Biology 333
Cellular & Molecular Neuroscience
Spring 2008
Syllabus

SYLLABUS

Description                
An advanced examination of neurons and synapses at the cellular, molecular, and genetic levels.  Topics include the cellular structure of neurons and glia, neurogenesis, synaptogenesis, the molecular basis of neuronal transmission and memory, and the genetics of behavior.  Special attention is paid to current issues such as stem cell transplantation, neuronal regeneration, and neurological disorders.  Weekly laboratory sessions emphasize methods to visualize neuronal morphology and synapses. 

Prerequisites            
• Biology 111 (Molecules, Genes, & Cells)
• Completion of at least one of the following upper level courses:
Biology 301 (Genetics)                            
Biology 304 (Molecular Biology)
Biology 306 (Developmental Biology)        
Biology 308 (Cell Biology)
Biology 309 (Genomics)                        
Biology 331/Psych 303 (Behavioral Neuroscience)
• Note: Bio333 is not recommended without a previous an upper level biology or neuroscience course

Instructor                  
Barbara Lom, Ph.D.                                            
balom "at" davidson.edu                  
261 Dana (office)                                                           
251 Dana (lab)                                       
704-894-2338 (office)                                          
704-xxx-xxxx (home)                             
704-894-2512 (fax)                                             
704-xxx-xxxx (cell – rarely on)
Office Hours: By appointment and Tuesdays 2:00-4:00

           

Meetings                   
Lectures: Tuesdays & Thursdays 10:00 – 11:15 • Sloan 201
Labs:Wednesday 1:30-4:30 or Thursday 1:00-4:00 & on own time as needed for experiments • Dana 220

Course Web Sites     
blackboard.davidson.edu                                       www.bio.davidson.edu/people/balom/333syll.html

Textbook                   
There is no textbook for this course – all reading will be provided as downloads on the library’s electronic reserves and/or Blackboard.  We will use chapters from several textbooks along with recent review articles and scientific research articles.

Attendance               
Regular attendance is essential and absences are discouraged.  If you do need to miss a class make appropriate arrangements with a classmate to get notes.  Lab attendance is required and any necessary absences must be cleared with the instructor in advance.

Course Grade                                                
A  100 — 95%
A- 94.9 — 90%
B+ 89.9 — 87%             
B  86.9 — 84%  
B- 83.9 — 80%   
C+ 79.9 — 77%             
C  76.9 — 74%
C- 73.9 — 70%
D+ 69.9 — 65%
D  64.9 — 60%
F 59.9 — 0%

Evaluation                 
In-class quizzes                                                    15%
Two exams (exam #1 = 12.5%; exam #2 = 17.5%)     30%
Oral presentation & associated assignments            30%
Lab assignments, images, data, movies, notes etc.       20%
Course participation, effort, teamwork, etc.             5%

In-class Quizzes       
Short pop quiz questions at the start of lectures will occur periodically.  Consequently, regular attendance, reading, and understanding of the lecture material is strongly recommended for success in this course.  Your lowest quiz grade will be dropped when determining your quiz score.

Exams                        
Two take-home exams will test your conceptual understanding and ability to apply your knowledge.  The format will be closed book and closed notes with generous time for completion.

Oral Presentation    
Each student will lead a 35-minute class on a topic of interest to the class that has been approved by the instructor.  Students will work in small teams to refine their lectures and give active feedback well before and during presentations.  At least two practice presentations must be executed (the Speaking Center is a wonderful resource) as well as a debriefing session with Dr. Lom as part of the assignments associated with this presentation. 

Seminars                   
Each student will attend at least two science-related seminars presented by visiting scientists before the Easter break and write short evaluations of the effectiveness of each speaker in preparation for their own oral presentation. 

Conference                
As a unique component of this lab course, each student will attend a regional neuroscience conference (SYNAPSE or SENN) during a weekend in March.  These conferences are wonderful opportunities to meet other neuroscientists, discuss data with other students, and learn more about careers in science.  We will arrange travel support, carpools, etc. to facilitate your attendance.  If you absolutely cannot attend either conference due to scheduling conflicts for work, interviews, athletics, etc. please talk to Dr. Lom immediately to discuss alternatives well ahead of the conference registration deadlines.

Class Meetings          
Neuroscience is a rapidly evolving and exciting field. We will be discussing many results that are hot off the presses.  Many important questions do not have answers (yet).  If you are having trouble understanding a concept, please raise the issue in class.  Chances are that some of your classmates will have similar questions.  Questions are particularly essential during the class periods in which we will be discussing primary research papers wherein you will be expected to be familiar with the reading.

Lab Notebook           
Students will keep an orderly lab notebook with careful records of observations and related assignments.  Use the question, "can another student replicate my experiments with only my notebook as a guide?" to direct your notebook record keeping and organization.

Lab Sessions              
Good laboratory work requires patience and perseverance.  You will be expected to work at times that do not occur during formal laboratory sessions.  Failure to attend to such details may seriously jeopardize the outcome of your experiments.  You are expected to abide by all laboratory guidelines in order to maintain a neat, clean, and safe laboratory experience for yourself and your classmates.  In addition, you must comply with all ethical standards for the responsible care and use of laboratory animals.  If you have issues with experimental manipulation of laboratory animals, you must speak to me before the first laboratory session.

Deadlines                   
Assignment deadlines are absolutely FIRM.  Assignments submitted late will incur penalty of 10% per hour late.  Sports, other academic commitments, and social/volunteer activities are unacceptable excuses for late work or extension requests.  Extension of due dates without penalty will only be considered in unforeseen and extreme circumstances.  In an emergency you must request an extension as soon as possible, preferably before the deadline.  Because minor unforeseen circumstances occasionally arise, each student is allocated one (indivisible) lifeline, a four-hour extension that can be redeemed on any individual assignment without explanation or penalty by simply writing the word “lifeline” near your name on the assignment.  Lifelines cannot be used on group assignments.

Backing Up               
A computer crash is devastating, but not an acceptable excuse for late submissions.  Get in the habit of backing up your work regularly.  You must retain electronic copies of all submitted work and hard copies of all returned work until after you have received your course grade for the semester.  You will likely be generating a lot of computer files in lab.  You are welcome to store files on the lab computers, but the safety of these files cannot be guaranteed.  All files on lab computers can be erased at any time (possibly without warning).  I strongly recommend that you develop a method to back up your data (flash/USB/thumb drives, recordable CD/DVDs, etc.).

Collaboration            
You are encouraged to develop knowledge and ideas from a large variety of resources throughout this course.  Most scientists get valuable ideas and feedback from conversations with colleagues.

Honor Code               
It is your responsibility to reaffirm the Davidson Honor Code on every assignment by stating the Honor Pledge and signing your name in ink.  Unpledged work will not be accepted.  Make sure to cite your sources so that your reader has the necessary information to locate your primary sources.  Please do not take risks with citation issues and consult with me if you are uncertain when citations are necessary.  Plagiarism is an academic violation with severe consequences.  Please consult the departmental web page on this topic: www.bio.davidson.edu/dept/plagiarism.html


COURSE SCHEDULE
(subject to modification as necessary – changes will be announced in class)


Tu 01/15         Course Introduction
Reviewchapters on Cells & Neurons/Nervous System in your Bio111/112 textbook

Th 01/17         Neuronal and Glial Cells – how to examine the unique and important features of these cells
Kandel et al. (2000) Chapter 4 (The Cytology of Neurons)
Alberts et al. (2002) Chapter 9 (Visualizing Cells)


Tu 01/22         Neurogenesis – making new neurons
Jessell & Sanes (2000) The generation and survival of nerve cells
Munoz-Sanjuan & Brivanlou (2002) Neural induction, the default model and embryonic stem cells

Tu 01/22         Biology Seminar - Dr. Fiona Watson (Davidson) - 4:00 – Dana 146
DSCAM: A Highly Variable Protein that Wires the Fly Nervous System

Th 01/24       Adult Neurogenesis – differences in research results between two labs
Specter (2001) Rethinking the brain
Gould et al. (1999) Neurogenesis in the neocortex of adult primates
Kornack & Rakic (2001) Cell proliferation without neurogenesis in adult primate neocortex     

Lab                  Introduction, safety, microscopes, begin lecture topic selection process, etc.
Bring your $10 lab fee (check made out to Davidson College (preferred) or exact change)


Tu 01/29         Growth cones – how do neurons travel to find synaptic partners?
Sanes et al. (2006) Chapter 5 (Axon Growth & Guidance)
Erskine & Herrera (2007) The retinal ganglion cell axon’s journey: Insights into molecular mechanisms of axon…           

Th 01/31         Axon guidance – what types of molecular cues guide growth cones?
McFarlane et al. (1995) FGF signaling and target recognition in the developing Xenopus visual system.
McFarlane et al. (1996) Inhibition of FGF receptor activity in retinal ganglion cell axons causes errors…

Lab                  Intro to tissue culture and time-lapse imaging of growth cones


Tu 02/05         Local translation – how do growth cones respond rapidly to guidance cues?
Lin & Holt (2007) Local translation and directional steering in axons
Leung et al. (2006) Assymetrical b-actin mRNA translation in growth cones mediates attractive turning…

Th 02/07         Synaptogenesis – how do two neurons form a new synapse?
Sanes & Jessel (2000) The formation and regeneration of synapses

 Fr 02/08          Biology Seminar - Dr. Bill Rebeck (Georgetown) – 2:30 (tentative) – location tba
Molecular Analysis of Alzheimer’s

Lab                  Intro to analysis of growth cone dynamics and ImagePro+ software


Tu 02/12         Synaptic refinement  - plasticity: which synapses stay vs. go and/or get stronger vs. weaker?
Sanes et al. (2006) Chapter 9 (Refinement of Synaptic Connections)

Th 02/14         Synaptic competition – battle at the neuromuscular junction
Kasthuri & Lichtman (2003) The role of neuronal identity in synaptic competition
Buffelli et al. (2003) Genetic evidence that relative synaptic efficacy biases the outcome of synaptic competition

Lab                  Discuss analysis results, refine methods, select parameters for experiments

 

Tu 02/19         Spinal cord regeneration – fixing damaged spinal cords
Kraft (2005) Mending the spinal cord
Bradbury & McMahon (2006) Spinal cord repair strategies: Why do they work?
Harel & Strittmatter (2006) Can regenerating axons recapitulate developmental guidance during recovery…

 

Th 02/21         Spinal cord regeneration – fixing damaged spinal cords (part II)
Yiu & He (2006) Glial inhibition of CNS axon regeneration
Thuret et al. (2006) Therapeutic interventions after spinal cord injury                   

Fr 02/22          Exam #1 available – take-home format; due 02/26/08

Lab                  Begin growth cone experiments


Tu 02/26         Exam #1 due – exam must be completed by 6:00 AM and turned in at the start of class
The Genetics of Human Neurological Disorders (Dr. Huda Zoghbi DVD lecture
Ross-Flanigan (2001) When the brain fails
Nuzzo (2006) Profile of Huda Y. Zoghbi

Th 02/28         Rett Syndrome – mutations in a transcriptional repressor that cause neurological disease
Chahrour & Zoghbi (2007) The story of Rett syndrome: From clinic to neurobiology

Lab                  Continue growth cone experiments

Spring Break


Tu 03/11         Homeostatic Synaptic Plasticity - Guest lecture by Jennifer Wilhelm, ’01 (Emory)
Turrigiano & Nelson (2004) Homeostatic plasticity in the developing nervous system
manuscript by Wilhelm and Wenner (tba)
userwww.service.emory.edu/~pwenner/index.html

Th 03/13         Genetic Regulation of Plasticity in Neural Circuits - Diane O’Dowd’s lab (UC Irvine)
www.healthaffairs.uci.edu/anatomy/odowd.html
Rohrbough et al. (2003) Cellular bases of behavioral plasticity: Establishing and modifying synaptic circuits…
Gu & O’Dowd (2006) Cholinergic synaptic transmission in adult Drosophila Kenyon cells in situ
Campusano et al. (2007) nAChR-mediated calcium responses and plasticity in Drosophila Kenyon cells

Lab                  Continue growth cone experiments

Sat 03/15        SYNAPSE Conference at College of Charleston (keynote address by Dr. O’Dowd)
www.cofc.edu/synapse


Tu 03/18         Neural Stem Cells
Flight (2007) Stem cells: Intrinsically different
Wu et al. (2007) Integrative genomic and functional analyses reveal neuronal subtype differentiation bias…
Svendsen et al. (2002) Neurons from stem cells: Preventing an identity crisis

Th 03/20         Catch-up/move ahead

Lab                  Finish growth cone experiments


Tu 03/25         No class – Easter break

Th 03/27         Neurobiology of Vocal Communication - Erich Jarvis’s lab (Duke)
www.jarvislab.net/
Wada et al. (2006) A molecular neuroethological approach for identifying and characterizing a cascade of…
Haesler et al. (2004) FoxP2 expression in avian vocal learners and non-learners

Lab                  Analyze growth cone experiments

Sat 03/28        Southeast Nerve Net Meeting at Georgia State University (keynote address by Dr. Jarvis)
biology.gsu.edu/senn/


Tu 04/01         Class-selected topics: presentations #1 & 2 (Readings tba)

Th 04/03         Class-selected topics: presentations #3 & 4 (Readings tba)

Lab                  Discuss experimental results in order to design follow-up experiments


Tu 04/08         Class-selected topics: presentations #5 &6 (Readings tba)

 Th 04/10         Class-selected topics: presentations #7 & 8 (Readings tba)

Lab                  Conduct follow-up experiments


Tu 04/15         Class-selected topics: presentations #9 & 10 (Readings tba)

Th 04/17         Class-selected topics: presentations #11 & 12 (Readings tba)

Lab                  Conduct follow-up experiments


Tu 04/22         Class-selected topics: presentations #13 & 14 (Readings tba)

Th 04/24         Class-selected topics: presentations #15 & 16 (Readings tba)

Lab                  Analyze follow-up experiments


Tu 04/29         Catch-up and/or review

Th 05/01        Exam #2 available (Optional Day)

Lab                  Present experimental results


Tu 05/06         Exam #2 due (Optional Day)


Peer Advice from students in the 2006 Cellular & Molecular Neuroscience class:

• Do all the readings assigned before class.  Always be prepared for the quizzes before class begins.

• Get things done early.

• Do the readings and go see Dr. Lom.  Devote time to the course.

• Be organized.  Write everything down.

• Read every article before class.  Focus on concepts over details.

• Read the articles slowly and carefully.  Start lab assignments early.

• Try to understand the material rather than reading it and half understanding.  Spend quality time rather than quantity.  Sometimes even just the introduction to the paper helps a lot more than reading every word and not understanding the paper.

• Keep up with the reading and especially the lab work, but mostly look at the “big picture” for tests instead of obsessing over details.

• Be prepared to discuss work and reading assignments.  Be careful with your wording.  Play close attention to instructions and deadlines.

• Read the papers, get to class on time, read assignments thoroughly, put reminders up on Outlook for when things are due.

• Make sure you understand the material.  Pay close attention to the syllabus because your hand’s not going to be held all along the way to make sure you remember deadlines.

• Do the readings, review notes, powerpoints, and papers before the tests.

• Go to Dr. Lom if you have questions.  Go to SYNAPSE.  Make a schedule for yourself to get lab stuff done.

• Complete lab assignments immediately after they are assigned, even if it makes for a hectic schedule.

 


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