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

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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

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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

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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;

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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

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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. 1:30-evening Projects

July 17 - Fri 9am-3pm Projects 3:30pm – 6pm Presentations 6:30pm End of Cycle Party

July 18 - Sat OFF

July 19 - Sun OFF (back by 6pm to meet next cycle faculty)

FACULTY Darcy Peterka Columbia Univ Erik Jorgensen Univ. of Utah JoAnn Buchanan Alan Brain Inst. Tom Reese NIH Sam Hess Univ. of Maine Ryohei Yasuda Max Planck FLA Yi Zuo UC Santa Cruz Sara Abrahamsson Rockefeller Univ. Shigeki Watanabe U. Utah

TA Jenny Hodges Team Zuo Andrew Neslon Team Hess Matt Valles Team Hess Joan Pulupa Team Abrahamsson Johannes Larsch Team Abrahamsson Jesse Jackson Team Peterka Christina Whiteus Team Yasuda Edward Hujber Team Jorgensen Thien Vu Team Jorgensen

LECTURERS Jeff Lichtman Harvard University Loren Looger Janelia Farms Marla Feller UC Berkeley

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NEURONAL CELL BIOLOGY July 21 - Aug 2 Section head: Tim Ryan Section Description: The objective of the will be to have an experimental immersion in modern neuronal cell biology. Students will pursue original research projects, designed and executed under the guidance of individual teams of faculty and TA. Projects will take advantage of the imaging principles and techniques that were introduced in the imaging section of the course. Projects will range from studies of synaptic vesicle recycling, glutamate receptor trafficking, neuronal regeneration, and the application of optogenetic techniques for control of neural function. Students will present research hypotheses and progress in periodic laboratory meetings so that all students gain an understanding of the projects being pursued in each individual research group.

Daily Schedule (some exceptions noted below) 9:00 – 10:30 or 11 Lecture 10:30-12:00 Lab 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 (at 8 PM)

July 19 - Sun 6pm Bar-B-Q in front of Loeb. Meet Imaging Faculty

July 20 - Mon 9am-12:00 Project Outlines; 15min/Faculty: ALL FACULTY 1:30-2:30 Students Pick Projects 3:00-evening Projects Begin 8pm Monday night Lecture – Susumu Tomita, Yale

July 21 - Tues 9am-11:00 Lecture: Tim Ryan– Bioenergetics of nerve terminals 1:30-evening Projects

July 22 - Wed 9am-11:00 Lecture: Mark Von Zastrow - Principles of Signaling 11:00-evening Projects

July 23 - Thur 9am-10:30 Lecture: Michael Higley: - synaptic inhibition in cortical circuits 10:30-evening Projects

July 24 - Fri 9am-10:30 Lecture: Shernaz Bamji – Activity mediated trafficking of synaptic proteins 10:30-evening Projects

July 25 - Sat 9am – 11:30 Lab Meeting: Present hypothesis, background, techniques and progress. – 20min per group 1:30-evening Projects

July 26 - Sun OFF

July 27 - Mon 9am-10:30 Lecture: Alvaro Sagasti – Neural Development 10:30-6pm: Projects 8:00pm Monday night Lecture: Vanessa Rutta - Rockefeller

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July 28 - Tues 9am-10:30 Lecture: Marc Hammarlund – Regeneration and Repair 10:30-6pm: Projects

July 29 - Wed 9am-10:30 Group Meeting – Progress Update: 10min per group 1:30-evening Projects

July 30 - Thurs 9am-10:30 Lecture Thomas Misgeld- The inner life of an axon: Imaging axon degeneration in vivo 1:30-evening Projects

July 31 - Fri 9am-10:30 All Faculty: Where do we go from here? 1:30-evening Projects

Sat Aug 1 9am-3pm CLEAN AND PACK COURSE – ALL STUDENTS/FACULTY 3:00-6pm Presentations 6pm - End of Course Party

FACULTY Tim Ryan Weill Cornell Shernaz Bamji UBC Alvaro Sagasti UCLA Mark Hammarlund Yale Thomas Misgeld Univ. Munich Mark Von Zastrow UCSF Mike Higley Yale

TA Damien Jullie Team Von Zastrow Matthew Shorey Team Sagasti Alexandra Byrne Team Hammarlund Caroline Fecher Team Misgeld Jordan Shimell Team Bamji Geraldine Gouzer Team Ryan Jaime de Juan Sanz Team Ryan Gyorgy "Gyuri" Lur Team Higley

LECTURERS Vanessa Ruta The Rockefeller University Susumu Tomita Yale University

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Kravitz Lecture: Dr. Michael Nitabach, PhD Associate Professor of Cellular and Molecular Physiology and of Genetics Yale University

Research Statement: Michael Nitabach is an Associate Professor of Cellular and Molecular Physiology and of Genetics at Yale University. The Nitabach lab is focused broadly on the use of genetic, physiological, and behavioral approaches to understanding the information processing principles by which neural circuits control animal behavior. Particular behaviors we are interested in include sleep, circadian rhythms, multisensory integration, and learning. This work is pursued using as model organisms Drosophila melanogaster fruit flies and Caenorhabditis elegans nematode fruit worms. Specific technical approaches employed include whole-cell patch-clamp electrophysiology, optical imaging of membrane voltage and intracellular second messengers, cell-specific genetic targeting of biophysical and biochemical effectors, and sophisticated behavioral assays.

Massey Lecture: Dr. Marla Feller, PhD Professor of Molecular and Cell Biology Head: Division of Neurobiology University of California, Berkeley

Research Statement: Marla Feller is Professor of Molecular and Cell Biology and Head of the Division of Neurobiology at the University of California, Berkeley. The Feller laboratory is interested in the mechanisms underlying spontaneous activity in the developing nervous system and the role this activity plays in the construction of neuronal circuits. There are several examples throughout the developing vertebrate nervous system, including the retina, spinal cord, hippocampus and neocortex, where immature neural circuits generate activity patterns that are distinct from the functioning adult circuitry. It has been proposed that these transitional circuits provide the test patterns necessary for normal development of the adult nervous system. The Feller lab uses a combination of electrophysiology, imaging, and anatomical techniques to address three major questions: 1) What are the cellular mechanisms underlying the generation and maintenance of retinal waves? 2) How do motion sensitive circuits arise during development?

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