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Kondengadan SM, Wang B. Quantitative Factors Introduced in the Feasibility Analysis of Reactive Oxygen Species (ROS)-Sensitive Triggers. Angew Chem Int Ed Engl 2024:e202403880. [PMID: 38630918 DOI: 10.1002/anie.202403880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
Reactive oxygen species (ROS) are critical for cellular signaling. Various pathophysiological conditions are also associated with elevated levels of ROS. Hence, ROS-sensitive triggers have been extensively used for selective payload delivery. Such applications are predicated on two key functions: (1) a sufficient magnitude of concentration difference for the interested ROS between normal tissue/cells and intended sites and (2) appropriate reaction kinetics to ensure a sufficient level of selectivity for payload release. Further, ROS refers to a group of species with varying reactivity, which should not be viewed as a uniform group. In this review, we critically analyze data on the concentrations of different ROS species under various pathophysiological conditions and examine how reaction kinetics affect the success of ROS-sensitive linker chemistry. Further, we discuss different ROS linker chemistry in the context of their applications in drug delivery and imaging. This review brings new insights into research in ROS-triggered delivery, highlights factors to consider in maximizing the chance for success and discusses pitfalls to avoid.
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Affiliation(s)
- Shameer M Kondengadan
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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2
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Qutbuddin Y, Guinart A, Gavrilović S, Al Nahas K, Feringa BL, Schwille P. Light-Activated Synthetic Rotary Motors in Lipid Membranes Induce Shape Changes Through Membrane Expansion. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311176. [PMID: 38215457 DOI: 10.1002/adma.202311176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/16/2023] [Indexed: 01/14/2024]
Abstract
Membranes are the key structures to separate and spatially organize cellular systems. Their rich dynamics and transformations during the cell cycle are orchestrated by specific membrane-targeted molecular machineries, many of which operate through energy dissipation. Likewise, man-made light-activated molecular rotary motors have previously shown drastic effects on cellular systems, but their physical roles on and within lipid membranes remain largely unexplored. Here, the impact of rotary motors on well-defined biological membranes is systematically investigated. Notably, dramatic mechanical transformations are observed in these systems upon motor irradiation, indicative of motor-induced membrane expansion. The influence of several factors on this phenomenon is systematically explored, such as motor concentration and membrane composition., Membrane fluidity is found to play a crucial role in motor-induced deformations, while only minor contributions from local heating and singlet oxygen generation are observed. Most remarkably, the membrane area expansion under the influence of the motors continues as long as irradiation is maintained, and the system stays out-of-equilibrium. Overall, this research contributes to a comprehensive understanding of molecular motors interacting with biological membranes, elucidating the multifaceted factors that govern membrane responses and shape transitions in the presence of these remarkable molecular machines, thereby supporting their future applications in chemical biology.
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Affiliation(s)
- Yusuf Qutbuddin
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Ainoa Guinart
- Stratingh Institute for Chemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Svetozar Gavrilović
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Kareem Al Nahas
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Ben L Feringa
- Stratingh Institute for Chemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Petra Schwille
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
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3
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Chen CC, Peng SJ, Chou YH, Lee CY, Lee PH, Hu RH, Ho MC, Chung MH, Hsiao FT, Tien YW, Tang SC. Human liver afferent and efferent nerves revealed by 3-D/Airyscan super-resolution imaging. Am J Physiol Endocrinol Metab 2024; 326:E107-E123. [PMID: 38170164 DOI: 10.1152/ajpendo.00205.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/31/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Neural regulation of hepatic metabolism has long been recognized. However, the detailed afferent and efferent innervation of the human liver has not been systematically characterized. This is largely due to the liver's high lipid and pigment contents, causing false-negative (light scattering and absorption) and false-positive (autofluorescence) results in in-depth fluorescence imaging. Here, to avoid the artifacts in three-dimensional (3-D) liver neurohistology, we embed the bleached human liver in the high-refractive-index polymer for tissue clearing and antifade 3-D/Airyscan super-resolution imaging. Importantly, using the paired substance P (SP, sensory marker) and PGP9.5 (pan-neuronal marker) labeling, we detect the sensory nerves in the portal space, featuring the SP+ varicosities in the PGP9.5+ nerve bundles/fibers, confirming the afferent liver innervation. Also, using the tyrosine hydroxylase (TH, sympathetic marker) labeling, we identify 1) condensed TH+ sympathetic nerves in the portal space, 2) extension of sympathetic nerves from the portal to the intralobular space, in which the TH+ nerve density is 2.6 ± 0.7-fold higher than that of the intralobular space in the human pancreas, and 3) the TH+ nerve fibers and varicosities contacting the ballooning cells, implicating potential sympathetic influence on hepatocytes with macrovesicular fatty change. Finally, using the vesicular acetylcholine transporter (VAChT, parasympathetic marker), PGP9.5, and CK19 (epithelial marker) labeling with panoramic-to-Airyscan super-resolution imaging, we detect and confirm the parasympathetic innervation of the septal bile duct. Overall, our labeling and 3-D/Airyscan imaging approach reveal the hepatic sensory (afferent) and sympathetic and parasympathetic (efferent) innervation, establishing a clinically related setting for high-resolution 3-D liver neurohistology.NEW & NOTEWORTHY We embed the human liver (vs. pancreas, positive control) in the high-refractive-index polymer for tissue clearing and antifade 3-D/Airyscan super-resolution neurohistology. The pancreas-liver comparison reveals: 1) sensory nerves in the hepatoportal space; 2) intralobular sympathetic innervation, including the nerve fibers and varicosities contacting the ballooning hepatocytes; and 3) parasympathetic innervation of the septal bile duct. Our results highlight the sensitivity and resolving power of 3-D/Airyscan super-resolution imaging in human liver neurohistology.
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Affiliation(s)
- Chien-Chia Chen
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Shih-Jung Peng
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ya-Hsien Chou
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Yuan Lee
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Huang Lee
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Department of Surgery, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Rey-Heng Hu
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Department of Surgery, National Taiwan University Hospital-Yunlin Branch, Yunlin, Taiwan
| | - Ming-Chih Ho
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Department of Surgery, National Taiwan University Hospital-Hsinchu Branch, Hsinchu, Taiwan
| | - Mei-Hsin Chung
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Pathology, National Taiwan University Hospital-Hsinchu Branch, Hsinchu, Taiwan
| | - Fu-Ting Hsiao
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Wen Tien
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Shiue-Cheng Tang
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
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4
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Ernst P, Kim S, Yang Z, Liu XM, Zhou L. Characterization of the far-red fluorescent probe MitoView 633 for dynamic mitochondrial membrane potential measurement. Front Physiol 2023; 14:1257739. [PMID: 37936577 PMCID: PMC10627182 DOI: 10.3389/fphys.2023.1257739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/13/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction: MitoView 633, a far-red fluorescent dye, exhibits the ability to accumulate within mitochondria in a membrane potential-dependent manner, as described by the Nernst equation. This characteristic renders it a promising candidate for bioenergetics studies, particularly as a robust indicator of mitochondrial membrane potential (DYm). Despite its great potential, its utility in live cell imaging has not been well characterized. Methods: This study seeks to characterize the spectral properties of MitoView 633 in live cells and evaluate its mitochondrial staining, resistance to photobleaching, and dynamics during DYm depolarization. The co-staining and imaging of MitoView 633 with other fluorophores such as MitoSOX Red and Fluo-4 AM were also examined in cardiomyocytes using confocal microscopy. Results and Discussion: Spectrum analysis showed that MitoView 633 emission could be detected at 660 ± 50 nm, and exhibited superior thermal stability compared to tetramethylrhodamine methyl ester (TMRM), a commonly used DYm indicator, which emits at 605 ± 25 nm. Confocal imaging unequivocally illustrated MitoView 633's specific localization within the mitochondrial matrix, corroborated by its colocalization with MitoTracker Green, a well-established mitochondrial marker. Furthermore, our investigation revealed that MitoView 633 exhibited minimal photobleaching at the recommended in vitro concentrations. Additionally, the dynamics of MitoView 633 fluoresce during carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP, a mitochondrial uncoupler)-induced DYm depolarization mirrored that of TMRM. Importantly, MitoView 633 demonstrated compatibility with co-staining alongside MitoSOX Red and Fluo-4 AM, enabling concurrent monitoring of DYm, mitochondrial ROS, and cytosolic Ca2+ in intact cells. Conclusion: These findings collectively underscore MitoView 633 as a superb molecular probe for the singular or combined assessment of DYm and other indicators in live cell imaging applications.
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Affiliation(s)
- Patrick Ernst
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Seulhee Kim
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, United States
| | - Zengqiao Yang
- Department of Surgery, The Ohio State University, Columbus, OH, United States
| | - Xiaoguang Margaret Liu
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | - Lufang Zhou
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, United States
- Department of Surgery, The Ohio State University, Columbus, OH, United States
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5
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Hsiao FT, Chien HJ, Chou YH, Peng SJ, Chung MH, Huang TH, Lo LW, Shen CN, Chang HP, Lee CY, Chen CC, Jeng YM, Tien YW, Tang SC. Transparent tissue in solid state for solvent-free and antifade 3D imaging. Nat Commun 2023; 14:3395. [PMID: 37296117 PMCID: PMC10256715 DOI: 10.1038/s41467-023-39082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Optical clearing with high-refractive-index (high-n) reagents is essential for 3D tissue imaging. However, the current liquid-based clearing condition and dye environment suffer from solvent evaporation and photobleaching, causing difficulties in maintaining the tissue optical and fluorescent features. Here, using the Gladstone-Dale equation [(n-1)/density=constant] as a design concept, we develop a solid (solvent-free) high-n acrylamide-based copolymer to embed mouse and human tissues for clearing and imaging. In the solid state, the fluorescent dye-labeled tissue matrices are filled and packed with the high-n copolymer, minimizing scattering in in-depth imaging and dye fading. This transparent, liquid-free condition provides a friendly tissue and cellular environment to facilitate high/super-resolution 3D imaging, preservation, transfer, and sharing among laboratories to investigate the morphologies of interest in experimental and clinical conditions.
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Affiliation(s)
- Fu-Ting Hsiao
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Hung-Jen Chien
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ya-Hsien Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Shih-Jung Peng
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Mei-Hsin Chung
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Pathology, National Taiwan University Hospital-Hsinchu Branch, Hsinchu, Taiwan
| | - Tzu-Hui Huang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Li-Wen Lo
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Ning Shen
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Pi Chang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Yuan Lee
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Chia Chen
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yung-Ming Jeng
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Wen Tien
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Shiue-Cheng Tang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan.
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
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6
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Leighton RE, Alperstein AM, Punihaole D, Silva WR, Frontiera RR. Stimulated Raman versus Inverse Raman: Investigating Depletion Mechanisms for Super-Resolution Raman Microscopy. J Phys Chem B 2023; 127:26-36. [PMID: 36576851 DOI: 10.1021/acs.jpcb.2c04415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Super-resolution fluorescence microscopy has been critical in elucidating the nanoscale structure of biological systems. However, fluorescent labels bring difficulties such as perturbative labeling steps and photobleaching. Thus, label-free super-resolution techniques are of great interest, like our group's 2016 stimulated Raman scattering (SRS) technique, stimulated Raman depletion microscopy (SRDM). Inspired by stimulated emission depletion microscopy, SRDM uses a toroidally shaped beam to deplete the signal formed on the edges of the focal spot, resulting in SRS signal being detected from only a subdiffraction limited region. In initial works, the cause of the depletion was not thoroughly characterized. Here, we conclusively demonstrate suppression mechanisms in SRDM, while also contrasting approaches to super-resolution Raman microscopy on the Stokes and anti-Stokes sides of the spectrum. By monitoring the depletion of both the SRS and inverse Raman scattering (IRS) signal at a range of depletion powers, we observed other four-wave coherent Raman pathways that correspond to the introduction of the femtosecond depletion beam. In addition, we showed the depletion of the IRS signal, paving the way for a super-resolution imaging technique based on IRS, inverse raman depletion microscopy (IRDM). Combined, SRDM and IRDM offer label-free super-resolution imaging over a large spectral range to accommodate a variety of different sample constraints.
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Affiliation(s)
- Ryan E Leighton
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Ariel M Alperstein
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - David Punihaole
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - W Ruchira Silva
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
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7
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Dubay MM, Acres J, Riekeles M, Nadeau JL. Recent advances in experimental design and data analysis to characterize prokaryotic motility. J Microbiol Methods 2023; 204:106658. [PMID: 36529156 DOI: 10.1016/j.mimet.2022.106658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying run distances and speeds, turn angles and behavior by surfaces or cell-cell interactions) remains a challenging task. A qualitative and quantitative understanding of bacterial motility is needed to bridge the gap between experimentation, omics analysis, and bacterial motility theory. In this review, we discuss the strengths and limitations of how phase contrast microscopy, fluorescence microscopy, and digital holographic microscopy have been used to quantify bacterial motility. Approaches to automated software analysis, including cell recognition, tracking, and track analysis, are also discussed with a view to providing a guide for experimenters to setting up the appropriate imaging and analysis system for their needs.
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Affiliation(s)
- Megan Marie Dubay
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Jacqueline Acres
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Max Riekeles
- Astrobiology Group, Center of Astronomy and Astrophysics, Technical University Berlin, Hardenbergstraße 36A, 10623 Berlin, Germany
| | - Jay L Nadeau
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America.
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8
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Tran Q, Osabe K, Entani T, Wazawa T, Hattori M, Nagai T. Application of Green-enhanced Nano-lantern as a bioluminescent ratiometric indicator for measurement of Arabidopsis thaliana root apoplastic fluid pH. PLANT, CELL & ENVIRONMENT 2022; 45:3157-3170. [PMID: 35864560 PMCID: PMC9542637 DOI: 10.1111/pce.14404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant root absorbs water and nutrients from the soil, and the root apoplastic fluid (AF) is an important intermediate between cells and the surrounding environment. The acid growth theory suggests that an acidic AF is needed for cell wall expansion during root growth. However, technical limitations have precluded the quantification of root apoplastic fluid pH (AF-pH). Here, we used Green-enhanced Nano-lantern (GeNL), a chimeric protein of the luciferase NanoLuc (Nluc) and the green fluorescent protein mNeonGreen (mNG), as a ratiometric pH indicator based on the pH dependency of bioluminescence resonance energy transfer efficiency from Nluc to mNG. Luminescence spectrum of GeNL changed reciprocally from pH 4.5 to 7.5, with a pKa of 5.5. By fusing GeNL to a novel signal peptide from Arabidopsis thaliana Cellulase 1, we localised GeNL in A. thaliana AF. We visualised AF dynamics at subcellular resolution over 30 min and determined flow velocity in the maturation zone to be 0.97± 0.06 μm/s. We confirmed that the developing root AF is acidic in the pH range of 5.1-5.7, suggesting that the AF-pH is tightly regulated during root elongation. These results support the acid growth theory and provide evidence for AF-pH maintenance despite changes in ambient pH.
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Affiliation(s)
- Quang Tran
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Kenji Osabe
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Tetsuyuki Entani
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
| | - Tetsuichi Wazawa
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
| | - Mitsuru Hattori
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Takeharu Nagai
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
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9
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Wüstner D. Image segmentation and separation of spectrally similar dyes in fluorescence microscopy by dynamic mode decomposition of photobleaching kinetics. BMC Bioinformatics 2022; 23:334. [PMID: 35962314 PMCID: PMC9373304 DOI: 10.1186/s12859-022-04881-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Background Image segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on significant intensity differences in individual image regions (intensity-based segmentation). These approaches fail, if dye fluorescence shows large spectral overlap with other employed probes or with strong cellular autofluorescence. Results Here, a novel model-free approach is presented which determines bleaching characteristics based on dynamic mode decomposition (DMD) and uses the inferred photobleaching kinetics to distinguish different probes or dye molecules from autofluorescence. DMD is a data-driven computational method for detecting and quantifying dynamic events in complex spatiotemporal data. Here, DMD is first used on synthetic image data and thereafter used to determine photobleaching characteristics of a fluorescent sterol probe, dehydroergosterol (DHE), compared to that of cellular autofluorescence in the nematode Caenorhabditis elegans. It is shown that decomposition of those dynamic modes allows for separating probe from autofluorescence without invoking a particular model for the bleaching process. In a second application, DMD of dye-specific photobleaching is used to separate two green-fluorescent dyes, an NBD-tagged sphingolipid and Alexa488-transferrin, thereby assigning them to different cellular compartments. Conclusions Data-based decomposition of dynamic modes can be employed to analyze spatially varying photobleaching of fluorescent probes in cells and tissues for spatial and temporal image segmentation, discrimination of probe from autofluorescence and image denoising. The new method should find wide application in analysis of dynamic fluorescence imaging data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04881-x.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology and Physics of Life Sciences (PhyLife) Center, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
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10
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Leighton RE, Alperstein AM, Frontiera RR. Label-Free Super-Resolution Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:37-55. [PMID: 35316608 PMCID: PMC9454238 DOI: 10.1146/annurev-anchem-061020-014723] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Biological and material samples contain nanoscale heterogeneities that are unresolvable with conventional microscopy techniques. Super-resolution fluorescence methods can break the optical diffraction limit to observe these features, but they require samples to be fluorescently labeled. Over the past decade, progress has been made toward developing super-resolution techniques that do not require the use of labels. These label-free techniques span a variety of different approaches, including structured illumination, transient absorption, infrared absorption, and coherent Raman spectroscopies. Many draw inspiration from widely successful fluorescence-based techniques such as stimulated emission depletion (STED) microscopy, photoactivated localization microscopy (PALM), and stochastic optical reconstruction microscopy (STORM). In this review, we discuss the progress made in these fields along with the current challenges and prospects in reaching resolutions comparable to those achieved with fluorescence-based methods.
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Affiliation(s)
- Ryan E Leighton
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Ariel M Alperstein
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA;
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11
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Fei K, Zhang J, Yuan J, Xiao P. Present Application and Perspectives of Organoid Imaging Technology. Bioengineering (Basel) 2022; 9:bioengineering9030121. [PMID: 35324810 PMCID: PMC8945799 DOI: 10.3390/bioengineering9030121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 03/13/2022] [Indexed: 11/18/2022] Open
Abstract
An organoid is a miniaturized and simplified in vitro model with a similar structure and function to a real organ. In recent years, the use of organoids has increased explosively in the field of growth and development, disease simulation, drug screening, cell therapy, etc. In order to obtain necessary information, such as morphological structure, cell function and dynamic signals, it is necessary and important to directly monitor the culture process of organoids. Among different detection technologies, imaging technology is a simple and convenient choice and can realize direct observation and quantitative research. In this review, the principle, advantages and disadvantages of imaging technologies that have been applied in organoids research are introduced. We also offer an overview of prospective technologies for organoid imaging. This review aims to help biologists find appropriate imaging techniques for different areas of organoid research, and also contribute to the development of organoid imaging systems.
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12
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Determination of two-photon absorption in nucleobase analogues: a QR-DFT perspective. Photochem Photobiol Sci 2022; 21:529-543. [PMID: 35179700 DOI: 10.1007/s43630-022-00182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
Abstract
With the prevalence of fluorescence spectroscopy in biological systems, and the benefits of two-photon absorption techniques, presented here is an assessment of the two-photon accessibility of modern fluorescent nucleobase analogues utilising quadratic response DFT. Due to the complex environment experienced by these nucleobases, the two-photon spectra of each analogue has been assessed in the presence of both [Formula: see text]-stacked and hydrogen-bonding interactions involving the canonical nucleobases. Findings suggest that the [Formula: see text]-stacking environment provides a more significant effect on the spectra of the analogues studies than a hydrogen-bonding environment; analogue structures presenting high two-photon cross-section values for one or more states coincide with polycyclic extensions to preserved canonical base structure, as observed in the qA family of analogues, while analogue structures more closely resembling the structure of the base in question present a much more muted spectra in comparison. Results from this investigation have also allowed for the derivation of a number of design rules for the development of potential, two-photon specific, analogues for future use in both imaging and potential photochemical activation.
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13
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Tasso TT, Baptista MS. Photosensitized Oxidation of Intracellular Targets: Understanding the Mechanisms to Improve the Efficiency of Photodynamic Therapy. Methods Mol Biol 2022; 2451:261-283. [PMID: 35505023 DOI: 10.1007/978-1-0716-2099-1_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The development of improved photosensitizers is a key aspect in the establishment of photodynamic therapy (PDT) as a reliable treatment modality. In this chapter, we discuss how molecular design can lead to photosensitizers with higher selectivity and better efficiency, with focus on the importance of specific intracellular targeting in determining the cell death mechanism and, consequently, the PDT outcome.
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Affiliation(s)
- Thiago Teixeira Tasso
- Chemistry Department, Institute of Exact Sciences, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Maurício S Baptista
- Biochemistry Department, Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil.
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14
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Kaya M, Stein F, Rouwkema J, Khalil ISM, Misra S. Serial imaging of micro-agents and cancer cell spheroids in a microfluidic channel using multicolor fluorescence microscopy. PLoS One 2021; 16:e0253222. [PMID: 34129617 PMCID: PMC8205435 DOI: 10.1371/journal.pone.0253222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022] Open
Abstract
Multicolor fluorescence microscopy is a powerful technique to fully visualize many biological phenomena by acquiring images from different spectrum channels. This study expands the scope of multicolor fluorescence microscopy by serial imaging of polystyrene micro-beads as surrogates for drug carriers, cancer spheroids formed using HeLa cells, and microfluidic channels. Three fluorophores with different spectral characteristics are utilized to perform multicolor microscopy. According to the spectrum analysis of the fluorophores, a multicolor widefield fluorescence microscope is developed. Spectral crosstalk is corrected by exciting the fluorophores in a round-robin manner and synchronous emitted light collection. To report the performance of the multicolor microscopy, a simplified 3D tumor model is created by placing beads and spheroids inside a channel filled with the cell culture medium is imaged at varying exposure times. As a representative case and a method for bio-hybrid drug carrier fabrication, a spheroid surface is coated with beads in a channel utilizing electrostatic forces under the guidance of multicolor microscopy. Our experiments show that multicolor fluorescence microscopy enables crosstalk-free and spectrally-different individual image acquisition of beads, spheroids, and channels with the minimum exposure time of 5.5 ms. The imaging technique has the potential to monitor drug carrier transportation to cancer cells in real-time.
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Affiliation(s)
- Mert Kaya
- Surgical Robotics Laboratory, Department of Biomechanical Engineering, University of Twente, Enschede, The Netherlands
- Surgical Robotics Laboratory, Department of Biomedical Engineering and University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Fabian Stein
- Vascularization Laboratory, Department of Biomechanical Engineering, University of Twente, Enschede, The Netherlands
| | - Jeroen Rouwkema
- Vascularization Laboratory, Department of Biomechanical Engineering, University of Twente, Enschede, The Netherlands
| | - Islam S. M. Khalil
- Surgical Robotics Laboratory, Department of Biomedical Engineering and University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Sarthak Misra
- Surgical Robotics Laboratory, Department of Biomechanical Engineering, University of Twente, Enschede, The Netherlands
- Surgical Robotics Laboratory, Department of Biomedical Engineering and University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
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15
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Guo J, Sesena Rubfiaro A, Lai Y, Moscoso J, Chen F, Liu Y, Wang X, He J. Dynamic single-cell intracellular pH sensing using a SERS-active nanopipette. Analyst 2020; 145:4852-4859. [PMID: 32542257 PMCID: PMC7425357 DOI: 10.1039/d0an00838a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glass nanopipettes have shown promise for applications in single-cell manipulation, analysis, and imaging. In recent years, plasmonic nanopipettes have been developed to enable surface-enhanced Raman spectroscopy (SERS) measurements for single-cell analysis. In this work, we developed a SERS-active nanopipette that can be used to perform long-term and reliable intracellular analysis of single living cells with minimal damage, which is achieved by optimizing the nanopipette geometry and the surface density of the gold nanoparticle (AuNP) layer at the nanopipette tip. To demonstrate its ability in single-cell analysis, we used the nanopipette for intracellular pH sensing. Intracellular pH (pHi) is vital to cells as it influences cell function and behavior and pathological conditions. The pH sensitivity was realized by simply modifying the AuNP layer with the pH reporter molecule 4-mercaptobenzoic acid. With a response time of less than 5 seconds, the pH sensing range is from 6.0 to 8.0 and the maximum sensitivity is 0.2 pH units. We monitored the pHi change of individual HeLa and fibroblast cells, triggered by the extracellular pH (pHe) change. The HeLa cancer cells can better resist pHe change and adapt to the weak acidic environment. Plasmonic nanopipettes can be further developed to monitor other intracellular biomarkers.
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Affiliation(s)
- Jing Guo
- Department of Physics, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
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16
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Allard C, Schué L, Fossard F, Recher G, Nascimento R, Flahaut E, Loiseau A, Desjardins P, Martel R, Gaufrès E. Confinement of Dyes inside Boron Nitride Nanotubes: Photostable and Shifted Fluorescence down to the Near Infrared. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001429. [PMID: 32483892 DOI: 10.1002/adma.202001429] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 05/28/2023]
Abstract
Fluorescence is ubiquitous in life science and used in many fields of research ranging from ecology to medicine. Among the most common fluorogenic compounds, dyes are being exploited in bioimaging for their outstanding optical properties from UV down to the near IR (NIR). However, dye molecules are often toxic to living organisms and photodegradable, which limits the time window for in vivo experiments. Here, it is demonstrated that organic dye molecules are passivated and photostable when they are encapsulated inside a boron nitride nanotube (dyes@BNNT). The results show that the BNNTs drive an aggregation of the encapsulated dyes, which induces a redshifted fluorescence from visible to NIR-II. The fluorescence remains strong and stable, exempt of bleaching and blinking, over a time scale longer than that of free dyes by more than 104 . This passivation also reduces the toxicity of the dyes and induces exceptional chemical robustness, even in harsh conditions. These properties are highlighted in bioimaging where the dyes@BNNT nanohybrids are used as fluorescent nanoprobes for in vivo monitoring of Daphnia Pulex microorganisms and for diffusion tracking on human hepatoblastoma cells with two-photon imaging.
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Affiliation(s)
- Charlotte Allard
- Département de génie physique, Polytechnique Montréal, Montréal, Québec, H3C 3A7, Canada
| | - Léonard Schué
- Département de chimie, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Frédéric Fossard
- Laboratoire d'Etude des Microstructures, ONERA-CNRS, UMR104, Université Paris-Saclay, BP 72, Châtillon, 92322, France
| | - Gaëlle Recher
- CNRS & Institut d'Optique, UMR 5298, Talence, F-33400, France
- LP2N, Laboratoire Photonique Numerique et Nanosciences, University of Bordeaux, Talence, F-33400, France
| | - Rafaella Nascimento
- Département de chimie, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Emmanuel Flahaut
- CIRIMAT, Université de Toulouse, CNRS, INPT, UPS, UMR CNRS-UPS-INP N°5085, Université Toulouse 3 Paul Sabatier, Bât. CIRIMAT, 118, route de Narbonne, Toulouse, 31062, France
| | - Annick Loiseau
- Laboratoire d'Etude des Microstructures, ONERA-CNRS, UMR104, Université Paris-Saclay, BP 72, Châtillon, 92322, France
| | - Patrick Desjardins
- Département de génie physique, Polytechnique Montréal, Montréal, Québec, H3C 3A7, Canada
| | - Richard Martel
- Département de chimie, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Etienne Gaufrès
- Laboratoire d'Etude des Microstructures, ONERA-CNRS, UMR104, Université Paris-Saclay, BP 72, Châtillon, 92322, France
- CNRS & Institut d'Optique, UMR 5298, Talence, F-33400, France
- LP2N, Laboratoire Photonique Numerique et Nanosciences, University of Bordeaux, Talence, F-33400, France
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17
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Tichá M, Hlaváčková K, Hrbáčková M, Ovečka M, Šamajová O, Šamaj J. Super-resolution imaging of microtubules in Medicago sativa. Methods Cell Biol 2020; 160:237-251. [PMID: 32896319 DOI: 10.1016/bs.mcb.2020.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Study of microtubules on cellular and subcellular levels is compromised by limited resolution of conventional fluorescence microscopy. However, it is possible to improve Abbe's diffraction-limited resolution by employment of super-resolution microscopy methods. Two of them, described herein, are structured-illumination microscopy (SIM) and Airyscan laser scanning microscopy (AM). Both methods allow high-resolution imaging of cortical microtubules in plant cells, thus contributing to the current knowledge on plant morphogenesis, growth and development. Both SIM and AM provide certain advantages and characteristic features, which are described here. We present immunofluorescence localization methods for microtubules in fixed plant cells achieving high signal efficiency, superb sample stability and sub-diffraction resolution. These protocols were developed for whole-mount immunolabeling of root samples of legume crop species Medicago sativa. They also contain tips for optimal sample preparation of plants germinated from seeds as well as plantlets regenerated from somatic embryos in vitro. We describe in detail all steps of optimized protocols for sample preparation, microtubule immunolabeling and super-resolution imaging.
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Affiliation(s)
- Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Kateřina Hlaváčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslava Hrbáčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
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18
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Demchenko AP. Photobleaching of organic fluorophores: quantitative characterization, mechanisms, protection. Methods Appl Fluoresc 2020; 8:022001. [PMID: 32028269 DOI: 10.1088/2050-6120/ab7365] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Photochemical stability is one of the most important parameters that determine the usefulness of organic dyes in different applications. This Review addresses key factors that determine the dye photostability. It is shown that photodegradation can follow different oxygen-dependent and oxygen-independent mechanisms and may involve both 1S1-3T1 and higher-energy 1Sn-3Tn excited states. Their involvement and contribution depends on dye structure, medium conditions, irradiation power. Fluorescein, rhodamine, BODIPY and cyanine dyes, as well as conjugated polymers are discussed as selected examples illustrating photobleaching mechanisms. The strategies for modulating and improving the photostability are overviewed. They include the improvement of fluorophore design, particularly by attaching protective and anti-fading groups, creating proper medium conditions in liquid, solid and nanoscale environments. The special conditions for biological labeling, sensing and imaging are outlined.
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Affiliation(s)
- Alexander P Demchenko
- Palladin Institute of Biochemistry, Leontovicha st. 9, Kyiv 01030, Ukraine. Yuriy Fedkovych National University, Chernivtsi, 58012, Ukraine
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19
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Vinçon B, Geisler C, Egner A. Pixel hopping enables fast STED nanoscopy at low light dose. OPTICS EXPRESS 2020; 28:4516-4528. [PMID: 32121686 DOI: 10.1364/oe.385174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/23/2020] [Indexed: 05/22/2023]
Abstract
The achievable image quality in fluorescence microscopy and nanoscopy is usually limited by photobleaching. Reducing the light dose imposed on the sample is thus a challenge for all these imaging techniques. Various approaches like CLEM, RESCue, MINFIELD, DyMIN and smart RESOLFT have been presented in the last years and have proven to significantly reduce the required light dose in diffraction-limited as well as super-resolution imaging, thus resulting in less photobleaching and phototoxicity. None of these methods has so far been able to transfer the light dose reduction into a faster recording at pixel dwell times of a few ten microseconds. By implementing a scan system with low latency and large field of view we could directly convert the light dose reduction of RESCue into a shorter acquisition time for STED nanoscopy. In this way, FastRESCue speeds up the acquisition locally up to 10-fold and allows overall for a 5 times faster acquisition at only 20% of the light dose in biological samples.
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20
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Ticli G, Prosperi E. In Situ Analysis of DNA-Protein Complex Formation upon Radiation-Induced DNA Damage. Int J Mol Sci 2019; 20:ijms20225736. [PMID: 31731696 PMCID: PMC6888283 DOI: 10.3390/ijms20225736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/05/2023] Open
Abstract
The importance of determining at the cellular level the formation of DNA–protein complexes after radiation-induced lesions to DNA is outlined by the evidence that such interactions represent one of the first steps of the cellular response to DNA damage. These complexes are formed through recruitment at the sites of the lesion, of proteins deputed to signal the presence of DNA damage, and of DNA repair factors necessary to remove it. Investigating the formation of such complexes has provided, and will probably continue to, relevant information about molecular mechanisms and spatiotemporal dynamics of the processes that constitute the first barrier of cell defense against genome instability and related diseases. In this review, we will summarize and discuss the use of in situ procedures to detect the formation of DNA-protein complexes after radiation-induced DNA damage. This type of analysis provides important information on the spatial localization and temporal resolution of the formation of such complexes, at the single-cell level, allowing the study of heterogeneous cell populations.
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Affiliation(s)
- Giulio Ticli
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Correspondence:
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21
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Nassar SJM, Wills C, Harriman A. Inhibition of the Photobleaching of Methylene Blue by Association with Urea. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900141] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sulafa Jamal M. Nassar
- Molecular Photonics Laboratory, SNES- ChemistryNewcastle University Newcastle upon Tyne NE1 7RU UK
| | - Corinne Wills
- NMR Laboratory School of Natural and Environmental ScienceNewcastle University Newcastle upon Tyne NE1 7RU UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, SNES- ChemistryNewcastle University Newcastle upon Tyne NE1 7RU UK
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22
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Graefe CT, Punihaole D, Harris CM, Lynch MJ, Leighton R, Frontiera RR. Far-Field Super-Resolution Vibrational Spectroscopy. Anal Chem 2019; 91:8723-8731. [PMID: 31251563 DOI: 10.1021/acs.analchem.9b01731] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Potential label-free alternatives to super-resolution fluorescence techniques have been the focus of considerable research due to the challenges intrinsic in the reliance on fluorescent tags. In this Feature, we discuss efforts to develop super-resolution techniques based on vibrational spectroscopies and address possible sample applications as well as future potential resolution enhancements.
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Affiliation(s)
- Christian T Graefe
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - David Punihaole
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Celina M Harris
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Michael J Lynch
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Ryan Leighton
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Renee R Frontiera
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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23
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Ruba A, Luo W, Kelich J, Tingey M, Yang W. 3D Tracking-Free Approach for Obtaining 3D Super-Resolution Information in Rotationally Symmetric Biostructures. J Phys Chem B 2019; 123:5107-5120. [PMID: 31117612 DOI: 10.1021/acs.jpcb.9b02979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, it is highly desirable but still challenging to obtain high-resolution (<50 nm) three-dimensional (3D) super-resolution information on structures in fixed specimens as well as for dynamic processes in live cells. Here we introduce a simple approach, without using 3D super-resolution microscopy or real-time 3D particle tracking, to estimate 3D sub-diffraction-limited structural or dynamic information in rotationally symmetric biostructures. This is a postlocalization analysis that transforms 2D super-resolution images or 2D single-molecule localization distributions into their corresponding 3D spatial probability distributions on the basis of prior known structural knowledge. This analysis is ideal in cases where the ultrastructure of a cellular structure is known but the substructural localization of a particular (usually mobile) protein is not. The method has been successfully applied to achieve 3D structural and functional sub-diffraction-limited information for 25-300 nm subcellular organelles that meet the rotational symmetry requirement, such as nuclear pore complex, primary cilium, and microtubule. In this Article, we will provide comprehensive analyses of this method by using experimental data and computational simulations. Finally, open source code of the 2D to 3D transformation algorithm (MATLAB) and simulations (Python) have also been developed.
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Affiliation(s)
- Andrew Ruba
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Wangxi Luo
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Joseph Kelich
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Mark Tingey
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Weidong Yang
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
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24
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Live Cell Imaging and Analysis to Capture T-Cell Motility in Real-Time. Methods Mol Biol 2019. [PMID: 30610596 DOI: 10.1007/978-1-4939-9036-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
T-lymphocytes are the principle coordinators of the immune defense system and play a major role in the protection of our body against infections, intruders of non-self, and malignancies. To mount an immune response, T-cells need to be effectively employed to tissue sites of infection or inflammation and establish contacts with antigen-presenting cells (APCs) or malignant cells. Understanding how T-cells navigate toward their recruitment sites would offer new therapeutic opportunities. Advancement in the hardware and software upgrades of microscopy technology has created several efficient and easy-to-operate live cell imaging platforms. In this protocol, we present a generalized and simple-to-follow protocol for live cell imaging of migrating T-cells, which can also be adopted to visualize real-time tracking of intracellular signaling events.
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25
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Roth S, Hadass O, Cohen M, Verbarg J, Wilsey J, Danielli A. Improving the Sensitivity of Fluorescence-Based Immunoassays by Photobleaching the Autofluorescence of Magnetic Beads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1803751. [PMID: 30411493 DOI: 10.1002/smll.201803751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/24/2018] [Indexed: 05/11/2023]
Abstract
In fluorescence-based assays, usually a target molecule is captured using a probe conjugated to a capture surface, and then detected using a second fluorescently labeled probe. One of the most common capture surfaces is a magnetic bead. However, magnetic beads exhibit strong autofluorescence, which often overlaps with the emission of the reporter fluorescent dyes and limits the analytical performance of the assay. Here, several widely used magnetic beads are photobleached and their autofluorescence is reduced to 1% of the initial value. Their autofluorescence properties, including their photobleaching decay rates and autofluorescence spectra pre- and post-photobleaching, and the stability of the photobleaching over a period of two months are analyzed. The photobleached beads are stable over time and their surface functionality is retained. In a high-sensitivity LX-200 system using photobleached magnetic beads, human interleukin-8 is detected with a threefold improvement in detection limit and signal-to-noise ratio over results achievable with nonbleached beads. Since many contemporary immunoassays rely on magnetic beads as capture surfaces, prebleaching the beads may significantly improve the analytical performance of these assays. Moreover, nonmagnetic beads with low autofluorescence are also successfully photobleached, suggesting that photobleaching can be applied to various capture surfaces used in fluorescence-based assays.
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Affiliation(s)
- Shira Roth
- Faculty of Engineering, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
| | - Orr Hadass
- MagBiosense, Inc., 4320 Forest Park Ave., Suite 304, St. Louis, MO, 63108, USA
| | - Meir Cohen
- Faculty of Engineering, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
| | - Jasenka Verbarg
- MagBiosense, Inc., 4320 Forest Park Ave., Suite 304, St. Louis, MO, 63108, USA
| | - Jennifer Wilsey
- MagBiosense, Inc., 4320 Forest Park Ave., Suite 304, St. Louis, MO, 63108, USA
| | - Amos Danielli
- Faculty of Engineering, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
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Abstract
Fluorescent optical probes have rapidly transformed our understanding of complex biological systems by providing specific information on biological targets in the natural living state. However, their utility is often limited by insufficient brightness, photostability, and multiplexing capacity. Here, we report a conceptually new optical probe, termed ‘reflectophore’, which is based on the spectral interference from a dielectric microsphere. Reflectophores are orders-of-magnitudes brighter than conventional fluorophores and are free from photobleaching, enabling practically unlimited readout at high fidelity. They also offer high-degree multiplexing, encoded in their optical size, which can be readily decoded through interferometric detection with nanoscale accuracy, even in turbid biological media. Furthermore, we showcase their biological applications in cellular barcoding and microenvironmental sensing of a target protein and local electric field. Tagging and tracking cells with multiplexed labels can help study complex cellular behaviors in living systems. Here, Jo et al. propose and demonstrate the use of Fabry-Perot-like resonances in dielectric microspheres as such a label and call these reflectophores.
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27
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Quantifying Embolism: Label‐Free Volumetric Mapping of Thrombus Structure and Kinesis in a Microfluidic System with Optical Holography. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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28
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Abstract
In the past decade, automated microscopy has become an important tool for the drug discovery and development process. The establishment of imaging modalities as screening tools depended on technological breakthroughs in the domain of automated microscopy and automated image analysis. These types of assays are often referred to as high content screening or high content analysis (HCS/HCA). The driving force to adopt imaging for drug development is the quantity and quality of cellular information that can be collected and the enhanced physiological relevance of cellular screening compared to biochemical screening. Most imaging in drug development is performed on fixed cells as this allows uncoupling the preparation of the cells from the acquisition of the images. Live-cell imaging is technically challenging, but is very useful for many aspects of the drug development pipeline such as kinetic studies of compound mode of action or to analyze the motion of cellular components. Most vendors of HCS microscopy systems offer the option of environmental chambers and onboard pipetting on their platforms. This reflects the wish and desire of many customers to have the ability to perform live-cell assays on their HCS automated microscopes. This book chapter summarizes the challenges and advantages of live-cell imaging in drug discovery. Examples of applications are presented and the motivation to perform these assays in kinetic mode is discussed.
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Affiliation(s)
- Milan Esner
- High Throughput Technology Development Studio (HT-TDS), Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00, Brno, Czech Republic
| | - Felix Meyenhofer
- High Throughput Technology Development Studio (HT-TDS), Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
- Département de Médecine, Faculté des Sciences, University of Fribourg, 1, Rte., Albert Gockel, Fribourg, 1700, Switzerland
| | - Marc Bickle
- High Throughput Technology Development Studio (HT-TDS), Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
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Purdey MS, Capon PK, Pullen BJ, Reineck P, Schwarz N, Psaltis PJ, Nicholls SJ, Gibson BC, Abell AD. An organic fluorophore-nanodiamond hybrid sensor for photostable imaging and orthogonal, on-demand biosensing. Sci Rep 2017; 7:15967. [PMID: 29162856 PMCID: PMC5698319 DOI: 10.1038/s41598-017-15772-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/02/2017] [Indexed: 11/21/2022] Open
Abstract
Organic fluorescent probes are widely used to detect key biomolecules; however, they often lack the photostability required for extended intracellular imaging. Here we report a new hybrid nanomaterial (peroxynanosensor, PNS), consisting of an organic fluorescent probe bound to a nanodiamond, that overcomes this limitation to allow concurrent and extended cell-based imaging of the nanodiamond and ratiometric detection of hydrogen peroxide. Far-red fluorescence of the nanodiamond offers continuous monitoring without photobleaching, while the green fluorescence of the organic fluorescent probe attached to the nanodiamond surface detects hydrogen peroxide on demand. PNS detects basal production of hydrogen peroxide within M1 polarised macrophages and does not affect macrophage growth during prolonged co-incubation. This nanosensor can be used for extended bio-imaging not previously possible with an organic fluorescent probe, and is spectrally compatible with both Hoechst 33342 and MitoTracker Orange stains for hyperspectral imaging.
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Affiliation(s)
- Malcolm S Purdey
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia.
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia.
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia.
- South Australian Health and Medical Research Institute (SAHMRI) and School of Medicine, The University of Adelaide, North Terrace, Adelaide, SA 5001, Australia.
| | - Patrick K Capon
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Benjamin J Pullen
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- South Australian Health and Medical Research Institute (SAHMRI) and School of Medicine, The University of Adelaide, North Terrace, Adelaide, SA 5001, Australia
| | - Philipp Reineck
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
- School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Nisha Schwarz
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
- South Australian Health and Medical Research Institute (SAHMRI) and School of Medicine, The University of Adelaide, North Terrace, Adelaide, SA 5001, Australia
| | - Peter J Psaltis
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
- South Australian Health and Medical Research Institute (SAHMRI) and School of Medicine, The University of Adelaide, North Terrace, Adelaide, SA 5001, Australia
| | - Stephen J Nicholls
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
- South Australian Health and Medical Research Institute (SAHMRI) and School of Medicine, The University of Adelaide, North Terrace, Adelaide, SA 5001, Australia
| | - Brant C Gibson
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
- School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia.
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia.
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia.
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High-Resolution Fluorescence Microscope Imaging of Erythroblast Structure. Methods Mol Biol 2017. [PMID: 29076092 DOI: 10.1007/978-1-4939-7428-3_12] [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
During erythropoiesis, erythroblasts undergo dramatic morphological changes to produce mature erythrocytes. Many unanswered questions regarding the molecular mechanisms behind these changes can be addressed with high-resolution fluorescence imaging. Immunofluoresence staining enables localization of specific molecules, organelles, and membrane components in intact cells at different phases of erythropoiesis. Confocal laser scanning microscopy can provide high-resolution, three-dimensional images of stained structures, which can be used to dissect the molecular mechanisms driving erythropoiesis. The sample preparation, staining procedure, imaging parameters, and image analysis methods used directly affect the quality of the confocal images and the amount and accuracy of information that they can provide. Here, we describe methods to dissect erythropoietic tissues from mice, to perform immunofluorescence staining and confocal imaging of various molecules, organelles and structures of interest in erythroblasts, and to present and quantitatively analyze the data obtained in these fluorescence images.
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31
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Hsu YP, Rittichier J, Kuru E, Yablonowski J, Pasciak E, Tekkam S, Hall E, Murphy B, Lee TK, Garner EC, Huang KC, Brun YV, VanNieuwenhze MS. Full color palette of fluorescent d-amino acids for in situ labeling of bacterial cell walls. Chem Sci 2017; 8:6313-6321. [PMID: 28989665 PMCID: PMC5628581 DOI: 10.1039/c7sc01800b] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/06/2017] [Indexed: 01/01/2023] Open
Abstract
Fluorescent d-amino acids (FDAAs) enable efficient in situ labeling of peptidoglycan in diverse bacterial species. Conducted by enzymes involved in peptidoglycan biosynthesis, FDAA labeling allows specific probing of cell wall formation/remodeling activity, bacterial growth and cell morphology. Their broad application and high biocompatibility have made FDAAs an important and effective tool for studies of peptidoglycan synthesis and dynamics, which, in turn, has created a demand for the development of new FDAA probes. Here, we report the synthesis of new FDAAs, with emission wavelengths that span the entire visible spectrum. We also provide data to characterize their photochemical and physical properties, and we demonstrate their utility for visualizing peptidoglycan synthesis in Gram-negative and Gram-positive bacterial species. Finally, we show the permeability of FDAAs toward the outer-membrane of Gram-negative organisms, pinpointing the probes available for effective labeling in these species. This improved FDAA toolkit will enable numerous applications for the study of peptidoglycan biosynthesis and dynamics.
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Affiliation(s)
- Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | | | - Erkin Kuru
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | - Jacob Yablonowski
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | - Erick Pasciak
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Srinivas Tekkam
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Edward Hall
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Brennan Murphy
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Timothy K Lee
- Department of Bioengineering , Stanford University , Stanford , CA 94305 , USA
| | - Ethan C Garner
- Molecular and Cellular Biology (FAS) Center for Systems Biology , Harvard University , Cambridge , Massachusetts 02138 , USA
| | - Kerwyn Casey Huang
- Department of Bioengineering , Stanford University , Stanford , CA 94305 , USA
- Department of Microbiology and Immunology , Stanford University School of Medicine , Stanford , CA 94305 , USA
| | - Yves V Brun
- Department of Biology , Indiana University , Bloomington , IN 47405 , USA .
| | - Michael S VanNieuwenhze
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
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32
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Tang Y, Thillier Y, Liu R, Li X, Lam KS, Gao T. Single-Bead Quantification of Peptide Loading Distribution for One-Bead One-Compound Library Synthesis Using Confocal Raman Spectroscopy. Anal Chem 2017; 89:7000-7008. [PMID: 28530391 DOI: 10.1021/acs.analchem.7b00516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report an analytical method to determine peptide loading of "one-bead one-compound" (OBOC) combinatorial peptide libraries at single-bead level. The quantification is based on a linear relationship between the amount of N-terminal amino groups on individual peptide beads and the intensity of Raman signal obtained from a specifically designed reporter labeled on amino groups. Confocal Raman spectroscopy was employed to characterize peptide loading of beads with defined peptide sequences and from OBOC combinatorial peptide libraries. Although amine loading of blank TentaGel beads was found to be uniform, peptide loading among beads of OBOC peptide libraries varied substantially, particularly for those libraries with long sequences. Construction of OBOC libraries can be monitored with this novel analytical technique so that synthetic conditions can be optimized for the preparation of high-quality OBOC peptide libraries. As the variability of peptide loading of individual library beads can significantly influence the screening results, quantitative information obtained by this method will allow us to gain insight into the complexity and challenge of OBOC library synthesis and screening.
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Affiliation(s)
- Yuchen Tang
- College of Chemistry, Central China Normal University , Wuhan 430079, China.,China Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China.,Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Yann Thillier
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Tingjuan Gao
- College of Chemistry, Central China Normal University , Wuhan 430079, China.,China Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
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33
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Prakash K. Investigating Chromatin Organisation Using Single Molecule Localisation Microscopy. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-52183-1_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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34
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Danan Y, Yariv I, Zalevsky Z, Sinvani M. Improved Margins Detection of Regions Enriched with Gold Nanoparticles inside Biological Phantom. MATERIALS (BASEL, SWITZERLAND) 2017; 10:E203. [PMID: 28772563 PMCID: PMC5459194 DOI: 10.3390/ma10020203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/12/2017] [Accepted: 02/14/2017] [Indexed: 02/06/2023]
Abstract
Utilizing the surface plasmon resonance (SPR) effect of gold nanoparticles (GNPs) enables their use as contrast agents in a variety of biomedical applications for diagnostics and treatment. These applications use both the very strong scattering and absorption properties of the GNPs due to their SPR effects. Most imaging methods use the light-scattering properties of the GNPs. However, the illumination source is in the same wavelength of the GNPs' scattering wavelength, leading to background noise caused by light scattering from the tissue. In this paper we present a method to improve border detection of regions enriched with GNPs aiming for the real-time application of complete tumor resection by utilizing the absorption of specially targeted GNPs using photothermal imaging. Phantoms containing different concentrations of GNPs were irradiated with a continuous-wave laser and measured with a thermal imaging camera which detected the temperature field of the irradiated phantoms. By modulating the laser illumination, and use of a simple post processing, the border location was identified at an accuracy of better than 0.5 mm even when the surrounding area got heated. This work is a continuation of our previous research.
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Affiliation(s)
- Yossef Danan
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan 5290002, Israel.
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Inbar Yariv
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan 5290002, Israel.
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Zeev Zalevsky
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan 5290002, Israel.
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Moshe Sinvani
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan 5290002, Israel.
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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Abstract
AbstractLive-cell and live-tissue imaging using fluorescence optical microscopes presents an inherent trade-off between image quality and photodamage. Spatially-controlled illumination microscopy (SCIM) aims to strike the right balance between obtaining good image quality and minimizing the risk of photodamage. In traditional imaging, illumination is performed with a spatially-uniform light dose resulting in spatially-variable detected signals. SCIM adopts an alternative imaging approach where illumination is performed with a spatially-variable light dose resulting in spatially-uniform detected signals. The actual image information of the biological specimen in SCIM is predominantly encoded in the illumination profile. SCIM uses real-time spatial control of illumination in the imaging of fluorescent biological specimens. This alternative imaging paradigm reduces the overall illumination light dose during imaging, which facilitates prolonged imaging of live biological specimens by minimizing photodamage without compromising image quality. Additionally, the dynamic range of a SCIM image is no longer limited by the dynamic range of the detector (or camera), since it employs a uniform detection strategy. The large dynamic range of SCIM is predominantly determined by the illumination profile, and is advantageous for imaging both live and fixed biological specimens. In the present review, the concept and working mechanisms of SCIM are discussed, together with its application in various types of optical microscopes.
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36
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Lee SA, Ponjavic A, Siv C, Lee SF, Biteen JS. Nanoscopic Cellular Imaging: Confinement Broadens Understanding. ACS NANO 2016; 10:8143-8153. [PMID: 27602688 DOI: 10.1021/acsnano.6b02863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In recent years, single-molecule fluorescence imaging has been reconciling a fundamental mismatch between optical microscopy and subcellular biophysics. However, the next step in nanoscale imaging in living cells can be accessed only by optical excitation confinement geometries. Here, we review three methods of confinement that can enable nanoscale imaging in living cells: excitation confinement by laser illumination with beam shaping; physical confinement by micron-scale geometries in bacterial cells; and nanoscale confinement by nanophotonics.
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Affiliation(s)
- Stephen A Lee
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Aleks Ponjavic
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Chanrith Siv
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Steven F Lee
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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Daetwyler S, Huisken J. Fast Fluorescence Microscopy with Light Sheets. THE BIOLOGICAL BULLETIN 2016; 231:14-25. [PMID: 27638692 DOI: 10.1086/689588] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In light sheet microscopy, optical sectioning by selective fluorescence excitation with a sheet of light is combined with fast full-frame acquisition. This illumination scheme provides minimal photobleaching and phototoxicity. Complemented with remote focusing and multi-view acquisition, light sheet microscopy is the method of choice for acquisition of very fast biological processes, large samples, and high-throughput applications in areas such as neuroscience, plant biology, and developmental biology. This review explains why light sheet microscopes are much faster and gentler than other established fluorescence microscopy techniques. New volumetric imaging schemes and highlights of selected biological applications are also discussed.
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Affiliation(s)
- Stephan Daetwyler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Jan Huisken
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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38
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Groot Nibbelink M, Daoudi K, Slegers S, Grootendorst D, Dantuma M, Steenbergen W, Karperien M, Manohar S, van Apeldoorn A. Opening the "White Box" in Tissue Engineering: Visualization of Cell Aggregates in Optically Scattering Scaffolds. Tissue Eng Part C Methods 2016; 22:534-42. [PMID: 27056242 DOI: 10.1089/ten.tec.2015.0462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The noninvasive and longitudinal imaging of cells or cell aggregates in large optically scattering scaffolds is still a largely unresolved problem in tissue engineering. In this work, we investigated the potential of near-infrared (NIR) photoacoustic (PA) tomography imaging to address this issue. We used clinically relevant sizes of highly light scattering polyethersulfone multibore(®) hollow fiber scaffolds seeded with cells. Since cells have little optical absorption at NIR wavelengths, we studied labeling of cells with absorbers. Four NIR labels were examined for their suitability based on absorption characteristics, resistance to bleaching, and influence on cell viability. On the basis of these criteria, carbon nanoparticles proved most suitable in a variety of cells. For PA imaging, we used a research setup, based on computed tomography geometry. As proof of principle, using this imager we monitored the distribution and clustering of labeled rat insulinoma beta cell aggregates in the scaffolds. This was performed for the duration of 1 week in a nondestructive manner. The results were validated using fluorescence imaging, histology, and light microscopy imaging. Based on our findings, we conclude that PA tomography is a powerful tool for the nondestructive imaging of cells in optically scattering tissue-engineered scaffolds.
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Affiliation(s)
- Milou Groot Nibbelink
- 1 Developmental Bioengineering, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Khalid Daoudi
- 2 Biomedical Photonic Imaging, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Sanne Slegers
- 2 Biomedical Photonic Imaging, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands .,3 Albert Schweitzer Hospital , Dordrecht, The Netherlands
| | - Diederik Grootendorst
- 2 Biomedical Photonic Imaging, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Maura Dantuma
- 2 Biomedical Photonic Imaging, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Wiendelt Steenbergen
- 2 Biomedical Photonic Imaging, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Marcel Karperien
- 1 Developmental Bioengineering, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Srirang Manohar
- 2 Biomedical Photonic Imaging, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Aart van Apeldoorn
- 1 Developmental Bioengineering, MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
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Ilovitsh T, Zalevsky Z. Temporal flickering of contrast agents for enhanced optical imaging. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 8:439-448. [PMID: 26371615 DOI: 10.1002/wnan.1375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 07/27/2015] [Accepted: 08/12/2015] [Indexed: 06/05/2023]
Abstract
The temporal flickering of contrast agents that labels a biological sample is a unique modality for cellular imaging with single molecule sensitivity. It improves the signal-to-noise ratio statistics associated with the noisy in vivo environment and has promising applications in single particle tracking and super-resolution microscopy techniques. The flickering can be triggered either statistically through the mechanism of temporal fluctuations of the emitter or through external modulation. The enriching toolbox of contrast agents that are feasible for biomedical imaging for the flickering methods will be discussed, with emphasis on the emerging field of flickering gold nanoparticles and the lock-in detection mechanism. WIREs Nanomed Nanobiotechnol 2016, 8:439-448. doi: 10.1002/wnan.1375 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Tali Ilovitsh
- Faculty of Engineering, Bar Ilan University, Ramat-Gan, Israel
| | - Zeev Zalevsky
- Faculty of Engineering, Bar Ilan University, Ramat-Gan, Israel
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Żurek-Biesiada D, Szczurek AT, Prakash K, Best G, Mohana GK, Lee HK, Roignant JY, Dobrucki JW, Cremer C, Birk U. Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe. Data Brief 2016; 7:157-71. [PMID: 27054149 PMCID: PMC4802433 DOI: 10.1016/j.dib.2016.01.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 01/07/2016] [Accepted: 01/20/2016] [Indexed: 02/02/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) is a recently emerged optical imaging method that was shown to achieve a resolution in the order of tens of nanometers in intact cells. Novel high resolution imaging methods might be crucial for understanding of how the chromatin, a complex of DNA and proteins, is arranged in the eukaryotic cell nucleus. Such an approach utilizing switching of a fluorescent, DNA-binding dye Vybrant® DyeCycle™ Violet has been previously demonstrated by us (Żurek-Biesiada et al., 2015) [1]. Here we provide quantitative information on the influence of the chemical environment on the behavior of the dye, discuss the variability in the DNA-associated signal density, and demonstrate direct proof of enhanced structural resolution. Furthermore, we compare different visualization approaches. Finally, we describe various opportunities of multicolor DNA/SMLM imaging in eukaryotic cell nuclei.
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Affiliation(s)
- Dominika Żurek-Biesiada
- Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | | | - Kirti Prakash
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Gerrit Best
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Giriram K Mohana
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Hyun-Keun Lee
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Jurek W Dobrucki
- Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
| | - Udo Birk
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
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42
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Kuznetsova DS, Shirmanova MV, Dudenkova VV, Subochev PV, Turchin IV, Zagaynova EV, Lukyanov SA, Shakhov BE, Kamensky VA. Photobleaching and phototoxicity of KillerRed in tumor spheroids induced by continuous wave and pulsed laser illumination. JOURNAL OF BIOPHOTONICS 2015; 8:952-960. [PMID: 25648724 DOI: 10.1002/jbio.201400130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/18/2014] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
The purpose of this study was to evaluate photobleaching of the genetically encoded photosensitizer KillerRed in tumor spheroids upon pulsed and continuous wave (CW) laser irradiation and to analyze the mechanisms of cancer cell death after the treatment. We observed the light-dose dependent mechanism of KillerRed photobleaching over a wide range of fluence rates. Loss of fluorescence was limited to 80% at light doses of 150 J/cm(2) and more. Based on the bleaching curves, six PDT regimes were applied for irradiation using CW and pulsed regimes at a power density of 160 mW/cm(2) and light doses of 140 J/cm(2) , 170 J/cm(2) and 200 J/cm(2). Irradiation of KillerRed-expressing spheroids in the pulsed mode (pulse duration 15 ns, pulse repetition rate 10 Hz) induced predominantly apoptotic cell death, while in the case of CW mode the cancer cells underwent necrosis. In general, these results improve our understanding of photobleaching mechanisms in GFP-like proteins and show the importance of appropriate selection of treatment mode for PDT with KillerRed. Representative fluorescence image of two KillerRed-expressing spheroids before and immediately after CW irradiation.
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Affiliation(s)
- Daria S Kuznetsova
- Nizhny Novgorod State Medical Academy, 603005, Minin and Pozharsky Sq., 10/1, Nizhny Novgorod, Russia.
- Lobachevsky State University of Nizhny Novgorod, 603950, Gagarin Ave., 23, Nizhny Novgorod, Russia.
| | - Marina V Shirmanova
- Nizhny Novgorod State Medical Academy, 603005, Minin and Pozharsky Sq., 10/1, Nizhny Novgorod, Russia
- Lobachevsky State University of Nizhny Novgorod, 603950, Gagarin Ave., 23, Nizhny Novgorod, Russia
| | - Varvara V Dudenkova
- Nizhny Novgorod State Medical Academy, 603005, Minin and Pozharsky Sq., 10/1, Nizhny Novgorod, Russia
- Lobachevsky State University of Nizhny Novgorod, 603950, Gagarin Ave., 23, Nizhny Novgorod, Russia
| | - Pavel V Subochev
- Institute of Applied Physics RAS, 603950, Ulyanov St., 46, Nizhny Novgorod, Russia
| | - Ilya V Turchin
- Institute of Applied Physics RAS, 603950, Ulyanov St., 46, Nizhny Novgorod, Russia
| | - Elena V Zagaynova
- Nizhny Novgorod State Medical Academy, 603005, Minin and Pozharsky Sq., 10/1, Nizhny Novgorod, Russia
- Lobachevsky State University of Nizhny Novgorod, 603950, Gagarin Ave., 23, Nizhny Novgorod, Russia
| | - Sergey A Lukyanov
- Nizhny Novgorod State Medical Academy, 603005, Minin and Pozharsky Sq., 10/1, Nizhny Novgorod, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Miklukho-Maklaya St., 16/10, Moscow, Russia
- Pirogov Russian National Research Medical University, 117997, Ostrovitianova St. 1, Moscow, Russia
| | - Boris E Shakhov
- Nizhny Novgorod State Medical Academy, 603005, Minin and Pozharsky Sq., 10/1, Nizhny Novgorod, Russia
| | - Vladislav A Kamensky
- Institute of Applied Physics RAS, 603950, Ulyanov St., 46, Nizhny Novgorod, Russia
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43
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Ilovitsh T, Ilovitsh A, Weiss A, Meir R, Zalevsky Z. Three dimensional imaging of gold-nanoparticles tagged samples using phase retrieval with two focus planes. Sci Rep 2015; 5:15473. [PMID: 26498517 PMCID: PMC4620448 DOI: 10.1038/srep15473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/24/2015] [Indexed: 01/17/2023] Open
Abstract
Optical sectioning microscopy can provide highly detailed three dimensional (3D) images of biological samples. However, it requires acquisition of many images per volume, and is therefore time consuming, and may not be suitable for live cell 3D imaging. We propose the use of the modified Gerchberg-Saxton phase retrieval algorithm to enable full 3D imaging of gold-particle tagged samples using only two images. The reconstructed field is free space propagated to all other focus planes using post processing, and the 2D z-stack is merged to create a 3D image of the sample with high fidelity. Because we propose to apply the phase retrieving on nano particles, the regular ambiguities typical to the Gerchberg-Saxton algorithm, are eliminated. The proposed concept is presented and validated both on simulated data as well as experimentally.
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Affiliation(s)
- Tali Ilovitsh
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Asaf Ilovitsh
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Aryeh Weiss
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Rinat Meir
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Zeev Zalevsky
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
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Sustarsic M, Kapanidis AN. Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells. Curr Opin Struct Biol 2015; 34:52-9. [DOI: 10.1016/j.sbi.2015.07.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 07/02/2015] [Indexed: 12/29/2022]
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45
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Brutkowski W, Dziob D, Bernas T. Increasing microscopy resolution with photobleaching and intensity cumulant analysis. Microsc Res Tech 2015; 78:958-68. [PMID: 26278779 DOI: 10.1002/jemt.22559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/24/2015] [Accepted: 07/22/2015] [Indexed: 11/10/2022]
Abstract
Super-resolution fluorescence microscopy and its applications for analysis of biological structures are evolving rapidly field. A number of approaches aimed at overcoming the fundamental limit imposed by diffraction have been proposed in recent years. Here we present a modification of super-resolution optical fluctuation imaging (SOFI), a technique based on spatio-temporal evaluation of the optical signal from independently fluctuating emitters. Instead of rapid, reversible photoswitching, photobleaching is used to produce irreversible transitions between emitting and nonemitting states of the fluorochrome molecules. Simulated images are used to demonstrate that, in the absence of noise, the proposed SOFI modification increases the efficiency of transfer of high spatial frequencies in a fluorescence microscope. Correspondingly, a decrease of the point spread function (PSF) width is obtained. Moreover, the modified SOFI algorithm is capable of resolving point emitters in the presence of simulated noise. Using real biological images we demonstrate that an increase of resolution is obtained in 2D optical sections through densely packed chromatin in cell nuclei and lamin layer at the nuclear envelope. Finally, the approach is extended to 3D wide-field microscopy, allowing reduction of out-of-focus image blurring.
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Affiliation(s)
- Wojtek Brutkowski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Daniel Dziob
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Krakow, Poland
| | - Tytus Bernas
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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46
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Ilovitsh T, Danan Y, Meir R, Meiri A, Zalevsky Z. Cellular superresolved imaging of multiple markers using temporally flickering nanoparticles. Sci Rep 2015; 5:10965. [PMID: 26020693 PMCID: PMC4447069 DOI: 10.1038/srep10965] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/11/2015] [Indexed: 11/09/2022] Open
Abstract
In this paper we present a technique aimed for simultaneous detection of multiple types of gold nanoparticles (GNPs) within a biological sample, using lock-in detection. We image the sample using a number of modulated laser beams that correspond to the number of GNP species that label a given sample. The final image where the GNPs are spatially separated is obtained computationally. The proposed method enables the simultaneous superresolved imaging of different areas of interest within biological sample and also the spatial separation of GNPs at sub-diffraction distances, making it a useful tool in the study of intracellular trafficking pathways in living cells.
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Affiliation(s)
- Tali Ilovitsh
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Yossef Danan
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Rinat Meir
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Amihai Meiri
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Zeev Zalevsky
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
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47
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Ilovitsh T, Danan Y, Meir R, Meiri A, Zalevsky Z. Cellular imaging using temporally flickering nanoparticles. Sci Rep 2015; 5:8244. [PMID: 25650019 PMCID: PMC4316156 DOI: 10.1038/srep08244] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/18/2014] [Indexed: 11/11/2022] Open
Abstract
Utilizing the surface plasmon resonance effect in gold nanoparticles enables their use as contrast agents in a variety of applications for compound cellular imaging. However, most techniques suffer from poor signal to noise ratio (SNR) statistics due to high shot noise that is associated with low photon count in addition to high background noise. We demonstrate an effective way to improve the SNR, in particular when the inspected signal is indistinguishable in the given noisy environment. We excite the temporal flickering of the scattered light from gold nanoparticle that labels a biological sample. By preforming temporal spectral analysis of the received spatial image and by inspecting the proper spectral component corresponding to the modulation frequency, we separate the signal from the wide spread spectral noise (lock-in amplification).
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Affiliation(s)
- Tali Ilovitsh
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Yossef Danan
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Rinat Meir
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Amihai Meiri
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Zeev Zalevsky
- Faculty of Engineering, Bar Ilan University, Ramat-Gan 5290002, Israel
- The Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar Ilan University, Ramat-Gan 5290002, Israel
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48
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Lehner P, Staudinger C, Borisov SM, Regensburger J, Klimant I. Intrinsic Artefacts in Optical Oxygen Sensors-How Reliable are our Measurements? Chemistry 2015; 21:3978-86. [DOI: 10.1002/chem.201406037] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Indexed: 11/07/2022]
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49
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Wüstner D, Christensen T, Solanko LM, Sage D. Photobleaching kinetics and time-integrated emission of fluorescent probes in cellular membranes. Molecules 2014; 19:11096-130. [PMID: 25076144 PMCID: PMC6271172 DOI: 10.3390/molecules190811096] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/04/2014] [Accepted: 07/10/2014] [Indexed: 12/02/2022] Open
Abstract
Since the pioneering work of Hirschfeld, it is known that time-integrated emission (TiEm) of a fluorophore is independent of fluorescence quantum yield and illumination intensity. Practical implementation of this important result for determining exact probe distribution in living cells is often hampered by the presence of autofluorescence. Using kinetic modelling of photobleaching combined with pixel-wise bleach rate fitting of decay models with an updated plugin to the ImageJ program, it is shown that the TiEm of a fluorophore in living cells can be determined exactly from the product of bleaching amplitude and time constant. This applies to mono-exponential bleaching from the first excited singlet and/or triplet state and to multi-exponential combinations of such processes. The TiEm can be used to correct for illumination shading and background autofluorescence without the need for fluorescent test layers or separate imaging of non-stained cells. We apply the method to simulated images and to images of cells, whose membranes were labelled with fluorescent sterols and sphingolipids. Our bleaching model can be extended to include a probability density function (PDF) of intrinsic bleach rate constants with a memory kernel. This approach results in a time-dependent bleach rate coefficient and is exemplified for fluorescent sterols in restricted intracellular environments, like lipid droplets. We show that for small deviations from the classical exponential bleaching, the TiEm of decay functions with rate coefficients remains largely independent of fluorescence lifetime and illumination, and thereby represents a faithful measure of probe distribution.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Tanja Christensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Lukasz M Solanko
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Daniel Sage
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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50
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Szczurek AT, Prakash K, Lee HK, Żurek-Biesiada DJ, Best G, Hagmann M, Dobrucki JW, Cremer C, Birk U. Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes. Nucleus 2014; 5:331-40. [PMID: 25482122 PMCID: PMC4152347 DOI: 10.4161/nucl.29564] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 12/12/2022] Open
Abstract
Several approaches have been described to fluorescently label and image DNA and chromatin in situ on the single-molecule level. These superresolution microscopy techniques are based on detecting optically isolated, fluorescently tagged anti-histone antibodies, fluorescently labeled DNA precursor analogs, or fluorescent dyes bound to DNA. Presently they suffer from various drawbacks such as low labeling efficiency or interference with DNA structure. In this report, we demonstrate that DNA minor groove binding dyes, such as Hoechst 33258, Hoechst 33342, and DAPI, can be effectively employed in single molecule localization microscopy (SMLM) with high optical and structural resolution. Upon illumination with low intensity 405 nm light, a small subpopulation of these molecules stochastically undergoes photoconversion from the original blue-emitting form to a green-emitting form. Using a 491 nm laser excitation, fluorescence of these green-emitting, optically isolated molecules was registered until "bleached". This procedure facilitated substantially the optical isolation and localization of large numbers of individual dye molecules bound to DNA in situ, in nuclei of fixed mammalian cells, or in mitotic chromosomes, and enabled the reconstruction of high-quality DNA density maps. We anticipate that this approach will provide new insights into DNA replication, DNA repair, gene transcription, and other nuclear processes.
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Affiliation(s)
| | - Kirti Prakash
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
| | - Hyun-Keun Lee
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
| | | | - Gerrit Best
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Martin Hagmann
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Jurek W Dobrucki
- Faculty of Biochemistry, Biophysics, and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Christoph Cremer
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
| | - Udo Birk
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
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