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Suthaharan S, Rossi EA, Snyder V, Chhablani J, Lejoyeux R, Sahel JA, Dansingani K. Laplacian feature detection and feature alignment for multimodal ophthalmic image registration using phase correlation and Hessian affine feature space. SIGNAL PROCESSING 2020; 177:107733. [PMID: 32943806 PMCID: PMC7491864 DOI: 10.1016/j.sigpro.2020.107733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Advances in multimodal imaging have revolutionized diagnostic and treatment monitoring in ophthalmic practice. In multimodal ophthalmic imaging, geometric deformations are inevitable and they contain inherent deformations arising from heterogeneity in the optical characteristics of imaging devices and patient related factors. The registration of ophthalmic images under such conditions is challenging. We propose a novel technique that overcomes these challenges, using Laplacian feature, Hessian affine feature space and phase correlation, to register blue autofluorescence, near-infrared reflectance and color fundus photographs of the ocular posterior pole with high accuracy. Our validation analysis - that used current feature detection and extraction techniques (speed-up robust features (SURF), a concept of wind approach (KAZE), and fast retina keypoint (FREAK)), and quantitative measures (Sørensen-Dice coefficient, Jaccard index, and Kullback-Leibler divergence scores) - showed that our approach has significant merit in registering multimodal images when compared with a mix-and-match SURF-KAZE-FREAK benchmark approach. Similarly, our evaluation analysis that used a state-of-the-art qualitative measure - the mean registration error (MRE) - showed that the proposed approach is significantly better than the mix-and-match SURF-KAZE-FREAK benchmark approach, as well as a cutting edge image registration technique - Linear Stack Alignment with SIFT (scale-invariant feature transform) - in registering multimodal ophthalmic images.
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Affiliation(s)
- Shan Suthaharan
- Department of Computer Science, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ethan A Rossi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Valerie Snyder
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jay Chhablani
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Raphael Lejoyeux
- Rothschild Foundation Hospital, 29 Rue Manin, 75019 Paris, France
| | - Jośe-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kunal Dansingani
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Trimmer JS. Recombinant Antibodies in Basic Neuroscience Research. CURRENT PROTOCOLS IN NEUROSCIENCE 2020; 94:e106. [PMID: 33151027 PMCID: PMC7665837 DOI: 10.1002/cpns.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Basic neuroscience research employs antibodies as key reagents to label, capture, and modulate the function of proteins of interest. Antibodies are immunoglobulin proteins. Recombinant antibodies are immunoglobulin proteins whose nucleic acid coding regions, or fragments thereof, have been cloned into expression plasmids that allow for unlimited production. Recombinant antibodies offer many advantages over conventional antibodies including their unambiguous identification and digital archiving via DNA sequencing, reliable expression, ease and reliable distribution as DNA sequences and as plasmids, and the opportunity for numerous forms of engineering to enhance their utility. Recombinant antibodies exist in many different forms, each of which offers potential advantages and disadvantages for neuroscience research applications. I provide an overview of recombinant antibodies and their development. Examples of their emerging use as valuable reagents in basic neuroscience research are also discussed. Many of these examples employ recombinant antibodies in innovative experimental approaches that cannot be pursued with conventional antibodies. © 2020 Wiley Periodicals LLC.
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Affiliation(s)
- James S Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, California
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53
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Verhaar ER, Woodham AW, Ploegh HL. Nanobodies in cancer. Semin Immunol 2020; 52:101425. [PMID: 33272897 DOI: 10.1016/j.smim.2020.101425] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/24/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023]
Abstract
For treatment and diagnosis of cancer, antibodies have proven their value and now serve as a first line of therapy for certain cancers. A unique class of antibody fragments called nanobodies, derived from camelid heavy chain-only antibodies, are gaining increasing acceptance as diagnostic tools and are considered also as building blocks for chimeric antigen receptors as well as for targeted drug delivery. The small size of nanobodies (∼15 kDa), their stability, ease of manufacture and modification for diverse formats, short circulatory half-life, and high tissue penetration, coupled with excellent specificity and affinity, account for their attractiveness. Here we review applications of nanobodies in the sphere of tumor biology.
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Affiliation(s)
- Elisha R Verhaar
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States
| | - Andrew W Woodham
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States; Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States; Department of Pediatrics, Harvard Medical School, Boston, MA, United States.
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54
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Messal HA, Almagro J, Zaw Thin M, Tedeschi A, Ciccarelli A, Blackie L, Anderson KI, Miguel-Aliaga I, van Rheenen J, Behrens A. Antigen retrieval and clearing for whole-organ immunofluorescence by FLASH. Nat Protoc 2020; 16:239-262. [PMID: 33247285 DOI: 10.1038/s41596-020-00414-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022]
Abstract
Advances in light-sheet and confocal microscopy now allow imaging of cleared large biological tissue samples and enable the 3D appreciation of cell and protein localization in their native organ environment. However, the sample preparations for such imaging are often onerous, and their capability for antigen detection is limited. Here, we describe FLASH (fast light-microscopic analysis of antibody-stained whole organs), a simple, rapid, fully customizable technique for molecular phenotyping of intact tissue volumes. FLASH utilizes non-degradative epitope recovery and membrane solubilization to enable the detection of a multitude of membranous, cytoplasmic and nuclear antigens in whole mouse organs and embryos, human biopsies, organoids and Drosophila. Retrieval and immunolabeling of epithelial markers, an obstacle for previous clearing techniques, can be achieved with FLASH. Upon volumetric imaging, FLASH-processed samples preserve their architecture and integrity and can be paraffin-embedded for subsequent histopathological analysis. The technique can be performed by scientists trained in light microscopy and yields results in <1 week.
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Affiliation(s)
- Hendrik A Messal
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK.,Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jorge Almagro
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - May Zaw Thin
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Antonio Tedeschi
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | | | - Laura Blackie
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Kurt I Anderson
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Irene Miguel-Aliaga
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK. .,Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK. .,Convergence Science Centre, Imperial College London, London, UK. .,The Institute of Cancer Research, London, UK.
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55
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de Beer MA, Giepmans BNG. Nanobody-Based Probes for Subcellular Protein Identification and Visualization. Front Cell Neurosci 2020; 14:573278. [PMID: 33240044 PMCID: PMC7667270 DOI: 10.3389/fncel.2020.573278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.
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Affiliation(s)
- Marit A de Beer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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56
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Quantitative Synaptic Biology: A Perspective on Techniques, Numbers and Expectations. Int J Mol Sci 2020; 21:ijms21197298. [PMID: 33023247 PMCID: PMC7582872 DOI: 10.3390/ijms21197298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022] Open
Abstract
Synapses play a central role for the processing of information in the brain and have been analyzed in countless biochemical, electrophysiological, imaging, and computational studies. The functionality and plasticity of synapses are nevertheless still difficult to predict, and conflicting hypotheses have been proposed for many synaptic processes. In this review, we argue that the cause of these problems is a lack of understanding of the spatiotemporal dynamics of key synaptic components. Fortunately, a number of emerging imaging approaches, going beyond super-resolution, should be able to provide required protein positions in space at different points in time. Mathematical models can then integrate the resulting information to allow the prediction of the spatiotemporal dynamics. We argue that these models, to deal with the complexity of synaptic processes, need to be designed in a sufficiently abstract way. Taken together, we suggest that a well-designed combination of imaging and modelling approaches will result in a far more complete understanding of synaptic function than currently possible.
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57
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Carrier M, Robert MÈ, González Ibáñez F, Desjardins M, Tremblay MÈ. Imaging the Neuroimmune Dynamics Across Space and Time. Front Neurosci 2020; 14:903. [PMID: 33071723 PMCID: PMC7539119 DOI: 10.3389/fnins.2020.00903] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
The immune system is essential for maintaining homeostasis, as well as promoting growth and healing throughout the brain and body. Considering that immune cells respond rapidly to changes in their microenvironment, they are very difficult to study without affecting their structure and function. The advancement of non-invasive imaging methods greatly contributed to elucidating the physiological roles performed by immune cells in the brain across stages of the lifespan and contexts of health and disease. For instance, techniques like two-photon in vivo microscopy were pivotal for studying microglial functional dynamics in the healthy brain. Through these observations, their interactions with neurons, astrocytes, blood vessels and synapses were uncovered. High-resolution electron microscopy with immunostaining and 3D-reconstruction, as well as super-resolution fluorescence microscopy, provided complementary insights by revealing microglial interventions at synapses (phagocytosis, trogocytosis, synaptic stripping, etc.). In addition, serial block-face scanning electron microscopy has provided the first 3D reconstruction of a microglial cell at nanoscale resolution. This review will discuss the technical toolbox that currently allows to study microglia and other immune cells in the brain, as well as introduce emerging methods that were developed and could be used to increase the spatial and temporal resolution of neuroimmune imaging. A special attention will also be placed on positron emission tomography and the development of selective functional radiotracers for microglia and peripheral macrophages, considering their strong potential for research translation between animals and humans, notably when paired with other imaging modalities such as magnetic resonance imaging.
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Affiliation(s)
- Micaël Carrier
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Marie-Ève Robert
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Fernando González Ibáñez
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Michèle Desjardins
- Axe Oncologie, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
- Department of Physics, Physical Engineering and Optics, Université Laval, Québec City, QC, Canada
| | - Marie-Ève Tremblay
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Université Laval, Québec City, QC, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
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58
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Pedersen H, Jensen RK, Jensen JMB, Fox R, Pedersen DV, Olesen HG, Hansen AG, Christiansen D, Mazarakis SMM, Lojek N, Hansen P, Gadeberg TAF, Zarantonello A, Laursen NS, Mollnes TE, Johnson MB, Stevens B, Thiel S, Andersen GR. A Complement C3-Specific Nanobody for Modulation of the Alternative Cascade Identifies the C-Terminal Domain of C3b as Functional in C5 Convertase Activity. THE JOURNAL OF IMMUNOLOGY 2020; 205:2287-2300. [PMID: 32938727 DOI: 10.4049/jimmunol.2000752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022]
Abstract
The complement system is an intricate cascade of the innate immune system and plays a key role in microbial defense, inflammation, organ development, and tissue regeneration. There is increasing interest in developing complement regulatory and inhibitory agents to treat complement dysfunction. In this study, we describe the nanobody hC3Nb3, which is specific for the C-terminal C345c domain of human and mouse complement component C3/C3b/C3c and potently inhibits C3 cleavage by the alternative pathway. A high-resolution structure of the hC3Nb3-C345c complex explains how the nanobody blocks proconvertase assembly. Surprisingly, although the nanobody does not affect classical pathway-mediated C3 cleavage, hC3Nb3 inhibits classical pathway-driven hemolysis, suggesting that the C-terminal domain of C3b has an important function in classical pathway C5 convertase activity. The hC3Nb3 nanobody binds C3 with low nanomolar affinity in an SDS-resistant complex, and the nanobody is demonstrated to be a powerful reagent for C3 detection in immunohistochemistry and flow cytometry. Overall, the hC3Nb3 nanobody represents a potent inhibitor of both the alternative pathway and the terminal pathway, with possible applications in complement research, diagnostics, and therapeutics.
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Affiliation(s)
- Henrik Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Rasmus K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Rachel Fox
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Dennis V Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Heidi G Olesen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Annette G Hansen
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Sofia M M Mazarakis
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Neal Lojek
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pernille Hansen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Trine A F Gadeberg
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Nick S Laursen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Tom Eirik Mollnes
- Research Laboratory, Nordland Hospital, 8092 Bodø, Norway.,K.G. Jebsen Thrombosis Research and Expertise Center, University of Tromsø, 9037 Tromsø, Norway.,Department of Immunology, Oslo University Hospital, University of Oslo, 0318 Oslo, Norway.,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway; and
| | - Matthew B Johnson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115
| | - Beth Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark
| | - Gregers R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark;
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59
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Guo J, Wang G, Tang W, Song D, Wang X, Hong J, Zhang Z. An optimized approach using cryofixation for high-resolution 3D analysis by FIB-SEM. J Struct Biol 2020; 212:107600. [PMID: 32798655 DOI: 10.1016/j.jsb.2020.107600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 01/10/2023]
Abstract
Compared with conventional two-dimensional transmission electron microscopy (TEM), focused ion beam scanning electron microscopy (FIB-SEM) can provide more comprehensive 3D information on cell substructures at the nanometer scale. Biological samples prepared by cryofixation using high-pressure freezing demonstrate optimal preservation of the morphology of cellular structures, as these are arrested instantly in their near-native states. However, samples from cryofixation often show a weak back-scatter electron signal and bad image contrast in FIB-SEM imaging. In addition, it is impossible to do large amounts of heavy metal staining. This is commonly achieved via established osmium impregnation (OTO) en bloc staining protocols. Here, we compared the FIB-SEM image quality of brain tissues prepared using several common freeze-substitution media, and we developed an approach that overcomes these limitations through a combination of osmium tetroxide, uranyl acetate, tannic acid, and potassium permanganate at proper concentrations, respectively. Using this optimized sample preparation protocol for high-pressure freezing and freeze-substitution, perfect smooth membrane morphology, even of the lipid bilayers of the cell membrane, was readily obtained using FIB-SEM. In addition, our protocol is broadly applicable and we demonstrated successful application to brain tissues, plant tissues, Caenorhabditis elegans, Candida albicans, and chlorella. This approach combines the potential of cryofixation for 3D large volume analysis of subcellular structures with the high-resolution capabilities of FIB-SEM.
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Affiliation(s)
- Jiansheng Guo
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058 Hangzhou, Zhejiang, China; Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, 310058 Hangzhou, Zhejiang, China
| | - Guan Wang
- Department of Neurobiology, Zhejiang University School of Medicine, 310058 Hangzhou, Zhejiang, China
| | - Wen Tang
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058 Hangzhou, Zhejiang, China
| | - Dandan Song
- Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, 310058 Hangzhou, Zhejiang, China
| | - Xinqiu Wang
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Jian Hong
- Center of Analysis and Measurement, Zhejiang University, Hangzhou 310029, China
| | - Zhongkai Zhang
- Biotechnology and Genetic Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation Ministry of Agriculture and Rural Affairs, Key Lab of Agricultural Biotechnology of Yunnan Province, Kunming 650205, Yunnan, China.
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60
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BRAIN Initiative: Cutting-Edge Tools and Resources for the Community. J Neurosci 2020; 39:8275-8284. [PMID: 31619497 DOI: 10.1523/jneurosci.1169-19.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
The overarching goal of the NIH BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Initiative is to advance the understanding of healthy and diseased brain circuit function through technological innovation. Core principles for this goal include the validation and dissemination of the myriad innovative technologies, tools, methods, and resources emerging from BRAIN-funded research. Innovators, BRAIN funding agencies, and non-Federal partners are working together to develop strategies for making these products usable, available, and accessible to the scientific community. Here, we describe several early strategies for supporting the dissemination of BRAIN technologies. We aim to invigorate a dialogue with the neuroscience research and funding community, interdisciplinary collaborators, and trainees about the existing and future opportunities for cultivating groundbreaking research products into mature, integrated, and adaptable research systems. Along with the accompanying Society for Neuroscience 2019 Mini-Symposium, "BRAIN Initiative: Cutting-Edge Tools and Resources for the Community," we spotlight the work of several BRAIN investigator teams who are making progress toward providing tools, technologies, and services for the neuroscience community. These tools access neural circuits at multiple levels of analysis, from subcellular composition to brain-wide network connectivity, including the following: integrated systems for EM- and florescence-based connectomics, advances in immunolabeling capabilities, and resources for recording and analyzing functional connectivity. Investigators describe how the resources they provide to the community will contribute to achieving the goals of the NIH BRAIN Initiative. Finally, in addition to celebrating the contributions of these BRAIN-funded investigators, the Mini-Symposium will illustrate the broader diversity of BRAIN Initiative investments in cutting-edge technologies and resources.
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61
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Carrington G, Tomlinson D, Peckham M. Exploiting nanobodies and Affimers for superresolution imaging in light microscopy. Mol Biol Cell 2020; 30:2737-2740. [PMID: 31609674 PMCID: PMC6789155 DOI: 10.1091/mbc.e18-11-0694] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibodies have long been the main approach used for localizing proteins of interest by light microscopy. In the past 5 yr or so, and with the advent of superresolution microscopy, the diversity of tools for imaging has rapidly expanded. One main area of expansion has been in the area of nanobodies, small single-chain antibodies from camelids or sharks. The other has been the use of artificial scaffold proteins, including Affimers. The small size of nanobodies and Affimers compared with the traditional antibody provides several advantages for superresolution imaging.
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Affiliation(s)
- Glenn Carrington
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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62
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Sograte-Idrissi S, Schlichthaerle T, Duque-Afonso CJ, Alevra M, Strauss S, Moser T, Jungmann R, Rizzoli SO, Opazo F. Circumvention of common labelling artefacts using secondary nanobodies. NANOSCALE 2020; 12:10226-10239. [PMID: 32356544 DOI: 10.1039/d0nr00227e] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A standard procedure to study cellular elements is via immunostaining followed by optical imaging. This methodology typically requires target-specific primary antibodies (1.Abs), which are revealed by secondary antibodies (2.Abs). Unfortunately, the antibody bivalency, polyclonality, and large size can result in a series of artifacts. Alternatively, small, monovalent probes, such as single-domain antibodies (nanobodies) have been suggested to minimize these limitations. The discovery and validation of nanobodies against specific targets are challenging, thus only a minimal amount of them are currently available. Here, we used STED, DNA-PAINT, and light-sheet microscopy, to demonstrate that secondary nanobodies (1) increase localization accuracy compared to 2.Abs; (2) allow direct pre-mixing with 1.Abs before staining, reducing experimental time, and enabling the use of multiple 1.Abs from the same species; (3) penetrate thick tissues more efficiently; and (4) avoid probe-induced clustering of target molecules observed with conventional 2.Abs in living or poorly fixed samples. Altogether, we show how secondary nanobodies are a valuable alternative to 2.Abs.
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Affiliation(s)
- Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany. and Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany and International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, 80539, Munich, Germany and Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Carlos J Duque-Afonso
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany and Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany and Multiscale Bioimaging Cluster of Excellence (MBExC), University of Göttingen, 37075 Göttingen, Germany and University of Göttingen, 37075, Göttingen, Germany
| | - Mihai Alevra
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany.
| | - Sebastian Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, 80539, Munich, Germany and Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany and Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany and Multiscale Bioimaging Cluster of Excellence (MBExC), University of Göttingen, 37075 Göttingen, Germany and University of Göttingen, 37075, Göttingen, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, 80539, Munich, Germany and Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Silvio O Rizzoli
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany. and Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany and Multiscale Bioimaging Cluster of Excellence (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany. and Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany and NanoTag Biotechnologies GmbH, 37079, Göttingen, Germany
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Ochs M, Hegermann J, Lopez-Rodriguez E, Timm S, Nouailles G, Matuszak J, Simmons S, Witzenrath M, Kuebler WM. On Top of the Alveolar Epithelium: Surfactant and the Glycocalyx. Int J Mol Sci 2020; 21:ijms21093075. [PMID: 32349261 PMCID: PMC7246550 DOI: 10.3390/ijms21093075] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022] Open
Abstract
Gas exchange in the lung takes place via the air-blood barrier in the septal walls of alveoli. The tissue elements that oxygen molecules have to cross are the alveolar epithelium, the interstitium and the capillary endothelium. The epithelium that lines the alveolar surface is covered by a thin and continuous liquid lining layer. Pulmonary surfactant acts at this air-liquid interface. By virtue of its biophysical and immunomodulatory functions, surfactant keeps alveoli open, dry and clean. What needs to be added to this picture is the glycocalyx of the alveolar epithelium. Here, we briefly review what is known about this glycocalyx and how it can be visualized using electron microscopy. The application of colloidal thorium dioxide as a staining agent reveals differences in the staining pattern between type I and type II alveolar epithelial cells and shows close associations of the glycocalyx with intraalveolar surfactant subtypes such as tubular myelin. These morphological findings indicate that specific spatial interactions between components of the surfactant system and those of the alveolar epithelial glycocalyx exist which may contribute to the maintenance of alveolar homeostasis, in particular to alveolar micromechanics, to the functional integrity of the air-blood barrier, to the regulation of the thickness and viscosity of the alveolar lining layer, and to the defence against inhaled pathogens. Exploring the alveolar epithelial glycocalyx in conjunction with the surfactant system opens novel physiological perspectives of potential clinical relevance for future research.
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Affiliation(s)
- Matthias Ochs
- Institute of Functional Anatomy, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
- German Center for Lung Research (DZL), 10117 Berlin, Germany; (M.W.); (W.M.K.)
- Correspondence:
| | - Jan Hegermann
- Research Core Unit Electron Microscopy and Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany;
| | - Elena Lopez-Rodriguez
- Institute of Functional Anatomy, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Sara Timm
- Core Facility Electron Microscopy, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Geraldine Nouailles
- Department of Infectious Diseases and Respiratory Medicine, and Division of Pulmonary Inflammation, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Jasmin Matuszak
- Institute of Physiology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; (J.M.); (S.S.)
| | - Szandor Simmons
- Institute of Physiology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; (J.M.); (S.S.)
| | - Martin Witzenrath
- German Center for Lung Research (DZL), 10117 Berlin, Germany; (M.W.); (W.M.K.)
- Department of Infectious Diseases and Respiratory Medicine, and Division of Pulmonary Inflammation, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Wolfgang M. Kuebler
- German Center for Lung Research (DZL), 10117 Berlin, Germany; (M.W.); (W.M.K.)
- Institute of Physiology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; (J.M.); (S.S.)
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64
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Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics. eNeuro 2020; 7:ENEURO.0328-19.2019. [PMID: 32094293 PMCID: PMC7174874 DOI: 10.1523/eneuro.0328-19.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 11/23/2022] Open
Abstract
Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed by imaging consecutive tissue slices, has proven to be a powerful tool for the investigation of brain anatomy. Between the process of cutting the slices, or “sections,” and imaging them, however, handling 10°−106 delicate sections remains a bottleneck in ssEM, especially for batches in the “mesoscale” regime, i.e., 102–103 sections. We present a tissue section handling device that transports and positions sections, accurately and repeatability, for automated, robotic section pick-up and placement onto an imaging substrate. The device interfaces with a conventional ultramicrotomy diamond knife, accomplishing in-line, exact-constraint trapping of sections with 100-μm repeatability. An associated mathematical model includes capillary-based and Stokes-based forces, accurately describing observed behavior and fundamentally extends the modeling of water-air interface forces. Using the device, we demonstrate and describe the limits of reliable handling of hundreds of slices onto a variety of electron and light microscopy substrates without significant defects (n = 8 datasets composed of 126 serial sections in an automated fashion with an average loss rate and throughput of 0.50% and 63 s/section, respectively. In total, this work represents an automated mesoscale serial sectioning system for scalable 3D-EM connectomics.
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65
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Torelli MD, Nunn NA, Shenderova OA. A Perspective on Fluorescent Nanodiamond Bioimaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902151. [PMID: 31215753 PMCID: PMC6881523 DOI: 10.1002/smll.201902151] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/03/2019] [Indexed: 05/28/2023]
Abstract
The field of fluorescent nanodiamonds (FNDs) has advanced greatly over the past few years. Though historically limited primarily to red fluorescence, the wavelengths available for nanodiamonds have increased due to continuous technical advancement. This Review summarizes the strides made in the synthesis, functionalization, and application of FNDs to bioimaging. Highlights range from super-resolution microscopy, through cellular and whole animal imaging, up to constantly emerging fields including sensing and hyperpolarized magnetic resonance imaging.
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Affiliation(s)
- Marco D. Torelli
- Adámas Nanotechnologies, Inc., 8100 Brownleigh Dr, Suite 120, Raleigh, NC 27617
| | - Nicholas A. Nunn
- Adámas Nanotechnologies, Inc., 8100 Brownleigh Dr, Suite 120, Raleigh, NC 27617
| | - Olga A. Shenderova
- Adámas Nanotechnologies, Inc., 8100 Brownleigh Dr, Suite 120, Raleigh, NC 27617
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66
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Dong JX, Lee Y, Kirmiz M, Palacio S, Dumitras C, Moreno CM, Sando R, Santana LF, Südhof TC, Gong B, Murray KD, Trimmer JS. A toolbox of nanobodies developed and validated for use as intrabodies and nanoscale immunolabels in mammalian brain neurons. eLife 2019; 8:48750. [PMID: 31566565 PMCID: PMC6785268 DOI: 10.7554/elife.48750] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/18/2019] [Indexed: 12/30/2022] Open
Abstract
Nanobodies (nAbs) are small, minimal antibodies that have distinct attributes that make them uniquely suited for certain biomedical research, diagnostic and therapeutic applications. Prominent uses include as intracellular antibodies or intrabodies to bind and deliver cargo to specific proteins and/or subcellular sites within cells, and as nanoscale immunolabels for enhanced tissue penetration and improved spatial imaging resolution. Here, we report the generation and validation of nAbs against a set of proteins prominently expressed at specific subcellular sites in mammalian brain neurons. We describe a novel hierarchical validation pipeline to systematically evaluate nAbs isolated by phage display for effective and specific use as intrabodies and immunolabels in mammalian cells including brain neurons. These nAbs form part of a robust toolbox for targeting proteins with distinct and highly spatially-restricted subcellular localization in mammalian brain neurons, allowing for visualization and/or modulation of structure and function at those sites.
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Affiliation(s)
- Jie-Xian Dong
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Yongam Lee
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Michael Kirmiz
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Stephanie Palacio
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Camelia Dumitras
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Claudia M Moreno
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States.,Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Richard Sando
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford School of Medicine, Stanford, United States
| | - L Fernando Santana
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford School of Medicine, Stanford, United States
| | - Belvin Gong
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Karl D Murray
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - James S Trimmer
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States.,Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
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67
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Sigmund F, Pettinger S, Kube M, Schneider F, Schifferer M, Schneider S, Efremova MV, Pujol-Martí J, Aichler M, Walch A, Misgeld T, Dietz H, Westmeyer GG. Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters. ACS NANO 2019; 13:8114-8123. [PMID: 31194509 DOI: 10.1021/acsnano.9b03140] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Multicolored gene reporters for light microscopy are indispensable for biomedical research, but equivalent genetic tools for electron microscopy (EM) are still rare despite the increasing importance of nanometer resolution for reverse engineering of molecular machinery and reliable mapping of cellular circuits. We here introduce the fully genetic encapsulin/cargo system of Quasibacillus thermotolerans (Qt), which in combination with the recently characterized encapsulin system from Myxococcus xanthus (Mx) enables multiplexed gene reporter imaging via conventional transmission electron microscopy (TEM) in mammalian cells. Cryo-electron reconstructions revealed that the Qt encapsulin shell self-assembles to nanospheres with T = 4 icosahedral symmetry and a diameter of ∼43 nm harboring two putative pore regions at the 5-fold and 3-fold axes. We also found that upon heterologous expression in mammalian cells, the native cargo is autotargeted to the inner surface of the shell and exhibits ferroxidase activity leading to efficient intraluminal iron biomineralization, which enhances cellular TEM contrast. We furthermore demonstrate that the two differently sized encapsulins of Qt and Mx do not intermix and can be robustly differentiated by conventional TEM via a deep learning classifier to enable automated multiplexed EM gene reporter imaging.
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Affiliation(s)
- Felix Sigmund
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Susanne Pettinger
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Massimo Kube
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Fabian Schneider
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Martina Schifferer
- Institute of Neuronal Cell Biology, TUM School of Medicine , Technical University of Munich , 80802 Munich , Germany
- German Center for Neurodegenerative Diseases (DZNE) , 81377 Munich , Germany
| | - Steffen Schneider
- Computational Neuroengineering, Department of Electrical and Computer Engineering , Technical University of Munich , 80333 Munich , Germany
- Tübingen AI Center , University of Tübingen , 72076 Tübingen , Germany
| | - Maria V Efremova
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Laboratory of Chemical Design of Bionanomaterials for Medical Applications, Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russian Federation
| | - Jesús Pujol-Martí
- Department "Circuits - Computation - Models" , Max Planck Institute of Neurobiology , 82152 Martinsried , Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Axel Walch
- Research Unit Analytical Pathology , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, TUM School of Medicine , Technical University of Munich , 80802 Munich , Germany
- German Center for Neurodegenerative Diseases (DZNE) , 81377 Munich , Germany
| | - Hendrik Dietz
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Gil G Westmeyer
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
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68
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Huang C, Li D, Ren J, Ji F, Jia L. Generation and Application of Fluorescent Anti-Human β2-Microglobulin VHHs via Amino Modification. Molecules 2019; 24:E2600. [PMID: 31319525 PMCID: PMC6680903 DOI: 10.3390/molecules24142600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/07/2019] [Accepted: 07/14/2019] [Indexed: 01/21/2023] Open
Abstract
The functionalization of VHHs enables their application in almost every aspect of biomedical inquiry. Amino modification remains a common strategy for protein functionalization, though is considered to be inferior to site-specific methods and cause protein property changes. In this paper, four anti-β2M VHHs were selected and modified on the amino group by NHS-Fluo. The impacts of amino modification on these VHHs were drastically different, and among all th examples, the modified NB-1 maintained the original stability, bioactivity and homogeneity of unmodified NB-1. Specific recognition of VHHs targeting β2M detected by fluorescence imaging explored the possible applications of VHHs. Via this study, we successfully functionalized the anti-β2M VHHs through amino modification and the results are able to instruct the simple and fast functionalization of VHHs in biomedical researches.
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Affiliation(s)
- Chundong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, Liaoning, China.
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69
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Baena V, Schalek RL, Lichtman JW, Terasaki M. Serial-section electron microscopy using automated tape-collecting ultramicrotome (ATUM). Methods Cell Biol 2019; 152:41-67. [PMID: 31326026 DOI: 10.1016/bs.mcb.2019.04.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Automated Tape-Collecting Ultramicrotome (ATUM) is a tape-reeling device that is placed in a water-filled diamond knife boat to collect serial sections as they are cut by a conventional ultramicrotome. The ATUM can collect thousands of sections of many different shapes and sizes, which are subsequently imaged by a scanning electron microscope. This method has been used for large-scale connectomics projects of mouse brain, and is well suited for other smaller-scale studies of tissues, cells, and organisms. Here, we describe basic procedures for preparing a block for ATUM sectioning, handling of the ATUM, tape preparation, post-treatment of sections, and considerations for mapping, imaging, and aligning the serial sections.
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Affiliation(s)
- Valentina Baena
- Deparment of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States
| | - Richard Lee Schalek
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, United States
| | - Jeff William Lichtman
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, United States
| | - Mark Terasaki
- Deparment of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States.
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70
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Shibata S, Iseda T, Mitsuhashi T, Oka A, Shindo T, Moritoki N, Nagai T, Otsubo S, Inoue T, Sasaki E, Akazawa C, Takahashi T, Schalek R, Lichtman JW, Okano H. Large-Area Fluorescence and Electron Microscopic Correlative Imaging With Multibeam Scanning Electron Microscopy. Front Neural Circuits 2019; 13:29. [PMID: 31133819 PMCID: PMC6517476 DOI: 10.3389/fncir.2019.00029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/08/2019] [Indexed: 01/21/2023] Open
Abstract
Recent improvements in correlative light and electron microscopy (CLEM) technology have led to dramatic improvements in the ability to observe tissues and cells. Fluorescence labeling has been used to visualize the localization of molecules of interest through immunostaining or genetic modification strategies for the identification of the molecular signatures of biological specimens. Newer technologies such as tissue clearing have expanded the field of observation available for fluorescence labeling; however, the area of correlative observation available for electron microscopy (EM) remains restricted. In this study, we developed a large-area CLEM imaging procedure to show specific molecular localization in large-scale EM sections of mouse and marmoset brain. Target molecules were labeled with antibodies and sequentially visualized in cryostat sections using fluorescence and gold particles. Fluorescence images were obtained by light microscopy immediately after antibody staining. Immunostained sections were postfixed for EM, and silver-enhanced sections were dehydrated in a graded ethanol series and embedded in resin. Ultrathin sections for EM were prepared from fully polymerized resin blocks, collected on silicon wafers, and observed by multibeam scanning electron microscopy (SEM). Multibeam SEM has made rapid, large-area observation at high resolution possible, paving the way for the analysis of detailed structures using the CLEM approach. Here, we describe detailed methods for large-area CLEM in various tissues of both rodents and primates.
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Affiliation(s)
- Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Taro Iseda
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | | | - Atsushi Oka
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Shindo
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Nobuko Moritoki
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Toshihiro Nagai
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Shinya Otsubo
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Takashi Inoue
- Central Institute for Experimental Animals, Kawasaki, Japan
| | - Erika Sasaki
- Central Institute for Experimental Animals, Kawasaki, Japan
| | - Chihiro Akazawa
- Department of Biochemistry and Biophysics, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takao Takahashi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Richard Schalek
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
| | - Jeff W Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
| | - Hideyuki Okano
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan.,Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wakō, Japan
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71
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Yang Y, Lu J, Zuo Y. Changes of Synaptic Structures Associated with Learning, Memory and Diseases. BRAIN SCIENCE ADVANCES 2019. [DOI: 10.26599/bsa.2018.2018.9050012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Synaptic plasticity is widely believed to be the cellular basis of learning and memory. It is influenced by various factors including development, sensory experiences, and brain disorders. Long-term synaptic plasticity is accompanied by protein synthesis and trafficking, leading to structural changes of the synapse. In this review, we focus on the synaptic structural plasticity, which has mainly been studied with in vivo two-photon laser scanning microscopy. We also discuss how a special type of synapses, the multi-contact synapses (including those formed by multi-synaptic boutons and multi-synaptic spines), are associated with experience and learning.
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Affiliation(s)
- Yang Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ju Lu
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
| | - Yi Zuo
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
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72
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Zhang Q, Lee WCA, Paul DL, Ginty DD. Multiplexed peroxidase-based electron microscopy labeling enables simultaneous visualization of multiple cell types. Nat Neurosci 2019; 22:828-839. [PMID: 30886406 PMCID: PMC6555422 DOI: 10.1038/s41593-019-0358-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/07/2019] [Indexed: 01/06/2023]
Abstract
Electron microscopy (EM) is a powerful tool for circuit mapping, but identifying specific cell types in EM datasets remains a major challenge. Here we describe a technique enabling simultaneous visualization of multiple, genetically identified neuronal populations so that synaptic interactions between them can be unequivocally defined. We present 15 AAV constructs and six mouse reporter lines for multiplexed EM labeling in the mammalian nervous system. These reporters feature dAPEX2, which exhibits dramatically improved signal compared to previously described ascorbate peroxidases. By targeting this enhanced peroxidase to different subcellular compartments, multiple orthogonal reporters can be simultaneously visualized and distinguished under EM using a protocol compatible with existing EM pipelines. Proof-of-principle double and triple EM labeling experiments demonstrated synaptic connections between primary afferents, descending cortical inputs, and inhibitory interneurons in the spinal cord dorsal horn. Our multiplexed peroxidase-based EM labeling system should therefore greatly facilitate analysis of connectivity in the nervous system.
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Affiliation(s)
- Qiyu Zhang
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Wei-Chung A Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - David L Paul
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - David D Ginty
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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73
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Chanier T, Chames P. Nanobody Engineering: Toward Next Generation Immunotherapies and Immunoimaging of Cancer. Antibodies (Basel) 2019; 8:E13. [PMID: 31544819 PMCID: PMC6640690 DOI: 10.3390/antib8010013] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
In the last decade, cancer immunotherapies have produced impressive therapeutic results. However, the potency of immunotherapy is tightly linked to immune cell infiltration within the tumor and varies from patient to patient. Thus, it is becoming increasingly important to monitor and modulate the tumor immune infiltrate for an efficient diagnosis and therapy. Various bispecific approaches are being developed to favor immune cell infiltration through specific tumor targeting. The discovery of antibodies devoid of light chains in camelids has spurred the development of single domain antibodies (also called VHH or nanobody), allowing for an increased diversity of multispecific and/or multivalent formats of relatively small sizes endowed with high tissue penetration. The small size of nanobodies is also an asset leading to high contrasts for non-invasive imaging. The approval of the first therapeutic nanobody directed against the von Willebrand factor for the treatment of acquired thrombotic thrombocypenic purpura (Caplacizumab, Ablynx), is expected to bolster the rise of these innovative molecules. In this review, we discuss the latest advances in the development of nanobodies and nanobody-derived molecules for use in cancer immunotherapy and immunoimaging.
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Affiliation(s)
- Timothée Chanier
- Aix Marseille University, CNRS, INSERM, Institute Paoli-Calmettes, CRCM, 13009 Marseille, France.
| | - Patrick Chames
- Aix Marseille University, CNRS, INSERM, Institute Paoli-Calmettes, CRCM, 13009 Marseille, France.
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