Automated Analysis of a Diverse Synapse Population

PLoS Computational Biology

Volumn 9, Issue 3, 2013, Pages

  Busse, Brad ^a,b   Smith, Stephen ^a  

^a STANFORD UNIVERSITY   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRAIN; CLASSIFICATION (OF INFORMATION); MAMMALS;

ACTIVITY-DEPENDENT; AUTOMATED ANALYSIS; BRAIN FUNCTIONS; CENTRAL NERVOUS SYSTEMS; HOMEOSTATIC MECHANISM; MEASUREMENTS OF; MEMORY MECHANISM; MOLECULAR COMPOSITIONS; PROPERTY; SPECIFIC SUBSET;

TOMOGRAPHY;

ARTICLE; AUTOANALYSIS; CLASSIFICATION ALGORITHM; CONNECTOME; CONTROLLED STUDY; CYTOARCHITECTURE; DECISION MAKING; HUMAN; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR IMAGING; MOUSE; NERVE CELL NETWORK; NERVE CELL PLASTICITY; NEUROANATOMY; NONHUMAN; PROTEOMICS; SOMATOSENSORY CORTEX; SYNAPSE; SYNAPTIC TRANSMISSION; VALIDATION PROCESS;

EID: 84876000308     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002976     Document Type: Article

References (41)

1. Grant S, (2007) Toward a molecular catalogue of synapses. Brain research reviews 55: 445-9.
2. Sheng M, Hoogenraad C, (2007) The postsynaptic architecture of excitatory synapses: a more quantitative view. Annual review of biochemistry 76: 823-47.
3. Sassoè-Pognetto M, Frola E, Pregno G, Briatore F, Patrizi A, (2011) Understanding the molecular diversity of gabaergic synapses. Frontiers in cellular neuroscience 5: 4.
4. Lein E, Hawrylycz M, Ao N, Ayres M, Bensinger A, et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445: 168-76.
5. O'Rourke N, Weiler N, Micheva K, Smith SJ, (2012) Deep molecular diversity of mammalian synapses: why it matters and how to measure it. Nature Reviews Neuroscience 13: 365-79.
6. Turrigiano G, Nelson S, (2004) Homeostatic plasticity in the developing nervous system. Nature reviews Neuroscience 5: 97-107.
7. Citri A, Malenka R, (2008) Synaptic plasticity: multiple forms, functions, and mechanisms. Neuropsychopharmacology: official publication of the American College of Neuropsychopharmacology 33: 18-41.
8. Garner C, Zhai R, Gundelfinger E, Ziv N, (2002) Molecular mechanisms of cns synaptogenesis. Trends in neurosciences 25: 243-51.
9. Hioki H, Fujiyama F, Nakamura K, Wu S, Matsuda W, et al. (2004) Chemically specific circuit composed of vesicular glutamate transporter 3- and preprotachykinin b-producing interneurons in the rat neocortex. Cerebral cortex (New York, NY: 1991) 14: 1266-75.
10. Gutiérrez R, (2005) The dual glutamatergic-gabaergic phenotype of hippocampal granule cells. Trends in neurosciences 28: 297-303.
11. Briggman K, Helmstaedter M, Denk W, (2011) Wiring specificity in the direction-selectivity circuit of the retina. Nature 471: 183-8.
12. Anderson J, Jones B, Watt C, Shaw M, Yang J, et al. (2011) Exploring the retinal connectome. Molecular vision 17: 355-79.
13. Li L, Tasic B, Micheva K, Ivanov V, Spletter M, et al. (2010) Visualizing the distribution of synapses from individual neurons in the mouse brain. PloS one 5: e11503.
14. Kuhlman S, Huang Z, (2008) High-resolution labeling and functional manipulation of specific neuron types in mouse brain by cre-activated viral gene expression. PloS one 3: e2005.
15. Katz Y, Menon V, Nicholson D, Geinisman Y, Kath W, et al. (2009) Synapse distribution suggests a two-stage model of dendritic integration in ca1 pyramidal neurons. Neuron 63: 171-7.
16. Davie J, Clark B, Husser M, (2008) The origin of the complex spike in cerebellar purkinje cells. The Journal of neuroscience: the official journal of the Society for Neuroscience 28: 7599-609.
17. Micheva K, Busse B, Weiler N, O'Rourke N, Smith S, (2010) Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers. Neuron 68: 639-53.
18. Bayés A, Grant S, (2009) Neuroproteomics: understanding the molecular organization and complexity of the brain. Nature reviews Neuroscience 10: 635-46.
19. Dani A, Huang B, Bergan J, Dulac C, Zhuang X, (2010) Superresolution imaging of chemical synapses in the brain. Neuron 68: 843-56.
20. De Camilli P, Cameron R, Greengard P, (1983) Synapsin 1 (protein 1), a nerve terminal-specific phosphoprotein. Journal of Cell Biology 96: 1337-1354.
21. Evans N, Facci L, Owen D, Soden P, Burbidge S, et al. (2008) Abeta(1-42) reduces synapse number and inhibits neurite outgrowth in primary cortical and hippocampal neurons: a quantitative analysis. Journal of neuroscience methods 175: 96-103.
22. Jackson JE, (1991) A User's Guide to Principal Components. John Wiley and Sons.
23. Belkacem-Boussaid K, Pennell M, Lozanski G, Shana'ah A, Gurcan M, (2010) Computer-aided classification of centroblast cells in follicular lymphoma. Analytical and quantitative cytology and histology/the International Academy of Cytology [and] American Society of Cytology 32: 254-260.
24. Breiman L, (2001) Random forests. Machine Learning 45: 5-3-2.
25. Bogen I, Boulland J, Mariussen E, Wright M, Fonnum F, et al. (2006) Absence of synapsin I and ii is accompanied by decreases in vesicular transport of specific neurotransmitters. Journal of neurochemistry 96: 1458-66.
26. Schüz A, Palm G, (1989) Density of neurons and synapses in the cerebral cortex of the mouse. The Journal of comparative neurology 286: 442-55.
27. Lawton D, Oswald W, McClure J, (1995) The biological reality of the interlacunar network in the embryonic, cartilaginous, skeleton: a thiazine dye/absolute ethanol/lr white resin protocol for visualizing the network with minimal tissue shrinkage. Journal of microscopy 178: 66-85.
28. Gonchar Y, Wang Q, Burkhalter A, (2007) Multiple distinct subtypes of gabaergic neurons in mouse visual cortex identified by triple immunostaining. Frontiers in neuroanatomy 1: 3.
29. Fremeau R, Burman J, Qureshi T, Tran C, Proctor J, et al. (2002) The identification of vesicular glutamate transporter 3 suggests novel modes of signaling by glutamate. Proceedings of the National Academy of Sciences of the United States of America 99: 14488-93.
30. Fremeau R, Voglmaier S, Seal R, Edwards R, (2004) Vgluts define subsets of excitatory neurons and suggest novel roles for glutamate. Trends in neurosciences 27: 98-103.
31. Fremeau R, Kam K, Qureshi T, Johnson J, Copenhagen D, et al. (2004) Vesicular glutamate transporters 1 and 2 target to functionally distinct synaptic release sites. Science (New York, NY) 304: 1815-9.
32. Dal Bo G, St-Gelais F, Danik M, Williams S, Cotton M, et al. (2004) Dopamine neurons in culture express vglut2 explaining their capacity to release glutamate at synapses in addition to dopamine. Journal of neurochemistry 88: 1398-405.
33. Kawano M, Kawasaki A, Sakata-Haga H, Fukui Y, Kawano H, et al. (2006) Particular subpopulations of midbrain and hypothalamic dopamine neurons express vesicular glutamate transporter 2 in the rat brain. The Journal of comparative neurology 498: 581-92.
34. Fu M, Zuo Y, (2011) Experience-dependent structural plasticity in the cortex. Trends in neurosciences 34: 177-87.
35. White JG, Southgate E, Thomson JN, Brenner S, (1986) The structure of the nervous system of the nematode caenorhabditis elegans. Philosophical Transactions of the Royal Society B: Biological Sciences 314: 1-340.
36. Cardona A, Saalfeld S, Arganda I, Pereanu W, Schindelin J, et al. (2010) Identifying neuronal lineages of drosophila by sequence analysis of axon tracts. The Journal of neuroscience: the official journal of the Society for Neuroscience 30: 7538-53.
37. Micheva K, O'Rourke N, Busse B, Smith S, (2010) Array tomography: high-resolution threedimensional immunouorescence. Cold Spring Harbor protocols 2010: pdb.top89.
38. Arganda-Carreras I, Sorzano C, Marabini R, Carazo J, Ortiz-de Solorzano C, et al. (2006) Consistent and elastic registration of histological sections using vector-spline regularization. Springer. 85-95 pp.
39. Wang G, Smith S, (2012) Sub-diffraction limit localization of proteins in volumetric space using bayesian restoration of uorescence images from ultrathin specimens. PLoS computational biology 8: e1002671.
40. Cohn D, Ghahramani Z, Jordan M, (1996) Active learning with statistical models. Journal of Artificial Intelligence 4: 129-145.
41. Settles B, (2009) Active learning literature survey. Computer Sciences Technical Report 1648. University of Wisconsin-Madison.