Ana Maria Barral

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Genomics at National University

Course Overview

Both courses are part of National University's BS Biology program. BIO407 is Molecular Biology (lecture) and BIO407A is Molecular Biology Lab. The 2 courses are run concurrently over an 8 week period.

Implementation

GEP is currently (May 2014) being implemented for the BIO407A course, planning to do annotation over 16-20 hours of laboratory time. Implementation experiences will be updated as the course progresses.

Lessons Learned and Future Plans


See summary presented at the 2014 August alumni workshop.
Suggestions for tools: "hands-on" introduction to gene structure: consider the Bioinformatics module of the Center for Biomolecular Modeling.
Electronic Lab Notebook: Lab Archives.

[1]

Syllabus for BIO407A Molecular Biology Lab


Class Location and Schedule
NU Spectrum Campus Laboratory and Room 193 (computer room) for annotation.
Wednesdays 5.30 pm between 5/7 and 6/25, as well as Saturdays 6/7 (changed from 5/17) and 6/14.
Instructor
Ana Maria Barral, Ph.D.
Best way to communicate is by email: abarral@nu.edu. I will respond to your emails within 24 hours. If you have emailed and I have not responded, please resend, or use annba29@gmail.com (and also check your spam folder).
Phone: (714) 429 5148 (office) or google phone (858) 480-9139 (please leave message and I will get back to you as soon as I can).
I will be on campus before class starts for any consultation or advising, or you can request a meeting time. We can also discuss via skype or google hangout.
Textbook
This course will use handouts for the laboratory experiments. For the bioinformatics assignments, materials from the GEP website will be used (http://gep.wustl.edu/)
All handouts and materials are available in electronic format. Students need to buy access to the LabArchives Electronic notebook system (see below) for $10.
Laboratory Notebook
Your Laboratory Notebook is electronic and housed at
https://mynotebook.labarchives.com/self_signup/MTkwNS44fDM3ODg5LzE0NjYvQ291cnNlLzEwMzM0OTc4NzF8NDgzNy44 in the LabArchives website. You will be able to record and upload your results and observations, both via computer or using the LabArchives App. That said, many students still prefer to write their observations on paper before transcribing it to an electronic document. Therefore I suggest bring a simple composition notebook or similar to take daily notes of your activities and also have a record of what documents you are uploading as part of the GEP project.
LabArchives allow real-life monitoring of your notebook. Be diligent and detail-oriented. The quality of your notebook is an important part of your grade (see below).


Course description
This course emphasizes techniques essential to molecular biology including DNA extraction, purification and quantification; polymerase chain reactions; and restriction enzyme digestion. An important component of this course is a bioinformatics Drosophila gene annotation project, as part of Washington University in St. Louis Genomics Education Partnership project.
Course Learning Objectives

Upon successful completion of this course, the student will be able to:
1. Isolate plasmid DNA from Escherichia coli by using the mini-prep and maxi-prep technique.
2. Amplify 16S rRNA gene fragments by polymerase chain reaction (PCR) and identify bacterial genera using Blast analysis.
3. Quantify DNA using a spectrophotometer, and perform restriction digestion and agarose gel electrophoresis.
4. Perform artificial transformation of bacterial competent cells.
5. Annotate a fosmid from D. biarmipes Muller F element or the D. ananassae Muller D element, a process that includes becoming familiar with online genomics tools such as FlyBase and UCSC Genome browser, as well as annotation strategies based on gene structure principles.

Assignments and Grading

Assignment Point value Date
Lab reports 6 x 25 p = 150p Please see schedule for due dates.
Midterm exam 100 p 6/4
Final exam 200 p 6/25
Annotation project 100 p Due latest 6/29
Total points 550 p

Lab Reports.
In the LabArchives Notebook, submit your lab reports under the folder Reports for Submission. Lab Reports are usually due one week after the exercise took place: consult your syllabus or the LabArchives Report placeholder for exact date. It is strongly recommended you do not leave completion of the report until the last minute. Continuous and early work on the report is beneficial for 2 reasons: 1) I can give you early feedback for improvement; 2) you remember better right after the completion of the lab.
In the Report for Submission Folder there will be pages corresponding to each report. As you hover under the title of the page, you will be links. Click on Edit and add text, pictures, tables etc. Remember to save your work and submit before it is due.
Lab Reports will be graded on the following aspects:
1. Completion of all sections (20p):
a. Purpose: 1-2 sentences
b. Brief description of the laboratory activity (1-2 paragraphs. No need for detailed procedures).
c. Experimental design: can be be either a detailed description of the setup, a diagram, or a table. For bioinformatics, make a list of the documents developed.
d. Results (data, observations, graphs etc.)
e. Conclusions and Discussion: it should address what was achieved, and if something went wrong, why do you think it did, and what can be done the next time.
2. Quality and presentation of content (5p). This is a holistic aspect, which evaluates how professional your report is, and includes:
a. Clarity of your writing (includes grammar, spelling)
b. Correctness of the information
c. Organization.
Exams
The midterm exam will mainly evaluate your understanding of basic molecular biology laboratory techniques and procedures. They may include calculations of dilutions and DNA/protein concentrations.
The final exam will further evaluate your understanding of basic molecular biology techniques and experimental design, as well as the basics of bioinformatics and gene annotation.

Annotation project
As a research project, this assignment is evaluated more on its thoroughness and organization. This is project you will be working on in pairs, and completion the requirements of the report form all but guarantees maximum points. However, as each sequence is different and may have particular challenges, you should work on this early on and discuss any potential difficulties during the last 2 weeks of the course.