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https://www.readbyqxmd.com/read/27899526/dynamic-pre-bcr-homodimers-fine-tune-autonomous-survival-signals-in-b-cell-precursor-acute-lymphoblastic-leukemia
#1
M Frank Erasmus, Ksenia Matlawska-Wasowska, Ichiko Kinjyo, Avanika Mahajan, Stuart S Winter, Li Xu, Michael Horowitz, Diane S Lidke, Bridget S Wilson
The pre-B cell receptor (pre-BCR) is an immature form of the BCR critical for early B lymphocyte development. It is composed of the membrane-bound immunoglobulin (Ig) heavy chain, surrogate light chain components, and the signaling subunits Igα and Igβ. We developed monovalent quantum dot (QD)-labeled probes specific for Igβ to study the behavior of pre-BCRs engaged in autonomous, ligand-independent signaling in live B cells. Single-particle tracking revealed that QD-labeled pre-BCRs engaged in transient, but frequent, homotypic interactions...
November 29, 2016: Science Signaling
https://www.readbyqxmd.com/read/27889810/rhodamine-bound-maghemite-as-a-long-term-dual-imaging-nanoprobe-of-adipose-tissue-derived-mesenchymal-stromal-cells
#2
Vratislav Cmiel, Josef Skopalik, Katerina Polakova, Jan Solar, Marketa Havrdova, David Milde, Ivan Justan, Massimiliano Magro, Zenon Starcuk, Ivo Provaznik
In the last few years, magnetically labeled cells have been intensively explored, and non-invasive cell tracking and magnetic manipulation methods have been tested in preclinical studies focused on cell transplantation. For clinical applications, it is desirable to know the intracellular pathway of nanoparticles, which can predict their biocompatibility with cells and the long-term imaging properties of labeled cells. Here, we quantified labeling efficiency, localization, and fluorescence properties of Rhodamine derivatized superparamagnetic maghemite nanoparticles (SAMN-R) in mesenchymal stromal cells (MSC)...
November 26, 2016: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27885259/trackntrace-a-simple-and-extendable-open-source-framework-for-developing-single-molecule-localization-and-tracking-algorithms
#3
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/27853188/lineage-mapper-a-versatile-cell-and-particle-tracker
#4
Joe Chalfoun, Michael Majurski, Alden Dima, Michael Halter, Kiran Bhadriraju, Mary Brady
The ability to accurately track cells and particles from images is critical to many biomedical problems. To address this, we developed Lineage Mapper, an open-source tracker for time-lapse images of biological cells, colonies, and particles. Lineage Mapper tracks objects independently of the segmentation method, detects mitosis in confluence, separates cell clumps mistakenly segmented as a single cell, provides accuracy and scalability even on terabyte-sized datasets, and creates division and/or fusion lineages...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27851944/segmentation-of-3d-trajectories-acquired-by-tsunami-microscope-an-application-to-egfr-trafficking
#5
Yen-Liang Liu, Evan P Perillo, Cong Liu, Peter Yu, Chao-Kai Chou, Mien-Chie Hung, Andrew K Dunn, Hsin-Chih Yeh
Whereas important discoveries made by single-particle tracking have changed our view of the plasma membrane organization and motor protein dynamics in the past three decades, experimental studies of intracellular processes using single-particle tracking are rather scarce because of the lack of three-dimensional (3D) tracking capacity. In this study we use a newly developed 3D single-particle tracking method termed TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) to investigate epidermal growth factor receptor (EGFR) trafficking dynamics in live cells at 16/43 nm (xy/z) spatial resolution, with track duration ranging from 2 to 10 min and vertical tracking depth up to tens of microns...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27848929/the-role-of-a-conserved-membrane-proximal-cysteine-in-altering-%C3%AE-ps2c%C3%AE-ps-integrin-diffusion
#6
Aleem Syed, Neha Arora, Thomas A Bunch, Emily A Smith
Cysteine residues (Cys) in the membrane proximal region are common post-translational modification (PTM) sites in transmembrane proteins. Herein, the effects of a highly conserved membrane proximal α-subunit Cys(1368) on the diffusion properties of αPS2CβPS integrins are reported. Sequence alignment shows that this cysteine is palmitoylated in human α3 and α6 integrin subunits. Replacing Cys(1368) in wild-type integrins with valine (Val(1368)) putatively blocks a PTM site and alters integrins' ligand binding and diffusion characteristics...
November 15, 2016: Physical Biology
https://www.readbyqxmd.com/read/27815876/quantitative-immunofluorescence-to-study-phagosome-maturation
#7
Roya M Dayam, Roberto J Botelho
Cells such as macrophages and neutrophils can internalize a diverse set of particulate matter, illustrated by bacteria and apoptotic bodies through the process of phagocytosis. These particles are sequestered into phagosomes, which then fuse with early and late endosomes, and ultimately with lysosomes to mature into phagolysosomes, through a process known as phagosome maturation. As phagosomes change, they acquire and divest proteins that are associated with the various stages of phagosome maturation. These changes can be assessed at the single-phagosome level by using immunofluorescence methods to study phagosome maturation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27796398/lipid-membrane-assisted-condensation-and-assembly-of-amphiphilic-janus-particles
#8
Mariah Chambers, Stewart Anthony Mallory, Heather Malone, Yuan Gao, Stephen M Anthony, Yi Yi, Angelo Cacciuto, Yan Yu
Amphiphilic Janus particles self-assemble into complex metastructures, but little is known about how their assembly might be modified by weak interactions with a nearby biological membrane surface. Here, we report an integrated experimental and molecular dynamics simulation study to investigate the self-assembly of amphiphilic Janus particles on a lipid membrane. We created an experimental system in which Janus particles are allowed to self-assemble in the same medium where zwitterionic lipids form giant unilamellar vesicles (GUVs)...
November 16, 2016: Soft Matter
https://www.readbyqxmd.com/read/27793291/interferometric-scattering-microscopy-for-the-study-of-molecular-motors
#9
J Andrecka, Y Takagi, K J Mickolajczyk, L G Lippert, J R Sellers, W O Hancock, Y E Goldman, P Kukura
Our understanding of molecular motor function has been greatly improved by the development of imaging modalities, which enable real-time observation of their motion at the single-molecule level. Here, we describe the use of a new method, interferometric scattering microscopy, for the investigation of motor protein dynamics by attaching and tracking the motion of metallic nanoparticle labels as small as 20nm diameter. Using myosin-5, kinesin-1, and dynein as examples, we describe the basic assays, labeling strategies, and principles of data analysis...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27776112/bright-photoactivatable-fluorophores-for-single-molecule-imaging
#10
Jonathan B Grimm, Brian P English, Heejun Choi, Anand K Muthusamy, Brian P Mehl, Peng Dong, Timothy A Brown, Jennifer Lippincott-Schwartz, Zhe Liu, Timothée Lionnet, Luke D Lavis
Small-molecule fluorophores are important tools for advanced imaging experiments. We previously reported a general method to improve small, cell-permeable fluorophores which resulted in the azetidine-containing 'Janelia Fluor' (JF) dyes. Here, we refine and extend the utility of these dyes by synthesizing photoactivatable derivatives that are compatible with live-cell labeling strategies. Once activated, these derived compounds retain the superior brightness and photostability of the JF dyes, enabling improved single-particle tracking and facile localization microscopy experiments...
October 24, 2016: Nature Methods
https://www.readbyqxmd.com/read/27775882/application-of-noncanonical-amino-acids-for-protein-labeling-in-a-genomically-recoded-escherichia-coli
#11
Kalle Kipper, Ebba Gregorsson Lundius, Vladimir Curic, Ivana Nikic, Edward A Lemke, Manfred Wiessler, Johan Elf
Small synthetic fluorophores are in many ways superior to fluorescent proteins as labels for imaging. A major challenge is to use them for a protein-specific labeling in living cells. Here, we report on our use of noncanonical amino acids that are genetically encoded via the pyrrolysyl-tRNA/pyrrolysyl-RNA synthetase pair at artificially introduced TAG codons in a recoded E. coli strain. The strain is lacking endogenous TAG codons and the TAG-specific release factor RF1. The amino acids contain bioorthogonal groups that can be clicked to externally supplied dyes, thus enabling protein-specific labeling in live cells...
October 24, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27767185/a-multimodality-imaging-model-to-track-viable-breast-cancer-cells-from-single-arrest-to-metastasis-in-the-mouse-brain
#12
Katie M Parkins, Amanda M Hamilton, Ashley V Makela, Yuanxin Chen, Paula J Foster, John A Ronald
Cellular MRI involves sensitive visualization of iron-labeled cells in vivo but cannot differentiate between dead and viable cells. Bioluminescence imaging (BLI) measures cellular viability, and thus we explored combining these tools to provide a more holistic view of metastatic cancer cell fate in mice. Human breast carcinoma cells stably expressing Firefly luciferase were loaded with iron particles, injected into the left ventricle, and BLI and MRI were performed on days 0, 8, 21 and 28. The number of brain MR signal voids (i...
October 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27748588/fluorescence-monitored-voltammetry-of-single-attolitre-droplets
#13
Christopher Batchelor-McAuley, Christopher A Little, Stanislav V Sokolov, Enno Kätelhön, Giorgia Zampardi, Richard G Compton
The lipid soluble fluorophore Nile Red (9-diethylamino-5-benzo[α]phenoxazinone) is used to fluorescently and electrochemically label an organic-in-water emulsion, where the organic phase is an ionic liquid [P6,6,6,14][FAP]/toluene mixture. The optical detection of the individual droplets is enabled facilitating the in-situ tracking and sizing of the suspended particles (average diameter = 530 nm, interquartile range = 180 nm). Through the use of a combined thin-layer optical/electrochemical cell, the irreversible accumulation of the droplets at an optically opaque carbon fibre electrode (diameter ~ 7...
October 17, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27725698/short-lived-cages-restrict-protein-diffusion-in-the-plasma-membrane
#14
Maria Goiko, John R de Bruyn, Bryan Heit
The plasma membrane is a heterogeneous environment characterized by anomalous diffusion and the presence of microdomains that are molecularly distinct from the bulk membrane. Using single particle tracking of the C-type lectin CD93, we have identified for the first time the transient trapping of transmembrane proteins in cage-like microdomains which restrict protein diffusion. These cages are stabilized by actin-dependent confinement regions, but are separate structures with sizes and lifespans uncorrelated to those of the underlying actin corral...
October 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27720951/ligand-binding-affinity-and-changes-in-the-lateral-diffusion-of-receptor-for-advanced-glycation-endproducts-rage
#15
Aleem Syed, Qiaochu Zhu, Emily A Smith
The effect of ligand on the lateral diffusion of receptor for advanced glycation endproducts (RAGE), a receptor involved in numerous pathological conditions, remains unknown. Single particle tracking experiments that use quantum dots specifically bound to hemagglutinin (HA)-tagged RAGE (HA-RAGE) are reported to elucidate the effect of ligand binding on HA-RAGE diffusion in GM07373 cell membranes. The ligand used in these studies is methylglyoxal modified-bovine serum albumin (MGO-BSA) containing advanced glycation end products modifications...
December 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27714348/nanoparticle-diffusion-in-crowded-and-confined-media
#16
Firoozeh Babayekhorasani, Dave E Dunstan, Ramanan Krishnamoorti, Jacinta C Conrad
We identify distinct mechanisms controlling slowing of nanoparticle diffusion through complex media featuring both rigid geometrical confinement and soft mobile crowders. Towards this end, we use confocal microscopy and single particle tracking to probe the diffusion of 400 nm nanoparticles suspended in Newtonian water, in a Newtonian glycerol/water mixture, or in a non-Newtonian polymer solution through a model porous medium, a packed bed of microscale glass beads. The mobility of nanoparticles, as quantified by the long-time diffusion coefficient extracted from the particle mean-squared displacement, slows as the average pore size of the packed bed media decreases for both Newtonian and non-Newtonian solutions...
October 12, 2016: Soft Matter
https://www.readbyqxmd.com/read/27714014/magnetophoretic-transistors-in-a-tri-axial-magnetic-field
#17
Roozbeh Abedini-Nassab, Daniel Y Joh, Faris Albarghouthi, Ashutosh Chilkoti, David M Murdoch, Benjamin B Yellen
The ability to direct and sort individual biological and non-biological particles into spatially addressable locations is fundamentally important to the emerging field of single cell biology. Towards this goal, we demonstrate a new class of magnetophoretic transistors, which can switch single magnetically labeled cells and magnetic beads between different paths in a microfluidic chamber. Compared with prior work on magnetophoretic transistors driven by a two-dimensional in-plane rotating field, the addition of a vertical magnetic field bias provides significant advantages in preventing the formation of particle clumps and in better replicating the operating principles of circuits in general...
October 18, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27713081/trackmate-an-open-and-extensible-platform-for-single-particle-tracking
#18
Jean-Yves Tinevez, Nick Perry, Johannes Schindelin, Genevieve M Hoopes, Gregory D Reynolds, Emmanuel Laplantine, Sebastian Y Bednarek, Spencer L Shorte, Kevin W Eliceiri
We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results...
October 3, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27699104/tracking-single-fluorescent-particles-in-three-dimensions-via-extremum-seeking
#19
Trevor T Ashley, Eric L Gan, Jane Pan, Sean B Andersson
The ability to track single fluorescent particles in three-dimensions with sub-diffraction limit precision as well as sub-millisecond temporal resolution has enabled the understanding of many biophysical phenomena at the nanometer scale. While there are several techniques for achieving this, most require complicated experimental setups that are expensive to implement. These methods can offer superb performance but their complexity may be overwhelming to the end-user whose aim is only to understand the feature being imaged...
September 1, 2016: Biomedical Optics Express
https://www.readbyqxmd.com/read/27697928/nanoscopic-compartmentalization-of-membrane-protein-motion-at-the-axon-initial-segment
#20
David Albrecht, Christian M Winterflood, Mohsen Sadeghi, Thomas Tschager, Frank Noé, Helge Ewers
The axon initial segment (AIS) is enriched in specific adaptor, cytoskeletal, and transmembrane molecules. During AIS establishment, a membrane diffusion barrier is formed between the axonal and somatodendritic domains. Recently, an axonal periodic pattern of actin, spectrin, and ankyrin forming 190-nm-spaced, ring-like structures has been discovered. However, whether this structure is related to the diffusion barrier function is unclear. Here, we performed single-particle tracking time-course experiments on hippocampal neurons during AIS development...
October 10, 2016: Journal of Cell Biology
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