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https://www.readbyqxmd.com/read/28646301/random-initialisation-of-the-spectral-variables-an-alternate-approach-for-initiating-multivariate-curve-resolution-alternating-least-square-mcr-als-analysis
#1
Keshav Kumar
Multivariate curve resolution alternating least square (MCR-ALS) analysis is the most commonly used curve resolution technique. The MCR-ALS model is fitted using the alternate least square (ALS) algorithm that needs initialisation of either contribution profiles or spectral profiles of each of the factor. The contribution profiles can be initialised using the evolve factor analysis; however, in principle, this approach requires that data must belong to the sequential process. The initialisation of the spectral profiles are usually carried out using the pure variable approach such as SIMPLISMA algorithm, this approach demands that each factor must have the pure variables in the data sets...
June 23, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28645380/comet-fish-for-ultrasensitive-strand-specific-detection-of-dna-damage-in-single-cells
#2
Manas Mondal, Jia Guo
The genome integrity of living organisms is constantly threatened by endogenous cellular metabolic processes and environmental agents. To quantify these low, physiologically relevant levels of DNA damage, a single-cell gel electrophoresis (comet) combined with strand-specific fluorescence in situ hybridization (FISH)-based approach has been developed. This approach enables the quantification of low levels of specific DNA lesions in each strand of the selected sequence at the single-molecule sensitivity, as well as in the genome overall in single cells...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28644802/fully-non-linear-sp3-approximation-based-fluorescence-optical-tomography
#3
Naren Naik, Nishigandha Patil, Yamini Yadav, Jerry Eriksson, Asima Pradhan
In fluorescence optical tomography, many works in literature focus on the linear reconstruction problem to obtain the fluorescent yield or the linearized reconstruction problem to obtain the absorption coefficient. The nonlinear reconstruction problem, to reconstruct the fluorophore absorption coefficient, is of interest in imaging studies as it presents the possibility of better reconstructions owing to a more appropriate model. Accurate and computationally efficient forward models are also critical in the reconstruction process...
June 21, 2017: IEEE Transactions on Medical Imaging
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/28641018/three-dimensional-imaging-of-transparent-tissues-via-metal-nanoparticle-labeling
#5
Abdullah Muhammad Syed, Shrey Sindhwani, Stefan Wilhelm, Benjamin R Kingston, Dennis S W Lee, Jennifer L Gommerman, Warren C W Chan
Chemical probes are key components of the bioimaging toolbox as they label biomolecules in cells and tissues. The new challenge in bioimaging is to design chemical probes for 3-Dimensional (3D) tissue imaging. Here, we discovered that the scattering of metal nanoparticles can provide imaging contrast in intact tissues in 3D. The nanoparticles can act as a template for chemically growing a metal layer to further enhance the scattering signal. The use of chemically-grown nanoparticles in whole tissues can amplify the scattering to produce a 1...
June 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28640518/a-carborane-containing-fluorophore-as-a-stain-of-cellular-lipid-droplets
#6
Andrew Wu, Jacek L Kolanowski, Badwi B Boumelhem, Kylie Yang, Rebecca Lee, Amandeep Kaur, Stuart T Fraser, Elizabeth J New, Louis M Rendina
The use of fluorescent markers and probes greatly enhances biological investigations but relies on the provision of an array of fluorophores with diverse properties. Herein we report a novel carborane-containing coumarin, 5, which is sufficiently lipophilic to localise in cellular lipid droplets. In non-polar solvents which show comparable polarities to those of a lipid environment, compound 5 exhibits a fluorescence quantum yield two orders of magnitude greater than found in aqueous solvents, adding a further degree of selectivity to lipid droplet imaging...
June 22, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28640486/dendrimer-based-signal-amplification-of-click-labelled-dna-in-situ
#7
Nada Raddaoui, Samuele Stazzoni, Leonhard Möckl, Bastien Viverge, Florian Geiger, Hanna Engelke, Christoph Bräuchle, Thomas Carell
The in vivo incorporation of alkyne modified bases into the genome of cells is today the basis for efficient detection of cell proliferation. Cells are grown in the presence of ethinyl-dU (EdU), fixed and permeabilized. The incorporated alkynes are then efficiently detected using azide-containing fluorophores and the Cu(I) catalyzed alkyne-azide click reaction. In a world where constant improvement of the sensitivity of a given method is driving diagnostic advancement, we developed azide and alkyne modified dendrimers that allow to establish sandwich-type detection assays that show significantly improved signal intensities and signal to noise ratios far beyond of what is currently possible...
June 22, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28639669/plasmon-enhanced-fluorescence-spectroscopy
#8
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/28638473/rapid-fluorescence-imaging-of-spinal-cord-following-epidural-administration-of-a-nerve-highlighting-fluorophore
#9
Wanguo Liu, Rui Gu, Qingsan Zhu, Chunsheng Xiao, Lanfeng Huang, Xinming Zhuang, Jingzhe Zhang, Lidi Liu, Ben Ma, Huailin Yang, Jianchao Ma, Zhipeng Hu, Chenglin Tang, Shuhua Zhao, Xuesi Chen
Iatrogenic spinal cord injury (SCI) is the most devastating complication of spine surgery, which usually results in permanent and serious disabilities of patients. Improvement of the visualization and discrimination of the spinal cord is critical for accuracy and safety during surgery; however, to date, there is no suitable technology to fulfill this clinical need. Here, we first show an efficient and rapid fluorescence imaging of the spinal cord in rabbit by epidural administration of a nerve-highlighting fluorophore, i...
2017: Theranostics
https://www.readbyqxmd.com/read/28638177/highly-luminescent-water-dispersible-nir-emitting-wurtzite-cuins2-zns-core-shell-colloidal-quantum-dots
#10
Chenghui Xia, Johannes D Meeldijk, Hans C Gerritsen, Celso de Mello Donega
Copper indium sulfide (CIS) quantum dots (QDs) are attractive as labels for biomedical imaging, since they have large absorption coefficients across a broad spectral range, size- and composition-tunable photoluminescence from the visible to the near-infrared, and low toxicity. However, the application of NIR-emitting CIS QDs is still hindered by large size and shape dispersions and low photoluminescence quantum yields (PLQYs). In this work, we develop an efficient pathway to synthesize highly luminescent NIR-emitting wurtzite CIS/ZnS QDs, starting from template Cu2-x S nanocrystals (NCs), which are converted by topotactic partial Cu(+) for In(3+) exchange into CIS NCs...
June 13, 2017: Chemistry of Materials: a Publication of the American Chemical Society
https://www.readbyqxmd.com/read/28636537/metabolic-pathway-for-the-universal-fluorescent-recognition-of-tumor-cells
#11
Ana Fernandez-Carrascal, Manuel Garcia-Algar, Moritz Nazarenus, Alicia Torres-Nuñez, Luca Guerrini, Neus Feliu, Wolfgang J Parak, Eduardo Garcia-Rico, Ramon A Alvarez-Puebla
Quantification of circulating tumor cells (CTCs) in blood samples from cancer patients is a non-invasive approach to monitoring the status of the disease. Most of the methods proposed in the recent years are phenomenological and rely on the use of antibodies labelled with fluorophores, magnetic particles, or immobilized on surfaces to capture the CTCs. Herein, we designed and optimized a method that employs a glucose analogue labelled with a fluorophore which takes advantage of the different metabolic pathways of cancer cells to discern them from normal ones...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636039/a-convenient-method-for-multicolour-labelling-of-proteins-with-bodipy-fluorophores-via-tyrosine-residues
#12
Miffy H Y Cheng, Huguette Savoie, Francesca Bryden, Ross W Boyle
Fluorescence is an essential imaging modality for labelling and visualising cells and sub-cellular structures. Multicolour labelling is especially challenging due to differences in physicochemical and photophysical behaviour of structurally unrelated fluorophores in the heterogeneous environments found in sub-cellular compartments. Herein, we report the conjugation of three azide-bearing BODIPYs with similar core structures but widely different emission wavelengths (green, red and NIR) to tyrosine residues of a model globular protein (BSA) via a common linking methodology...
June 21, 2017: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/28636018/fluorescence-lifetime-microscopy-reveals-the-biologically-related-photophysical-heterogeneity-of-oxyblepharismin-in-light-adapted-blue-blepharisma-japonicum-cells
#13
G Checcucci, B Storti, F Ghetti, G Signore, R Bizzarri
The step-up photophobic response of the heterotrich ciliate Blepharisma japonicum is mediated by a hypericinic pigment, blepharismin, which is not present in any of the known six families of photoreceptors, namely rhodopsins, phytochromes, xanthopsins, cryptochromes, phototropins, and BLUF proteins. Upon irradiation, native cells become light-adapted (blue) by converting blepharismin into the photochemically stable oxyblepharismin (OxyBP). So far, OxyBP has been investigated mainly from a photophysical point of view in vitro, either alone or complexed with proteins...
June 21, 2017: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/28632960/snap-tag-based-subcellular-proteins-labeling-and-fluorescent-imaging-with-naphthalimides
#14
Chao Wang, Xinbo Song, Yi Xiao
Genetically encoded technologies provide methods for specific labeling and imaging of proteins, which is essential for the understanding of their subcellular localization and function. Herein, we employ naphthalimide, an efficient two-photon fluorophore, to develop O6-benzylguanine (BG) derivatives for specific labeling of subcellular proteins and fluorescent imaging through the SNAP-tag. The three naphthalimide-BG derivatives, TNI-BG, QNI-BG and ONI-BG are conveniently synthesized through modular "click chemistry" with high yields...
June 20, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28632383/taking-advantage-of-disorder-small-molecule-organic-glasses-for-radiation-detection-and-particle-discrimination
#15
Joseph S Carlson, Peter Marleau, Ryan A Zarkesh, Patrick L Feng
A series of fluorescent silyl-fluorene molecules were synthesized and studied with respect to their photophysical properties and response toward ionizing neutron and gamma-ray radiation. Optically transparent and stable organic glasses were prepared from these materials using a bulk melt-casting procedure. The prepared organic glass monoliths provided fluorescence quantum yields and radiation detection properties exceeding the highest-performing benchmark materials such as solution-grown trans-stilbene crystals...
June 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28631591/comparative-evaluation-of-veriflow-%C3%A2-listeria-species-to-usda-culture-based-method-for-the-detection-of-listeria-spp-in-food-and-environmental-samples
#16
Adam C Joelsson, Shawn P Terkhorn, Ashley S Brown, Amrita Puri, Benjamin J Pascal, Zara E Gaudioso, Nicholas A Siciliano
Veriflow(®)Listeria species (Veriflow LS) isa molecular-based assay for the presumptive detection of Listeria spp. from environmental surfaces (stainless steel, sealed concrete, plastic, and ceramic tile) and ready-to-eat (RTE) food matrixes (hot dogs and deli meat). The assay utilizes a PCR detection method coupled with a rapid, visual, flow-based assay that develops in 3 min post-PCR amplification and requires only a 24 h enrichment for maximum sensitivity. The Veriflow LS system eliminates the need for sample purification, gel electrophoresis, or fluorophore-based detection of target amplification and does not require complex data analysis...
June 20, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28631590/comparative-evaluation-of-veriflow-%C3%A2-salmonella-species-to-usda-and-fda-culture-based-methods-for-the-detection-of-salmonella-spp-in-food-and-environmental-samples
#17
Amrita Puri, Adam C Joelsson, Shawn P Terkhorn, Ashley S Brown, Zara E Gaudioso, Nicholas A Siciliano
Veriflow(®)Salmonella species (Veriflow SS)is a molecular-based assay for the presumptive detection of Salmonella spp. from environmental surfaces (stainless steel, sealed concrete, plastic, and ceramic tile), dairy (2% milk), raw meat (20% fat ground beef), chicken carcasses, and ready-to-eat (RTE) food (hot dogs). The assay utilizes a PCR detection method coupled with a rapid, visual, flow-based assay that develops in 3 min post-PCR amplification and requires only an 18 h enrichment for maximum sensitivity...
June 20, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28631482/carbohydrate-bis-acetal-based-substrates-as-tunable-fluorescence-quenched-probes-for-monitoring-exo-glycosidase-activity
#18
Samy Cecioni, David J Vocadlo
Tunable Förster resonance energy transfer (FRET)-quenched substrates are useful for monitoring the activity of various enzymes within their relevant physiological environments. Development of FRET-quenched substrates for exo-glycosidases, however, has been hindered by their constrained pocket-shaped active sites. Here we report the design of a new class of substrate that overcomes this problem. These Bis-Acetal-Based Substrates (BABS) bear a hemiacetal aglycon leaving group that tethers fluorochromes in close proximity, also positioning them distant from the active site pocket...
June 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28630487/multicolor-two-photon-imaging-of-endogenous-fluorophores-in-living-tissues-by-wavelength-mixing
#19
Chiara Stringari, Lamiae Abdeladim, Guy Malkinson, Pierre Mahou, Xavier Solinas, Isabelle Lamarre, Sébastien Brizion, Jean-Baptiste Galey, Willy Supatto, Renaud Legouis, Ana-Maria Pena, Emmanuel Beaurepaire
Two-photon imaging of endogenous fluorescence can provide physiological and metabolic information from intact tissues. However, simultaneous imaging of multiple intrinsic fluorophores, such as nicotinamide adenine dinucleotide(phosphate) (NAD(P)H), flavin adenine dinucleotide (FAD) and retinoids in living systems is generally hampered by sequential multi-wavelength excitation resulting in motion artifacts. Here, we report on efficient and simultaneous multicolor two-photon excitation of endogenous fluorophores with absorption spectra spanning the 750-1040 nm range, using wavelength mixing...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630286/efficient-switching-of-mcherry-fluorescence-using-chemical-caging
#20
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
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