201
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The quantification and regulation of microtubule dynamics in the mitotic spindle. Curr Opin Cell Biol 2019; 60:36-43. [PMID: 31108428 DOI: 10.1016/j.ceb.2019.03.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/20/2019] [Accepted: 03/30/2019] [Indexed: 12/18/2022]
Abstract
Microtubules play essential roles in cellular organization, cargo transport, and chromosome segregation during cell division. During mitosis microtubules form a macromolecular structure known as the mitotic spindle that is responsible for the accurate segregation of chromosomes between the two daughter cells. This is accomplished thanks to finely tuned control of microtubule dynamics. Even small changes in microtubule dynamics during spindle formation and/or operation may lead to chromosome mis-segregation, chromosome instability and aneuploidy. These three events are directly correlated with human diseases like cancer and developmental defects. Precise measurements of microtubule dynamics in the spindle will allow us to discover new molecules involved in regulating microtubule dynamics and enable a deeper understanding of the mechanisms that underlie mitosis and cancer emergence and development. Moreover, many chemotherapeutic agents for cancer treatment are targeted to microtubules, so continued investigation of their dynamics with utmost precision will facilitate the development of new drugs. Measuring microtubule dynamics in the spindle has been a difficult task until recently. With the development of new and gentler microscopic techniques, and new computer programs, we can perform better and more accurate measurements of microtubule dynamics during mitosis.
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202
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Boyman L, Coleman AK, Zhao G, Wescott AP, Joca HC, Greiser BM, Karbowski M, Ward CW, Lederer WJ. Dynamics of the mitochondrial permeability transition pore: Transient and permanent opening events. Arch Biochem Biophys 2019; 666:31-39. [PMID: 30930285 PMCID: PMC6538282 DOI: 10.1016/j.abb.2019.03.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022]
Abstract
A gentle optical examination of the mitochondrial permeability transition pore (mPTP) opening events was carried out in isolated quiescent ventricular myocytes by tracking the inner membrane potential (ΔΨM) using TMRM (tetramethylrhodamine methyl ester). Zeiss Airyscan 880 ″super-resolution" or "high-resolution" imaging was done with very low levels of illumination (0.009% laser power). In cellular areas imaged every 9 s (ROI or regions of interest), transient depolarizations of variable amplitudes occurred at increasing rates for the first 30 min. The time to first depolarization events was 8.4 min (±1.1 SEM n = 21 cells). At longer times, essentially permanent and irreversible depolarizations occurred at an increasing fraction of all events. In other cellular areas surrounding the ROI, mitochondria were rarely illuminated (once per 5 min) and virtually no permanent depolarization events occurred for over 1 h of imaging. These findings suggest that photon stress due to the imaging itself plays an important role in the generation of both the transient mPTP opening events as well as the permanent mPTP opening events. Consistent with the evidence that photon "stress" in mitochondria loaded with virtually any photon absorbing substance, generates reactive oxygen species (ROS) [1-5], we show that cyclosporine-A (CsA, 10 μM) and the antioxidant n-acetyl cysteine (NAC, 10 mM), reduced the number of events by 80% and 93% respectively. Furthermore, CsA and NAC treatment led to the virtual disappearance of permanent depolarization events. Nevertheless, all transient depolarization events in any condition (control, CsA and NAC) appeared to repolarize with a similar half-time of 30 ± 6 s (n = 478) at 37 °C. Further experiments showed quantitatively similar results in cerebral vascular smooth muscle cells, using a different confocal system, and different photon absorbing reagent (TMRE; tetramethylrhodamine ethyl ester). In these experiments, using modest power (1% laser power) transient depolarization events were seen in only 8 out of 23 cells while with higher power (8%), all cells showed transient events, which align with the level of photon stress being the driver of the effect. Together, our findings suggest that photon-induced ROS is sufficient to cause depolarization events of individual mitochondria in quiescent cells; without electrical or mechanical activity to stimulates mitochondrial metabolism, and without raising the mitochondrial matrix Ca2+. In a broad context, these findings neither support nor deny the relevance or occurrence of ΔΨM depolarization events in specific putatively physiologic mitochondrial behaviors such as MitoFlashes [6,7] or MitoWinks [8]. Instead, our findings raise a caution with regards to the physiological and pathophysiological functions attributed to singular ΔΨM depolarization events when those functions are investigated using photon absorbing substances. Nevertheless, using photon stress as a tool ("Optical Stress-Probe"), we can extract information on the activation, reversibility, permanency and kinetics of mitochondrial depolarization. These data may provide new information on mPTP, help identify the mPTP protein complex, and establish the physiological function of the mPTP protein complex and their links to MitoFlashes and MitoWinks.
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Affiliation(s)
- Liron Boyman
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA.
| | - Andrew K Coleman
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA
| | - Guiling Zhao
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA
| | - Andrew P Wescott
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA
| | - Humberto C Joca
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA
| | - B Maura Greiser
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA
| | - Mariusz Karbowski
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA
| | - Chris W Ward
- Department of Orthopedics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - W J Lederer
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA.
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203
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Jost APT, Waters JC. Designing a rigorous microscopy experiment: Validating methods and avoiding bias. J Cell Biol 2019; 218:1452-1466. [PMID: 30894402 PMCID: PMC6504886 DOI: 10.1083/jcb.201812109] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 01/06/2023] Open
Abstract
Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.
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204
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Corsetti S, Gunn-Moore F, Dholakia K. Light sheet fluorescence microscopy for neuroscience. J Neurosci Methods 2019; 319:16-27. [DOI: 10.1016/j.jneumeth.2018.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/03/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022]
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205
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Abstract
The goal of this protocol is to characterize how membrane compartments form and transform in live cells of budding yeast. Many intracellular compartments in yeast are dynamic, and a full understanding of their properties requires time-lapse imaging. Multi-color 4D confocal fluorescence microscopy is a powerful method for tracking the behavior and composition of an intracellular compartment on a time scale of 5-15 min. Rigorous analysis of compartment dynamics requires the capture of thousands of optical sections. To achieve this aim, photobleaching and phototoxicity are minimized by scanning rapidly at very low laser power, and the pixel dimensions and Z-step intervals are set to the largest values that are compatible with sampling the image at full resolution. The resulting 4D data sets are noisy but can be smoothed by deconvolution. Even with high quality data, the analysis phase is challenging because intracellular structures are often numerous, heterogeneous, and mobile. To meet this need, custom ImageJ plugins were written to array 4D data on a computer screen, identify structures of interest, edit the data to isolate individual structures, quantify the fluorescence time courses, and make movies of the projected Z-stacks. 4D movies are particularly useful for distinguishing stable compartments from transient compartments that turn over by maturation. Such movies can also be used to characterize events such as compartment fusion, and to test the effects of specific mutations or other perturbations.
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Affiliation(s)
- Natalie Johnson
- Department of Molecular Genetics and Cell Biology, University of Chicago
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago;
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206
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Schloetel JG, Heine J, Cowman AF, Pasternak M. Guided STED nanoscopy enables super-resolution imaging of blood stage malaria parasites. Sci Rep 2019; 9:4674. [PMID: 30886187 PMCID: PMC6423018 DOI: 10.1038/s41598-019-40718-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/19/2019] [Indexed: 12/27/2022] Open
Abstract
Malaria remains a major burden world-wide, but the disease-causing parasites from the genus Plasmodium are difficult to study in vitro. Owing to the small size of the parasites, subcellular imaging poses a major challenge and the use of super-resolution techniques has been hindered by the parasites' sensitivity to light. This is particularly apparent during the blood-stage of the Plasmodium life cycle, which presents an important target for drug research. The iron-rich food vacuole of the parasite undergoes disintegration when illuminated with high-power lasers such as those required for high resolution in Stimulated Emission Depletion (STED) microscopy. This causes major damage to the sample precluding the use of this super-resolution technique. Here we present guided STED, a novel adaptive illumination (AI) STED approach, which takes advantage of the highly-reflective nature of the iron deposit in the cell to identify the most light-sensitive parts of the sample. Specifically in these parts, the high-power STED laser is deactivated automatically to prevent local damage. Guided STED nanoscopy finally allows super-resolution imaging of the whole Plasmodium life cycle, enabling multicolour imaging of blood-stage malaria parasites with resolutions down to 35 nm without sample destruction.
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Affiliation(s)
| | - Jörn Heine
- Abberior Instruments GmbH, 37077, Göttingen, Germany
| | - Alan F Cowman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Michał Pasternak
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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207
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Imaging Flies by Fluorescence Microscopy: Principles, Technologies, and Applications. Genetics 2019; 211:15-34. [PMID: 30626639 PMCID: PMC6325693 DOI: 10.1534/genetics.118.300227] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023] Open
Abstract
The development of fluorescent labels and powerful imaging technologies in the last two decades has revolutionized the field of fluorescence microscopy, which is now widely used in diverse scientific fields from biology to biomedical and materials science. Fluorescence microscopy has also become a standard technique in research laboratories working on Drosophila melanogaster as a model organism. Here, we review the principles of fluorescence microscopy technologies from wide-field to Super-resolution microscopy and its application in the Drosophila research field.
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208
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Abstract
We introduce Field Synthesis, a theorem that can be used to synthesize any scanned or dithered light-sheet, including those used in lattice light-sheet microscopy (LLSM), from an incoherent superposition of one-dimensional intensity distributions. This user-friendly and modular approach offers a drastically simplified optical design, higher light-throughput, simultaneous multicolor illumination, and a 100% spatial duty cycle that provides biological imaging with low rates of photobleaching.
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209
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Huang T, Phelps C, Wang J, Lin LJ, Bittel A, Scott Z, Jacques S, Gibbs SL, Gray JW, Nan X. Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophys J 2019; 114:301-310. [PMID: 29401428 DOI: 10.1016/j.bpj.2017.11.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
Single-molecule tracking (SMT) offers rich information on the dynamics of underlying biological processes, but multicolor SMT has been challenging due to spectral cross talk and a need for multiple laser excitations. Here, we describe a single-molecule spectral imaging approach for live-cell tracking of multiple fluorescent species at once using a single-laser excitation. Fluorescence signals from all the molecules in the field of view are collected using a single objective and split between positional and spectral channels. Images of the same molecule in the two channels are then combined to determine both the location and the identity of the molecule. The single-objective configuration of our approach allows for flexible sample geometry and the use of a live-cell incubation chamber required for live-cell SMT. Despite a lower photon yield, we achieve excellent spatial (20-40 nm) and spectral (10-15 nm) resolutions comparable to those obtained with dual-objective, spectrally resolved Stochastic Optical Reconstruction Microscopy. Furthermore, motions of the fluorescent molecules did not cause loss of spectral resolution owing to the dual-channel spectral calibration. We demonstrate SMT in three (and potentially more) colors using spectrally proximal fluorophores and single-laser excitation, and show that trajectories of each species can be reliably extracted with minimal cross talk.
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Affiliation(s)
- Tao Huang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Carey Phelps
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Jing Wang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Li-Jung Lin
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Amy Bittel
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Zubenelgenubi Scott
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Steven Jacques
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Summer L Gibbs
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Joe W Gray
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.
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210
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Liimatainen K, Kananen L, Latonen L, Ruusuvuori P. Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks. BMC Bioinformatics 2019; 20:80. [PMID: 30767778 PMCID: PMC6376647 DOI: 10.1186/s12859-019-2605-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With deep learning, cells can be detected with high accuracy, but manually annotated training data is required. We propose a method for cell detection that requires annotated training data for one cell line only, and generalizes to other, unseen cell lines. RESULTS Training a deep learning model with one cell line only can provide accurate detections for similar unseen cell lines (domains). However, if the new domain is very dissimilar from training domain, high precision but lower recall is achieved. Generalization capabilities of the model can be improved with training data transformations, but only to a certain degree. To further improve the detection accuracy of unseen domains, we propose iterative unsupervised domain adaptation method. Predictions of unseen cell lines with high precision enable automatic generation of training data, which is used to train the model together with parts of the previously used annotated training data. We used U-Net-based model, and three consecutive focal planes from brightfield image z-stacks. We trained the model initially with PC-3 cell line, and used LNCaP, BT-474 and 22Rv1 cell lines as target domains for domain adaptation. Highest improvement in accuracy was achieved for 22Rv1 cells. F1-score after supervised training was only 0.65, but after unsupervised domain adaptation we achieved a score of 0.84. Mean accuracy for target domains was 0.87, with mean improvement of 16 percent. CONCLUSIONS With our method for generalized cell detection, we can train a model that accurately detects different cell lines from brightfield images. A new cell line can be introduced to the model without a single manual annotation, and after iterative domain adaptation the model is ready to detect these cells with high accuracy.
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Affiliation(s)
- Kaisa Liimatainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lauri Kananen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leena Latonen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Pekka Ruusuvuori
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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211
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Li X, Wang X, Zhao C, Shao L, Lu J, Tong Y, Chen L, Cui X, Sun H, Liu J, Li M, Deng X, Wu Y. From one to all: self-assembled theranostic nanoparticles for tumor-targeted imaging and programmed photoactive therapy. J Nanobiotechnology 2019; 17:23. [PMID: 30711005 PMCID: PMC6359812 DOI: 10.1186/s12951-019-0450-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background In recent years, multifunctional theranostic nanoparticles have been fabricated by integrating imaging and therapeutic moieties into one single nano-formulations. However, Complexity of production and safety issues limits their further application. Results Herein, we demonstrated self-assembled nanoparticles with single structure as a “from one to all” theranostic platform for tumor-targeted dual-modal imaging and programmed photoactive therapy (PPAT). The nanoparticles were successfully developed through self-assembling of hyaluronic acid (HA)-cystamine-cholesterol (HSC) conjugate, in which IR780 was simultaneously incorporated (HSCI NPs). Due to the proper hydrodynamic size and intrinsic targeting ability of HA, the HSCI NPs could accumulate at the tumor site effectively after systemic administration. In the presence of incorporated IR780, in vivo biodistribution and accumulation behaviors of HSCI NPs could be monitored by photoacoustic imaging. After cellular uptake, the HSCI NPs would disintegrate resulting from cystamine reacting with over-expressed GSH. The released IR780 would induce fluorescence “turn-on” conversion, which could be used to image tumor sites effectively. Upon treatment with 808 nm laser irradiation, PPAT could be achieved in which generated reactive oxygen species (ROS) would produce photodynamic therapy (PDT), and subsequently the raised temperature would be beneficial to tumor photothermal therapy (PTT). Conclusion The self-assembled HSCI NPs could act as “from one to all” theranostic platform for high treatment efficiency via PPAT pattern, which could also real-time monitor NPs accumulation by targeted and dual-modal imaging in a non-invasive way.![]() Electronic supplementary material The online version of this article (10.1186/s12951-019-0450-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianlei Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xuan Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Caiyan Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Leihou Shao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jianqing Lu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China
| | - Yujia Tong
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China
| | - Long Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xinyue Cui
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China
| | - Huiling Sun
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China
| | - Junxing Liu
- The First Affiliated Hospital of Jiamusi University, Jiamusi, 154003, China
| | - Mingjun Li
- The First Affiliated Hospital of Jiamusi University, Jiamusi, 154003, China.
| | - Xiongwei Deng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China.
| | - Yan Wu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 First North Road, Zhongguancun, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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212
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Moreno-Layseca P, Icha J, Hamidi H, Ivaska J. Integrin trafficking in cells and tissues. Nat Cell Biol 2019; 21:122-132. [PMID: 30602723 PMCID: PMC6597357 DOI: 10.1038/s41556-018-0223-z] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022]
Abstract
Cell adhesion to the extracellular matrix is fundamental to metazoan multicellularity and is accomplished primarily through the integrin family of cell-surface receptors. Integrins are internalized and enter the endocytic-exocytic pathway before being recycled back to the plasma membrane. The trafficking of this extensive protein family is regulated in multiple context-dependent ways to modulate integrin function in the cell. Here, we discuss recent advances in understanding the mechanisms and cellular roles of integrin endocytic trafficking.
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Affiliation(s)
- Paulina Moreno-Layseca
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jaroslav Icha
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Hellyeh Hamidi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
- Department of Biochemistry, University of Turku, Turku, Finland.
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213
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Tortarolo G, Sun Y, Teng KW, Ishitsuka Y, Lanzanó L, Selvin PR, Barbieri B, Diaspro A, Vicidomini G. Photon-separation to enhance the spatial resolution of pulsed STED microscopy. NANOSCALE 2019; 11:1754-1761. [PMID: 30624448 DOI: 10.1039/c8nr07485b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Stimulated emission depletion microscopy (STED) is one of the pivotal super-resolution techniques. It overcomes the spatial resolution limit imposed by the diffraction by using an additional laser beam, the STED beam, intensity of which is directly related to the achievable resolution. Despite reaching nanometer resolution, much effort in recent years has been devoted to reducing the STED beam intensity because it may lead to photo-damaging effects. Accessing the spatial information encoded in the temporal dynamics of the detected fluorescent photons has been proved to be a powerful strategy and has contributed to the separation by lifetime tuning (SPLIT) technique. The SPLIT method uses the phasor analysis to efficiently distinguish photons emitted from the center and the periphery of the excitation spot. It thus improves the resolution without increasing the STED beam intensity. This method was proposed for architectures based on the STED beam running in continuous waves (CW-STED microscopy). Here, we extend it to pulsed STED beam implementations (pSTED microscopy). We show, through simulated and experimental data, that the pSTED-SPLIT method reduces the detection volume of the pSTED microscope without significantly decreasing the signal-to-noise ratio of the final image, thus effectively improving the resolution without increasing the STED beam intensity.
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Affiliation(s)
- Giorgio Tortarolo
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
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Gruβmayer KS, Yserentant K, Herten DP. Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting. Methods Appl Fluoresc 2019; 7:012003. [DOI: 10.1088/2050-6120/aaf2eb] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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215
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Valente AJ, Fonseca J, Moradi F, Foran G, Necakov A, Stuart JA. Quantification of Mitochondrial Network Characteristics in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:183-196. [DOI: 10.1007/978-981-13-8367-0_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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216
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Li H, Guo C, Kim-Holzapfel D, Li W, Altshuller Y, Schroeder B, Liu W, Meng Y, French JB, Takamaru KI, Frohman MA, Jia S. Fast, volumetric live-cell imaging using high-resolution light-field microscopy. BIOMEDICAL OPTICS EXPRESS 2019; 10:29-49. [PMID: 30775081 PMCID: PMC6363205 DOI: 10.1364/boe.10.000029] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/26/2018] [Accepted: 10/10/2018] [Indexed: 05/03/2023]
Abstract
Visualizing diverse anatomical and functional traits that span many spatial scales with high spatio-temporal resolution provides insights into the fundamentals of living organisms. Light-field microscopy (LFM) has recently emerged as a scanning-free, scalable method that allows for high-speed, volumetric functional brain imaging. Given those promising applications at the tissue level, at its other extreme, this highly-scalable approach holds great potential for observing structures and dynamics in single-cell specimens. However, the challenge remains for current LFM to achieve a subcellular level, near-diffraction-limited 3D spatial resolution. Here, we report high-resolution LFM (HR-LFM) for live-cell imaging with a resolution of 300-700 nm in all three dimensions, an imaging depth of several micrometers, and a volume acquisition time of milliseconds. We demonstrate the technique by imaging various cellular dynamics and structures and tracking single particles. The method may advance LFM as a particularly useful tool for understanding biological systems at multiple spatio-temporal levels.
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Affiliation(s)
- Haoyu Li
- Department of Biomedical Engineering, Stony Brook University (SUNY), Stony Brook, New York, USA
- Ultra-Precision Optoelectronic Instrument Engineering Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Changliang Guo
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Deborah Kim-Holzapfel
- Department of Biochemistry and Cell Biology and Department of Chemistry, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Weiyi Li
- Department of Materials Science and Chemical Engineering, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Yelena Altshuller
- Department of Pharmacological Sciences, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Bryce Schroeder
- Department of Biomedical Engineering, Stony Brook University (SUNY), Stony Brook, New York, USA
- Medical Scientist Training Program, School of Medicine, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Wenhao Liu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Yizhi Meng
- Department of Materials Science and Chemical Engineering, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Jarrod B. French
- Department of Biochemistry and Cell Biology and Department of Chemistry, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Ken-Ichi Takamaru
- Department of Pharmacological Sciences, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Michael A. Frohman
- Department of Pharmacological Sciences, Stony Brook University (SUNY), Stony Brook, New York, USA
- Medical Scientist Training Program, School of Medicine, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Shu Jia
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
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217
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Choosing the right microscope to image mitosis in zebrafish embryos: A practical guide. Methods Cell Biol 2018. [PMID: 29957200 DOI: 10.1016/bs.mcb.2018.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Tissue growth and organismal development require orchestrated cell proliferation. To understand how cell division guides development, it is important to explore mitosis at the tissue-wide, cellular, and subcellular scale. At the tissue level this includes determining a tissue's mitotic index, at the cellular level the tracing of cell lineages, and at the subcellular level the characterization of intracellular components. These different tasks can be addressed by different imaging approaches (e.g., laser-scanning confocal, spinning disk confocal, and light-sheet fluorescence microscopy). Here, we summarize three protocols for exploring different facets of mitosis in developing zebrafish embryos. Zebrafish embryos are transparent and their rapid external development greatly facilitates the study of cellular processes and developmental dynamics using microscopy. A critical step in all imaging studies of mitosis in development is to choose the most suitable microscope for each scientific question. This choice is important in order to ensure a balance between the required temporal and spatial resolution and minimal phototoxicity that could otherwise perturb the process of interest. The use of different microscopy techniques, best suited for the purpose of each experiment, thus permits to generate a comprehensive and unbiased view on how mitosis influences development.
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218
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Weigert M, Schmidt U, Boothe T, Müller A, Dibrov A, Jain A, Wilhelm B, Schmidt D, Broaddus C, Culley S, Rocha-Martins M, Segovia-Miranda F, Norden C, Henriques R, Zerial M, Solimena M, Rink J, Tomancak P, Royer L, Jug F, Myers EW. Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat Methods 2018; 15:1090-1097. [PMID: 30478326 DOI: 10.1038/s41592-018-0216-7] [Citation(s) in RCA: 480] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/10/2018] [Indexed: 02/05/2023]
Abstract
Fluorescence microscopy is a key driver of discoveries in the life sciences, with observable phenomena being limited by the optics of the microscope, the chemistry of the fluorophores, and the maximum photon exposure tolerated by the sample. These limits necessitate trade-offs between imaging speed, spatial resolution, light exposure, and imaging depth. In this work we show how content-aware image restoration based on deep learning extends the range of biological phenomena observable by microscopy. We demonstrate on eight concrete examples how microscopy images can be restored even if 60-fold fewer photons are used during acquisition, how near isotropic resolution can be achieved with up to tenfold under-sampling along the axial direction, and how tubular and granular structures smaller than the diffraction limit can be resolved at 20-times-higher frame rates compared to state-of-the-art methods. All developed image restoration methods are freely available as open source software in Python, FIJI, and KNIME.
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Affiliation(s)
- Martin Weigert
- Center for Systems Biology Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Uwe Schmidt
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Tobias Boothe
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Alexandr Dibrov
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Akanksha Jain
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Benjamin Wilhelm
- Center for Systems Biology Dresden, Dresden, Germany
- University of Konstanz, Konstanz, Germany
| | | | - Coleman Broaddus
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Mauricio Rocha-Martins
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Caren Norden
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michele Solimena
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Jochen Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Loic Royer
- Center for Systems Biology Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- CZ Biohub, San Francisco, CA, USA.
| | - Florian Jug
- Center for Systems Biology Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Eugene W Myers
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Department of Computer Science, Technical University Dresden, Dresden, Germany
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219
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Wu Y, Shroff H. Faster, sharper, and deeper: structured illumination microscopy for biological imaging. Nat Methods 2018; 15:1011-1019. [PMID: 30478322 DOI: 10.1038/s41592-018-0211-z] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/02/2018] [Indexed: 11/09/2022]
Abstract
Structured illumination microscopy (SIM) allows rapid, super-resolution (SR) imaging in live specimens. We review recent technical advances in SR-SIM, with emphasis on imaging speed, resolution, and depth. Since its introduction decades ago, the technique has grown to offer myriad implementations, each with its own strengths and weaknesses. We discuss these, aiming to provide a practical guide for biologists and to highlight which approach is best suited to a given application.
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Affiliation(s)
- Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
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221
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Recent progress in the green synthesis of rare-earth doped upconversion nanophosphors for optical bioimaging from cells to animals. Chin J Chem Eng 2018. [DOI: 10.1016/j.cjche.2018.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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222
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Ovečka M, von Wangenheim D, Tomančák P, Šamajová O, Komis G, Šamaj J. Multiscale imaging of plant development by light-sheet fluorescence microscopy. NATURE PLANTS 2018; 4:639-650. [PMID: 30185982 DOI: 10.1038/s41477-018-0238-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.
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Affiliation(s)
- Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Daniel von Wangenheim
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pavel Tomančák
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic.
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223
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Multi-scale imaging techniques to investigate solute transport across articular cartilage. J Biomech 2018; 78:10-20. [DOI: 10.1016/j.jbiomech.2018.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/11/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
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224
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Smith PJ, Darzynkiewicz Z, Errington RJ. Nuclear cytometry and chromatin organization. Cytometry A 2018; 93:771-784. [PMID: 30144297 DOI: 10.1002/cyto.a.23521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022]
Abstract
The nuclear-targeting chemical probe, for the detection and quantification of DNA within cells, has been a mainstay of cytometry-from the colorimetric Feulgen stain to smart fluorescent agents with tuned functionality. The level of nuclear structure and function at which the probe aims to readout, or indeed at which a DNA-targeted drug acts, is shadowed by a wide range of detection modalities and analytical methods. These methods are invariably limited in terms of the resolution attainable versus the volume occupied by targeted chromatin structures. The scalar challenge arises from the need to understand the extent and different levels of compaction of genomic DNA and how such structures can be re-modeled, reported, or even perturbed by both probes and drugs. Nuclear cytometry can report on the complex levels of chromatin order, disorder, disassembly, and even active disruption by probes and drugs. Nuclear probes can report defining features of clinical and therapeutic interest as in NETosis and other cell death processes. New cytometric approaches continue to bridge the scalar challenges of analyzing chromatin organization. Advances in super-resolution microscopy address the resolution and depth of analysis issues in cellular systems. Typical of recent insights into chromatin organization enabled by exploiting a DNA interacting probe is ChromEM tomography (ChromEMT). ChromEMT uses the unique properties of the anthraquinone-based cytometric dye DRAQ5™ to reveal that local and global 3D chromatin structures effect differences in compaction. The focus of this review is nuclear and chromatin cytometry, with linked reference to DNA targeting probes and drugs as exemplified by the anthracenediones.
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Affiliation(s)
- Paul J Smith
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Zbigniew Darzynkiewicz
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, Valhalla, New York, 10595
| | - Rachel J Errington
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
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225
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Low irradiance multiphoton imaging with alloyed lanthanide nanocrystals. Nat Commun 2018; 9:3082. [PMID: 30082844 PMCID: PMC6079005 DOI: 10.1038/s41467-018-05577-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/16/2018] [Indexed: 12/22/2022] Open
Abstract
Multiphoton imaging techniques that convert low-energy excitation to higher energy emission are widely used to improve signal over background, reduce scatter, and limit photodamage. Lanthanide-doped upconverting nanoparticles (UCNPs) are among the most efficient multiphoton probes, but even UCNPs with optimized lanthanide dopant levels require laser intensities that may be problematic. Here, we develop protein-sized, alloyed UCNPs (aUCNPs) that can be imaged individually at laser intensities >300-fold lower than needed for comparably sized doped UCNPs. Using single UCNP characterization and kinetic modeling, we find that addition of inert shells changes optimal lanthanide content from Yb3+, Er3+-doped NaYF4 nanocrystals to fully alloyed compositions. At high levels, emitter Er3+ ions can adopt a second role to enhance aUCNP absorption cross-section by desaturating sensitizer Yb3+ or by absorbing photons directly. Core/shell aUCNPs 12 nm in total diameter can be imaged through deep tissue in live mice using a laser intensity of 0.1 W cm−2. By using a near-IR optical excitation, upconverting nanoparticles may enable high-resolution imaging deep in tissue. Here, Tian et al. introduce alloyed upconverting nanoparticles with improved brightness due to newly described energy transfer pathways.
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226
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Tay YD, Leda M, Goryachev AB, Sawin KE. Local and global Cdc42 guanine nucleotide exchange factors for fission yeast cell polarity are coordinated by microtubules and the Tea1-Tea4-Pom1 axis. J Cell Sci 2018; 131:jcs.216580. [PMID: 29930085 PMCID: PMC6080602 DOI: 10.1242/jcs.216580] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/14/2018] [Indexed: 12/30/2022] Open
Abstract
The conserved Rho-family GTPase Cdc42 plays a central role in eukaryotic cell polarity. The rod-shaped fission yeast Schizosaccharomyces pombe has two Cdc42 guanine nucleotide exchange factors (GEFs), Scd1 and Gef1, but little is known about how they are coordinated in polarized growth. Although the microtubule cytoskeleton is normally not required for polarity maintenance in fission yeast, we show here that when scd1 function is compromised, disruption of microtubules or the polarity landmark proteins Tea1, Tea4 or Pom1 leads to disruption of polarized growth. Instead, cells adopt an isotropic-like pattern of growth, which we term PORTLI growth. Surprisingly, PORTLI growth is caused by spatially inappropriate activity of Gef1. Although most Cdc42 GEFs are membrane associated, we find that Gef1 is a broadly distributed cytosolic protein rather than a membrane-associated protein at cell tips like Scd1. Microtubules and the Tea1–Tea4–Pom1 axis counteract inappropriate Gef1 activity by regulating the localization of the Cdc42 GTPase-activating protein Rga4. Our results suggest a new model of fission yeast cell polarity regulation, involving coordination of ‘local’ (Scd1) and ‘global’ (Gef1) Cdc42 GEFs via microtubules and microtubule-dependent polarity landmarks. Highlighted Article: Cell polarity in fission yeast is regulated by two different Cdc42 guanine nucleotide exchange factors, coordinated by the microtubule-dependent landmark system.
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Affiliation(s)
- Ye Dee Tay
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Marcin Leda
- SynthSys - Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Andrew B Goryachev
- SynthSys - Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Kenneth E Sawin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
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227
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Shaw M, Zhan H, Elmi M, Pawar V, Essmann C, Srinivasan MA. Three-dimensional behavioural phenotyping of freely moving C. elegans using quantitative light field microscopy. PLoS One 2018; 13:e0200108. [PMID: 29995960 PMCID: PMC6040744 DOI: 10.1371/journal.pone.0200108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/19/2018] [Indexed: 11/19/2022] Open
Abstract
Behavioural phenotyping of model organisms is widely used to investigate fundamental aspects of organism biology, from the functioning of the nervous system to the effects of genetic mutations, as well as for screening new drug compounds. However, our capacity to observe and quantify the full range and complexity of behavioural responses is limited by the inability of conventional microscopy techniques to capture volumetric image information at sufficient speed. In this article we describe how combining light field microscopy with computational depth estimation provides a new method for fast, quantitative assessment of 3D posture and movement of the model organism Caenorhabditis elegans (C. elegans). We apply this technique to compare the behaviour of cuticle collagen mutants, finding significant differences in 3D posture and locomotion. We demonstrate the ability of quantitative light field microscopy to provide new fundamental insights into C. elegans locomotion by analysing the 3D postural modes of a freely swimming worm. Finally, we consider relative merits of the method and its broader application for phenotypic imaging of other organisms and for other volumetric bioimaging applications.
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Affiliation(s)
- Michael Shaw
- Department of Computer Science, University College London, London, United Kingdom
- Biometrology Group, National Physical Laboratory, Teddington, United Kingdom
- * E-mail:
| | - Haoyun Zhan
- Department of Computer Science, University College London, London, United Kingdom
| | - Muna Elmi
- Department of Computer Science, University College London, London, United Kingdom
| | - Vijay Pawar
- Department of Computer Science, University College London, London, United Kingdom
| | - Clara Essmann
- Department of Computer Science, University College London, London, United Kingdom
| | - Mandayam A. Srinivasan
- Department of Computer Science, University College London, London, United Kingdom
- MIT TouchLab, Research Laboratory of Electronics and Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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228
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Stockmar I, Feddersen H, Cramer K, Gruber S, Jung K, Bramkamp M, Shin JY. Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy. Sci Rep 2018; 8:10137. [PMID: 29973667 PMCID: PMC6031688 DOI: 10.1038/s41598-018-28472-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/19/2018] [Indexed: 11/08/2022] Open
Abstract
mNeonGreen fluorescent protein is capable of photo-switching, hence in principle applicable for super-resolution imaging. However, difficult-to-control blinking kinetics that lead to simultaneous emission of multiple nearby mNeonGreen molecules impedes its use for PALM. Here, we determined the on- and off- switching rate and the influence of illumination power on the simultaneous emission. Increasing illumination power reduces the probability of simultaneous emission, but not enough to generate high quality PALM images. Therefore, we introduce a simple data post-processing step that uses temporal and spatial information of molecule localizations to further reduce artifacts arising from simultaneous emission of nearby emitters. We also systematically evaluated various sample preparation steps to establish an optimized protocol to preserve cellular morphology and fluorescence signal. In summary, we propose a workflow for super-resolution imaging with mNeonGreen based on optimization of sample preparation, data acquisition and simple post-acquisition data processing. Application of our protocol enabled us to resolve the expected double band of bacterial cell division protein DivIVA, and to visualize that the chromosome organization protein ParB organized into sub-clusters instead of the typically observed diffraction-limited foci. We expect that our workflow allows a broad use of mNeonGreen for super-resolution microscopy, which is so far difficult to achieve.
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Affiliation(s)
- Iris Stockmar
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Max Plank Institute for Biochemistry, Martinsried, Germany
| | - Helge Feddersen
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kimberly Cramer
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Max Plank Institute for Biochemistry, Martinsried, Germany
| | - Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
| | - Jae Yen Shin
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
- Max Plank Institute for Biochemistry, Martinsried, Germany.
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229
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Mullineaux PM, Exposito-Rodriguez M, Laissue PP, Smirnoff N. ROS-dependent signalling pathways in plants and algae exposed to high light: Comparisons with other eukaryotes. Free Radic Biol Med 2018; 122:52-64. [PMID: 29410363 DOI: 10.1016/j.freeradbiomed.2018.01.033] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 01/09/2023]
Abstract
Like all aerobic organisms, plants and algae co-opt reactive oxygen species (ROS) as signalling molecules to drive cellular responses to changes in their environment. In this respect, there is considerable commonality between all eukaryotes imposed by the constraints of ROS chemistry, similar metabolism in many subcellular compartments, the requirement for a high degree of signal specificity and the deployment of thiol peroxidases as transducers of oxidising equivalents to regulatory proteins. Nevertheless, plants and algae carry out specialised signalling arising from oxygenic photosynthesis in chloroplasts and photoautotropism, which often induce an imbalance between absorption of light energy and the capacity to use it productively. A key means of responding to this imbalance is through communication of chloroplasts with the nucleus to adjust cellular metabolism. Two ROS, singlet oxygen (1O2) and hydrogen peroxide (H2O2), initiate distinct signalling pathways when photosynthesis is perturbed. 1O2, because of its potent reactivity means that it initiates but does not transduce signalling. In contrast, the lower reactivity of H2O2 means that it can also be a mobile messenger in a spatially-defined signalling pathway. How plants translate a H2O2 message to bring about changes in gene expression is unknown and therefore, we draw on information from other eukaryotes to propose a working hypothesis. The role of these ROS generated in other subcellular compartments of plant cells in response to HL is critically considered alongside other eukaryotes. Finally, the responses of animal cells to oxidative stress upon high irradiance exposure is considered for new comparisons between plant and animal cells.
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Affiliation(s)
- Philip M Mullineaux
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
| | | | | | - Nicholas Smirnoff
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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230
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Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours. Commun Biol 2018; 1:73. [PMID: 30271954 PMCID: PMC6123791 DOI: 10.1038/s42003-018-0079-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 05/31/2018] [Indexed: 12/14/2022] Open
Abstract
Imaging living organisms at high spatial resolution requires effective and innocuous immobilization. Long-term imaging places further demands on sample mounting with minimal perturbation of the organism. Here we present a simple, inexpensive method for rapid encapsulation of small animals of any developmental stage within a photo-crosslinked polyethylene glycol (PEG) hydrogel, gently restricting movement within their confined spaces. Immobilized animals maintain their original morphology in a hydrated environment compatible with chemical treatment, optical stimulation, and light-sheet microscopy. We demonstrate prolonged three-dimensional imaging of neural responses in the nematode Caenorhabditis elegans, recovery of viable organisms after 24 h, and imaging of larger squid hatchlings. We characterize a range of hydrogel and illumination conditions for immobilization quality, and identify paralytic-free conditions suitable for high-resolution single-cell imaging. Overall, PEG hydrogel encapsulation provides fast, versatile, and gentle mounting of small living organisms, from yeast to zebrafish, for continuous observation over hours. Kyra Burnett et al. present a simple and economical method to encapsulate small living organisms for long-term microscopy in a photo-crosslinked polyethylene glycol hydrogel. This method provides a fast and gentle mounting for continuous imaging over hours, and works with light-sheet microscopy and optogenetic stimulation.
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231
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Shin S, Kim D, Kim K, Park Y. Super-resolution three-dimensional fluorescence and optical diffraction tomography of live cells using structured illumination generated by a digital micromirror device. Sci Rep 2018; 8:9183. [PMID: 29907828 PMCID: PMC6004010 DOI: 10.1038/s41598-018-27399-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/24/2018] [Indexed: 11/26/2022] Open
Abstract
We present a multimodal approach for measuring the three-dimensional (3D) refractive index (RI) and fluorescence distributions of live cells by combining optical diffraction tomography (ODT) and 3D structured illumination microscopy (SIM). A digital micromirror device is utilized to generate structured illumination patterns for both ODT and SIM, which enables fast and stable measurements. To verify its feasibility and applicability, the proposed method is used to measure the 3D RI distribution and 3D fluorescence image of various samples, including a cluster of fluorescent beads, and the time-lapse 3D RI dynamics of fluorescent beads inside a HeLa cell, from which the trajectory of the beads in the HeLa cell is analyzed using spatiotemporal correlations.
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Affiliation(s)
- Seungwoo Shin
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Doyeon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Tomocube, Inc., 48, Yuseong-daero 1184beon-gil, Yuseong-Gu, Daejeon, 34051, Republic of Korea
| | - Kyoohyun Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea.
- Tomocube, Inc., 48, Yuseong-daero 1184beon-gil, Yuseong-Gu, Daejeon, 34051, Republic of Korea.
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232
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Parthasarathy R. Monitoring microbial communities using light sheet fluorescence microscopy. Curr Opin Microbiol 2018; 43:31-37. [PMID: 29175679 PMCID: PMC5963963 DOI: 10.1016/j.mib.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/10/2017] [Accepted: 11/06/2017] [Indexed: 01/20/2023]
Abstract
Microbes often live in dense, dynamic, multi-species communities whose architecture and function are intimately intertwined. Imaging these complex, three-dimensional ensembles presents considerable technical challenges, however. In this review, I describe light sheet fluorescence microscopy, a technique that enables rapid acquisition of three-dimensional images over large fields of view and over long durations, and I highlight recent applications of this method to microbial systems that include artificial closed ecosystems, bacterial biofilms, and gut microbiota. I comment also on the history of light sheet imaging and the many variants of the method. Light sheet techniques have tremendous potential for illuminating the workings of microbial communities, a potential that is just beginning to be realized.
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233
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Abstract
RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred from DNA to proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution. We review current theoretical models for describing transcription and translation that were generated by single-molecule and single-cell studies. These methods provide a basis to study how single-molecule interactions generate phenotypes, fundamentally changing our understating of gene expression regulation.
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Affiliation(s)
- Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;,
| | - Nathan M. Livingston
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;,
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461
- Cellular Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Bin Wu
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21205;,
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234
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Dobrowolski JC, Lipiński PFJ, Karpińska G. Substituent Effect in the First Excited Singlet State of Monosubstituted Benzenes. J Phys Chem A 2018; 122:4609-4621. [PMID: 29698609 DOI: 10.1021/acs.jpca.8b02209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
sEDA, pEDA, and cSAR descriptors of the substituent effect were determined for >30 monosubstituted benzenes in the first excited singlet S1 state at the LC-ωB97XD/aug-cc-pVTZ level. It was found that in the S1 state, the σ- and π-valence electrons are a bit less and a bit more affected, respectively, than in the S0 state, but basically, the effect in both states remains the same. In the S0 and S1 states, the d(C-X) distances to the substituent's first atom and the ring perimeter correlate with the sEDA and pEDA in the appropriate states, respectively. The energies and the gap of the frontier orbitals in the two states are linearly correlated and for the HOMO(S1), LUMO(S1), and HOMO(S1)-LUMO(S1) gap correlate also with the pEDA(S1) and cSAR(S1) descriptors. In all studied correlations, three similar groups of substituents can be distinguished, for which correlations (i) are very good, (ii) deviate slightly, and (iii) deviate significantly. Comparison of the shape of the HOMO(S0) and HOMO(S1) orbitals shows that for case (i) HOMO orbitals exhibit almost perfect antisymmetry against the benzene plane, for case (ii) the antisymmetry of HOMO in one of the states is either perturbed or changed, and for case (iii) one HOMO state has σ-character.
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Affiliation(s)
- Jan Cz Dobrowolski
- Department for Medicines Biotechnology and Bioinformatics , National Medicines Institute , 30/34 Chełmska Street , 00-725 Warsaw , Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides , Mossakowski Medical Research Centre PAS , 5 Pawińskiego Street , 02-106 Warsaw , Poland
| | - Grażyna Karpińska
- Department for Medicines Biotechnology and Bioinformatics , National Medicines Institute , 30/34 Chełmska Street , 00-725 Warsaw , Poland
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235
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Riani YD, Matsuda T, Takemoto K, Nagai T. Green monomeric photosensitizing fluorescent protein for photo-inducible protein inactivation and cell ablation. BMC Biol 2018; 16:50. [PMID: 29712573 PMCID: PMC5928576 DOI: 10.1186/s12915-018-0514-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/06/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Photosensitizing fluorescent proteins, which generate reactive oxygen species (ROS) upon light irradiation, are useful for spatiotemporal protein inactivation and cell ablation. They give us clues about protein function, intracellular signaling pathways and intercellular interactions. Since ROS generation of a photosensitizer is specifically controlled by certain excitation wavelengths, utilizing colour variants of photosensitizing protein would allow multi-spatiotemporal control of inactivation. To expand the colour palette of photosensitizing protein, here we developed SuperNova Green from its red predecessor, SuperNova. RESULTS SuperNova Green is able to produce ROS spatiotemporally upon blue light irradiation. Based on protein characterization, SuperNova Green produces insignificant amounts of singlet oxygen and predominantly produces superoxide and its derivatives. We utilized SuperNova Green to specifically inactivate the pleckstrin homology domain of phospholipase C-δ1 and to ablate cancer cells in vitro. As a proof of concept for multi-spatiotemporal control of inactivation, we demonstrate that SuperNova Green can be used with its red variant, SuperNova, to perform independent protein inactivation or cell ablation studies in a spatiotemporal manner by selective light irradiation. CONCLUSION Development of SuperNova Green has expanded the photosensitizing protein toolbox to optogenetically control protein inactivation and cell ablation.
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Affiliation(s)
- Yemima Dani Riani
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Tomoki Matsuda
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan
| | - Kiwamu Takemoto
- Graduate School of Medicine, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, 236-0027, Japan
| | - Takeharu Nagai
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan. .,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan.
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236
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Abstract
Mitotic cell division in plants is a dynamic process playing a key role in plant morphogenesis, growth, and development. Since progress of mitosis is highly sensitive to external stresses, documentation of mitotic cell division in living plants requires fast and gentle live-cell imaging microscopy methods and suitable sample preparation procedures. This chapter describes, both theoretically and practically, currently used advanced microscopy methods for the live-cell visualization of the entire process of plant mitosis. These methods include microscopy modalities based on spinning disk, Airyscan confocal laser scanning, structured illumination, and light-sheet bioimaging of tissues or whole plant organs with diverse spatiotemporal resolution. Examples are provided from studies of mitotic cell division using microtubule molecular markers in the model plant Arabidopsis thaliana, and from deep imaging of mitotic microtubules in robust plant samples, such as legume crop species Medicago sativa.
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237
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Liu TL, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 2018; 360:eaaq1392. [PMID: 29674564 PMCID: PMC6040645 DOI: 10.1126/science.aaq1392] [Citation(s) in RCA: 317] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/19/2018] [Indexed: 01/10/2023]
Abstract
True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution, without inducing undue stress on either. We combined lattice light-sheet microscopy with adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.
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Affiliation(s)
- Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Srigokul Upadhyayula
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ved Singh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kai Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ian A Swinburne
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Kishore R Mosaliganti
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Zach M Collins
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Tom W Hiscock
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Abraham Q Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Taylor N Medwig
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Daphne Dambournet
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Forster
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brian Cunniff
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Yuan Ruan
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hanako Yashiro
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steffen Scholpp
- Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Elliot M Meyerowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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238
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Nylk J, McCluskey K, Preciado MA, Mazilu M, Yang Z, Gunn-Moore FJ, Aggarwal S, Tello JA, Ferrier DEK, Dholakia K. Light-sheet microscopy with attenuation-compensated propagation-invariant beams. SCIENCE ADVANCES 2018; 4:eaar4817. [PMID: 29740614 PMCID: PMC5938225 DOI: 10.1126/sciadv.aar4817] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/15/2018] [Indexed: 05/18/2023]
Abstract
Scattering and absorption limit the penetration of optical fields into tissue. We demonstrate a new approach for increased depth penetration in light-sheet microscopy: attenuation-compensation of the light field. This tailors an exponential intensity increase along the illuminating propagation-invariant field, enabling the redistribution of intensity strategically within a sample to maximize signal and minimize irradiation. A key attribute of this method is that only minimal knowledge of the specimen transmission properties is required. We numerically quantify the imaging capabilities of attenuation-compensated Airy and Bessel light sheets, showing that increased depth penetration is gained without compromising any other beam attributes. This powerful yet straightforward concept, combined with the self-healing properties of the propagation-invariant field, improves the contrast-to-noise ratio of light-sheet microscopy up to eightfold across the entire field of view in thick biological specimens. This improvement can significantly increase the imaging capabilities of light-sheet microscopy techniques using Airy, Bessel, and other propagation-invariant beam types, paving the way for widespread uptake by the biomedical community.
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Affiliation(s)
- Jonathan Nylk
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
- Corresponding author.
| | - Kaley McCluskey
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
| | - Miguel A. Preciado
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
| | - Michael Mazilu
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
| | - Zhengyi Yang
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
| | - Frank J. Gunn-Moore
- School of Biology, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Sanya Aggarwal
- School of Medicine, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Javier A. Tello
- School of Medicine, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - David E. K. Ferrier
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, East Sands, St. Andrews, Fife KY16 8LB, UK
| | - Kishan Dholakia
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
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Aulner N, Danckaert A, Fernandes J, Nicola MA, Roux P, Salles A, Tinevez JY, Shorte SL. Fluorescence imaging host pathogen interactions: fifteen years benefit of hindsight…. Curr Opin Microbiol 2018; 43:193-198. [PMID: 29567588 DOI: 10.1016/j.mib.2018.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 01/24/2023]
Abstract
We consider in review current state-of-the-art fluorescence microscopy for investigating the host-pathogen interface. Our perspective is honed from years with literally thousands of microbiologists using the variety of imaging technologies available within our dedicated BSL2/BSL3 optical imaging research service facilities at the Institut Pasteur Paris founded from scratch in 2001. During fifteen years learning from the success and failures of introducing different fluorescence imaging technologies, methods, and technical development strategies we provide here a synopsis review of our experience to date and a synthesis of how we see the future in perspective for fluorescence imaging at the host-pathogen interface.
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Affiliation(s)
- Nathalie Aulner
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Anne Danckaert
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Julien Fernandes
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Marie-Anne Nicola
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Pascal Roux
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Audrey Salles
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Spencer L Shorte
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
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240
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Fadero TC, Gerbich TM, Rana K, Suzuki A, DiSalvo M, Schaefer KN, Heppert JK, Boothby TC, Goldstein B, Peifer M, Allbritton NL, Gladfelter AS, Maddox AS, Maddox PS. LITE microscopy: Tilted light-sheet excitation of model organisms offers high resolution and low photobleaching. J Cell Biol 2018; 217:1869-1882. [PMID: 29490939 PMCID: PMC5940309 DOI: 10.1083/jcb.201710087] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/26/2018] [Accepted: 02/16/2018] [Indexed: 11/22/2022] Open
Abstract
Fadero et al. present lateral interference tilted excitation (LITE) microscopy–a tilted light-sheet method to illuminate high-numerical-aperture objectives for fluorescence microscopy. LITE can be implemented unobtrusively on most microscope systems and combines low photodamage with high resolution and efficient detection in imaging fluorescent organisms. Fluorescence microscopy is a powerful approach for studying subcellular dynamics at high spatiotemporal resolution; however, conventional fluorescence microscopy techniques are light-intensive and introduce unnecessary photodamage. Light-sheet fluorescence microscopy (LSFM) mitigates these problems by selectively illuminating the focal plane of the detection objective by using orthogonal excitation. Orthogonal excitation requires geometries that physically limit the detection objective numerical aperture (NA), thereby limiting both light-gathering efficiency (brightness) and native spatial resolution. We present a novel live-cell LSFM method, lateral interference tilted excitation (LITE), in which a tilted light sheet illuminates the detection objective focal plane without a sterically limiting illumination scheme. LITE is thus compatible with any detection objective, including oil immersion, without an upper NA limit. LITE combines the low photodamage of LSFM with high resolution, high brightness, and coverslip-based objectives. We demonstrate the utility of LITE for imaging animal, fungal, and plant model organisms over many hours at high spatiotemporal resolution.
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Affiliation(s)
- Tanner C Fadero
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Therese M Gerbich
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kishan Rana
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Aussie Suzuki
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew DiSalvo
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and Raleigh, NC
| | - Kristina N Schaefer
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jennifer K Heppert
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Thomas C Boothby
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bob Goldstein
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mark Peifer
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nancy L Allbritton
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and Raleigh, NC
| | - Amy S Gladfelter
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Amy S Maddox
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Paul S Maddox
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC
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241
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Vicidomini G, Bianchini P, Diaspro A. STED super-resolved microscopy. Nat Methods 2018; 15:173-182. [DOI: 10.1038/nmeth.4593] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022]
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242
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Osman S, Dalmay D, Mahaut-Smith M. Fluorescence Approaches to Image and Quantify the Demarcation Membrane System in Living Megakaryocytes. Methods Mol Biol 2018; 1812:195-215. [PMID: 30171580 DOI: 10.1007/978-1-4939-8585-2_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The demarcation membrane system (DMS) develops to provide additional surface membrane for the process of platelet production. The DMS is an invagination of the plasma membrane that can extend throughout the extranuclear volume of mature megakaryocytes and its lumen is continuous with the extracellular solution. DMS ultrastructure in fixed samples has been extensively studied using transmission electron microscopy (TEM) and more recently with focused ion beam scanning EM. In addition, whole cell patch clamp membrane capacitance provides a direct measurement of DMS content in living megakaryocytes. However, fluorescence methods to image and quantify the DMS in living megakaryocytes provide several advantages. For example, confocal fluorescence microscopy is easier to use compared to EM or electrophysiological methods and the required equipment is more readily available. In addition, use of living cells avoids artifacts known to occur during the fixation, dehydration, or embedding steps used to prepare EM samples. Here we describe the use of styryl dyes such as FM 1-43 or di-8-ANEPPS and impermeant fluorescent indicators of the extracellular space as simple approaches for imaging and quantification of the DMS.
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Affiliation(s)
- Sangar Osman
- Department of Molecular and Cell Biology, Lancaster Road, University of Leicester, Leicester, UK
| | - Daniel Dalmay
- Department of Molecular and Cell Biology, Lancaster Road, University of Leicester, Leicester, UK
| | - Martyn Mahaut-Smith
- Department of Molecular and Cell Biology, Lancaster Road, University of Leicester, Leicester, UK.
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Kim K, Park WS, Na S, Kim S, Kim T, Heo WD, Park Y. Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging. BIOMEDICAL OPTICS EXPRESS 2017; 8:5688-5697. [PMID: 29296497 PMCID: PMC5745112 DOI: 10.1364/boe.8.005688] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 05/20/2023]
Abstract
Optical diffraction tomography (ODT) provides label-free three-dimensional (3D) refractive index (RI) measurement of biological samples. However, due to the nature of the RI values of biological specimens, ODT has limited access to molecular specific information. Here, we present an optical setup combining ODT with three-channel 3D fluorescence microscopy, to enhance the molecular specificity of the 3D RI measurement. The 3D RI distribution and 3D deconvoluted fluorescence images of HeLa cells and NIH-3T3 cells are measured, and the cross-correlative analysis between RI and fluorescence of live cells are presented.
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Affiliation(s)
- Kyoohyun Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141, South Korea
- Current address: Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Wei Sun Park
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | | | | | | | - Won Do Heo
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141, South Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
- KI for Health Science and Technology (KIHST), KAIST, Daejeon 34141, South Korea
- TomoCube Inc., Daejeon 34051, South Korea
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Hejna M, Jorapur A, Song JS, Judson RL. High accuracy label-free classification of single-cell kinetic states from holographic cytometry of human melanoma cells. Sci Rep 2017; 7:11943. [PMID: 28931937 PMCID: PMC5607248 DOI: 10.1038/s41598-017-12165-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/31/2017] [Indexed: 02/07/2023] Open
Abstract
Digital holographic cytometry (DHC) permits label-free visualization of adherent cells. Dozens of cellular features can be derived from segmentation of hologram-derived images. However, the accuracy of single cell classification by these features remains limited for most applications, and lack of standardization metrics has hindered independent experimental comparison and validation. Here we identify twenty-six DHC-derived features that provide biologically independent information across a variety of mammalian cell state transitions. When trained on these features, machine-learning algorithms achieve blind single cell classification with up to 95% accuracy. Using classification accuracy to guide platform optimization, we develop methods to standardize holograms for the purpose of kinetic single cell cytometry. Applying our approach to human melanoma cells treated with a panel of cancer therapeutics, we track dynamic changes in cellular behavior and cell state over time. We provide the methods and computational tools for optimizing DHC for kinetic single adherent cell classification.
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Affiliation(s)
- Miroslav Hejna
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, 61801, USA
| | - Aparna Jorapur
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, Box# 3111, San Francisco, CA, 94158, USA.,Department of Dermatology, University of California, San Francisco, 1701 Divisadero Street, San Francisco, CA, 94115, USA
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, 61801, USA.
| | - Robert L Judson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, Box# 3111, San Francisco, CA, 94158, USA. .,Department of Dermatology, University of California, San Francisco, 1701 Divisadero Street, San Francisco, CA, 94115, USA.
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