1
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Shi J, Yin W, Chen W. Mathematical models of TCR initial triggering. Front Immunol 2024; 15:1411614. [PMID: 39091495 PMCID: PMC11291225 DOI: 10.3389/fimmu.2024.1411614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
T cell receptors (TCRs) play crucial roles in regulating T cell response by rapidly and accurately recognizing foreign and non-self antigens. The process involves multiple molecules and regulatory mechanisms, forming a complex network to achieve effective antigen recognition. Mathematical modeling techniques can help unravel the intricate network of TCR signaling and identify key regulators that govern it. In this review, we introduce and briefly discuss relevant mathematical models of TCR initial triggering, with a focus on kinetic proofreading (KPR) models with different modified structures. We compare the topology structures, biological hypotheses, parameter choices, and simulation performance of each model, and summarize the advantages and limitations of them. Further studies on TCR modeling design, aiming for an optimized balance of specificity and sensitivity, are expected to contribute to the development of new therapeutic strategies.
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Affiliation(s)
- Jiawei Shi
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Weiwei Yin
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Wei Chen
- Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- Department of Cell Biology, School of Medicine, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
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2
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Liu X, Yu W, Mu X, Zhang W, Wang X, Gu Q. A fluorescence probe based on carbon dots for determination of dopamine utilizing its self-polymerization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 287:122112. [PMID: 36395584 DOI: 10.1016/j.saa.2022.122112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
A rapid and sensitive strategy for sensing dopamine (DA) was proposed based on the fluorescence quenching effects of polydopamine (PDA) on carbon dots (CDs). The green-emission fluorescence CDs were synthesized via a facile one-pot hydrothermal approach by employing p-phenylenediamine and ethanol as reagents. In alkaline environments, DA would polymerize to form PDA on surface of CDs, resulting in the fluorescence quenching of the detection system owing to the effects of fluorescence resonance energy transfer (FERT) and inner filter effect (IFE). The proposed fluorescence probe exhibits good selectivity and sensitivity to DA in the concentration range of 0.1-15 μM, with a limit of detection (LOD) of 37 nM. Results of detecting DA in serum samples indicate the broad potential of the proposed strategy for future application in diagnosis of DA-related diseases.
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Affiliation(s)
- Xin Liu
- College of Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Wei Yu
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun 130033, China
| | - Xiaowei Mu
- College of Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Wei Zhang
- College of Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Xinghua Wang
- College of Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China.
| | - Qiang Gu
- College of Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China.
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3
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Mahato J, Ray S, Maji SK, Chowdhury A. Spectrally Resolved FRET Microscopy of α-Synuclein Phase-Separated Liquid Droplets. Methods Mol Biol 2023; 2551:425-447. [PMID: 36310218 DOI: 10.1007/978-1-0716-2597-2_27] [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] [Indexed: 06/16/2023]
Abstract
Liquid-liquid phase separation (LLPS) has emerged as an important phenomenon associated with formation of membraneless organelles. Recently, LLPS has been shown to act as nucleation centers for disease-associated protein aggregation and amyloid fibril formation. Phase-separated α-synuclein droplets gradually rigidify during the course of protein aggregation, and it is very challenging to understand the biomolecular interactions that lead to liquid-like to solid-like transition using conventional ensemble measurements. Here, we describe a spectrally-resolved fluorescence microscopy based Förster resonance energy transfer (FRET) imaging to probe interactions of α-synuclein in individual droplets during LLPS-mediated aggregation. By acquiring entire emission spectral profiles of individual droplets upon sequential excitation of acceptors and donors therein, this technique allows for the quantification of sensitized emission proportional to the extent of FRET, which enables interrogation of the evolution of local interactions of donor-/acceptor-labeled α-synuclein molecules within each droplet. The present study on single droplets is not only an important development for studying LLPS but can also be used to investigate self-assembly or aggregation in biomolecular systems and soft materials.
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Affiliation(s)
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India.
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4
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Umabharathi PS, Karpagam S. Real scenario of metal ion sensor: is conjugated polymer helpful to detect hazardous metal ion. REV INORG CHEM 2022. [DOI: 10.1515/revic-2022-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Metal ions from natural and anthropogenic sources cause pollution to society and the environment is major concern in the present scenario. The deposition and contamination of metal ions in soil and water affect the biogeochemical cycles. Thus, it threatens the everyday life of living and non-living organisms. Reviews on the detection of metal ions through several techniques (Analytical methods, electrochemical techniques, and sensors) and materials (Nanoparticles, carbon dots (quantum dots), polymers, chiral molecules, metal-organic framework, carbon nanotubes, etc.) are addressed separately in the present literature. This review reveals the advantages and disadvantages of the techniques and materials for metal ion sensing with crucial factors. Furthermore, it focus on the capability of conjugated polymers (CPs) as metal ion sensors able to detect/sense hazardous metal ions from environmental samples. Six different routes can synthesize this type of CPs to get specific properties and better metal ion detecting capability in vast research areas. The metal ion detection by CP is time-independent, simple, and low cost compared to other materials/techniques. This review outlines recent literature on the conjugated polymer for cation, anion, and dual ion sensors. Over the last half decades published articles on the conjugated polymer are discussed and compared.
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Affiliation(s)
| | - Subramanian Karpagam
- Department of Chemistry , School of Advanced Sciences, Vellore Institute of Technology , Vellore - 14 , Tamil Nadu , India
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5
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Fujimoto KJ, Miyashita T, Dewa T, Yanai T. Determination of FRET orientation factor between artificial fluorophore and photosynthetic light-harvesting 2 complex (LH2). Sci Rep 2022; 12:15091. [PMID: 36065053 PMCID: PMC9445053 DOI: 10.1038/s41598-022-19375-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
The orientation factor of fluorescence resonance energy transfer (FRET) between photosynthetic light-harvesting 2 complex (LH2) and artificial fluorophore (Alexa Fluor 647: A647) was theoretically investigated. The orientation factor of 2/3, i.e., the isotropic mean, is widely used to predict the donor–acceptor distance from FRET measurements. However, this approximation seems inappropriate because the movement of A647 is possibly restricted by the bifunctional linker binding to LH2. In this study, we performed molecular dynamics (MD) simulations and electronic coupling calculations on the LH2-A647 conjugate to analyze its orientation factor. The MD results showed that A647 keeps a position approximately 26 Å away from the bacteriochlorophyll (BChl) assembly in LH2. The effective orientation factor was extracted from the electronic coupling calculated using the transition charge from electrostatic potential (TrESP) method. With MD snapshots, an averaged orientation factor was predicted to be 1.55, significantly different from the isotropic mean value. The analysis also suggested that the value of the refractive index employed in the previous studies is not suitable for this system. Furthermore, optimal orientations of A647 with larger orientation factors to improve FRET efficiency were searched using Euler angles. The present approach is useful for extending the applicability of FRET analysis.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan. .,Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan.
| | - Tomoya Miyashita
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Takehisa Dewa
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Takeshi Yanai
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan. .,Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan.
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6
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Sánchez-Álvarez M, Del Pozo MÁ, Bosch M, Pol A. Insights Into the Biogenesis and Emerging Functions of Lipid Droplets From Unbiased Molecular Profiling Approaches. Front Cell Dev Biol 2022; 10:901321. [PMID: 35756995 PMCID: PMC9213792 DOI: 10.3389/fcell.2022.901321] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Lipid droplets (LDs) are spherical, single sheet phospholipid-bound organelles that store neutral lipids in all eukaryotes and some prokaryotes. Initially conceived as relatively inert depots for energy and lipid precursors, these highly dynamic structures play active roles in homeostatic functions beyond metabolism, such as proteostasis and protein turnover, innate immunity and defense. A major share of the knowledge behind this paradigm shift has been enabled by the use of systematic molecular profiling approaches, capable of revealing and describing these non-intuitive systems-level relationships. Here, we discuss these advances and some of the challenges they entail, and highlight standing questions in the field.
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Affiliation(s)
- Miguel Sánchez-Álvarez
- Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Miguel Ángel Del Pozo
- Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Marta Bosch
- Lipid Trafficking and Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Department of Biomedical Sciences, Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Albert Pol
- Lipid Trafficking and Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Department of Biomedical Sciences, Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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7
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High-throughput optical assays for sensing serine hydrolases in living systems and their applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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9
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Kohrman AQ, Kim-Yip RP, Posfai E. Imaging developmental cell cycles. Biophys J 2021; 120:4149-4161. [PMID: 33964274 PMCID: PMC8516676 DOI: 10.1016/j.bpj.2021.04.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/30/2021] [Indexed: 01/05/2023] Open
Abstract
The last decade has seen a major expansion in development of live biosensors, the tools needed to genetically encode them into model organisms, and the microscopic techniques used to visualize them. When combined, these offer us powerful tools with which to make fundamental discoveries about complex biological processes. In this review, we summarize the availability of biosensors to visualize an essential cellular process, the cell cycle, and the techniques for single-cell tracking and quantification of these reporters. We also highlight studies investigating the connection of cellular behavior to the cell cycle, particularly through live imaging, and anticipate exciting discoveries with the combination of these technologies in developmental contexts.
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Affiliation(s)
- Abraham Q Kohrman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Rebecca P Kim-Yip
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey.
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10
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Cai C, Sun H, Hu L, Fan Z. Visualization of integrin molecules by fluorescence imaging and techniques. ACTA ACUST UNITED AC 2021; 45:229-257. [PMID: 34219865 PMCID: PMC8249084 DOI: 10.32604/biocell.2021.014338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Integrin molecules are transmembrane αβ heterodimers involved in cell adhesion, trafficking, and signaling. Upon activation, integrins undergo dynamic conformational changes that regulate their affinity to ligands. The physiological functions and activation mechanisms of integrins have been heavily discussed in previous studies and reviews, but the fluorescence imaging techniques -which are powerful tools for biological studies- have not. Here we review the fluorescence labeling methods, imaging techniques, as well as Förster resonance energy transfer assays used to study integrin expression, localization, activation, and functions.
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Affiliation(s)
- Chen Cai
- Department of Immunology, School of Medicine, UConn Health, Farmington, 06030, USA
| | - Hao Sun
- Department of Medicine, University of California, San Diego, La Jolla, 92093, USA
| | - Liang Hu
- Cardiovascular Institute of Zhengzhou University, Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450051, China
| | - Zhichao Fan
- Department of Immunology, School of Medicine, UConn Health, Farmington, 06030, USA
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11
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Nichani K, Li J, Suzuki M, Houston JP. Evaluation of Caspase-3 Activity During Apoptosis with Fluorescence Lifetime-Based Cytometry Measurements and Phasor Analyses. Cytometry A 2020; 97:1265-1275. [PMID: 32790129 PMCID: PMC7738394 DOI: 10.1002/cyto.a.24207] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/30/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
Caspase-3 is a well-described protease with many roles that impact the fate of a cell. During apoptosis, caspase-3 acts as an executioner caspase with important proteolytic functions that lead to the final stages of programmed cell death. Owing to this key role, caspase-3 is exploited intracellularly as a target of control of apoptosis for therapeutic outcomes. Yet the activation of caspase-3 during apoptosis is challenged by other roles and functions (e.g., paracrine signaling). This brief report presents a way to track caspase-3 levels using a flow cytometer that measures excited state fluorescence lifetimes and a signal processing approach that leads to a graphical phasor-based interpretation. An established Förster resonance energy transfer (FRET) bioprobe was used for this test; the connected donor and acceptor fluorophore is cleavable by caspase-3 during apoptosis induction. With the cell-by-cell decay kinetic data and phasor analyses we generate a caspase activation trajectory, which is used to interpret activation throughout apoptosis. When lifetime-based cytometry is combined with a FRET bioprobe and phasor analyses, enzyme activation can be simplified and quantified with phase and modulation data. We envision extrapolating this approach to high content screening, and reinforce the power of phasor approaches with cytometric data. Analyses such as these can be used to cluster cells by their phase and modulation "lifetime fingerprint" when the intracellular fluorescent probe is utilized as a sensor of enzyme activity. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Kapil Nichani
- Department of Chemical & Materials EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Jianzhi Li
- Department of Chemical & Materials EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Miho Suzuki
- Department of Functional Materials and ScienceGraduate School of Science and Engineering, Saitama UniversitySaitama338‐8570Japan
| | - Jessica P. Houston
- Department of Chemical & Materials EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
- Department of Functional Materials and ScienceGraduate School of Science and Engineering, Saitama UniversitySaitama338‐8570Japan
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12
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Talbert LE, Julian RR. Methionine and Selenomethionine as Energy Transfer Acceptors for Biomolecular Structure Elucidation in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1601-1608. [PMID: 31222676 PMCID: PMC6697561 DOI: 10.1007/s13361-019-02262-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 06/09/2023]
Abstract
Mass spectrometry affords rapid and sensitive analysis of peptides and proteins. Coupling spectroscopy with mass spectrometry allows for the development of new methods to enhance biomolecular structure determination. Herein, we demonstrate two new energy acceptors that can be utilized for action-excitation energy transfer experiments. In the first system, C-S bonds in methionine act as energy acceptors from native chromophores, including tyrosine, tryptophan, and phenylalanine. Comparison among chromophores reveals that tyrosine transfers energy most efficiently at 266 nm, but phenylalanine and tryptophan also transfer energy with comparable efficiencies. Overall, the C-S bond dissociation yields following energy transfer are low for methionine, which led to an investigation of selenomethionine, a common analog that is found in many naturally occurring proteins. Sulfur and selenium are chemically similar, but C-Se bonds are weaker than C-S bonds and have lower lying σ* anti-bonding orbitals. Excitation of peptides containing tyrosine and tryptophan results in efficient energy transfer to selenomethionine and abundant C-Se bond dissociation. A series of helical peptides were examined where the positions of the donor or acceptor were systematically scanned to explore the influence of distance and helix orientation on energy transfer. The distance was found to be the primary factor affecting energy transfer efficiency, suggesting that selenomethionine may be a useful acceptor for probing protein structure in the gas phase.
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Affiliation(s)
- Lance E Talbert
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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13
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FÖrster resonance energy transfer (FRET)-based biosensors for biological applications. Biosens Bioelectron 2019; 138:111314. [DOI: 10.1016/j.bios.2019.05.019] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022]
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14
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Du Y, Pan J, Choi JH. A review on optical imaging of DNA nanostructures and dynamic processes. Methods Appl Fluoresc 2019; 7:012002. [PMID: 30523978 DOI: 10.1088/2050-6120/aaed11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA self-assembly offers a powerful means to construct complex nanostructures and program dynamic molecular processes such as strand displacement. DNA nanosystems pack high structural complexity in a small scale (typically, <100 nm) and span dynamic features over long periods of time, which bring new challenges for characterizations. The spatial and temporal features of DNA nanosystems require novel experimental methods capable of high resolution imaging over long time periods. This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.
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Affiliation(s)
- Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907
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15
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Moroz P, Royo Romero L, Zamkov M. Colloidal semiconductor nanocrystals in energy transfer reactions. Chem Commun (Camb) 2019; 55:3033-3048. [DOI: 10.1039/c9cc00162j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Excitonic energy transfer is a versatile mechanism by which colloidal semiconductor nanocrystals can interact with a variety of nanoscale species. This feature article will discuss the latest research on the key scenarios under which semiconductor nanocrystals can engage in energy transfer with other nanoparticles, organic fluorophores, and plasmonic nanostructures, highlighting potential technological benefits to be gained from such processes.
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Affiliation(s)
- Pavel Moroz
- Department of Physics and Astronomy
- Bowling Green State University
- Bowling Green
- USA
- The Center for Photochemical Sciences
| | - Luis Royo Romero
- Department of Physics and Astronomy
- Bowling Green State University
- Bowling Green
- USA
| | - Mikhail Zamkov
- Department of Physics and Astronomy
- Bowling Green State University
- Bowling Green
- USA
- The Center for Photochemical Sciences
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16
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Wang M, Su K, Cao J, She Y, Abd El-Aty AM, Hacımüftüoğlu A, Wang J, Yan M, Hong S, Lao S, Wang Y. "Off-On" non-enzymatic sensor for malathion detection based on fluorescence resonance energy transfer between β-cyclodextrin@Ag and fluorescent probe. Talanta 2018; 192:295-300. [PMID: 30348392 DOI: 10.1016/j.talanta.2018.09.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/08/2018] [Accepted: 09/18/2018] [Indexed: 01/01/2023]
Abstract
Here, we developed a novel non-enzymatic rapid testing method for determination of organophosphate pesticide (malathion) in water. In principle, target molecule can block the Fluorescence resonance energy transfer (FRET) between chemical fluorescent probe (energy donor) and β-cyclodextrin-coated silver nanoparticles (@AgNP) (receptor). The effects of malathion on the dynamics of fluorescent probe and β-cyclodextrin@AgNP were evaluated and their properties were further characterized. The current methodology showed a good sensitivity of 0.01 μg/mL represented as a limit of detection (LOD) and the calibration curve was linear over the concentration range of 0.1-25 μg/mL. Recovery rate from water samples spiked at 3 different concentration levels (0.3, 0.4, and 0.6 μg/mL) showed satisfactory range between 83% and 101%.
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Affiliation(s)
- Miao Wang
- Institute of Quality Standardization & Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100193 Beijing, China; Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture, 100193 Beijing, China
| | - Kun Su
- Institute of Quality Standardization & Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100193 Beijing, China; Baotou Medical College, 014040 Baotou, China
| | - Jing Cao
- Institute of Quality Standardization & Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Yongxin She
- Institute of Quality Standardization & Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100193 Beijing, China; Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture, 100193 Beijing, China.
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt; Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
| | - Ahmet Hacımüftüoğlu
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
| | - Jing Wang
- Institute of Quality Standardization & Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100193 Beijing, China; Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture, 100193 Beijing, China; Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, 53003 Nanning, China.
| | - Mengmeng Yan
- Institute of Quality Standardization & Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100193 Beijing, China; Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture, 100193 Beijing, China
| | - Sihui Hong
- Institute of Quality Standardization & Testing Technology for Agro-products, Chinese Academy of Agricultural Sciences, 100193 Beijing, China; Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture, 100193 Beijing, China
| | - Shuibing Lao
- Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, 53003 Nanning, China
| | - Yanli Wang
- Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, 53003 Nanning, China
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17
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Moroz P, Jin Z, Sugiyama Y, Lara D, Razgoniaeva N, Yang M, Kholmicheva N, Khon D, Mattoussi H, Zamkov M. Competition of Charge and Energy Transfer Processes in Donor-Acceptor Fluorescence Pairs: Calibrating the Spectroscopic Ruler. ACS NANO 2018; 12:5657-5665. [PMID: 29883087 DOI: 10.1021/acsnano.8b01451] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sensing strategies utilizing Förster resonance energy transfer (FRET) are widely used for probing biological phenomena. FRET sensitivity to the donor-acceptor distance makes it ideal for measuring the concentration of a known analyte or determining the spatial separation between fluorescent labels in a macromolecular assembly. The difficulty lies in extracting the FRET efficiency from the acceptor-induced quenching of the donor emission, which may contain a significant non-FRET contribution. Here, we demonstrate a general spectroscopic approach for differentiating between charge transfer and energy transfer (ET) processes in donor-acceptor assemblies and apply the developed method for unravelling the FRET/non-FRET contributions in cyanine dye-semiconductor quantum dot (QD) constructs. The present method relies on correlating the amplitude of the acceptor emission to specific changes in the donor excitation profile in order to extract ET-only transfer efficiencies. Quenching of the donor emission is then utilized to determine the non-ET component, tentatively attributed to the charge transfer. We observe that the latter accounts for 50-99% of donor emission quenching in QD-Cy5 and QD-Cy7 systems, stressing the importance of determining the non-FRET efficiency in a spectroscopic ruler and other FRET-based sensing applications.
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Affiliation(s)
| | - Zhicheng Jin
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32303 , United States
| | - Yuya Sugiyama
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32303 , United States
| | - D'Andree Lara
- Department of Chemistry and Biochemistry , St. Mary's University , San Antonio , Texas 78228 , United States
| | | | | | | | - Dmitriy Khon
- Department of Chemistry and Biochemistry , St. Mary's University , San Antonio , Texas 78228 , United States
| | - Hedi Mattoussi
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32303 , United States
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18
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Chen B, Su Q, Kong W, Wang Y, Shi P, Wang F. Energy transfer-based biodetection using optical nanomaterials. J Mater Chem B 2018; 6:2924-2944. [DOI: 10.1039/c8tb00614h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review focuses on recent progress in the development of FRET probes and the applications of FRET-based sensing systems.
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Affiliation(s)
- Bing Chen
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Qianqian Su
- Institute of Nanochemistry and Nanobiology
- Shanghai University
- Shanghai 200444
- China
| | - Wei Kong
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Yuan Wang
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
- China
| | - Peng Shi
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
- China
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
| | - Feng Wang
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
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19
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Lehner F, Kudlinzki D, Richter C, Müller-Werkmeister HM, Eberl KB, Bredenbeck J, Schwalbe H, Silvers R. Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding. Chembiochem 2017; 18:2340-2350. [DOI: 10.1002/cbic.201700437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Florian Lehner
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Denis Kudlinzki
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium; DKTK; German Cancer Research Center; DKFZ; Im Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Christian Richter
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | | | - Katharina B. Eberl
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Jens Bredenbeck
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Robert Silvers
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- Present address: Francis Bitter Magnet Laboratory; Massachusetts Institute of Technology; Cambridge MA 02139 USA
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20
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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21
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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22
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Zhang Z, Zhang M, Wu XY, Chang Z, Lee YI, Huy BT, Sakthivel K, Liu JF, Jiang GB. Upconversion fluorescence resonance energy transfer—a novel approach for sensitive detection of fluoroquinolones in water samples. Microchem J 2016. [DOI: 10.1016/j.microc.2015.08.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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23
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Lagarrigue F, Vikas Anekal P, Lee HS, Bachir AI, Ablack JN, Horwitz AF, Ginsberg MH. A RIAM/lamellipodin-talin-integrin complex forms the tip of sticky fingers that guide cell migration. Nat Commun 2015; 6:8492. [PMID: 26419705 PMCID: PMC4589889 DOI: 10.1038/ncomms9492] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/26/2015] [Indexed: 01/10/2023] Open
Abstract
The leading edge of migrating cells contains rapidly translocating activated integrins associated with growing actin filaments that form 'sticky fingers' to sense extracellular matrix and guide cell migration. Here we utilized indirect bimolecular fluorescence complementation to visualize a molecular complex containing a Mig-10/RIAM/lamellipodin (MRL) protein (Rap1-GTP-interacting adaptor molecule (RIAM) or lamellipodin), talin and activated integrins in living cells. This complex localizes at the tips of growing actin filaments in lamellipodial and filopodial protrusions, thus corresponding to the tips of the 'sticky fingers.' Formation of the complex requires talin to form a bridge between the MRL protein and the integrins. Moreover, disruption of the MRL protein-integrin-talin (MIT) complex markedly impairs cell protrusion. These data reveal the molecular basis of the formation of 'sticky fingers' at the leading edge of migrating cells and show that an MIT complex drives these protrusions.
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Affiliation(s)
- Frederic Lagarrigue
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Praju Vikas Anekal
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Ho-Sup Lee
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Alexia I Bachir
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jailal N Ablack
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Alan F Horwitz
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Mark H Ginsberg
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
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24
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Fluorescent CD4 probe for potential HIV-1 gp120 protein detection. Bioorg Med Chem Lett 2015; 25:1182-5. [DOI: 10.1016/j.bmcl.2015.01.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 02/02/2023]
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25
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26
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Dou QQ, Rengaramchandran A, Selvan ST, Paulmurugan R, Zhang Y. Core-shell upconversion nanoparticle - semiconductor heterostructures for photodynamic therapy. Sci Rep 2015; 5:8252. [PMID: 25652742 PMCID: PMC4317689 DOI: 10.1038/srep08252] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/09/2015] [Indexed: 12/27/2022] Open
Abstract
Core-shell nanoparticles (CSNPs) with diverse chemical compositions have been attracting greater attention in recent years. However, it has been a challenge to develop CSNPs with different crystal structures due to the lattice mismatch of the nanocrystals. Here we report a rational design of core-shell heterostructure consisting of NaYF4:Yb,Tm upconversion nanoparticle (UCN) as the core and ZnO semiconductor as the shell for potential application in photodynamic therapy (PDT). The core-shell architecture (confirmed by TEM and STEM) enables for improving the loading efficiency of photosensitizer (ZnO) as the semiconductor is directly coated on the UCN core. Importantly, UCN acts as a transducer to sensitize ZnO and trigger the generation of cytotoxic reactive oxygen species (ROS) to induce cancer cell death. We also present a firefly luciferase (FLuc) reporter gene based molecular biosensor (ARE-FLuc) to measure the antioxidant signaling response activated in cells during the release of ROS in response to the exposure of CSNPs under 980 nm NIR light. The breast cancer cells (MDA-MB-231 and 4T1) exposed to CSNPs showed significant release of ROS as measured by aminophenyl fluorescein (APF) and ARE-FLuc luciferase assays, and ~45% cancer cell death as measured by MTT assay, when illuminated with 980 nm NIR light.
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Affiliation(s)
- Qing Qing Dou
- Institute of Materials Research and Engineering (IMRE), A * STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| | - Adith Rengaramchandran
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Palo Alto, California 94304, USA
| | - Subramanian Tamil Selvan
- 1] Institute of Materials Research and Engineering (IMRE), A * STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602 [2] Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Palo Alto, California 94304, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575
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27
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Khrenova M, Topol I, Collins J, Nemukhin A. Estimating orientation factors in the FRET theory of fluorescent proteins: the TagRFP-KFP pair and beyond. Biophys J 2015; 108:126-32. [PMID: 25564859 PMCID: PMC4286598 DOI: 10.1016/j.bpj.2014.11.1859] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/20/2014] [Accepted: 11/06/2014] [Indexed: 11/29/2022] Open
Abstract
The orientation factor κ(2), one of the key parameters defining Förster resonance energy transfer efficiency, is determined by the transition dipole moment orientations of the donor and acceptor species. Using the results of quantum chemical and quantum mechanical/molecular mechanical calculations for the chromophore-containing pockets in selected colored proteins of the green fluorescent protein family, we derived transition dipole moments corresponding to the S0,min → S1 excitation for green fluorescent protein, red fluorescent protein (TagRFP), and kindling fluorescent protein, and the S1,min → S0 emission for TagRFP. These data allowed us to estimate κ(2) values for the TagRFP-linker-kindling fluorescent protein tetrameric complex required for constructing novel sensors.
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Affiliation(s)
- Maria Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Igor Topol
- Advanced Biomedical Computing Center, Information Systems Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland.
| | - Jack Collins
- Advanced Biomedical Computing Center, Information Systems Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation; Emanuel Institute of Biochemical Physics, Moscow, Russian Federation
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28
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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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29
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Hendricks N, Lareau NM, Stow SM, McLean JA, Julian RR. Bond-specific dissociation following excitation energy transfer for distance constraint determination in the gas phase. J Am Chem Soc 2014; 136:13363-70. [PMID: 25174489 PMCID: PMC4183596 DOI: 10.1021/ja507215q] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Indexed: 01/02/2023]
Abstract
Herein, we report chemistry that enables excitation energy transfer (EET) to be accurately measured via action spectroscopy on gaseous ions in an ion trap. It is demonstrated that EET between tryptophan or tyrosine and a disulfide bond leads to excited state, homolytic fragmentation of the disulfide bond. This phenomenon exhibits a tight distance dependence, which is consistent with Dexter exchange transfer. The extent of fragmentation of the disulfide bond can be used to determine the distance between the chromophore and disulfide bond. The chemistry is well suited for the examination of protein structure in the gas phase because native amino acids can serve as the donor/acceptor moieties. Furthermore, both tyrosine and tryptophan exhibit unique action spectra, meaning that the identity of the donating chromophore can be easily determined in addition to the distance between donor/acceptor. Application of the method to the Trpcage miniprotein reveals distance constraints that are consistent with a native-like fold for the +2 charge state in the gas phase. This structure is stabilized by several salt bridges, which have also been observed to be important previously in proteins that retain native-like structures in the gas phase. The ability of this method to measure specific distance constraints, potentially at numerous positions if combined with site-directed mutagenesis, significantly enhances our ability to examine protein structure in the gas phase.
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Affiliation(s)
- Nathan
G. Hendricks
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Nichole M. Lareau
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology (VICB), and
Vanderbilt Institute for Integrative Biosystems Research and Education
(VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sarah M. Stow
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology (VICB), and
Vanderbilt Institute for Integrative Biosystems Research and Education
(VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology (VICB), and
Vanderbilt Institute for Integrative Biosystems Research and Education
(VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ryan R. Julian
- Department
of Chemistry, University of California, Riverside, California 92521, United States
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30
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Kelkar SS, Xue L, Turner SR, Reineke TM. Lanthanide-Containing Polycations for Monitoring Polyplex Dynamics via Lanthanide Resonance Energy Transfer. Biomacromolecules 2014; 15:1612-24. [DOI: 10.1021/bm401870z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sneha S. Kelkar
- Department
of Chemistry and Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
- Wake Forest Institute for Regenerative Medicine and Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Winston-Salem, North Carolina 27101, United States
| | - Lian Xue
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - S. Richard Turner
- Department
of Chemistry and Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Theresa M. Reineke
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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31
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Rehman S, Gladman JT, Periasamy A, Sun Y, Mahadevan MS. Development of an AP-FRET based analysis for characterizing RNA-protein interactions in myotonic dystrophy (DM1). PLoS One 2014; 9:e95957. [PMID: 24781112 PMCID: PMC4004549 DOI: 10.1371/journal.pone.0095957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/31/2014] [Indexed: 01/09/2023] Open
Abstract
Förster Resonance Energy Transfer (FRET) microscopy is a powerful tool used to identify molecular interactions in live or fixed cells using a non-radiative transfer of energy from a donor fluorophore in the excited state to an acceptor fluorophore in close proximity. FRET can be a very sensitive tool to study protein-protein and/or protein-nucleic acids interactions. RNA toxicity is implicated in a number of disorders; especially those associated with expanded repeat sequences, such as myotonic dystrophy. Myotonic dystrophy (DM1) is caused by a (CTG)n repeat expansion in the 3′ UTR of the DMPK gene which results in nuclear retention of mutant DMPK transcripts in RNA foci. This results in toxic gain-of-function effects mediated through altered functions of RNA-binding proteins (e.g. MBNL1, hnRNPH, CUGBP1). In this study we demonstrate the potential of a new acceptor photobleaching assay to measure FRET (AP-FRET) between RNA and protein. We chose to focus on the interaction between MBNL1 and mutant DMPK mRNA in cells from DM1 patients due to the strong microscopic evidence of their co-localization. Using this technique we have direct evidence of intracellular interaction between MBNL1 and the DMPK RNA. Furthermore using the AP-FRET assay and MBNL1 mutants, we show that all four zinc-finger motifs in MBNL1 are crucial for MBNL1-RNA foci interactions. The data derived using this new assay provides compelling evidence for the interaction between RNA binding proteins and RNA foci, and mechanistic insights into MBNL1-RNA foci interaction demonstrating the power of AP-FRET in examining RNA-Protein interactions in DM1.
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Affiliation(s)
- Shagufta Rehman
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jordan T Gladman
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ammasi Periasamy
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Yuansheng Sun
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mani S Mahadevan
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
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32
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Chuang C, Knoester J, Cao J. Scaling Relations and Optimization of Excitonic Energy Transfer Rates between One-Dimensional Molecular Aggregates. J Phys Chem B 2014; 118:7827-34. [DOI: 10.1021/jp4124502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chern Chuang
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jasper Knoester
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh
4, AG Groningen 9747, The Netherlands
| | - Jianshu Cao
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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33
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Beutler M, Heisterkamp IM, Piltz B, Stief P, De Beer D. Microscopic oxygen imaging based on fluorescein bleaching efficiency measurements. Microsc Res Tech 2014; 77:341-7. [PMID: 24610786 DOI: 10.1002/jemt.22350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 01/25/2014] [Accepted: 02/18/2014] [Indexed: 11/09/2022]
Abstract
Photobleaching of the fluorophore fluorescein in an aqueous solution is dependent on the oxygen concentration. Therefore, the time-dependent bleaching behavior can be used to measure of dissolved oxygen concentrations. The method can be combined with epi-fluorescence microscopy. The molecular states of the fluorophore can be expressed by a three-state energy model. This leads to a set of differential equations which describe the photobleaching behavior of fluorescein. The numerical solution of these equations shows that in a conventional wide-field fluorescence microscope, the fluorescence of fluorescein will fade out faster at low than at high oxygen concentration. Further simulation showed that a simple ratio function of different time-points during a fluorescence decay recorded during photobleaching could be used to describe oxygen concentrations in an aqueous solution. By careful choice of dye concentration and excitation light intensity the sensitivity in the oxygen concentration range of interest can be optimized. In the simulations, the estimation of oxygen concentration by the ratio function was very little affected by the pH value in the range of pH 6.5-8.5. Filming the fluorescence decay by a charge-coupled-device (ccd) camera mounted on a fluorescence microscope allowed a pixelwise estimation of the ratio function in a microscopic image. Use of a microsensor and oxygen-consuming bacteria in a sample chamber enabled the calibration of the system for quantification of absolute oxygen concentrations. The method was demonstrated on nitrifying biofilms growing on snail and mussel shells, showing clear effects of metabolic activity on oxygen concentrations.
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Affiliation(s)
- Martin Beutler
- bionsys GmbH, Fahrenheitstraße 1, 28359, Bremen, Germany
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Lee JW, Lee S, Jang S, Han KY, Kim Y, Hyun J, Kim SK, Lee Y. Preparation of non-aggregated fluorescent nanodiamonds (FNDs) by non-covalent coating with a block copolymer and proteins for enhancement of intracellular uptake. MOLECULAR BIOSYSTEMS 2013; 9:1004-11. [PMID: 23364398 DOI: 10.1039/c2mb25431j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescent nanodiamonds (FNDs) are very promising fluorophores for use in biosystems due to their high biocompatibility and photostability. To overcome their tendency to aggregate in physiological solutions, which severely limits the biological applications of FNDs, we developed a new non-covalent coating method using a block copolymer, PEG-b-P(DMAEMA-co-BMA), or proteins such as BSA and HSA. By simple mixing of the block copolymer with FNDs, the cationic DMAEMA and hydrophobic BMA moieties can strongly interact with the anionic and hydrophobic moieties on the FND surface, while the PEG block can form a shell to prevent the direct contact between FNDs. The polymer-coated FNDs, along with BSA- and HSA-coated FNDs, showed non-aggregation characteristics and maintained their size at the physiological salt concentration. The well-dispersed, polymer- or protein-coated FNDs in physiological solutions showed enhanced intracellular uptake, which was confirmed by CLSM. In addition, the biocompatibility of the coated FNDs was expressly supported by a cytotoxicity assay. Our simple non-covalent coating with the block copolymer, which can be easily modified by various chemical methods, projects a very promising outlook for future biomedical applications, especially in comparison with covalent coating or protein-based coating.
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Affiliation(s)
- Jong Woo Lee
- WCU Department of Biophysics and Chemical Biology, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, Republic of Korea
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Duarte JM, Biyani N, Baskaran K, Capitani G. An analysis of oligomerization interfaces in transmembrane proteins. BMC STRUCTURAL BIOLOGY 2013; 13:21. [PMID: 24134166 PMCID: PMC4015793 DOI: 10.1186/1472-6807-13-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/11/2013] [Indexed: 01/05/2023]
Abstract
BACKGROUND The amount of transmembrane protein (TM) structures solved to date is now large enough to attempt large scale analyses. In particular, extensive studies of oligomeric interfaces in the transmembrane region are now possible. RESULTS We have compiled the first fully comprehensive set of validated transmembrane protein interfaces in order to study their features and assess what differentiates them from their soluble counterparts. CONCLUSIONS The general features of TM interfaces do not differ much from those of soluble proteins: they are large, tightly packed and possess many interface core residues. In our set, membrane lipids were not found to significantly mediate protein-protein interfaces. Although no G protein-coupled receptor (GPCR) was included in the validated set, we analyzed the crystallographic dimerization interfaces proposed in the literature. We found that the putative dimer interfaces proposed for class A GPCRs do not show the usual patterns of stable biological interfaces, neither in terms of evolution nor of packing, thus they likely correspond to crystal interfaces. We cannot however rule out the possibility that they constitute transient or weak interfaces. In contrast we do observe a clear signature of biological interface for the proposed dimer of the class F human Smoothened receptor.
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Affiliation(s)
- Jose M Duarte
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, 5232, Switzerland
| | - Nikhil Biyani
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, 5232, Switzerland
| | - Kumaran Baskaran
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, 5232, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, 5232, Switzerland
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Wang Y, Xia J, Wang LV. Deep-tissue photoacoustic tomography of Förster resonance energy transfer. JOURNAL OF BIOMEDICAL OPTICS 2013; 18:101316. [PMID: 23884608 PMCID: PMC3719951 DOI: 10.1117/1.jbo.18.10.101316] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/01/2013] [Accepted: 07/03/2013] [Indexed: 05/20/2023]
Abstract
Förster resonance energy transfer (FRET) is a distance-dependent process that transfers excited state energy from a donor molecule to an acceptor molecule without the emission of a photon. The FRET rate is determined by the proximity between the donor and the acceptor molecules; it becomes significant only when the proximity is within several nanometers. Therefore, FRET has been applied to visualize interactions and conformational changes of biomolecules, such as proteins, lipids, and nucleic acids that cannot be resolved by optical microscopy. Here, we report photoacoustic tomography of FRET efficiency at a 1-cm depth in chicken breast tissue, whereas conventional high-resolution fluorescence imaging is limited to <0.1 cm. Photoacoustic tomography is expected to facilitate the examination of FRET phenomena in living organisms.
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Affiliation(s)
- Yu Wang
- Washington University in St. Louis, Department of Biomedical Engineering, Optical Imaging Laboratory, 1 Brookings Dr., St. Louis, Missouri 63130
| | - Jun Xia
- Washington University in St. Louis, Department of Biomedical Engineering, Optical Imaging Laboratory, 1 Brookings Dr., St. Louis, Missouri 63130
| | - Lihong V. Wang
- Washington University in St. Louis, Department of Biomedical Engineering, Optical Imaging Laboratory, 1 Brookings Dr., St. Louis, Missouri 63130
- Address all correspondence to: Lihong V. Wang, Washington University in St. Louis, Department of Biomedical Engineering, Optical Imaging Laboratory, 1 Brookings Dr., St. Louis, Missouri 63130. Tel: (314) 935-6152; Fax: (314) 935-7448; E-mail:
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Chen S, Fahmi NE, Wang L, Bhattacharya C, Benkovic SJ, Hecht SM. Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids. J Am Chem Soc 2013; 135:12924-7. [PMID: 23941571 PMCID: PMC3785542 DOI: 10.1021/ja403007r] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Two fluorescent amino acids, including the novel fluorescent species 4-biphenyl-l-phenylalanine (1), have been incorporated at positions 17 and 115 of dihydrofolate reductase (DHFR) to enable a study of conformational changes associated with inhibitor binding. Unlike most studies involving fluorescently labeled proteins, the fluorophores were incorporated into the amino acid side chains, and both probes [1 and L-(7-hydroxycoumarin-4-yl)ethylglycine (2)] were smaller than fluorophores typically used for such studies. The DHFR positions were chosen as potentially useful for Förster resonance energy transfer (FRET) measurements on the basis of their estimated separation (17-18 Å) and the expected change in distance along the reaction coordinate. Also of interest was the steric accessibility of the two sites: Glu17 is on the surface of DHFR, while Ile115 is within a folded region of the protein. Modified DHFR I (1 at position 17; 2 at position 115) and DHFR II (2 at position 17; 1 at position 115) were both catalytically competent. However, DHFR II containing the potentially rotatable biphenylphenylalanine moiety at sterically encumbered position 115 was significantly more active than DHFR I. Irradiation of the modified DHFRs at 280 nm effected excitation of 1, energy transfer to 2, and emission by 2 at 450 nm. However, the energy transfer was substantially more efficient in DHFR II. The effect of inhibitor binding was also measured. Trimethoprim mediated concentration-dependent diminution of the emission observed at 450 nm for DHFR II but not for DHFR I. These findings demonstrate that amino acids containing small fluorophores can be introduced into DHFR with minimal disruption of function and in a fashion that enables sensitive monitoring of changes in DHFR conformation.
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Affiliation(s)
- Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nour Eddine Fahmi
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Lin Wang
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Chandrabali Bhattacharya
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J. Benkovic
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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Laverty DJ, Kury AL, Kuksin D, Pirani A, Flanagan K, Chan LLY. Automated quantification of budding Saccharomyces cerevisiae using a novel image cytometry method. ACTA ACUST UNITED AC 2013; 40:581-8. [DOI: 10.1007/s10295-013-1263-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
Abstract
Abstract
The measurements of concentration, viability, and budding percentages of Saccharomyces cerevisiae are performed on a routine basis in the brewing and biofuel industries. Generation of these parameters is of great importance in a manufacturing setting, where they can aid in the estimation of product quality, quantity, and fermentation time of the manufacturing process. Specifically, budding percentages can be used to estimate the reproduction rate of yeast populations, which directly correlates with metabolism of polysaccharides and bioethanol production, and can be monitored to maximize production of bioethanol during fermentation. The traditional method involves manual counting using a hemacytometer, but this is time-consuming and prone to human error. In this study, we developed a novel automated method for the quantification of yeast budding percentages using Cellometer image cytometry. The automated method utilizes a dual-fluorescent nucleic acid dye to specifically stain live cells for imaging analysis of unique morphological characteristics of budding yeast. In addition, cell cycle analysis is performed as an alternative method for budding analysis. We were able to show comparable yeast budding percentages between manual and automated counting, as well as cell cycle analysis. The automated image cytometry method is used to analyze and characterize corn mash samples directly from fermenters during standard fermentation. Since concentration, viability, and budding percentages can be obtained simultaneously, the automated method can be integrated into the fermentation quality assurance protocol, which may improve the quality and efficiency of beer and bioethanol production processes.
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Affiliation(s)
- Daniel J Laverty
- Department of Technology R&D, Nexcelom Bioscience LLC 360 Merrimack St. Building 9 01843 Lawrence MA USA
- grid.419758.6 0000 0001 2236 9819 Center for Biotechnology and Biomedical Sciences, Merrimack College 01845 North Andover MA USA
| | - Alexandria L Kury
- Department of Technology R&D, Nexcelom Bioscience LLC 360 Merrimack St. Building 9 01843 Lawrence MA USA
- grid.419758.6 0000 0001 2236 9819 Center for Biotechnology and Biomedical Sciences, Merrimack College 01845 North Andover MA USA
| | - Dmitry Kuksin
- Department of Technology R&D, Nexcelom Bioscience LLC 360 Merrimack St. Building 9 01843 Lawrence MA USA
- grid.419758.6 0000 0001 2236 9819 Center for Biotechnology and Biomedical Sciences, Merrimack College 01845 North Andover MA USA
| | - Alnoor Pirani
- Department of Applications, Nexcelom Bioscience LLC 01843 Lawrence MA USA
| | - Kevin Flanagan
- Department of Software Development, Nexcelom Bioscience LLC 01843 Lawrence MA USA
| | - Leo Li-Ying Chan
- Department of Technology R&D, Nexcelom Bioscience LLC 360 Merrimack St. Building 9 01843 Lawrence MA USA
- grid.419758.6 0000 0001 2236 9819 Center for Biotechnology and Biomedical Sciences, Merrimack College 01845 North Andover MA USA
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Rinnenthal JL, Börnchen C, Radbruch H, Andresen V, Mossakowski A, Siffrin V, Seelemann T, Spiecker H, Moll I, Herz J, Hauser AE, Zipp F, Behne MJ, Niesner R. Parallelized TCSPC for dynamic intravital fluorescence lifetime imaging: quantifying neuronal dysfunction in neuroinflammation. PLoS One 2013; 8:e60100. [PMID: 23613717 PMCID: PMC3629055 DOI: 10.1371/journal.pone.0060100] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 02/22/2013] [Indexed: 01/27/2023] Open
Abstract
Two-photon laser-scanning microscopy has revolutionized our view on vital processes by revealing motility and interaction patterns of various cell subsets in hardly accessible organs (e.g. brain) in living animals. However, current technology is still insufficient to elucidate the mechanisms of organ dysfunction as a prerequisite for developing new therapeutic strategies, since it renders only sparse information about the molecular basis of cellular response within tissues in health and disease. In the context of imaging, Förster resonant energy transfer (FRET) is one of the most adequate tools to probe molecular mechanisms of cell function. As a calibration-free technique, fluorescence lifetime imaging (FLIM) is superior for quantifying FRET in vivo. Currently, its main limitation is the acquisition speed in the context of deep-tissue 3D and 4D imaging. Here we present a parallelized time-correlated single-photon counting point detector (p-TCSPC) (i) for dynamic single-beam scanning FLIM of large 3D areas on the range of hundreds of milliseconds relevant in the context of immune-induced pathologies as well as (ii) for ultrafast 2D FLIM in the range of tens of milliseconds, a scale relevant for cell physiology. We demonstrate its power in dynamic deep-tissue intravital imaging, as compared to multi-beam scanning time-gated FLIM suitable for fast data acquisition and compared to highly sensitive single-channel TCSPC adequate to detect low fluorescence signals. Using p-TCSPC, 256×256 pixel FLIM maps (300×300 µm(2)) are acquired within 468 ms while 131×131 pixel FLIM maps (75×75 µm(2)) can be acquired every 82 ms in 115 µm depth in the spinal cord of CerTN L15 mice. The CerTN L15 mice express a FRET-based Ca-biosensor in certain neuronal subsets. Our new technology allows us to perform time-lapse 3D intravital FLIM (4D FLIM) in the brain stem of CerTN L15 mice affected by experimental autoimmune encephalomyelitis and, thereby, to truly quantify neuronal dysfunction in neuroinflammation.
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Affiliation(s)
- Jan Leo Rinnenthal
- German Rheumatism Research Center, Berlin, Germany
- Charité – University of Medicine, Berlin, Germany
| | - Christian Börnchen
- Department of Dermatology and Venerology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Helena Radbruch
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité – University of Medicine, Berlin, Germany
| | | | - Agata Mossakowski
- German Rheumatism Research Center, Berlin, Germany
- Charité – University of Medicine, Berlin, Germany
| | - Volker Siffrin
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Neurology Department, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | - Ingrid Moll
- Department of Dermatology and Venerology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Josephine Herz
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité – University of Medicine, Berlin, Germany
| | - Anja E. Hauser
- German Rheumatism Research Center, Berlin, Germany
- Charité – University of Medicine, Berlin, Germany
| | - Frauke Zipp
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Neurology Department, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin J. Behne
- Department of Dermatology and Venerology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Raluca Niesner
- German Rheumatism Research Center, Berlin, Germany
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité – University of Medicine, Berlin, Germany
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Lu Y, Chen X, Wu Y, Wang Y, He Y, Wu Y. Directly transforming PCR-amplified DNA fragments into plant cells is a versatile system that facilitates the transient expression assay. PLoS One 2013; 8:e57171. [PMID: 23468926 PMCID: PMC3582559 DOI: 10.1371/journal.pone.0057171] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 01/17/2013] [Indexed: 01/21/2023] Open
Abstract
A circular plasmid containing a gene coding sequence has been broadly used for studying gene regulation in cells. However, to accommodate a quick screen plasmid construction and preparation can be time consuming. Here we report a PCR amplified dsDNA fragments (PCR-fragments) based transient expression system (PCR-TES) for suiting in the study of gene regulation in plant cells. Instead of transforming plasmids into plant cells, transient expression of PCR-fragments can be applicable. The transformation efficiency and expression property of PCR-fragments are comparable to transformation using plasmids. We analyzed the transformation efficiency in PCR-TES at transcription and protein levels. Our results indicate that the PCR-TES is as versatile as the conventional transformation system using plasmid DNA. Through reconstituting PYR1-mediated ABA signaling pathway in Arabidopsis mesophyll protoplasts, we were not only validating the practicality of PCR-TES but also screening potential candidates of CDPK family members which might be involved in the ABA signaling. Moreover, we determined that phosphorylation of ABF2 by CPK4 could be mediated by ABA-induced PYR1 and ABI1, demonstrating a crucial role of CDPKs in the ABA signaling. In summary, PCR-TES can be applicable to facilitate analyzing gene regulation and for the screen of putative regulatory molecules at the high throughput level in plant cells.
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Affiliation(s)
- Yuming Lu
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Xi Chen
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yuxuan Wu
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yanping Wang
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yuqing He
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yan Wu
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
- * E-mail:
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Vilela M, Halidi N, Besson S, Elliott H, Hahn K, Tytell J, Danuser G. Fluctuation analysis of activity biosensor images for the study of information flow in signaling pathways. Methods Enzymol 2013; 519:253-76. [PMID: 23280114 DOI: 10.1016/b978-0-12-405539-1.00009-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Comprehensive understanding of cellular signal transduction requires accurate measurement of the information flow in molecular pathways. In the past, information flow has been inferred primarily from genetic or protein-protein interactions. Although useful for overall signaling, these approaches are limited in that they typically average over populations of cells. Single-cell data of signaling states are emerging, but these data are usually snapshots of a particular time point or limited to averaging over a whole cell. However, many signaling pathways are activated only transiently in specific subcellular regions. Protein activity biosensors allow measurement of the spatiotemporal activation of signaling molecules in living cells. These data contain highly complex, dynamic information that can be parsed out in time and space and compared with other signaling events as well as changes in cell structure and morphology. We describe in this chapter the use of computational tools to correct, extract, and process information from time-lapse images of biosensors. These computational tools allow one to explore the biosensor signals in a multiplexed approach in order to reconstruct the sequence of signaling events and consequently the topology of the underlying pathway. The extraction of this information, dynamics and topology, provides insight into how the inputs of a signaling network are translated into its biochemical or mechanical outputs.
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Affiliation(s)
- Marco Vilela
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
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42
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Upconversion nanoparticle-based fluorescence resonance energy transfer assay for Cr(III) ions in urine. Anal Chim Acta 2013; 761:178-85. [DOI: 10.1016/j.aca.2012.11.035] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/15/2012] [Accepted: 11/17/2012] [Indexed: 01/13/2023]
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Zadran S, Standley S, Wong K, Otiniano E, Amighi A, Baudry M. Fluorescence resonance energy transfer (FRET)-based biosensors: visualizing cellular dynamics and bioenergetics. Appl Microbiol Biotechnol 2012; 96:895-902. [PMID: 23053099 DOI: 10.1007/s00253-012-4449-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
Abstract
Förster (or fluorescence) resonance energy transfer (FRET) is a process involving the radiation-less transfer of energy from a "donor" fluorophore to an "acceptor" fluorophore. FRET technology enables the quantitative analysis of molecular dynamics in biophysics and in molecular biology, such as the monitoring of protein-protein interactions, protein-DNA interactions, and protein conformational changes. FRET-based biosensors have been utilized to monitor cellular dynamics not only in heterogeneous cellular populations, but also at the single-cell level in real time. Lately, applications of FRET-based biosensors range from basic biological to biomedical disciplines. Despite the diverse applications of FRET, FRET-based sensors still face many challenges. There is an increasing need for higher fluorescence resolution and improved specificity of FRET biosensors. Additionally, as more FRET-based technologies extend to medical diagnostics, the affordability of FRET reagents becomes a significant concern. Here, we will review current advances and limitations of FRET-based biosensor technology and discuss future FRET applications.
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Affiliation(s)
- Sohila Zadran
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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Berkes CA, Chan LLY, Wilkinson A, Paradis B. Rapid quantification of pathogenic fungi by Cellometer image-based cytometry. J Microbiol Methods 2012; 91:468-76. [PMID: 22985717 DOI: 10.1016/j.mimet.2012.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/08/2012] [Accepted: 09/09/2012] [Indexed: 11/19/2022]
Abstract
The objective of this study was to develop an image-based cytometric methodology for the quantification of viable pathogenic yeasts, which can offer increased sensitivity and efficiency when compared to the traditional colony forming unit (CFU) assay. Live/dead yeast quantification by flow cytometry has been previously demonstrated, however, adoption of flow cytometric detection of pathogenic yeasts has been limited for a number of practical reasons including its high cost and biosafety considerations. Our studies focus on detection of two human fungal pathogens: Histoplasma capsulatum and Candida albicans. H. capsulatum colonizes alveolar macrophages by replicating within the macrophage phagosome. Here, we quantitatively assess the growth of H. capsulatum yeasts within RAW 264.7 macrophages using acridine orange/propidium iodide staining in combination with Cellometer image-based cytometry; this method faithfully recapitulates growth trends as measured by traditional CFU enumeration, but with significantly increased sensitivity. Additionally, we directly assess infection of bone marrow-derived macrophages with a GFP-expressing strain of C. albicans. To demonstrate that image-based cytometry can be used as a tool to assess the susceptibility of fungi to antifungal drugs, we perform dose response experiments with the antifungal drugs amphotericin B and itraconazole and show that image-based cytometry allows rapid assessment of the kinetics of cytotoxicity induced by these antifungals. Our methodology offers a rapid, accurate, and economical means for detection and quantification of important human fungal pathogens, either alone or in association with host cells.
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Wang Y, Wang LV. Förster resonance energy transfer photoacoustic microscopy. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:086007. [PMID: 23224194 PMCID: PMC3414237 DOI: 10.1117/1.jbo.17.8.086007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/10/2012] [Accepted: 07/12/2012] [Indexed: 05/19/2023]
Abstract
Förster, or fluorescence, resonance energy transfer (FRET) provides fluorescence signals sensitive to intra- and inter-molecular distances in the 1 to 10 nm range. Widely applied in the fluorescence imaging environment, FRET enables visualization of physicochemical processes in molecular interactions and conformations. In this paper, we report photoacoustic imaging of FRET, based on nonradiative decay that produces heat and subsequent acoustic waves. Estimates of the energy transfer efficiency by photoacoustic microscopy were compared to those obtained by fluorescence confocal microscopy. The experimental results in tissue phantoms show that photoacoustic microscopy is capable of FRET imaging with an enhanced penetration depth. Through its ability to three-dimensionally image tissue with scalable resolution, photoacoustic microscopy could be a beneficial biomedical tool to broaden the in vivo application of FRET.
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Affiliation(s)
- Yu Wang
- Washington University in St. Louis, Department of Biomedical Engineering, Optical Imaging Laboratory, 1 Brookings Drive, St. Louis, Missouri, 63130
| | - Lihong V. Wang
- Washington University in St. Louis, Department of Biomedical Engineering, Optical Imaging Laboratory, 1 Brookings Drive, St. Louis, Missouri, 63130
- Address all correspondence to: Lihong V. Wang, Washington University in St. Louis, Department of Biomedical Engineering, Optical Imaging Laboratory, 1 Brookings Dr., St. Louis, Missouri, 63130. Tel: 314-935-9586; Fax: 314-935-7448; E-mail:
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Chan LL, Wilkinson AR, Paradis BD, Lai N. Rapid image-based cytometry for comparison of fluorescent viability staining methods. J Fluoresc 2012; 22:1301-11. [PMID: 22718197 DOI: 10.1007/s10895-012-1072-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 05/29/2012] [Indexed: 11/24/2022]
Abstract
The ability to accurately measure cell viability is important for any cell-based research. Traditionally, viability measurements have been performed using trypan blue exclusion method on hemacytometer, which allowed researchers to visually distinguish viable from nonviable cells. However, the trypan blue method is often limited to only cell lines or primary cells that have been rigorously purified. In the recent years, small desktop image-based cell counters have been developed for rapid cell concentration and viability measurement due to advances in imaging and optics technologies as well as novel fluorescent stains. In this work, we employed the Cellometer image-based cytometer to demonstrate the ability to simplify viability detection compared to the current methods. We compared various fluorescence viability detection methods using single- or dual-staining technique. Single-staining method using nucleic acid stains including ethidium bromide, propidium iodide, 7AAD, DAPI, Sytox Green and Sytox Red, and enzymatic stains including CFDA and Calcein AM were performed. All stains produced comparable results to trypan blue exclusion method for cell line samples. Dual-staining method using AO/PI, CFDA/PI, Calcein AM/PI and Hoechst 33342/PI that enumerates viable and non-viable cells was tested on primary cell samples with high debris contents. This method allowed exclusion of cellular debris and non-nucleated cells from analysis, which can eliminate the need to perform purification step during sample preparation, and improves the efficiency of viability detection method. Overall, these image-based fluorescent cell counters can simplify assay procedures as well as capture images for visual confirmation.
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Affiliation(s)
- Leo L Chan
- Department of Technology R&D, Nexcelom Bioscience LLC, 360 Merrimack St. Building 9, Lawrence, MA 01843, USA,
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47
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Xie F, Zhu J, Deng C, Huang G, Mitchelson K, Cheng J. General and reliable quantitative measurement of fluorescence resonance energy transfer using three fluorescence channels. Analyst 2012; 137:1013-9. [PMID: 22234659 DOI: 10.1039/c2an15902c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we describe a comprehensive general system adapted for quantitative fluorescence resonance energy transfer (FRET) measurement using signals from three channels of a fluorescence instrument. The general FRET measurement system involves two established methods, as well as two novel approaches. Unlike the previous measurements, which can be taken correctly only when the quantity of the acceptor is greater than or equal to that of the donor, one of our novel methods can overcome this obstacle and take quantitative FRET measurements when the donor is in excess of the acceptor. Hence the general FRET measurement system allowed one to determine the exact distance when the donor and acceptor were present in different quantities, and integrated the methods for quantitative FRET measurements. The uniformity of measured values and utility of each method were validated using molecular standards based on DNA oligonucleotide rulers. We also discussed and validated the use of a novel method for estimating the relative quantities of the donor and acceptor fluorophores when they were not known before an appropriate method of this system can be selected.
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Affiliation(s)
- Fengbo Xie
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing, 100084, China
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48
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Abstract
Integrins play critical adhesion and signaling roles during development, wound healing, immunity, and cancer. Central to their function is a unique ability to dynamically modulate their adhesiveness and signaling properties through changes in conformation, both homo- and heterotypic protein-protein interactions and cellular distribution. Genetic, biochemical and structural studies have been instrumental in uncovering overall functions, describing ligand and regulatory protein interactions and elucidating the molecular architecture of integrins. However, such approaches alone are inadequate to describe how dynamic integrin behaviors are orchestrated in intact cells. To fill this void, a wide array of distinct light microscopy (largely fluorescence-based) imaging approaches have been developed and employed. Various microscopy technologies, including wide-field, optical sectioning (laser-scanning confocal, spinning-disk confocal, and multiphoton), TIRF and range of novel "Super-Resolution" techniques have been used in combination with diverse imaging modalities (such as IRM, FRET, FRAP, CALI, and fluorescence speckle imaging) to address distinct aspects of integrin function and regulation. This chapter provides an overview of these imaging approaches and how they have advanced our understanding of integrins.
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Affiliation(s)
- Christopher V Carman
- Center for Vascular Biology Research, Division of Molecular and Vascular Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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49
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Tian Z, Wu W, Wan W, Li ADQ. Photoswitching-induced frequency-locked donor-acceptor fluorescence double modulations identify the target analyte in complex environments. J Am Chem Soc 2011; 133:16092-100. [PMID: 21863862 DOI: 10.1021/ja205124g] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Precisely identifying biological targets and accurately extracting their relatively weak signals from complicated physiological environments represent daunting challenges in biological detection and biomedical diagnosis. Fluorescence techniques have become the method of choice and offer minimally invasive and ultrasensitive detections, thus, providing a wealth of information regarding the biological mechanisms in living systems. Despite fluorescence analysis has advanced remarkably, conventional detections still encounter considerable limitations. This stems from the fact that the fluorescence intensity signal (I) is sensitive and liable to numerous external factors including temperature, light source, medium characteristics, and dye concentration. The interferences exasperatingly undermine the precision of measurements, and frequently render the signal undetectable. For example, fluorescence from single-molecule emitters can be measured on glass substrates under optimum conditions, but single-molecule events in complicated physiological environments such as live cells can hardly be detected because of autofluorescence interference and other factors. Furthermore, traditional intensity (I) and wavelength (λ) measurements do not reveal the interactive nature between the donor and the acceptor. Thus, innovative detection strategies to circumvent these aforementioned limitations of the conventional techniques are critically needed. With the use of photoswitching-induced donor-acceptor-fluorescence double modulations, we present a novel strategy that introduces three additional physical parameters: modulation amplitude (A), phase shift (ΔΦ), and lock-in frequency (ω), and demonstrate that such a strategy can circumvent the limitation of the conventional fluorescence detection techniques. Together, these five physical quantities (I, λ, A, ΔΦ, ω) reveal insightful information regarding molecular interactive strength between the probe and the analyte and enable extracting weak-fluorescence spectra from large interfering noises in complex environments.
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Affiliation(s)
- Zhiyuan Tian
- College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, Beijing, PR China 100049.
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50
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Fogarty KH, Zhang W, Grigsby IF, Johnson JL, Chen Y, Mueller JD, Mansky LM. New insights into HTLV-1 particle structure, assembly, and Gag-Gag interactions in living cells. Viruses 2011; 3:770-93. [PMID: 21994753 PMCID: PMC3185773 DOI: 10.3390/v3060770] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 05/20/2011] [Accepted: 05/20/2011] [Indexed: 11/16/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) has a reputation for being extremely difficult to study in cell culture. The challenges in propagating HTLV-1 has prevented a rigorous analysis of how these viruses replicate in cells, including the detailed steps involved in virus assembly. The details for how retrovirus particle assembly occurs are poorly understood, even for other more tractable retroviral systems. Recent studies on HTLV-1 using state-of-the-art cryo-electron microscopy and fluorescence-based biophysical approaches explored questions related to HTLV-1 particle size, Gag stoichiometry in virions, and Gag-Gag interactions in living cells. These results provided new and exciting insights into fundamental aspects of HTLV-1 particle assembly-which are distinct from those of other retroviruses, including HIV-1. The application of these and other novel biophysical approaches promise to provide exciting new insights into HTLV-1 replication.
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Affiliation(s)
- Keir H. Fogarty
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
| | - Wei Zhang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Iwen F. Grigsby
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jolene L. Johnson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
| | - Yan Chen
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
| | - Joachim D. Mueller
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M. Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
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