Core Courses

NBIO 722-723:
722: Molecular and Cellular Neuroscience
723: Systems and Translational Neuroscience
(Cross listed as PHYI and PHCO 722-723)

Course Director: Garret Stuber, PhD

2014-2015 Schedule
Course Description

Purpose of the course:

The purpose of this course in Cellular and Molecular Neurobiology is to explore the experimental and theoretical basis for our current concepts of nervous system function. The course runs as a series of three Blocks in the fall semester and three Blocks in the spring semester. This is NOT a survey course in neurobiology. The goals of the course are not so much to inform as to foster an understanding of how we accumulate our knowledge and hypotheses; not to provide a complete textbook picture of the func-tioning nervous system as we know it in 2011, but to provide the intellectual tools and skills to evaluate current and future hypotheses; not so much to provide answers to questions as to attempt to define the unanswered questions.

In order to create a climate for active discussion and exploration of ideas, each Block is limited to 24 students. All students are required to obtain permission from the Course Director to enroll. Because of the BBSP, we do not know how many applicants we will have for the course in Fall 2012. Priority is given to (1) students entering the Neurobiology Curriculum, as they are required to take the entire course, and to (2) students from departments affiliated with the course and who intend to register for all six Blocks of the course. Students should acquaint themselves with the course description and schedule and, if they are willing to take on the responsibilities of the course, email Denise Kenney for permission to enroll; Denise will contact the Course Director. The email should state for how many Blocks the student intends to register and why he or she wants to take the course.

Neurobiology as an experimental and health science:
We strive to enhance the development of our graduate students not only as experimentalists, but also as health professionals who are cognizant of the diseases that affect our society. Thus, an entire block of the required course is devoted to disease mechanisms. In addition a number of our students take additional training in translational science in an HHMI funded “Grad-to-Med” training program.

Competencies that we aim to achieve related to experimental science include:

  • Knowledge and application of the scientific method.
  • Determination of the accuracy and validity of scientific results.
  • Understanding of the methodology of measurements conducted in biological systems
  • Proficiency with the interpretation of both qualitative and quantitative experimental data.
  • Exposure and training in scientific ethics as applied to the neurosciences.

Competencies that we aim to achieve related to health science include:

  • Understanding the impact of neurobiological disease on health and society.
  • Understanding the importance of translational research bridging the basic and clinical sciences.

Teaching methods:
Instructors in NBIO 722 and 723 achieve these goals using a variety of teaching methods to convey core information as well as to shape students’ scientific thinking and perspective. Students are instructed using a variety of active learning techniques.

  • Didactic instruction: Lectures serve to convey and synthesize a body of complex material.  While didactic lectures are usually perceived as a passive teaching tool, this does not have be to be case (Hansen, 2002, Richardson, 2008). To engage students and encourage discussion, we limit enrollment to approximately 18 students (a few non-NBIO students can enroll with permission). Most students must take all 6 blocks so faculty and students get to know each other well. Faculty continually encourage discussion by asking students to address limitations related to the current state of the literature.
  • Paper based discussions: Paper based discussion is used throughout to immerse students in the primary literature as well as to give students training in assessing the strengths and weaknesses of original investigations.  The class is broken into 4 small groups.  Groups take turns presenting papers while the rest of the class critiques and asks questions related to the study.  Importantly, paper based discussion counts toward students’ final grades.
  • Workshops and group projects: In the first two blocks, workshops and group projects are designed to provide background knowledge and to actively engage students.  One example is a planned module centered on the Allen Brain Atlas. Working in small groups, students will be assigned genes implicated in neurobiological disorders. Students will then examine gene expression profiles, research neuroanatomical connectivity between genetically defined cell types, and design experiments to manipulate gene expression or neural circuit activity within these defined cell populations.
  • Problem sets: In many of the blocks, problem sets are handed out as homework assignments to actively engage students and further reinforce material.
  • Open Book Exams: Blocks end in an open book, take-home exam.  Exam questions often ask students to design an experiment of set of experiments to address a particular hypothesis, complete with controls and a discussion of feasibility (as one must do in preparing a grant application).  In addition to testing knowledge of block material, the exams encourage students to develop elegance and clarity in writing.

BLOCK 1 - Neurobiology Bootcamp: Introduction to Techniques Used in Studying the Nervous System/Electrical Signaling (NBIO 722A) Because the students taking the Core course have diverse backgrounds, this block is divided into two sections.

Block 1a: Neurobiology Bootcamp: Introduction to Techniques Used in Studying the Nervous System Because the students taking the Core course have diverse backgrounds, the first block serves as an introduction to neurobiology as well as an overview of many of the techniques students will encounter while reading materials and papers for the rest of the course. Examples of topics covered include statistics and hypothesis testing, molecular biology and genetic engineering, confocal microscopy, and functional anatomy of the rodent brain.

Block 1b: Electrical Signaling This block introduces materials related to electrical excitability of neurons. Topics include ion channels, membrane potentials, generation and propagation of action potentials, dendritic excitability, and computational neuroscience as it relates to electrical signaling of neurons.

BLOCK 2 - Neurotransmitter Receptors (NBIO 722B) This block focuses on neurotransmitter signaling through distinct receptor subclasses. Topics include G-protein coupled receptors and associated signaling, receptor binding theory, ionotropic and metabotropic glutamate and GABA receptors, receptor trafficking and localization.

BLOCK 3 - Synaptic Transmission and Intracellular Signaling (NBIO 722C) This block focuses on synaptic mechanisms of neurotransmitter release and termination of signaling, as well as intracellular signaling cascades that are regulated by synaptic transmission. Topics include electrophysiological and molecular analysis of neurotransmitter release, short-term plasticity in neurotransmitter release, synaptic plasticity, calcium signaling and regulation of intracellular signaling cascades and gene expression.

BLOCK 4 - Development of the Nervous System (NBIO 723A) This block focuses on molecular mechanisms of neuronal development and their relation to disease. Topics include neurogenesis, neural stem cells, molecular control of axonal guidance and neuronal migration, and cell and synaptic adhesions molecules.

BLOCK 5 - Anatomy and Function of Sensory and Motor Systems (NBIO 723B) This block focuses on the neural circuitry that comprises sensory and motor systems. Topics include organization and function of the retina, and visual cortex, mechanosensation, genetically defined circuits for nociception, organization and function of somatosensory cortex, motor cortex, basal ganglia neural circuitry, and cerebellar organization and function.

BLOCK 6 - Neurobiology of Disease (NBIO 723C) This block focuses on the neurobiological underpinnings of disease. For each topic, the disease and its impact on society is introduced, and then detailed discussions of the molecular, genetic underpinnings and circuit and behavioral consequences of the disorder are presented. Topics include epilepsy, addiction, fear and anxiety circuitry, schizophrenia, autism, Alzheimer’s disease, and Parkinson’s disease. This block also includes two classes devoted to human neuroimaging methods such at fMRI and DTI.

NBIO 850
Communication of Scientific Results
NBIO 850 (cross-listed: (PHYI 705/706)
2012-2013 Syllabus/Course Requirements
One faculty member from the Cell Biology & Physiology Department or the Neurobiology Curriculum will attend each session that involves student presentations.
Rehearsal Groups:
There are five rehearsal groups, each comprised of 4 students (Table 1). One member of each group is a senior student who took P Class last year; their job is to act as a coach/advisor during rehearsal sessions. When a member of your rehearsal group is scheduled to present in P Class, the whole rehearsal group will meet at least two days before the presentation to rehearse that student. The presenter organizes the group (email addresses are provided in Table 1) and finds a room. If possible the presenter should use a projector. What looks good on your computer screen sometimes does not project well.
Presentation:
For the Fall semester, each student will prepare and deliver a 10 minute talk describing his or her research. As you know, each of you is also obligated to give a formal departmental “Research in Progress” seminar this Fall, and I have organized it so that your P Class talk precedes your departmental talk. If you have a non-negotiable conflict with your assigned dates, let me know and we will find a way to work it out.
For your presentation, a good (but not ironclad) rule of thumb is 1 slide/min. Slides should illustrate the talk (this means diagrams and photos; text should be kept to a minimum). Bullets should be used wisely. A talk generally follows an outline like this:
•The larger scientific question being addressed and its general background.
•The particular question being addressed or hypothesis tested.
•Background, including results from the lab you are in. Please attribute these results to whomever did the experiments. Don't just say "our lab" or "a postdoc in the lab."
•Your results or expected results.
•A memorable, succinct summary, with graphics if possible.
•Future directions. Future directions can also be successfully intercalated into the talk instead of as a slide at the end.
•Acknowledgments, if they have not been inserted into the body of the talk.
The presenter will be introduced by a member of his or her rehearsal group. You are all expected to perform an introduction twice during the semester – once in P Class, and once at one of the formal departmental “Research in Progress” seminars. Making a relaxed, gracious, and interesting introduction, and managing the question session at the end of a talk, are skills that improve with practice. The presenter should provide the introducer with information about his or her background, including something to make the introduction more interesting—perhaps a hobby or an accomplishment.
The presenter must thank the introducer in a gracious manner. Walk to the "podium" (a table with the computer on it in 3118); stop; take a breath; look at the introducer; and attempt to be genuine, not scripted, in your thanks. (Say something other than “Thank you for that lovely introduction.” Notice what invited seminar speakers say at departmental talks.)
Scientific questions to the presenter:
Each student presentations in P Class will be followed by scientific questions. It is important for speakers-in-training to practice rephrasing and answering questions about their work in a professional and dignified way without getting flustered or becoming long-winded. It is important for audience members-in-training to develop skill in asking interesting questions without aggressive embellishments. In a professional setting, intelligent questions make your invited speaker feel welcomed and appreciated, and let them know that the audience was paying attention and was interested in the seminar.
For professional talks you should get into the habit of repeating/rephrasing the question before answering it. Repeating gives you time to think. It guarantees that you have understood the question. It makes sure everyone in the audience has heard the question. Do not, under any circumstances, start answering a question before the questioner has finished asking it. Allow them to come to a full stop before you reply!
Critique of the student’s presentation by the class:
As audience members, please be prepared to comment on the following (on paper, and verbally if time permits – remember to bring a pen or pencil to class!):
•Was the talk well organized?
•Was the speaker engaged with the audience (or did he or she face the slides and avoid looking at people)?
•Could you follow the talk easily -- was it paced properly? Too fast (common)?
•Was PPT used to best advantage? Comment on the slides, the use of space and color, use of animation, the content of the titles, the font sizes, etc.
•Could you describe the essence of the talk later to a colleague?
The video:
There will be two forms of feedback on your talk. First, you will receive written feedback from each member of the class (as detailed above). Second, I will make a video movie of your presentation and provide you with a DVD; you will meet with me for about an hour in the following week to review the written comments and the DVD in detail.
Formal public talk:
Near the end of the fall semester, each second-year student will give a formal, public “RIP” (Research in Progress) talk in the Bioinformatics or G202 Auditorium. You will be introduced by a member of your rehearsal group. You will be expected to thank the introducer graciously after arriving at the podium and getting settled, not on the way up the stairs. The introducer will also monitor and terminate the question session, keeping careful track of the time, and solving any problems (for example, difficulty with the lights).
End of semester luncheon
At the end of the semester the course will sponsor a catered lunch for the students and the faculty who have attended the class during that semester.

NBIO 850 Communication of Scientific Results
(Cross-listed: PHYI 705/706)

Course Director: Spencer Smith, PhD

Also known as PClass, this course is focused on the principles for effective scientific communication. The major component is focused on developing and giving scientific talks. The course also covers how to introduce speakers, prepare slides, and speak with the public about science. Finally, a written component is focused on preparation of specific aims for fellowship and grant application. Spencer Smith currently directs the course, with additional faculty participating. The class is limited to Neurobiology Curriculum students. Students prepare talks, refine them in small groups (3-4 students), and then present them in class. The in-class talk is videotaped, and these tapes are reviewed by the students in a session with their peers. After another round of refining with their small group, the students give their polished talks to the department in a formal setting. Writing is critiqued in class, with peers and guest faculty all offering input. Together, these components help the students develop their own effective speaking and writing methods, and prepare students for the next stage in their scientific careers. Fall semester.

BBSP 710 Statististics for Lab Scientists 

Course Director: Eric Bair, PhD

BBSP 710 introduces the basic concepts and methods of statistics with emphasis on applications in the experimental biological sciences.  Students should have a basic understanding of algebra and arithmetic.  No previous background in probability or staitistics is required, nor is experience with statistical  computing.  The objectives of this course are to provide graduate students in biomedical research programs familiarity with basic experimental design and elementary statistical methods.  By the end of the course, students should understand the principles of experimental design, be familiar with basic statistical methods (and how they are implemented in R), and know which methods are appropriate in a given circumstance.