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Neurobiology, 2009 MBL Neurobiology 2015 NEUROBIOLOGY COURSE SYLLABUS 2015 Directors: Grae Davis, Tim Ryan Course Assistants: Roya Huang GENOMICS BOOT CAMP June 7-13 Section head: Elva Diaz Section Description: The objective of the ‘Genomics Boot camp’ in the Neurobiology course (2015) is to introduce the students to cutting edge genomic methodology. This year we will focus specifically on RNA-seq- based, gene expression profiling of isolated Drosophila neurons. Students will be introduced to micro-dissection, RNA isolation and amplification methods for working with very small samples, library construction and sequencing protocols, and detailed analysis methods. Experimentally, we will define how the homeostatic modulation of neural function is achieved within a defined neural circuit, with implications for the stabilization of neural circuits throughout the life of an organism. A detailed understanding of this phenomenon may lead to new insight into neurological disease characterized by unstable or altered function of neural circuits including epilepsy and schizophrenia. We hope that this ‘Genomic Bootcamp’ will both educate the students in methodology and empower students to pursue these types of experiments in their own research programs at their home institutions. While it is not expected that the students will become completely proficient in these techniques, they will have established important contacts with expert faculty and will gain sufficient experience to understand the power and potential limitations of this approach. The foundation in genomics will become a common theme throughout the rest of the Neurobiology Course in 2015 during which students will also become versed in electrophysiology, super-resolution microscopy, optogenetic manipulation of neural circuitry and modern approaches toward understanding the cell biology of the neuron. June 7 – Sunday afternoon 3:00 pm - Meet in Loeb 108. Course introduction. Student and faculty introductions. Project overview and experimental design. Fly larvae dissection demo/training. 5:30pm – Pizza in courtyard outside Loeb (in common room if weather does not cooperate). General Daily Schedule 9:00 - 10:30am: Lecture 10:30am: Begin experimentation 12:00 – 1:30 pm: Lunch/ Free time 1:30 – 6:00 pm: Lab and Breakout/discussion 6:00 – 7:00 pm: Dinner/Free time 7:00 pm – midnight: Lab Jun 8-Mon Lab Goal: Dissections, RNA isolation and amplification 9:00-10:30 Genomics of CNS disease Stephan Sanders 10:30-12:00 Lab 12:00-1:30 Lunch and free time 1:30-4pm Lab 4:00 pm- Breakout/discussion - Linux tutorial Stephan Sanders Jun 9-Tue Lab Goal: Library preparation 9:00-10:30 RNA-seq analysis Charlie Kim 10:30-12:00 Lab 1 MBL Neurobiology 2015 12:00-1:30 Lunch and free time 1:30-4pm Lab 4:00 pm - R tutorial Donna Werling and Claire Williams Jun 10-Wed Lab Goal: Library QC and submit for sequencing 9:00-10:30 Gene expression in the CNS Elva Diaz 11:00-12:00 Lab 12:00-1:30 Lunch and free time 1:30-4pm Lab 4:00 pm - Breakout/discussion – Single cells All faculty Jun 11-Thu Lab Goal: Analyze dataset of sorted cells 9:00-10:30 Genomics and dendritic patterning Jay Parrish 11:00-12:00 Lab 12:00-1:30 Lunch and free time 1:30-4pm Lab 4:00 pm - Breakout/discussion – Online tools All faculty Jun 12-Fri Lab Goal: Data analysis and prepare presentations 9:00-10:30 Genomics and synapse aging Ben Eaton 11:00-12:00 Lab 12:00-1:30 Lunch and free time 1:30- Lab 4:00 pm - Breakout/discussion All faculty Jun 13-Sat Lab Goal: Student presentations 3:00 – 6:00 Student Presentations 7 pm - End of section PARTY Jun 14-Sun Day-Off (Back by 3pm to meet faculty for next section) Faculty: Elva Diaz UC Davis Grae Davis UCSF Ben Eaton UTHSCSA Jay Parrish U Washington Stephan Sanders UCSF Charlie Kim UCSF Teaching Assistants: Claire Williams U Washington Donna Werling UCSF Jorge Azpurua UTHSCSA Jenna Whippen UCSF Course Assistants: Allison Aghjayan Roya Huang 2 MBL Neurobiology 2014 ELECTROPHYSIOLOGY June 16 – July 5th Section head: Carlos Aizenman Section Description: The objective of the electrophysiology section is to learn electrophysiology from first principles to practical application. Students will receive lectures from leading scientists that range from the basics of whole cell recordings to ion channel structure/function to the molecular basis and modulation of synaptic transmission. Students will rotate through a series of experimental preparations that include the invertebrate neuromuscular junction, single channel recording and analysis in cultured cells, whole cell currents in cultured cells, and in vivo patch clamp recordings in tissue slices and intact central nervous system. Rotations will be followed by independent research projects. These projects will be short, original research projects designed and executed under the guidance of individual teams of faculty and TAs. The goal is attain a basic understanding of the theory and application of a wide range of modern electrophysiological techniques and the application of these techniques toward solving outstanding questions in modern neuroscience. Daily Schedule (some exceptions noted below) 9:00 – 12:00: Lecture 12:00 – 1:30 pm: Lunch/ Free time 1:30 – 6:00 pm: Lab 6:00 – 7:00 pm: Dinner/Free time 7:00 pm – evening: Lab and/or evening seminar June 14 - Sun 6pm-9pm: Bar-B-Q in front of Loeb. Meet Physiology Faculty June 15 - Mon 9am-12:00 Lecture: Jon Sack – Introduction to Voltage Clamp 1:30-6pm: Model Cell Demo, Rig tour 8:00pm Monday Night Lecture: Eve Marder, Brandeis June 16 - Tues 9am-12:00 Lecture: Jon Sack – Single Channel Recording 1:30-evening: Rotations June 17 - Wed 9am-12:00 Lecture: Diana Bautista – TRP Channels 1:30-evening: Rotations June 18 - Thurs 9am-12:00 Lecture: Bruce Bean – Voltage Gated Channels 1:30-evening: Rotations June 19 - Fri 9am-12:00 Lecture: Rod McKinnon – Structure of Ion Channels 1:30-evening: Rotations June 20 - Sat OFF June 21 - Sun OFF June 22 - Mon 9am-12:00 Lecture: Ellen Lumpkin- Mechanotransduction channels 1:30-6pm: Rotations 8:00pm Monday Night “Kravitz” Lecture: Michael Nitabach, Yale Univ. June 23 - Tues 9am-12:00 Lecture: Chris Moore – Optogenetics and Neural Dynamics 1:30-evening: Rotations Evening: Ephys Review June 24 - Wed 9am-12:00 Lecture: Dan Johnston – Dendritic Integration 3 MBL Neurobiology 2014 1:30-6pm: Rotations Evening: Projects Meeting June 25 – Thur 9am-12:00 Lecture: Martin Muller – Ca2+ Signaling & Synaptic Transmission 1:30-evening: Projects June 26 - Fri 9am-12:00 Lecture: Ricardo Araneda – Olfactory Processing 1:30-evening: Projects June 27 - Sat Day/Evening: Projects June 28 - Sun OFF June 29 - Mon 9am- 10:30 Lecture: Alfredo Kirkwood – Synaptic Plasticity 1:30-evening: Projects 8:00pm Monday Night Lecture: Alfredo Kirkwood, Johns Hopkins Univ. June 30 - Tues 9am-12:00 Lecture: Carlos Aizenman – Modulation of intrinsic excitability 1:30-evening: Projects July 1 - Wed 9am-12:00 Lecture: Patrick Kanold – Development of Neural Circuits 1:30-evening: Projects - Last Day of recordings! 4:30-6pm: Meeting with Electron Microscopy Faculty July 2 - Thur 9am-12:00 no Lecture: Grae Davis – Homeostatic Signaling 1:30-evening: Presentation prep, data analysis, etc. July 3 - Fri 9am-12:00: Parade Prep 3:00-5:30pm: Presentations 6:30pm: End of Cycle Party July 4 - Sat OFF (4th of July Parade – all lab participation) July 5 - Sun OFF (start of Imaging Cycle Bar-B-Q in evening, 6pm Loeb Patio) FACULTY Carolos Aizenman Brown University Diana Bautista UC Berkeley Ellen Lumpkin Columbia Univ. Ricardo Araneda Univ. Maryland Jon Sack UC Davis Juan Angueyra Univ. Washington Martin Mueller Univ. Zurich Patrick Kanold Univ. of Maryland TA Eric James Team Aizenman Ruilong Hu Team Araneda Carolyn Walsh Team Lumpkin/Bautista Yoshi Baba Team Lumpkin/Bautista Vanessa Hoop Team Mueller; Jennifer Keim Team Mueller; Rongkang Deng Team Kanold; 4 MBL Neurobiology 2014 LECTURERS Bruce Bean Harvard Medical School Rod MacKinnon Rockefeller University Ellen Lumpkin Columbia University Eve Marder Brandeis University Michael Nitabach Yale University Medical School Alfredo Kirkwood Johns Hopkins University Daniel Johnston UT Austin Chris Moore Brown University IMAGING July 5 – July 19 Section head: Tim Ryan Section Description: The objective of the imaging section will be to learn modern tools of microscopy from first principle optics to the application of super-resolution microscopy in modern neuroscience. Students will receive lectures from leading scientists on optics, resolution, super-resolution light microscopy, electron microscopy, array tomography and the application of imaging toward solving outstanding questions in neurobiology. Students will be able to rotate through several imaging systems, gaining hands-on experience with a range of imaging systems. Students will pursue original research projects, designed and executed under the guidance of individual teams of faculty and TA. Daily Schedule (some exceptions noted below) 9:00 – 12:00: Lecture 12:00 – 1:30 pm: Lunch/ Free time 1:30 – 6:00 pm: Lab 6:00 – 7:00 pm: Dinner/Free time 7:00 pm – evening: Lab and/or evening seminar July 5 - Sun 6pm Bar-B-Q in front of Loeb. Meet Imaging Faculty July 6 - Mon 9am-12:00 Lecture: Jeff Lichtman – Introduction to Microscopy 1:30-evening Rotations 8 pm Monday Night Lecture: Loren Looger, Janelia Farms, HHMI July 7 - Tues 9am-12:00 Lecture: Jeff Lichtman – Fluorescence Microscopy 1:30-evening Rotations July 8 - Wed 9am-12:00 Lecture: Darcy Peterka – Scanning fluorescence microscopy for functional Imaging 1:30-evening Rotations July 9 - Thurs 9am-12:00 Lecture Sam Hess – Super Resolution methods 1:30-evening Projects begin July 10 - Fri 9am-10:30 Lecture: Yi Zuo - Structural Plasticity in vivo 1:30-evening Projects July 11 - Sat 10:30 am- evening Projects 5 MBL Neurobiology 2014 July 12 - Sun OFF July 13 - Mon 9am-12:00 Tom Reese, JoAnn Buchanan, Shigeki Watanabe: Electron Microscopy 1:30-6pm: Projects 8:00pm Monday Night Lecture: Massey Lecture – Marla Feller July 14 - Tue 9am-12:00 Sara Abrahamsson -Multi-focal plane, SIM and light sheet microscopy 1:30-evening: Projects July 15 - Wed 9am-12:00 Lecture: Ryohei Yasuda – FRET and FLIM 1:30-evening Projects July 16 - Thurs 9am-10:30 Erik Jorgensen: things I do when I am bored.
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