title: Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex.
abstract: Neocortical circuits can be altered by sensory and motor experience, with experimental evidence supporting both anatomical and electrophysiological changes in synaptic properties. Previous studies have focused on changes in specific neurons or pathways-for example, the thalamocortical circuitry, layer 4-3 (L4-L3) synapses, or in the apical dendrites of L5 neurons- but a broad-scale analysis of experience-induced changes across the cortical column has been lacking. Without this comprehensive approach, a full understanding of how cortical circuits adapt during learning or altered sensory input will be impossible. Here we adapt an electron microscopy technique that selectively labels synapses, in combination with a machine-learning algorithm for semiautomated synapse detection, to perform an unbiased analysis of developmental and experience-dependent changes in synaptic properties across an entire cortical column in mice. Synapse density and length were compared across development and during whisker-evoked plasticity. Between postnatal days 14 and 18, synapse density significantly increases most in superficial layers, and synapse length increases in L3 and L5B. Removal of all but a single whisker row for 24 h led to an apparent increase in synapse density in L2 and a decrease in L6, and a significant increase in length in L3. Targeted electrophysiological analysis of changes in miniature EPSC and IPSC properties in L2 pyramidal neurons showed that mEPSC frequency nearly doubled in the whisker-spared column, a difference that was highly significant. Together, this analysis shows that data-intensive analysis of column-wide changes in synapse properties can generate specific and testable hypotheses about experience-dependent changes in cortical organization.
  
  
  CONCLUSIONS
  Development and sensory experience can change synapse properties in the neocortex. Here we use a semiautomated analysis of electron microscopy images for an unbiased, column-wide analysis of synapse changes. This analysis reveals new loci for synaptic change that can be verified by targeted electrophysiological investigation. This method can be used as a platform for generating new hypotheses about synaptic changes across different brain areas and experimental conditions.
authors.affiliation: Department of Biological Sciences and Center for the Neural Basis of Cognition and.
authors.forename: Santosh
authors.identifier: http://orcid.org/0000-0002-0686-6556
authors.initials: S
authors.lastname: Chandrasekaran
authors.affiliation: Integrative Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037.
authors.forename: Saket
authors.initials: S
authors.lastname: Navlakha
authors.affiliation: Department of Biological Sciences and Center for the Neural Basis of Cognition and.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Audette
authors.affiliation: Department of Biological Sciences and Center for the Neural Basis of Cognition and.
authors.forename: Dylan D
authors.identifier: http://orcid.org/0000-0003-3822-1338
authors.initials: DD
authors.lastname: McCreary
authors.affiliation: Department of Biological Sciences and Center for the Neural Basis of Cognition and.
authors.forename: Joe
authors.initials: J
authors.lastname: Suhan
authors.affiliation: Machine Learning Department and Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and.
authors.forename: Ziv
authors.initials: Z
authors.lastname: Bar-Joseph
authors.affiliation: Department of Biological Sciences and Center for the Neural Basis of Cognition and barth@cmu.edu.
authors.forename: Alison L
authors.initials: AL
authors.lastname: Barth
mesh_terms: D000222:Adaptation, Physiological; D000465:Algorithms; D000818:Animals; D019706:Excitatory Postsynaptic Potentials; D005260:Female; D007206:Individuality; D007858:Learning; D000069550:Machine Learning; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008854:Microscopy, Electron / Q000379:methods*; D019579:Neocortex / Q000254:growth & development / Q000473:pathology*; D009415:Nerve Net / Q000473:pathology; D009473:Neuronal Plasticity; D018408:Patch-Clamp Techniques; D017966:Pyramidal Cells / Q000473:pathology; D013569:Synapses / Q000473:pathology*; D014738:Vibrissae / Q000294:innervation
keywords: automated; development; electron microscopy; machine learning; synapse detection; synaptic plasticity