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Single molecule microscopy

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https://www.readbyqxmd.com/read/27919801/folic-acid-capped-pegylated-magnetic-nanoparticles-enter-cancer-cells-mostly-via-clathrin-dependent-endocytosis
#1
Emilie Allard-Vannier, Katel Hervé-Aubert, Karine Kaaki, Thibaut Blondy, Anastasia Shebanova, Konstantin V Shaitan, Anastasia A Ignatova, Marie-Louise Saboungi, Alexey V Feofanov, Igor Chourpa
BACKGROUND: This work is focused on mechanisms of uptake in cancer cells of rationally designed, covalently assembled nanoparticles, made of superparamagnetic iron oxide nanoparticles (SPIONs), fluorophores (doxorubicin or Nile Blue), polyethylene glycol (PEG) and folic acid (FA), referred hereinafter as SFP-FA. METHODS: SFP-FA were characterized by DLS, zetametry and fluorescence spectroscopy. The SFP-FA uptake in cancer cells was monitored using fluorescence-based methods like fluorescence-assisted cell sorting, LSCM with single-photon and two-photon excitation...
December 2, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27919690/comparative-analysis-of-different-xanthan-samples-by-atomic-force-microscopy
#2
Julia Teckentrup, Orooba Al-Hammood, Tim Steffens, Hanna Bednarz, Volker Walhorn, Karsten Niehaus, Dario Anselmetti
The polysaccharide xanthan which is produced by the γ-proteobacterium Xanthomonas campestris is used as a food thickening agent and rheologic modifier in numerous food, cosmetics and technical applications. Its great commercial importance stimulated biotechnological approaches to optimize the xanthan production. By targeted genetic modification the metabolism of Xanthomonas can be modified in such a way that the xanthan production efficiency and/or the shear-thickening potency is optimized. Using atomic force microscopy (AFM) the secondary structure of single xanthan polymers produced by the wild type Xanthomonas campestris B100 and several genetically modified variations were analyzed...
December 2, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27916824/graphene-oxide-nanoribbons-induce-autophagic-vacuoles-in-neuroblastoma-cell-lines
#3
Emanuela Mari, Stefania Mardente, Emanuela Morgante, Marco Tafani, Emanuela Lococo, Flavia Fico, Federica Valentini, Alessandra Zicari
Since graphene nanoparticles are attracting increasing interest in relation to medical applications, it is important to understand their potential effects on humans. In the present study, we prepared graphene oxide (GO) nanoribbons by oxidative unzipping of single-wall carbon nanotubes (SWCNTs) and analyzed their toxicity in two human neuroblastoma cell lines. Neuroblastoma is the most common solid neoplasia in children. The hallmark of these tumors is the high number of different clinical variables, ranging from highly metastatic, rapid progression and resistance to therapy to spontaneous regression or change into benign ganglioneuromas...
November 29, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27906373/efficient-homogeneous-illumination-and-optical-sectioning-for-quantitative-single-molecule-localization-microscopy
#4
Joran Deschamps, Andreas Rowald, Jonas Ries
Single-molecule localization microscopy (SMLM) relies on the switching of fluorescent molecules between a fluorescent and a dark state to achieve super resolution. This process is inherently dependent on the intensity distribution of the laser light used for both activation from the dark state and excitation of the bright state. Typically, laser light is coupled directly or via a single-mode fiber into the microscope, which leads to a Gaussian intensity profile in total internal reflection (TIR) or epi illumination...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27905323/plasmonic-nano-protrusions-hierarchical-nanostructures-for-single-molecule-raman-spectroscopy
#5
Sagnik Basuray, Avinash Pathak, Sangho Bok, Biyan Chen, Steven C Hamm, Cherian J Mathai, Suchismita Guha, Keshab Gangopadhyay, Shubhra Gangopadhyay
Classical methods for enhancing the electromagnetic field from substrates for spectroscopic applications, such as surface-enhanced Raman spectroscopy (SERS), have involved the generation of hotspots through directed self-assembly of nanoparticles or by patterning nanoscale features using expensive nanolithography techniques. A novel large-area, cost-effective soft lithographic technique involving glancing angle deposition (GLAD) of silver on polymer gratings is reported here. This method produces hierarchical nanostructures with high enhancement factors capable of analyzing single-molecule SERS...
December 1, 2016: Nanotechnology
https://www.readbyqxmd.com/read/27896559/antiviral-activity-of-hemolymph-of-podalia-against-rubella-virus
#6
N D Carvalho, R Z Mendonça, M I Oliveira, S P Curti, T F Barbosa, P E Silva, N N Taniwaki, M Tonelotto, D N S Giovanni, R H P Moraes, C A Figueiredo
Many active principles produced by animals, plants and microorganisms have been employed in the development of new drugs for the treatment of human diseases. Among animals known to produce pharmacologically active molecules that interfere in human cell physiology. Rubella virus (genus Rubivirus, family Togaviridae) is a single stranded RNA virus of positive genome polarity. Rubella virus infection of susceptible women during the first trimester of pregnancy often results in long-term virus persistence in the fetus causing multiple organ abnormalities...
November 28, 2016: Cytotechnology
https://www.readbyqxmd.com/read/27892536/investigation-of-cell-substrate-adhesion-properties-of-living-chondrocyte-by-measuring-adhesive-shear-force-and-detachment-using-afm-and-inverse-fea
#7
Trung Dung Nguyen, YuanTong Gu
It is well-known that cell adhesion is important in many biological processes such as cell migration and proliferation. A better understanding of the cell adhesion process will shed insight into these cellular biological responses as well as cell adhesion-related diseases treatment. However, there is little research which has attempted to investigate the process of cell adhesion and its mechanism. Thus, this paper aims to study the time-dependent adhesion properties of single living chondrocytes using an advanced coupled experimental-numerical approach...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27888215/super-resolution-microscopy-reveals-the-reorganization-of-glut4-on-plasma-membrane-regulated-by-insulin-resistance
#8
Lan Gao, Junling Chen, Jing Gao, Hongda Wang, Wenyong Xiong
GLUT4 is essential for glucose uptake in skeletal muscles and adipocytes, which play central roles in whole-body glucose metabolism. Here, using direct stochastic optical reconstruction microscopy (dSTORM) to investigate the characteristics of the plasma membrane (PM) fused GLUT4 at the single-molecule level, we demonstrated that insulin and insulin resistance regulated the spatial organization of GLUT4 in adipocytes. Stimulation of insulin shifted the balance of GLUT4 on the PM toward a more dispersed configuration...
November 25, 2016: Journal of Cell Science
https://www.readbyqxmd.com/read/27885259/trackntrace-a-simple-and-extendable-open-source-framework-for-developing-single-molecule-localization-and-tracking-algorithms
#9
Simon Christoph Stein, Jan Thiart
Super-resolution localization microscopy and single particle tracking are important tools for fluorescence microscopy. Both rely on detecting, and tracking, a large number of fluorescent markers using increasingly sophisticated computer algorithms. However, this rise in complexity makes it difficult to fine-tune parameters and detect inconsistencies, improve existing routines, or develop new approaches founded on established principles. We present an open-source MATLAB framework for single molecule localization, tracking and super-resolution applications...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27883140/single-molecule-fluorescence-resonance-energy-transfer-in-molecular-biology
#10
REVIEW
Dibyendu K Sasmal, Laura E Pulido, Shan Kasal, Jun Huang
Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics...
November 24, 2016: Nanoscale
https://www.readbyqxmd.com/read/27883139/clustered-localization-of-egfrviii-in-glioblastoma-cells-as-detected-by-high-precision-localization-microscopy
#11
Philip S Boyd, Nina Struve, Margund Bach, Jan Philipp Eberle, Martin Gote, Florian Schock, Christoph Cremer, Malte Kriegs, Michael Hausmann
For receptor tyrosine kinases supramolecular organization on the cell membrane is critical for their function. Super-resolution fluorescence microscopy techniques have offered new opportunities for the analysis of single receptor localization. Here, we analysed the cluster formation of the epidermal growth factor receptor variant III (EGFRvIII), a deletion variant which is expressed in glioblastoma. The constitutively activated variant EGFRvIII is expressed in cells with an egfr gene amplification and is thought to enhance the tumorigenic potential especially of glioblastoma cells...
November 24, 2016: Nanoscale
https://www.readbyqxmd.com/read/27883134/non-fluorescent-quantification-of-single-mrna-with-transient-absorption-microscopy
#12
Jing Liu, Joseph M K Irudayaraj
Single molecule detection is confounded by the background signals from the biological environment, such as autofluorescence, Rayleigh scattering, or turbidity in cells and tissues. In this article, we report on the utilization of gold nanoparticles (AuNPs) as an orthogonal probe for non-fluorescence detection of single molecules with a transient absorption microscopy (TAM). The developed system and concepts were validated by quantitative evaluation of human epidermal receptor 2 (Her2) mRNA in cancer cells and tissues at single copy sensitivity...
November 24, 2016: Nanoscale
https://www.readbyqxmd.com/read/27876857/smart-aggregation-imaging-for-single-molecule-localisation-with-spad-cameras
#13
Istvan Gyongy, Amy Davies, Neale A W Dutton, Rory R Duncan, Colin Rickman, Robert K Henderson, Paul A Dalgarno
Single molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27872870/nanoscale-organization-of-synaptic-adhesion-proteins-revealed-by-single-molecule-localization-microscopy
#14
Ingrid Chamma, Florian Levet, Jean-Baptiste Sibarita, Matthieu Sainlos, Olivier Thoumine
The advent of superresolution imaging has created a strong need for both optimized labeling strategies and analysis methods to probe the nanoscale organization of complex biological structures. We present a thorough description of the distribution of synaptic adhesion proteins at the nanoscopic scale, namely presynaptic neurexin-[Formula: see text] ([Formula: see text]), and its two postsynaptic binding partners neuroligin-1 (Nlg1) and leucine-rich-repeat transmembrane protein 2 (LRRTM2). We monitored these proteins in the membrane of neurons by direct stochastic optical reconstruction microscopy, after live surface labeling with Alexa647-conjugated monomeric streptavidin...
October 2016: Neurophotonics
https://www.readbyqxmd.com/read/27870840/single-nanotube-tracking-reveals-the-nanoscale-organization-of-the-extracellular-space-in-the-live-brain
#15
Antoine G Godin, Juan A Varela, Zhenghong Gao, Noémie Danné, Julien P Dupuis, Brahim Lounis, Laurent Groc, Laurent Cognet
The brain is a dynamic structure with the extracellular space (ECS) taking up almost a quarter of its volume. Signalling molecules, neurotransmitters and nutrients transit via the ECS, which constitutes a key microenvironment for cellular communication and the clearance of toxic metabolites. The spatial organization of the ECS varies during sleep, development and aging and is probably altered in neuropsychiatric and degenerative diseases, as inferred from electron microscopy and macroscopic biophysical investigations...
November 21, 2016: Nature Nanotechnology
https://www.readbyqxmd.com/read/27866079/multimodal-plasmonic-biosensing-nanostructures-prepared-by-dna-directed-immobilization-of-multifunctional-dna-gold-nanoparticles
#16
Nuria Tort, J-Pablo Salvador, M-Pilar Marco
Biofunctional multimodal plasmonic nanostructures suitable for multiplexed localized surface plasmon resonance (LSPR) biosensing have been created by DNA-directed immobilization (DDI) of two distinct multifunctional biohybrid gold nanoparticles. Gold nanoparticles (AuNP) of distinct sizes, and therefore showing distinct plasmon resonant peaks (RP), have been biofunctionalized and codified with two different single stranded-DNA (ssDNA) chains. One of these oligonucleotide chains has been specifically designed to direct each AuNP to a distinct location of the surface of a DNA microarray chip through specific hybridization with complementary oligonucleotide strands...
November 11, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27865982/hide-and-seek-how-do-dna-glycosylases-locate-oxidatively-damaged-dna-bases-amidst-a-sea-of-undamaged-bases
#17
Andrea J Lee, Susan S Wallace
The first step of the base excision repair (BER) pathway responsible for removing oxidative DNA damage utilizes DNA glycosylases to find and remove the damaged DNA base. How glycosylases find the damaged base amidst a sea of undamaged bases has long been a question in the BER field. Single molecule total internal reflection fluorescence microscopy (SM TIRFM) experiments have allowed for an exciting look into this search mechanism and have found that DNA glycosylases scan along the DNA backbone in a bidirectional and random fashion...
November 16, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27864920/design-of-small-molecule-inhibitors-of-type-iii-secretion-system-atpase-escn-from-enteropathogenic-eecherichia-coli
#18
Lukasz Bzdzion, Hanna Krezel, Karol Wrzeszcz, Irmina Grzegorek, Katarzyna Nowinska, Grzegorz Chodaczek, Wieslaw Swietnicki
Enteropathogenic E. coli (EPEC) is a human pathogen using type III secretion system for delivery of proteins directly into the human host. The system contains a single ATPase, EscN, which is essential for uncoupling of proteins from their complexes with chaperones before the delivery. The structure of EscN ATPase (PDB code: 2obm) was used to screen computationally for small molecule inhibitors blocking its active site. Two lead candidates were examined but only one, Compound 54, was selected for further optimization...
November 18, 2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27859821/covalent-modification-of-highly-ordered-pyrolytic-graphite-with-a-stable-organic-free-radical-using-diazonium-chemistry
#19
Gonca Seber, Alexander Rudnev, Andrea Droghetti, Ivan Rungger, Jaume Veciana, Marta Mas-Torrent, Concepció Rovira, Núria Crivillers
A novel, persistent, electrochemically active perchlorinatedtriphenylmethyl (PTM) radical with a diazonium functionality has been covalently attached onto highly ordered pyrolytic graphite by electrografting in a single-step process. Electrochemical scanning tunneling microscopy (EC-STM) and Raman spectrocopy measurements revealed that PTM molecules have a higher tendency to covalently react at the HOPG step edges. The cross-section profiles from EC-STM images showed that there is current enhancement at the functionalized areas, which can be explained by redox mediated electron tunneling through surface-confined redox-active molecules...
November 18, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27854362/a-bayesian-cluster-analysis-method-for-single-molecule-localization-microscopy-data
#20
Juliette Griffié, Michael Shannon, Claire L Bromley, Lies Boelen, Garth L Burn, David J Williamson, Nicholas A Heard, Andrew P Cope, Dylan M Owen, Patrick Rubin-Delanchy
Cell function is regulated by the spatiotemporal organization of the signaling machinery, and a key facet of this is molecular clustering. Here, we present a protocol for the analysis of clustering in data generated by 2D single-molecule localization microscopy (SMLM)-for example, photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). Three features of such data can cause standard cluster analysis approaches to be ineffective: (i) the data take the form of a list of points rather than a pixel array; (ii) there is a non-negligible unclustered background density of points that must be accounted for; and (iii) each localization has an associated uncertainty in regard to its position...
December 2016: Nature Protocols
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