Biology 351 (Group Investigation)
Microscopy & Imaging in Neuroscience
Fall 2006
Syllabus

Description:               
Original in vitro and/or in vivo neuroscience research using microscopy and imaging techniques

Goals:                         
• Each student will demonstrate working knowledge of light microscopy and expertise in biological imaging
• Each student will demonstrate practical understanding of experimental design, analysis, and communication
• Each student will produce an electronic image portfolio using a variety of microscopy techniques
• Students will collaboratively determine how neuronal activity affects RGC dendritic morphology in vivo  
• Students will collaboratively update Davidson’s confocal microscopy website & create a protocol website

Prerequisites           
Biology 111 & instructor permission

Meeting Time         
1:30 – 4:20 Monday afternoons in Dr. Lom’s office/lab AND on your own time as needed to perform experiments and complete assignments.  Expect to invest at least 10 hours/week for this course.

Instructors:
Barbara Lom, Ph.D.
balom@davidson.edu
261 Dana (office) or 251 Dana (lab)
704-894-2338 (office)

Fiona Watson, Ph.D.
fiwatson@davidson.edu
283 Watson (office) or 251 Dana (lab)

Office hours:
Dr. Lom:
Wednesdays 10:00-12:00 (except 10/18)
most Fridays 2:30-4:00 (except  9/1, 9/15, 10/6, 11/3, & 12/8)
and by appointment
If it is helpful in setting up appointments, a copy of Dr. Lom's Fall 2006 schedule can be viewed at: http://www.bio.davidson.edu/people/balom/lomschedule.gif

Dr. Watson:
Wednesdays 12:30-1:30
(except 10/18)

Lab Technician:         
Ms. Cyndi Payne (Dana 251)
cypayne@davidson.edu                                                   
704-894-2905 (lab)                                                          

Email:                         
We will make e-mail announcements outside of class as necessary (and encourage you to do the same).  Please check your e-mail regularly, and respond promptly and politely to all requests.

Textbooks:                
As this course emphasizes independent research, you are strongly encouraged to read sections of the texts beyond what is assigned, read papers in the scientific literature, and learn to identify other sources of info.

Required Texts:          
• Optimizing Light Microscopy for Biological and Clinical Laboratories (1997) by Barbara Foster
• Mead Spiral Five Star Notebook (6.5 x 9.5 inch) - for your lab notes
($10.00 – purchase both directly from the instructors)
• At the Bench: A Laboratory Navigator (2005) by Kathy Barker
• 3-Ring Binder to organize your papers, protocols, etc.

Web"Texts":                
Nikon’s Microscopy U
www.microscopyu.com/
Molecular Expressions microscopy.fsu.edu/index.html
(These interlaced websites provide comprehensive information on light microscopy, including tutorials, animations, and a huge photomicrograph image gallery.)

Lab Notebook:          
You are expected to store your notebook in the lab at all times.  Record daily and comprehensive notes.

Weekly Questions:   
Each student will regularly address the following questions in their notebook and send both Drs. Watson and Lom a weekly email update (usually by 9:30 AM on Mondays) addressing these four specific questions directly within an email (no attachments please):
Q#1 – Describe your time and efforts this week.
Q#2 – What do you know?
Q#3 – What don’t you know?
Q#4 – How can you find out what you don’t know?
Q#5 – What are your frustrations?

Reading Questions:   
For each original research paper that we discuss in class please come to class with written notes to address the following items:
1) What is the purpose of this study?  (experimental question, hypothesis)
2) What did the authors find? (results)
3) Do you believe their results? (strengths/weaknesses of their experiments)
4) Do the interpretations/conclusions made follow soundly from the data presented?
5) What is the contribution to the field?
(what was already known about this subject- is it a me-too paper, a big deal, etc.?)

Image Portfolio:       
Each student will generate a web-based portfolio of microscope images collected during the semester.  Specific portfolio assignments are indicated in the course schedule.  In addition to the specified portfolio images, portfolios must include at least five additional “wild card” images using various forms of light microscopy.  All images should be scientifically relevant, aesthetically composed, and include a scale bar and a descriptive legend.  We will use these images to generate a Bio351 2007 calendar.

Grading:                                            
A 95-100%
A- 90-94.9%
B+ 87-89.9%      
B  83-86.9% 
B- 80-82.9%
C+ 77-79.9%     
C 73-76.9% 
C- 70-72.9%
D+ 67-69.9% 

D 60-66.9%       
F 0-59.9%

35%

Image Portfolio, Web Sites, Protocol(s), Class Discussion, Oral Presentation, etc.

35%

Personal Effort, Initiative, Original Thought, Participation, Courtesy, Attention to Detail, Engagement, Ability to Generate Results, Ability to Work with Team, etc.

30%

Lab Notebook, Weekly Questions, Data Organization, etc.

Feedback:                 
We ask that students give us formal and/or informal feedback on what works well and what can be improved in this course so that you may learn more effectively.  Please make us aware of potential concerns as early as possible so that we can attend to them appropriately.  We cannot try to fix problems if we are not aware of them.

Deadlines:                  
Assignment deadlines are absolutely FIRM
.  Assignments will not be accepted past the deadline without significant penalty.  Sports, work for other courses, and social activities are unacceptable excuses for late work.  Extension of due dates will be considered only in unforeseen and extreme circumstances.  In an emergency, please request an extension before the deadline (if possible). 

Lifeline:                      
Because unforeseen minor circumstances occasionally arise, each student is allocated one lifeline for the semester.  A lifeline is a four-hour extension that can be redeemed on any single individual (non-group) assignment without explanation or penalty.  To redeem your lifeline simply indicate the word “lifeline” somewhere obvious on your assignment.

Honesty:                   
You are encouraged to develop knowledge and ideas from a large variety of resources throughout this course.  Many scientists get valuable ideas and feedback from conversations with their colleagues.  Such collegial conversation is encouraged in class and out of class.  We encourage you to study in groups and discuss your research with your classmates.  This course will involve a combination of individual and group work.  Please do not take risks (intentional or unintentional); ASK if you have questions, as plagiarism is an academic violation with severe consequences.  Reaffirm the Davidson Honor Pledge in writing and sign your name on every assignment you submit.  Assignments without the honor pledge will not be accepted.  The Davidson College Biology Department’s statement on plagiarism can be found at: www.bio.davidson.edu/dept/plagiarism.html

Microscopes:             
We are extremely fortunate to have many state-of-the-art microscopes available for this course including a laser-scanning confocal microscope.  These microscopes are very delicate and expensive.  You must treat all microscopes with ultimate care and concern.  Careless use of the instruments can cause thousands of dollars of damage and impair everyone’s ability to do their research.  Consequently it is imperative that you understand what you are doing whenever you are using a microscope, ask when you have questions, and exercise caution and good judgment.  Failure to respect these instruments will negatively (and significantly) impact your grade and/or your lab privileges.

Tools:                         
You will be provided with two sets (live and fix) of dissection tools.  These are expensive, delicate, and important instruments.  Treat the tools with great care by keeping them clean and capped when not in use.  Do not borrow anyone else’s tools without permission.

Lab Guidelines:          
• Safety comes first.  Period. 
• No food in the lab.  Ever.
• No unlabeled liquids, powders, solutions, experiments, etc. even if it’s just water.
• Clean up after yourself.  Always.
• Notice when supplies run low and inform Dr. Lom, Dr. Watson, and/or Cyndi BEFORE we are out.
• When using a computer, priority goes to research needs.
• Take your turn with dishwashing and lab cleaning duties (trading weeks is allowed).
• You will have catcard access to Dana 220 and 256 (to get to the prep room in between).  Please do not interrupt lab sessions in progress in either of those rooms.
• Lab, microscope room, culture room, and cryostat room access is via key.  (Combo =  __________.)
• Confocal room access is via key.  (Combo =  __________.)
• Never confuse fix (black) vs. live (white) tools or vessels.  Any live tool that touch fix should be converted to a fix (black) tool.
• Use animals ethically, responsibly, and humanely.  Please ask if you have questions.
• The hard drives on the lab computers fill up very rapidly.  You are welcome to keep a folder on the computer, but please be mindful of the computer space available.  DVDs, CDs, and flash drives are available for you to back up your data.  Please get in the habit of backing up your data regularly.
• Never wear open-toed shoes in the lab.
• Never use equipment that you are not trained to use.

Lab Courtesy:            
You will be working with others throughout the semester so it is imperative that you work in considerate and collegial manners.  Coordinate your plans with your classmates, use (and respect) sign-up sheets, and keep safety your first priority.  Always leave your work area cleaner than you found it, anticipate, notice, and/or communicate situations that could become problematic such as supplies running low, etc.  Music is welcome in the lab, but any lab member can veto music volume or selection without explanation.

No Fragrances:         
Because of extreme chemical sensitivity issues we respectfully ask everyone to avoid wearing perfumes, colognes, or any sort of scented products to class.

Data Storage:           
You will generate many images this semester that will take up a considerable amount of computer space.  I strongly recommended that you purchase your own USB/flash/thumb drive (any brand) of >512 Mb and a few recordable CDs/DVDs for backing up your images, movies, etc.  The lab has a few USB drives that you may share.  Any files left on a shared USB drive can be deleted by the next user, so please use the USB drives for data transfer (not storage).  Backing up your data is your responsibility and you must take it seriously and develop a regular plan for saving your images and movies in a coordinated and logical fashion.  Lost or erased files are unacceptable excuses for submitting late work.

Lab Storage:              
Each person in the lab has a “cubby” for storage of personal items such as tool boxes, lab notebooks, papers, etc.  Please keep your items in your cubby whenever possible to minimize clutter in the lab.  You may keep a pair of closed toe shoes in the shoe area below the cubbies if you want to wear sandals to and from the lab.  Please also use the cubby system for leaving notes, etc. for your lab mates.

Shared Lab Duties:   
Throughout the semester you will be responsible for cleaning the lab areas.  Your duties include doing all the dishes, noticing if we are low on supplies or solutions, picking up clutter, wiping down the countertops, watering the plants, filling paper towel dispensers, etc.  If you would like to swap weeks for lab cleaning duties you are welcome to do that as long as both parties agree to the swap.

Peer Advice:              
2005 Bio351 students answer the question, “If a friend asked you how to be successful in this course, what specific advice would you give based on your experiences this semester?”

It is important to learn how to communicate with your peers early on.  This will be invaluable in the future.  Also, plan ahead.  If you have your project organized, then you can set goals for yourself, as well as deadlines.  That way, when the deadline approaches, you are not frantically rushing to get everything done.

Start communication with the group members as soon as possible.  It helps so much to use each other’s strengths and weaknesses to get the tasks completed.  Don’t be afraid to ask for help.  The sooner you know if you’re going in the right direction, the better things will be.

Make sure to start assignments earlier.  Set really good things aside for final presentation throughout the course.  Check the quality of photos with the instructor throughout the project.  Start projects as soon as you understand all the techniques.  Divide up tasks by your strengths and schedules.

Ask questions.  Plan ahead.  Always leave more than enough time to complete the project at hand.  Start work early.

Communicate daily with your lab mates about progress/questions/tips.  Establish good relationships with all lab mates.

Be prepared to be on top of your schedule.  Make sure to have good time management skills because it often is what determines whether or not the projects in this class proceed.  Do not be afraid to take a leadership role.

Communicate with other lab members.  Find your strengths and go with them.  Use all of your resources (i.e. Dr. Lom/Cyndi).


Bio 351 • Course Schedule
expect alterations as necessary – this is a research-based course and will require flexibility

Week 1
8/21 Meeting:     
Introduction to the research question, RGCs, etc.
Observe frog squeezing and embryo fertilization
Learn to use staging tables to identify tadpole ages
Introduction to PTU-treating tadpoles, anesthetizing tadpoles, fixing tadpoles, etc.
Discuss lab safety and courtesy
Discuss how to keep good lab notebooks, data, etc.                       
Introduction to stereomicroscopes, cameras, ImagePro+, and PhotoShop software
Discuss lab duties, using the dishwasher, tool boxes, etc.

Reading:            
Barker   Chapter 1- Getting Oriented
Web     Pictorial Atlas of Xenopus Development www.bio.davidson.edu/people/balom/StagingTable/xenopushome.html
Web     Intro to Stereomicroscopy   www.microscopyu.com/articles/stereomicroscopy/stereointro.html
(try the Nikon SMZ1500 Stereomicroscope Interactive Flash Tutorial)
Web     Intro to Microscope Ergonomics microscopy   fsu.edu/primer/anatomy/ergonomics/ergointro.html
(try the Proper Microscope Posture Tutorial)
Web     Cleaning, Care, and Maintenance of Microscopes   microscopy.fsu.edu/primer/anatomy/cleaning.html

Lab Work:        
Generate stereomicroscope tadpole & “unknown” images for 1st portfolio assignment (due 9:30 AM 08/28/06)
Email five questions to Drs. Watson & Lom (and include copy in your notebook – due 9:30 AM Monday 08/28/06)
Complete schedule form and submit as soon as your schedule is solidified

Lab Duties:         All

 

Week 2          
8/28 Meeting:     
Animal training by Amy Becton – meet at 1:30 outside her office
Introduction to in vitro TTX/RGC results, more background, etc.
Discuss stereomicroscope tadpole images (1st portfolio assignment)
Introduction to retinal microinjections
Introduction to fluorescence microscopy
Discuss today’s assigned reading and any questions that arose from last week’s reading

Reading:            
Lom (2003) NSF Grant Proposal
McAllister (2000) Cellular and molecular mechanisms of dendrite growth
Foster   p 72-78 (Chapter 7 – Contrast Techniques Part III – Fluorescence)
Barker   Chapter 16 - Microscopy
Web     Intro to Fluorescence Microscopy    microscopy.fsu.edu/primer/lightandcolor/fluorointroduction.html
Optional:            Dr. McAllister’s website: http://sandtiger.dbs.ucdavis.edu/FacultyProfiles/NeuroGG/DisplayFacultyProfile.cfm?ResearcherID=1118

Lab Work:        
Perform/practice retinal microinjections
Fluorescent images of retinal injections & more “unknowns” (Portfolio assignment #2 - due 9:30 AM 09/04/06)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 09/04/06)

Lab Duties:         Tamar

 

Week 3          
09/04 Meeting:   
Discuss images of retinal microinjections (Portfolio assignment #2)
Introduction to tectal injections, screening tadpoles, and flatmounting retinas
Discuss this week’s readings – particularly methods

Reading:            
Rigel & Lom (2004) Xenopus laevis retinal ganglion cell dendritic arbors develop independently of visual…             
Lom & Cohen-Cory (1999) Brain-derived neurotrophic factor differentially regulates retinalfocus on the methods
Lom et al. (2002) Local and target-derived brain-derived neurotrophic factor…. – focus on the methods                 

Lab Work:        
Perform/practice tectal injections, screening, and flatmounting
Fluorescent images of tectal microinjections & more “unknowns” (Portfolio assignment #3 - due 9:30 AM 09/11/06)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 09/11/06)

Lab Duties:         Page

 

Week 4  
09/11 Meeting:   
Discuss images of tectal microinjections (Portfolio assignment #3)
Introduction to confocal microscopy
Discuss article(s) listed below

Reading:            
Scott & Luo (2001) How do dendrites take their shape?
Foster   p 63-66 (Chapter 6 – Contrast II – Phase Contrast)
Foster   p 133-134 (Chapter 10 – What’s Next? - Confocal Microscopy)
Web     Introduction to Confocal Microscopy    www.olympusconfocal.com/theory/confocalintro.html
Optional:            Dr. Luo’s web site: http://www.stanford.edu/group/luolab/index.shtml

Lab Work:        
Perform/practice flatmounting and imaging RGC dendrites with the confocal microscope
Widefield vs. confocal images of RGC dendritic arbors & $100 slide(s) (Portfolio assignment #4 – due 9:30 09/18/06)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 09/18/06)

Lab Duties:         Cyndi

 

Week 5          
09/18 Meeting:   
Discuss widefield versus confocal images (Portfolio assignment #4)
Introduction to analyzing RGC dendritic arbors

Reading:            
Sakaguchi (1989) The development of retinal ganglion cells deprived of their targets
Sakaguchi et al. (1984)  The development of retinal ganglion cells in a tetraploid strain of Xenopus laevis.: A morphological study utilizing intracellular dye injection
Optional:            Dr. Sakaguchi’s web site: http://www.public.iastate.edu/~zoogen/saklab.html

Lab Work:        
Analyze RGC dendritic arbors from confocal stacks
RGC dendritic arbor analysis images and data (Portfolio assignment #5 – due 9:30 AM 10/02/06)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 09/25/06)

Lab Duties:         Tamar

Week 6          
09/25 Meeting:   
Discuss RGC analysis (Portfolio assignment #5)
Discuss plans for executing/analyzing experiment

Reading:            
Cohen-Cory (1999) BDNF modulates, but does not mediate, activity-dependent branching and remodeling of optic axon arbors in vivo
Cline  (2001) Dendritic arbor development and synaptogenesis
Foster   p 124-130 (Chapter 7 – What’s Next? – Measurements Under the Light Microscope)
Optional:            Dr. Cohen-Cory’s web site: http://cohen-corylab.bio.uci.edu/

Lab Work:        
Conduct/analyze experiment (exact duties tba)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 10/02/06)

Lab Duties:         Page

 

Week 7          
10/02 Meeting:   
Discuss experimental status
Discuss confocal microscopy & protocol websites

Reading:            
Campbell et al (1997) Dendritic development of retinal ganglion cells after prenatal intracranial infusion of TTX
Chen & Ghosh (2005) Regulation of dendritic development by neuronal activity
Optional:            Dr. Ghosh’s website: http://www.biology.ucsd.edu/labs/ghosh/

Lab Work:       
Work on experiment (exact duties tba)
Email five questions to Drs. Lom & Watson (due 9:30 AM Wednesday 10/11/06)

Lab Duties:         Cyndi

 

Week 8 (No Monday meeting – fall break)
Lab Work:        
Work on experiment (exact duties tba)
Work on confocal & protocol web site

Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 10/16/06)

Lab Duties:         Tamar

 

Week 9  (No Monday meeting – BL, CP, & FW at SfN meeting)      
Lab Work:        
Work on confocal & protocol web sites
Work on experiment (exact duties tba)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 10/23/06)

Lab Duties:         Page

Week 10
10/23 Meeting:   
Discuss SfN meeting highlights, progress of experiment, websites, and assigned reading

Reading:            
Wong et al. (1991) Remodeling of retinal ganglion cell dendrites in the absence of action potential activity
Wong & Wong (2000) Rapid dendritic movements during synapse formation and rearrangement
Optional:           Dr. Wong’s website: http://thalamus.wustl.edu/wonglab/

Lab Work:        
Work on experiment (exact duties tba)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 10/30/06)

Lab Duties:         Cyndi   

 

Week 11 
10/30 Meeting:   
Discuss progress of experiment, websites, and assigned reading

Reading:            
Dalva et al. (1994) Independent control of dendritic and axonal form in the developing lateral geniculate nucleus
Whitford et al. (2002) Molecular control of cortical dendrite development
Optional:            Dr. Shatz’s website: http://neuro.med.harvard.edu/site/faculty/shatz.html      

Lab Work:        
Work on experiment (exact duties tba)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 11/06/06)

Lab Duties:         Tamar

 

Week 12
11/06 Meeting:   
Discuss analytical methods and statistics
Discuss progress of experiment, websites, and assigned reading

Reading:            
Bloomfield (1996) Effect of spike blockade on the receptive-field size of amacrine and ganglion cells in the rabbit
Jan & Jan (2003) The control of dendrite development
Optional:            The Jan lab website: http://www.ucsf.edu/jan/index.html

Lab Work:        
Work on experiment (exact duties tba)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 11/13/06)

Lab Duties:         Page

 

Week 13
11/13 Meeting:   
Discuss progress of experiment, websites, and assigned reading
Discuss 2007 Bio351 Microscopy Calendar

Reading:            
Article on PhotoShop dos and don’ts (tba)
Portera-Cailliau et al. (2003) Activity-regulated dynamic behavior of early dendritic protrusions
Yuste (2005) Fluorescence microscopy today
Optional:            Dr. Yuste’s website: http://www.columbia.edu/cu/biology/faculty-data/rafael-yuste/faculty.html

Lab Work:        
Work on experiment (exact duties tba)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 11/20/06)

Lab Duties:         Cyndi

 

Week 14
11/20 Meeting:   
Finalize analysis of experiment
Discuss what makes a good oral presentation
Discuss progress of experiment, websites, and assigned reading

Reading:            
Barker – Chapter 6 – presenting yourself and your data
Jaffe (2003) Graph with gusto
Ruthazer et al. (2003) Control of axon branch dynamics by correlated activity in vivo
Van Aelst & Cline (2004) Rho GTPases and activity-dependent dendrite development
Optional:            Dr. Cline’s website: http://clinelab.cshl.edu/

Lab Work:        
Finalize experimental analysis (exact duties tba)
Collaboratively prepare a good draft of oral presentation (due 9:30 AM Monday 11/27/06)
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 11/27/06)

Lab Duties:         Tamar

 

Week 15        
11/27 Meeting:   
Practice and revise oral presentation
Schedule rehearsals for oral presentation this week
Finish/print Bio 351 2007 microscopy calendar

Lab Work:        
Finalize analysis of experiments
Email five questions to Drs. Lom & Watson (due 9:30 AM Monday 12/04/06)

Lab Duties:         Page

 

Week 16    
12/04 Meeting:   
Class collaboratively presents semester’s results to the biology department.
Course evaluations
Debrief on presentation

Lab Work:        
Organize data, lab notes, etc. (exact duties tba)
Email final five questions to Drs. Lom & Watson (due 9:30 AM Wednesday 12/06/06)

Lab Duties:         Cyndi

 

            updated 20 August 2006 by B. Lom

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