Biology 351 (Group Investigation)
Microscopy & Imaging in Neuroscience
Fall 2007 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
• Each student will learn primary cell culture, immunostaining, and morphological analysis using imaging
• Students will collaboratively determine how neuronal activity affects RGC dendritic morphology in vitro
• Students will collaboratively update the lab’s protocol websites
• Students will collaboratively create an image calendar for 2008
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.
Instructor: Barbara Lom, PhD   
Office Hours: Wednesdays 11:30-1:00 (except 11/07)
By appointment (When proposing appointments first view my schedule at:
Lab Technician:  Julie Ruble, ‘06
Email: We will make e-mail announcements outside of class as necessary check your e-mail regularly, and respond promptly and politely to all requests from your teammates.
Textbooks: There is no textbook for this course, but a variety of books on microscopy and scientific research are available in the lab and library. 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.

Recommended 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
• At the Bench: A Laboratory Navigator (2005) by Kathy Barker
• 3-Ring Binder to organize your papers, protocols, etc.

Nikon’s Microscopy U
Molecular Expressions

Lab Notebook: You are expected to store your notebook in the lab at all times. Record daily and comprehensive notes. Your notebooks will be subject to unannounced checks for detail, accuracy, and completeness.
Weekly Questions: Each student will send Dr. Lom a weekly email update (by 9:30 AM on Mondays) addressing these five 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?
Image Portfolio: Each student will generate a portfolio of microscope images collected during the semester. Specific image assignments are indicated in the course schedule. In addition to the specified portfolio images, portfolios must include at least 12 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. These images will contribute to the class calendar, website, and presentation.
Seminars: In order to prepare for the final class presentation, each student will attend three science seminars of their choice before Thanksgiving break. Within 48 hours of the seminar please send me a brief email noting three presentation aspects that the scientist executed effectively and three aspects that could be improved.
  B+ 87-89.9% C+ 77-79.9% D+ 67-69.9%  
A 95-100% B 83-86.9% C 73-76.9% D 60-66.9% F 0-59.9%
A- 90-94.9% B- 80-82.9% C- 70-72.9%    

45% Image Assignments, Web Sites, Journal Club, Presentation, etc.
40% Personal Effort, Initiative, Understanding, Original Thought, Participation, Courtesy, Attention to Detail, Engagement, Ability to Generate Results, Ability to Work with Team, etc.
15% Lab Notebook, Weekly Questions, Data Organization, etc.

Feedback: I ask that students give me 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 me aware of potential concerns as early as possible so that I can attend to them appropriately. I cannot try to fix problems if I am 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 and submit the assignment up to four hours past the deadline.
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. I encourage you to study in groups and discuss your research with your classmates. Lab presentations and written reports 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:
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 the 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 impact your grade and/or your lab privileges.
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 and/or Julie BEFORE we are out.
• When using a lab 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.
• Please do not wear open-toed shoes in the lab (you are welcome to keep a pair of shoes in 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.
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 but there are not enough for everybody to have their own USB drive all semester. 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.
Tools: You will be provided with forceps and other 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 Cubby Systems: Each person in the lab has a “cubby” for storage of personal items such as toolboxes, 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 lab-approved shoes in the shoe area below the cubbies if you want to wear your flip-flops to and from the lab. Please also use the cubby system for leaving notes, etc. for your lab mates.
Shared Lab Duties: Twice during 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. in our lab, the confocal room, the microscope room, the culture room, and the cryostat room. 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:

Previous 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/tech).


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

Week One


8/27 Meeting: Brief introduction to the research question, RGCs, etc.
Observe frog squeezing and embryo fertilization
Learn to use staging tables to identify tadpole ages
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: Pictorial Atlas of Xenopus Development
Intro to Stereomicroscopy
(try the Nikon SMZ1500 Stereomicroscope Interactive Flash Tutorial)
Intro to Microscope Ergonomics microscopy
(try the Proper Microscope Posture Tutorial)
Cleaning, Care, and Maintenance of Microscopes

Lab Work: Each student generates a graph and stereomicroscope tadpole images for staging assignment (due 9:30 AM 09/03/07)
Complete schedule form and submit as soon as your schedule is solidified.

Lab Duties: All – demo

Week Two

09/03 Meeting: Introduction to in vitro TTX/RGC results
Animal training
Discuss staging graphs and tadpole images (first assignment)
Demonstrate eyebud dissection and dissociation

Lab Work: Perform/practice eyebud dissections on fixed and live tads and dissociations on live tissue
Generate more/better staged tadpole images and revise staging graph (due 9:30 AM 09/10/07)

Lab Duties: Kathryn

Week Three

09/10 Meeting: Critique tadpole images (second assignment)
Demonstrate full culturing technique
Discuss Rigel & Lom (2004) and NSF grant (articles on Blackboard)

Lab Work: Perform/practice explant and dissociated cultures
Generate images of “unknowns” with stereomicroscope (due 9:30 AM 09/17/07)

Lab Duties: Courtney

Week Four

09/17 Meeting: Critique unknown images (third assignment)
Introduction to brightfield and phase contrast microscopy and immunostaining
Discuss Spitzer (2006) article (on Blackboard)

Lab Work: Perform/practice explant and dissociated cultures with immunostaining
Generate images of cultured neurons and “misc. slides” using phase and brightfield (due 9:30 09/24/07)

Lab Duties: Jordan

Week Five

09/24 Meeting: Critique phase and brightfield images (fourth assignment)
Introduction to widefield (conventional) fluorescence microscopy
Discuss journal article (article tbd)

Lab Work: Perform/practice explant and dissociated cultures with immunostaining
Generate images of immunostained neurons using phase and fluorescence (due 9:30 AM 10/01/07)

Lab Duties: Dom

Week Six

10/01 Meeting: Critique fluorescent images (fifth assignment)
Introduction to measuring neuronal morphology
Discuss journal article (article tbd)

Lab Work: Continue culture and/or immunostaining as needed
Measure neurons and generate fluorescent images from “$100 slides” (due 9:30 AM 10/08/07)

Lab Duties: Kim

Week Seven

10/08 Meeting: Critique morphological analysis and fluorescent images (sixth assignment)
Discuss protocol websites
Discuss plan for experiments
Introduction to confocal microscopy
Determine journal club presentation schedule

Note: no meeting on 10/15 (fall break)

Lab Work: Work on techniques (culturing, immunostaining, and/or analysis) that need more practice, improvement, etc. (tbd)
Update protocols web site
Schedule confocal training to generate confocal versus fluorescence images of $100 slides (due 9:30 AM 10/22/07)

Lab Duties: Tara (week 7) & Julie (week 8)

Week Eight 10/22 Meeting: Critique confocal and fluorescence images (seventh assignment)
Design game plan for experiments
Journal club presentation by Students #1 & 2 (article tbd)

Lab Work: Generate more images, work on websites, and/or work on experiment (exact duties tbd)

Lab Duties: Kathryn
Week Nine

10/29 Meeting: Discuss images and experiments
Journal club presentation by Students #3 & 4 (article tbd)

Lab Work: Generate more images, work on websites, and/or work on experiment (exact duties tbd)

Lab Duties: Courtney

Week Ten

11/05 Meeting: Discuss experiments
Discuss class calendar images

Note: Dr. Lom will be out of town at the Society for Neuroscience meeting this week

Lab Work: Generate more images, work on websites, and/or work on experiment (exact duties tbd)

Lab Duties: Jordan

Week Eleven

11/12 Meeting: Discuss experiments & Society for Neuroscience meeting
Journal club presentation by Students #5 & 6 (article tbd)

Lab Work: Generate more images, work on websites, and/or work on experiment (exact duties tbd)

Lab Duties: Dom

Week Twelve

11/19 Meeting: Discuss progress of experiment, websites, calendar, etc.

Lab Work: Generate more images, work on websites, and/or work on experiment (exact duties tbd)

Lab Duties: Julie

Week Thirteen

11/26 Meeting: Discuss progress of experiment, websites, calendar, etc.
Discuss what makes a good oral presentation (use observations from seminars attended earlier in the semester)

Lab Work: Finalize experimental analysis (exact duties tbd)
Collaboratively prepare a good draft of oral presentation (due 9:30 AM Monday 12/03)

Lab Duties: Kim

Week Fourteen

12/03 Meeting: Revise oral presentation and schedule rehearsals for oral presentation

Lab Work: Practice presentation, address loose ends in lab, etc.

Lab Duties: Tara

Week Fifteen

12/10 Meeting: Class collaboratively presents semester’s results to the biology department.
Debrief on class presentation and chedule individual debriefing sessions with Dr. Lom
Course evaluations

Lab Work: Organize data, lab notes, etc. (exact duties tbd)

Lab Duties: Julie