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NEU466G, Dr. Harris · Class documents

Overview

These are the papers for each week, in the order of the schedule. Each entry gives the authors, year, title, journal and a DOI link. Open each paper through its DOI link.

The course does not host the papers. Canvas has a copy of each one in its Reading page for that week. Read the papers before class and use them for your weekly discussion question (see Assignments).

Unless an entry says Optional, the paper is required. Week 1 has no reading.

Week 2: Dendrites: excitatory postsynaptic structure

Two reviews on the ultrastructure of synapses and dendrites, and on the role of synapse and dendrite plasticity in disease.

  • Required. Harris, K. M., & Weinberg, R. J. (2012). Ultrastructure of synapses in the mammalian brain. Cold Spring Harbor Perspectives in Biology, 4, a005587. https://doi.org/10.1101/cshperspect.a005587
  • Required. Forrest, M. P., Parnell, E., & Penzes, P. (2018). Dendritic structural plasticity and neuropsychiatric disease. Nature Reviews Neuroscience, 19, 215-234. https://doi.org/10.1038/nrn.2018.16

Week 3: Presynaptic boutons, vesicles, and mitochondria

Presynaptic vesicles

The lecture draws heavily on the first paper, so it is there to help, but it is not required. Its first two sections ("Holding synapses together..." and "Presynaptic components...") are the most useful, since postsynaptic function was covered earlier. The 2019 review covers how vesicles and membranes are recycled in presynaptic boutons. The 2025 review summarizes the ultrastructural evidence for enhanced presynaptic cycling with LTP.

  • Optional. Chua, J. J. E., Kindler, S., Boyken, J., & Jahn, R. (2010). The architecture of an excitatory synapse. Journal of Cell Science, 123, 819-823. https://doi.org/10.1242/jcs.052696
  • Required. Chanaday, N. L., Cousin, M. A., Milosevic, I., Watanabe, S., & Morgan, J. R. (2019). The synaptic vesicle cycle revisited: New insights into the modes and mechanisms. The Journal of Neuroscience, 39, 8209-8216. https://doi.org/10.1523/JNEUROSCI.1158-19.2019
  • Required. Harris, K. M. (2025). Enhanced cycling of presynaptic vesicles during long-term potentiation in rat hippocampus. The Journal of Physiology, 603, 6001-6013. https://doi.org/10.1113/JP286983

Presynaptic mitochondria

A review of the roles of mitochondria beyond energy production, and a research paper on how presynaptic mitochondria support vesicle mobilization after LTP.

  • Required. Pekkurnaz, G., & Wang, X. (2022). Mitochondrial heterogeneity and homeostasis through the lens of a neuron. Nature Metabolism, 4, 802-812. https://doi.org/10.1038/s42255-022-00594-w
  • Required. Smith, H. L., Bourne, J. N., Cao, G., Chirillo, M. A., Ostroff, L. E., Watson, D. J., & Harris, K. M. (2016). Mitochondrial support of persistent presynaptic vesicle mobilization with age-dependent synaptic growth after LTP. eLife, 5, e15275. https://doi.org/10.7554/eLife.15275

Week 4: Methods: sample preparation and imaging

A review of electron microscopy modes and what they are used for, and the paper that introduced the transmission-mode scanning electron microscope (tSEM). The Harris Lab built that microscope and used it to image your class series; you see it on the lab tour.

  • Required. McCafferty, C. L., Klumpe, S., Amaro, R. E., Kukulski, W., Collinson, L., & Engel, B. D. (2024). Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell, 187, 563-584. https://doi.org/10.1016/j.cell.2024.01.005
  • Required. Kuwajima, M., Mendenhall, J. M., Lindsey, L. F., & Harris, K. M. (2013). Automated transmission-mode scanning electron microscopy (tSEM) for large volume analysis at nanoscale resolution. PLoS ONE, 8, e59573. https://doi.org/10.1371/journal.pone.0059573

Week 5: Smooth endoplasmic reticulum (SER) and recycling endosomes

Two primary research papers on how LTP changes SER and endosomes at dendritic spines, in young (Kulik et al.) and adult (Chirillo et al.) hippocampal area CA1.

  • Required. Kulik, Y. D., Watson, D. J., Cao, G., Kuwajima, M., & Harris, K. M. (2019). Structural plasticity of dendritic secretory compartments during LTP-induced synaptogenesis. eLife, 8, e46356. https://doi.org/10.7554/eLife.46356
  • Required. Chirillo, M. A., Waters, M. S., Lindsey, L. F., Bourne, J. N., & Harris, K. M. (2019). Local resources of polyribosomes and SER promote synapse enlargement and spine clustering after long-term potentiation in adult rat hippocampus. Scientific Reports, 9, 3861. https://doi.org/10.1038/s41598-019-40520-x

Week 6: Polyribosomes (PR) and local protein synthesis

A review of how neurons regulate protein concentration (proteostasis) across the large span of dendrites and synapses, and a research paper on where polyribosomes accumulate at synapses after LTP.

  • Required. Hanus, C., & Schuman, E. M. (2013). Proteostasis in complex dendrites. Nature Reviews Neuroscience, 14, 638-648. https://doi.org/10.1038/nrn3546
  • Required. Ostroff, L. E., Watson, D. J., Cao, G., Parker, P. H., Smith, H., & Harris, K. M. (2018). Shifting patterns of polyribosome accumulation at synapses over the course of hippocampal long-term potentiation. Hippocampus, 28, 416-430. https://doi.org/10.1002/hipo.22841

Weeks 7 to 14: Class research project

To be decided

Dr. Harris chooses the readings for the class project weeks, including the paper for the student-led paper discussion in Week 8. They will be listed here when they are set.

More readings

These papers were readings in an earlier term. They are not assigned this term, but they are useful for your lab reports and the class project.

Cytoskeleton: microtubules, actin, and neurofilaments

A review of the cytoskeletal proteins in neurons and their role in synapse function and plasticity, and a primary research paper that uses 3DEM to relate microtubule number in dendrites to synapse density.

  • Bucher, M., Fanutza, T., & Mikhaylova, M. (2019). Cytoskeletal makeup of the synapse: Shaft versus spine. Cytoskeleton, 77, 55-64. https://doi.org/10.1002/cm.21583
  • Harris, K. M., Hubbard, D. D., Kuwajima, M., Abraham, W. C., Bourne, J. N., Bowden, J. B., Haessly, A., Mendenhall, J. M., Parker, P. H., Shi, B., & Spacek, J. (2022). Dendritic spine density scales with microtubule number in rat hippocampal dendrites. Neuroscience, 489, 84-97. https://doi.org/10.1016/j.neuroscience.2022.02.021

Inhibitory synapses, cell adhesion molecules, and gap junctions

Two reviews on inhibitory synapses: activity-dependent structural plasticity of GABAergic synapses (2014), and the functional implications of where inhibitory synapses sit on pyramidal neuron dendrites (2018).

  • Flores, C. E., & Méndez, P. (2014). Shaping inhibition: Activity dependent structural plasticity of GABAergic synapses. Frontiers in Cellular Neuroscience, 8, 327. https://doi.org/10.3389/fncel.2014.00327
  • Boivin, J. R., & Nedivi, E. (2018). Functional implications of inhibitory synapse placement on signal processing in pyramidal neuron dendrites. Current Opinion in Neurobiology, 51, 16-22. https://doi.org/10.1016/j.conb.2018.01.013

Connectomics

A short review of synaptic connectomics, and a paper that looks at hippocampal neuropil from the connectomics view.

Development of synapses and LTP

Nascent zones and spaced learning

  • Bell, M. E., Bourne, J. N., Chirillo, M. A., Mendenhall, J. M., Kuwajima, M., & Harris, K. M. (2014). Dynamics of nascent and active zone ultrastructure as synapses enlarge during long-term potentiation in mature hippocampus. Journal of Comparative Neurology, 522, 3861-3884. https://doi.org/10.1002/cne.23646
  • Harris, K. M., Kuwajima, M., Flores, J. C., & Zito, K. (2024). Synapse-specific structural plasticity that protects and refines local circuits during LTP and LTD. Philosophical Transactions of the Royal Society B, 379, 20230224. https://doi.org/10.1098/rstb.2023.0224

Perisynaptic astroglia

A 2017 review of the roles of astrocytes and microglia in forming and remodeling synaptic circuits, and a 2025 paper on how perisynaptic astroglia respond structurally to LTP and concurrent LTD in the dentate gyrus of adult rats.

  • Stogsdill, J. A., & Eroglu, C. (2017). The interplay between neurons and glia in synapse development and plasticity. Current Opinion in Neurobiology, 42, 1-8. https://doi.org/10.1016/j.conb.2016.09.016
  • Nam, A. J., Kuwajima, M., Parker, P. H., Bowden, J. B., Abraham, W. C., & Harris, K. M. (2025). Perisynaptic astroglial response to in vivo long-term potentiation and concurrent long-term depression in the hippocampal dentate gyrus. The Journal of Neuroscience, 45, e0943252025. https://doi.org/10.1523/JNEUROSCI.0943-25.2025

Staff-provided material (Canvas only)

  • Example reviewer comments. The reviewer comments for Harris (2025), "Enhanced cycling of presynaptic vesicles during long-term potentiation (LTP) in rat hippocampus," The Journal of Physiology (https://doi.org/10.1113/JP286983), one of the Week 3 readings. The teaching team provides this file on Canvas only, as an example of how reviewers respond to a paper.