141 results on '"Derek Toomre"'
Search Results
2. Longitudinal Association of COVID-19 Hospitalization and Death with Online Search for Loss of Smell or Taste
- Author
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Derek Toomre, Sasikiran Kandula, and Jeffrey Shaman
- Subjects
COVID-19 ,SARS-CoV-2 ,coronavirus disease ,severe acute respiratory syndrome coronavirus 2 ,viruses ,zoonoses ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Surveillance of COVID-19 is challenging but critical for mitigating disease, particularly if predictive of future disease burden. We report a robust multiyear lead-lag association between internet search activity for loss of smell or taste and COVID-19–associated hospitalization and deaths. These search data could help predict COVID-19 surges.
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- 2023
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3. An active tethering mechanism controls the fate of vesicles
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Seong J. An, Felix Rivera-Molina, Alexander Anneken, Zhiqun Xi, Brian McNellis, Vladimir I. Polejaev, and Derek Toomre
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Science - Abstract
Molecular tethers physically bridge transport vesicles to their target membranes as a prerequisite step for fusion. Here the authors control vesicle tethering using optogenetic approaches to study the interplay between vesicle tethering and fusion.
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- 2021
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4. Endothelial β‐arrestins regulate mechanotransduction by the type II bone morphogenetic protein receptor in primary cilia
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Saejeong Park, Zhiyuan Ma, Georgia Zarkada, Irinna Papangeli, Sarin Paluri, Nour Nazo, Felix Rivera‐Molina, Derek Toomre, Sudarshan Rajagopal, and Hyung J. Chun
- Subjects
beta‐arrestin ,BMPR2 ,endothelial cells ,primary cilia ,shear stress ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 ,Diseases of the respiratory system ,RC705-779 - Abstract
Abstract Modulation of endothelial cell behavior and phenotype by hemodynamic forces involves many signaling components, including cell surface receptors, intracellular signaling intermediaries, transcription factors, and epigenetic elements. Many of the signaling mechanisms that underlie mechanotransduction by endothelial cells are inadequately defined. Here we sought to better understand how β‐arrestins, intracellular proteins that regulate agonist‐mediated desensitization and integration of signaling by transmembrane receptors, may be involved in the endothelial cell response to shear stress. We performed both in vitro studies with primary endothelial cells subjected to β‐arrestin knockdown, and in vivo studies using mice with endothelial specific deletion of β‐arrestin 1 and β‐arrestin 2. We found that β‐arrestins are localized to primary cilia in endothelial cells, which are present in subpopulations of endothelial cells in relatively low shear states. Recruitment of β‐arrestins to cilia involved its interaction with IFT81, a component of the flagellar transport protein complex in the cilia. β‐arrestin knockdown led to marked reduction in shear stress response, including induction of NOS3 expression. Within the cilia, β‐arrestins were found to associate with the type II bone morphogenetic protein receptor (BMPR‐II), whose disruption similarly led to an impaired endothelial shear response. β‐arrestins also regulated Smad transcription factor phosphorylation by BMPR‐II. Mice with endothelial specific deletion of β‐arrestin 1 and β‐arrestin 2 were found to have impaired retinal angiogenesis. In conclusion, we have identified a novel role for endothelial β‐arrestins as key transducers of ciliary mechanotransduction that play a central role in shear signaling by BMPR‐II and contribute to vascular development.
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- 2022
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5. Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells
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Jonathan Tyson, Kevin Hu, Shuai Zheng, Phylicia Kidd, Neville Dadina, Ling Chu, Derek Toomre, Joerg Bewersdorf, and Alanna Schepartz
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Chemistry ,QD1-999 - Published
- 2021
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6. Modeling the effectiveness of olfactory testing to limit SARS-CoV-2 transmission
- Author
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Daniel B. Larremore, Derek Toomre, and Roy Parker
- Subjects
Science - Abstract
A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Here, the authors evaluate an alternative strategy based on the monitoring of olfactory dysfunction with a mathematical model.
- Published
- 2021
- Full Text
- View/download PDF
7. Novel ecto-tagged integrins reveal their trafficking in live cells
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Clotilde Huet-Calderwood, Felix Rivera-Molina, Daniel V. Iwamoto, Emil B. Kromann, Derek Toomre, and David A. Calderwood
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Science - Abstract
Integrins are cell-surface adhesion receptors that are modulated by endo-exocytic trafficking, but existing tools to study this process can interfere with function. Here the authors develop β1 integrins carrying traceable tags in the extracellular domain; a pH-sensitive pHlourin tag or a HaloTag to facilitate dye attachment.
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- 2017
- Full Text
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8. Acylation – A New Means to Control Traffic Through the Golgi
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Andreas M. Ernst, Derek Toomre, and Jonathan S. Bogan
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Golgi ,palmitoylation ,acylation ,anterograde transport ,Golgi bypass ,membrane traffic ,Biology (General) ,QH301-705.5 - Abstract
The Golgi is well known to act as center for modification and sorting of proteins for secretion and delivery to other organelles. A key sorting step occurs at the trans-Golgi network and is mediated by protein adapters. However, recent data indicate that sorting also occurs much earlier, at the cis-Golgi, and uses lipid acylation as a novel means to regulate anterograde flux. Here, we examine an emerging role of S-palmitoylation/acylation as a mechanism to regulate anterograde routing. We discuss the critical Golgi-localized DHHC S-palmitoyltransferase enzymes that orchestrate this lipid modification, as well as their diverse protein clients (e.g., MAP6, SNAP25, CSP, LAT, β-adrenergic receptors, GABA receptors, and GLUT4 glucose transporters). Critically, for integral membrane proteins, S-acylation can act as new a “self-sorting” signal to concentrate these cargoes in rims of Golgi cisternae, and to promote their rapid traffic through the Golgi or, potentially, to bypass the Golgi. We discuss this mechanism and examine its potential relevance to human physiology and disease, including diabetes and neurodegenerative diseases.
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- 2019
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9. YES to junctions, no to Src
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Michael Simons and Derek Toomre
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Article - Abstract
Regulation of the endothelial barrier function is critical to physiological function of the vasculature, which must dynamically change in a number of physiologic and pathologic settings. A new study emphasizes the complex relationship between VE-cadherin phosphorylation , the critical role of YES in this process, and the vascular leak
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- 2022
10. Unraveling cellular complexity with unlimited multiplexed super-resolution imaging
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Florian Schueder, Felix Rivera-Molina, Maohan Su, Phylicia Kidd, James E. Rothman, Derek Toomre, and Joerg Bewersdorf
- Abstract
SummaryMapping the intricate spatial relationships between the many different molecules inside a cell is essential to understanding cellular functions in all their complexity. Super-resolution fluorescence microscopy offers the required spatial resolution but struggles to reveal more than four different targets simultaneously. Exchanging labels in subsequent imaging rounds for multiplexed imaging extends this number but is limited by its low throughput. Here we present a novel imaging method for rapid multiplexed super-resolution microscopy of a nearly unlimited number of molecular targets by leveraging fluorogenic labeling in conjunction with Transient Adapter-mediated switching for high-throughput DNA-PAINT (FLASH-PAINT). We demonstrate the cell biological versatility of FLASH-PAINT in mammalian cells in four applications: i) mapping nine proteins in a single mammalian cell, ii) elucidating the functional organization of primary cilia by nine-target imaging, iii) revealing the changes in proximity of twelve different targets in unperturbed and dissociated Golgi stacks and iv) investigating inter-organelle contacts at 3D super-resolution.
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- 2023
11. Use of Ecto-Tagged Integrins to Monitor Integrin Exocytosis and Endocytosis
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Clotilde Huet-Calderwood, Felix Rivera-Molina, Derek Toomre, and David A. Calderwood
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- 2023
12. A Bayesian method for 3D estimation of subcellular particle features in multi-angle TIRF microscopy.
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Liang Liang, Hongying Shen, Yingke Xu, Pietro De Camilli, Derek Toomre, and James S. Duncan
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- 2012
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13. An Expectation Maximization Based Method for Subcellular Particle Tracking Using Multi-angle TIRF Microscopy.
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Liang Liang, Hongying Shen, Pietro De Camilli, Derek Toomre, and James S. Duncan
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- 2011
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14. Regulation of EGF-stimulated activation of the PI-3K/AKT pathway by exocyst-mediated exocytosis
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Seong J. An, Alexander Anneken, Zhiqun Xi, Changseon Choi, Joseph Schlessinger, and Derek Toomre
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ErbB Receptors ,Extracellular Vesicles ,Multidisciplinary ,Epidermal Growth Factor ,Humans ,Phosphatidylinositol 3-Kinase ,Proto-Oncogene Proteins c-akt ,Exocytosis - Abstract
The phosphoinositide-3 kinase (PI-3K)/AKT cell survival pathway is an important pathway activated by EGFR signaling. Here we show, that in addition to previously described critical components of this pathway, i.e., the docking protein Gab1, the PI-3K/AKT pathway in epithelial cells is regulated by the exocyst complex, which is a vesicle tether that is essential for exocytosis. Using live-cell imaging, we demonstrate that PI(3,4,5)P 3 levels fluctuate at the membrane on a minutes time scale and that these fluctuations are associated with local PI(3,4,5)P 3 increases at sites where recycling vesicles undergo exocytic fusion. Supporting a role for exocytosis in PI(3,4,5)P 3 generation, acute promotion of exocytosis by optogenetically driving exocyst-mediated vesicle tethering up-regulates PI(3,4,5)P 3 production and AKT activation. Conversely, acute inhibition of exocytosis using Endosidin2, a small-molecule inhibitor of the exocyst subunit Exo70 (also designated EXOC7), or inhibition of exocyst function by siRNA-mediated knockdown of the exocyst subunit Sec15 (EXOC6), impairs PI(3,4,5)P 3 production and AKT activation induced by EGF stimulation of epithelial cells. Moreover, prolonged inhibition of EGF signaling by EGFR tyrosine kinase inhibitors results in spontaneous reactivation of AKT without a concomitant relief of EGFR inhibition. However, this reactivation can be negated by acutely inhibiting the exocyst. These experiments demonstrate that exocyst-mediated exocytosis—by regulating PI(3,4,5)P 3 levels at the plasma membrane—subserves activation of the PI-3K/AKT pathway by EGFR in epithelial cells.
- Published
- 2022
15. Estimation of 3D Geometry of Microtubules Using Multi-angle Total Internal Reflection Fluorescence Microscopy.
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Qian Yang, Alexander Karpikov, Derek Toomre, and James S. Duncan
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- 2010
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16. 3-D reconstruction and measurement of microtubules from multiple angle-total internal reflection fluorescence microscopy.
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Qian Yang, Alexander Karpikov, Derek Toomre, and James S. Duncan
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- 2009
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17. Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells
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Alanna Schepartz, Jonathan Tyson, Neville Dadina, Ling Chu, Kevin Hu, Derek Toomre, Phylicia Kidd, Joerg Bewersdorf, and Shuai Zheng
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Fluorophore ,General Chemical Engineering ,Quantum yield ,Context (language use) ,010402 general chemistry ,01 natural sciences ,law.invention ,03 medical and health sciences ,chemistry.chemical_compound ,Live cell imaging ,law ,Microscopy ,QD1-999 ,030304 developmental biology ,Biological evaluation ,0303 health sciences ,General Chemistry ,Laser ,0104 chemical sciences ,Chemistry ,chemistry ,Chemical Sciences ,Biophysics ,Generic health relevance ,Research Article ,Biotechnology ,Intracellular organelles - Abstract
New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multicolor, live-cell, single-molecule localization microscopy (SMLM). Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR-emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives., The bright and near-IR-emitting spontaneously blinking fluorophore Yale676sb is paired with HMSiR to enable two-color live-cell single-molecule localization microscopy with no chemical additives and a single 642 nm laser.
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- 2021
18. Estimating the Duration of Endocytic Events.
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Rafael Sebastián, Guillermo Ayala, María Elena Díaz, Roberto Zoncu, and Derek Toomre
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- 2007
- Full Text
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19. Fuzzy Temporal Random Sets with an Application to Cell Biology.
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Teresa León, Rafael Sebastián, Guillermo Ayala, María Elena Díaz, Roberto Zoncu, and Derek Toomre
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- 2007
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20. Tracking the motion of the outer tips of microtubules.
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Stathis Hadjidemetriou, Derek Toomre, and James S. Duncan
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- 2006
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21. Analysis of spatial dependencies of endocytic proteins based on temporal random sets.
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Rafael Sebastián, María Elena Díaz, Guillermo Ayala, Roberto Zoncu, and Derek Toomre
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- 2006
- Full Text
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22. Imaging Single-Vesicle Exocytosis with Total Internal Reflection Fluorescence Microscopy (TIRFM)
- Author
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Yingke, Xu, Luhong, Jin, and Derek, Toomre
- Subjects
Mice ,Microscopy, Fluorescence ,3T3-L1 Cells ,Cell Membrane ,Adipocytes ,Animals ,Exocytosis - Abstract
Total internal reflection fluorescence microscopy (TIRFM) provides extremely thin optical sectioning with excellent signal-to-noise ratios, which allows for visualization of membrane dynamics at the cell surface with superb spatiotemporal resolution. In this chapter, TIRFM is used to record and analyze exocytosis of single glucose transporter-4 (GLUT4) containing vesicles in 3T3-L1 adipocytes.
- Published
- 2022
23. Segmentation and 3D Reconstruction of Microtubules in Total Internal Reflection Fluorescence Microscopy (TIRFM).
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Stathis Hadjidemetriou, Derek Toomre, and James S. Duncan
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- 2005
- Full Text
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24. Automatic Quantification of Microtubule Dynamics.
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Stathis Hadjidemetriou, James S. Duncan, Derek Toomre, and David Tuck
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- 2004
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25. Two-color nanoscopy of organelles for extended times with HIDE probes
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Jonathan Tyson, Derek Toomre, Felix Rivera-Molina, Anthony J. Koleske, Ling Chu, Juliana E. Shaw, and Alanna Schepartz
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0301 basic medicine ,General Physics and Astronomy ,02 engineering and technology ,01 natural sciences ,Fluorescent dyes ,Imaging ,chemistry.chemical_compound ,Nanotechnology ,Super-resolution microscopy ,lcsh:Science ,Pediatric ,Physics ,Microscopy ,0303 health sciences ,Microscopy, Confocal ,Photobleaching ,Multidisciplinary ,STED microscopy ,021001 nanoscience & nanotechnology ,Chemical biology ,Confocal ,0210 nano-technology ,Fluorophore ,Science ,Cellular imaging ,010402 general chemistry ,Time-Lapse Imaging ,Fluorescence ,Article ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,03 medical and health sciences ,Imaging, Three-Dimensional ,Confocal imaging ,Organelle ,Human Umbilical Vein Endothelial Cells ,Humans ,Fluorescent Dyes ,030304 developmental biology ,Organelles ,General Chemistry ,0104 chemical sciences ,030104 developmental biology ,Microscopy, Fluorescence ,chemistry ,Hela Cells ,Three-Dimensional ,Biophysics ,lcsh:Q ,Extended time ,HeLa Cells - Abstract
Performing multi-color nanoscopy for extended times is challenging due to the rapid photobleaching rate of most fluorophores. Here we describe a new fluorophore (Yale-595) and a bio-orthogonal labeling strategy that enables two-color super-resolution (STED) and 3D confocal imaging of two organelles simultaneously for extended times using high-density environmentally sensitive (HIDE) probes. Because HIDE probes are small, cell-permeant molecules, they can visualize dual organelle dynamics in hard-to-transfect cell lines by super-resolution for over an order of magnitude longer than with tagged proteins. The extended time domain possible using these tools reveals dynamic nanoscale targeting between different organelles., High density environmentally sensitive (HIDE) probes allow for long time-lapse super-resolution imaging of live cells. Here the authors develop a second HIDE probe with a bio-orthogonal labelling strategy to enable two-color nanoscopy of two organelles over extended periods.
- Published
- 2020
26. Endosome motility defects revealed at super-resolution in live cells using HIDE probes
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Aarushi Gupta, Derek Toomre, Felix Rivera-Molina, Zhiqun Xi, and Alanna Schepartz
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In situ ,Endosome ,Confocal ,Motility ,Endosomes ,Article ,03 medical and health sciences ,Organelle ,Humans ,Molecular Biology ,Fluorescent Dyes ,030304 developmental biology ,0303 health sciences ,Membrane Glycoproteins ,Chemistry ,030302 biochemistry & molecular biology ,Biological Transport ,Cell Biology ,Carbocyanines ,Fibroblasts ,Small molecule ,3. Good health ,Cell biology ,Transport protein ,Protein Transport ,Cholesterol ,Microscopy, Fluorescence ,NPC1 ,Carrier Proteins ,Lysosomes ,HeLa Cells - Abstract
We report new lipid-based, high-density, environmentally sensitive (HIDE) probes that accurately and selectively image endo-lysosomes and their dynamics at super-resolution for extended times. Treatment of live cells with the small molecules DiIC16TCO or DiIC16’TCO followed by in situ tetrazine ligation reaction with the silicon-rhodamine dye SiR-Tz generates the HIDE probes DiIC16-SiR and DiIC16’-SiR in the endo-lysosomal membrane. These new probes support the acquisition of super-resolution videos of organelle dynamics in primary cells for more than 7 minutes with no detectable change in endosome structure or function. Using DiIC16-SiR and DiIC16’-SiR, we describe the first direct evidence of endosome motility defects in cells from patients with Niemann-Pick Type-C disease. In wild-type fibroblasts, the probes reveal distinct but rare inter-endosome kiss-and-run events that cannot be observed using confocal methods. Our results shed new light on the role of NPC1 in organelle motility and cholesterol trafficking.
- Published
- 2020
27. Imaging Single-Vesicle Exocytosis with Total Internal Reflection Fluorescence Microscopy (TIRFM)
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Yingke Xu, Luhong Jin, and Derek Toomre
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- 2022
28. Exocyst complex mediates recycling of internal cilia
- Author
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Elena Reales, Derek Toomre, Felix Rivera-Molina, Bryan Wang, Zhiqun Xi, National Institutes of Health (US), Junta de Andalucía, and European Commission
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Cytoplasm ,Ciliogenesis ,Cilium ,Cell Membrane ,Vesicular Transport Proteins ,Exocyst ,Biology ,respiratory system ,General Biochemistry, Genetics and Molecular Biology ,Exocytosis ,Cell biology ,Ciliary pocket ,Live cell imaging ,Extracellular ,Humans ,Recycling ,Cilia ,General Agricultural and Biological Sciences ,Ciliary base - Abstract
Primary cilia are slender, cellular antennae that sense extracellular stimuli, and their absence or dysfunction plays a role in numerous human diseases. Prior work has indicated a role of the exocyst tethering complex in cilia biogenesis and maintenance, with the underlying paradigm that the exocyst targets vesicles to the ciliary base to deliver ciliary cargoes. However, the role of the exocyst vis-à-vis to primary cilia in living cells and during stimulation is unknown. Herein, using advanced imaging and quantitative analysis reveals that serum stimulation increases the exocyst's localization to cilia by three-fold. This serum-stimulated localization is highly dynamic, and FRAP experiments show that exocysts at the cilia are highly mobile (60%–80%). Super resolution imaging reveals that the xocyst extends past the cilia base to the entire ciliary pocket. To visualize cilia exocytosis, we conducted live cell imaging with pH-sensitive cilia reporters in combination with extracellular pH switching. Strikingly, we observed that an exocyst-positive internal cilia fuses with the cell surface. These live cell results support a novel and dynamic role of the exocyst complex in the delivery of internalized cilia to the cell surface. Moreover, they suggest a novel pathway may be used to recycle primary cilia to the cell surface that engages the exocyst in response to stimuli. This new remarkable plasticity in cilia presence on the surface in response to extracellular stimuli suggest new means to potentially modulate cilia signaling., This work was supported by NIH grants R01 GM 118486-03 and R21HD078851-02 and Andalucia Talent Hub Marie Curie Fellowship (Agencia Andaluza del Conocimiento de la Junta de Andalucia [Spain] y FP7-PEOPLE-COFUND-Marie Curie) (E.R.).
- Published
- 2021
29. Modeling the effectiveness of olfactory testing to limit SARS-CoV-2 transmission
- Author
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Derek Toomre, Daniel B. Larremore, and Roy Parker
- Subjects
2019-20 coronavirus outbreak ,Time Factors ,Coronavirus disease 2019 (COVID-19) ,Epidemiology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Science ,Anosmia ,Cost-Benefit Analysis ,General Physics and Astronomy ,Bioinformatics ,General Biochemistry, Genetics and Molecular Biology ,Article ,law.invention ,03 medical and health sciences ,0302 clinical medicine ,law ,Prevalence ,Medicine ,Humans ,Mass Screening ,030212 general & internal medicine ,030223 otorhinolaryngology ,Multidisciplinary ,business.industry ,COVID-19 ,General Chemistry ,Models, Theoretical ,Viral Load ,Olfaction test ,Transmission (mechanics) ,Viral infection ,COVID-19 Nucleic Acid Testing ,Communicable Disease Control ,business ,Viral load ,Alternative strategy - Abstract
A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Molecular tests that detect viral RNAs or antigens will be unable to rise to this challenge unless testing capacity increases by at least an order of magnitude while decreasing turnaround times. Here, we evaluate an alternative strategy based on the monitoring of olfactory dysfunction, a symptom identified in 76–83% of SARS-CoV-2 infections—including those with no other symptoms—when a standardized olfaction test is used. We model how screening for olfactory dysfunction, with reflexive molecular tests, could be beneficial in reducing community spread of SARS-CoV-2 by varying testing frequency and the prevalence, duration, and onset time of olfactory dysfunction. We find that monitoring olfactory dysfunction could reduce spread via regular screening, and could reduce risk when used at point-of-entry for single-day events. In light of these estimated impacts, and because olfactory tests can be mass produced at low cost and self-administered, we suggest that screening for olfactory dysfunction could be a high impact and cost-effective method for broad COVID-19 screening and surveillance., A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Here, the authors evaluate an alternative strategy based on the monitoring of olfactory dysfunction with a mathematical model.
- Published
- 2021
30. New software for automated cilia detection in cells (ACDC)
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Wen-Qi Wu, Derek Toomre, Wei Luo, Feng Yu, Tianqi Zhu, and Max C. Lauring
- Subjects
False negative ,False positives and false negatives ,Biology ,Image analysis ,03 medical and health sciences ,0302 clinical medicine ,Software ,Primary cilia ,Ciliogenesis ,F1 score ,medicine ,False positive ,lcsh:QH573-671 ,030304 developmental biology ,0303 health sciences ,Ground truth ,business.industry ,lcsh:Cytology ,ACDC ,Automated cilia analysis ,Methodology ,Pattern recognition ,Cell Biology ,medicine.disease ,Data set ,Artificial intelligence ,business ,030217 neurology & neurosurgery - Abstract
Background Primary cilia frequency and length are key metrics in studies of ciliogenesis and ciliopathies. Typically, quantitative cilia analysis is done manually, which is very time-consuming. While some open-source and commercial image analysis software applications can segment input data, they still require the user to optimize many parameters, suffer from user bias, and often lack rigorous performance quality assessment (e.g., false positives and false negatives). Further, optimal parameter combinations vary in detection accuracy depending on cilia reporter, cell type, and imaging modality. A good automated solution would analyze images quickly, robustly, and adaptably—across different experimental data sets—without significantly compromising the accuracy of manual analysis. Methods To solve this problem, we developed a new software for automated cilia detection in cells (ACDC). The software operates through four main steps: image importation, pre-processing, detection auto-optimization, and analysis. From a data set, a representative image with manually selected cilia (i.e., Ground Truth) is used for detection auto-optimization based on four parameters: signal-to-noise ratio, length, directional score, and intensity standard deviation. Millions of parameter combinations are automatically evaluated and optimized according to an accuracy ‘F1’ score, based on the amount of false positives and false negatives. Afterwards, the optimized parameter combination is used for automated detection and analysis of the entire data set. Results The ACDC software accurately and adaptably detected nuclei and primary cilia across different cell types (NIH3T3, RPE1), cilia reporters (AcTub, Smo-GFP, Arl13b), and image magnifications (60×, 40×). We found that false-positive and false-negative rates for Arl13b-stained cilia were 1–6%, yielding high F1 scores of 0.96–0.97 (max. = 1.00). The software detected significant differences in mean cilia length between control and cytochalasin D-treated cell populations and could monitor dynamic changes in cilia length from movie recordings. Automated analysis offered up to a 96-fold speed enhancement compared to manual analysis, requiring around 5 s/image, or nearly 18,000 cilia analyzed/hour. Conclusion The ACDC software is a solution for robust automated analysis of microscopic images of ciliated cells. The software is extremely adaptable, accurate, and offers immense time-savings compared to traditional manual analysis. Electronic supplementary material The online version of this article (10.1186/s13630-019-0061-z) contains supplementary material, which is available to authorized users.
- Published
- 2019
31. Modeling the effectiveness of olfactory testing to limit SARS-CoV-2 transmission
- Author
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Derek Toomre, Daniel B. Larremore, and Roy Parker
- Subjects
2019-20 coronavirus outbreak ,Transmission (mechanics) ,Coronavirus disease 2019 (COVID-19) ,business.industry ,law ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Medicine ,business ,Bioinformatics ,Olfaction test ,law.invention ,Alternative strategy - Abstract
A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Molecular tests that detect viral RNAs or antigens will be unable to rise to this challenge unless testing capacity increases by at least an order of magnitude while decreasing turnaround times. Here, we evaluate an alternative strategy based on the monitoring of olfactory dysfunction, a symptom identified in 76-83% of SARS-CoV-2 infections—including those with no other symptoms—when a standardized olfaction test is used. We model how screening for olfactory dysfunction, with reflexive molecular tests, could be beneficial in reducing community spread of SARS-CoV-2 by varying testing frequency and the prevalence, duration, and onset time of olfactory dysfunction. We find that monitoring olfactory dysfunction could reduce spread via regular screening, and could reduce risk when used at point-of-entry for single-day events. In light of these estimated impacts, and because olfactory tests can be mass produced at low cost and self-administered, we suggest that screening for olfactory dysfunction could be a high impact and cost-effective method for broad COVID-19 screening and surveillance.
- Published
- 2020
32. DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells
- Author
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Erdem Karatekin, Zhiqun Xi, Farren J. Isaacs, Derek Toomre, John T. Powell, Julien Berro, Nathan D. Williams, Wenjiao Zhou, Chenxiang Lin, Ane Landajuela, and Ravikiran Kasula
- Subjects
Brightness ,Fluorescence-lifetime imaging microscopy ,Quantification methods ,Microscope ,Bioengineering ,Nanotechnology ,02 engineering and technology ,Article ,law.invention ,Live cell imaging ,law ,Fluorescence microscope ,DNA origami ,Animals ,General Materials Science ,Fluorescent Dyes ,chemistry.chemical_classification ,Mechanical Engineering ,Biomolecule ,Proteins ,General Chemistry ,DNA ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Fluorescence ,chemistry ,Microscopy, Fluorescence ,Quantitative Microscopy ,0210 nano-technology - Abstract
Fluorescence microscopy has been one of the most discovery-rich methods in biology. In the digital age, the discipline is becoming increasingly quantitative. Virtually all biological laboratories have access to fluorescence microscopes, but abilities to quantify biomolecule copy numbers are limited by the complexity and sophistication associated with current quantification methods. Here, we present DNA-origami-based fluorescence brightness standards for counting 5–300 copies of proteins in mammalian and bacterial cells, tagged with fluorescent proteins or organic dyes. Compared to conventional quantification techniques, our brightness standards are robust, straightforward to use, and compatible with nearly all fluorescence imaging applications, thereby providing a practical and versatile tool to quantify biomolecules via fluorescence microscopy.
- Published
- 2020
33. Platelet P-selectin initiates cross-presentation and dendritic cell differentiation in blood monocytes
- Author
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Patrick Han, Douglas Hanlon, Najla Arshad, Jung Seok Lee, Kazuki Tatsuno, Alp Yurter, Eve Robinson, Renata Filler, Olga Sobolev, Christine Cote, Felix Rivera-Molina, Derek Toomre, Tarek Fahmy, and Richard Edelson
- Subjects
0303 health sciences ,Multidisciplinary ,P-selectin ,Chemistry ,Monocyte ,Antigen presentation ,Cross-presentation ,Dendritic cell differentiation ,In vitro ,Calcium in biology ,3. Good health ,Cell biology ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,medicine ,Platelet ,030304 developmental biology ,030215 immunology - Abstract
Dendritic cells (DCs) are adept at cross-presentation and initiation of antigen-specific immunity. Clinically, however, DCs produced by in vitro differentiation of monocytes in the presence of exogenous cytokines have been met with limited success. We hypothesized that DCs produced in a physiological manner may be more effective and found that platelets activate a cross-presentation program in peripheral blood monocytes with rapid (18 hours) maturation into physiological DCs (phDCs). Differentiation of monocytes into phDCs was concomitant with the formation of an “adhesion synapse,” a biophysical junction enriched with platelet P-selectin and monocyte P-selectin glycoprotein ligand 1, followed by intracellular calcium fluxing and nuclear localization of nuclear factor κB. phDCs were more efficient than cytokine-derived DCs in generating tumor-specific T cell immunity. Our findings demonstrate that platelets mediate a cytokine-independent, physiologic maturation of DC and suggest a novel strategy for DC-based immunotherapies.
- Published
- 2020
34. Leptin Is Produced by Parathyroid Glands and Stimulates Parathyroid Hormone Secretion
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Samuel Kim, Glenda G. Callender, Derek Toomre, Nathalie Abitbol, Julie Ann Sosa, Xiaopan Yao, Felix Rivera-Molina, Alexander Y. Li, Fangyong Li, Niclas Broer, Sanziana A. Roman, Deepak Narayan, Christine A. Simpson, Gloria R. Sue, and Don Hoang
- Subjects
Adenoma ,Leptin ,0301 basic medicine ,Parathyroidectomy ,medicine.medical_specialty ,medicine.medical_treatment ,Parathyroid hormone ,030209 endocrinology & metabolism ,Parathyroid Glands ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,medicine ,Animals ,Humans ,Prospective Studies ,RNA, Messenger ,Microscopy, Immunoelectron ,Cells, Cultured ,Mice, Knockout ,Calcium metabolism ,Hyperparathyroidism ,Hyperplasia ,Microscopy, Confocal ,Leptin receptor ,Parathyroid neoplasm ,business.industry ,Parathyroid chief cell ,medicine.disease ,Immunohistochemistry ,Parathyroid Neoplasms ,030104 developmental biology ,Endocrinology ,Microscopy, Fluorescence ,Parathyroid Hormone ,Receptors, Leptin ,Parathyroid hormone secretion ,Surgery ,business ,hormones, hormone substitutes, and hormone antagonists - Abstract
Objective We asked if leptin and its cognate receptor were present in normal and diseased parathyroid glands, and if so, whether they had any functional effects on parathyroid hormone (PTH) secretion in parathyroid neoplasms. Background The parathyroid glands acting through PTH play a critical role in the regulation of serum calcium. Based on leptin's recently discovered role in bone metabolism, we hypothesized these glands were the sites of a functional interaction between these 2 hormones. Methods From July 2010 to July 2011, 96 patients were enrolled in a prospective study of leptin and hyperparathyroidism, all of whom were enrolled based on their diagnosis of hyperparathyroidism, and their candidacy for surgical intervention provided informed consent. Immediately after parathyroidectomy, 100 to 300 mg of adenomatous or hyperplastic diseased parathyroid tissue was prepared and processed according to requirements of the following: in situ hybridization, immunohistochemistry, immunofluorescence by conventional and spinning disc confocal microscopy, electron microscopy, parathyroid culture, whole organ explant, and animal model assays. Results Leptin, leptin receptor (long isoform), and PTH mRNA transcripts and protein were detected in an overlapping fashion in parathyroid chief cells in adenoma and hyperplastic glands, and also in normal parathyroid by in situ hybridization, qRT-PCR, and immunohistochemistry. Confocal microscopy confirmed active exogenous leptin uptake in cultured parathyroid cells. PTH secretion in explants increased in response to leptin and decreased with leptin receptor signaling inhibition by AG490, a JAK2/STAT3 inhibitor. Ob/ob mice injected with mouse leptin exhibited increased PTH levels from baseline. Conclusions Taken together, these data suggest that leptin is a functionally active product of the parathyroid glands and stimulates PTH release.
- Published
- 2017
35. Long-Term Live-Cell STED Nanoscopy of Primary and Cultured Cells with the Plasma Membrane HIDE Probe DiI-SiR
- Author
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Mitchell H. Omar, Alexander D. Thompson, Derek Toomre, Alanna Schepartz, Anthony J. Koleske, Felix Rivera-Molina, and Zhiqun Xi
- Subjects
0301 basic medicine ,Fluorophore ,neurons ,Bioengineering ,010402 general chemistry ,01 natural sciences ,Catalysis ,Article ,Fluorescence ,Cell membrane ,chemistry.chemical_compound ,03 medical and health sciences ,0302 clinical medicine ,super-resolution microscopy ,medicine ,Tumor Cells, Cultured ,fluorophores ,Humans ,Nanotechnology ,Fluorescent Dyes ,Microscopy ,Cultured ,Molecular Structure ,Super-resolution microscopy ,Cell Membrane ,Optical Imaging ,Organic Chemistry ,STED microscopy ,General Chemistry ,Transfection ,General Medicine ,bioorthogonal chemistry ,eye diseases ,0104 chemical sciences ,Tumor Cells ,medicine.anatomical_structure ,030104 developmental biology ,chemistry ,Biochemistry ,Microscopy, Fluorescence ,membranes ,Temporal resolution ,Hela Cells ,Chemical Sciences ,Biophysics ,Bioorthogonal chemistry ,Filopodia ,030217 neurology & neurosurgery ,HeLa Cells - Abstract
Super-resolution imaging of live cells over extended time periods with high temporal resolution requires high-density labeling and extraordinary fluorophore photostability. Here we achieve this goal by combining the attributes of the high-density plasma membrane probe DiI-TCO and the photostable STED dye SiR-Tz. These components undergo rapid tetrazine ligation within the plasma membrane to generate the HIDE probe DiI-SiR. Using DiI-SiR, we visualized filopodia dynamics in HeLa cells over 25 min at 0.5 sec temporal resolution, and visualized dynamic contact-mediated repulsion events in primary mouse hippocampal neurons over 9 min at 2 sec temporal resolution. HIDE probes such as DiI-SiR are non-toxic and do not require transfection, and their apparent photostability significantly improves the ability to monitor dynamic processes in live cells at super-resolution over biologically relevant timescales.
- Published
- 2017
36. Long time-lapse nanoscopy with spontaneously blinking membrane probes
- Author
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Hideo Takakura, Derek Toomre, Felix Rivera-Molina, Alexander D. Thompson, Shin-nosuke Uno, Mako Kamiya, Joerg Bewersdorf, Alanna Schepartz, Yongdeng Zhang, Yasuteru Urano, Roman S. Erdmann, Brian McNellis, Yu Lin, and James E. Rothman
- Subjects
0301 basic medicine ,Fluorophore ,Biomedical Engineering ,Bioengineering ,010402 general chemistry ,01 natural sciences ,Applied Microbiology and Biotechnology ,Article ,03 medical and health sciences ,symbols.namesake ,chemistry.chemical_compound ,Microscopy ,Humans ,Nanotechnology ,Fluorescent Dyes ,Super-resolution microscopy ,Chemistry ,Endoplasmic reticulum ,Golgi apparatus ,Cellular Structures ,0104 chemical sciences ,030104 developmental biology ,Membrane ,Microscopy, Fluorescence ,symbols ,Biophysics ,Molecular Medicine ,Spatiotemporal resolution ,Filopodia ,HeLa Cells ,Biotechnology - Abstract
Imaging cellular structures and organelles in living cells by long time-lapse super-resolution microscopy is challenging, as it requires dense labeling, bright and highly photostable dyes, and non-toxic conditions. We introduce a set of high-density, environment-sensitive (HIDE) membrane probes, based on the membrane-permeable silicon-rhodamine dye HMSiR, that assemble in situ and enable long time-lapse, live-cell nanoscopy of discrete cellular structures and organelles with high spatiotemporal resolution. HIDE-enabled nanoscopy movies span tens of minutes, whereas movies obtained with labeled proteins span tens of seconds. Our data reveal 2D dynamics of the mitochondria, plasma membrane and filopodia, and the 2D and 3D dynamics of the endoplasmic reticulum, in living cells. HIDE probes also facilitate acquisition of live-cell, two-color, super-resolution images, expanding the utility of nanoscopy to visualize dynamic processes and structures in living cells.
- Published
- 2017
37. Differential requirement forN-ethylmaleimide-sensitive factor in endosomal trafficking of transferrin receptor from anterograde trafficking of vesicular stomatitis virus glycoprotein G
- Author
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Yonghong Sun, Yanli Wang, Derek Toomre, Xiaoxu Zhou, Cuifang Kuang, Yingke Xu, Jiannan Fan, and Xu Liu
- Subjects
0301 basic medicine ,Endosome ,Biophysics ,Golgi Apparatus ,Transferrin receptor ,Endosomes ,Endocytosis ,Biochemistry ,Exocytosis ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Viral Envelope Proteins ,Structural Biology ,Receptors, Transferrin ,Genetics ,Humans ,Transport Vesicles ,N-Ethylmaleimide-Sensitive Proteins ,Molecular Biology ,Adenosine Triphosphatases ,chemistry.chemical_classification ,Membrane Glycoproteins ,biology ,Chemistry ,Cell Biology ,Golgi apparatus ,biology.organism_classification ,Virology ,Cell biology ,Vesicular transport protein ,Protein Transport ,030104 developmental biology ,Vesicular stomatitis virus ,Transferrin ,Gene Knockdown Techniques ,Mutation ,symbols ,RNA Interference ,030217 neurology & neurosurgery ,HeLa Cells - Abstract
N-ethylmaleimide-sensitive fusion factor (NSF) is an ATPase that plays a crucial role in vesicular transport. Here, we examined the effects of NSF knockdown on Golgi structure and different vesicle trafficking pathways in mammalian cells. NSF knockdown caused Golgi fragmentation and abolished transferrin receptor exocytosis, defects that were rescued by RNAi-resistant NSF. Strikingly, NSF deficiency in HeLa cells barely affected cell viability, anterograde trafficking of vesicular stomatitis virus glycoprotein G and transferrin endocytosis. These results confirm the central role of NSF in Golgi structure and reveal differential requirement of NSF for exocytic recycling and constitutive trafficking pathways.
- Published
- 2017
38. Palmitoylated Proteins in Plasmodium falciparum-Infected Erythrocytes: Investigation with Click Chemistry and Metabolic Labeling
- Author
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Derek Toomre, Andreas M. Ernst, Yongdeng Zhang, Giles Hooker, Choukri Ben Mamoun, Nicole Kilian, and Lauren C LaMonica
- Subjects
Erythrocytes ,Confocal ,Transgene ,Plasmodium falciparum ,Biology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,parasitic diseases ,medicine ,Parasite hosting ,Humans ,Malaria, Falciparum ,030304 developmental biology ,0303 health sciences ,medicine.disease ,biology.organism_classification ,3. Good health ,Microscopy, Electron ,Biochemistry ,Metabolic labeling ,Click chemistry ,Click Chemistry ,030217 neurology & neurosurgery ,Malaria - Abstract
The examination of the complex cell biology of the human malaria parasite Plasmodium falciparum usually relies on the time-consuming generation of transgenic parasites. Here, metabolic labeling and click chemistry are employed as a fast transfection-independent method for the microscopic examination of protein S-palmitoylation, an important post-translational modification during the asexual intraerythrocytic replication of P. falciparum. Applying various microscopy approaches such as confocal, single-molecule switching, and electron microscopy, differences in the extent of labeling within the different asexual developmental stages of P. falciparum and the host erythrocytes over time are observed.
- Published
- 2019
39. Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags
- Author
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James E. Rothman, Rebecca F. Wissner, Derek Toomre, Daniel St Johnston, Stephanie Wood Baguley, Alanna Schepartz, Joerg Bewersdorf, Nicholas Lowe, Edward S. Allgeyer, Roman S. Erdmann, Jennifer H. Richens, Richard Butler, Sheng Zhong, Zhiqun Xi, Alexander D. Thompson, Richens, Jennifer [0000-0002-8241-4826], Allgeyer, Edward [0000-0002-2187-4423], Butler, Richard [0000-0002-3885-1332], St Johnston, Daniel [0000-0001-5582-3301], and Apollo - University of Cambridge Repository
- Subjects
Confocal ,Recombinant Fusion Proteins ,Clinical Biochemistry ,Green Fluorescent Proteins ,Biology ,HaloTag ,nanoscopy ,self-labeling proteins ,01 natural sciences ,Biochemistry ,Article ,live-cell imaging ,Fluorescence ,Rhodamine ,chemistry.chemical_compound ,Live cell imaging ,super-resolution microscopy ,Drug Discovery ,Microscopy ,fluorophores ,Animals ,Humans ,Molecular Biology ,Fluorescent Dyes ,Pharmacology ,SNAP-tag ,Microscopy, Confocal ,Staining and Labeling ,010405 organic chemistry ,Super-resolution microscopy ,Rhodamines ,STED microscopy ,Proteins ,3. Good health ,0104 chemical sciences ,STED ,Microscopy, Fluorescence ,chemistry ,microscopy ,Biophysics ,Molecular Medicine ,Drosophila ,HeLa Cells - Abstract
Summary Super-resolution microscopy requires that subcellular structures are labeled with bright and photostable fluorophores, especially for live-cell imaging. Organic fluorophores may help here as they can yield more photons—by orders of magnitude—than fluorescent proteins. To achieve molecular specificity with organic fluorophores in live cells, self-labeling proteins are often used, with HaloTags and SNAP-tags being the most common. However, how these two different tagging systems compare with each other is unclear, especially for stimulated emission depletion (STED) microscopy, which is limited to a small repertoire of fluorophores in living cells. Herein, we compare the two labeling approaches in confocal and STED imaging using various proteins and two model systems. Strikingly, we find that the fluorescent signal can be up to 9-fold higher with HaloTags than with SNAP-tags when using far-red rhodamine derivatives. This result demonstrates that the labeling strategy matters and can greatly influence the duration of super-resolution imaging., Highlights • Systematic comparison of SNAP versus Halo tag labeling by confocal and STED microscopy • Target proteins, fluorophores, and model systems are compared • Large differences in Halo versus SNAP intensity with silicon rhodamine fluorophores • Guidelines for one- and two-color super-resolution imaging are provided, Self-labeling proteins leverage the superior photophysical properties of organic fluorophores and are the method of choice for live-cell nanoscopy. Comparing SNAP-tags and HaloTags, Erdmann et al. show that Halo tagging with silicon rhodamine fluorophores provides brighter labeling for confocal and STED nanoscopy.
- Published
- 2019
40. An active tethering mechanism controls the fate of vesicles
- Author
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Vladimir I. Polejaev, Zhiqun Xi, Brian McNellis, Alexander Anneken, Derek Toomre, Felix Rivera-Molina, and Seong An
- Subjects
Cell biology ,Vesicle fusion ,Science ,Recombinant Fusion Proteins ,Vesicular Transport Proteins ,General Physics and Astronomy ,Gene Expression ,Exocyst ,Membrane trafficking ,Optogenetics ,Exosomes ,Membrane Fusion ,General Biochemistry, Genetics and Molecular Biology ,Article ,Exocytosis ,Genes, Reporter ,Receptors, Transferrin ,Humans ,Fusion ,Microscopy ,Multidisciplinary ,Chemistry ,Tethering ,Vesicle ,Secretory Vesicles ,Cell Membrane ,General Chemistry ,Cryptochromes ,Luminescent Proteins ,Membrane ,Microscopy, Fluorescence ,rab GTP-Binding Proteins ,Biophysics ,Intracellular ,HeLa Cells - Abstract
Vesicle tethers are thought to underpin the efficiency of intracellular fusion by bridging vesicles to their target membranes. However, the interplay between tethering and fusion has remained enigmatic. Here, through optogenetic control of either a natural tether—the exocyst complex—or an artificial tether, we report that tethering regulates the mode of fusion. We find that vesicles mainly undergo kiss-and-run instead of full fusion in the absence of functional exocyst. Full fusion is rescued by optogenetically restoring exocyst function, in a manner likely dependent on the stoichiometry of tether engagement with the plasma membrane. In contrast, a passive artificial tether produces mostly kissing events, suggesting that kiss-and-run is the default mode of vesicle fusion. Optogenetic control of tethering further shows that fusion mode has physiological relevance since only full fusion could trigger lamellipodial expansion. These findings demonstrate that active coupling between tethering and fusion is critical for robust membrane merger., Molecular tethers physically bridge transport vesicles to their target membranes as a prerequisite step for fusion. Here the authors control vesicle tethering using optogenetic approaches to study the interplay between vesicle tethering and fusion.
- Published
- 2019
41. Seeing the long tail: A novel green fluorescent protein, SiriusGFP, for ultra long timelapse imaging
- Author
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Dhasakumar Navaratnam, Felix Rivera-Molina, Alberto Rivetta, Joseph Santos-Sacchi, Sheng Zhong, and Derek Toomre
- Subjects
0301 basic medicine ,Microscopy, Confocal ,General Neuroscience ,Confocal ,Green Fluorescent Proteins ,Photobleaching ,Fluorescence ,Green fluorescent protein ,03 medical and health sciences ,Light intensity ,030104 developmental biology ,0302 clinical medicine ,HEK293 Cells ,Membrane protein ,Microscopy, Fluorescence ,Cytoplasm ,Biophysics ,Humans ,Bacterial outer membrane ,030217 neurology & neurosurgery ,HeLa Cells - Abstract
Background Fluorescent proteins (FPs) have widespread uses in cell biology. However, the practical applications of FPs are significantly limited due to their rapid photobleaching and misfolding when fused to target proteins. New Method Using a combination of novel and known mutations to eGFP, we developed a well folded and very photostable variant, SiriusGFP. Results The fluorescence spectrum indicated that the excitation and emission peaks of SiriusGFP were red-shifted by 16 and 8 nm, respectively. Co- operative effects of two key mutations, S147R and S205 V, contribute to its photostability. SiriusGFP tagged to the mitochondrial outer membrane protein Omp25 showed sustained fluorescence during continuous 3D-scanning confocal imaging (4D confocal) compared to eGFP-tagged Omp25. Furthermore, with super-resolution structured illumination microscopy (SIM) we demonstrate marked improvements in image quality and resolution (130 nm in XY axis, and 310 nm in Z axis), as well as, decreased artifacts due to photobleaching. Comparison with Existing Method(s) Compared to eGFP. SiriusGFP shows a 2-fold increase in photostability in vitro, and folds well when fused to the N- and C- termini of cytoplasmic and membrane proteins. While its quantum yield is ˜3 fold lower than eGFP, its decreased brightness was more than compensated by its increasedphotostability in different experimental paradigms allowing practical experimentation without dynamic adjustment of light intensity or fluorescence sampling times. Conclusions We have developed a variant of eGFP, SiriusGFP, that shows over a two fold increase in photostability with utility in methods requiring sustained or high intensity excitation as in 4D confocal or SIM imaging.
- Published
- 2018
42. S-Palmitoylation Sorts Membrane Cargo for Anterograde Transport in the Golgi
- Author
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Francesca Bottanelli, Frederic Pincet, Patrik Björkholm, James E. Rothman, Felix Rivera-Molina, Saad Syed, Moritz Hacke, Andreas M. Ernst, Derek Toomre, Omar Zaki, Zhiqun Xi, Aleksander A. Rebane, David Baddeley, Hong Zheng, Morven Graham, CSIRO: Digital Productivity and Services, Laboratoire de Physique Statistique de l'ENS (LPS), Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Physiology and Cellular Biophysics [New York, NY, USA], and Columbia University College of Physicians and Surgeons
- Subjects
0301 basic medicine ,Lipoylation ,Golgi Apparatus ,macromolecular substances ,Biology ,Endoplasmic Reticulum ,environment and public health ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Palmitoylation ,Golgi ,Humans ,Protein palmitoylation ,Molecular Biology ,Cells, Cultured ,030304 developmental biology ,Golgi membrane ,0303 health sciences ,Membranes ,Trafficking ,[PHYS.PHYS]Physics [physics]/Physics [physics] ,Chemistry ,Vesicle ,Sorting ,technology, industry, and agriculture ,Biological Transport ,Intracellular Membranes ,Cell Biology ,Golgi apparatus ,Cell biology ,Transport protein ,Transmembrane domain ,Protein Transport ,030104 developmental biology ,Membrane ,S-palmitoylation ,Membrane protein ,Axoplasmic transport ,Biophysics ,Posttranslational modification ,symbols ,lipids (amino acids, peptides, and proteins) ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
International audience; While retrograde cargo selection in the Golgi is known to depend on specific signals, it is unknown whether anterograde cargo is sorted, and anterograde signals have not been identified. We suggest here that S-palmitoylation of anterograde cargo at the Golgi membrane interface is an anterograde signal and that it results in concentration in curved regions at the Golgi rims by simple physical chemistry. The rate of transport across the Golgi of two S-palmitoylated membrane proteins is controlled by S-palmitoylation. The bulk of S-palmitoylated proteins in the Golgi behave analogously, as revealed by click chemistry-based fluorescence and electron microscopy. These palmitoylated cargos concentrate in the most highly curved regions of the Golgi membranes, including the fenestrated perimeters of cisternae and associated vesicles. A palmitoylated transmembrane domain behaves similarly in model systems.
- Published
- 2018
43. Assessing photodamage in live-cell STED microscopy
- Author
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Derek Toomre, Giles Hooker, Nicole Kilian, Alexander Goryaynov, Joerg Bewersdorf, Mark D. Lessard, and James E. Rothman
- Subjects
0301 basic medicine ,Photolysis ,Chemistry ,Extramural ,Cell ,STED microscopy ,Oxidation reduction ,Cell Biology ,Photochemical Processes ,Biochemistry ,Fluorescence ,Article ,03 medical and health sciences ,030104 developmental biology ,medicine.anatomical_structure ,Microscopy, Fluorescence ,Microscopy ,medicine ,Biophysics ,Humans ,Molecular Biology ,Oxidation-Reduction ,Biotechnology ,HeLa Cells - Published
- 2018
44. The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135
- Author
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Kavita Mistry, Emily H. Stoops, Michael J. Caplan, Jennifer L. Harder, Felix Rivera-Molina, Christina Olesen, Michael Hull, and Derek Toomre
- Subjects
animal structures ,Physiology ,Biology ,Microtubules ,Madin Darby Canine Kidney Cells ,03 medical and health sciences ,Dogs ,0302 clinical medicine ,Contactin 1 ,Report ,Cell polarity ,Animals ,Humans ,Cilia ,Research Articles ,030304 developmental biology ,Epithelial polarity ,0303 health sciences ,Membrane Glycoproteins ,Staining and Labeling ,Cilium ,Cell Membrane ,Cell Polarity ,Epithelial Cells ,Apical constriction ,Cell Biology ,Basolateral plasma membrane ,Apical membrane ,Actin cytoskeleton ,Transport protein ,Cell biology ,Actin Cytoskeleton ,Protein Transport ,sense organs ,030217 neurology & neurosurgery ,trans-Golgi Network - Abstract
The apical glycoprotein gp135 is delivered to a ring at the base of the primary cilium and subsequently moves in a radial fashion away from the cilium in a microtubule-dependent manner., In polarized epithelial cells, newly synthesized cell surface proteins travel in carrier vesicles from the trans Golgi network to the apical or basolateral plasma membrane. Despite extensive research on polarized trafficking, the sites of protein delivery are not fully characterized. Here we use the SNAP tag system to examine the site of delivery of the apical glycoprotein gp135. We show that a cohort of gp135 is delivered to a ring surrounding the base of the primary cilium, followed by microtubule-dependent radial movement away from the cilium. Delivery to the periciliary ring was specific to newly synthesized and not recycling protein. A subset of this newly delivered protein traverses the basolateral membrane en route to the apical membrane. Crumbs3a, another apical protein, was not delivered to the periciliary region, instead making its initial apical appearance in a pattern that resembled its steady-state distribution. Our results demonstrate a surprising “hot spot” for gp135 protein delivery at the base of the primary cilium and suggest the existence of a novel microtubule-based directed movement of a subset of apical surface proteins.
- Published
- 2015
45. HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution
- Author
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Alanna Schepartz, Joerg Bewersdorf, Alexander D. Thompson, and Derek Toomre
- Subjects
0301 basic medicine ,Biochemistry & Molecular Biology ,Time Factors ,High density ,Medical Biochemistry and Metabolomics ,Biology ,Signal-To-Noise Ratio ,Biochemistry ,Article ,Imaging modalities ,Medicinal and Biomolecular Chemistry ,03 medical and health sciences ,Organelle ,Humans ,Organelles ,Endoplasmic reticulum ,Dynamics (mechanics) ,Intracellular Membranes ,Superresolution ,Cell biology ,Molecular Imaging ,030104 developmental biology ,Hela Cells ,Biophysics ,Generic health relevance ,Biochemistry and Cell Biology ,HeLa Cells - Abstract
Living cells are complex and dynamic assemblies that carefully sequester and orchestrate multiple diverse processes that enable growth, division, regulation, movement, and communication. Membrane-bound organelles such as the endoplasmic reticulum, mitochondria, plasma membrane, and others are integral to these processes, and their functions demand dynamic reorganization in both space and time. Visualizing these dynamics in live cells over long time periods demands probes that label discrete organelles specifically, at high density, and withstand long-term irradiation. Here we describe the evolution of our work on the development of a set of high-density environmentally sensitive (HIDE) membrane probes that enable long-term, live-cell nanoscopy of the dynamics of multiple organelles in live cells using single-molecule switching and stimulated emission depletion imaging modalities.
- Published
- 2017
46. A novel physiological role for ARF1 in the formation of bidirectional tubules from the Golgi
- Author
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David Baddeley, Roman S. Erdmann, Lena K. Schroeder, James E. Rothman, Emil B. Kromann, Derek Toomre, Felix Rivera-Molina, Alanna Schepartz, Joerg Bewersdorf, Andreas M. Ernst, Francesca Bottanelli, Mark D. Lessard, Nicole Kilian, and Glick, Benjamin S
- Subjects
0301 basic medicine ,GTP' ,Coated vesicle ,Golgi Apparatus ,Clathrin ,Medical and Health Sciences ,GTP Phosphohydrolases ,Coat Protein Complex I ,03 medical and health sciences ,symbols.namesake ,Genetics ,Humans ,Molecular Biology ,Secretory pathway ,biology ,Vesicle ,Hydrolysis ,Cell Biology ,COPI ,Articles ,Intracellular Membranes ,Golgi apparatus ,Biological Sciences ,Cell biology ,030104 developmental biology ,Coatomer ,Membrane Trafficking ,Hela Cells ,biology.protein ,symbols ,ADP-Ribosylation Factor 1 ,Guanosine Triphosphate ,COP-Coated Vesicles ,HeLa Cells ,Biotechnology ,Developmental Biology - Abstract
Besides its well-established role in generating COPI vesicles by recruiting coatomer at the Golgi, the small GTPase ARF1 is additionally involved in the formation of anterograde and retrograde tubular carriers at the Golgi., Capitalizing on CRISPR/Cas9 gene-editing techniques and super-resolution nanoscopy, we explore the role of the small GTPase ARF1 in mediating transport steps at the Golgi. Besides its well-established role in generating COPI vesicles, we find that ARF1 is also involved in the formation of long (∼3 µm), thin (∼110 nm diameter) tubular carriers. The anterograde and retrograde tubular carriers are both largely free of the classical Golgi coat proteins coatomer (COPI) and clathrin. Instead, they contain ARF1 along their entire length at a density estimated to be in the range of close packing. Experiments using a mutant form of ARF1 affecting GTP hydrolysis suggest that ARF1[GTP] is functionally required for the tubules to form. Dynamic confocal and stimulated emission depletion imaging shows that ARF1-rich tubular compartments fall into two distinct classes containing 1) anterograde cargoes and clathrin clusters or 2) retrograde cargoes and coatomer clusters.
- Published
- 2017
47. Excess cholesterol inhibits glucose-stimulated fusion pore dynamics in insulin exocytosis
- Author
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Mingming Hao, Derek Toomre, Yingke Xu, and Jonathan S. Bogan
- Subjects
0301 basic medicine ,Phosphatidylinositol 4,5-Diphosphate ,medicine.medical_treatment ,Type 2 diabetes ,Membrane Fusion ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,Insulin-Secreting Cells ,fusion pore ,glucose ,diabetes ,VAMP2‐pHluorin ,Molecular Medicine ,Original Article ,Beta cell ,Signal Transduction ,Dynamins ,medicine.medical_specialty ,insulin ,total internal reflection fluorescence microscopy ,Biology ,Models, Biological ,Exocytosis ,03 medical and health sciences ,Internal medicine ,Diabetes mellitus ,Cell Line, Tumor ,medicine ,Animals ,Humans ,Phosphatidylinositol ,Dynamin ,Cholesterol ,Insulin ,Secretory Vesicles ,Cell Membrane ,cholesterol ,Cell Biology ,Original Articles ,medicine.disease ,beta cell ,030104 developmental biology ,Endocrinology ,chemistry ,Diabetes Mellitus, Type 2 ,Gene Expression Regulation ,Microscopy, Fluorescence ,030217 neurology & neurosurgery - Abstract
Type 2 diabetes is caused by defects in both insulin sensitivity and insulin secretion. Glucose triggers insulin secretion by causing exocytosis of insulin granules from pancreatic β‐cells. High circulating cholesterol levels and a diminished capacity of serum to remove cholesterol from β‐cells are observed in diabetic individuals. Both of these effects can lead to cholesterol accumulation in β‐cells and contribute to β‐cell dysfunction. However, the molecular mechanisms by which cholesterol accumulation impairs β‐cell function remain largely unknown. Here, we used total internal reflection fluorescence microscopy to address, at the single‐granule level, the role of cholesterol in regulating fusion pore dynamics during insulin exocytosis. We focused particularly on the effects of cholesterol overload, which is relevant to type 2 diabetes. We show that excess cholesterol reduced the number of glucose‐stimulated fusion events, and modulated the proportion of full fusion and kiss‐and‐run fusion events. Analysis of single exocytic events revealed distinct fusion kinetics, with more clustered and compound exocytosis observed in cholesterol‐overloaded β‐cells. We provide evidence for the involvement of the GTPase dynamin, which is regulated in part by cholesterol‐induced phosphatidylinositol 4,5‐bisphosphate enrichment in the plasma membrane, in the switch between full fusion and kiss‐and‐run fusion. Characterization of insulin exocytosis offers insights into the role that elevated cholesterol may play in the development of type 2 diabetes.
- Published
- 2017
48. STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells
- Author
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Roman S. Erdmann, Derek Toomre, and Alanna Schepartz
- Subjects
0301 basic medicine ,Ceramide ,Fluorophore ,Bioorthogonal chemistry ,Confocal ,1.1 Normal biological development and functioning ,Golgi Apparatus ,Fluorophores ,Ceramides ,Article ,Fluorescence ,Imaging ,03 medical and health sciences ,chemistry.chemical_compound ,symbols.namesake ,Imaging, Three-Dimensional ,Drug Stability ,Underpinning research ,Organelle ,Humans ,Super-resolution microscopy ,Inverse electron demand Diels-Alder reaction ,Fluorescent Dyes ,Microscopy ,Membranes ,Chemistry ,Rhodamines ,Click chemistry ,STED microscopy ,Golgi apparatus ,Cell biology ,030104 developmental biology ,Microscopy, Fluorescence ,Hela Cells ,Three-Dimensional ,symbols ,lipids (amino acids, peptides, and proteins) ,Generic health relevance ,Biochemistry and Cell Biology ,Other Chemical Sciences ,HeLa Cells ,Developmental Biology - Abstract
Long time-lapse super-resolution imaging in live cells requires a labeling strategy that combines a bright, photostable fluorophore with a high-density localization probe. Lipids are ideal high-density localization probes, as they are >100 times more abundant than most membrane-bound proteins and simultaneously demark the boundaries of cellular organelles. Here, we describe Cer-SiR, a two-component, high-density lipid probe that is exceptionally photostable. Cer-SiR is generated in cells via a bioorthogonal reaction of two components: a ceramide lipid tagged with trans-cyclooctene (Cer-TCO) and a reactive, photostable Si-rhodamine dye (SiR-Tz). These components assemble within the Golgi apparatus of live cells to form Cer-SiR. Cer-SiR is benign to cellular function, localizes within the Golgi at a high density, and is sufficiently photostable to enable visualization of Golgi structure and dynamics by 3D confocal or long time-lapse STED microscopy.
- Published
- 2017
49. Super-Resolution Imaging of the Golgi in Live Cells with a Bioorthogonal Ceramide Probe
- Author
-
Hideo Takakura, Edward S. Allgeyer, Joerg Bewersdorf, Felix Rivera-Molina, Derek Toomre, Alanna Schepartz, Alexander D. Thompson, and Roman S. Erdmann
- Subjects
Ceramide ,Cell Survival ,1.1 Normal biological development and functioning ,Confocal ,Golgi Apparatus ,Ceramides ,Fluorescence ,Article ,Catalysis ,chemistry.chemical_compound ,symbols.namesake ,Underpinning research ,fluorophores ,Humans ,Coloring Agents ,Microscopy ,Microscopy, Confocal ,Endoplasmic reticulum ,Organic Chemistry ,STED microscopy ,General Chemistry ,Golgi apparatus ,bioorthogonal chemistry ,3. Good health ,STED ,Membrane ,Microscopy, Fluorescence ,chemistry ,Biochemistry ,membranes ,Hela Cells ,click chemistry ,Chemical Sciences ,Click chemistry ,Biophysics ,symbols ,lipids (amino acids, peptides, and proteins) ,Generic health relevance ,Bioorthogonal chemistry ,HeLa Cells - Abstract
We report a lipid-based strategy to visualize Golgi structure and dynamics at super-resolution in live cells. The method is based on two novel reagents: a trans-cyclooctene-containing ceramide lipid (Cer-TCO) and a highly reactive, tetrazine-tagged near-IR dye (SiR-Tz). These reagents assemble via an extremely rapid ‘tetrazine-click’ reaction into Cer-SiR, a highly photostable ‘vital dye’ that enables prolonged live cell imaging of the Golgi apparatus by 3D confocal and STED microscopy. Cer-SiR is non-toxic at concentrations as high as 2 μM and does not perturb the mobility of Golgi-resident enzymes or the traffic of cargo from the endoplasmic reticulum through the Golgi and to the plasma membrane.
- Published
- 2014
50. A Network of Interactions Enables CCM3 and STK24 to Coordinate UNC13D-Driven Vesicle Exocytosis in Neutrophils
- Author
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Titus J. Boggon, Dianqing Wu, Derek Toomre, Wenwen Tang, Weijun Pan, Yingke Xu, Haifeng Zhang, Wang Min, Jiasheng Zhang, Xiaofeng Niu, Yong Zhang, and Kun Gao
- Subjects
Neutrophils ,Cell Degranulation ,Regulator ,Protein Serine-Threonine Kinases ,Biology ,Kidney ,Exocytosis ,Article ,General Biochemistry, Genetics and Molecular Biology ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Animals ,UNC13D ,Molecular Biology ,030304 developmental biology ,Mice, Knockout ,0303 health sciences ,Innate immune system ,Intracellular Signaling Peptides and Proteins ,Membrane Proteins ,Munc-18 ,Cell Biology ,Immunity, Innate ,Protein Structure, Tertiary ,3. Good health ,Cell biology ,Mice, Inbred C57BL ,Specific granule ,Reperfusion Injury ,Neutrophil degranulation ,Apoptosis Regulatory Proteins ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Neutrophil degranulation plays an important role in acute innate immune responses and is tightly regulated because the granule contents can cause tissue damage. However, this regulation remains poorly understood. Here we identify the complex of STK24 and CCM3 as being an important regulator of neutrophil degranulation. Lack of either STK24 or CCM3 increases the release of a specific granule pool without affecting other neutrophil functions. STK24 appears to suppress exocytosis by interacting and competing with UNC13D C2B domain for lipid binding, whereas CCM3 has dual roles in exocytosis regulation. While CCM3 stabilizes STK24, it counteracts STK24-mediated inhibition of exocytosis by recruiting STK24 away from the C2B domain through its Ca2+-sensitive interaction with UNC13D C2A domain. This STK24/CCM3-regulated exocytosis plays an important role in protection of kidneys from ischemia-reperfusion injury. Together, these findings reveal a previously unknown function of the STK24 and CCM3 complex in the regulation of ligand-stimulated exocytosis.
- Published
- 2013
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