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Hainsworth AH, Lee S, Foot P, Patel A, Poon WW, Knight AE. Super-resolution imaging of subcortical white matter using stochastic optical reconstruction microscopy (STORM) and super-resolution optical fluctuation imaging (SOFI). Neuropathol Appl Neurobiol 2017; 44:417-426. [PMID: 28696566 DOI: 10.1111/nan.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 01/25/2023]
Abstract
AIMS The spatial resolution of light microscopy is limited by the wavelength of visible light (the 'diffraction limit', approximately 250 nm). Resolution of sub-cellular structures, smaller than this limit, is possible with super resolution methods such as stochastic optical reconstruction microscopy (STORM) and super-resolution optical fluctuation imaging (SOFI). We aimed to resolve subcellular structures (axons, myelin sheaths and astrocytic processes) within intact white matter, using STORM and SOFI. METHODS Standard cryostat-cut sections of subcortical white matter from donated human brain tissue and from adult rat and mouse brain were labelled, using standard immunohistochemical markers (neurofilament-H, myelin-associated glycoprotein, glial fibrillary acidic protein, GFAP). Image sequences were processed for STORM (effective pixel size 8-32 nm) and for SOFI (effective pixel size 80 nm). RESULTS In human, rat and mouse, subcortical white matter high-quality images for axonal neurofilaments, myelin sheaths and filamentous astrocytic processes were obtained. In quantitative measurements, STORM consistently underestimated width of axons and astrocyte processes (compared with electron microscopy measurements). SOFI provided more accurate width measurements, though with somewhat lower spatial resolution than STORM. CONCLUSIONS Super resolution imaging of intact cryo-cut human brain tissue is feasible. For quantitation, STORM can under-estimate diameters of thin fluorescent objects. SOFI is more robust. The greatest limitation for super-resolution imaging in brain sections is imposed by sample preparation. We anticipate that improved strategies to reduce autofluorescence and to enhance fluorophore performance will enable rapid expansion of this approach.
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Affiliation(s)
- A H Hainsworth
- Molecular and Clinical Sciences Research Institute, St Georges University of London, London, UK.,Neurology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - S Lee
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - P Foot
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - A Patel
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - W W Poon
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - A E Knight
- National Physical Laboratory, Teddington, UK
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Abstract
INTRODUCTION Platelet granule deficiencies lead to bleeding disorders, but their specific diagnosis typically requires whole mount transmission electron microscopy, which is often not available and has a number of important limitations. We recently proposed the use of advanced forms of fluorescence microscopy - the so-called 'super-resolution' microscopies - as a possible solution. Areas covered: In this special report, we review the diagnosis of platelet granule deficiencies, and discuss how recent developments in fluorescence microscopy may be useful in improving diagnostic approaches to these and related disorders. In particular, we conclude that super-resolution fluorescence microscopy may have advantages over transmission electron microscopy in this application. Expert commentary: The value of the super-resolution microscopies has been amply demonstrated in research; however, their potential in diagnostic applications is ripe for further exploration. Hematology is a field particularly likely to benefit because of the relative simplicity of sample preparation. We anticipate that the costs of the necessary instrumentation will continue to fall rapidly, making these technologies widely accessible to clinicians.
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Affiliation(s)
- Alex E Knight
- a Biotechnology Group , National Physical Laboratory , Middlesex , UK
| | - Keith Gomez
- b Katherine Dormandy Haemophilia Centre and Thrombosis Unit , Royal Free London NHS Foundation Trust , London , UK
| | - Daniel F Cutler
- c MRC Laboratory for Molecular Cell Biology , University College London , London , UK
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Hainsworth AH, Lee S, Patel A, Foot P, Knight AE. P2‐071: Super Resolution Microscopy of Intact Brain White Matter. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Sarah Lee
- St Georges Healthcare NHS TrustLondonUnited Kingdom
| | - Anita Patel
- St Georges Healthcare NHS TrustLondonUnited Kingdom
| | - Peter Foot
- St Georges Healthcare NHS TrustLondonUnited Kingdom
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Westmoreland D, Shaw M, Grimes W, Metcalf DJ, Burden JJ, Gomez K, Knight AE, Cutler DF. Super-resolution microscopy as a potential approach to diagnosis of platelet granule disorders. J Thromb Haemost 2016; 14:839-49. [PMID: 26806224 PMCID: PMC4982064 DOI: 10.1111/jth.13269] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Many platelet functions are dependent on bioactive molecules released from their granules. Deficiencies of these granules in number, shape or content are associated with bleeding. The small size of these granules is such that imaging them for diagnosis has traditionally required electron microscopy. However, recently developed super-resolution microscopes provide sufficient spatial resolution to effectively image platelet granules. When combined with automated image analysis, these methods provide a quantitative, unbiased, rapidly acquired dataset that can readily and reliably reveal differences in platelet granules between individuals. OBJECTIVE To demonstrate the ability of structured illumination microscopy (SIM) to efficiently differentiate between healthy volunteers and three patients with Hermansky-Pudlak syndrome. METHODS Blood samples were taken from three patients with Hermansky-Pudlak syndrome and seven controls. Patients 1-3 have gene defects in HPS1, HPS6 and HPS5, respectively; all controls were healthy volunteers. Platelet-rich plasma was isolated from blood and the platelets fixed, stained for CD63 and processed for analysis by immunofluorescence microscopy, using a custom-built SIM microscope. RESULTS SIM can successfully resolve CD63-positive structures in fixed platelets. A determination of the number of CD63-positive structures per platelet allowed us to conclude that each patient was significantly different from all of the controls with 99% confidence. CONCLUSIONS A super-resolution imaging approach is effective and rapid in objectively differentiating between patients with a platelet bleeding disorder and healthy volunteers. CD63 is a useful marker for predicting Hermansky-Pudlak syndrome and could be used in the diagnosis of patients suspected of other platelet granule disorders.
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Affiliation(s)
- D Westmoreland
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Endothelial Cell Biology Laboratory, London, UK
| | - M Shaw
- Analytical Science Division, National Physical Laboratory, Teddington, Middlesex, London, UK
| | - W Grimes
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Endothelial Cell Biology Laboratory, London, UK
- Imaging Informatics Division, Bioinformatics Institute, Singapore, Singapore
| | | | - J J Burden
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Electron Microscopy Laboratory, London, UK
| | - K Gomez
- Katherine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
| | - A E Knight
- Analytical Science Division, National Physical Laboratory, Teddington, Middlesex, London, UK
| | - D F Cutler
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Endothelial Cell Biology Laboratory, London, UK
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Knight AE, Peckham M. Recent innovations in super-resolution microscopy. Methods 2015; 88:1-2. [PMID: 26255962 DOI: 10.1016/j.ymeth.2015.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Alex E Knight
- Biotechnology Group, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Michelle Peckham
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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Grove J, Metcalf DJ, Knight AE, Wavre-Shapton ST, Sun T, Protonotarios ED, Griffin LD, Lippincott-Schwartz J, Marsh M. Flat clathrin lattices: stable features of the plasma membrane. Mol Biol Cell 2014; 25:3581-94. [PMID: 25165141 PMCID: PMC4230618 DOI: 10.1091/mbc.e14-06-1154] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) is a fundamental property of eukaryotic cells. Classical CME proceeds via the formation of clathrin-coated pits (CCPs) at the plasma membrane, which invaginate to form clathrin-coated vesicles, a process that is well understood. However, clathrin also assembles into flat clathrin lattices (FCLs); these structures remain poorly described, and their contribution to cell biology is unclear. We used quantitative imaging to provide the first comprehensive description of FCLs and explore their influence on plasma membrane organization. Ultrastructural analysis by electron and superresolution microscopy revealed two discrete populations of clathrin structures. CCPs were typified by their sphericity, small size, and homogeneity. FCLs were planar, large, and heterogeneous and present on both the dorsal and ventral surfaces of cells. Live microscopy demonstrated that CCPs are short lived and culminate in a peak of dynamin recruitment, consistent with classical CME. In contrast, FCLs were long lived, with sustained association with dynamin. We investigated the biological relevance of FCLs using the chemokine receptor CCR5 as a model system. Agonist activation leads to sustained recruitment of CCR5 to FCLs. Quantitative molecular imaging indicated that FCLs partitioned receptors at the cell surface. Our observations suggest that FCLs provide stable platforms for the recruitment of endocytic cargo.
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Affiliation(s)
- Joe Grove
- MRC Laboratory for Molecular Cell Biology, London WC1E 6BT, United Kingdom Institute of Immunity and Transplantation, University College London, London NW3 2PF, United Kingdom
| | - Daniel J Metcalf
- Biophysics and Diagnostics, National Physical Laboratory, Teddington TW11 0LW, United Kingdom
| | - Alex E Knight
- Biophysics and Diagnostics, National Physical Laboratory, Teddington TW11 0LW, United Kingdom
| | | | - Tony Sun
- MRC Laboratory for Molecular Cell Biology, London WC1E 6BT, United Kingdom
| | | | - Lewis D Griffin
- CoMPLEX, University College London, London WC1E 6BT, United Kingdom
| | - Jennifer Lippincott-Schwartz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, London WC1E 6BT, United Kingdom
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Abstract
AbstractTotal internal reflection fluorescence (TIRF) is a popular illumination technique in microscopy, with many applications in cell and molecular biology and biophysics. The chief advantage of the technique is the high contrast that can be achieved by restricting fluorescent excitation to a thin layer. We summarise the optical theory needed to understand the technique and various aspects required for a practical implementation of it, including the merits of different TIRF geometries. Finally, we discuss a variety of applications including super-resolution microscopy and high-throughput DNA sequencing technologies.
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Affiliation(s)
- Alex E. Knight
- 1Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
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Ferraro F, Kriston-Vizi J, Metcalf DJ, Martin-Martin B, Freeman J, Burden JJ, Westmoreland D, Dyer CE, Knight AE, Ketteler R, Cutler DF. A two-tier Golgi-based control of organelle size underpins the functional plasticity of endothelial cells. Dev Cell 2014; 29:292-304. [PMID: 24794632 PMCID: PMC4022834 DOI: 10.1016/j.devcel.2014.03.021] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 02/03/2014] [Accepted: 03/27/2014] [Indexed: 01/10/2023]
Abstract
Weibel-Palade bodies (WPBs), endothelial-specific secretory granules that are central to primary hemostasis and inflammation, occur in dimensions ranging between 0.5 and 5 μm. How their size is determined and whether it has a functional relevance are at present unknown. Here, we provide evidence for a dual role of the Golgi apparatus in controlling the size of these secretory carriers. At the ministack level, cisternae constrain the size of nanostructures (“quanta”) of von Willebrand factor (vWF), the main WPB cargo. The ribbon architecture of the Golgi then allows copackaging of a variable number of vWF quanta within the continuous lumen of the trans-Golgi network, thereby generating organelles of different sizes. Reducing the WPB size abates endothelial cell hemostatic function by drastically diminishing platelet recruitment, but, strikingly, the inflammatory response (the endothelial capacity to engage leukocytes) is unaltered. Size can thus confer functional plasticity to an organelle by differentially affecting its activities. Cisternal length within Golgi ministacks controls the size of vWF cargo nanostructures The Golgi ribbon allows copackaging of vWF nanostructures into WPBs of variable size Endothelial cells with small WPBs display a reduced platelet recruitment capability Control of organelle size may confer hemostatic plasticity to endothelia
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Affiliation(s)
- Francesco Ferraro
- Endothelial Cell Biology Laboratory, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Janos Kriston-Vizi
- Translational Research Resource Center, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK; Bioinformatics Image Core, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Daniel J Metcalf
- Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK
| | - Belen Martin-Martin
- Endothelial Cell Biology Laboratory, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Jamie Freeman
- Translational Research Resource Center, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Jemima J Burden
- Electron Microscopy Laboratory, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - David Westmoreland
- Endothelial Cell Biology Laboratory, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Clare E Dyer
- Endothelial Cell Biology Laboratory, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Alex E Knight
- Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK
| | - Robin Ketteler
- Translational Research Resource Center, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Daniel F Cutler
- Endothelial Cell Biology Laboratory, Laboratory for Molecular and Cellular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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Sinkó J, Kákonyi R, Rees E, Metcalf D, Knight AE, Kaminski CF, Szabó G, Erdélyi M. TestSTORM: Simulator for optimizing sample labeling and image acquisition in localization based super-resolution microscopy. Biomed Opt Express 2014; 5:778-87. [PMID: 24688813 PMCID: PMC3959829 DOI: 10.1364/boe.5.000778] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 05/12/2023]
Abstract
Localization-based super-resolution microscopy image quality depends on several factors such as dye choice and labeling strategy, microscope quality and user-defined parameters such as frame rate and number as well as the image processing algorithm. Experimental optimization of these parameters can be time-consuming and expensive so we present TestSTORM, a simulator that can be used to optimize these steps. TestSTORM users can select from among four different structures with specific patterns, dye and acquisition parameters. Example results are shown and the results of the vesicle pattern are compared with experimental data. Moreover, image stacks can be generated for further evaluation using localization algorithms, offering a tool for further software developments.
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Affiliation(s)
- József Sinkó
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720 Hungary
| | - Róbert Kákonyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720 Hungary
| | - Eric Rees
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA, UK
| | - Daniel Metcalf
- Analytical Science Division, National Physical Laboratory, Teddington, Middlesex, TW11 0LW, UK
| | - Alex E. Knight
- Analytical Science Division, National Physical Laboratory, Teddington, Middlesex, TW11 0LW, UK
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA, UK
| | - Gábor Szabó
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720 Hungary
- MTA-SZTE Research Group on Photoacoustic Spectroscopy, Szeged, Dóm tér 9, 6720 Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720 Hungary
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10
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Abstract
STORM is a recently developed super-resolution microscopy technique with up to 10 times better resolution than standard fluorescence microscopy techniques. However, as the image is acquired in a very different way than normal, by building up an image molecule-by-molecule, there are some significant challenges for users in trying to optimize their image acquisition. In order to aid this process and gain more insight into how STORM works we present the preparation of 3 test samples and the methodology of acquiring and processing STORM super-resolution images with typical resolutions of between 30-50 nm. By combining the test samples with the use of the freely available rainSTORM processing software it is possible to obtain a great deal of information about image quality and resolution. Using these metrics it is then possible to optimize the imaging procedure from the optics, to sample preparation, dye choice, buffer conditions, and image acquisition settings. We also show examples of some common problems that result in poor image quality, such as lateral drift, where the sample moves during image acquisition and density related problems resulting in the 'mislocalization' phenomenon.
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Erdelyi M, Rees E, Metcalf D, Schierle GSK, Dudas L, Sinko J, Knight AE, Kaminski CF. Correcting chromatic offset in multicolor super-resolution localization microscopy. Opt Express 2013; 21:10978-88. [PMID: 23669954 DOI: 10.1364/oe.21.010978] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Localization based super-resolution microscopy techniques require precise drift correction methods because the achieved spatial resolution is close to both the mechanical and optical performance limits of modern light microscopes. Multi-color imaging methods require corrections in addition to those dealing with drift due to the static, but spatially-dependent, chromatic offset between images. We present computer simulations to quantify this effect, which is primarily caused by the high-NA objectives used in super-resolution microscopy. Although the chromatic offset in well corrected systems is only a fraction of an optical wavelength in magnitude (<50 nm) and thus negligible in traditional diffraction limited imaging, we show that object colocalization by multi-color super-resolution methods is impossible without appropriate image correction. The simulated data are in excellent agreement with experiments using fluorescent beads excited and localized at multiple wavelengths. Finally we present a rigorous and practical calibration protocol to correct for chromatic optical offset, and demonstrate its efficacy for the imaging of transferrin receptor protein colocalization in HeLa cells using two-color direct stochastic optical reconstruction microscopy (dSTORM).
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Affiliation(s)
- Miklos Erdelyi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, UK.
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Abstract
Single-molecule enzymology has a longer history than is often supposed, with the first measurements being made as early as 1961. However, the development of new technologies has meant that most of the progress has been made in the last two decades. I review the development of single-molecule enzymology, focussing on five key papers which are milestones in the field. In particular, I discuss the 1961 paper by Boris Rotman, which made inventive use of what now seems like primitive technology, and continues to be influential to this day.
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Affiliation(s)
- Alex E Knight
- Analytical Science Division, National Physical Laboratory, Teddington, Middlesex, UK.
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Klauenberg K, Ebert B, Voigt J, Walzel M, Noble JE, Knight AE, Elster C. Bayesian analysis of an international ELISA comparability study. Clin Chem Lab Med 2011; 49:1459-68. [DOI: 10.1515/cclm.2011.648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Damianoglou A, Crust EJ, Hicks MR, Howson SE, Knight AE, Ravi J, Scott P, Rodger A. A new reference material for UV-visible circular dichroism spectroscopy. Chirality 2008; 20:1029-38. [DOI: 10.1002/chir.20566] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Noble JE, Knight AE, Reason AJ, Di Matola A, Bailey MJA. A comparison of protein quantitation assays for biopharmaceutical applications. Mol Biotechnol 2008; 37:99-111. [PMID: 17914170 DOI: 10.1007/s12033-007-0038-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 10/23/2022]
Abstract
Dye-based protein determination assays are widely used to estimate protein concentration, however various reports suggest that the response is dependent on the composition and sequence of the protein, limiting confidence in the resulting concentration estimates. In this study a diverse set of model proteins representing various sizes of protein and covalent modifications, some typical of biopharmaceuticals have been used to assess the utility of dye-based protein concentration assays. The protein concentration assays (Bicinchoninic acid (BCA), Bradford, 3-(4-carboxybenzoyl)quinoline-2-carboxaldehyde (CBQCA), DC, Fluorescamine and Quant-i) were compared to the 'gold standard' assay, quantitative amino acid analysis (AAA). The assays that displayed the lowest variability between proteins, BCA and DC, also generated improved estimates when BSA was used as a standard, when compared to AAA derived concentrations. Assays read out by absorbance tended to display enhanced robustness and repeatability, whereas the fluorescence based assays had wider quantitation ranges and lower limits of detection. Protein modification, in the form of glycosylation and PEGylation, and the addition of excipients, were found to affect the estimation of protein concentration for some of the assays when compared to the unmodified protein. We discuss the suitability and limitations of the selected assays for the estimation of protein concentration in biopharmaceutical applications.
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Affiliation(s)
- J E Noble
- National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK.
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Noble JE, Wang L, Cerasoli E, Knight AE, Porter RA, Gray E, Howe C, Hannes E, Corbisier P, Wang J, Wu L, Altieri I, Patriarca M, Hoffman A, Resch-Genger U, Ebert B, Voigt J, Shigeri Y, Vonsky MS, Konopelko LA, Gaigalas AK, Bailey MJ. An international comparability study to determine the sources of uncertainty associated with a non-competitive sandwich fluorescent ELISA. Clin Chem Lab Med 2008; 46:1033-45. [DOI: 10.1515/cclm.2008.182] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gaunt JA, Knight AE, Windsor SA, Chechik V. Stability and quantum yield effects of small molecule additives on solutions of semiconductor nanoparticles. J Colloid Interface Sci 2005; 290:437-43. [PMID: 16153904 DOI: 10.1016/j.jcis.2005.04.073] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 04/20/2005] [Accepted: 04/22/2005] [Indexed: 10/25/2022]
Abstract
The effect of additives on the photostability of semiconductor nanoparticles was studied using CdSe, CdSe/ZnSe and CdSe/ZnS particles of various sizes and composition. The additives included phosphine oxides, amines, and antioxidants. Strong initial enhancement of band edge emission by hexadecylamine was observed for the uncoated particles but stability over a week period in light and air was shown to be poor. Inorganic coatings rendered the nanoparticles initially insensitive to additive but provided little extra stability in terms of photoluminescence. Antioxidant was shown to be effective at reducing the rate of photooxidative degradation for all particles in chloroform but not in toluene.
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Affiliation(s)
- Joseph A Gaunt
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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Abstract
Recent technological advances in lasers and optical detectors have enabled a variety of new, single molecule technologies to be developed. Using intense and highly collimated laser light sources in addition to super-sensitive cameras, the fluorescence of single fluorophores can now be imaged in aqueous solution. Also, laser optical tweezers have enabled the piconewton forces produced by pair of interacting biomolecules to be measured directly. However, for a researcher new to the field to begin to use such techniques in their own research might seem a daunting prospect. Most of the equipment that is in use is custom-built. However, most of the equipment is essence fairly simple and the aim of this article is to provide an entry point to the field for a newcomer. It focuses mainly on those practical aspects which are not particularly well covered in the literature, and aims to provide an overview of the field as a whole with references and web links to more detailed sources elsewhere. Indeed, the opportunity to publish an article such as this on the Internet affords many new opportunities (and more space!) for presenting scientific ideas and information. For example, we have illustrated the nature of optical trap data with an interactive Java simulation; provided links to relevant web sites and technical documents, and included a large number of colour figures and plots. Our group's research focuses on molecular motors, and the bias of this article reflects this. It turns out that molecular motors have been a paradigm (or prototype) for single molecule research and the field has seen a rapid development in the techniques. It is hoped that the methods described here will be broadly applicable to other biological systems.
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Affiliation(s)
- Alex E Knight
- Quality of Life Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK.
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Mashanov GI, Tacon D, Knight AE, Peckham M, Molloy JE. Visualizing single molecules inside living cells using total internal reflection fluorescence microscopy. Methods 2003; 29:142-52. [PMID: 12606220 DOI: 10.1016/s1046-2023(02)00305-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Over the past 10 years, advances in laser and detector technologies have enabled single fluorophores to be visualized in aqueous solution. Here, we describe methods based on total internal reflection fluorescence microscopy (TIRFM) that we have developed to study the behavior of individual protein molecules within living mammalian cells. We have used cultured myoblasts that were transiently transfected with DNA plasmids encoding a target protein fused to green fluorescent protein (GFP). Expression levels were quantified from confocal images of control dilutions of GFP and cells with 1-100 nM GFP were then examined using TIRFM. An evanescent field was produced by a totally internally reflected, argon ion laser beam that illuminated a shallow region (50-100 nm deep) at the glass-water interface. Individual GFP-tagged proteins that entered the evanescent field appeared as individual, diffraction-limited spots of light, which were clearly resolved from background fluorescence. Molecules that bound to the basal cell membrane remained fixed in position for many seconds, whereas those diffusing freely in the cytoplasm disappeared within a few milliseconds. We developed automated detection and tracking methods to recognize and characterize the behavior of single molecules in recorded video sequences. This enabled us to measure the kinetics of photobleaching and lateral diffusion of membrane-bound molecules.
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Affiliation(s)
- G I Mashanov
- Biology Department, University of York, Heslington, York YO1 5DD, UK
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20
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Abstract
Whereas we have a great deal of information about myosin, there remain fundamental questions about its mechanism (and those of other motor proteins). Single-molecule technologies enable us to make measurements we cannot make from large ensembles of molecules. Optical tweezers (and similar techniques) are used to measure the mechanical aspects of actomyosin interactions, including force, displacement and stiffness. Single-molecule fluorescence has been used to observe the binding and release of nucleotide by myosins. A combination of these measurements has the potential to solve the problem of coupling of ATP hydrolysis to mechanical work in motor proteins.
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Affiliation(s)
- A E Knight
- Biology Department, University of York, P.O. Box 373, York YO10 5YW, U.K
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21
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Abstract
The troponin-tropomyosin-linked regulation of striated muscle contraction occurs through allosteric control by both Ca(2+) and myosin. The thin filament fluctuates between two extreme states: the inactive "off" state and the active "on" state. Intermediate states have been proposed from structural studies and transient kinetic measurements. However, in contrast to the well-characterised, on and off states, the mechanochemical properties of the intermediate states are much less well understood because of the instability of those states. In the present study, we have characterized a myosin-induced intermediate that is stabilized by cross-linking myosin motor domains (S1) to actin filaments (with a maximum of one S1 molecule for 50 actin monomers). A single S1 molecule is known to interact with two adjacent actin monomers. A detailed analysis revealed that thin filaments containing S1 molecules cross-linked to just one actin monomer (actin(1)-S1 complexes) are regulated with a 79% inhibition of the ATPase in the absence of Ca(2+). In contrast, filaments containing S1 molecules cross-linked at two positions, to two adjacent actin monomers (actin(2)-S1 complexes) totally lose their regulation in a highly cooperative manner. This loss of regulation was due both to an enhancement of the ATPase activity without calcium and an inhibition of the ATPase with calcium. Filaments containing actin(2)-S1 complexes, with significant ATPase activity in the absence of calcium (about 50%), did not move on a myosin-coated surface unless calcium was present. This partial uncoupling between the ATPase activity and in vitro motility in the absence of calcium demonstrates that the mechanical steps require actin-myosin contacts, which take place only in the on state and not in the off or intermediate states. These data provide new insights concerning the difference in cooperativity of Ca(2+) regulation that exists between the biochemical and mechanical cycles of the actin-myosin motor.
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22
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Knight AE, Veigel C, Chambers C, Molloy JE. Analysis of single-molecule mechanical recordings: application to acto-myosin interactions. Prog Biophys Mol Biol 2001; 77:45-72. [PMID: 11473786 DOI: 10.1016/s0079-6107(01)00010-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Several laboratories have now developed methods to make single-molecule mechanical recordings from interacting pairs of biological molecules. The mechanical work done (product of force and distance) by a single biomolecular interaction is usually of the same order as thermal energy. Recordings made from non-processive, intermittently interacting, molecular motors such as acto-myosin therefore contain a large background of thermal noise. We have applied Page's test to analyse mechanical interactions between muscle myosin II's and F-actin recorded using an optical tweezers based single-molecule mechanical transducer. We compare Page's test with other variance-based methods and find it to be a robust method for analysing both simulated and real data sets. We discuss some of the problems associated with automatic detection of transient mechanical events in noisy data signals, and show that if the start and end points of individual events are known accurately then the events may be synchronised and combined to give more detailed information about different mechanical states.
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Affiliation(s)
- A E Knight
- Biology Department, University of York, P.O. Box 373, York YO10 5YW, UK.
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23
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Reichelt S, Knight AE, Hodge TP, Baluska F, Samaj J, Volkmann D, Kendrick-Jones J. Characterization of the unconventional myosin VIII in plant cells and its localization at the post-cytokinetic cell wall. Plant J 1999; 19:555-67. [PMID: 10504577 DOI: 10.1046/j.1365-313x.1999.00553.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Myosins are a large superfamily of motor proteins which, in association with actin, are involved in intra- cellular motile processes. In addition to the conventional myosins involved in muscle contractility, there is, in animal cells, a wide range of unconventional myosins implicated in membrane-associated processes, such as vesicle transport and membrane dynamics. In plant cells, however, very little is known about myosins. We have raised an antibody to the recombinant tail region of Arabidopsis thaliana myosin 1 (a class VIII myosin) and used it in immunofluorescence and EM studies on root cells from cress and maize. The plant myosin VIII is found to be concentrated at newly formed cross walls at the stage in which the phragmoplast cytoskeleton has depolymerized and the new cell plate is beginning to mature. These walls are rich in plasmodesmata and we show that they are the regions where the longitudinal actin cables appear to attach. Myosin VIII appears to be localized in these plasmodesmata and we suggest that this protein is involved in maturation of the cell plate and the re-establishment of cytoplasmic actin cables at sites of intercellular communication.
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Affiliation(s)
- S Reichelt
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
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24
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25
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Buss F, Kendrick-Jones J, Lionne C, Knight AE, Côté GP, Paul Luzio J. The localization of myosin VI at the golgi complex and leading edge of fibroblasts and its phosphorylation and recruitment into membrane ruffles of A431 cells after growth factor stimulation. J Biophys Biochem Cytol 1998; 143:1535-45. [PMID: 9852149 PMCID: PMC2132970 DOI: 10.1083/jcb.143.6.1535] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Myosin VI is an unconventional myosin that may play a role in vesicular membrane traffic through actin rich regions of the cytoplasm in eukaryotic cells. In this study we have cloned and sequenced a cDNA encoding a chicken intestinal brush border myosin VI. Polyclonal antisera were raised to bacterially expressed fragments of this myosin VI. The affinity purified antibodies were highly specific for myosin VI by immunoblotting and immunoprecipitation and were used to study the localization of the protein by immunofluorescence and immunoelectron microscopy. It was found that in NRK and A431 cells, myosin VI was associated with both the Golgi complex and the leading, ruffling edge of the cell as well as being present in a cytosolic pool. In A431 cells in which cell surface ruffling was stimulated by EGF, myosin VI was phosphorylated and recruited into the newly formed ruffles along with ezrin and myosin V. In vitro experiments suggested that a p21-activated kinase (PAK) might be the kinase responsible for phosphorylation in the motor domain. These results strongly support a role for myosin VI in membrane traffic on secretory and endocytic pathways.
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Affiliation(s)
- F Buss
- Department of Clinical Biochemistry, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 2QR, United Kingdom.
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26
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Edgar AJ, Knight AE, Bennett JP. Chicken myosin IB mRNA is highly expressed in lymphoid tissues. J Anat 1996; 189 ( Pt 2):451-6. [PMID: 8886967 PMCID: PMC1167762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Little is known about the functions of members of the myosin I family in vertebrates. Chicken myosin IB is a member of the amoeba-type subclass of myosin I molecules and tissue localisation studies may provide possible clues to the functions of these myosin I molecules. The expression of the mRNA of this unconventional myosin IB was analysed by in situ hybridization and compared with that of the well characterised brush border myosin I on frozen sections of tissues from the adult domestic chicken. High levels of myosin IB mRNA were found in the intestine and spleen, but were not found in other tissues examined such as brain, heart, lung, liver and kidney. In the intestine, myosin IB mRNA was much more abundant in the lamina propria than in the enterocytes, whereas brush border myosin I mRNA was restricted to the enterocytes. In the spleen, myosin IB mRNA expression was abundant in regions of white pulp, namely germinal centres, periellipsoid lymphocyte sheaths and periarteriolar lymphocyte sheaths. Lymphocytes are the major cell type in both the lamina propria and the white pulp of the spleen, which suggests that chicken myosin IB is highly expressed in lymphocytes. Lymphocyte recirculation depends on their migration through the endothelial layer and it is possible that myosin IB may have a role to play in this type of cell motility.
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Affiliation(s)
- A J Edgar
- Department of Anatomy and Cell Biology, Imperial College School of Medicine at St Mary's, London, UK
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27
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Blake DJ, Tinsley JM, Davies KE, Knight AE, Winder SJ, Kendrick-Jones J. Coiled-coil regions in the carboxy-terminal domains of dystrophin and related proteins: potentials for protein-protein interactions. Trends Biochem Sci 1995; 20:133-5. [PMID: 7770909 DOI: 10.1016/s0968-0004(00)88986-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- D J Blake
- Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK
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28
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Abstract
During the past year significant progress has been made in understanding how dystrophin deficiency leads to muscle cell necrosis in Duchenne muscular dystrophy and Becker muscular dystrophy. Dystrophin interacts with a glycoprotein complex spanning the muscle sarcolemma, effectively linking the actin cytoskeleton to the extracellular matrix. The carboxyl terminus of dystrophin is required for glycoprotein binding. Interestingly, at least three mRNAs transcribed from the distal end of the DMD gene in tissues other than muscle have been shown to encode this domain. Deficiency of a second component of the dystrophin-associated glycoprotein complex has been shown to occur in another muscle-wasting disorder, severe childhood autosomal recessive muscular dystrophy. Sequence analysis of the entire cDNA for the autosomal dystrophin-related protein utrophin has shown that dystrophin and utrophin are closely related. Furthermore, both of these proteins have been shown to bind to the same or a similar glycoprotein complex in muscle.
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Affiliation(s)
- J M Tinsley
- Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK
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29
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Abstract
As part of a study of the diversity of myosins, we have cloned a cDNA encoding a myosin-like protein from Arabidopsis thaliana. This is the first molecular motor of any kind to be cloned from a higher plant. The predicted polypeptide (molecular weight 131 kDa) has a motor domain (head) very similar to those of other myosins, but the remainder of the sequence is unusual. The tail contains four potential calmodulin binding sites ("IQ-motifs"), but no sequence motifs suggestive of actin or phospholipid binding, like those found in other myosins. There is also a small region of probable alpha-helical coiled-coil, which suggests that the molecule could be dimeric, though unlikely to form filaments. The N-terminal and C-terminal regions of the molecule are unique. We present a phylogenetic analysis of myosin head sequences, which suggests that this is a new type of myosin.
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Affiliation(s)
- A E Knight
- MRC Laboratory of Molecular Biology, Cambridge, U.K
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30
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Abstract
We have deduced the amino acid sequences of four sea urchin (Strongylocentrotus purpuratus; SP) kinesin light chain (KLC) isoforms (SPKLC 1-4) and compared them to rat brain light chain sequences. Examination of the SPKLC open reading frames (SPKLC1, 649; SPKLC2, 677; SPKLC3, 686; and SPKLC4, 451 amino acid residues) reveals that the first 500 or so residues of the KLCs are highly conserved but the C-terminal ends of rat and sea urchin light chains are divergent; SPKLCs 1, 2 and 3 share a highly basic, 86 residue C-terminal segment that is missing from the shorter rat light chains and SPKLC4. The insertion of 28 and 37 residue segments at residue 563 of SPKLCs 2 and 3, respectively, gives rise to sequence heterogeneity at the C-terminal ends of the sea urchin KLCs. C-terminal sequence differences between light chains may provide inter- and intraspecies differences in the functional properties of the presumptive cargo attachment elements of kinesin.
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Affiliation(s)
- K P Wedaman
- Division of Biological Sciences, University of California, Davis 95616
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31
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Tinsley JM, Blake DJ, Roche A, Fairbrother U, Riss J, Byth BC, Knight AE, Kendrick-Jones J, Suthers GK, Love DR. Primary structure of dystrophin-related protein. Nature 1992; 360:591-3. [PMID: 1461283 DOI: 10.1038/360591a0] [Citation(s) in RCA: 313] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dystrophin-related protein (DRP or 'utrophin') is localized in normal adult muscle primarily at the neuromuscular junction. In the absence of dystrophin in Duchenne muscular dystrophy (DMD) patients, DRP is also present in the sarcolemma. DRP is expressed in fetal and regenerating muscle and may play a similar role to dystrophin in early development, although it remains to be determined whether DRP can functionally replace dystrophin in adult tissue. Previously we described a 3.5-kilobase complementary DNA clone that exhibits 80 per cent homology to the C-terminal domain of dystrophin. This sequence identifies a 13-kilobase transcript that maps to human chromosome 6 (refs 2, 11). Antibodies raised against the gene product identify a polypeptide with a relative molecular mass of about 400K in all tissues examined. To investigate the relationship between DRP and dystrophin in more detail, we have cloned and sequenced the whole DRP cDNA. Homology between DRP and dystrophin extends over their entire length, suggesting that they derive from a common ancestral gene. Comparative analysis of primary sequences highlights regions of functional importance, including those that may mediate the localization of DRP and dystrophin in the muscle cell.
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Affiliation(s)
- J M Tinsley
- Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK
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32
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Abstract
This paper gives details of a family in which there are numerous examples of the heterozygous Kdegree state. The study was initiated by the presence of anti-Kpb in the serum of the propositus. Reactions with anti-K, anti-Ku, anti-Jsb and anti-K13 confirm that the Kdegree gene in trans with Kpa results in weaker expression of these Kell antigens. One example of anti-K showed some evidence of dosage effect with kKpb/Kdegree cells, but these results were not confirmed by quantitation studies.
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