Cortical Column and Whole-brain Imaging with Molecular Contrast and Nanoscale Resolution

Overview

Journal Science

Specialty Science

Date 2019 Jan 19

PMID 30655415

Citations 145

Authors

Ruixuan Gao

Shoh M Asano

Srigokul Upadhyayula

Igor Pisarev

Daniel E Milkie

Tsung-Li Liu

Ved Singh

Austin Graves

Grace H Huynh

Yongxin Zhao

John Bogovic

Jennifer Colonell

Carolyn M Ott

Christopher Zugates

Susan Tappan

Alfredo Rodriguez

Kishore R Mosaliganti

Shu-Hsien Sheu

H Amalia Pasolli

Song Pang

C Shan Xu

Sean G Megason

Harald Hess

Jennifer Lippincott-Schwartz

Adam Hantman

Gerald M Rubin

Tom Kirchhausen

Stephan Saalfeld

Yoshinori Aso

Edward S Boyden

Eric Betzig

Affiliations

Soon will be listed here.

Abstract

Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.

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References

Duchen M . Mitochondria in health and disease: perspectives on a new mitochondrial biology. Mol Aspects Med. 2004; 25(4):365-451. DOI: 10.1016/j.mam.2004.03.001. View

Economo M, Clack N, Lavis L, Gerfen C, Svoboda K, Myers E . A platform for brain-wide imaging and reconstruction of individual neurons. Elife. 2016; 5:e10566. PMC: 4739768. DOI: 10.7554/eLife.10566. View

Takasaki K, Sabatini B . Super-resolution 2-photon microscopy reveals that the morphology of each dendritic spine correlates with diffusive but not synaptic properties. Front Neuroanat. 2014; 8:29. PMC: 4019874. DOI: 10.3389/fnana.2014.00029. View

Jenett A, Rubin G, Ngo T, Shepherd D, Murphy C, Dionne H . A GAL4-driver line resource for Drosophila neurobiology. Cell Rep. 2012; 2(4):991-1001. PMC: 3515021. DOI: 10.1016/j.celrep.2012.09.011. View

Butcher N, Friedrich A, Lu Z, Tanimoto H, Meinertzhagen I . Different classes of input and output neurons reveal new features in microglomeruli of the adult Drosophila mushroom body calyx. J Comp Neurol. 2012; 520(10):2185-201. DOI: 10.1002/cne.23037. View

Thomas U . Modulation of synaptic signalling complexes by Homer proteins. J Neurochem. 2002; 81(3):407-13. DOI: 10.1046/j.1471-4159.2002.00869.x. View

Tomassy G, Berger D, Chen H, Kasthuri N, Hayworth K, Vercelli A . Distinct profiles of myelin distribution along single axons of pyramidal neurons in the neocortex. Science. 2014; 344(6181):319-24. PMC: 4122120. DOI: 10.1126/science.1249766. View

Emmenlauer M, Ronneberger O, Ponti A, Schwarb P, Griffa A, Filippi A . XuvTools: free, fast and reliable stitching of large 3D datasets. J Microsc. 2009; 233(1):42-60. DOI: 10.1111/j.1365-2818.2008.03094.x. View

Li D, Shao L, Chen B, Zhang X, Zhang M, Moses B . ADVANCED IMAGING. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science. 2015; 349(6251):aab3500. PMC: 4659358. DOI: 10.1126/science.aab3500. View

10.

Zonouzi M, Scafidi J, Li P, McEllin B, Edwards J, Dupree J . GABAergic regulation of cerebellar NG2 cell development is altered in perinatal white matter injury. Nat Neurosci. 2015; 18(5):674-82. PMC: 4459267. DOI: 10.1038/nn.3990. View

11.

Einheber S, Zanazzi G, Ching W, Scherer S, Milner T, Peles E . The axonal membrane protein Caspr, a homologue of neurexin IV, is a component of the septate-like paranodal junctions that assemble during myelination. J Cell Biol. 1998; 139(6):1495-506. PMC: 2132621. DOI: 10.1083/jcb.139.6.1495. View

12.

Tonnesen J, Inavalli V, Nagerl U . Super-Resolution Imaging of the Extracellular Space in Living Brain Tissue. Cell. 2018; 172(5):1108-1121.e15. DOI: 10.1016/j.cell.2018.02.007. View

13.

RUSHTON W . A theory of the effects of fibre size in medullated nerve. J Physiol. 1951; 115(1):101-22. PMC: 1392008. DOI: 10.1113/jphysiol.1951.sp004655. View

14.

Sharma K, Schmitt S, Bergner C, Tyanova S, Kannaiyan N, Manrique-Hoyos N . Cell type- and brain region-resolved mouse brain proteome. Nat Neurosci. 2015; 18(12):1819-31. PMC: 7116867. DOI: 10.1038/nn.4160. View

15.

Palmer L, Stuart G . Site of action potential initiation in layer 5 pyramidal neurons. J Neurosci. 2006; 26(6):1854-63. PMC: 6793621. DOI: 10.1523/JNEUROSCI.4812-05.2006. View

16.

Azuma T, Kei T . Super-resolution spinning-disk confocal microscopy using optical photon reassignment. Opt Express. 2015; 23(11):15003-11. DOI: 10.1364/OE.23.015003. View

17.

Liu Q, Shio H . Mitochondrial morphogenesis, dendrite development, and synapse formation in cerebellum require both Bcl-w and the glutamate receptor delta2. PLoS Genet. 2008; 4(6):e1000097. PMC: 2405952. DOI: 10.1371/journal.pgen.1000097. View

18.

Owald D, Fouquet W, Schmidt M, Wichmann C, Mertel S, Depner H . A Syd-1 homologue regulates pre- and postsynaptic maturation in Drosophila. J Cell Biol. 2010; 188(4):565-79. PMC: 2828917. DOI: 10.1083/jcb.200908055. View

19.

Micheva K, Smith S . Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron. 2007; 55(1):25-36. PMC: 2080672. DOI: 10.1016/j.neuron.2007.06.014. View

20.

Pfeiffer B, Ngo T, Hibbard K, Murphy C, Jenett A, Truman J . Refinement of tools for targeted gene expression in Drosophila. Genetics. 2010; 186(2):735-55. PMC: 2942869. DOI: 10.1534/genetics.110.119917. View