Jacob Kagey

From GEP Wiki
Jump to: navigation, search

Genetics Laboratory at University of Detroit Mercy

Course Overview

Genetics Laboratory (BIO2710) is an upper level laboratory course that meets once a week for three hours. This lab course accompanies the Genetics lecture (BIO2700), and though the lab course is not required it does count as an upper level laboratory elective for Biology and Biochemistry majors. The course is built around students conducting two hypotheses driven Genetics research projects. The first project involves the characterization and mapping of an unknown Drosophila melanogaster growth mutant. Students work to characterize the overgrowth phenotype while they become familiar with the basic techniques of fly husbandry. Next, students utilize complementation mapping to identify the genomic region that houses this particular mutant. Further rounds of complementation mapping identify the actual gene that is mutated and this serves as a transition into molecular genetics. In this part of the project students work to isolate DNA from their mutant flies, utilize PCR to amplify the gene, and submit the amplified gene for DNA sequencing. The last week of this module involves students using web-based genomic tools to analyze the sequencing data and determine the level of evolutionary conservation between their gene and the human homolog. This entire experimental module takes 10 weeks. A 4-week module in which the students work in pairs on the Drosophila annotation project follows the student of the growth mutant. Further details of this module will be outlined below in the implementation section.


The annotation module was conducted in four three-hour class periods. Students were given the choice to work individually or with partners to annotate one contig as a group.

Week one: Introduction
The first week was used to introduce the GEP program, genomic sequencing, and the annotation. As a class we worked through the GEP D. virilis contig. We worked through one entire gene and then the students were given the remainder of the class (approximately 30 minutes) to work on a second gene and ask questions. During the class period students were given an annotation guide and encouraged to take extensive notes and ask questions.

Weeks 2-4: Annotation
Starting at the beginning of week two students were assigned a particular contig and were given the annotation report guidelines. During the class period, which was held in a computer lab, students worked either individually or with their partner to annotate their contig. There were two facilitators (myself and a trained TA) and we spent the class period answer questions and helping the students to trouble shoot the annotation. After the week 4 class, the students were given the weekend to complete their annotation report and submit the report for grading the following Monday.

Lessons Learned and Future Plans

Lessons learned: Overall, the module was a success. All students were able to submit an annotation report. The three weeks of in class time to work on the project (9 hours) was an ideal amount of class time. I selected simpler contigs (each with 2 genes) and feedback from the students indicated that these projects were completed somewhere between 10-15 hours of work. This required the students to put in some additional work outside of class. Most students worked as partners and after observing the students work, I am confidant that the majority of student groups benefitted from working in groups. Even students that were not partner were helping each other, creating a culture of collaborative learning. Students struggled in the first week of work, which was to be expected, and by the forth week students were working on making improvements to their annotation guide and helping other students through common pitfalls and difficulties.
Improvements for next year: I plan to utilize actual annotation projects next year. This year, since it was the first time I had implemented this course, I utilized already annotated projects from the ‘sandbox’. Furthermore, I only selected 2 contigs meaning that a number of groups were annotating the same contig. Next year I plan to give each group their own unique contig. This course runs in the winter semester, this fall, two students who took the course and will serve as TAs next year are going to conduct independent research with me. For their research project, the students will be working on annotations throughout the semester, this will help them to update the user manual as well as become experts on troubleshooting.

Syllabus for BIO2710

BIO2710 – Genetics Laboratory - #23206
Thursday 2:00 – 5:00 PM  Ford Life Sciences Building Room 201  Term II, 2013
Instructor: Dr. Jacob Kagey, Ph.D. Office: Ford Life Sciences 218
Email: kageyja@udmercy.edu Lab: Ford Life Sciences 219
Office Hours: M/W/F 11 – 1 Phone: 313-993-1408
And by appointment

Courses Description: This course is designed to educate students in the design, implementation, and interpretation of experiments within the field of Genetics. During this course we will work to map and characterize a homozygous lethal Drosophila melanogaster mutant identified from a screen to identify genes that regulate cell growth and cell division. The last portion of the semester, we will be contributing to the Genomics Education Partnership to aide in the annotation of the genome of other Drosophila species. Students will be exposed to techniques from classical genetics, molecular genetics, and bioinformatics.

Prerequisites: Biology 1200, Biology 1220, and Biology 2700. (2700 can be taken concurrently).

Course Textbook: All course material will be available on the course Knowledge site. The Genetics textbook by Snusted and Simon may be useful as a supplement.

Knowledge: The Knowledge site for this course will be used for announcements, provide each week’s laboratory manual, and data collected through the digital camera.

Electronics: Electronics not used for academic purposes must be turned off or silenced. No texting, Facebook updating, tweeting, etc. should be done during class under any circumstance. Students violating this policy will be asked to leave.

Students with Disabilities: UDM is committed to all students achieving their potential. If a student has a disability or believes that s/he may have a disability (including a physical, mental, or emotional disability) that may require an accommodation, students should contact Emilie Gallegos in the University Academic Services (UAS) office for further discussion. The UAS office is located on the third floor of the Library. Because accommodations often require adequate time to implement, students should make arrangements to contact the UAS as soon as possible.

Grading: Your grade for this course will be based on four components. Each component is discussed in detail below.
45% - Three laboratory reports (15% each)
15% - Annotation Project
20% - Weekly quizzes (2% each)
10% - Laboratory notebook
10% - Poster Presentation

94-100 A 77-79 C+
90-93 A- 73-76 C
87-89 B+ 70-72 C-
83-86 B 60-69 D
80-82 B- <60 F

Lab Reports: Periodically throughout the semester you will be asked to summarize the current findings in the laboratory with a 2-page lab report. Each lab report has a two-page limit and must include the following sections: introduction, methods, results, and discussion. Figures for each laboratory report do not count towards the page limit and are to be included at the end of the lab report. Each laboratory report must be appropriately cited and reflect the findings of your research.
*Though students will be working with lab partners throughout the semester on the execution and interpretation of experiments, lab reports are to be completed individually. Each lab report will be submitted to SafeAssign prior to submission. Any plagiarism of the lab report from another student or external source will result in an automatic zero and referral the Dean of Students.

Weekly Quizzes: Each week following the pre-laboratory lecture, a quiz will be given. The quiz will consist of material to be covered that week in lab and also in the previous week’s laboratory. The lowest 2 quiz scores will be dropped.

Laboratory Notebook: Each week I will check the previous week’s notebook. Your notebook must be completed in entirety before laboratory begins to receive full credit. I recommend getting a three ring-notebook to keep each week’s laboratory handout and figures.

Poster Presentation: On April 15, 2013 we will have a poster presentation during class time. This poster presentation will serve as your final exam. The poster should include the following components: abstract, introduction, methods, data, and conclusions. Your grade will be based on the quality of your poster and your ability to answer questions regarding your research.

Attendance: Attendance for laboratory is mandatory. Students needing to miss laboratory for an excused absence are encouraged to discuss their absence with me prior to missing laboratory. If you miss lab, you cannot makeup the grade for your lab notebook or quiz. Students are responsible for any material from missed laboratories.

Academic Integrity: Everything submitted for grading is expected to be a student’s own work. Anything suspected otherwise will be dealt with according to the University policy. See specific details under ‘lab reports’.

Extra Credit: Extra credit assignments will not be given.

Email: When emailing me about this course please utilize your udmercy.edu email address. There are certain types of information that I cannot give out to other email addresses.

*Subject to change

Lab Topic Date
1 Fly husbandry and Genetic Screens January 9
2 Deficiency Mapping 1/ Gene naming January 16
3 Deficiency Mapping 2 January 23
4 Molecular Basics/DNA isolation
Lab Report #1 Due (Labs 1-3) January 30
5 Primer Design/DNA quantification February 6
6 PCR February 13
7 Gel Electrophoresis/Ligation/Transformation
Lab Report #2 Due (Labs 4-6) February 20
8 Plasmid Isolation/Restriction Digest February 27
Spring Break March 6
10 DNA sequence analysis/Evolutionary Conservation March 11
11 Genome Annotation - overview
Lab Report #3 Due (Labs 7-9) March 13
12  Annotation work Day 1 March 20
13 Annotation work Day 2 March 27
14 Annotation work Day 3 April 3
15 Poster Presentation Preparation
Annotation Project Due April 10

Poster Presentations April 17th

This course syllabus provides a general plan for the course; deviations may be necessary as the data dictates.