51
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Tsai TY, Huang MT, Sung PS, Peng CY, Tao MH, Yang HI, Chang WC, Yang AS, Yu CM, Lin YP, Bau CY, Huang CJ, Pan MH, Wu CY, Hsiao CD, Yeh YH, Duan S, Paulson JC, Hsieh SL. SIGLEC-3 (CD33) serves as an immune checkpoint receptor for HBV infection. J Clin Invest 2021; 131:e141965. [PMID: 34060491 DOI: 10.1172/jci141965] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Chronic hepatitis B (CHB) infection is rarely eradicated by current antiviral nucleos(t)ide analogues. We found that α2,6-biantennary sialoglycans of HBV surface antigen (HBsAg) bound human SIGLEC-3 (CD33) by IP and ELISA, and the binding affinity between SIGLEC-3 and α2,6-biantennary sialoglycans was determined by biolayer interferometry (equilibrium dissociation constant [KD]: 1.95 × 10-10 ± 0.21 × 10-10 M). Moreover, HBV activated SIGLEC-3 on myeloid cells and induced immunosuppression by stimulating immunoreceptor tyrosine-based inhibitory motif phosphorylation and SHP-1/-2 recruitment via α2,6-biantennary sialoglycans on HBsAg. An antagonistic anti-SIGLEC-3 mAb reversed this effect and enhanced cytokine production in response to TLR-7 agonist GS-9620 in PBMCs from CHB patients. Moreover, anti-SIGLEC-3 mAb alone was able to upregulate the expression of molecules involved in antigen presentation, such as CD80, CD86, CD40, MHC-I, MHC-II, and PD-L1 in CD14+ cells. Furthermore, SIGLEC-3 SNP rs12459419 C, which expressed a higher amount of SIGLEC-3, was associated with increased risk of hepatocellular carcinoma (HCC) in CHB patients (HR: 1.256, 95% CI: 1.027-1.535, P = 0.0266). Thus, blockade of SIGLEC-3 is a promising strategy to reactivate host immunity to HBV and lower the incidence of HCC in the CHB patient population.
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Affiliation(s)
- Tsung-Yu Tsai
- PhD Program for Translational Medicine, China Medical University and Academia Sinica, Taichung, Taiwan.,Center for Digestive Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | | | - Pei-Shan Sung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yuan Peng
- Center for Digestive Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan.,School of Medicine, China Medical University, Taichung, Taiwan
| | - Mi-Hua Tao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Ping Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Yu Bau
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Jen Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Hung Pan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Hung Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shiteng Duan
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Shie-Liang Hsieh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute for Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan
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52
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Fisher RS, Jimenez RM, Soto E, Kalev D, Elbaum-Garfinkle S. An apparent core/shell architecture of polyQ aggregates in the aging Caenorhabditis elegans neuron. Protein Sci 2021; 30:1482-1486. [PMID: 33966305 DOI: 10.1002/pro.4105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 01/28/2023]
Abstract
Huntington's disease is caused by a polyglutamine (polyQ) expansion in the huntingtin protein which results in its abnormal aggregation in the nervous system. Huntingtin aggregates are linked to toxicity and neuronal dysfunction, but a comprehensive understanding of the aggregation mechanism in vivo remains elusive. Here, we examine the morphology of polyQ aggregates in Caenorhabditis elegans mechanosensory neurons as a function of age using confocal and fluorescence lifetime imaging microscopy. We find that aggregates in young worms are mostly spherical with homogenous intensity, but as the worm ages aggregates become substantially more heterogeneous. Most prominently, in older worms we observe an apparent core/shell morphology of polyQ assemblies with decreased intensity in the center. The fluorescence lifetime of polyQ is uniform across the aggregate indicating that the dimmed intensity in the assembly center is most likely not due to quenching or changes in local environment, but rather to displacement of fluorescent polyQ from the central region. This apparent core/shell architecture of polyQ aggregates in aging C. elegans neurons contributes to the diverse landscape of polyQ aggregation states implicated in Huntington's disease.
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Affiliation(s)
- Rachel S Fisher
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Rosa Meyo Jimenez
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Elizabeth Soto
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Darin Kalev
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA.,Ph.D. Programs in Biochemistry and Biology, The Graduate Center, CUNY, New York, New York, USA
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53
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High-speed compressed-sensing fluorescence lifetime imaging microscopy of live cells. Proc Natl Acad Sci U S A 2021; 118:2004176118. [PMID: 33431663 DOI: 10.1073/pnas.2004176118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We present high-resolution, high-speed fluorescence lifetime imaging microscopy (FLIM) of live cells based on a compressed sensing scheme. By leveraging the compressibility of biological scenes in a specific domain, we simultaneously record the time-lapse fluorescence decay upon pulsed laser excitation within a large field of view. The resultant system, referred to as compressed FLIM, can acquire a widefield fluorescence lifetime image within a single camera exposure, eliminating the motion artifact and minimizing the photobleaching and phototoxicity. The imaging speed, limited only by the readout speed of the camera, is up to 100 Hz. We demonstrated the utility of compressed FLIM in imaging various transient dynamics at the microscopic scale.
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54
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Jadavi S, Bianchini P, Cavalleri O, Dante S, Canale C, Diaspro A. Correlative nanoscopy: A multimodal approach to molecular resolution. Microsc Res Tech 2021; 84:2472-2482. [PMID: 33955625 PMCID: PMC8518117 DOI: 10.1002/jemt.23800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/11/2021] [Indexed: 11/24/2022]
Abstract
Atomic force microscopy (AFM) is a nano‐mechanical tool uniquely suited for biological studies at the molecular scale. AFM operation is based on mechanical interaction between the tip and the sample, a mechanism of contrast capable of measuring different information, including surface topography, mechanical, and electrical properties. However, the lack of specificity highlights the need to integrate AFM data with other techniques providing compositional hints. In particular, optical microscopes based on fluorescence as a mechanism of contrast can access the local distribution of specific molecular species. The coupling between AFM and super‐resolved fluorescence microscopy solves the resolution mismatch between AFM and conventional fluorescence optical microscopy. Recent advances showed that also the inherently label‐free imaging capabilities of the AFM are fundamental to complement the fluorescence images. In this review, we have presented a brief historical view on correlative microscopy, and, finally, we have summarized the progress of correlative AFM‐super‐resolution microscopy in biological research.
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Affiliation(s)
- Samira Jadavi
- DIFILAB, Department of Physics, University of Genova, Genova, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genova, Italy
| | - Paolo Bianchini
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Silvia Dante
- Materials Characterization Facility, Istituto Italiano di Tecnologia, Genova, Italy
| | - Claudio Canale
- DIFILAB, Department of Physics, University of Genova, Genova, Italy
| | - Alberto Diaspro
- DIFILAB, Department of Physics, University of Genova, Genova, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genova, Italy
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55
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Wang S, Li Y, Zhao Y, Lin F, Qu J, Liu L. Investigating tunneling nanotubes in ovarian cancer based on two-photon excitation FLIM-FRET. BIOMEDICAL OPTICS EXPRESS 2021; 12:1962-1973. [PMID: 33996210 PMCID: PMC8086450 DOI: 10.1364/boe.418778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 05/13/2023]
Abstract
Precise and efficient cell-to-cell communication is critical to the growth and differentiation of organisms, the formation of various organism, the maintenance of tissue function and the coordination of their various physiological activities, especially to the growth and invasion of cancer cells. Tunneling nanotubes (TNTs) were discovered as a new method of cell-to-cell communication in many cell lines. In this paper, we investigated TNTs-like structures in ovarian cancer cells and proved their elements by fluorescent staining, which showed that TNTs are comprised of natural lipid bilayers with microtubules as the skeleton that can transmit ions and organelles between adjacent cells. We then used fluorescence resonance energy transfer (FRET) based on two-photon excitation fluorescence lifetime imaging microscopy (FLIM) (TP-FLIM-FRET) to detect material transport in TNTs. The experimental results showed that the number of TNTs have an impact on the drug treatment of cancer cells, which provided a new perspective for TNTs involvement in cancer treatment. Our results also showed that TP-FLIM-FRET would potentially become a new optical method for TNTs study.
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56
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Su Z, Dhusia K, Wu Y. A multiscale study on the mechanisms of spatial organization in ligand-receptor interactions on cell surfaces. Comput Struct Biotechnol J 2021; 19:1620-1634. [PMID: 33868599 PMCID: PMC8026753 DOI: 10.1016/j.csbj.2021.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/21/2021] [Accepted: 03/21/2021] [Indexed: 01/11/2023] Open
Abstract
The binding of cell surface receptors with extracellular ligands triggers distinctive signaling pathways, leading into the corresponding phenotypic variation of cells. It has been found that in many systems, these ligand-receptor complexes can further oligomerize into higher-order structures. This ligand-induced oligomerization of receptors on cell surfaces plays an important role in regulating the functions of cell signaling. The underlying mechanism, however, is not well understood. One typical example is proteins that belong to the tumor necrosis factor receptor (TNFR) superfamily. Using a generic multiscale simulation platform that spans from atomic to subcellular levels, we compared the detailed physical process of ligand-receptor oligomerization for two specific members in the TNFR superfamily: the complex formed between ligand TNFα and receptor TNFR1 versus the complex formed between ligand TNFβ and receptor TNFR2. Interestingly, although these two systems share high similarity on the tertiary and quaternary structural levels, our results indicate that their oligomers are formed with very different dynamic properties and spatial patterns. We demonstrated that the changes of receptor’s conformational fluctuations due to the membrane confinements are closely related to such difference. Consistent to previous experiments, our simulations also showed that TNFR can preassemble into dimers prior to ligand binding, while the introduction of TNF ligands induced higher-order oligomerization due to a multivalent effect. This study, therefore, provides the molecular basis to TNFR oligomerization and reveals new insights to TNFR-mediated signal transduction. Moreover, our multiscale simulation framework serves as a prototype that paves the way to study higher-order assembly of cell surface receptors in many other bio-systems.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Kalyani Dhusia
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
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57
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Rivas S, Hanif K, Chakouri N, Ben-Johny M. Probing ion channel macromolecular interactions using fluorescence resonance energy transfer. Methods Enzymol 2021; 653:319-347. [PMID: 34099178 DOI: 10.1016/bs.mie.2021.01.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ion channels are macromolecular complexes whose functions are exquisitely tuned by interacting proteins. Fluorescence resonance energy transfer (FRET) is a powerful methodology that is adept at quantifying ion channel protein-protein interactions in living cells. For FRET experiments, the interacting partners are tagged with appropriate donor and acceptor fluorescent proteins. If the fluorescently-labeled molecules are in close proximity, then photoexcitation of the donor results in non-radiative energy transfer to the acceptor, and subsequent fluorescence emission of the acceptor. The stoichiometry of ion channel interactions and their relative binding affinities can be deduced by quantifying both the FRET efficiency and the total number of donors and acceptors in a given cell. In this chapter, we discuss general considerations for FRET analysis of biological interactions, various strategies for estimating FRET efficiencies, and detailed protocols for construction of binding curves and determination of stoichiometry. We focus on implementation of FRET assays using a flow cytometer given its amenability for high-throughput data acquisition, enhanced accessibility, and robust analysis. This versatile methodology permits mechanistic dissection of dynamic changes in ion channel interactions.
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Affiliation(s)
- Sharen Rivas
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | | | - Nourdine Chakouri
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States.
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58
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A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells. PLoS Comput Biol 2021; 17:e1008825. [PMID: 33684103 PMCID: PMC7971848 DOI: 10.1371/journal.pcbi.1008825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/18/2021] [Accepted: 02/21/2021] [Indexed: 11/19/2022] Open
Abstract
The activation and differentiation of T-cells are mainly directly by their co-regulatory receptors. T lymphocyte-associated protein-4 (CTLA-4) and programed cell death-1 (PD-1) are two of the most important co-regulatory receptors. Binding of PD-1 and CTLA-4 with their corresponding ligands programed cell death-ligand 1 (PD-L1) and B7 on the antigen presenting cells (APC) activates two central co-inhibitory signaling pathways to suppress T cell functions. Interestingly, recent experiments have identified a new cis-interaction between PD-L1 and B7, suggesting that a crosstalk exists between two co-inhibitory receptors and the two pairs of ligand-receptor complexes can undergo dynamic oligomerization. Inspired by these experimental evidences, we developed a coarse-grained model to characterize the assembling of an immune complex consisting of CLTA-4, B7, PD-L1 and PD-1. These four proteins and their interactions form a small network motif. The temporal dynamics and spatial pattern formation of this network was simulated by a diffusion-reaction algorithm. Our simulation method incorporates the membrane confinement of cell surface proteins and geometric arrangement of different binding interfaces between these proteins. A wide range of binding constants was tested for the interactions involved in the network. Interestingly, we show that the CTLA-4/B7 ligand-receptor complexes can first form linear oligomers, while these oligomers further align together into two-dimensional clusters. Similar phenomenon has also been observed in other systems of cell surface proteins. Our test results further indicate that both co-inhibitory signaling pathways activated by B7 and PD-L1 can be down-regulated by the new cis-interaction between these two ligands, consistent with previous experimental evidences. Finally, the simulations also suggest that the dynamic and the spatial properties of the immune complex assembly are highly determined by the energetics of molecular interactions in the network. Our study, therefore, brings new insights to the co-regulatory mechanisms of T cell activation. The activation of a T cell can be regulated by the receptors on its surface, such as CTLA-4 and PD-1. People used to think that these two receptors inhibit T cell activation through distinct pathways. However, recent experiments discovered that the ligands of these two receptors, B7 and PD-L1, can interact with each other on the same surface of antigen presenting cells. Here we utilized computational simulations to investigate functional roles of this newly discovered interaction in T cell coregulation. The specific environment of interface between T cell and antigen presenting cell has been taken into account of our model. Ligand and receptors randomly diffuse within this interface area. They further involve in different types of interactions, with each other from the same side or the opposite side of cell surface. Using this method, we found ligands and receptors can not only form complexes, but also aggregate into large-scale clusters. We also demonstrated that the engagement between B7 and PD-L1 can reduce the interactions with their corresponding receptors. This study, therefore, offers new insights to our understanding of signal regulation in T cells.
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59
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Michalet X. Continuous and discrete phasor analysis of binned or time-gated periodic decays. AIP ADVANCES 2021; 11:035331. [PMID: 33786208 PMCID: PMC7990508 DOI: 10.1063/5.0027834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/22/2021] [Indexed: 05/29/2023]
Abstract
The time-resolved analysis of periodically excited luminescence decays by the phasor method in the presence of time-gating or binning is revisited. Analytical expressions for discrete configurations of square gates are derived, and the locus of the phasors of such modified periodic single-exponential decays is compared to the canonical universal semicircle. The effects of instrument response function offset, decay truncation, and gate shape are also discussed. Finally, modified expressions for the phase and modulus lifetimes are provided for some simple cases. A discussion of a modified phasor calibration approach is presented, and an illustration of the new concepts with examples from the literature concludes this work.
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Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, 607 Charles E. Young Drive E., Los Angeles, California 90095, USA
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60
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Enhancmentation of Photo-Thermal Lens of Fluorescence Molecules by Fluorescence Resonance Energy Transfer Mechanism. J Fluoresc 2021; 31:587-593. [PMID: 33484368 DOI: 10.1007/s10895-020-02676-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
The photo-thermal lens technique is based on the measurement of the gradient temperature that is produced in an illuminated sample by laser beam as a result of non-radiative relaxation. The sensitivity of photo-thermal lens is higher than conventional absorption techniques, due to the direct measurement of absorbed energy. However, the main drawback of the photo-thermal lens technique is the inability to measure molecules that release their excess energy of absorption in the form of radiation relaxation. In fluorescence molecules, because their excess energy is released by radiation, the photo-thermal lens is insignificant. In this research, we aim to increase the photo-thermal lens sensitivity of the fluorescence molecules by selecting the appropriate acceptor for the fluorescence molecules as the donor. We investigated the effect of the presence of AuNPs on the photo-thermal lens of di-triazene (DTA) as fluorescence molecules. We observed that AuNPs enhanced the photo-thermal lens of DTA. The quantum yield of DTA was calculated to be 90.45%. The energy transfer from DTA to AuNPs occurs by fluorescence resonance energy transfer (FRET) mechanism. The FRET efficiency was 83.43%. In the presence of AuNPs, the photo-thermal lens of the DTA was amplified by four times more. The calibration curve of DTA is linear in the range of 0.1 to 110 ng/mL. The limited of detection (LOD) value of 0.08 ng/mL is calculated.
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61
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Lone MS, Bhat PA, Afzal S, Chat OA, Dar AA. Energy transduction through FRET in self-assembled soft nanostructures based on surfactants/polymers: current scenario and prospects. SOFT MATTER 2021; 17:425-446. [PMID: 33400748 DOI: 10.1039/d0sm01625j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The self-assembled systems of surfactants/polymers, which are capable of supporting energy funneling between fluorophores, have recently gained significant attraction. Surfactant and polymeric micelles form nanoscale structures spanning a radius of 2-10 nm are generally suitable for the transduction of energy among fluorophores. These systems have shown great potential in Förster resonance energy transfer (FRET) due to their unique characteristics of being aqueous based, tendency to remain self-assembled, spontaneous formation, tunable nature, and responsiveness to different external stimuli. This review presents current developments in the field of energy transfer, particularly the multi-step FRET processes in the self-assembled nanostructures of surfactants/polymers. The part one of this review presents a background and brief overview of soft systems and discusses certain aspects of the self-assemblies of surfactants/polymers and their co-solubilization property to bring fluorophores to close proximity to transduce energy. The second part of this review deals with single-step and multi-step FRET in the self-assemblies of surfactants/polymers and links FRET systems with advanced smart technologies including multicolor formation, data encryption, and artificial antenna systems. This review also discusses the diverse examples in the literature to present the emerging applications of FRET. Finally, the prospects regarding further improvement of FRET in self-assembled soft systems are outlined.
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Affiliation(s)
- Mohd Sajid Lone
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
| | - Parvaiz Ahmad Bhat
- Department of Chemistry, Government Degree College, Pulwama-192301, J&K, India.
| | - Saima Afzal
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
| | - Oyais Ahmad Chat
- Department of Chemistry, Government Degree College, Pulwama-192301, J&K, India.
| | - Aijaz Ahmad Dar
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
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62
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Alspaugh G, Roarke B, Chand A, Penjweini R, Andreoni A, Knutson JR. Developing Analysis Protocols for Monitoring Intracellular Oxygenation Using Fluorescence Lifetime Imaging of Myoglobin-mCherry. Methods Mol Biol 2021; 2304:315-337. [PMID: 34028725 PMCID: PMC8813554 DOI: 10.1007/978-1-0716-1402-0_17] [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] [Indexed: 06/12/2023]
Abstract
Oxygen (O2) is a critical metabolite for cellular function as it fuels aerobic cellular metabolism; further, it is a known regulator of gene expression. Monitoring oxygenation within cells and organelles can provide valuable insights into how O2, or lack thereof, both influences and responds to cell processes. In recent years, fluorescence lifetime imaging microscopy (FLIM) has been used to track several probe concentration independent intracellular phenomena, such as pH, viscosity, and, in conjunction with Förster resonance energy transfer (FRET), protein-protein interactions. Here, we describe methods for synthesizing and expressing the novel FLIM-FRET intracellular O2 probe Myoglobin-mCherry (Myo-mCherry) in cultured cell lines, as well as acquiring FLIM images using a laser scanning confocal microscope configured for two-photon excitation and a time-correlated single photon counting (TCSPC) module. Finally, we provide step-by-step protocols for FLIM analysis of Myo-mCherry using the commercial software SPCImage and conversion of fluorescence lifetime values in each pixel to apparent intracellular oxygen partial pressures (pO2).
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Affiliation(s)
- Greg Alspaugh
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Branden Roarke
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexandra Chand
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alessio Andreoni
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jay R Knutson
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA.
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63
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Ophiopogonin D Increases SERCA2a Interaction with Phospholamban by Promoting CYP2J3 Upregulation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8857906. [PMID: 33488937 PMCID: PMC7790559 DOI: 10.1155/2020/8857906] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/12/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022]
Abstract
Ophiopogonin D (OPD), a compound from the Chinese herb Radix Ophiopogonis, reportedly induces increased levels of cytochrome P450 2J3 (CYP2J3)/epoxyeicosatrienoic acids (EETs) and Ca2+ in rat cardiomyocytes. Little is known regarding the specific mechanism between CYP2J3 and Ca2+ homeostasis. Here, we investigated whether CYP2J3 is involved in the protective action of OPD on the myocardium by activating the Ca2+ homeostasis-related protein complex (SERCA2a and PLB) in H9c2 rat cardiomyoblast cells. The interaction between SERCA2a and PLB was measured using fluorescence resonance energy transfer. OPD attenuated heart failure and catalyzed the active transport of Ca2+ into the sarcoplasmic reticulum by inducing the phosphorylation of PLB and promoting the SERCA2a activity. These beneficial effects of OPD on heart failure were abolished after knockdown of CYP2J3 in a model of heart failure. Together, our results identify CYP2J3 as a critical intracellular target for OPD and unravel a mechanism of CYP2J3-dependent regulation of intracellular Ca2+.
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64
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Bagheri Y, Ali AA, You M. Current Methods for Detecting Cell Membrane Transient Interactions. Front Chem 2020; 8:603259. [PMID: 33365301 PMCID: PMC7750205 DOI: 10.3389/fchem.2020.603259] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Short-lived cell membrane complexes play a key role in regulating cell signaling and communication. Many of these complexes are formed based on low-affinity and transient interactions among various lipids and proteins. New techniques have emerged to study these previously overlooked membrane transient interactions. Exciting functions of these transient interactions have been discovered in cellular events such as immune signaling, host-pathogen interactions, and diseases such as cancer. In this review, we have summarized current experimental methods that allow us to detect and analyze short-lived cell membrane protein-protein, lipid-protein, and lipid-lipid interactions. These methods can provide useful information about the strengths, kinetics, and/or spatial patterns of membrane transient interactions. However, each method also has its own limitations. We hope this review can be used as a guideline to help the audience to choose proper approaches for studying membrane transient interactions in different membrane trafficking and cell signaling events.
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Affiliation(s)
| | | | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
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65
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Abstract
This protocol highlights the use of FRET-based biosensors to investigate signaling events during microglia activation in real time. Understanding microglia activation has gained momentum as it can help decipher signaling mechanisms underlying the neurodegenerative process occurring in neurological disorders. Unlike more traditional methods widely employed in the microglia field, FRET allows microglia signaling events to be studied in real time with exquisite subcellular resolution. However, FRET-based live-cell imaging requires application-specific biosensors and specialized imaging systems, limiting its use in in vivo studies. For complete details on the use and execution of this protocol, please refer to Socodato et al. (2020), Portugal et al. (2017), and Socodato et al. (2018).
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66
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Bednarkiewicz A, Chan EM, Prorok K. Enhancing FRET biosensing beyond 10 nm with photon avalanche nanoparticles. NANOSCALE ADVANCES 2020; 2:4863-4872. [PMID: 36132913 PMCID: PMC9417941 DOI: 10.1039/d0na00404a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/12/2020] [Indexed: 05/24/2023]
Abstract
Förster Resonance Energy Transfer (FRET) between donor (D) and acceptor (A) molecules is a phenomenon commonly exploited to study or visualize biological interactions at the molecular level. However, commonly used organic D and A molecules often suffer from photobleaching and spectral bleed-through, and their spectral properties hinder quantitative analysis. Lanthanide-doped upconverting nanoparticles (UCNPs) as alternative D species offer significant improvements in terms of photostability, spectral purity and background-free luminescence detection, but they bring new challenges related to multiple donor ions existing in a single large size UCNP and the need for nanoparticle biofunctionalization. Considering the relatively short Förster distance (typically below 5-7 nm), it becomes a non-trivial task to assure sufficiently strong D-A interaction, which translates directly to the sensitivity of such bio-sensors. In this work we propose a solution to these issues, which employs the photon avalanche (PA) phenomenon in lanthanide-doped materials. Using theoretical modelling, we predict that these PA systems would be highly susceptible to the presence of A and that the estimated sensitivity range extends to distances 2 to 4 times longer (i.e. 10-25 nm) than those typically found in conventional FRET systems. This promises high sensitivity, low background and spectral or temporal biosensing, and provides the basis for a radically novel approach to combine luminescence imaging and self-normalized bio-molecular interaction sensing.
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Affiliation(s)
- Artur Bednarkiewicz
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences Okolna 2 50-422 Wroclaw Poland
| | - Emory M Chan
- The Molecular Foundry, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Katarzyna Prorok
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences Okolna 2 50-422 Wroclaw Poland
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67
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Huang W, Tan M, Wang Y, Liu L, Pan Y, Li J, Ouyang M, Long C, Qu X, Liu H, Liu C, Wang J, Deng L, Xiang Y, Qin X. Increased intracellular Cl - concentration improves airway epithelial migration by activating the RhoA/ROCK Pathway. Theranostics 2020; 10:8528-8540. [PMID: 32754261 PMCID: PMC7392015 DOI: 10.7150/thno.46002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022] Open
Abstract
In the airway, Cl- is the most abundant anion and is critically involved in transepithelial transport. The correlation of the abnormal expression and activation of chloride channels (CLCs), such as cystic fibrosis transmembrane conductance regulators (CFTRs), anoctamin-1, and CLC-2, with cell migration capability suggests a relationship between defective Cl- transport and epithelial wound repair. However, whether a correlation exists between intracellular Cl- and airway wound repair capability has not been explored thus far, and the underlying mechanisms involved in this relationship are not fully defined. Methods: In this work, the alteration of intracellular chloride concentration ([Cl-]i) was measured by using a chloride-sensitive fluorescent probe (N-[ethoxycarbonylmethyl]-6-methoxyquinolium bromide). Results: We found that clamping with high [Cl-]i and 1 h of treatment with the CLC inhibitor CFTR blocker CFTRinh-172 and chloride intracellular channel inhibitor IAA94 increased intracellular Cl- concentration ([Cl-]i) in airway epithelial cells. This effect improved epithelial cell migration. In addition, increased [Cl-]i in cells promoted F-actin reorganization, decreased cell stiffness, and improved RhoA activation and LIMK1/2 phosphorylation. Treatment with the ROCK inhibitor of Y-27632 and ROCK1 siRNA significantly attenuated the effects of increased [Cl-]i on LIMK1/2 activation and cell migration. In addition, intracellular Ca2+ concentration was unaffected by [Cl-]i clamping buffers and CFTRinh-172 and IAA94. Conclusion: Taken together, these results suggested that Cl- accumulation in airway epithelial cells could activate the RhoA/ROCK/LIMK cascade to induce F-actin reorganization, down-regulate cell stiffness, and improve epithelial migration.
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Affiliation(s)
- Wenjie Huang
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
- Affiliated Liutie Central Hospital of Guangxi medical university, Liuzhou, Guangxi 545007, China
| | - Meiling Tan
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Yue Wang
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou, Jiangsu 213164, China
- School of Nursing, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Lei Liu
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou, Jiangsu 213164, China
| | - Yan Pan
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou, Jiangsu 213164, China
| | - Jingjing Li
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou, Jiangsu 213164, China
| | - Mingxing Ouyang
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou, Jiangsu 213164, China
| | - Chunjiao Long
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Xiangping Qu
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Huijun Liu
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Chi Liu
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Jia Wang
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Linhong Deng
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou, Jiangsu 213164, China
| | - Yang Xiang
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Xiaoqun Qin
- School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
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68
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Ghosh A, Enderlein J, Butkevich E. Dimerization of Human Drebrin-like Protein Governs Its Biological Activity. Biochemistry 2020; 59:1553-1558. [PMID: 32282191 DOI: 10.1021/acs.biochem.9b01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drebrin-like protein (DBNL) is a multidomain F-actin-binding protein, which also interacts with other molecules within different intracellular pathways. Here, we present quantitative measurements on the size and conformation of human DBNL. Using dual-focus fluorescence correlation spectroscopy, we determined the hydrodynamic radius of the DBNL monomer. Native gel electrophoresis and dual-color fluorescence cross-correlation spectroscopy show that both endogenous DBNL and recombinant DBNL exist as dimers under physiological conditions. We demonstrate that C-terminal truncations of DBNL downstream of the coiled-coil domain result in its oligomerization at nanomolar concentrations. In contrast, the ADF-H domain alone is a monomer, which displays a concentration-dependent self-assembly. In vivo FLIM-FRET imaging shows that the presence of only actin-binding domains is not sufficient for DBNL to localize properly at the actin filament inside the cell. In summary, our work provides detailed insight into the structure-function relationship of human drebrin-like protein.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Eugenia Butkevich
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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69
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Levitt JA, Poland SP, Krstajic N, Pfisterer K, Erdogan A, Barber PR, Parsons M, Henderson RK, Ameer-Beg SM. Quantitative real-time imaging of intracellular FRET biosensor dynamics using rapid multi-beam confocal FLIM. Sci Rep 2020; 10:5146. [PMID: 32198437 PMCID: PMC7083966 DOI: 10.1038/s41598-020-61478-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/14/2020] [Indexed: 01/21/2023] Open
Abstract
Fluorescence lifetime imaging (FLIM) is a quantitative, intensity-independent microscopical method for measurement of diverse biochemical and physical properties in cell biology. It is a highly effective method for measurements of Förster resonance energy transfer (FRET), and for quantification of protein-protein interactions in cells. Time-domain FLIM-FRET measurements of these dynamic interactions are particularly challenging, since the technique requires excellent photon statistics to derive experimental parameters from the complex decay kinetics often observed from fluorophores in living cells. Here we present a new time-domain multi-confocal FLIM instrument with an array of 64 visible beamlets to achieve parallelised excitation and detection with average excitation powers of ~ 1–2 μW per beamlet. We exemplify this instrument with up to 0.5 frames per second time-lapse FLIM measurements of cAMP levels using an Epac-based fluorescent biosensor in live HeLa cells with nanometer spatial and picosecond temporal resolution. We demonstrate the use of time-dependent phasor plots to determine parameterisation for multi-exponential decay fitting to monitor the fractional contribution of the activated conformation of the biosensor. Our parallelised confocal approach avoids having to compromise on speed, noise, accuracy in lifetime measurements and provides powerful means to quantify biochemical dynamics in living cells.
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Affiliation(s)
- James A Levitt
- Microscopy Innovation Centre, Guy's Campus, Kings College, London, SE1 1UL, UK.,Richard Dimbleby Laboratories, School of Cancer and Pharmaceutical Sciences, Guy's Campus, Kings College London, London, SE1 1UL, UK
| | - Simon P Poland
- Richard Dimbleby Laboratories, School of Cancer and Pharmaceutical Sciences, Guy's Campus, Kings College London, London, SE1 1UL, UK
| | - Nikola Krstajic
- Institute for Microelectronics and Nanosystems, School of Engineering, College of Science and Engineering, University of Edinburgh, Edinburgh, EH9 3FB, UK
| | - Karin Pfisterer
- Randall Centre for Cell and Molecular Biophysics, Guy's Campus, Kings College, London, SE1 1UL, UK
| | - Ahmet Erdogan
- Institute for Microelectronics and Nanosystems, School of Engineering, College of Science and Engineering, University of Edinburgh, Edinburgh, EH9 3FB, UK
| | - Paul R Barber
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, Guy's Campus, Kings College, London, SE1 1UL, UK
| | - Robert K Henderson
- Institute for Microelectronics and Nanosystems, School of Engineering, College of Science and Engineering, University of Edinburgh, Edinburgh, EH9 3FB, UK
| | - Simon M Ameer-Beg
- Richard Dimbleby Laboratories, School of Cancer and Pharmaceutical Sciences, Guy's Campus, Kings College London, London, SE1 1UL, UK.
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70
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Maares M, Haase H. A Guide to Human Zinc Absorption: General Overview and Recent Advances of In Vitro Intestinal Models. Nutrients 2020; 12:E762. [PMID: 32183116 PMCID: PMC7146416 DOI: 10.3390/nu12030762] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/23/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022] Open
Abstract
Zinc absorption in the small intestine is one of the main mechanisms regulating the systemic homeostasis of this essential trace element. This review summarizes the key aspects of human zinc homeostasis and distribution. In particular, current knowledge on human intestinal zinc absorption and the influence of diet-derived factors on bioaccessibility and bioavailability as well as intrinsic luminal and basolateral factors with an impact on zinc uptake are discussed. Their investigation is increasingly performed using in vitro cellular intestinal models, which are continually being refined and keep gaining importance for studying zinc uptake and transport via the human intestinal epithelium. The vast majority of these models is based on the human intestinal cell line Caco-2 in combination with other relevant components of the intestinal epithelium, such as mucin-secreting goblet cells and in vitro digestion models, and applying improved compositions of apical and basolateral media to mimic the in vivo situation as closely as possible. Particular emphasis is placed on summarizing previous applications as well as key results of these models, comparing their results to data obtained in humans, and discussing their advantages and limitations.
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Affiliation(s)
- Maria Maares
- Technische Universität Berlin, Chair of Food Chemistry and Toxicology, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Hajo Haase
- Technische Universität Berlin, Chair of Food Chemistry and Toxicology, Straße des 17. Juni 135, 10623 Berlin, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany
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71
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Argyrousi EK, Heckman PRA, Prickaerts J. Role of cyclic nucleotides and their downstream signaling cascades in memory function: Being at the right time at the right spot. Neurosci Biobehav Rev 2020; 113:12-38. [PMID: 32044374 DOI: 10.1016/j.neubiorev.2020.02.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 01/23/2023]
Abstract
A plethora of studies indicate the important role of cAMP and cGMP cascades in neuronal plasticity and memory function. As a result, altered cyclic nucleotide signaling has been implicated in the pathophysiology of mnemonic dysfunction encountered in several diseases. In the present review we provide a wide overview of studies regarding the involvement of cyclic nucleotides, as well as their upstream and downstream molecules, in physiological and pathological mnemonic processes. Next, we discuss the regulation of the intracellular concentration of cyclic nucleotides via phosphodiesterases, the enzymes that degrade cAMP and/or cGMP, and via A-kinase-anchoring proteins that refine signal compartmentalization of cAMP signaling. We also provide an overview of the available data pointing to the existence of specific time windows in cyclic nucleotide signaling during neuroplasticity and memory formation and the significance to target these specific time phases for improving memory formation. Finally, we highlight the importance of emerging imaging tools like Förster resonance energy transfer imaging and optogenetics in detecting, measuring and manipulating the action of cyclic nucleotide signaling cascades.
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Affiliation(s)
- Elentina K Argyrousi
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, 6200 MD, the Netherlands
| | - Pim R A Heckman
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, 6200 MD, the Netherlands
| | - Jos Prickaerts
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, 6200 MD, the Netherlands.
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72
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Cao R, Wallrabe H, Siller K, Periasamy A. Optimization of FLIM imaging, fitting and analysis for auto-fluorescent NAD(P)H and FAD in cells and tissues. Methods Appl Fluoresc 2020; 8:024001. [PMID: 31972557 DOI: 10.1088/2050-6120/ab6f25] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Increasingly, the auto-fluorescent coenzymes NAD(P)H and FAD are being tracked by multi-photon fluorescence lifetime microscopy (FLIM) and used as versatile markers for changes in mammalian metabolism. The cellular redox state of different cell model systems, organoids and tissue sections is investigated in a range of pathologies where the metabolism is disrupted or reprogrammed; the latter is particularly relevant in cancer biology. Yet, the actual optimized process of acquiring images by FLIM, execute a correct lifetime fitting procedure and subsequent processing and analysis can be challenging for new users. Questions remain of how to optimize FLIM experiments, whether any potential photo-bleaching affects FLIM results and whether fixed specimens can be used in experiments. We have broken down the multi-step sequence into best-practice application of FLIM for NAD(P)H and FAD imaging, with images generated by a time-correlated-single-photon-counting (TCSPC) system, fitted with Becker & Hickl software and further processed with open-source ImageJ/Fiji and Python software.
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Affiliation(s)
- Ruofan Cao
- The W.M. Keck Center for Cellular Imaging, University of Virginia, Charlottesville, VA, United States of America
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73
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Rout J, Swain BC, Biswas S, Das AK, Tripathy U. A simulation study on the influence of energy migration and relative interaction strengths of homo- and hetero-FRET on the net FRET efficiency. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117599. [PMID: 31751800 DOI: 10.1016/j.saa.2019.117599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful method for probing biomolecular conformations and dynamics in bulk as well as at a single-molecule level. FRET utilizes non-radiative mechanisms to transfer energy between fluorophores, donor and acceptor when placed in close proximity. The FRET efficiency has a strong distance dependence and serves as a direct read-out for molecular interaction. In case of a significant overlap of donor emission and absorption spectra, the excited state energy can be exchanged between the identical donors in close proximity, which eventually migrates back and forth until it gets dissipated. This form of energy transfer is called energy migration or homo-FRET. Here, we have simulated FRET efficiency by considering the donor-donor interaction strength (ξDD) and donor-acceptor interaction strength (ξDA) under conditions of non-uniform distribution of molecules. Our earlier studies indicate that energy migration modulate the FRET efficiency for various values of ξDD and ξDA. We, therefore, determined the limiting values of acceptor concentration (CLA) that will allow the determination of FRET efficiency in the absence and presence of energy migration. Taken together, our study optimizes the conditions for meaningful FRET efficiency for a given FRET pair for better reporting of molecular interactions.
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Affiliation(s)
- Janmejaya Rout
- Department of Applied Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India
| | - Bikash Chandra Swain
- Department of Applied Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India
| | - Shrutidhara Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781029, India
| | - Anand Kant Das
- Department of Applied Physics, Vienna University of Technology, Getreidemarkt-9, Vienna, 1060, Austria
| | - Umakanta Tripathy
- Department of Applied Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India.
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74
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Zou W, Le K, Zastrow ML. Live‐Cell Copper‐Induced Fluorescence Quenching of the Flavin‐Binding Fluorescent Protein CreiLOV. Chembiochem 2020; 21:1356-1363. [DOI: 10.1002/cbic.201900669] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Wenping Zou
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
| | - Khoa Le
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
| | - Melissa L. Zastrow
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
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75
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Eltyshev AK, Minin AS, Smoliuk LT, Benassi E, Belskaya NP. 2-Aryl-2,4-dihydro-5H-[1,2,3]triazolo[4,5-d]pyrimidin-5-ones as a New Platform for the Design and Synthesis of Biosensors and Chemosensors. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Artem S. Minin
- Ural Federal University; 19 Mira Str. 620002 Yekaterinburg Russia
- M. N. Mikheev Institute of Metal Physics; Ural Branch of Russian Academy of Science; 18 S. Kovalevskaya Str. 620108 Yekaterinburg Russia
| | - Leonid T. Smoliuk
- Institute of Immunology and Physiology; Ural Branch of Russian Academy of Science; 20 S. Kovalevskaya Str. 620049 Yekaterinburg Russia
| | - Enrico Benassi
- Lanzhou Institute of Chemical Physics; Chinese Academy of Science; 18 Tianshui Middle Rd 73000020 Lanzhou Shi Gansu Sheng P.R. China
- Department of Chemistry; Hexi University; 734000 Zhangye P. R. China
| | - Nataliya P. Belskaya
- Ural Federal University; 19 Mira Str. 620002 Yekaterinburg Russia
- I. Ya. Postovsky Institute of Organic Synthesis; Ural Branch of Russian Academy of Science; 20 S. Kovalevskaya Str. 620219 Yekaterinburg Russia
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76
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Cao R, Wallrabe H, Periasamy A. Multiphoton FLIM imaging of NAD(P)H and FAD with one excitation wavelength. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-16. [PMID: 31920048 PMCID: PMC6951488 DOI: 10.1117/1.jbo.25.1.014510] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/12/2019] [Indexed: 05/07/2023]
Abstract
Two-photon fluorescence lifetime imaging microscopy (FLIM) is widely used to capture autofluorescence signals from cellular components to investigate dynamic physiological changes in live cells and tissues. Among these intrinsic fluorophores, nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD)-essential coenzymes in cellular respiration-have been used as intrinsic fluorescent biomarkers for metabolic states in cancer and other pathologies. Traditional FLIM imaging for NAD(P)H, FAD, and in particular fluorescence lifetime redox ratio (FLIRR) requires a sequential multiwavelength excitation to avoid spectral bleed-through (SBT). This sequential imaging complicates image acquisition, may introduce motion artifacts, and reduce temporal resolution. Testing several two-photon excitation wavelengths in combination with optimized emission filters, we have proved a FLIM imaging protocol, allowing simultaneous image acquisition with a single 800-nm wavelength excitation for NADH and FAD with negligible SBT. As a first step, standard NADH and FAD single and mixed solutions were tested that mimic biological sample conditions. After these optimization steps, the assay was applied to two prostate cancer live cell lines: African-American (AA) and Caucasian-American (LNCaP), used in our previous publications. FLIRR result shows that, in cells, the 800-nm two-photon excitation wavelength is suitable for NADH and FAD FLIM imaging with negligible SBT. While NAD(P)H signals are decreased, sufficient photons are present for accurate lifetime fitting and FAD signals are measurably increased at lower laser power, compared with the common 890-nm excitation conditions. This single wavelength excitation allows a simplification of NADH and FAD FLIM imaging data analysis, decreasing the total imaging time. It also avoids motion artifacts and increases temporal resolution. This simplified assay will also make it more suitable to be applied in a clinical setting.
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Affiliation(s)
- Ruofan Cao
- University of Virginia, WM Keck Center for Cellular Imaging, Department of Biology, Charlottesville, Virginia, United States
| | - Horst Wallrabe
- University of Virginia, WM Keck Center for Cellular Imaging, Department of Biology, Charlottesville, Virginia, United States
| | - Ammasi Periasamy
- University of Virginia, WM Keck Center for Cellular Imaging, Department of Biology, Charlottesville, Virginia, United States
- University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States
- Address all correspondence to Ammasi Periasamy, E-mail:
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77
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Petazzi RA, Aji AK, Chiantia S. Fluorescence microscopy methods for the study of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:1-41. [DOI: 10.1016/bs.pmbts.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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78
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Farazi S, Chen F, Foster H, Boquiren R, McAlpine SR, Chapman R. Real time monitoring of peptide delivery in vitro using high payload pH responsive nanogels. Polym Chem 2020. [DOI: 10.1039/c9py01120j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A pH responsive pMAA nanogel that demonstrates high loading capacity and rapid intracellular delivery of hydrophilic peptides.
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Affiliation(s)
- Shegufta Farazi
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
| | - Fan Chen
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
| | - Henry Foster
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
| | | | | | - Robert Chapman
- School of Chemistry
- UNSW Sydney
- Australia
- Centre for Advanced Macromolecular Design (CAMD)
- UNSW Sydney
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79
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Godet J, Mély Y. Exploring protein-protein interactions with large differences in protein expression levels using FLIM-FRET. Methods Appl Fluoresc 2019; 8:014007. [PMID: 31791032 DOI: 10.1088/2050-6120/ab5dd2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Many molecular processes within a cell are carried out by molecular machines built from a large number of proteins organized by their protein-protein interactions (PPIs). Exploring PPIs in their cellular context is critical to better understand the proteins functions. Förster resonance energy transfer measured by fluorescence lifetime imaging (FLIM-FRET) enables to monitor PPIs and to map their spatial organization in a living cell with high spatial and temporal specificity. But both the accurate measurement and the interpretation of multi-exponential FLIM-FRET data associated to mixtures of interacting and non-interacting proteins are difficult. Here we show that a simple diagram plot can find interesting visualization properties by clustering pixels with similar decay signatures. FLIM diagram plot can be used to provide valuable information about stoichiometry and binding mode in PPIs, even in the presence of large differences in protein expression levels of the different interacting partners. The proposed FLIM diagram plot is a useful visual approach for a more straightforward interpretation of complex lifetime data. This approach was applied for revealing critical features of PPIs in live Pseudomonas aeruginosa.
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Affiliation(s)
- Julien Godet
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, Illkirch, France. Groupe Méthode Recherche Clinique, Pôle de Santé Publique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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80
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Dumas JP, Jiang JY, Gates EM, Hoffman BD, Pierce MC, Boustany NN. FRET efficiency measurement in a molecular tension probe with a low-cost frequency-domain fluorescence lifetime imaging microscope. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-11. [PMID: 31884745 PMCID: PMC6935677 DOI: 10.1117/1.jbo.24.12.126501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
We demonstrate the possibility of measuring FRET efficiency with a low-cost frequency-domain fluorescence lifetime imaging microscope (FD-FLIM). The system utilizes single-frequency-modulated excitation, which enables the use of cost-effective laser sources and electronics, simplification of data acquisition and analysis, and a dual-channel detection capability. Following calibration with coumarin 6, we measured the apparent donor lifetime in mTFP1-mVenus FRET standards expressed in living cells. We evaluated the system's sensitivity by differentiating the short and long lifetimes of mTFP1 corresponding to the known standards' high and low FRET efficiency, respectively. Furthermore, we show that the lifetime of the vinculin tension sensor, VinTS, at focal adhesions (2.30 ± 0.16 ns) is significantly (p < 10 - 6) longer than the lifetime of the unloaded TSMod probe (2.02 ± 0.16 ns). The pixel dwell time was 6.8 μs for samples expressing the FRET standards, with signal typically an order of magnitude higher than VinTS. The apparent FRET efficiency (<inline-formula>EFRETapp</inline-formula>) of the standards, calculated from the measured apparent lifetime, was linearly related to their known FRET efficiency by a factor of 0.92 to 0.99 (R2 = 0.98). This relationship serves as a calibration curve to convert apparent FRET to true FRET and circumvent the need to measure multiexponential lifetime decays. This approach yielded a FRET efficiency of 18% to 19.5%, for VinTS, in agreement with published values. Taken together, our results demonstrate a cost-effective, fast, and sensitive FD-FLIM approach with the potential to facilitate applications of FLIM in mechanobiology and FRET-based biosensing.
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Affiliation(s)
- John-Paul Dumas
- Rutgers University, Department of Biomedical Engineering, Piscataway, New Jersey, United States
- Thorlabs Inc., Newton, New Jersey, United States
| | | | - Evan M. Gates
- Duke University, Department of Biomedical Engineering, Durham, North Carolina, United States
| | - Brenton D. Hoffman
- Duke University, Department of Biomedical Engineering, Durham, North Carolina, United States
| | - Mark C. Pierce
- Rutgers University, Department of Biomedical Engineering, Piscataway, New Jersey, United States
| | - Nada N. Boustany
- Rutgers University, Department of Biomedical Engineering, Piscataway, New Jersey, United States
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81
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Liu W, Irudayaraj J. Understanding the dynamics and structure of epigenetic states with single-molecule fluorescence microscopy. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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82
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Vinegoni C, Feruglio PF, Gryczynski I, Mazitschek R, Weissleder R. Fluorescence anisotropy imaging in drug discovery. Adv Drug Deliv Rev 2019; 151-152:262-288. [PMID: 29410158 PMCID: PMC6072632 DOI: 10.1016/j.addr.2018.01.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Non-invasive measurement of drug-target engagement can provide critical insights in the molecular pharmacology of small molecule drugs. Fluorescence polarization/fluorescence anisotropy measurements are commonly employed in protein/cell screening assays. However, the expansion of such measurements to the in vivo setting has proven difficult until recently. With the advent of high-resolution fluorescence anisotropy microscopy it is now possible to perform kinetic measurements of intracellular drug distribution and target engagement in commonly used mouse models. In this review we discuss the background, current advances and future perspectives in intravital fluorescence anisotropy measurements to derive pharmacokinetic and pharmacodynamic measurements in single cells and whole organs.
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Affiliation(s)
- Claudio Vinegoni
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Paolo Fumene Feruglio
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Ignacy Gryczynski
- University of North Texas Health Science Center, Institute for Molecular Medicine, Fort Worth, TX, United States
| | - Ralph Mazitschek
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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83
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Algar WR, Hildebrandt N, Vogel SS, Medintz IL. FRET as a biomolecular research tool — understanding its potential while avoiding pitfalls. Nat Methods 2019; 16:815-829. [DOI: 10.1038/s41592-019-0530-8] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 07/15/2019] [Indexed: 01/14/2023]
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84
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Trümper V, von Knethen A, Preuß A, Ermilov E, Hackbarth S, Kuchler L, Gunne S, Schäfer A, Bornhütter T, Vereb G, Ujlaky-Nagy L, Brüne B, Röder B, Schindler M, Parnham MJ, Knape T. Flow cytometry-based FRET identifies binding intensities in PPARγ1 protein-protein interactions in living cells. Theranostics 2019; 9:5444-5463. [PMID: 31534496 PMCID: PMC6735382 DOI: 10.7150/thno.29367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 05/01/2019] [Indexed: 01/10/2023] Open
Abstract
PPARγ is a pharmacological target in inflammatory and metabolic diseases. Upon agonistic treatment or following antagonism, binding of co-factors is altered, which consequently affects PPARγ-dependent transactivation as well as its DNA-independent properties. Therefore, establishing techniques to characterize these interactions is an important issue in living cells. Methods: Using the FRET pair Clover/mRuby2, we set up a flow cytometry-based FRET assay by analyzing PPARγ1 binding to its heterodimerization partner RXRα. Analyses of PPARγ-reporter and co-localization studies by laser-scanning microscopy validated this system. Refining the system, we created a new readout to distinguish strong from weak interactions, focusing on PPARγ-binding to the co-repressor N-CoR2. Results: We observed high FRET in cells expressing Clover-PPARγ1 and mRuby2-RXRα, but no FRET when cells express a mRuby2-RXRα deletion mutant, lacking the PPARγ interaction domain. Focusing on the co-repressor N-CoR2, we identified in HEK293T cells the new splice variant N-CoR2-ΔID1-exon. Overexpressing this isoform tagged with mRuby2, revealed no binding to Clover-PPARγ1, nor in murine J774A.1 macrophages. In HEK293T cells, binding was even lower in comparison to N-CoR2 constructs in which domains established to mediate interaction with PPARγ binding are deleted. These data suggest a possible role of N-CoR2-ΔID1-exon as a dominant negative variant. Because binding to N-CoR2-mRuby2 was not altered following activation or antagonism of Clover-PPARγ1, we determined the effect of pharmacological treatment on FRET intensity. Therefore, we calculated flow cytometry-based FRET efficiencies based on our flow cytometry data. As with PPARγ antagonism, PPARγ agonist treatment did not prevent binding of N-CoR2. Conclusion: Our system allows the close determination of protein-protein interactions with a special focus on binding intensity, allowing this system to characterize the role of protein domains as well as the effect of pharmacological agents on protein-protein interactions.
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Affiliation(s)
- Verena Trümper
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
| | - Andreas von Knethen
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Annegret Preuß
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Eugeny Ermilov
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Steffen Hackbarth
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Laura Kuchler
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
| | - Sandra Gunne
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Anne Schäfer
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
| | - Tobias Bornhütter
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Lázló Ujlaky-Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Bernhard Brüne
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Beate Röder
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Michael Schindler
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Karls University Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen
| | - Michael J. Parnham
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Tilo Knape
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
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85
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Lu L, Zhang L, Yuan L, Zhu T, Chen W, Wang G, Wang Q. Artificial Cellulosome Complex from the Self-Assembly of Ni-NTA-Functionalized Polymeric Micelles and Cellulases. Chembiochem 2019; 20:1394-1399. [PMID: 30697892 DOI: 10.1002/cbic.201900061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Indexed: 12/17/2023]
Abstract
Polymer-protein core-shell nanoparticles have been explored for enzyme immobilization. This work reports on the development of functional polymeric micelles for immobilizing His6 -tagged cellulases with controlled spatial orientation of enzymes, resulting in "artificial cellulosomes" for effective cellulose hydrolysis. Poly(styrene)-b-poly(styrene-alt-maleic anhydride) was prepared through one-pot reversible addition-fragmentation chain-transfer polymerization and modified with nitrilotriacetic acid (NTA) to afford an amphiphilic block copolymer. The self-assembled polymer was mixed with a solution of NiSO4 to form Ni-NTA-functionalized micelles, which could successfully capture His6 -tagged cellulases and form hierarchically structured core-shell nanoparticles with cellulases as the corona. Because the anchored enzymes are site-specifically oriented and in close proximity, synergistic catalysis that results in over twofold activity enhancement has been achieved.
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Affiliation(s)
- Lin Lu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Liang Yuan
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Tianyu Zhu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE, 19716, USA
| | - Guiren Wang
- Department of Mechanical Engineering, University of South Carolina, 301 Main Street, Columbia, SC, 29208, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
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86
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Reichmann NT, Tavares AC, Saraiva BM, Jousselin A, Reed P, Pereira AR, Monteiro JM, Sobral RG, VanNieuwenhze MS, Fernandes F, Pinho MG. SEDS-bPBP pairs direct lateral and septal peptidoglycan synthesis in Staphylococcus aureus. Nat Microbiol 2019; 4:1368-1377. [PMID: 31086309 DOI: 10.1038/s41564-019-0437-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/25/2019] [Indexed: 11/09/2022]
Abstract
Peptidoglycan (PGN) is the major component of the bacterial cell wall, a structure that is essential for the physical integrity and shape of the cell. Bacteria maintain cell shape by directing PGN incorporation to distinct regions of the cell, namely, through the localization of late-stage PGN synthesis proteins. These include two key protein families, SEDS transglycosylases and bPBP transpeptidases, proposed to function in cognate pairs. Rod-shaped bacteria have two SEDS-bPBP pairs, involved in elongation and division. Here, we elucidate why coccoid bacteria, such as Staphylococcus aureus, also possess two SEDS-bPBP pairs. We determined that S. aureus RodA-PBP3 and FtsW-PBP1 probably constitute cognate pairs of interacting proteins. A lack of RodA-PBP3 resulted in more spherical cells due to deficient sidewall PGN synthesis, whereas depletion of FtsW-PBP1 arrested normal septal PGN incorporation. Although PBP1 is an essential protein, a mutant lacking PBP1 transpeptidase activity is viable, showing that this protein has a second function. We propose that the FtsW-PBP1 pair has a role in stabilizing the divisome at midcell. In the absence of these proteins, the divisome appears as multiple rings or arcs that drive lateral PGN incorporation, leading to cell elongation. We conclude that RodA-PBP3 and FtsW-PBP1 mediate sidewall and septal PGN incorporation, respectively, and that their activity must be balanced to maintain coccoid morphology.
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Affiliation(s)
- Nathalie T Reichmann
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Andreia C Tavares
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Bruno M Saraiva
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ambre Jousselin
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Patricia Reed
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana R Pereira
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - João M Monteiro
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Rita G Sobral
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,Departamento de Ciências da Vida e UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | | | - Fábio Fernandes
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.,Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Mariana G Pinho
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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87
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Stelson AC, Liu M, Little CAE, Long CJ, Orloff ND, Stephanopoulos N, Booth JC. Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics. Nat Commun 2019; 10:1174. [PMID: 30862776 PMCID: PMC6414672 DOI: 10.1038/s41467-019-09017-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/11/2019] [Indexed: 01/23/2023] Open
Abstract
Detection of conformational changes in biomolecular assemblies provides critical information into biological and self-assembly processes. State-of-the-art in situ biomolecular conformation detection techniques rely on fluorescent labels or protein-specific binding agents to signal conformational changes. Here, we present an on-chip, label-free technique to detect conformational changes in a DNA nanomechanical tweezer structure with microwave microfluidics. We measure the electromagnetic properties of suspended DNA tweezer solutions from 50 kHz to 110 GHz and directly detect two distinct conformations of the structures. We develop a physical model to describe the electrical properties of the tweezers, and correlate model parameters to conformational changes. The strongest indicator for conformational changes in DNA tweezers are the ionic conductivity, while shifts in the magnitude of the cooperative water relaxation indicate the addition of fuel strands used to open the tweezer. Microwave microfluidic detection of conformational changes is a generalizable, non-destructive technique, making it attractive for high-throughput measurements. Methods to study conformational changes in biomolecules are limited in resolution and require labelling or other modifications of target analytes. Here the authors present a label-free, microwave microfluidic approach to detect conformational changes of DNA nanostructures based on ionic conductivity.
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Affiliation(s)
- Angela C Stelson
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Minghui Liu
- School of Molecular Sciences, Arizona State University, 551 E University Dr, Tempe, AZ, 85281, USA.,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 727 E. Tyler St., Tempe, AZ, 85281, USA
| | - Charles A E Little
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Christian J Long
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Nathan D Orloff
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, 551 E University Dr, Tempe, AZ, 85281, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 727 E. Tyler St., Tempe, AZ, 85281, USA.
| | - James C Booth
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA.
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88
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Cominelli A, Acconcia G, Labanca I, Ghioni M, Rech I. Accurate non-invasive measurement of the turn-on transition of fast gated single photon avalanche diodes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:033102. [PMID: 30927784 DOI: 10.1063/1.5056222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Recently developed Active Quenching Circuits (AQCs) with fast-gating capabilities allow us to control a single photon avalanche diode with gate windows in the nanosecond and sub-nanosecond range, thus paving the way to advanced applications, especially in the field of time-correlated single photon counting. In this scenario, an accurate measurement of the time needed by the AQC to turn-on the detector is of utmost importance. Indeed, it permits us to evaluate the impact of the system in specific applications and provides a tool to designers to understand AQC limitations and to enhance its performance. Here we propose a simple non-invasive technique to accurately measure the time needed by a gated system to turn on the detector. The effectiveness of the measure has been proved on a gated system, and results have been compared to those obtained starting from the distribution of recorded photons under constant illumination, which is a widely used approach in the literature. The great advantage of the proposed approach is that it avoids typical artifacts that affect other kinds of measurements.
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Affiliation(s)
- A Cominelli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - G Acconcia
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - I Labanca
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - M Ghioni
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - I Rech
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
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89
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Lugovik KI, Eltyshev AK, Suntsova PO, Smoluk LT, Belousova AV, Ulitko MV, Minin AS, Slepukhin PA, Benassi E, Belskaya NP. Fluorescent boron complexes based on new N,O-chelates as promising candidates for flow cytometry. Org Biomol Chem 2019; 16:5150-5162. [PMID: 29963677 DOI: 10.1039/c8ob00868j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This study presents the synthesis and optical properties of a new class of bright green-yellow fluorescent dyes with potential applications in bioimaging. A facile synthetic route via the chelation of aryl(hetaryl)aminoacryloylthiophene scaffolds with a BF2 fragment is presented. The photophysical properties of the dyes are attributed to the nature and position of electron-donating and electron-withdrawing substituents. Upon coordination to a BF2 fragment, characteristic emission was observed, with λem ranging from 503 to 543 nm and quantum yields of 0.14-0.42. Compared with parent aryl(hetaryl)aminoacryloylthiophenes, a significant red shift in absorption (up to 480 nm in solution) and emission (up to 543 nm in solution and 610 nm in the solid state) and high chemical stability and photostability were observed. The electron-accepting character of the substituents on the terminal aromatic ring or replacing this fragment with pyridine or pyrazine moieties resulted in increased quantum yields. To gain insight into the electronic structures and optical properties, quantum mechanical calculations were performed. The results of (TD-)DFT calculations supported the structural and spectroscopic data and showed the features of electronic distribution in the frontier molecular orbitals and active electrophilic and nucleophilic sites in the compounds investigated. Synthesized BF2 complexes are promising dyes for cell imaging and flow cytometry owing to their ready penetration and accumulation in cells.
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Affiliation(s)
- Kseniya I Lugovik
- Ural Federal University, 19 Mira Str., Yekaterinburg, 620002, Russian Federation.
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90
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Cao R, Wallrabe H, Siller K, Rehman Alam S, Periasamy A. Single-cell redox states analyzed by fluorescence lifetime metrics and tryptophan FRET interaction with NAD(P)H. Cytometry A 2019; 95:110-121. [PMID: 30604477 DOI: 10.1002/cyto.a.23711] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/12/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022]
Abstract
Redox changes in live HeLa cervical cancer cells after doxorubicin treatment can either be analyzed by a novel fluorescence lifetime microscopy (FLIM)-based redox ratio NAD(P)H-a2%/FAD-a1%, called fluorescence lifetime redox ratio or one of its components (NAD(P)H-a2%), which is actually driving that ratio and offering a simpler and alternative metric and are both compared. Auto-fluorescent NAD(P)H, FAD lifetime is acquired by 2- photon excitation and Tryptophan by 3-photon, at 4 time points after treatment up to 60 min demonstrating early drug response to doxorubicin. Identical Fields-of-view (FoV) at each interval allows single-cell analysis, showing heterogeneous responses to treatment, largely based on their initial control redox state. Based on a discrete ROI selection method, mitochondrial OXPHOS and cytosolic glycolysis are discriminated. Furthermore, putative FRET interaction and energy transfer between tryptophan residue carrying enzymes and NAD(P)H correlate with NAD(P)H-a2%, as does the NADPH/NADH ratio, highlighting a multi-parametric assay to track metabolic changes in live specimens. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Ruofan Cao
- The W.M. Keck Center for Cellular Imaging, Physical and Life Sciences Building (PLSB), University of Virginia, 90 Geldard Drive, Charlottesville, Virginia, 22904.,Department of Biology, University of Virginia, 409 McCormick Road, Charlottesville, Virginia, 22904
| | - Horst Wallrabe
- The W.M. Keck Center for Cellular Imaging, Physical and Life Sciences Building (PLSB), University of Virginia, 90 Geldard Drive, Charlottesville, Virginia, 22904.,Department of Biology, University of Virginia, 409 McCormick Road, Charlottesville, Virginia, 22904
| | - Karsten Siller
- Advanced Research Computing Services, Division of St-VP Information Technology, University of Virginia, 1023 Millmont Street, Charlottesville, Virginia, 22904
| | - Shagufta Rehman Alam
- The W.M. Keck Center for Cellular Imaging, Physical and Life Sciences Building (PLSB), University of Virginia, 90 Geldard Drive, Charlottesville, Virginia, 22904
| | - Ammasi Periasamy
- The W.M. Keck Center for Cellular Imaging, Physical and Life Sciences Building (PLSB), University of Virginia, 90 Geldard Drive, Charlottesville, Virginia, 22904.,Department of Biology, University of Virginia, 409 McCormick Road, Charlottesville, Virginia, 22904.,Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22904
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91
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Neagu AN. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:55-98. [PMID: 31347042 DOI: 10.1007/978-3-030-15950-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
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92
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Zhou B, Zhang X, Wang G, Barbour KW, Berger FG, Wang Q. Drug screening assay based on the interaction of intact Keap1 and Nrf2 proteins in cancer cells. Bioorg Med Chem 2019; 27:92-99. [PMID: 30473361 DOI: 10.1016/j.bmc.2018.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND The Nrf2-Keap1 interaction is the major regulatory pathway for cytoprotective responses against oxidative and electrophilic stresses. Keap1, a substrate protein of a Cul3-dependent E3 ubiquitin ligase complex, is a negative regulator of Nrf2. The use of chemicals to regulate the interaction between Keap1 and Nrf2 has been proposed as a strategy for the chemoprevention of degenerative diseases and cancers. RESULTS The interactions between Keap1 and Nrf2 in vitro and in vivo were investigated using fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) strategies in our study. Nrf2 with its N-terminal fused to eGFP and Keap1 with its C-terminal fused to mCherry were expressed and purified in vitro. When purified eGFP-Nrf2 and Keap1-mChrry proteins were mixed together, a strong FRET signal could be detected, indicating an efficient energy transfer from eGFP to mCherry. Moreover, the FRET was detected in vivo using confocal microscopy in colon cancer HCT-116 cells that were co-transfected with eGFP-Nrf2 and Keap1-mCherry. Finally, using an eGFP BiFC approach, the Keap1-Nrf2 interaction was also detected in MCF7 cells by transfecting eGFP N-terminal fused to Nrf2 (eN158-Nrf2) and eGFP C-terminal fused to Keap1 (eC159-Keap1). Using the BiFC and FRET systems, we demonstrated that the prototypical Nrf2-activiting compound tBHQ and the antitumor drug F-dUrd might interfere with the intracellular interaction between Keap1 and Nrf2 whereas the 5-Fu have little role in activating the protective response of Nrf2 pathway in cancer cells. CONCLUSIONS By analyzing the perturbation of the energy transfer between the donor and acceptor fluorophores and the bimolecular fluorescence complementation of eGFP, we can screen potential inhibitors for the interaction between Keap1 and Nrf2.
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Affiliation(s)
- Bo Zhou
- College of Life Science, Northeast Forestry University, Harbin, China; Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Xiaolei Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Guiren Wang
- Biomedical Engineering Program and Mechanical Engineering Department, University of South Carolina, Columbia, SC, USA.
| | - Karen W Barbour
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC, USA.
| | - Franklin G Berger
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC, USA.
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA.
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93
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Pedretti E, Tanner MG, Choudhary TR, Krstajić N, Megia-Fernandez A, Henderson RK, Bradley M, Thomson RR, Girkin JM, Dhaliwal K, Dalgarno PA. High-speed dual color fluorescence lifetime endomicroscopy for highly-multiplexed pulmonary diagnostic applications and detection of labeled bacteria. BIOMEDICAL OPTICS EXPRESS 2019; 10:181-195. [PMID: 30775092 PMCID: PMC6363193 DOI: 10.1364/boe.10.000181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 05/03/2023]
Abstract
We present a dual-color laser scanning endomicroscope capable of fluorescence lifetime endomicroscopy at one frame per second (FPS). The scanning system uses a coherent imaging fiber with 30,000 cores. High-speed lifetime imaging is achieved by distributing the signal over an array of 1024 parallel single-photon avalanche diode detectors (SPADs), minimizing detection dead-time maximizing the number of photons detected per excitation pulse without photon pile-up to achieve the high frame rate. This also enables dual color fluorescence imaging by temporally shifting the dual excitation lasers, with respect to each other, to separate the two spectrally distinct fluorescent decays in time. Combining the temporal encoding, to provide spectral separation, with lifetime measurements we show a one FPS, multi-channel endomicroscopy platform for clinical applications and diagnosis. We demonstrate the potential of the system by imaging SmartProbe labeled bacteria in ex vivo samples of human lung using lifetime to differentiate bacterial fluorescence from the strong background lung autofluorescence which was used to provide structural information.
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Affiliation(s)
- Ettore Pedretti
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot–Watt University, Edinburgh EH14 4AS,
UK
- EPSRC Proteus Hub, Centre for Inflammation Research, Queen’s Medical Research Centre, University of Edinburgh, Edinburgh EH16 4TJ,
UK
- Currently with the Leibniz-Institute für Astrophysik Potsdam, Potsdam,
Germany
| | - Michael G. Tanner
- Scottish Universities Physics Alliance (SUPA), Institute of Photonics and Quantum Sciences, School of Engineering and Physical Sciences, Heriot–Watt University, Edinburgh EH14 4AS,
UK
- EPSRC Proteus Hub, Centre for Inflammation Research, Queen’s Medical Research Centre, University of Edinburgh, Edinburgh EH16 4TJ,
UK
| | - Tushar R. Choudhary
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot–Watt University, Edinburgh EH14 4AS,
UK
- EPSRC Proteus Hub, Centre for Inflammation Research, Queen’s Medical Research Centre, University of Edinburgh, Edinburgh EH16 4TJ,
UK
| | - Nikola Krstajić
- EPSRC Proteus Hub, Centre for Inflammation Research, Queen’s Medical Research Centre, University of Edinburgh, Edinburgh EH16 4TJ,
UK
- Institute for Integrated Micro and Nano Systems, School of Engineering, University of Edinburgh, Edinburgh EH9 3FF,
UK
- Currently with the University of Dundee, School of Science and Engineering, Dundee,
UK
| | | | - Robert K. Henderson
- Institute for Integrated Micro and Nano Systems, School of Engineering, University of Edinburgh, Edinburgh EH9 3FF,
UK
| | - Mark Bradley
- EPSRC Proteus Hub, Centre for Inflammation Research, Queen’s Medical Research Centre, University of Edinburgh, Edinburgh EH16 4TJ,
UK
- EaStChem, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ,
UK
| | - Robert R. Thomson
- Scottish Universities Physics Alliance (SUPA), Institute of Photonics and Quantum Sciences, School of Engineering and Physical Sciences, Heriot–Watt University, Edinburgh EH14 4AS,
UK
- EPSRC Proteus Hub, Centre for Inflammation Research, Queen’s Medical Research Centre, University of Edinburgh, Edinburgh EH16 4TJ,
UK
| | - John M. Girkin
- Department of Physics, University of Durham, Durham DH1 3LE,
UK
| | - Kevin Dhaliwal
- EPSRC Proteus Hub, Centre for Inflammation Research, Queen’s Medical Research Centre, University of Edinburgh, Edinburgh EH16 4TJ,
UK
| | - Paul A. Dalgarno
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot–Watt University, Edinburgh EH14 4AS,
UK
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94
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Gates EM, LaCroix AS, Rothenberg KE, Hoffman BD. Improving Quality, Reproducibility, and Usability of FRET-Based Tension Sensors. Cytometry A 2018; 95:201-213. [PMID: 30523675 DOI: 10.1002/cyto.a.23688] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/30/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023]
Abstract
Mechanobiology, the study of how mechanical forces affect cellular behavior, is an emerging field of study that has garnered broad and significant interest. Researchers are currently seeking to better understand how mechanical signals are transmitted, detected, and integrated at a subcellular level. One tool for addressing these questions is a Förster resonance energy transfer (FRET)-based tension sensor, which enables the measurement of molecular-scale forces across proteins based on changes in emitted light. However, the reliability and reproducibility of measurements made with these sensors has not been thoroughly examined. To address these concerns, we developed numerical methods that improve the accuracy of measurements made using sensitized emission-based imaging. To establish that FRET-based tension sensors are versatile tools that provide consistent measurements, we used these methods, and demonstrated that a vinculin tension sensor is unperturbed by cell fixation, permeabilization, and immunolabeling. This suggests FRET-based tension sensors could be coupled with a variety of immuno-fluorescent labeling techniques. Additionally, as tension sensors are frequently employed in complex biological samples where large experimental repeats may be challenging, we examined how sample size affects the uncertainty of FRET measurements. In total, this work establishes guidelines to improve FRET-based tension sensor measurements, validate novel implementations of these sensors, and ensure that results are precise and reproducible. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- Evan M Gates
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708
| | - Andrew S LaCroix
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708
| | - Katheryn E Rothenberg
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708
| | - Brenton D Hoffman
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708
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95
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Aluko J, Perrin C, Devauges V, Nedbal J, Poland S, Matthews D, Whittaker J, Ameer-Beg S. Semi-autonomous real-time programmable fluorescence lifetime segmentation with a digital micromirror device. OPTICS EXPRESS 2018; 26:31055-31074. [PMID: 30650697 DOI: 10.1364/oe.26.031055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/22/2018] [Indexed: 06/09/2023]
Abstract
Time-correlated single-photon counting (TCSPC) is the gold standard for performing lifetime spectroscopy in biological assays. Traditional fluorescence lifetime imaging (FLIM) using laser scanning microscopes are inherently slow due to point scanning all pixels in the field-of-view. Wide-field implementations of TCSPC spectroscopy using microchannel plates benefit from particularly fast acquisition times at the expense of temporal resolution, and are fundamentally limited by photon counting rates. Here, we introduce programmable lifetime imaging (PLI), combining the advantages of wide-field imaging using total internal reflection excitation with state-of-the-art TCSPC detector technology for accurate lifetime determination in an object-oriented manner using a digital micromirror device (DMD). The fluorescent emission is projected onto the DMD to facilitate the sequential segmentation of fluorescence from individual objects in the field-of-view, allowing for both image acquisition and fluorescence lifetime determination of the assay. The sensitivity of PLI is demonstrated by manually segmenting fluorescence from fixed cell assays. We also demonstrate an automated implementation of PLI, using a camera as a feedback mechanism to segment fluorescence produced by emitting objects of interest in the imaging field-of-view, highlighting the advantages of measurement only in areas where valuable information exists. As a result, PLI is able to reduce acquisition time of fluorescence lifetime data by at least an order of magnitude compared to laser scanning implementations.
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96
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Teunissen AJP, Pérez-Medina C, Meijerink A, Mulder WJM. Investigating supramolecular systems using Förster resonance energy transfer. Chem Soc Rev 2018; 47:7027-7044. [PMID: 30091770 PMCID: PMC6441672 DOI: 10.1039/c8cs00278a] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Supramolecular systems have applications in areas as diverse as materials science, biochemistry, analytical chemistry, and nanomedicine. However, analyzing such systems can be challenging due to the wide range of time scales, binding strengths, distances, and concentrations at which non-covalent phenomena take place. Due to their versatility and sensitivity, Förster resonance energy transfer (FRET)-based techniques are excellently suited to meet such challenges. Here, we detail the ways in which FRET has been used to study non-covalent interactions in both synthetic and biological supramolecular systems. Among other topics, we examine methods to measure molecular forces, determine protein conformations, monitor assembly kinetics, and visualize in vivo drug release from nanoparticles. Furthermore, we highlight multiplex FRET techniques, discuss the field's limitations, and provide a perspective on new developments.
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Affiliation(s)
- Abraham J. P. Teunissen
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Carlos Pérez-Medina
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Andries Meijerink
- Department of Chemistry, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Willem J. M. Mulder
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Laboratory of Chemical biology, Department of Biomedical Engineering and Institute for Complex Molecular systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, The Netherlands
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97
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Ochoa M, Pian Q, Yao R, Ducros N, Intes X. Assessing patterns for compressive fluorescence lifetime imaging. OPTICS LETTERS 2018; 43:4370-4373. [PMID: 30211866 PMCID: PMC6261333 DOI: 10.1364/ol.43.004370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A novel hyperspectral single pixel system was used to compare different compressive basis patterns for intensity imaging, lifetime imaging, and FRET quantification. Six popular basis patterns were compared experimentally in a phantom containing two fluorescent dyes. The basis patterns that performed best for lifetime quantification were used to measure FRET occurrence in well-plate samples with varying acceptor-donor ratios. The ABS-WP approach using Haar patterns and the compressive sensing approach with Hadamard Ranked patterns displayed the best overall performances at a 50% compression ratio.
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Affiliation(s)
- M. Ochoa
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Q. Pian
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - R. Yao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - N. Ducros
- University Lyon, INSA Lyon, UCB Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS UMR 5220, U1206, Lyon 69621, France
| | - X. Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
- Corresponding author:
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99
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Saari H, Lisitsyna E, Rautaniemi K, Rojalin T, Niemi L, Nivaro O, Laaksonen T, Yliperttula M, Vuorimaa-Laukkanen E. FLIM reveals alternative EV-mediated cellular up-take pathways of paclitaxel. J Control Release 2018; 284:133-143. [DOI: 10.1016/j.jconrel.2018.06.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/04/2018] [Accepted: 06/10/2018] [Indexed: 12/17/2022]
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100
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Cortes CL, Jacob Z. Fundamental figures of merit for engineering Förster resonance energy transfer. OPTICS EXPRESS 2018; 26:19371-19387. [PMID: 30114111 DOI: 10.1364/oe.26.019371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/01/2018] [Indexed: 06/08/2023]
Abstract
Over the past 15 years there has been an ongoing debate regarding the influence of the photonic environment on Förster resonance energy transfer (FRET). Disparate results corresponding to enhancement, suppression and null effect of the photonic environment have led to a lack of consensus between the traditional theory of FRET and experiments. Here we show that the quantum electrodynamic theory (QED) of FRET near an engineered nanophotonic environment is exactly equivalent to an effective near-field model describing electrostatic dipole-dipole interactions. This leads to an intuitive and rigorously exact description of FRET, previously unavailable, bridging the gap between experimental observations and theoretical interpretations. Furthermore, we show that the widely used concept of Purcell factor variation is only important for understanding spontaneous emission and is an incorrect figure of merit (FOM) for analyzing FRET. To this end, we analyze the figures of merit which characterize FRET in a photonic environment 1) the FRET rate enhancement factor (FET), 2) FRET efficiency enhancement factor (Feff) and 3) Two-point spectral density (SEE) which is the photonic property of the environment governing FRET analogous to the local density of states that controls spontaneous emission. Counterintuitive to existing knowledge, we show that suppression of the Purcell factor is in fact necessary for enhancing the efficiency of the FRET process. We place fundamental bounds on the FRET figures of merit arising from material absorption in the photonic environment as well as key properties of emitters including intrinsic quantum efficiencies and orientational dependence. Finally, we use our approach to conclusively explain multiple recent experiments and predict regimes where the FRET rate is expected to be enhanced, suppressed or remain the same. Our work paves for a complete theory of FRET with predictive power for designing the ideal photonic environment to control FRET.
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