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Ganji M, Schlichthaerle T, Eklund AS, Strauss S, Jungmann R. Quantitative Assessment of Labeling Probes for Super-Resolution Microscopy Using Designer DNA Nanostructures. Chemphyschem 2021; 22:911-914. [PMID: 33720501 PMCID: PMC8251534 DOI: 10.1002/cphc.202100185] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/22/2022]
Abstract
Improving labeling probes for state-of-the-art super-resolution microscopy is becoming of major importance. However, there is currently a lack of tools to quantitatively evaluate probe performance regarding efficiency, precision, and achievable resolution in an unbiased yet modular fashion. Herein, we introduce designer DNA origami structures combined with DNA-PAINT to overcome this issue and evaluate labeling efficiency, precision, and quantification using antibodies and nanobodies as exemplary labeling probes. Whereas current assessment of binders is mostly qualitative, e. g. based on an expected staining pattern, we herein present a quantitative analysis platform of the antigen labeling efficiency and achievable resolution, allowing researchers to choose the best performing binder. The platform can furthermore be readily adapted for discovery and precise quantification of a large variety of additional labeling probes.
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Affiliation(s)
- Mahipal Ganji
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Current Address: Department of Biochemistry, Indian Institute of Science, CV Raman Road, 560012, Bengaluru, India
| | - Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Current Address: Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexandra S Eklund
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Sebastian Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
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Pezzulo G, LaPalme J, Durant F, Levin M. Bistability of somatic pattern memories: stochastic outcomes in bioelectric circuits underlying regeneration. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190765. [PMID: 33550952 PMCID: PMC7935058 DOI: 10.1098/rstb.2019.0765] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
Nervous systems' computational abilities are an evolutionary innovation, specializing and speed-optimizing ancient biophysical dynamics. Bioelectric signalling originated in cells' communication with the outside world and with each other, enabling cooperation towards adaptive construction and repair of multicellular bodies. Here, we review the emerging field of developmental bioelectricity, which links the field of basal cognition to state-of-the-art questions in regenerative medicine, synthetic bioengineering and even artificial intelligence. One of the predictions of this view is that regeneration and regulative development can restore correct large-scale anatomies from diverse starting states because, like the brain, they exploit bioelectric encoding of distributed goal states-in this case, pattern memories. We propose a new interpretation of recent stochastic regenerative phenotypes in planaria, by appealing to computational models of memory representation and processing in the brain. Moreover, we discuss novel findings showing that bioelectric changes induced in planaria can be stored in tissue for over a week, thus revealing that somatic bioelectric circuits in vivo can implement a long-term, re-writable memory medium. A consideration of the mechanisms, evolution and functionality of basal cognition makes novel predictions and provides an integrative perspective on the evolution, physiology and biomedicine of information processing in vivo. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy
| | - Joshua LaPalme
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Fallon Durant
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA
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