intensities is the undetermined cell refractive index (RI). Here, we use a combination of TIRF excitation and supercritical angle fluorescence emission detection to directly measure the average RI in the "footprint" region of the cell during image acquisition...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28494367/enhanced-detection-sensitivity-of-carcinoembryonic-antigen-on-a-plasmonic-nanoimmunosensor-by-transmission-grating-based-total-internal-reflection-scattering-microscopy
#20
Sujin Ahn, Hyunung Yu, Seong Ho Kang
Carcinoembryonic antigen (CEA) is a glycoprotein associated with colorectal carcinomas and is commonly used as a clinical tumor marker. Enhanced detection sensitivity for the assay of CEA molecules was achieved on a plasmonic nanoimmunosensor by wavelength-dependent transmission grating (TG)-based total internal reflection scattering microscopy (TIRSM). The plasmonic nanoparticles were placed in an evanescent field layer on a glass nanoimmunosensor that produced evanescent wave scattering by the total internal reflection of light from two lasers...
May 4, 2017: Biosensors & Bioelectronics
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