Contact information
    Dr. Fane
    Office: Keating Building (BIO5), Room 229
    Phone: 626-6634
    Email: bfane@email.arizona.edu

Course Objectives

The objective of this course is to introduce students to virology research and skills used for the study of viruses. Although some feasibility studies have been conducted, the experiments in the course have not been conducted before and represent novel lines of investigation. Although preliminary hypotheses will be discussed, unlike most undergraduate laboratory exercises, experimental results cannot be predicted. They will test hypotheses, which may be incorrect. Moreover, since many experiments are being conducted for the first time, problems may arise. Thus, the syllabus should be regarded as a tentative schedule.

Ideally the hypotheses and experiments around which this course has been designed should be of interest to the virology research community. It is conceivable that results generated in this course will be published, as was the case the last time this course was taught (Cherwa et al. 2009). However, it is unlikely that all the research required for publication will be completed during the course. Therefore, there may be the opportunity for an interested student to finish the research as an independent study.

Experiments and hypotheses to be tested

Single-stranded viral DNA replication cycles are generally more complex and more stringently regulated than double-stranded DNA replication cycles. Upon infection, the single-stranded DNA genome is converted to a double stranded DNA molecule. Host cell proteins are usually necessary and sufficient for this initial round of DNA replication (Stage I). Thus, no viral proteins are required. The second round of DNA replication (Stage II) involves the selective amplification of double-stranded viral DNA (replicative-form DNA), which may or may not require viral proteins. In the last stage of DNA replication (Stage III), only one strand of the replicative-form DNA is synthesized. As host proteins cannot perform strand-selective DNA replication, a viral protein is required. In addition to selective strand replication, these proteins also inhibit double-strand DNA synthesis. The experiments are designed to test hypotheses regarding the switch from Stage II -> Stage III DNA synthesis. For the Microviruses, the switch is most likely mediated by the relative intracellular concentrations of the host cell single-stranded DNA binding protein ssB and protein C, which is encoded within the viral genome.

Specific hypotheses to be tested:

1. The over expression of the viral C gene will lower viral yields by prematurely inhibiting double-stranded DNA replication. As double stranded viral DNA is required for transcription, this will also lead to decreases in viral protein synthesis.

2. The over expression of the host cell ssB gene will lower viral leads by inhibiting Stage III DNA replication. This will lead to the production of empty capsids, DNA-less particles.

3. To accomplish the switch from Stage II to Stage III DNA synthesis, the viral C protein interacts with the viral A protein, which is involved in both Stage II and Stage III DNA synthesis. Thus, C proteins from related viruses will not always cross-function. 

Grading: Grades will be based on two take-away exams, the lab notebook, each worth 100 points, and an additional 30 points for lab conduct and effort. A student can receive a total of 330 points in the course. Grades, however, will be calculated by dividing the points obtained by 300. No exams are dropped. Distribution 90%-110% A; 80%-90% B; 70%-80% C; Below 70% E. Note that the D grade is not used in this course.

 Take-away exams: the take-away exams are open book and internet. Students are allowed to seek advice from other students in the course. Although discussion is strongly encouraged, answers must be in the student's own words. 

Lab notebook: Students will be given a lab notebook at the beginning of the course. As the data generated in this course may be published, the lab notebook must be 100% comprehensible to me! The notebook should contain protocols, data, observations, conclusions and experimental rationales. It should not contain lecture notes and drafts of protocols. Keep a second notebook for that purpose. 

Lab conduct and effort: At large universities there are many more students that wish to conduct research than there are available spaces in research laboratories. The impetus of this course is to provide a bona fide research experience, as opposed to a lab course with predictable results, which is much easier to establish and execute. Thus, I expect students to make a serious effort to understand course material, to conduct experiments carefully, to be respectful of the support staff and other students in the course, and to act in a responsible and professional manner.

Attendance: If a student has more than one unexcused absence from the course. S/he will be dropped from the course. I understand that the course is labor-intensive and spans five weeks. Thus, each student is allowed one personal business or sick day, although it is not recommended.  Please be considerate to your lab partner. If taking a personal business day please

1. Inform me of this 48 hours in advance.

2. Clear this with his/her lab partner 48 hours in advance.

3. Both lab partners cannot have an absence on the same day.

4. The student is 100% responsible for obtaining lecture notes and data.

Office hours: by appointment. However, both the TA and the professor will be in the laboratory. Often there is "down" time during experiments, which provides a wonderful time to ask questions.

Safety procedures: A list of safety procedures and lab rules will be circulated. Students are to read this carefully and sign the bottom of the page, which attests to their understanding of the safety procedures. If a student does not wish to sign this agreement, s/he will have to drop the course. If a student fails to abide by the safety rules, the TA and/or the professor has the authority to ask him/her to leave for the period. 

Take-away exam 1

Take-away exam 2