Lab Methods in Molecular Biology 446/546, Fall 2015
(BIOL 10693; BIOL 11850)
Lectures will be given by Drs Don Natvig & Coen Adema. There contact details are given below.
Dr. Coen Adema
Room 2428 Castetter Hall (Dept. of Biology)
Tel: 277-2743
E-mail: coenadem@unm.edu
Dr. Don Natvig
Room 206E, Castetter Hall (Dept. of Biology)
Tel: 277-5977
E-mail: dnatvig@unm.edu
Teaching assistant:
Miriam Hutchinson
Room 203 Castetter Hall (Dept. of Biology)
Tel: 277-2388
E-mail miramira@unm.edu
Office Hours: will be announced in class. Please don’t hesitate to come in with your questions.
Your participation in this class acknowledges that you have read and accept the information contained in this
syllabus. Students are expected be familiar with, and follow the principles laid out in, the Student Code of
Conduct published in the Student Handbook, Pathfinder.
Special needs: If there is any student in this class with a disability, please inform us of your needs as soon as
possible to ensure that your needs are met.
Class times: Monday & Friday 1:00-3:50 PM, Castetter Hall 37
Course information such as lectures, suggested reading, handouts, and homework assignments will be posted online at:
http://biology.unm.edu/cmadema/4546/4546.html
Textbook: NOTE there is no mandatory book for this class.
Readings will be provided through the above website in the form of protocols, scientific papers, also check out
http://www.ncbi.nlm.nih.gov/sites/entrez?db=Books
For those that prefer textbook for background information, we recommend: Molecular Biology of the Gene (7th
ed), Watson, Baker, Bell, Gann, Levine, Losick; Published by Pearson student edition ISBN 13:978-0-321-76243-6,
ISBN 10: 0-321-76243-6
Philosophy and major objective of the Course:
It is easy to follow a recipe, it is harder to follow it well, and most difficult to make it work. The major
objective is to teach you to get things to work in the lab, this may not be difficult for some of you, but it may
require a personality change for others.
There are 5 identifiable goals in this course:
(1) To introduce you to modern techniques used in molecular biology research.
(2) To teach you to use computer- and internet-based bioinformatics tools for sequence analysis
(3) To teach you to perform research carefully so that your scientific observations stand on solid ground.
(4) To troubleshoot experiments, but also, to persevere when nothing works.
(5) To give you experience in communicating research findings to the scientific community.
Ideally, this course will give you a better understanding of what a scientific career that uses molecular
techniques would be like and inspire you to pursue additional studies.
Grading (400 points undergrad/500 points for grad students)
Your final grade will depend on a midterm examination (100), a 15 minute class presentation (50), your lab
book (25), homework/in class troubleshooting exercises (50), class attendance/participation (75), and a final
paper (100). The final paper will be in the format of a submission-type manuscript for a scientific journal,
instructions will be provided. Additionally, graduate students will be required to give the class a 30 minute
presentation on their proposed research (100). Excessive or unexcused absences will lower your final grade.
Do not make it a habit of arriving to class late. The class depends on you to be here so that we can start and
finish class on time. FYI-you will work in groups of two or three throughout the semester. Your partner and
you are a team, so don’t let him or her down. Do your share of the work, be respectful of each other’s grasp of
the material, help each other whenever possible. As is common in science, you will collaborate on the writing
on your final paper and turn one paper in per group.
Warning: There is always a slow groups in the class. Please be respectful. It is our experience that these are
often the groups that get the best results.
Laboratory Rules and Guidelines: Laboratory work involves the use of dangerous equipment and chemicals,
which will be specially noted at the beginning of each lab. If you are unsure about any procedure, ask the
instructors or TA. This is important when handling dangerous chemicals or expensive equipment;
spectrophotometers, adjustable pipettors, and other equipment can be easily damaged.
Laboratory etiquette (for your safety):
No food (includes chewing gum) or drink is allowed in the lab.
Cell phones, music players and other electronic devices should be turned off.
Books (other than your notebook and lab manual), backpacks, clothing, and personal belongings should not be
kept on lab benches.
Lab coats and protective eyewear are recommended when conducting experiments. Lab gloves should be worn
whenever working with chemicals or solutions. Do not wear shoes with open toes in the lab.
Handle all equipment carefully and don’t goof around in the lab.
Wash and rinse all glassware when you finish using it.
Return individual items to your drawer at the end of each lab.
Notify the instructor if any spills occur or if equipment is damaged, and assist as instructed for the clean-up.
Notify the instructor if anything is spilled on your lab notebook or manual. It is important not to take
contaminated material out of the lab.
Cleaning glassware:
Clean glassware is essential to accurate and reproducible results. A single rinse is definitely not sufficient. For
this class, the recommended procedure is as follows:
1. Clean the glassware thoroughly with laboratory soap (only small amounts of soap are necessary, excess soap
just makes good rinsing more difficult and is a serious source of contamination).
2. Rinse all surfaces several times with tap water.
3. Rinse three times with distilled water.
If the glass is clean the water will adhere as a film and not collect as drops. Allow glassware to drain dry unless
needed immediately.
Sharps disposal:
Glass and sharp objects should be disposed of in special containers found around the lab. Never, under any
circumstances, put sharp things in the regular trash. This presents a very real hazard for maintenance
workers. All other waste (tips, tubes, cultures) can be collected in beakers on the bench but is ultimately to be
placed in the biohazard bags (front of the class room).
Course fee: The amount charged contributes to the purchase of kits and chemicals that are needed throughout
the semester.
Computers: Computers are made available for in class analysis. The software needed for bioinformatics will
either be provided or can be downloaded from the web. This provides a good opportunity to display and or hone
your computer/internet skills.
Lab Notebook:
Scientists have a responsibility to document their work. Publication is the formal documentation, but a
well kept lab notebook is the authoritative foundation for publication. Details about experimental procedure
often seem so obvious that they need not be written down in a formal way, but 6 weeks later, many details will
be impossible to recall. For graduate students it is important that the major professor be able to figure out how
an experiment was done, while for industrial scientists the employer must be able to follow what experiments
were done. Laboratory notebooks can be very important for claims of priority when sorting out patent disputes.
Many scientists working in areas which can lead to patents have their notebooks notarized to strengthen any
subsequent claim of priority. There have also been cases in which scientists charged with fraud could not easily
refute the charge because of poor record keeping. In one case, the US Secret Service was called upon to study a
researcher's notebook. But for the most part the lab notebook is your personal diary of what you did in the lab.
It need not be pretty, just accurate and complete.
You are required to keep a lab notebook for this class. This should be a running commentary with your
ideas and notes to yourself, together with all of the raw data and any calculations you make from the raw data.
Information about the equipment you use should be listed as should information about the chemicals you use.
You may refer to specific pages in the Laboratory Manual so long as you carefully note where any changes
were made. It should be possible for someone generally familiar with your area of study to pick up your
notebook and pick up with experiments where you left off.
All of the exercises will require making calculations or summarizing your results in a notebook. This
should be done during the scheduled lab period for two reasons. First, it is usually easier to do calculations
when the data is fresh in your mind and you are more accurate in recalling details for your summaries when you
write them immediately. Second, the instructor will be available during the lab period and may not be available
later. One of the criteria on which you will be graded is how current you notebook is. Lab notebooks will be
checked by us periodically.
General Guidelines:
1. Use a bound book of decent size with numbered pages (hand numbering is okay).
2. Make all entries in ink, beginning with your name and some identification about the notebook.
3. Leave 5 pages or more in the front for a table of contents. For each experiment or set of closely related
experiments, make an entry in the table of contents followed by the date of the experimental work, and the page
number where the research is described in detail.
4. Each experiment should list the
Title and date
One or two sentences about the experiment
Methods (including calculations and materials)
Summary of the results (generally with some sort of graph or diagram)
Short conclusion stating important findings and/or problems encountered.
5. Changes on previous pages, when needed, should be made by crossing out the old information with one line
and putting the new information nearby. Date any changes made to your notebook.
6. Raw data such as photos of your gels can be cut out and taped into the notebook. When particularly
voluminous raw data is involved, it is best to store this separately, but with a good cross reference system so
that the data and the description of the data can be put together later.
7. Rough graphs can be drawn directly in the notebook; more formal graphs should be drawn on appropriate
graph paper or with a graphing program, and taped into the notebook.
Evaluation: You will be evaluated on the basis of the laboratory notebook you will keep. You should record
everything of interest to you in the lab in this notebook. It is not necessary to reproduce methods spelled out in
the handouts, but everything else should be in your notebook. Not everything has to be polished, for example,
if you want to do a small calculation, do it in your notebook, not on a paper towel (formerly the record keeping
choice of most scientists). Within the last few years society has given clear signals that it expects scientists to
keep reasonable records and we must all learn to do this. All written communication in the lab will be in this
notebook, including feedback from the instructors. Do not write your raw data on paper towels intending to
transfer it to the notebook later. If you want to have a neat record of your results and feel you cannot do this as
the experiment progresses, take the raw data on one page, and then copy it to a later page in the notebook. You
will not be graded on neatness.
References:
Alley, Michael. 1996. The Craft of Scientific Writing. 3rd Edition. , Springer, NY.
Kanare, Howard M. 1985. Writing the Laboratory Notebook. Washington, D.C.: American Chemical Society.
(Much of the above was kindly provided by Dr. David Hanson from his Biology 478L Laboratory manual)