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https://www.readbyqxmd.com/read/28415349/decorrelation-correction-for-nanoparticle-tracking-analysis-of-dilute-polydisperse-suspensions-in-bulk-flow
#1
John Hartman, Brian Kirby
Nanoparticle tracking analysis, a multiprobe single particle tracking technique, is a widely used method to quickly determine the concentration and size distribution of colloidal particle suspensions. Many popular tools remove non-Brownian components of particle motion by subtracting the ensemble-average displacement at each time step, which is termed dedrifting. Though critical for accurate size measurements, dedrifting is shown here to introduce significant biasing error and can fundamentally limit the dynamic range of particle size that can be measured for dilute heterogeneous suspensions such as biological extracellular vesicles...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415337/mean-squared-displacement-statistical-test-for-fractional-brownian-motion
#2
Grzegorz Sikora, Krzysztof Burnecki, Agnieszka Wyłomańska
Anomalous diffusion in crowded fluids, e.g., in cytoplasm of living cells, is a frequent phenomenon. A common tool by which the anomalous diffusion of a single particle can be classified is the time-averaged mean square displacement (TAMSD). A classical mechanism leading to the anomalous diffusion is the fractional Brownian motion (FBM). A validation of such process for single-particle tracking data is of great interest for experimentalists. In this paper we propose a rigorous statistical test for FBM based on TAMSD...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28402886/three-dimensional-super-resolution-in-eukaryotic-cells-using-the-double-helix-point-spread-function
#3
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
https://www.readbyqxmd.com/read/28402875/tracking-low-copy-transcription-factors-in-living-bacteria-the-case-of-the-lac-repressor
#4
Federico Garza de Leon, Laura Sellars, Mathew Stracy, Stephen J W Busby, Achillefs N Kapanidis
Transcription factors control the expression of genes by binding to specific sites in DNA and repressing or activating transcription in response to stimuli. The lac repressor (LacI) is a well characterized transcription factor that regulates the ability of bacterial cells to uptake and metabolize lactose. Here, we study the intracellular mobility and spatial distribution of LacI in live bacteria using photoactivated localization microscopy combined with single-particle tracking. Since we track single LacI molecules in live cells by stochastically photoactivating and observing fluorescent proteins individually, there are no limitations on the copy number of the protein under study; as a result, we were able to study the behavior of LacI in bacterial strains containing the natural copy numbers (∼40 monomers), as well as in strains with much higher copy numbers due to LacI overexpression...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28398558/studying-the-structural-optical-chemical-and-electrochemical-etching-changes-of-cr-39-for-dosemetric-applications
#5
M F Zaki, Y H Elshaer, Doaa H Taha
The present work shows the induced modification of the structural, optical, chemical etching and electrochemical etching parameters of CR-39 irradiated with alpha-particles. CR-39 polymer track detectors were irradiated with different fluences (1.62 × 106, 2.72 × 106, 3.82 × 106 and 5.21 × 106 particles/cm2) of alpha-particles using 241Am source. The structural and optical properties were measured by FT-IR spectroscopy, X-ray diffraction and UV/Vis spectroscopy, respectively. The FT-IR spectra reveal that no major changes in the typical functional groups of irradiated polymer detectors...
April 7, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/28396602/nanoplasmonic-upconverting-nanoparticles-as-orientation-sensors-for-single-particle-microscopy
#6
Kory K Green, Janina Wirth, Shuang F Lim
We showed that the anisotropic disk shape of nanoplasmonic upconverting nanoparticles (NP-UCNPs) creates changes in fluorescence intensity during rotational motion. We determined the orientation by a three-fold change in fluorescence intensity. We further found that the luminescence intensity was strongly dependent on the particle orientation and on polarization of the excitation light. The luminescence intensity showed a three-fold difference between flat and on-edge orientations. The intensity also varied sinusoidally with the polarization of the incident light, with an Imax/Imin ratio of up to 2...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28394326/intraflagellar-transport-dynein-is-autoinhibited-by-trapping-of-its-mechanical-and-track-binding-elements
#7
Katerina Toropova, Miroslav Mladenov, Anthony J Roberts
Cilia are multifunctional organelles that are constructed using intraflagellar transport (IFT) of cargo to and from their tip. It is widely held that the retrograde IFT motor, dynein-2, must be controlled in order to reach the ciliary tip and then unleashed to power the return journey. However, the mechanism is unknown. Here, we systematically define the mechanochemistry of human dynein-2 motors as monomers, dimers, and multimotor assemblies with kinesin-II. Combining these data with insights from single-particle EM, we discover that dynein-2 dimers are intrinsically autoinhibited...
April 10, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28379846/sted-microscopy-visualizes-energy-deposition-of-single-ions-in-a-solid-state-detector-beyond-diffraction-limit
#8
M Niklas, M Henrich, O Jäkel, J Engelhardt, A Abdollahi, S Greilich
Fluorescent nuclear track detectors (FNTDs) allow for visualization of single-particle traversal in clinical ion beams. The point spread function of the confocal readout has so far hindered a more detailed characterization of the track spots-the ion's characteristic signature left in the FNTD. Here we report on the readout of the FNTD by optical nanoscopy, namely stimulated emission depletion microscopy. It was firstly possible to visualize the track spots of carbon ions and protons beyond the diffraction limit of conventional light microscopy with a resolving power of approximately 80 nm (confocal: 320 nm)...
April 5, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28371581/single-particle-tracking-of-human-immunodeficiency-virus-type-1-productive-entry-into-human-primary-macrophages
#9
Qin Li, Wei Li, Wen Yin, Jia Guo, Zhi-Ping Zhang, Dejun Zeng, Xiaowei Zhang, Yuntao Wu, Xian-En Zhang, Zongqiang Cui
Macrophages are one of the major targets of human immunodeficiency virus (HIV-1), but the viral entry pathway remains poorly understood in these cells. Noninvasive virus labeling and single-virus tracking are effective tools for studying virus entry. Here, we constructed a quantum dot (QD)-encapsulated infectious HIV-1 particle to track viral entry at a single-particle level in live human primary macrophages. QDs were encapsulated in HIV-1 virions by incorporating viral accessory protein Vpr-conjugated QDs during virus assembly...
April 6, 2017: ACS Nano
https://www.readbyqxmd.com/read/28368853/three-dimensional-reconstruction-of-therapeutic-carbon-ion-beams-in-phantoms-using-single-secondary-ion-tracks
#10
Anna Merle Reinhart, Claudia Katharina Spindeldreier, Jan Jakubek, Maria Martisikova
Carbon ion beam radiotherapy enables a very localised dose deposition. However, already small changes in the patient geometry or positioning errors can significantly distort the dose distribution. A live, non-invasive monitoring system of the beam delivery within the patient is therefore highly desirable and could improve patient treatment. We present a novel three-dimensional imaging method of the beam in the irradiated object, exploiting the measured tracks of single secondary ions emerging under irradiation...
April 3, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28365760/smoldyn-particle-based-simulation-with-rule-based-modeling-improved-molecular-interaction-and-a-library-interface
#11
Steven S Andrews
Motivation: Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features. Results: Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which is better for complicated models...
March 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28350474/detachment-of-membrane-bound-virions-by-competitive-ligand-binding-induced-receptor-depletion
#12
Nagma Parveen, Stephan Block, Vladimir P Zhdanov, Gustaf E Rydell, Fredrik Höök
Multivalent receptor-mediated interactions between virions and a lipid membrane can be weakened using competitive nonpathogenic ligand binding. In particular, the subsequent binding of such ligands can induce detachment of bound virions, a phenomenon of crucial relevance for the development of new antiviral drugs. Focusing on the simian virus 40 (SV40) and recombinant cholera toxin B subunit (rCTB), and using (monosialotetrahexosyl)ganglioside (GM1) as their common receptor in a supported lipid bilayer (SLB), we present the first detailed investigation of this phenomenon by employing the quartz crystal microbalance with dissipation (QCM-D) and total internal reflection fluorescence (TIRF) microscopy assisted 2D single particle tracking (SPT) techniques...
April 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28344779/accuracy-of-the-detection-of-binding-events-using-3d-single-particle-tracking
#13
Sara Carozza, Jamie Culkin, John van Noort
BACKGROUND: Nanoparticles can be used as markers to track the position of biomolecules, such as single proteins, inside living cells. The activity of a protein can sometimes be inferred from changes in the mobility of the attached particle. Mean Square Displacement analysis is the most common method to obtain mobility information from trajectories of tracked particles, such as the diffusion coefficient D. However, the precision of D sets a limit to discriminate changes in mobility caused by biological events from changes that reflect the stochasticity inherent to diffusion...
2017: BMC Biophysics
https://www.readbyqxmd.com/read/28340764/revisiting-the-fission-track-method-for-the-analysis-of-particles-in-safeguards-environmental-samples
#14
N Dzigal, E Chinea-Cano, S Walsh, A Limbeck
This paper details an improved approach to environmental particle analysis for safeguards by means of a combination of an upgraded version of the so-called fission track method with state-of-the-art microscope and microprobe techniques. Improvements to the fission track method comprise a novel sample assembly, the automation of several of its steps and the extensive use of correlative microscopy. This is followed by an automated isolation of particles-of-interest by means of laser micro-dissection (LMD) and their collection onto a harvester for transfer to other micro-analytical instruments for further analysis...
May 15, 2017: Talanta
https://www.readbyqxmd.com/read/28339189/polymerization-induced-self-assembly-pisa-control-over-the-morphology-of-19-f-containing-polymeric-nano-objects-for-cell-uptake-and-tracking
#15
Wei Zhao, Hang T Ta, Cheng Zhang, Andrew K Whittaker
Fluorine-containing polymeric materials are receiving increasing attention as imaging probes in fluorine-19 magnetic resonance imaging ((19)F MRI), for example to enable quantitative in vivo detection of cells. Here we describe the one-pot polymerization synthesis of (19)F-containing functional poly(oligo(ethylene glycol) methyl ether methacrylate-co-2,2,2-trifluoroethyl acrylate-b-poly(styrene-co-3-vinylbenzaldehyde) (poly(OEGA-co-TFEA)-b-poly(St-co-VBA)) copolymers as a new class of fluorinated MRI agent...
March 30, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28321960/hiv-infection-is-influenced-by-dynamin-at-three-independent-points-in-the-viral-life-cycle
#16
Anupriya Aggarwal, Tina L Hitchen, Lars Ootes, Samantha McAllery, Andrew Wong, Khanh Nguyen, Adam McCluskey, Phillip J Robinson, Stuart G Turville
CD4 T cells are important cellular targets for HIV-1, yet the primary site of HIV fusion remains unresolved. Candidate fusion sites are either the plasma membrane or from within endosomes. One area of investigation compounding the controversy of this field, is the role of the protein dynamin in the HIV life cycle. To understand the role of dynamin in primary CD4 T cells we combined dynamin inhibition with a series of complementary assays based on single particle tracking, HIV fusion, detection of HIV DNA products and active viral transcription...
March 21, 2017: Traffic
https://www.readbyqxmd.com/read/28317988/using-single-nanoparticle-tracking-obtained-by-nanophotonic-force-microscopy-to-simultaneously-characterize-nanoparticle-size-distribution-and-nanoparticle-surface-interactions
#17
Delyan R Hristov, Dong Ye, Joao Medeiros de Araújo, Colby Ashcroft, Brian DiPaolo, Robert Hart, Christopher Earhart, Hender Lopez, Kenneth A Dawson
Comprehensive characterization of nanomaterials for medical applications is a challenging and complex task due to the multitude of parameters which need to be taken into consideration in a broad range of conditions. Routine methods such as dynamic light scattering or nanoparticle tracking analysis provide some insight into the physicochemical properties of particle dispersions. For nanomedicine applications the information they supply can be of limited use. For this reason, there is a need for new methodologies and instruments that can provide additional data on nanoparticle properties such as their interactions with surfaces...
March 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28294967/single-lipid-molecule-dynamics-on-supported-lipid-bilayers-with-membrane-curvature
#18
Philip P Cheney, Alan W Weisgerber, Alec M Feuerbach, Michelle K Knowles
The plasma membrane is a highly compartmentalized, dynamic material and this organization is essential for a wide variety of cellular processes. Nanoscale domains allow proteins to organize for cell signaling, endo- and exocytosis, and other essential processes. Even in the absence of proteins, lipids have the ability to organize into domains as a result of a variety of chemical and physical interactions. One feature of membranes that affects lipid domain formation is membrane curvature. To directly test the role of curvature in lipid sorting, we measured the accumulation of two similar lipids, 1,2-Dihexadecanoyl-sn-glycero-3-phosphoethanolamine (DHPE) and hexadecanoic acid (HDA), using a supported lipid bilayer that was assembled over a nanopatterned surface to obtain regions of membrane curvature...
March 15, 2017: Membranes
https://www.readbyqxmd.com/read/28290531/mapping-cell-surface-adhesion-by-rotation-tracking-and-adhesion-footprinting
#19
Isaac T S Li, Taekjip Ha, Yann R Chemla
Rolling adhesion, in which cells passively roll along surfaces under shear flow, is a critical process involved in inflammatory responses and cancer metastasis. Surface adhesion properties regulated by adhesion receptors and membrane tethers are critical in understanding cell rolling behavior. Locally, adhesion molecules are distributed at the tips of membrane tethers. However, how functional adhesion properties are globally distributed on the individual cell's surface is unknown. Here, we developed a label-free technique to determine the spatial distribution of adhesive properties on rolling cell surfaces...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28268807/3d-limb-movement-tracking-and-analysis-for-neurological-dysfunctions-of-neonates-using-multi-camera-videos
#20
Irene Yu-Hua Gu, Grzegorz Sowulewski, Yixiao Yun, Anders Flisberg, Magnus Thordstein
Central nervous system dysfunction in infants may be manifested through inconsistent, rigid and abnormal limb movements. Detection of limb movement anomalies associated with such neurological dysfunctions in infants is the first step towards early treatment for improving infant development. This paper addresses the issue of detecting and quantifying limb movement anomalies in infants through non-invasive 3D image analysis methods using videos from multiple camera views. We propose a novel scheme for tracking 3D time trajectories of markers on infant's limbs by video analysis techniques...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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