Genomics at University of Northern Colorado
I implemented the GEP curriculum for the first time in the 2012-2013 academic year. I teach sophomore-level Genetics (BIO 220), and organize the lab associated with that course. BIO 220 is a required course for our biology majors. In the Fall there are usually two lab sections of 20-24 students each, and in the spring there are three laboratory sections. I wished to use the GEP as one module in the laboratory aspect of the course. I essentially followed the curriculum outline developed by Julie Emerson at Amherst. We spend four weeks (four lab periods of three hours each) near the end of the semester performing gene annotation.
I use the GEP curriculum in a four-week laboratory module in BIO 220 (sophomore genetics). In the weeks leading up the project, we cover transcription and gene structure in lecture. Just prior to the start of the laboratory project, I do one lecture on evidence-based gene annotation, introducing the "big picture" of gene annotation, and what evidence we use to locate genes in an unknown DNA sequence. I also very briefly introduce the interests of the larger research project.
Week 1: Students work through the BLAST tutorial in lab. Then each student must complete an online quiz on using BLAST prior to the next lab period.
Week 2: Students work through A Sample Annotation Problem, and an introduction to the Gene Model Checker in lab.
Weeks 3&4: Each group of two or three students is assigned a gene to annotate. Most groups are assigned one isoform of one gene (4-6 exons on average). Some genes only have two or three exons, and I assign multiple genes or isoforms if they have a very small gene. Each group goes through the process of verifying the melanogaster ortholog, mapping each exon by BLAST, fine-mapping each exon-intron border, then checking and verifying their gene model with Gene Model Checker. For grading purposes, each group completes the GEP annotation report for their gene, and a more detailed annotation report in which they detail the evidence they used to create their gene model.
Since I now do GEP annotation every semester, at the end of the semester I ask for volunteers to act as undergraduate teaching assistants for the next semester. These undergrad TAs receive one university credit for this activity, and the credit counts toward their upper division electives for a biology major. The TAs and I set up a weekly one hour meeting, and begin to meet at the beginning of the semester. I claim several fosmids for annotation, and each week I assign the TAs one gene/isoform to annotate. We then go over their findings in our weekly meeting, and roughly annotate each gene by the time the project starts in BIO 220. This helps the TAs to become very proficient annotators, well able to assist the students in BIO 220. It also helps us identify very difficult/tricky genes, which we do not assign to the BIO 220 students. We are concerned that such a short module can leave students feeling very frustrated, so we try to only assign straighforward projects. The TAs then attend each lab section, and help to answer student questions. The TAs also help to compile the final reports in one report for each fosmid in preparation to submit them to the GEP.
Lessons Learned and Future Plans
I teach one lab section per semester, and I supervise a graduate student TA who teaches the other lab sections (this grad student was also trained at WashU last summer). In the first semester, one thing we quickly realized was that the normal ratio of one lab instructor to 20-24 students was completely inadequate for this project. The use of undergraduate TAs has solved this problem, and it is a good experience for the TAs as well.
Syllabus Biology 220 Genetics
Lecture: Ross 2295, MWF 11:15-12:05
Lab: Ross 1611 Thursdays 11 and 2:30.
Instructor: Judy Leatherman, Ph.D.
Office: Ross 2510, 351-2453
Office hours: Monday 2:30-4, Wednesday 10-11:30, or by appointment.
'1. 'Textbook: Introduction to Genetic Analysis (10th edition, 2010), Griffiths, Wessler, Carroll, and Doebley.
'2. 'Lab coursepack (bookstore, $29.50)
'3. 'Clicker: Turning Technologies response card. I will give you a one week grace period to get your clicker; starting next Monday, I will have graded items that require a clicker. Once you get your clicker, register your device number on blackboard.
By the end of the course, students will be able to:
1. Connect the concepts of chromosome segregation during meiosis to Mendelian inheritance of genes/alleles.
2. Solve probability problems related to genetic inheritance in complex crosses and multigenerational pedigrees.
3. Predict inheritance patterns with various types of allele relationships (dominant, recessive, codominant, homozygous lethal), and with multiple genes that act on the same trait.
4. Utilize linkage analysis to predict the chromosomal location of a gene, or to predict whether certain individuals in a pedigree carry a disease allele.
5. Describe the components of a gene at the DNA level, and the molecular machinery involved in the processes of the central dogma: DNA replication, transcription, and translation.
6. Describe the processes involved in the inheritance and regulation of the genetic material, including key differences between eukaryotes and prokaryotes.
7. Apply the Hardy-Weinberg equation to problems to predict allele and genotype frequencies in populations, and to assess whether alleles are in equilibrium in a population.
Grading: Your grade for the lecture portion of the course will be based on exams, quizzes, online homework, and class participation. There will be four exams and a final (comprehensive) exam. The first exam will be given during the Thursday lab session; the other exams will be given during the normal class period, and the final exam will be given during the scheduled final exam period. Online homework on Blackboard will be assigned for certain chapters. For other chapters, quizzes (announced) will be administered in class. Announcements about homework due-dates and quizzes will primarily be made in class, if you are not there you may miss those announcements—it is your responsibility to find out about any assignments if you miss class.<o:p></o:p>
I value the engagement of students in this course. For full participation points for the lecture aspect of the course, you will need to come to class regularly. We will have learning activities/assignments in class throughout the semester which you will turn in for “participation credit”—if you are not present, you cannot get these points. I will frequently give participation credit for clicker answering. It is your responsibility toalways bring your clicker to class.
The laboratory portion of the course will include three large projects: a Drosophila experiment on X-linkage and homologous recombination, and a molecular project with a recombinant plasmid called pGLO, and a genomics (computer-based) project on gene annotation. Attendance in laboratory is mandatory; you will lose 20 points from your lab grade for the first time you miss lab, 30 points for the second time, and if you miss a third time, you will receive a zero for the entire lab portion of the course. If you have a personal emergency (death in the family, hospitalization), you must provide documentation in order to be excused from missing lab. Things like dentist/doctor appointments and work schedules will not be approved excuses. The laboratory will constitute approximately ¼ of your grade.
Four Exams (80 pts each) 320
Final Exam 80
Online homework and quizzes 70
Class Participation 30
Lab book checks & quiz 25
Mitosis/Meiosis animation 20
Drosophila Lab Report 40
pGLO Lab Report 50
Online BLAST quiz 10
Gene annotation report 30
The grading scale will be no more rigorous than: A: 90-100%, B: 80-89%, C: 70-79%, D: 60-69%, F: below 60%.
Blackboard: All documents relating to the
class will be posted on the class blackboard web
site. Please make sure you can access the site.
Lecture slides will usually be available on blackboard
no later than the evening prior to
the class period. If you want them
printed out, you will need to do that yourself.
Assignment/test grades will also be posted on Blackboard. Please make sure you check your UNC email
regularly, I may use this email to communicate with you.
Students with Disabilities: Any student requesting
disability accommodation for this class must inform the instructor giving
appropriate notice. Students are
encouraged to contact Disability Support Services at (970)351-2289 to certify
documentation of disability and to ensure appropriate accommodations are
implemented in a timely manner.
Cheating and Plagiarism: One of the student
responsibilities at UNC is to act in accordance with commonly accepted
standards of academic conduct. If a
student is found to be cheating or plagiarizing, they will receive a zero for
the assignment in question. Depending
upon the nature of the infraction, the student may also receive a grade of F
for the course and be referred to the University for disciplinary action. For more information please see the Dean of
Student’s website at www.unco.edu/dos.<o:p></o:p>
Hints for success: Read the chapters in advance. Don’t let yourself get behind. Come to class, and ask questions if you don’t understand. Print out the lecture slides and write your own notes on them. In class, find people you like to sit next to, and participate in the in-class problems, and work together with your neighbor on the problems. Do the suggested textbook problems, if you have trouble understanding the problems, you probably do not understand the material. Take action early; ask for help before the exam on that chapter. Find a study partner to work on problems together. For lab, read through the lab manual in advance. Don’t rely on your instructor or your lab partner to check up on you and make sure you did things correctly. Our lab exercises are multi-week projects—make sure you save the appropriate sample(s) for the next week’s experiments. <o:p></o:p>