1
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Sarkar M, Raj R R, Maliekal TT. Finding the partner: FRET and beyond. Exp Cell Res 2024; 441:114166. [PMID: 39029572 DOI: 10.1016/j.yexcr.2024.114166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
Given the importance of aberrant protein-protein interactions (PPIs) in disease, the recent drug discovery focuses on targeting the altered PPIs to treat the disease. In this context, identifying the atypical PPIs underlying the disease is critical for the development of diagnostics and therapeutics. Various biochemical, biophysical, and genetic methods have been reported to study PPIs. Here, we are giving a short account of those techniques with more emphasis on Förster resonance energy transfer (FRET), which can be used to monitor macromolecular interactions in live cells. Besides the basics of FRET, we explain the modifications of its application, like Single molecule FRET (smFRET), Fluorescence Lifetime Imaging Microscopy-FRET (FLIM-FRET), and photoswitching FRET. While smFRET is extensively used for evaluating the biology of nucleic acids and also to develop diagnostics, FLIM-FRET is widely exploited to study the PPIs underlying neurological disorders and cancer. Photoswitching FRET is a relatively newer technique and it has tremendous potential to unravel the significance of different PPIs. Besides these modifications, there are several advancements in the field by introducing new fluorophores. Identification of lanthanide chelates, quantum dots, and other nanoparticle fluorophores has revolutionized the applications of FRET in diagnostics and basic biology. Yet, these methods can be employed to study the interactions of only two molecules. Since the majority of the PPIs are multimeric complexes, we still need to improve our technologies to study these interactions in live cells in real-time.
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Affiliation(s)
- Meghna Sarkar
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Reshma Raj R
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India.
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2
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Chen H, Tian P, Guo J, Sun M, Zhu W, Li Z, Liu Z. Synergistic synthesis of gold nanoflowers as upconversion near-infrared nanoprobe energy acceptor and recognition unit for improved hydrogen sulfide sensing. Talanta 2024; 273:125908. [PMID: 38503119 DOI: 10.1016/j.talanta.2024.125908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/03/2024] [Accepted: 03/09/2024] [Indexed: 03/21/2024]
Abstract
A highly sensitive and selective upconversion near-infrared (NIR) fluorescence and colorimetric dual readout hydrogen sulfide (H2S) nanoprobe was constructed based on the excellent NIR fluorescence emission performance of upconversion nanomaterials (UCNPs), the specific recognition effect of synergistically synthesized gold nanoflowers (trypsin-stabled AuNFs (Try-AuNFs)) and the effective NIR fluorescence quenching capability. In this assay, the sensing strategy included three processes. First of all, the synthesized UCNPs can emit 803 nm NIR fluorescence when they were excited by 980 nm excitation light. Secondly, as a result of the principle of fluorescence resonance energy transfer (FRET), Try-AuNFs can effectively quench the NIR fluorescence of UCNPs at 803 nm, which can effectively improve the signal-to-background ratio of nanoprobes, thereby improving the sensitivity of the probes. Thirdly, in the presence of H2S, the Try protective layer on the surface of Try-AuNFs was specifically penetrated, which will subsequently cleave Try-AuNFs via the strong S-Au bond. As such, the NIR fluorescence of UCNPs will be restored, achieving high selectivity and sensitivity detection of H2S. Under optimized conditions, the linear response range of H2S was 0.1-300 μM, and the detection limit was 53 nM. It is worth noting that the Try on the surface of Try-AuNFs via the synergistic effect can increase the steric hindrance of the probe, and this can effectively prevent the interaction between the probe with biothiols (cysteine (Cys), homocysteine (Hcy)) and other natural amino acids (non-thiol-containing) with resultant in the high selectivity regarding the detection of H2S in human serum, which is unlikely to be achieved by AuNFs synthesized by the gold seed method (Se-AuNFs). This work not only provided a new type of UCNPs fluorescence quencher and recognition unit, but also exemplified that the use of the physical properties (steric hindrance) of protein ligands on the surface of nanoflowers can improve the specificity of the probe. This will provide new ideas for the design of other nanoprobes.
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Affiliation(s)
- Hongyu Chen
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China.
| | - Peipei Tian
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Jiayi Guo
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Manman Sun
- College of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466001, China.
| | - Wenping Zhu
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Zhendong Li
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Zengchen Liu
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China.
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3
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Zhao T, Wu D, Zhang X, Lyu H. A fluorescent sensor based on single band bright red luminescent core-shell UCNPs for the high-sensitivity detection of glucose and glutathione. Anal Chim Acta 2024; 1295:342323. [PMID: 38355224 DOI: 10.1016/j.aca.2024.342323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
As the reliable biomarkers to evaluate the diabetes and neurological disease, sensitive and accurate detection of glucose and glutathione (GSH) in biological samples is necessary for early precaution and diagnosis of related-diseases. The single red upconversion nanoparticles (UCNPs) especially with core-shell structure can penetrate deeper biological tissues and cause less energy loss and thus have higher sensitivity and accuracy. Additionally, an enzyme-controlled cascade signal amplification (ECSAm) strategy will further enhance sensitivity. Herein, using single red UCNPs with core-shell structure as the luminescent material, a fluorescent sensor based on ECSAm was developed for the highly sensitive and accurate detection of glucose and GSH. Under the optimal conditions, the limits of detection for glucose and GSH by fluorescent method were 0.03 μM and 0.075 μM, separately. This assay was used to analyze the content of glucose and GSH in serum samples, and the obtained data was close to that of commercial blood glucose and GSH detection kit. The developed sensor platform based on single red UCNPs with core-shell structure and ECSAm can be a promising method for the accurate and sensitive detection of glucose and GSH in biological samples.
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Affiliation(s)
- Tianlu Zhao
- College of Materials Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Dongzhi Wu
- Department of Orthopedics Institute, Fuzhou Second Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, China; Department of Orthopedics Institute, Fuzhou Second Hospital, Fuzhou, 350007, China
| | - Xuecheng Zhang
- College of Materials Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Haixia Lyu
- College of Materials Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
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4
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Devkota S, Zhou R, Nagarajan V, Maesako M, Do H, Noorani A, Overmeyer C, Bhattarai S, Douglas JT, Saraf A, Miao Y, Ackley BD, Shi Y, Wolfe MS. Familial Alzheimer mutations stabilize synaptotoxic γ-secretase-substrate complexes. Cell Rep 2024; 43:113761. [PMID: 38349793 PMCID: PMC10941010 DOI: 10.1016/j.celrep.2024.113761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/19/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Mutations that cause familial Alzheimer's disease (FAD) are found in amyloid precursor protein (APP) and presenilin, the catalytic component of γ-secretase, that together produce amyloid β-peptide (Aβ). Nevertheless, whether Aβ is the primary disease driver remains controversial. We report here that FAD mutations disrupt initial proteolytic events in the multistep processing of APP substrate C99 by γ-secretase. Cryoelectron microscopy reveals that a substrate mimetic traps γ-secretase during the transition state, and this structure aligns with activated enzyme-substrate complex captured by molecular dynamics simulations. In silico simulations and in cellulo fluorescence microscopy support stabilization of enzyme-substrate complexes by FAD mutations. Neuronal expression of C99 and/or presenilin-1 in Caenorhabditis elegans leads to synaptic loss only with FAD-mutant transgenes. Designed mutations that stabilize the enzyme-substrate complex and block Aβ production likewise led to synaptic loss. Collectively, these findings implicate the stalled process-not the products-of γ-secretase cleavage of substrates in FAD pathogenesis.
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Affiliation(s)
- Sujan Devkota
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
| | - Rui Zhou
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | | | - Masato Maesako
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hung Do
- Center for Computational Biology, University of Kansas, Lawrence, KS, USA
| | - Arshad Noorani
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
| | - Caitlin Overmeyer
- Graduate Program in Neurosciences, University of Kansas, Lawrence, KS, USA
| | - Sanjay Bhattarai
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
| | - Justin T Douglas
- Nuclear Magnetic Resonance Core Lab, University of Kansas, Lawrence, KS, USA
| | - Anita Saraf
- Mass Spectrometry and Analytical Proteomic Laboratory, University of Kansas, Lawrence, KS, USA
| | - Yinglong Miao
- Center for Computational Biology, University of Kansas, Lawrence, KS, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Brian D Ackley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Yigong Shi
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China; Westlake Laboratory of Life Science and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Michael S Wolfe
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA; Graduate Program in Neurosciences, University of Kansas, Lawrence, KS, USA.
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5
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Sławski J, Maciejewski J, Szukiewicz R, Gieczewska K, Grzyb J. Quantum Dots Assembled with Photosynthetic Antennae on a Carbon Nanotube Platform: A Nanohybrid for the Enhancement of Light Energy Harvesting. ACS OMEGA 2023; 8:41991-42003. [PMID: 37969970 PMCID: PMC10633852 DOI: 10.1021/acsomega.3c07673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/17/2023]
Abstract
The construction of artificial systems for solar energy harvesting is still a challenge. There needs to be a light-harvesting antenna with a broad absorption spectrum and then the possibility to transfer harvested energy to the reaction center, converting photons into a storable form of energy. Bioinspired and bioderivative elements may help in achieving this aim. Here, we present an option for light harvesting: a nanobiohybrid of colloidal, semiconductor quantum dots (QDs) and natural photosynthetic antennae assembled on the surface of a carbon nanotube. For that, we used QDs of cadmium telluride and cyanobacterial phycobilisome rods (PBSr) or light-harvesting complex II (LHCII) of higher plants. For this nanobiohybrid, we confirmed composition and organization using infrared spectroscopy, X-ray photoelectron spectroscopy, and high-resolution confocal microscopy. Then, we proved that within such an assembly, there is a resonance energy transfer from QD to PBSr or LHCII. When such a nanobiohybrid was further combined with thylakoids, the energy was transferred to photosynthetic reaction centers and efficiently powered the photosystem I reaction center. The presented construct is proof of a general concept, combining interacting elements on a platform of a nanotube, allowing further variation within assembled elements.
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Affiliation(s)
- Jakub Sławski
- Department
of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Jan Maciejewski
- Department
of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Rafał Szukiewicz
- Faculty
of Physics and Astronomy, University of
Wrocław, Maxa Borna
9, 50-204 Wrocław, Poland
| | - Katarzyna Gieczewska
- Department
of Plant Anatomy and Cytology, Institute of Experimental Plant Biology
and Biotechnology, Faculty of Biology, University
of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Joanna Grzyb
- Department
of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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6
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Wu Q, Duan XJ, Lv HT, Wang LT. Red-emitting carbon dots as fluorescent probes for the rapid detection of brilliant blue FCF in foods. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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7
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Gooz M, Maldonado EN. Fluorescence microscopy imaging of mitochondrial metabolism in cancer cells. Front Oncol 2023; 13:1152553. [PMID: 37427141 PMCID: PMC10326048 DOI: 10.3389/fonc.2023.1152553] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Mitochondrial metabolism is an important contributor to cancer cell survival and proliferation that coexists with enhanced glycolytic activity. Measuring mitochondrial activity is useful to characterize cancer metabolism patterns, to identify metabolic vulnerabilities and to identify new drug targets. Optical imaging, especially fluorescent microscopy, is one of the most valuable tools for studying mitochondrial bioenergetics because it provides semiquantitative and quantitative readouts as well as spatiotemporal resolution of mitochondrial metabolism. This review aims to acquaint the reader with microscopy imaging techniques currently used to determine mitochondrial membrane potential (ΔΨm), nicotinamide adenine dinucleotide (NADH), ATP and reactive oxygen species (ROS) that are major readouts of mitochondrial metabolism. We describe features, advantages, and limitations of the most used fluorescence imaging modalities: widefield, confocal and multiphoton microscopy, and fluorescent lifetime imaging (FLIM). We also discus relevant aspects of image processing. We briefly describe the role and production of NADH, NADHP, flavins and various ROS including superoxide and hydrogen peroxide and discuss how these parameters can be analyzed by fluorescent microscopy. We also explain the importance, value, and limitations of label-free autofluorescence imaging of NAD(P)H and FAD. Practical hints for the use of fluorescent probes and newly developed sensors for imaging ΔΨm, ATP and ROS are described. Overall, we provide updated information about the use of microscopy to study cancer metabolism that will be of interest to all investigators regardless of their level of expertise in the field.
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Affiliation(s)
- Monika Gooz
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Eduardo N. Maldonado
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
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8
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Prajapati GK, Kumar A, Wany A, Pandey DM. Molecular Beacon Probe (MBP)-Based Real-Time PCR. Methods Mol Biol 2023; 2638:273-287. [PMID: 36781649 DOI: 10.1007/978-1-0716-3024-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In the advancement of molecular biology techniques, several probe-based techniques, like molecular beacon probe (MBP) assay, TaqMan probe, and minor groove binder (MGB) probe assay, have been reported to identify specific sequences through real-time polymerase chain reaction (PCR). All probe-based methods are more sensitive than the conventional PCR for the detection and quantification of target genes. MBP is a hydrolysis probe that emits fluorescence when getting the specific sequences on the gene. Here, we describe the application of MBP for the identification of the motif sequences present in the promoters of differentially expressed genes.
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Affiliation(s)
- Gopal Kumar Prajapati
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,R & D Biologics Division, Promea Therapeutics Pvt Ltd, Sultanpur, Hyderabad, India
| | - Ashutosh Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Aakanksha Wany
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.
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9
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Smolen JA, Wooley KL. Fluorescence lifetime image microscopy prediction with convolutional neural networks for cell detection and classification in tissues. PNAS NEXUS 2022; 1:pgac235. [PMID: 36712353 PMCID: PMC9802238 DOI: 10.1093/pnasnexus/pgac235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/11/2022] [Indexed: 12/05/2022]
Abstract
Convolutional neural networks (CNNs) and other deep-learning models have proven to be transformative tools for the automated analysis of microscopy images, particularly in the domain of cellular and tissue imaging. These computer-vision models have primarily been applied with traditional microscopy imaging modalities (e.g. brightfield and fluorescence), likely due to the availability of large datasets in these regimes. However, more advanced microscopy imaging techniques could, potentially, allow for improved model performance in various computational histopathology tasks. In this work, we demonstrate that CNNs can achieve high accuracy in cell detection and classification without large amounts of data when applied to histology images acquired by fluorescence lifetime imaging microscopy (FLIM). This accuracy is higher than what would be achieved with regular single or dual-channel fluorescence images under the same settings, particularly for CNNs pretrained on publicly available fluorescent cell or general image datasets. Additionally, generated FLIM images could be predicted from just the fluorescence image data by using a dense U-Net CNN model trained on a subset of ground-truth FLIM images. These U-Net CNN generated FLIM images demonstrated high similarity to ground truth and improved accuracy in cell detection and classification over fluorescence alone when used as input to a variety of commonly used CNNs. This improved accuracy was maintained even when the FLIM images were generated by a U-Net CNN trained on only a few example FLIM images.
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Affiliation(s)
| | - Karen L Wooley
- Departments of Chemistry, Chemical Engineering, and Materials Science and Engineering, Texas A&M University, College Station, TX 77842, USA
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10
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Fluorescence resonance energy transfer-based nanomaterials for the sensing in biological systems. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.12.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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McKendell AK, Houser MCQ, Mitchell SPC, Wolfe MS, Berezovska O, Maesako M. In-Depth Characterization of Endo-Lysosomal Aβ in Intact Neurons. BIOSENSORS 2022; 12:bios12080663. [PMID: 36005059 PMCID: PMC9406119 DOI: 10.3390/bios12080663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/21/2022]
Abstract
Amyloid-beta (Aβ) peptides are produced within neurons. Some peptides are released into the brain parenchyma, while others are retained inside the neurons. However, the detection of intracellular Aβ remains a challenge since antibodies against Aβ capture Aβ and its precursor proteins (i.e., APP and C99). To overcome this drawback, we recently developed 1) the C99 720-670 biosensor for recording γ-secretase activity and 2) a unique multiplexed immunostaining platform that enables the selective detection of intracellular Aβ with subcellular resolution. Using these new assays, we showed that C99 is predominantly processed by γ-secretase in late endosomes and lysosomes, and intracellular Aβ is enriched in the same subcellular loci in intact neurons. However, the detailed properties of Aβ in the acidic compartments remain unclear. Here, we report using fluorescent lifetime imaging microscopy (FLIM) that intracellular Aβ includes both long Aβ intermediates bound to γ-secretase and short peptides dissociated from the protease complex. Surprisingly, our results also suggest that the dissociated Aβ is bound to the glycoproteins on the inner membrane of lysosomes. Furthermore, we show striking cell-to-cell heterogeneity in intracellular Aβ levels in primary neurons and APP transgenic mouse brains. These findings provide a basis for the further investigation of the role(s) of intracellular Aβ and its relevance to Alzheimer’s disease (AD).
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Affiliation(s)
- Alec K. McKendell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, 114, 16th street, Charlestown, MA 02129, USA
| | - Mei C. Q. Houser
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, 114, 16th street, Charlestown, MA 02129, USA
| | - Shane P. C. Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, 114, 16th street, Charlestown, MA 02129, USA
| | - Michael S. Wolfe
- Department of Medicinal Chemistry, University of Kansas, 1567 Irving Hill Rd, Lawrence, Kansas City, KS 66045, USA
| | - Oksana Berezovska
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, 114, 16th street, Charlestown, MA 02129, USA
| | - Masato Maesako
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, 114, 16th street, Charlestown, MA 02129, USA
- Correspondence: ; Tel.: +1-617-724-2579
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12
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Duan Z, Li K, Duan W, Zhang J, Xing J. Probing membrane protein interactions and signaling molecule homeostasis in plants by Förster resonance energy transfer analysis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:68-77. [PMID: 34610124 DOI: 10.1093/jxb/erab445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Membrane proteins have key functions in signal transduction, transport, and metabolism. Therefore, deciphering the interactions between membrane proteins provides crucial information on signal transduction and the spatiotemporal organization of protein complexes. However, detecting the interactions and behaviors of membrane proteins in their native environments remains difficult. Förster resonance energy transfer (FRET) is a powerful tool for quantifying the dynamic interactions and assembly of membrane proteins without disrupting their local environment, supplying nanometer-scale spatial information and nanosecond-scale temporal information. In this review, we briefly introduce the basic principles of FRET and assess the current state of progress in the development of new FRET techniques (such as FRET-FLIM, homo-FRET, and smFRET) for the analysis of plant membrane proteins. We also describe the various FRET-based biosensors used to quantify the homeostasis of signaling molecules and the active state of kinases. Furthermore, we summarize recent applications of these advanced FRET sensors in probing membrane protein interactions, stoichiometry, and protein clustering, which have shed light on the complex biological functions of membrane proteins in living plant cells.
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Affiliation(s)
- Zhikun Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Kaiwen Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wenwen Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jingjing Xing
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
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13
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Polaske NW, Kelly BD, Smith MA, Haura EB, Belosludtsev YY. Fully Automated Protein Proximity Assay in Formalin-Fixed, Paraffin-Embedded Tissue Using Caged Haptens. Bioconjug Chem 2020; 31:1635-1640. [PMID: 32395983 DOI: 10.1021/acs.bioconjchem.0c00193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ability to interrogate for the presence and distribution of protein-protein complexes (PPCs) is of high importance for the advancement of diagnostic capabilities such as determining therapeutic effects in the context of pharmaceutical development. Herein, we report a novel assay for detecting and visualizing PPCs on formalin-fixed, paraffin-embedded material using a caged hapten. To this end, we synthetically modified a nitropyrazole hapten with an alkaline phosphatase (AP)-responsive self-immolative caging group. The AP-labile caging group abrogates antibody binding; however, upon exposure to AP, the native hapten is regenerated. These caged haptens were applied in a proximity assay format by the use of a first antibody labeled with caged haptens that can be uncaged by AP conjugated to the second antibody. Only when the two epitopes of interest are in close proximity to one another will the AP interact with the caged hapten and uncage it. The native hapten, which represents the population of PPCs, was then visualized by an anti-hapten antibody conjugated to horseradish peroxidase, followed by diaminobenzidine detection. We provide proof of concept for the detection of protein proximity pairs (β-catenin-E-cadherin and EGFR-GRB2), and confirm assay specificity through technical controls involving reagent omission experiments, and biologically by treatment with small-molecule kinase inhibitors that interrupt kinase-adaptor complexes.
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Affiliation(s)
- Nathan W Polaske
- Tissue Research & Early Development, Roche Tissue Diagnostics, Tucson, Arizona 85755, United States
| | - Brian D Kelly
- Tissue Research & Early Development, Roche Tissue Diagnostics, Tucson, Arizona 85755, United States
| | - Matthew A Smith
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Eric B Haura
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Yuri Y Belosludtsev
- Tissue Research & Early Development, Roche Tissue Diagnostics, Tucson, Arizona 85755, United States
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14
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Datta R, Heaster TM, Sharick JT, Gillette AA, Skala MC. Fluorescence lifetime imaging microscopy: fundamentals and advances in instrumentation, analysis, and applications. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-43. [PMID: 32406215 PMCID: PMC7219965 DOI: 10.1117/1.jbo.25.7.071203] [Citation(s) in RCA: 312] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/24/2020] [Indexed: 05/18/2023]
Abstract
SIGNIFICANCE Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to distinguish the unique molecular environment of fluorophores. FLIM measures the time a fluorophore remains in an excited state before emitting a photon, and detects molecular variations of fluorophores that are not apparent with spectral techniques alone. FLIM is sensitive to multiple biomedical processes including disease progression and drug efficacy. AIM We provide an overview of FLIM principles, instrumentation, and analysis while highlighting the latest developments and biological applications. APPROACH This review covers FLIM principles and theory, including advantages over intensity-based fluorescence measurements. Fundamentals of FLIM instrumentation in time- and frequency-domains are summarized, along with recent developments. Image segmentation and analysis strategies that quantify spatial and molecular features of cellular heterogeneity are reviewed. Finally, representative applications are provided including high-resolution FLIM of cell- and organelle-level molecular changes, use of exogenous and endogenous fluorophores, and imaging protein-protein interactions with Förster resonance energy transfer (FRET). Advantages and limitations of FLIM are also discussed. CONCLUSIONS FLIM is advantageous for probing molecular environments of fluorophores to inform on fluorophore behavior that cannot be elucidated with intensity measurements alone. Development of FLIM technologies, analysis, and applications will further advance biological research and clinical assessments.
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Affiliation(s)
- Rupsa Datta
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Tiffany M. Heaster
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Joe T. Sharick
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Amani A. Gillette
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Melissa C. Skala
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
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15
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Huang X, Jiang C, Yu L, Yang A. Current and Emerging Approaches for Studying Inter-Organelle Membrane Contact Sites. Front Cell Dev Biol 2020; 8:195. [PMID: 32292782 PMCID: PMC7118198 DOI: 10.3389/fcell.2020.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 12/24/2022] Open
Abstract
Inter-organelle membrane contact sites (MCSs) are classically defined as areas of close proximity between heterologous membranes and established by specific proteins (termed tethers). The interest on MCSs has rapidly increased in the last years, since MCSs play a crucial role in the transfer of cellular components between different organelles and have been involved in important cellular functions such as apoptosis, organelle division and biogenesis, and cell growth. Recently, an unprecedented depth and breadth in insights into the details of MCSs have been uncovered. On one hand, extensive MCSs (organelles interactome) are revealed by comprehensive analysis of organelle network with high temporal-spatial resolution at the system level. On the other hand, more and more tethers involving in MCSs are identified and further works are focusing on addressing the role of these tethers in regulating the function of MCSs at the molecular level. These enormous progresses largely depend on the powerful approaches, including several different types of microscopies and various biochemical techniques. These approaches have greatly accelerated recent advances in MCSs at the system and molecular level. In this review, we summarize the current and emerging approaches for studying MCSs, such as various microscopies, proximity-driven fluorescent signal generation and proximity-dependent biotinylation. In addition, we highlight the advantages and disadvantages of the techniques to provide a general guidance for the study of MCSs.
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Affiliation(s)
- Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chen Jiang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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16
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Rohilla S, Krämer B, Koberling F, Gregor I, Hocke AC. Multi-target immunofluorescence by separation of antibody cross-labelling via spectral-FLIM-FRET. Sci Rep 2020; 10:3820. [PMID: 32123277 PMCID: PMC7052234 DOI: 10.1038/s41598-020-60877-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/17/2020] [Indexed: 11/10/2022] Open
Abstract
In biomedical research, indirect immunofluorescence labelling by use of primary and secondary antibodies is central for revealing the spatial distribution of multiple cellular antigens. However, labelling is regularly restricted to few antigens since species variation of primary and corresponding secondary antibodies is limited bearing the risk of unspecific cross-labelling. Here, we introduce a novel microscopic procedure for leveraging undesirable cross-labelling effects among secondary antibodies thereby increasing the number of fluorophore channels. Under cross-labelling conditions, commonly used fluorophores change chemical-physical properties by ‘Förster resonance energy transfer’ leading to defined changes in spectral emission and lifetime decay. By use of spectral fluorescence lifetime imaging and pattern-matching, we demonstrate precise separation of cross-labelled cellular antigens where conventional imaging completely fails. Consequently, this undesired effect serves for an innovative imaging procedure to separate critical antigens where antibody species variation is limited and allows for multi-target labelling by attribution of new fluorophore cross-labelling channels.
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Affiliation(s)
- Sumeet Rohilla
- PicoQuant Innovations GmbH, Rudower Chaussee 29 (IGZ), 12489, Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charitéplatz 1, 10117, Berlin, Germany
| | - Benedikt Krämer
- PicoQuant GmbH, Rudower Chaussee 29 (IGZ), 12489, Berlin, Germany
| | - Felix Koberling
- PicoQuant GmbH, Rudower Chaussee 29 (IGZ), 12489, Berlin, Germany
| | - Ingo Gregor
- Third Institute of Physics, Georg-August-University, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Andreas C Hocke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charitéplatz 1, 10117, Berlin, Germany.
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17
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Poudel C, Mela I, Kaminski CF. High-throughput, multi-parametric, and correlative fluorescence lifetime imaging. Methods Appl Fluoresc 2020; 8:024005. [PMID: 32028271 PMCID: PMC8208541 DOI: 10.1088/2050-6120/ab7364] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/18/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
In this review, we discuss methods and advancements in fluorescence lifetime imaging microscopy that permit measurements to be performed at faster speed and higher resolution than previously possible. We review fast single-photon timing technologies and the use of parallelized detection schemes to enable high-throughput and high content imaging applications. We appraise different technological implementations of fluorescence lifetime imaging, primarily in the time-domain. We also review combinations of fluorescence lifetime with other imaging modalities to capture multi-dimensional and correlative information from a single sample. Throughout the review, we focus on applications in biomedical research. We conclude with a critical outlook on current challenges and future opportunities in this rapidly developing field.
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Affiliation(s)
- Chetan Poudel
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
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18
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Castellani CM, Torres-Ocampo AP, Breffke J, White AB, Chambers JJ, Stratton MM, Maresca TJ. Live-cell FLIM-FRET using a commercially available system. Methods Cell Biol 2020; 158:63-89. [PMID: 32423651 PMCID: PMC8006575 DOI: 10.1016/bs.mcb.2020.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Förster resonance energy transfer (FRET)-based sensors have been powerful tools in cell biologists' toolkit for decades. Informed by fundamental understanding of fluorescent proteins, protein-protein interactions, and the structural biology of reporter components, researchers have been able to employ creative design approaches to build sensors that are uniquely capable of probing a wide range of phenomena in living cells including visualization of localized calcium signaling, sub-cellular activity gradients, and tension generation to name but a few. While FRET sensors have significantly impacted many fields, one must also be cognizant of the limitations to conventional, intensity-based FRET measurements stemming from variation in probe concentration, sensitivity to photobleaching, and bleed-through between the FRET fluorophores. Fluorescence lifetime imaging microscopy (FLIM) largely overcomes the limitations of intensity-based FRET measurements. In general terms, FLIM measures the time, which for the reporters described in this chapter is nanoseconds (ns), between photon absorption and emission by a fluorophore. When FLIM is applied to FRET sensors (FLIM-FRET), measurement of the donor fluorophore lifetime provides valuable information such as FRET efficiency and the percentage of reporters engaged in FRET. This chapter introduces fundamental principles of FLIM-FRET toward informing the practical application of the technique and, using two established FRET reporters as proofs of concept, outlines how to use a commercially available FLIM system.
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Affiliation(s)
| | - Ana P. Torres-Ocampo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
| | | | | | - James J. Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA
| | - Margaret M. Stratton
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
| | - Thomas J. Maresca
- Biology Department, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
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19
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CuO Nanoparticle-Protein Bioconjugate: Characterization of CuO Nanoparticles for the Study of the Interaction and Dynamic of Energy Transfer with Bovine Serum Albumin. BIONANOSCIENCE 2019. [DOI: 10.1007/s12668-019-00687-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Cui Y, Zhang X, Yu M, Zhu Y, Xing J, Lin J. Techniques for detecting protein-protein interactions in living cells: principles, limitations, and recent progress. SCIENCE CHINA-LIFE SCIENCES 2019; 62:619-632. [DOI: 10.1007/s11427-018-9500-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/12/2019] [Indexed: 01/07/2023]
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21
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Mintz KJ, Zhou Y, Leblanc RM. Recent development of carbon quantum dots regarding their optical properties, photoluminescence mechanism, and core structure. NANOSCALE 2019; 11:4634-4652. [PMID: 30834912 PMCID: PMC6467229 DOI: 10.1039/c8nr10059d] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Carbon quantum dots (CDs) are a relatively new class of carbon nanomaterials which have been studied very much in the last fifteen years to improve their already favorable properties. The optical properties of CDs have drawn particular interest as they display the unusual trait of excitation-dependent emission, as well as high fluorescence quantum yields (QY), long photoluminescence (PL) decay lifetimes, and photostability. These qualities naturally lead researchers to apply CDs in the field of imaging (particularly bio-imaging) and sensing. Since the amount of publications regarding CDs has been growing nearly exponentially in the last ten years, many improvements have been made in the optical properties of CDs such as QY and PL lifetime. However, a great deal of confusion remains regarding the PL mechanism of CDs as well as their structural properties. Therefore, presented in this review is a summary and discussion of the QYs and PL lifetimes reported in recent years. The effect of method as well as precursor has been evaluated and discussed appropriately. The current theories regarding the PL mechanism of CDs are discussed, with special attention to the concept of surface state-controlled PL. With this knowledge, the improvement of preparation and applications of CDs related to their optical properties will be easily accomplished. Further improvements can be made to CDs through the understanding of their structural and optical properties.
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Affiliation(s)
- Keenan J Mintz
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA.
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22
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Raicu V. Ab Initio Derivation of the FRET Equations Resolves Old Puzzles and Suggests Measurement Strategies. Biophys J 2019; 116:1313-1327. [PMID: 30885378 DOI: 10.1016/j.bpj.2019.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/27/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022] Open
Abstract
Quantitative imaging methods based on Förster resonance energy transfer (FRET) rely on the determination of an apparent FRET efficiency (Eapp), as well as donor and acceptor concentrations, to uncover the identity and relative abundance of the supramolecular (or quaternary) structures of associating macromolecules. Theoretical work has provided "structure-based" relationships between Eapp distributions and the quaternary structure models that underlie them. By contrast, the body of work that predicates the "signal-based" dependence of Eapp on directly measurable quantities (i.e., fluorescence emission of donors and acceptors) relies largely on plausibility arguments, one of which is the seemingly obvious assumption that the fraction of fluorescent molecules in the ground state pretty nearly equals the total concentration of molecules. In this work, we use the kinetic models of fluorescence in the presence and absence of FRET to rigorously derive useful relationships between Eapp and measurable fluorescence signals. Analysis of these relationships reveals a few anticipated results and some unexpected explanations for known experimental FRET puzzles, and it provides theoretical foundations for optimizing measurement strategies.
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Affiliation(s)
- Valerica Raicu
- Physics Department and Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin.
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23
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Stixová L, Komůrková D, Svobodová Kovaříková A, Bártová E. UVA irradiation strengthened an interaction between UBF1/2 proteins and H4K20 di-/tri-methylation. Chromosome Res 2019; 27:41-55. [PMID: 30610403 DOI: 10.1007/s10577-018-9596-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/29/2022]
Abstract
Repair of ribosomal DNA (rDNA) is a very important nuclear process due to the most active transcription of ribosomal genes. Proper repair of rDNA is required for physiological biogenesis of ribosomes. Here, we analyzed the epigenetics of the DNA damage response in a nucleolar compartment, thus in the ribosomal genes studied in nonirradiated and UVA-irradiated mouse embryonic fibroblasts (MEFs). We found that the promoter of ribosomal genes is not abundant on H4K20me2, but it is densely occupied by H4K20me3. Ribosomal genes, regulated via UBF1/2 proteins, were characterized by an interaction between UBF1/2 and H4K20me2/me3. This interaction was strengthened by UVA irradiation that additionally causes a focal accumulation of H4K20me3 in the nucleolus. No interaction has been found between UBF1/2 and H3K9me3. Interestingly, UVA irradiation decreases the levels of H3K9me3 and H4K20me3 at 28S rDNA. Altogether, the UVA light affects the epigenetic status of ribosomal genes at 28S rDNA and strengthens an interaction between UBF1/2 proteins and H4K20me2/me3.
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Affiliation(s)
- Lenka Stixová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic
| | - Denisa Komůrková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic
| | - Alena Svobodová Kovaříková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic.
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24
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Tardif C, Nadeau G, Labrecque S, Côté D, Lavoie-Cardinal F, De Koninck P. Fluorescence lifetime imaging nanoscopy for measuring Förster resonance energy transfer in cellular nanodomains. NEUROPHOTONICS 2019; 6:015002. [PMID: 30746389 PMCID: PMC6354015 DOI: 10.1117/1.nph.6.1.015002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/28/2018] [Indexed: 05/08/2023]
Abstract
Microscopy methods used to measure Förster resonance energy transfer (FRET) between fluorescently labeled proteins can provide information on protein interactions in cells. However, these methods are diffraction-limited, thus do not enable the resolution of the nanodomains in which such interactions occur in cells. To overcome this limitation, we assess FRET with an imaging system combining fluorescence lifetime imaging microscopy with stimulated emission depletion, termed fluorescence lifetime imaging nanoscopy (FLIN). The resulting FRET-FLIN approach utilizes immunolabeling of proteins in fixed cultured neurons. We demonstrate the capacity to discriminate nanoclusters of synaptic proteins exhibiting variable degrees of interactions with labeled binding partners inside dendritic spines of hippocampal neurons. This method enables the investigation of FRET within nanodomains of cells, approaching the scale of molecular signaling.
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Affiliation(s)
| | | | | | - Daniel Côté
- CERVO Brain Research Center, Québec (QC), Canada
- Université Laval, Département de physique, de génie physique et d’optique, Québec (QC), Canada
| | | | - Paul De Koninck
- CERVO Brain Research Center, Québec (QC), Canada
- Université Laval, Département de biochimie, de microbiologie et de bio-informatique, Québec (QC), Canada
- Address all correspondence to Paul De Koninck, E-mail:
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25
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Santra K, Smith EA, Song X, Petrich JW. A Bayesian Approach for Extracting Fluorescence Lifetimes from Sparse Data Sets and Its Significance for Imaging Experiments. Photochem Photobiol 2018; 95:773-779. [DOI: 10.1111/php.13057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/06/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Kalyan Santra
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
| | - Emily A. Smith
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
| | - Xueyu Song
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
| | - Jacob W. Petrich
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
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26
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Montaseri H, Forbes PBC. A triclosan turn-ON fluorescence sensor based on thiol-capped core/shell quantum dots. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 204:370-379. [PMID: 29958126 DOI: 10.1016/j.saa.2018.06.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Triclosan (TCS) is a common antimicrobial found in many personal care products. A large amount of TCS thus enters the wastewater system leading to the accumulation thereof in water sources. In this work, core-shell structured GSH-CdSe/ZnS fluorescent quantum dots (QDs) were synthesized based on organometallic synthesis with a thiol ligand capping agent. The GSH-CdSe/ZnS QDs showed excellent photostability and a photoluminescence quantum yield of 89%. The fluorescence of the GSH-CdSe/ZnS QDs was enhanced by the introduction of TCS, likely owing to fluorescence resonance energy transfer from TCS to the QDs, allowing for its use as a "turn on" fluorescence probe for the detection and determination of TCS. A linear response was observed in the range of 10-300 nmol L-1 with limits of detection and quantification of 3.7 and 12.4 nmol L-1 respectively. The probe displayed good recoveries (94%-117.5%) for the determination of TCS in tap and river water samples which demonstrated the suitability of this novel sensor for a monitoring application of environmental relevance.
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Affiliation(s)
- Hanieh Montaseri
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa
| | - Patricia B C Forbes
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa.
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27
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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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28
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Wang L, Xue Y, Xing J, Song K, Lin J. Exploring the Spatiotemporal Organization of Membrane Proteins in Living Plant Cells. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:525-551. [PMID: 29489393 DOI: 10.1146/annurev-arplant-042817-040233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plasma membrane proteins have important roles in transport and signal transduction. Deciphering the spatiotemporal organization of these proteins provides crucial information for elucidating the links between the behaviors of different molecules. However, monitoring membrane proteins without disrupting their membrane environment remains difficult. Over the past decade, many studies have developed single-molecule techniques, opening avenues for probing the stoichiometry and interactions of membrane proteins in their native environment by providing nanometer-scale spatial information and nanosecond-scale temporal information. In this review, we assess recent progress in the development of labeling and imaging technology for membrane protein analysis. We focus in particular on several single-molecule techniques for quantifying the dynamics and assembly of membrane proteins. Finally, we provide examples of how these new techniques are advancing our understanding of the complex biological functions of membrane proteins.
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Affiliation(s)
- Li Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Yiqun Xue
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jingjing Xing
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kai Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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29
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Herrington KA, Trinh AL, Dang C, O'Shaughnessy E, Hahn KM, Gratton E, Digman MA, Sütterlin C. Spatial analysis of Cdc42 activity reveals a role for plasma membrane-associated Cdc42 in centrosome regulation. Mol Biol Cell 2017; 28:2135-2145. [PMID: 28539409 PMCID: PMC5509425 DOI: 10.1091/mbc.e16-09-0665] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 11/11/2022] Open
Abstract
The ability of the small GTPase Cdc42 to regulate diverse cellular processes depends on tight spatial control of its activity. Cdc42 function is best understood at the plasma membrane (PM), where it regulates cytoskeletal organization and cell polarization. Active Cdc42 has also been detected at the Golgi, but its role and regulation at this organelle are only partially understood. Here we analyze the spatial distribution of Cdc42 activity by moni-toring the dynamics of the Cdc42 FLARE biosensor using the phasor approach to FLIM-FRET. Phasor analysis revealed that Cdc42 is active at all Golgi cisternae and that this activity is controlled by Tuba and ARHGAP10, two Golgi-associated Cdc42 regulators. To our surprise, FGD1, another Cdc42 GEF at the Golgi, was not required for Cdc42 regulation at the Golgi, although its depletion decreased Cdc42 activity at the PM. Similarly, changes in Golgi morphology did not affect Cdc42 activity at the Golgi but were associated with a substantial reduction in PM-associated Cdc42 activity. Of interest, cells with reduced Cdc42 activity at the PM displayed altered centrosome morphology, suggesting that centrosome regulation may be mediated by active Cdc42 at the PM. Our study describes a novel quantitative approach to determine Cdc42 activity at specific subcellular locations and reveals new regulatory principles and functions of this small GTPase.
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Affiliation(s)
- Kari A Herrington
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
| | - Andrew L Trinh
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697
| | - Carolyn Dang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
| | - Ellen O'Shaughnessy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Enrico Gratton
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697.,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697.,Centre for Bioactive Discovery in Health and Ageing, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
| | - Michelle A Digman
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697.,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697.,Centre for Bioactive Discovery in Health and Ageing, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
| | - Christine Sütterlin
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
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30
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Upconversion ratiometric fluorescence and colorimetric dual-readout assay for uric acid. Biosens Bioelectron 2016; 86:664-670. [DOI: 10.1016/j.bios.2016.07.055] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/15/2016] [Accepted: 07/16/2016] [Indexed: 12/20/2022]
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31
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Zhang Y, Cuyt A, Lee WS, Lo Bianco G, Wu G, Chen Y, Li DDU. Towards unsupervised fluorescence lifetime imaging using low dimensional variable projection. OPTICS EXPRESS 2016; 24:26777-26791. [PMID: 27857408 DOI: 10.1364/oe.24.026777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Analyzing large fluorescence lifetime imaging (FLIM) data is becoming overwhelming; the latest FLIM systems easily produce massive amounts of data, making an efficient analysis more challenging than ever. In this paper we propose the combination of a custom-fit variable projection method, with a Laguerre expansion based deconvolution, to analyze bi-exponential data obtained from time-domain FLIM systems. Unlike nonlinear least squares methods, which require a suitable initial guess from an experienced researcher, the new method is free from manual interventions and hence can support automated analysis. Monte Carlo simulations are carried out on synthesized FLIM data to demonstrate the performance compared to other approaches. The performance is also illustrated on real-life FLIM data obtained from the study of autofluorescence of daisy pollen and the endocytosis of gold nanorods (GNRs) in living cells. In the latter, the fluorescence lifetimes of the GNRs are much shorter than the full width at half maximum of the instrument response function. Overall, our proposed method contains simple steps and shows great promise in realising automated FLIM analysis of large data sets.
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32
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Wang L, Bi Y, Hou J, Li H, Xu Y, Wang B, Ding H, Ding L. Facile, green and clean one-step synthesis of carbon dots from wool: Application as a sensor for glyphosate detection based on the inner filter effect. Talanta 2016; 160:268-275. [PMID: 27591613 DOI: 10.1016/j.talanta.2016.07.020] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 07/01/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
Abstract
In this work, we reported a green route for the fabrication of fluorescent carbon dots (CDs). Wool, a kind of nontoxic and natural raw material, was chosen as the precursor to prepare CDs via a one-step microwave-assisted pyrolysis process. Compared with previously reported methods for preparation of CDs based on biomass materials, this method was simple, facile and free of any additives, such as acids, bases, or salts, which avoid the complicated post-treatment process to purify the CDs. The CDs have a high quantum yield (16.3%) and their fluorescence could be quenched by silver nanoparticles (AgNPs) based on inner filter effect (IFE). The presence of glyphosate could induce the aggregation of AgNPs and thus result in the fluorescence recovery of the quenched CDs. Based on this phenomenon, we constructed a fluorescence system (CDs/AgNPs) for determination of glyphosate. Under the optimized conditions, the fluorescence intensity of the CDs/AgNPs system was proportional to the concentration of glyphosate in the range of 0.025-2.5μgmL(-1), with a detection limit of 12ngmL(-1). Furthermore, the established method has been successfully used for glyphosate detection in the cereal samples with satisfactory results.
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Affiliation(s)
- Long Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Yidan Bi
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Juan Hou
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Huiyu Li
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Yuan Xu
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Bo Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Hong Ding
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Lan Ding
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China.
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Chen H, Fang A, He L, Zhang Y, Yao S. Sensitive fluorescent detection of H 2O 2 and glucose in human serum based on inner filter effect of squaric acid-iron(III) on the fluorescence of upconversion nanoparticle. Talanta 2016; 164:580-587. [PMID: 28107976 DOI: 10.1016/j.talanta.2016.10.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/23/2016] [Accepted: 10/02/2016] [Indexed: 12/24/2022]
Abstract
Diabetes mellitus is an epidemic disease that it has became a worldwide public health problem. Thus, blood glucose monitoring has attracted extensive attention. Here, we report a nanosensor based on inner filter effect (IFE) between upconversion nanoparticles (UCNPs) and squaric acid (SQA)-iron(III) for the highly sensitive and selective detection of glucose levels in human serum. In this assay, GOx-catalyzed oxidization of glucose produces gluconic acid and hydrogen peroxide (H2O2). The latter can catalytically oxidize iron(II) to iron(III) which can rapidly (<1min) coordinate with the SQA to produce (SQA)-iron(III). The absorption band of (SQA)-iron(III) largely covered the emission band of UCNPs, resulting the fluorescence emission of UCNPs was effectively quenched. Therefore, the glucose can be monitored based on the formation of SQA-iron(III). Under the optimal condition, the fluorescence quenching efficiency shows a good linear response to glucose concentration in the ranges of 7-340μmol/L with a detection limit of 2.3μmol/L. The developed method has been further applied to monitor glucose levels in human serum with satisfactory results. Compared with other fluorescence methods, current method displayed high sensitivity and signal-to-noise ratio. Meanwhile, this nanosystem is also generalizable and can be easily expanded to the detection of various H2O2-involved analytes.
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Affiliation(s)
- Hongyu Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
| | - Aijin Fang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
| | - Li He
- Hospital of Hunan Normal University, Hunan Normal University, Changsha 410081, PR China
| | - Youyu Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China.
| | - Shouzhuo Yao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
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Sivasankaran U, Cyriac ST, Menon S, Kumar KG. Fluorescence Turn off Sensor for Brilliant Blue FCF- an Approach Based on Inner Filter Effect. J Fluoresc 2016; 27:69-77. [PMID: 27639570 DOI: 10.1007/s10895-016-1935-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/07/2016] [Indexed: 10/21/2022]
Abstract
A nanosensor with fluorometric readout based on L-cysteine capped cadmium sulphide quantum dots for discriminative detection and determination of Brilliant blue FCF (BB) (in 0.5 M Tris buffer solution of pH 9.5) over other synthetic food colourants is developed. Mechanism of the nanosensor is based on inner filter effect (IFE). The addition of BB into quantum dot solution might induce the quenching of fluorescence. The nanosensor described in this report reveals its simplicity and flexibility due to less laborious and more cost-effective synthesis. The developed fluorescence sensor showed excellent selectivity towards BB, and allows the detection as low as 3.50 × 10-7 M. The developed sensor exhibited a linear concentration range of 4.00 × 10-5 to 4.50 × 10-6 M. More importantly, the proposed sensor exhibit sensitive responses toward BB in food samples such as sports drink and candies, demonstrating its potential in food analysis, which might be significant in food quality control in the future.
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Affiliation(s)
- Unni Sivasankaran
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, 22, India
| | - Soumya T Cyriac
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, 22, India
| | - Shalini Menon
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, 22, India
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Yu H, Saleeb R, Dalgarno P, Day-Uei Li D. Estimation of Fluorescence Lifetimes Via Rotational Invariance Techniques. IEEE Trans Biomed Eng 2016; 63:1292-300. [DOI: 10.1109/tbme.2015.2491364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Fang A, Long Q, Wu Q, Li H, Zhang Y, Yao S. Upconversion nanosensor for sensitive fluorescence detection of Sudan I–IV based on inner filter effect. Talanta 2016; 148:129-34. [DOI: 10.1016/j.talanta.2015.10.048] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/13/2015] [Accepted: 10/18/2015] [Indexed: 01/13/2023]
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37
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Niehörster T, Löschberger A, Gregor I, Krämer B, Rahn HJ, Patting M, Koberling F, Enderlein J, Sauer M. Multi-target spectrally resolved fluorescence lifetime imaging microscopy. Nat Methods 2016; 13:257-62. [PMID: 26808668 DOI: 10.1038/nmeth.3740] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/16/2015] [Indexed: 01/09/2023]
Abstract
We introduce a pattern-matching technique for efficient identification of fluorophore ratios in complex multidimensional fluorescence signals using reference fluorescence decay and spectral signature patterns of individual fluorescent probes. Alternating pulsed laser excitation at three different wavelengths and time-resolved detection on 32 spectrally separated detection channels ensures efficient excitation of fluorophores and a maximum gain of fluorescence information. Using spectrally resolved fluorescence lifetime imaging microscopy (sFLIM), we were able to visualize up to nine different target molecules simultaneously in mouse C2C12 cells. By exploiting the sensitivity of fluorescence emission spectra and the lifetime of organic fluorophores on environmental factors, we carried out fluorescence imaging of three different target molecules in human U2OS cells with the same fluorophore. Our results demonstrate that sFLIM can be used for super-resolution multi-target imaging by stimulated emission depletion (STED).
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Affiliation(s)
- Thomas Niehörster
- Department of Biotechnology &Biophysics, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Anna Löschberger
- Department of Biotechnology &Biophysics, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Ingo Gregor
- Drittes Physikalisches Institut, Georg-August-Universität, Göttingen, Germany
| | | | | | | | | | - Jörg Enderlein
- Drittes Physikalisches Institut, Georg-August-Universität, Göttingen, Germany
| | - Markus Sauer
- Department of Biotechnology &Biophysics, Julius Maximilian University of Würzburg, Würzburg, Germany
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38
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Measuring NLR Oligomerization IV: Using Förster Resonance Energy Transfer (FRET)-Fluorescence Lifetime Imaging Microscopy (FLIM) to Determine the Close Proximity of Inflammasome Components. Methods Mol Biol 2016; 1417:169-83. [PMID: 27221489 DOI: 10.1007/978-1-4939-3566-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Intracellular signaling and cellular activation have been demonstrated to reside on multi-protein complexes rather than in isolated proteins. Consequently, techniques to resolve these complexes have gained much attention over the last few years. Förster Resonance Energy Transfer (FRET) coupled with Fluorescence Lifetime Imaging Microscopy (FLIM) is a powerful tool to discriminate direct interactions between two proteins within a multi-protein complex. Here, we present the use of FRET-FLIM as an experimental tool for the interpretation of the inflammasome composition. We also introduce some considerations required for the correct use of this technique and the control experiments that should be implemented.
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39
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Omer T, Intes X, Hahn J. Temporal Data Set Reduction Based on D-Optimality for Quantitative FLIM-FRET Imaging. PLoS One 2015; 10:e0144421. [PMID: 26658308 PMCID: PMC4686107 DOI: 10.1371/journal.pone.0144421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/18/2015] [Indexed: 12/13/2022] Open
Abstract
Fluorescence lifetime imaging (FLIM) when paired with Förster resonance energy transfer (FLIM-FRET) enables the monitoring of nanoscale interactions in living biological samples. FLIM-FRET model-based estimation methods allow the quantitative retrieval of parameters such as the quenched (interacting) and unquenched (non-interacting) fractional populations of the donor fluorophore and/or the distance of the interactions. The quantitative accuracy of such model-based approaches is dependent on multiple factors such as signal-to-noise ratio and number of temporal points acquired when sampling the fluorescence decays. For high-throughput or in vivo applications of FLIM-FRET, it is desirable to acquire a limited number of temporal points for fast acquisition times. Yet, it is critical to acquire temporal data sets with sufficient information content to allow for accurate FLIM-FRET parameter estimation. Herein, an optimal experimental design approach based upon sensitivity analysis is presented in order to identify the time points that provide the best quantitative estimates of the parameters for a determined number of temporal sampling points. More specifically, the D-optimality criterion is employed to identify, within a sparse temporal data set, the set of time points leading to optimal estimations of the quenched fractional population of the donor fluorophore. Overall, a reduced set of 10 time points (compared to a typical complete set of 90 time points) was identified to have minimal impact on parameter estimation accuracy (≈5%), with in silico and in vivo experiment validations. This reduction of the number of needed time points by almost an order of magnitude allows the use of FLIM-FRET for certain high-throughput applications which would be infeasible if the entire number of time sampling points were used.
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Affiliation(s)
- Travis Omer
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States of America
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States of America
| | - Juergen Hahn
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States of America
- Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States of America
- * E-mail:
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40
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Quantum dots-fluorescence resonance energy transfer-based nanosensors and their application. Biosens Bioelectron 2015; 74:562-74. [DOI: 10.1016/j.bios.2015.06.076] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/02/2023]
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41
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Mohamad NR, Marzuki NHC, Buang NA, Huyop F, Wahab RA. An overview of technologies for immobilization of enzymes and surface analysis techniques for immobilized enzymes. BIOTECHNOL BIOTEC EQ 2015; 29:205-220. [PMID: 26019635 PMCID: PMC4434042 DOI: 10.1080/13102818.2015.1008192] [Citation(s) in RCA: 704] [Impact Index Per Article: 78.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/07/2014] [Indexed: 01/28/2023] Open
Abstract
The current demands of sustainable green methodologies have increased the use of enzymatic technology in industrial processes. Employment of enzyme as biocatalysts offers the benefits of mild reaction conditions, biodegradability and catalytic efficiency. The harsh conditions of industrial processes, however, increase propensity of enzyme destabilization, shortening their industrial lifespan. Consequently, the technology of enzyme immobilization provides an effective means to circumvent these concerns by enhancing enzyme catalytic properties and also simplify downstream processing and improve operational stability. There are several techniques used to immobilize the enzymes onto supports which range from reversible physical adsorption and ionic linkages, to the irreversible stable covalent bonds. Such techniques produce immobilized enzymes of varying stability due to changes in the surface microenvironment and degree of multipoint attachment. Hence, it is mandatory to obtain information about the structure of the enzyme protein following interaction with the support surface as well as interactions of the enzymes with other proteins. Characterization technologies at the nanoscale level to study enzymes immobilized on surfaces are crucial to obtain valuable qualitative and quantitative information, including morphological visualization of the immobilized enzymes. These technologies are pertinent to assess efficacy of an immobilization technique and development of future enzyme immobilization strategies.
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Affiliation(s)
- Nur Royhaila Mohamad
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Nur Haziqah Che Marzuki
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Nor Aziah Buang
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
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42
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Flynn DC, Bhagwat AR, Brenner MH, Núñez MF, Mork BE, Cai D, Swanson JA, Ogilvie JP. Pulse-shaping based two-photon FRET stoichiometry. OPTICS EXPRESS 2015; 23:3353-72. [PMID: 25836193 PMCID: PMC4394757 DOI: 10.1364/oe.23.003353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
Förster Resonance Energy Transfer (FRET) based measurements that calculate the stoichiometry of intermolecular interactions in living cells have recently been demonstrated, where the technique utilizes selective one-photon excitation of donor and acceptor fluorophores to isolate the pure FRET signal. Here, we present work towards extending this FRET stoichiometry method to employ two-photon excitation using a pulse-shaping methodology. In pulse-shaping, frequency-dependent phases are applied to a broadband femtosecond laser pulse to tailor the two-photon excitation conditions to preferentially excite donor and acceptor fluorophores. We have also generalized the existing stoichiometry theory to account for additional cross-talk terms that are non-vanishing under two-photon excitation conditions. Using the generalized theory we demonstrate two-photon FRET stoichiometry in live COS-7 cells expressing fluorescent proteins mAmetrine as the donor and tdTomato as the acceptor.
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Affiliation(s)
- Daniel C. Flynn
- Macromolecular Science and Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109
USA
| | - Amar R. Bhagwat
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
| | - Meredith H. Brenner
- Applied Physics Program, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
| | - Marcos F. Núñez
- Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
USA
| | - Briana E. Mork
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
| | - Dawen Cai
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109
USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109
USA
| | - Joel A. Swanson
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109
USA
| | - Jennifer P. Ogilvie
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
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Abstract
Optical imaging assays, especially fluorescence molecular assays, are minimally invasive if not completely noninvasive, and thus an ideal technique to be applied to live specimens. These fluorescence imaging assays are a powerful tool in biomedical sciences as they allow the study of a wide range of molecular and physiological events occurring in biological systems. Furthermore, optical imaging assays bridge the gap between the in vitro cell-based analysis of subcellular processes and in vivo study of disease mechanisms in small animal models. In particular, the application of Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM), well-known techniques widely used in microscopy, to the optical imaging assay toolbox, will have a significant impact in the molecular study of protein-protein interactions during cancer progression. This review article describes the application of FLIM-FRET to the field of optical imaging and addresses their various applications, both current and potential, to anti-cancer drug delivery and cancer research.
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Affiliation(s)
- Shilpi Rajoria
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
| | - Lingling Zhao
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Xavier Intes
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Margarida Barroso
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
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44
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Li DDU, Yu H, Chen Y. Fast bi-exponential fluorescence lifetime imaging analysis methods. OPTICS LETTERS 2015; 40:336-9. [PMID: 25680041 DOI: 10.1364/ol.40.000336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A new hardware-friendly bi-exponential fluorescence lifetime imaging (FLIM) algorithm has been proposed. Compared to conventional FLIM software, the proposed algorithms are noniterative offering direct calculation of lifetimes and therefore suitable for real-time applications. They are applicable to single-channel or 2D multichannel time-correlated single-photon counting (TCSPC) systems. The proposed methods have been tested on both synthesized and realistic FLIM data, and we have compared their performances with other recently proposed nonfitting bi-exponential techniques showing promising applications in future massive solid-state TCSPC imagers.
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45
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Marchetti L, Luin S, Bonsignore F, de Nadai T, Beltram F, Cattaneo A. Ligand-induced dynamics of neurotrophin receptors investigated by single-molecule imaging approaches. Int J Mol Sci 2015; 16:1949-79. [PMID: 25603178 PMCID: PMC4307343 DOI: 10.3390/ijms16011949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/05/2015] [Indexed: 01/14/2023] Open
Abstract
Neurotrophins are secreted proteins that regulate neuronal development and survival, as well as maintenance and plasticity of the adult nervous system. The biological activity of neurotrophins stems from their binding to two membrane receptor types, the tropomyosin receptor kinase and the p75 neurotrophin receptors (NRs). The intracellular signalling cascades thereby activated have been extensively investigated. Nevertheless, a comprehensive description of the ligand-induced nanoscale details of NRs dynamics and interactions spanning from the initial lateral movements triggered at the plasma membrane to the internalization and transport processes is still missing. Recent advances in high spatio-temporal resolution imaging techniques have yielded new insight on the dynamics of NRs upon ligand binding. Here we discuss requirements, potential and practical implementation of these novel approaches for the study of neurotrophin trafficking and signalling, in the framework of current knowledge available also for other ligand-receptor systems. We shall especially highlight the correlation between the receptor dynamics activated by different neurotrophins and the respective signalling outcome, as recently revealed by single-molecule tracking of NRs in living neuronal cells.
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Affiliation(s)
- Laura Marchetti
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Stefano Luin
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Fulvio Bonsignore
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Teresa de Nadai
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
| | - Fabio Beltram
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Antonino Cattaneo
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
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46
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Liu X, Qiu J. Recent advances in energy transfer in bulk and nanoscale luminescent materials: from spectroscopy to applications. Chem Soc Rev 2015; 44:8714-46. [DOI: 10.1039/c5cs00067j] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We discuss optical energy transfer involving ions, QDs, molecules etc., together with the relevant applications in different areas.
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Affiliation(s)
- Xiaofeng Liu
- State Key Laboratory of Modern Optical Instrumentation
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Jianrong Qiu
- State Key Laboratory of Modern Optical Instrumentation
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
- China
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47
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Sun Y, Periasamy A. Localizing protein-protein interactions in living cells using fluorescence lifetime imaging microscopy. Methods Mol Biol 2015; 1251:83-107. [PMID: 25391796 DOI: 10.1007/978-1-4939-2080-8_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the past decade, advances in fluorescence lifetime imaging have extensively applied in the life sciences, from fundamental biological investigations to advanced clinical diagnosis. Fluorescence lifetime imaging microscopy (FLIM) is now routinely used in the biological sciences to monitor dynamic signaling events inside living cells, e.g., Protein-Protein interactions. In this chapter, we describe the calibration of both time-correlated single-photon counting (TCSPC) and frequency domain (FD) FLIM systems and the acquisition and analysis of FLIM-FRET data for investigating Protein-Protein interactions in living cells.
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Affiliation(s)
- Yuansheng Sun
- W.M. Keck Center for Cellular Imaging, Biology, University of Virginia, B005 Physical and Life Sciences Building, White Head Road, Charlottesville, VA, 22904, USA
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48
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De Vos WH, Beghuin D, Schwarz CJ, Jones DB, van Loon JJWA, Bereiter-Hahn J, Stelzer EHK. Invited review article: Advanced light microscopy for biological space research. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:101101. [PMID: 25362364 DOI: 10.1063/1.4898123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.
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Affiliation(s)
- Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | | | - David B Jones
- Institute for Experimental Orthopaedics and Biomechanics, Philipps University, Marburg, Germany
| | - Jack J W A van Loon
- Department of Oral and Maxillofacial Surgery/Oral Pathology, VU University Medical Center and Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, Amsterdam, The Netherlands
| | | | - Ernst H K Stelzer
- Physical Biology, BMLS (FB15, IZN), Goethe University, Frankfurt am Main, Germany
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49
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Omer T, Zhao L, Intes X, Hahn J. Reduced temporal sampling effect on accuracy of time-domain fluorescence lifetime Förster resonance energy transfer. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:086023. [PMID: 25166472 PMCID: PMC4147194 DOI: 10.1117/1.jbo.19.8.086023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/30/2014] [Indexed: 05/04/2023]
Abstract
Fluorescence lifetime imaging (FLIM) aims at quantifying the exponential decay rate of fluorophores to yield lifetime maps over the imaged sample. When combined with Förster resonance energy transfer (FRET), the technique can be used to indirectly sense interactions at the nanoscale such as protein–protein interactions, protein–DNA interactions, and protein conformational changes. In the case of FLIM-FRET, the fluorescence intensity decays are fitted to a biexponential model in order to estimate the lifetime and fractional amplitude coefficients of each component of the population of the donor fluorophore (quenched and nonquenched). Numerous time data points, also called temporal or time gates, are typically employed for accurately estimating the model parameters, leading to lengthy acquisition times and significant computational demands. This work investigates the effect of the number and location of time gates on model parameter estimation accuracy. A detailed model of a FLIM-FRET imaging system is used for the investigation, and the simulation outcomes are validated with in vitro and in vivo experimental data. In all cases investigated, it is found that 10 equally spaced time gates allow robust estimation of model-based parameters with accuracy similar to that of full temporal datasets (90 gates).
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Affiliation(s)
- Travis Omer
- Rensselaer Polytechnic Institute, Department of Biomedical Engineering, 110 8th Street, Troy, New York 12180, United States
| | - Lingling Zhao
- Rensselaer Polytechnic Institute, Department of Biomedical Engineering, 110 8th Street, Troy, New York 12180, United States
| | - Xavier Intes
- Rensselaer Polytechnic Institute, Department of Biomedical Engineering, 110 8th Street, Troy, New York 12180, United States
| | - Juergen Hahn
- Rensselaer Polytechnic Institute, Departments of Biomedical Engineering and Chemical & Biological Engineering, 110 8th Street, Troy, New York 12180, United States
- Address all correspondence to: Juergen Hahn, E-mail:
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Liu J, Pampillo M, Guo F, Liu S, Cooperman BS, Farrell I, Dahary D, Gan BS, O'Gorman DB, Smilansky Z, Babwah AV, Leask A. Monitoring collagen synthesis in fibroblasts using fluorescently labeled tRNA pairs. J Cell Physiol 2014; 229:1121-9. [PMID: 24676899 DOI: 10.1002/jcp.24630] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 12/13/2022]
Abstract
There is a critical need for techniques that directly monitor protein synthesis within cells isolated from normal and diseased tissue. Fibrotic disease, for which there is no drug treatment, is characterized by the overexpression of collagens. Here, we use a bioinformatics approach to identify a pair of glycine and proline isoacceptor tRNAs as being specific for the decoding of collagen mRNAs, leading to development of a FRET-based approach, dicodon monitoring of protein synthesis (DiCoMPS), that directly monitors the synthesis of collagen. DiCoMPS aimed at detecting collagen synthesis will be helpful in identifying novel anti-fibrotic compounds in cells derived from patients with fibrosis of any etiology, and, suitably adapted, should be widely applicable in monitoring the synthesis of other proteins in cells.
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Affiliation(s)
- Jiaqi Liu
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada; Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
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