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single particle tracking

Yiqun Xue, Jingjing Xing, Yinglang Wan, Xueqin Lv, Lusheng Fan, Yongdeng Zhang, Kai Song, Li Wang, Xiaohua Wang, Xin Deng, Frantisek Baluska, John M Christie, Jinxing Lin
Phototropin (phot)-mediated signaling initiated by blue light (BL) plays a critical role in optimizing photosynthetic light capture at the plasma membrane (PM) in plants. However, the mechanisms underlying the regulation of phot activity at the PM in response to BL remain largely unclear. In this study, by single-particle tracking and step-wise photobleaching analysis we demonstrated that in the dark phot1-GFP proteins remain in an inactive state and mostly present as a monomer. The phot1-GFP diffusion rate and its dimerization increased in a dose-dependent manner in response to BL...
April 21, 2018: Molecular Plant
Nadia Peerboom, Eneas Schmidt, Edward Trybala, Stephan Block, Tomas Bergström, Hudson P Pace, Marta Bally
Discovery and development of new antiviral therapies essentially rely on two key factors: an in-depth understanding of the mechanisms involved in viral infection and the development of fast and versatile drug screening platforms. To meet those demands, we present a biosensing platform to probe virus-cell membrane interactions on a single particle level. Our method is based on the formation of supported lipid bilayers from cell membrane material. Using total internal reflection fluorescence microscopy, we report the contribution of viral and cellular components to the interaction kinetics of herpes simplex virus type 1 with the cell membrane...
April 24, 2018: ACS Infectious Diseases
Anna-Karin Gustavsson, Petar N Petrov, Maurice Y Lee, Yoav Shechtman, W E Moerner
To obtain a complete picture of subcellular nanostructures, cells must be imaged with high resolution in all three dimensions (3D). Here, we present tilted light sheet microscopy with 3D point spread functions (TILT3D), an imaging platform that combines a novel, tilted light sheet illumination strategy with engineered long axial range point spread functions (PSFs) for low-background, 3D super localization of single molecules as well as 3D super-resolution imaging in thick cells. TILT3D is built upon a standard inverted microscope and has minimal custom parts...
February 2018: Proceedings of SPIE
Shunsuke Teraguchi, Yutaro Kumagai
BACKGROUND: Time course measurement of single molecules on a cell surface provides detailed information about the dynamics of the molecules that would otherwise be inaccessible. To extract the quantitative information, single particle tracking (SPT) is typically performed. However, trajectories extracted by SPT inevitably have linking errors when the diffusion speed of single molecules is high compared to the scale of the particle density. METHODS: To circumvent this problem, we develop an algorithm to estimate diffusion constants without relying on SPT...
April 11, 2018: BMC Systems Biology
Aaron M Keller, Matthew S DeVore, Dominik G Stich, Dung M Vu, Timothy Causgrove, James H Werner
Single molecule Fluorescence Resonance Energy Transfer (smFRET) remains a widely utilized and powerful tool for quantifying heterogeneous interactions and conformational dynamics of biomolecules. However, traditional smFRET experiments are either limited to short observation times (typically less than 1 ms) in the case of "burst" confocal measurements, or require surface immo-bilization which usually has a temporal resolution limited by the camera framing rate. We developed a smFRET 3D tracking micro-scope that is capable of observing single particles for extended periods of time with high temporal resolution...
April 19, 2018: Analytical Chemistry
Laura Avogaro, Emmanuelle Querido, Myriam Dalachi, Michael F Jantsch, Pascal Chartrand, Emilio Cusanelli
Telomeres cap the ends of eukaryotic chromosomes, protecting them from degradation and erroneous recombination events which may lead to genome instability. Telomeres are transcribed giving rise to telomeric repeat-containing RNAs, called TERRA. The TERRA long noncoding RNAs have been proposed to play important roles in telomere biology, including heterochromatin formation and telomere length homeostasis. While TERRA RNAs are predominantly nuclear and localize at telomeres, little is known about the dynamics and function of TERRA molecules expressed from individual telomeres...
April 16, 2018: RNA Biology
Xuegeng Yang, Dominik Baczyzmalski, Christian Cierpka, Gerd Mutschke, Kerstin Eckert
Electrolytic gas evolution is a fundamental phenomenon occurring in a large number of industrial applications. In these processes gas bubbles are formed at the electrode from a supersaturated solution. Since dissolved gases can change the surface tension, a gas concentration gradient may cause the surface tension to vary locally at the interface of the gas bubble. Surface tension gradients may also form due to temperature gradients generated by ohmic heating of the electrolyte. In both cases, the resulting shear stress imposes a convection in the electrolyte and the gas bubble (Marangoni effect)...
April 13, 2018: Physical Chemistry Chemical Physics: PCCP
Marie-Lena I E Harwardt, Marina S Dietz, Mike Heilemann, Thorsten Wohland
The dynamics of biomolecules in the plasma membrane is of fundamental importance to understanding cellular processes. Cellular signaling often starts with extracellular ligand binding to a membrane receptor, which then transduces an intracellular signal. Ligand binding and receptor-complex activation often involve a complex rearrangement of proteins in the membrane, which results in changes in diffusion properties. Two widely used methods to characterize biomolecular diffusion are single-particle tracking (SPT) and imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS)...
April 9, 2018: Biophysical Journal
Vladimir A Volkov, Pim J Huis In 't Veld, Marileen Dogterom, Andrea Musacchio
Presence of multiple copies of the microtubule-binding NDC80 complex is an evolutionary conserved feature of kinetochores, points of attachment of chromosomes to spindle microtubules. This may enable multivalent interactions with microtubules, with implications that remain unexplored. Using recombinant human kinetochore components, we show that while single NDC80 complexes do not track depolymerizing microtubules, reconstituted particles containing the NDC80 receptor CENP-T bound to three or more NDC80 complexes do so effectively, as expected for a kinetochore force coupler...
April 9, 2018: ELife
Laura Martínez-Muñoz, José Miguel Rodríguez-Frade, Rubén Barroso, Carlos Óscar S Sorzano, Juan A Torreño-Pina, César A Santiago, Carlo Manzo, Pilar Lucas, Eva M García-Cuesta, Enric Gutierrez, Laura Barrio, Javier Vargas, Graciela Cascio, Yolanda R Carrasco, Francisco Sánchez-Madrid, María F García-Parajo, Mario Mellado
A current challenge in cell motility studies is to understand the molecular and physical mechanisms that govern chemokine receptor nanoscale organization at the cell membrane, and their influence on cell response. Using single-particle tracking and super-resolution microscopy, we found that the chemokine receptor CXCR4 forms basal nanoclusters in resting T cells, whose extent, dynamics, and signaling strength are modulated by the orchestrated action of the actin cytoskeleton, the co-receptor CD4, and its ligand CXCL12...
April 5, 2018: Molecular Cell
Mohak Patel, Susan E Leggett, Alexander K Landauer, Ian Y Wong, Christian Franck
Spatiotemporal tracking of tracer particles or objects of interest can reveal localized behaviors in biological and physical systems. However, existing tracking algorithms are most effective for relatively low numbers of particles that undergo displacements smaller than their typical interparticle separation distance. Here, we demonstrate a single particle tracking algorithm to reconstruct large complex motion fields with large particle numbers, orders of magnitude larger than previously tractably resolvable, thus opening the door for attaining very high Nyquist spatial frequency motion recovery in the images...
April 3, 2018: Scientific Reports
I-Hsuan Wang, Christoph J Burckhardt, Artur Yakimovich, Urs F Greber
Viruses have a dual nature: particles are “passive substances” lacking chemical energy transformation, whereas infected cells are “active substances” turning-over energy. How passive viral substances convert to active substances, comprising viral replication and assembly compartments has been of intense interest to virologists, cell and molecular biologists and immunologists. Infection starts with virus entry into a susceptible cell and delivers the viral genome to the replication site...
March 31, 2018: Viruses
Camille A Bayas, Jiarui Wang, Marissa K Lee, Jared M Schrader, Lucy Shapiro, W E Moerner
We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single-particle tracking and superresolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in Escherichia coli , where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
Yongzhuang Zhou, Paul Zammit, Guillem Carles, Andrew R Harvey
A new single-aperture 3D particle-localization and tracking technique is presented that demonstrates an increase in depth range by more than an order of magnitude without compromising optical resolution and throughput. We exploit the extended depth range and depth-dependent translation of an Airy-beam PSF for 3D localization over an extended volume in a single snapshot. The technique is applicable to all bright-field and fluorescence modalities for particle localization and tracking, ranging from super-resolution microscopy through to the tracking of fluorescent beads and endogenous particles within cells...
March 19, 2018: Optics Express
Abdollah Saboori, Simona Tusacciu, Mattia Busatto, Manuel Lai, Sara Biamino, Paolo Fino, Mariangela Lombardi
Directed Energy Deposition (DED), which is an additive manufacturing technique, involves the creation of a molten pool with a laser beam where metal powder is injected as particles. In general, this technique is employed to either fabricate or repair different components. In this technique, the final characteristics are affected by many factors. Indeed, one of the main tasks in building components by DED is the optimization of process parameters (such as laser power, laser speed, focus, etc.) which is usually carried out through an extensive experimental investigation...
March 13, 2018: Journal of Visualized Experiments: JoVE
Rafael L Schoch, Itay Barel, Frank L H Brown, Gilad Haran
Supported lipid bilayers (SLBs) have been studied extensively as simple but powerful models for cellular membranes. Yet, potential differences in the dynamics of the two leaflets of a SLB remain poorly understood. Here, using single particle tracking, we obtain a detailed picture of bilayer dynamics. We observe two clearly separate diffusing populations, fast and slow, that we associate with motion in the distal and proximal leaflets of the SLB, respectively, based on fluorescence quenching experiments. We estimate diffusion coefficients using standard techniques as well as a new method based on the blur of images due to motion...
March 28, 2018: Journal of Chemical Physics
Mehdi Molaei, Ehsan Atefi, John C Crocker
The complex rotational and translational Brownian motion of anisotropic particles depends on their shape and the viscoelasticity of their surroundings. Because of their strong optical scattering and chemical versatility, gold nanorods would seem to provide the ultimate probes of rheology at the nanoscale, but the suitably accurate orientational tracking required to compute rheology has not been demonstrated. Here we image single gold nanorods with a laser-illuminated dark-field microscope and use optical polarization to determine their three-dimensional orientation to better than one degree...
March 16, 2018: Physical Review Letters
Sicheng Tang, Yang Zhang, Pravat Dhakal, Laura Ravelo, Cheyenne L Anderson, Kevin M Collins, Françisco M Raymo
A photochemical strategy to encode fluorescence signals in vivo with spatial control was designed around the unique properties of a photoactivatable borondipyrromethene (BODIPY). The photoinduced disconnection of two oxazines, flanking a single BODIPY, in two consecutive steps produces a mixture of three emissive molecules with resolved fluorescence inside polymer beads. The relative amounts and emission intensities of the three fluorophores can be regulated precisely in each bead by adjusting the dose of activating photons to mark individual particles with distinct codes of fluorescence signals...
March 21, 2018: Journal of the American Chemical Society
Karthika Suresh, Dharmendar Kumar Sharma, Ramya Chulliyil, Ketan Dinkar Sarode, V Ravi Kumar, Arindam Chowdhury, Guruswamy Kumaraswamy
We use single particle tracking to investigate colloidal dynamics in hybrid assemblies comprising colloids enmeshed in a crosslinked polymer network. These assemblies are prepared using ice templating and are macroporous monolithic structures. We investigate microstructure-property relations in assemblies that appear chemically identical, but show qualitatively different mechanical response. Specifically, we contrast elastic assemblies that can recover from large compressive deformations with plastic assemblies that fail on being compressed...
March 20, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Alvaro Marin, Henri Lhuissier, Massimiliano Rossi, Christian J Kähler
The flow of a charged-stabilized suspension through a single constricted channel is studied experimentally by tracking the particles individually. Surprisingly, the behavior is found to be qualitatively similar to that of inertial dry granular systems: For small values of the neck-to-particle size ratio (D/d<3), clogs form randomly as arches of the particle span the constriction. The statistics of the clogging events are Poissonian as reported for granular systems and agree for moderate particle volume fraction (ϕ≈20%) with a simple stochastic model for the number of particles at the neck...
February 2018: Physical Review. E
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