1
|
Wei C, Lei X, Yu S. Multiplexed Detection Strategies for Biosensors Based on the CRISPR-Cas System. ACS Synth Biol 2024; 13:1633-1646. [PMID: 38860462 DOI: 10.1021/acssynbio.4c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
A growing number of applications require simultaneous detection of multiplexed nucleic acid targets in a single reaction, which enables higher information density in combination with reduced assay time and cost. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-Cas system have broad applications for the detection of nucleic acids due to their strong specificity, high sensitivity, and excellent programmability. However, realizing multiplexed detection is still challenging for the CRISPR-Cas system due to the nonspecific collateral cleavage activity, limited signal reporting strategies, and possible cross-reactions. In this review, we summarize the principles, strategies, and features of multiplexed detection based on the CRISPR-Cas system and further discuss the challenges and perspective.
Collapse
Affiliation(s)
- Cong Wei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
2
|
Kitzberger F, Yang SM, Týč J, Bílý T, Nebesářová J. An advanced fast method for the evaluation of multiple immunolabelling using gold nanoparticles based on low-energy STEM. Sci Rep 2024; 14:10150. [PMID: 38698090 PMCID: PMC11065996 DOI: 10.1038/s41598-024-60314-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/21/2024] [Indexed: 05/05/2024] Open
Abstract
We present a powerful method for the simultaneous detection of Au nanoparticles located on both sides of ultrathin sections. The method employs a high-resolution scanning electron microscope (HRSEM) operating in scanning transmission electron microscopy (STEM) mode in combination with the detection of backscattered electrons (BSE). The images are recorded simultaneously during STEM and BSE imaging at the precisely selected accelerating voltage. Under proper imaging conditions, the positions of Au nanoparticles on the top or bottom sides can be clearly differentiated, hence showing this method to be suitable for multiple immunolabelling using Au nanoparticles (NPs) as markers. The difference between the upper and lower Au NPs is so large that it is possible to apply common software tools (such as ImageJ) to enable their automatic differentiation. The effects of the section thickness, detector settings and accelerating voltage on the resulting image are shown. Our experimental results correspond to the results modelled in silico by Monte Carlo (MC) simulations.
Collapse
Affiliation(s)
- František Kitzberger
- Laboratory of Electron Microscopy, Institute of Parasitology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Shun-Min Yang
- Laboratory of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Jiří Týč
- Laboratory of Electron Microscopy, Institute of Parasitology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic
| | - Tomáš Bílý
- Laboratory of Electron Microscopy, Institute of Parasitology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Jana Nebesářová
- Laboratory of Electron Microscopy, Institute of Parasitology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic.
| |
Collapse
|
3
|
Vasconcelos MH, Alcaro S, Arechavala-Gomeza V, Baumbach J, Borges F, Brevini TAL, Rivas JDL, Devaux Y, Hozak P, Keinänen-Toivola MM, Lattanzi G, Mohr T, Murovska M, Prusty BK, Quinlan RA, Pérez-Sala D, Scheibenbogen C, Schmidt HHHW, Silveira I, Tieri P, Tolios A, Riganti C. Joining European Scientific Forces to Face Pandemics. Trends Microbiol 2020; 29:92-97. [PMID: 33288385 PMCID: PMC7716745 DOI: 10.1016/j.tim.2020.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/26/2022]
Abstract
Despite the international guidelines on the containment of the coronavirus disease 2019 (COVID-19) pandemic, the European scientific community was not sufficiently prepared to coordinate scientific efforts. To improve preparedness for future pandemics, we have initiated a network of nine European-funded Cooperation in Science and Technology (COST) Actions that can help facilitate inter-, multi-, and trans-disciplinary communication and collaboration.
Collapse
Affiliation(s)
- M Helena Vasconcelos
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, PT-4200-135 Porto, Portugal; Cancer Drug Resistance Group, IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, PT-4200-135 Porto, Portugal; Department of Biological Sciences, FFUP-Faculty of Pharmacy, University of Porto, PT-4050-313 Porto, Portugal
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università Magna Græcia di Catanzaro, Viale Europa, IT-88100, Catanzaro, Italy; Net4Science srl, Università Magna Græcia di Catanzaro, Viale Europa, IT-88100, Catanzaro, Italy
| | - Virginia Arechavala-Gomeza
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, ES-48903, Barakaldo, Spain; Ikerbasque, Basque Foundation for Science, ES-48009, Bilbao, Spain
| | - Jan Baumbach
- Experimental Bioinformatics, School of Life Sciences Weihenstephan, Technical University of Munich, DE-85354, Munich, Germany
| | - Fernanda Borges
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, PT-4169-007, Porto, Portugal
| | - Tiziana A L Brevini
- Laboratory of Biomedical Embryology, Center for Stem Cell Research UniSTEM, University of Milan, IT-20133 Milan, Italy
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IMBCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas and University of Salamanca, Campus Miguel de Unamuno, ES-37007 Salamanca, Spain
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, Czech Academy of Sciences, CZ-14220, Prague, Czech Republic
| | | | - Giovanna Lattanzi
- CNR, National Research Council of Italy, Institute of Molecular Genetics Unit of Bologna, IT-40136, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, IT-40136, Bologna, Italy
| | - Thomas Mohr
- ScienceConsult, DI Thomas Mohr KG, AT-2353, Guntramsdorf, Austria; Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center Vienna, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Modra Murovska
- Rīga Stradiņš University, Institute of Microbiology and Virology, LV-1007, Riga, Latvia
| | - Bhupesh K Prusty
- Julius-Maximilians-Universität, Institute for Virology and Immunobiology, DE-97078, Würzburg, Germany
| | - Roy A Quinlan
- Department of Biosciences, University of Durham, Upper Mountjoy Science Site, Durham DH1 3LE, UK
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, ES-28040 Madrid, Spain
| | - Carmen Scheibenbogen
- Institut für Med. Immunologie, Charité Campus Virchow Klinikum, DE-13353, Berlin, Germany
| | - Harald H H W Schmidt
- Department of Pharmacology and Personalised Medicine, MeHNS, FHML, Maastricht University, NL-6200 Maastricht, The Netherlands
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, PT-4200-135 Porto, Portugal; IBMC, Institute for Molecular and Cell Biology, Universidade do Porto, PT-4200-135 Porto, Portugal
| | - Paolo Tieri
- CNR Consiglio Nazionale delle Ricerche, IAC Istituto per le Applicazioni del Calcolo, IT-00185, Rome, Italy
| | - Alexander Tolios
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, AT-1090, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, AT-1090, Vienna, Austria; Center for Medical Statistics, Informatics, and Intelligent Systems, Institute for Artificial Intelligence and Decision Support, Medical University of Vienna, AT-1090, Vienna, Austria
| | - Chiara Riganti
- Department of Oncology, University of Turin, IT-10126, Turin, Italy.
| |
Collapse
|
4
|
Keevend K, Coenen T, Herrmann IK. Correlative cathodoluminescence electron microscopy bioimaging: towards single protein labelling with ultrastructural context. NANOSCALE 2020; 12:15588-15603. [PMID: 32677648 DOI: 10.1039/d0nr02563a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies heavily on the assessment of structure-function relationships at the nanoscale. Ever since the development of the first optical microscope, the reliance of scientists across disciplines on microscopy has increased. The development of the first electron microscope and with it the access to information at the nanoscale has prompted numerous disruptive discoveries. While fluorescence imaging allows identification of specific entities based on the labelling with fluorophores, the unlabelled constituents of the samples remain invisible. In electron microscopy on the other hand, structures can be comprehensively visualized based on their distinct electron density and geometry. Although electron microscopy is a powerful tool, it does not implicitly provide information on the location and activity of specific organic molecules. While correlative light and electron microscopy techniques have attempted to unify the two modalities, the resolution mismatch between the two data sets poses major challenges. Recent developments in optical super resolution microscopy enable high resolution correlative light and electron microscopy, however, with considerable constraints due to sample preparation requirements. Labelling of specific structures directly for electron microscopy using small gold nanoparticles (i.e. immunogold) has been used extensively. However, identification of specific entities solely based on electron contrast, and the differentiation from endogenous dense granules, remains challenging. Recently, the use of correlative cathodoluminescence electron microscopy (CCLEM) imaging based on luminescent inorganic nanocrystals has been proposed. While nanometric resolution can be reached for both the electron and the optical signal, high energy electron beams are potentially damaging to the sample. In this review, we discuss the opportunities of (volumetric) multi-color single protein labelling based on correlative cathodoluminescence electron microscopy, and its prospective impact on biomedical research in general. We elaborate on the potential challenges of correlative cathodoluminescence electron microscopy-based bioimaging and benchmark CCLEM against alternative high-resolution correlative imaging techniques.
Collapse
Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St Gallen, Switzerland.
| | | | | |
Collapse
|
5
|
Doh JK, Chang YH, Enns CA, Lόpez CS, Beatty KE. Imaging VIPER-labeled Cellular Proteins by Correlative Light and Electron Microscopy. Bio Protoc 2019; 9:e3414. [PMID: 33654913 PMCID: PMC7853974 DOI: 10.21769/bioprotoc.3414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 01/02/2023] Open
Abstract
Advances in fluorescence microscopy (FM), electron microscopy (EM), and correlative light and EM (CLEM) offer unprecedented opportunities for studying diverse proteins and nanostructures involved in fundamental cell biology. It is now possible to visualize and quantify the spatial organization of cellular proteins and other macromolecules by FM, EM, and CLEM. However, tagging and tracking cellular proteins across size scales is restricted by the scarcity of methods for attaching appropriate reporter chemistries to target proteins. Namely, there are few genetic tags compatible with EM. To overcome these issues we developed Versatile Interacting Peptide (VIP) tags, genetically-encoded peptide tags that can be used to image proteins by fluorescence and EM. VIPER, a VIP tag, can be used to label cellular proteins with bright, photo-stable fluorophores for FM or electron-dense nanoparticles for EM. In this Bio-Protocol, we provide an instructional guide for implementing VIPER for imaging a cell-surface receptor by CLEM. This protocol is complemented by two other Bio-Protocols outlining the use of VIPER ( Doh et al., 2019a and 2019b).
Collapse
Affiliation(s)
- Julia K. Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Caroline A. Enns
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Claudia S. Lόpez
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, USA
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Kimberly E. Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, USA
| |
Collapse
|
6
|
Malatesta M. Ultrastructural histochemistry in biomedical research: Alive and kicking. Eur J Histochem 2018; 62. [PMID: 30418011 PMCID: PMC6250102 DOI: 10.4081/ejh.2018.2990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023] Open
Abstract
The high-resolution images provided by the electron microscopy has constituted a limitless source of information in any research field of life and materials science since the early Thirties of the last century. Browsing the scientific literature, electron microscopy was especially popular from the 1970’s to 80’s, whereas during the 90’s, with the advent of innovative molecular techniques, electron microscopy seemed to be downgraded to a subordinate role, as a merely descriptive technique. Ultra -structural histochemistry was crucial to promote the Renaissance of electron microscopy, when it became evident that a precise localization of molecules in the biological environment was necessary to fully understand their functional role. Nowadays, electron microscopy is still irreplaceable for ultrastructural morphology in basic and applied biomedical research, while the application of correlative light and electron microscopy and of refined ultrastructural histochemical techniques gives electron microscopy a central role in functional cell and tissue biology, as a really unique tool for high-resolution molecular biology in situ.
Collapse
Affiliation(s)
- Manuela Malatesta
- University of Verona, Department of Neurosciences, Biomedicine and Movement Sciences.
| |
Collapse
|
7
|
ColorEM: analytical electron microscopy for element-guided identification and imaging of the building blocks of life. Histochem Cell Biol 2018; 150:509-520. [PMID: 30120552 PMCID: PMC6182685 DOI: 10.1007/s00418-018-1707-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 12/22/2022]
Abstract
Nanometer-scale identification of multiple targets is crucial to understand how biomolecules regulate life. Markers, or probes, of specific biomolecules help to visualize and to identify. Electron microscopy (EM), the highest resolution imaging modality, provides ultrastructural information where several subcellular structures can be readily identified. For precise tagging of (macro)molecules, electron-dense probes, distinguishable in gray-scale EM, are being used. However, practically these genetically-encoded or immune-targeted probes are limited to three targets. In correlated microscopy, fluorescent signals are overlaid on the EM image, but typically without the nanometer-scale resolution and limited to visualization of few targets. Recently, analytical methods have become more sensitive, which has led to a renewed interest to explore these for imaging of elements and molecules in cells and tissues in EM. Here, we present the current state of nanoscale imaging of cells and tissues using energy dispersive X-ray analysis (EDX), electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and touch upon secondary ion mass spectroscopy at the nanoscale (NanoSIMS). ColorEM is the term encompassing these analytical techniques the results of which are then displayed as false-color at the EM scale. We highlight how ColorEM will become a strong analytical nano-imaging tool in life science microscopy.
Collapse
|
8
|
Pastorek L, Sobol M, Hozák P. Colocalization coefficients evaluating the distribution of molecular targets in microscopy methods based on pointed patterns. Histochem Cell Biol 2016; 146:391-406. [PMID: 27460592 PMCID: PMC5037163 DOI: 10.1007/s00418-016-1467-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 01/28/2023]
Abstract
In biomedical studies, the colocalization is commonly understood as the overlap between distinctive labelings in images. This term is usually associated especially with quantitative evaluation of the immunostaining in fluorescence microscopy. On the other hand, the evaluation of the immunolabeling colocalization in the electron microscopy images is still under-investigated and biased by the subjective and non-quantitative interpretation of the image data. We introduce a novel computational technique for quantifying the level of colocalization in pointed patterns. Our approach follows the idea included in the widely used Manders' colocalization coefficients in fluorescence microscopy and represents its counterpart for electron microscopy. In presented methodology, colocalization is understood as the product of the spatial interactions at the single-particle (single-molecule) level. Our approach extends the current significance testing in the immunoelectron microscopy images and establishes the descriptive colocalization coefficients. To demonstrate the performance of the proposed coefficients, we investigated the level of spatial interactions of phosphatidylinositol 4,5-bisphosphate with fibrillarin in nucleoli. We compared the electron microscopy colocalization coefficients with Manders' colocalization coefficients for confocal microscopy and super-resolution structured illumination microscopy. The similar tendency of the values obtained using different colocalization approaches suggests the biological validity of the scientific conclusions. The presented methodology represents a good basis for further development of the quantitative analysis of immunoelectron microscopy data and can be used for studying molecular interactions at the ultrastructural level. Moreover, this methodology can be applied also to the other super-resolution microscopy techniques focused on characterization of discrete pointed structures.
Collapse
Affiliation(s)
- Lukáš Pastorek
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
- Laboratory of Epigenetics of the Cell Nucleus, Division BIOCEV, Institute of Molecular Genetics of the ASCR v. v. i., Průmyslová 595, 252 50, Vestec, Czech Republic.
| |
Collapse
|
9
|
Novel method of simultaneous multiple immunogold localization on resin sections in high resolution scanning electron microscopy. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2015; 12:105-8. [PMID: 26472050 DOI: 10.1016/j.nano.2015.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/15/2015] [Accepted: 09/22/2015] [Indexed: 11/23/2022]
Abstract
We present a new method of multiple immunolabeling that is suitable for a broad spectrum of biomedical applications. The general concept is to label both sides of the ultrathin section with the thickness of 70-80 nm with different antibodies conjugated to gold nanoparticles and to distinguish the labeled side by advanced imaging methods with high resolution scanning electron microscopy, such as by correlating images acquired at different energies of primary electrons using different signals. From the Clinical Editor: The use of transmission electron microscopy has become an indispensible tool in the detection of cellular proteins. In this short but interesting article, the authors described their new method of labeling and the identification of four different proteins simultaneously, which represents another advance in imaging technique.
Collapse
|
10
|
de Boer P, Hoogenboom JP, Giepmans BNG. Correlated light and electron microscopy: ultrastructure lights up! Nat Methods 2015; 12:503-13. [PMID: 26020503 DOI: 10.1038/nmeth.3400] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/15/2015] [Indexed: 12/15/2022]
Abstract
Microscopy has gone hand in hand with the study of living systems since van Leeuwenhoek observed living microorganisms and cells in 1674 using his light microscope. A spectrum of dyes and probes now enable the localization of molecules of interest within living cells by fluorescence microscopy. With electron microscopy (EM), cellular ultrastructure has been revealed. Bridging these two modalities, correlated light microscopy and EM (CLEM) opens new avenues. Studies of protein dynamics with fluorescent proteins (FPs), which leave the investigator 'in the dark' concerning cellular context, can be followed by EM examination. Rare events can be preselected at the light microscopy level before EM analysis. Ongoing development-including of dedicated probes, integrated microscopes, large-scale and three-dimensional EM and super-resolution fluorescence microscopy-now paves the way for broad CLEM implementation in biology.
Collapse
Affiliation(s)
- Pascal de Boer
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| |
Collapse
|
11
|
Mayhew T. Morphomics: An integral part of systems biology of the human placenta. Placenta 2015; 36:329-40. [DOI: 10.1016/j.placenta.2015.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 01/03/2023]
|
12
|
Mayhew TM, Lucocq JM. From gross anatomy to the nanomorphome: stereological tools provide a paradigm for advancing research in quantitative morphomics. J Anat 2015; 226:309-21. [PMID: 25753334 DOI: 10.1111/joa.12287] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 01/08/2023] Open
Abstract
The terms morphome and morphomics are not new but, recently, a group of morphologists and cell biologists has given them clear definitions and emphasised their integral importance in systems biology. By analogy to other '-omes', the morphome refers to the distribution of matter within 3-dimensional (3D) space. It equates to the totality of morphological features within a biological system (virus, single cell, multicellular organism or populations thereof) and morphomics is the systematic study of those structures. Morphomics research has the potential to generate 'big data' because it includes all imaging techniques at all levels of achievable resolution and all structural scales from gross anatomy and medical imaging, via optical and electron microscopy, to molecular characterisation. As with other '-omics', quantification is an important part of morphomics and, because biological systems exist and operate in 3D space, precise descriptions of form, content and spatial relationships require the quantification of structure in 3D. Revealing and quantifying structural detail inside the specimen is achieved currently in two main ways: (i) by some form of reconstruction from serial physical or tomographic slices or (ii) by using randomly-sampled sections and simple test probes (points, lines, areas, volumes) to derive stereological estimates of global and/or individual quantities. The latter include volumes, surfaces, lengths and numbers of interesting features and spatial relationships between them. This article emphasises the value of stereological design, sampling principles and estimation tools as a template for combining with alternative imaging techniques to tackle the 'big data' issue and advance knowledge and understanding of the morphome. The combination of stereology, TEM and immunogold cytochemistry provides a practical illustration of how this has been achieved in the sub-field of nanomorphomics. Applying these quantitative tools/techniques in a carefully managed study design offers us a deeper appreciation of the spatiotemporal relationships between the genome, metabolome and morphome which are integral to systems biology.
Collapse
Affiliation(s)
- Terry M Mayhew
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK; School of Medicine, University of St Andrews, St Andrews, UK
| | | |
Collapse
|
13
|
The Histochemistry and Cell Biology pandect: the year 2014 in review. Histochem Cell Biol 2015; 143:339-68. [PMID: 25744491 DOI: 10.1007/s00418-015-1313-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2015] [Indexed: 02/07/2023]
Abstract
This review encompasses a brief synopsis of the articles published in 2014 in Histochemistry and Cell Biology. Out of the total of 12 issues published in 2014, two special issues were devoted to "Single-Molecule Super-Resolution Microscopy." The present review is divided into 11 categories, providing an easy format for readers to quickly peruse topics of particular interest to them.
Collapse
|
14
|
Mayhew TM. Quantitative immunocytochemistry at the ultrastructural level: a stereology-based approach to molecular nanomorphomics. Cell Tissue Res 2014; 360:43-59. [PMID: 25403623 DOI: 10.1007/s00441-014-2038-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/15/2014] [Indexed: 12/16/2022]
Abstract
Biological systems span multiple levels of structural organisation from the macroscopic, via the microscopic, to the nanoscale. Therefore, comprehensive investigation of systems biology requires application of imaging modalities that reveal structure at multiple resolution scales. Nanomorphomics is the part of morphomics devoted to the systematic study of functional morphology at the nanoscale and an important element of its achievement is the combination of immunolabelling and transmission electron microscopy (TEM). The ultimate goal of quantitative immunocytochemistry is to estimate numbers of target molecules (usually peptides, proteins or protein complexes) in biological systems and to map their spatial distributions within them. Immunogold cytochemistry utilises target-specific affinity markers (primary antibodies) and visualisation aids (e.g., colloidal gold particles or silver-enhanced nanogold particles) to detect and localise target molecules at high resolution in intact cells and tissues. In the case of post-embedding labelling of ultrathin sections for TEM, targets are localised as a countable digital readout by using colloidal gold particles. The readout comprises a spatial distribution of gold particles across the section and within the context of biological ultrastructure. The observed distribution across structural compartments (whether volume- or surface-occupying) represents both specific and non-specific labelling; an assessment by eye alone as to whether the distribution is random or non-random is not always possible. This review presents a coherent set of quantitative methods for testing whether target molecules exhibit preferential and specific labelling of compartments and for mapping the same targets in two or more groups of cells as their TEM immunogold-labelling patterns alter after experimental manipulation. The set also includes methods for quantifying colocalisation in multiple-labelling experiments and mapping absolute numbers of colloidal gold particles across compartments at specific positions within cells having a point-like inclusion (e.g., centrosome, nucleolus) and a definable vertical axis. Although developed for quantifying colloidal gold particles, the same methods can in principle be used to quantify other electron-dense punctate nanoparticles, including quantum dots.
Collapse
Affiliation(s)
- Terry M Mayhew
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, E Floor, Nottingham, NG7 2UH, UK,
| |
Collapse
|