Please note that there was no lab corresponding to lectures 1, 12, 14, and 15.
| SES # | TOPICS | READINGS |
|---|---|---|
| 1 | Course Introduction; Overview of Neurotechnology | Refresh your memory of the concepts of diffraction-limited resolution, point spread function, combining tube lenses and objective lenses, and fluorescence excitation and emission at Nikon’s MicroscopyU. |
| 2 |
Advanced Microscopy Guest lecturers: Prof. Elly Nedivi, Prof. Peter So |
Chen, Jerry L., Walter C. Lin, et al. “Structural Basis for the Role of Inhibition in Facilitating Adult Brain Plasticity.” Nature Neuroscience 14, no. 5 (2011): 587–94. Chen, Jerry L., Katherine L. Villa, et al. “Clustered Dynamics of Inhibitory Synapses and Dendritic Spines in the Adult Neocortex.” Neuron 74, no. 2 (2012): 361–73. So, Peter T. C., Chen Y. Dong, et al. “Two-photon Excitation Fluorescence Microscopy.” Annual Review of Biomedical Engineering 2, no. 1 (2000): 399–429. So, Peter T. C., Elijah Y. S. Yew, et al. “High-throughput Nonlinear Optical Microscopy.” Biophysical Journal 105, no. 12 (2013): 2641–54. |
| Lab 2 |
Advanced Microscopy Imaging Guest Lecturer: Kalen Berry, Elijah Yew |
|
| 3 |
High-density Electrophysiology Guest lecturer: Prof. Matt Wilson |
Brown, Emery N., Robert E. Kass, et al. “Multiple Neural Spike Train Data Analysis: State-of-the-art and Future Challenges.” Nature Neuroscience 7, no. 5 (2004): 456–61. Buzsáki, György, Costas A. Anastassiou, et al. “The Origin of Extracellular Fields and Currents—EEG, ECoG, LFP and Spikes.” Nature Reviews Neuroscience 13, no. 6 (2012): 407–20. Womelsdorf, Thilo, Jan-Mathijs Schoffelen, et al. “Modulation of Neuronal Interactions through Neuronal Synchronization.” Science 316, no. 5831 (2007): 1609–12. |
| Lab 3 |
Digital Electrophysiology Guest Lecturer: Jon Newman |
|
| 4 |
Microfluidics and Cell Engineering Guest Lecturers: Prof. Roger Kamm & Sebastien Uzel |
Kothapalli, Chandrasekhar R., Ed van Veen, et al. “A High-throughput Microfluidic Assay to Study Neurite Response to Growth Factor Gradients.” Lab on a Chip 11, no. 3 (2011): 497–507. Park, Jae Woo, Hyung Joon Kim, et al. “Advances in Microfluidics-based Experimental Methods for Neuroscience Research.” Lab on a Chip 13, no. 4 (2013): 509–21. Shin, Yoojin, Sewoon Han, et al. “Microfluidic Assay for Simultaneous Culture of Multiple Cell Types on Surfaces or within Hydrogels.” Nature Protocols 7, no. 7 (2012): 1247–59. |
| Lab 4 | Microfluidics and Cell Engineering (cont.) | |
| 5 |
EM-based Connectomics Guest Lecturer: Dr. Daniel Berger |
Lichtman, Jeff W., and Winfried Denk. “The Big and The Small: Challenges of Imaging the Brain’s Circuits.” Science 334, no. 6056 (2011): 618–23. Briggman, Kevin L., and Davi D. Bock. “Volume Electron Microscopy for Neuronal Circuit Reconstruction.” Current Opinion in Neurobiology 22, no. 1 (2012): 154–61. Marx, Vivien. “Neurobiology: Brain Mapping in High Resolution.” Nature 503, no. 7474 (2013): 147–52. Tomassy, Giulio Srubek, Daniel R. Berger, et al. “Distinct Profiles of Myelin Distribution along Single Axons of Pyramidal Neurons in the Neocortex.” Science 344, no. 6181 (2014): 319–24. |
| Lab 5 |
EM-based Connectomics (cont.) Field Trip: Lichtman lab at Harvard |
|
| 6 | Optogenetics |
Kodandaramaiah, Suhasa B., Giovanni Talei Franzesi, et al. “Automated Whole-cell Patch-clamp Electrophysiology of Neurons in Vivo.” Nature Methods 9, no. 6 (2012): 585–87. Klapoetke, Nathan C., Yasunobu Murata, et al. “Independent Optical Excitation of Distinct Neural Populations.” Nature Methods 11, no. 3 (2014): 338–46. Chuong, Amy S., Mitra L. Miri, et al. “Noninvasive Optical Inhibition with a Red-shifted Microbial Rhodopsin.” Nature Neuroscience 17, no. 8 (2014): 1123–29. Prevedel, Robert, Young-Gyu Yoon, et al. “Simultaneous Whole-Animal 3D Imaging of Neuronal Activity Using Light-field Microscopy.” Nature Methods 11, no. 7 (2014): 727–30. |
| Lab 6a | Optogenetics (cont.) | |
| Lab 6b | Auto Patch Clamping | |
| 7 & Lab |
Virus Engineering Guest Lecturer: Dr. Ian Wickersham |
Atasoy, Deniz, Yexica Aponte, et al. “A FLEX Switch Targets Channelrhodopsin-2 to Multiple Cell Types for Imaging and Long-range Circuit Mapping.” The Journal of Neuroscience 28, no. 28 (2008): 7025–30. Wickersham, Ian R., David C. Lyon, et al. “Monosynaptic Restriction of Transsynaptic Tracing from Single, Genetically Targeted Neurons.” Neuron 53, no. 5 (2007): 639–47. |
| 8 |
Magnetoencephalography (MEG) Guest Lecturer: Prof. Dimitrios Pantazis |
Cichy, Radoslaw Martin, Dimitrios Pantazis, et al. “Resolving Human Object Recognition in Space and Time.” Nature Neuroscience 17, no. 3 (2014): 455–62. Baillet, Sylvain, John C. Mosher, et al. “Electromagnetic Brain Mapping.” (PDF) IEEE S_ignal Processing Magazine_ 18, no. 6 (2001): 14–30. |
| Lab 8 | MEG (cont.) | |
| 9 |
Structural Magnetic Resonance Imaging (MRI) Guest Lecturer: Dr. Atsushi Takahashi |
Huettel, Scott A., Allen W. Song, and Gregory McCarthy. Functional Magnetic Resonance Imaging. Vol. 1. Sinauer Associates, 2004. ISBN: 9780878932887. Mesulam, Marsel. “The Evolving Landscape of Human Cortical Connectivity: Facts and Inferences.” Neuroimage 62, no. 4 (2012): 2182–89. |
| Lab 9 | Structural MRI | |
| 10 |
Functional and Molecular MRI Guest Lecturer: Dr. Atsushi Takahashi |
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| Lab 10 | Functional and Molecular MRI (cont.) | |
| 11 |
High Throughput Neuroscience Guest Lecturer: Dr. Limor Freifeld |
Grewe, Benjamin F., and Fritjof Helmchen. “Optical Probing of Neuronal Ensemble Activity.” Current Opinion in Neurobiology 19, no. 5 (2009): 520–29. Looger, Loren L., and Oliver Griesbeck. “Genetically Encoded Neural Activity Indicators.” Current Opinion in Neurobiology 22, no. 1 (2012): 18–23. Lemon, William C., and Philipp J. Keller. “Live Imaging of Nervous System Development and Function using Light‐sheet Microscopy.” Molecular Reproduction and Development (2013). |
| Lab 11 | High Throughput Neuroscience Yanik Lab | |
| 12 | Discussion of Final Project Guidelines | |
| 13 |
Whole-brain Optical Imaging Guest Lecturer: Prof. Kwanghun Chung |
Chung, Kwanghun, Jenelle Wallace, et al. “Structural and Molecular Interrogation of Intact Biological Systems.” Nature 497, no. 7449 (2013): 332–37. |
| Lab 13 | CLARITY | |
| 14 | Final Presentations I | |
| 15 | Final Presentations II |
