Don Paetkau Saint Mary's College

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Genomics at Saint Mary's College

Course Overview

I have implemented a number of the GEP materials into an ever evolving BIO331: Biotechnology course at Saint Mary's.  Prior to attending the workshop, I used the "Investigating a Mutation in HIV-1" excercise as a stand alone lab section.  This was after students had worked on a multi-week project that included experimental design, PCR primer design, sequence comparison and database searching to determine which gene in a specific Drosophila region was responsible for a particular mutant phenotype.  This course also covered a number of other areas of Biotechnology (Microbial, Human Disease, Forensics, etc).  Since attending the workshop, I have committed half of the course to Annotation.  I implemented this change in the Fall 2009 semester and that is the syllabus presented below.  Due to changes in our program, I was able to teach the Biotech class in the Spring 2012 semester as a stand alone Genomics course.  The whole course was dedicated to finishing and annotation. 

Implementation

I attended the Summer 2009 Workshop and had a TA attend the Summer 2009 TA Workshop (separate workshops). 

The Biotechnology course is an upper-level (Juniors and Seniors)  Biology requirement for the Molecular/Cell Concentration of our Biology Degree.  It has the prerequisite of Molecular Cell Biology which has the prereq of Genetics, which has the prereq of the Introductory Biology Course.

2009-10 Implementation - Annotation

The middle 8 weeks of this course was dedicated to Annotation (listed as Genomics on the schedule).  Both lecture and lab were dedicated to Annotation.  Due to a scheduling conflict the Thursday 11-12:15 lecture and 2-5 lab were taught in a 20 computer Mac lab on one side of campus, while the Tuesday 11-12:15 lecture was taught in a 30 computer PC lab on the other side of campus. This set-up (switching from Macs to PCs) caused less troubles than the computer arrangements.  The PCs were arranged in rows - like a typical classroom - while the Macs were arranged around the outside of the room.  The Mac arrangement was much easier to work with, though it would have been better to have them all around a room instead of spread out along the back and sides.   

There were 17 students in the class. 

It took longer to annotate then we anticipated and students spent so much time on their presentations that they were unwilling to do another presentation, so we ended up scrapping the last presentations and moving to a straight professor lecture style for the remaining couple of weeks. 


2012 Implementation - Finishing and Annotation

There were 18 students in the class, 16 seniors and 2 juniors.  One TA who had taken annotation but not finishing.  Very enthusiastic and willing to learn which is more important than past experience in some cases.  She picked up the finishing, working ahead of the class throughout the first part of the semester and was able to keep up given her annotation background.


We implemented a 1 hour discussion per week of the original research papers.  Mostly papers from the website and then a few rescent articles thrown in for good measure.  1-2 papers a week, with two 9 person discussion groups (1 lead by me and 1 by the TA) at the beginning of our 3 hour lab session.  We switched groups each week.  This was a very important addition as it showed the students that the research was real, published and relavant.  The published human evolution papers we looked at were also very interesting to students and made the As, Cs, Gs and Ts of their work more interesting. 


Problems:  Presentations of the same material over and over.  So, we had students pair up for the first presentations which meant that only nine groups presented.  We did have a little trouble with one or two partners not sharing work equally, which was a draw back of this approach.  For the annotation presentations, we ran out of time so we cut the presentations down to 4 slides: Original project graphic, end project graphic, synteny and one interesting aspect of the project.

Lessons Learned and Future Plans

Lessons Learned:

1.  Assessment requires some type of insentive.  I usually provide class time for both the GEP students and the controls.  The controls require a colleague willing to use some of their lab time for the assessment and some type of insentive (I usually use chocolate cake).


2.  Two clear points should be made from the beginning of the course:

   a) What is the use of Genomics/Annotation in general - especially to a pre-med student. 

       This should not be a hard sell, as the AAMC has stressed the need for Genomics in the 

       undergraduate curriculum and considering that we are finding:

        - new RNA species

        - orthologs that provide disease study models.

        - new methods to control gene expression (which is ultimately a disease related study)   

          including new possible uses for pseudogenes in expression control.

       Even so, this should be made explicit at the beginning, middle and end of the course.

   b) What is the end point goal.  Students feel overwhelmed.  Have the teaching assistant 

       show her talk early in the course and make sure the report guidelines are clearly stated 

       early. 


3. Do not rely on the GEP color grading scheme, or at least know its basis.  Green ones that have no D. melanogaster orthologs are not conceptually easy starting points for students working on annotation.


4.  Emphasis the biological relevance of the project.  This means leaving time for what I call the post-annotation section of the study.  This includes, but is not limited to: synteny analysis; comparing repeat density to control region repeat density for discussion of hetero vs euchromatin; analyzing genes found during annotation - function, cellular location, orthologs, possible disease ramifications, etc.; assessing reliability of computer based gene predictors.  This type of analysis is especially important for independent research students but should also be available for all GEP research students.


5.  Include successful, clean submissions to the GEP as part of the course grade.  This will save you a ton of summer work.


Future Plans:

Convert the Biotech course to the Finishing/Annotation GEP course in the Spring 2012 semester. 

Syllabus

General Information and Syllabus: BIO331: Biotechnology (4 credits)
Saint Mary’s College, Fall Semester 2009

Lecture Time: Tuesday/Thursday 11:00-12:15 Science Hall 132
Lab Time: Thursday 2:00-4:45 Science Hall 227
Sept – Nov: Thurs. Lab and Lecture Regina 145

Prerequisites: Mol. Cell Bio. (BIO230)

Instructor: Dr. Don W. Paetkau (Pāt-kō)
Office: Science Hall 278
Office Phone: 284-4684
Home Phone: 1 (574) 533-9972 (Long distance from campus: 7am-11pm)
E-mail address: dpaetkau@saintmarys.edu

Course Overview
In this course, we will investigate current topics in biotechnology and observe their impact on society. A number of areas of biotechnology (bacterial, plant, animal, medical, etc.) will be explored with a strong emphasis on genomics this year. Our exploration will include lectures, labs, student presentations, student lectures, discussions, group genomics research annotation projects that lead to the publication of the data in Genbank, field trips and tastings. Time will also be spent discussing the social implications of specific biotechnologies. This year’s format is new and I am confident that it will be a enjoyable learning experience for all of us.

Learning Objectives
At the conclusion of this course you should be able to:
1. … perform experiments in the field of biotechnology and present the results of these experiments clearly.
2. … analyze data from biotech experiments, make logical conclusions from the data and design future experiments to extend the knowledge gained from that data.
3. … comprehend, discuss and critique recent literature in the field of biotechnology (including primary research articles).
4. … describe in detail and be able to communicate to others (teach) current technologies in the biotech industry.
5. … identify and discuss issues that arise from the use of biotechnology in today’s society.
6. …work collaboratively both in the lab and in class to enhance each other’s learning.
7. ...demonstrate proficiency in oral presentation.

The assignments in this course are designed to achieve these goals. Therefore you will be asked to: read the assigned readings before you attend class; ask questions; read, present and critique literature in the field of biotechnology; analyze data on your exams and in the lab; and participate in class discussions. The course consists of three distinct sections. The first quarter includes lectures and labs designed to introduce several general areas of biotechnology and techniques used in these areas. The second component involves an eight week section devoted to a integrated lab/lecture genomics research project. The third section involves student presentations of specific topics in Biotechnology, group discussions and a field trip to the South Bend Medical Foundation. You will also have a chance to assess each others projects and provide critical evaluations to improve your classmates’ oral and written presentations.


Lectures
Lectures will meet on Tuesdays and Thursdays: 11:00am-12:15pm.
Lecture attendance is mandatory. Because the format of the course places a high emphasis on class presentation and discussion, you will be unable to participate in this process if you do not attend lectures. If you know you will be unable to attend a class (for reasons such as a graduate/medical school interview), please let me know in advance so we may arrange substitute assignments.

Laboratories
Please purchase a 1” 3-ring binder, a 3 hole punched single subject notebook and a flash drive for lab.

Laboratory sessions will generally meet on Thursdays from 2 to 5 pm. However, during the eight week genomics project, the lab and lecture will be much more integrated, so please bring you lab book with you to those lecture times as well. You will also need to work outside of the lab time to complete the genomics project.

The lab manual will be handed out in class. Please read the lab procedure prior to lab, as well as any assigned readings.

Your lab notebook will hold all of your data. It is critical to maintain the notebook well as it is your primary resource for the lab reports. EVERYTHING YOU WRITE DOWN IN LAB SHOULD GO INTO YOUR NOTEBOOK, NOT ON SCRAP PIECES OF PAPER. You should also continually save screen shots and print your data from the genomics portion of this course. Use your flash drive to save the data as the network is not always the easiest tool to use. Bring your notebook and binder to both lab and lecture as the integrated nature of this course will mean that we will constantly being going back and forth between lab and lecture.

We will also have two field trips this semester to observe first hand the practical uses of biotechnology. It is a good idea to bring your lab notebook on the field trips.

Textbook
This course will use a combination of textbook readings and current literature. The primary textbook for this course, which is available in the bookstore, is Biotechnology: An Introduction by Susan R. Barnum (ISBN 0-534-49296-7). Further readings will be handed out in class or posted on the Blackboard site.

Blackboard Website
This course has a Blackboard website. It will be used for communication, as a class material resource site and as an assessment tool. Your grades will also be available to you on this site.

Office Hours
I will have formal office hours. I suggest the following times: MWF 9-11am. I am also readily available for meetings outside of class by appointment. You can set up an appointment before or after class, by telephone or by email. Review sessions will be scheduled by student/professor consensus prior to each exam.


Evaluations
Course performance will be evaluated by exams, short weekly quizzes, written assignments, oral presentations, lab exercises and peer reviews of some of your work. The distribution towards the final grade is:

Final Grade Distribution
Part 1: Bacterial, Plant and Animal Biotech
Ethanol Essay                            30 points
GMO Report                               20 points 
Weekly Quizzes                         40 points
Exam 1                                    100 points

Part 2: Genomics
Problem Sets
Exercise #1                                35 points
Exercise #2                                35 points
Exercise #3                                30 points
Homework Assignments              20 points
Final Report (Written and Oral)   100 points (75 +25)

Part 3: Student Presentations
Presentation                               50 points
Weekly Quizzes                         15 points
Final Exam                               100 points
Total                                         575 points

The midterm exam will be given during the class period. The final exam is scheduled for 10:30am-12:30pm Friday, December 18. A small part of the final exam may be cumulative in that knowledge you gain throughout the semester will be needed to answer questions that integrate a number of concepts on the final exam. If there are any problems with the midterm exam schedule, please contact me as soon as possible. Make-up midterm exams will only be given in extreme cases with a documented excuse (i.e. a written excuse from a doctor) and must be made up within 48 hours. If you know beforehand that you will be missing a midterm exam, you must take the exam before the scheduled time. The final exam time can not be changed without permission from the student advising office.

The student presentations will address specific topics in biotechnology by groups of three to four students. Topics will be chosen after the first section is complete from a list of suggested topics. Students are to research the topic, prepare and present a one hour PowerPoint based lecture/discussion and provide questions for review and the final exam. In addition, presenters will provide background readings for their fellow students (to be read prior to the presentation) from the textbook and at least one other source. Meetings with the professor will be set up prior to the presentation to aid in preparations. In addition to PowerPoint, students are invited to use any other reasonable means to enhance the learning of their classmates (questions, problem sets, props, etc).

Presentations notes (PowerPoint slides) and reading assignments must be handed in for posting on Blackboard at least one day before class.

Final Exam
The final exam is scheduled for 10:30am-12:30pm Friday, December 18. This date and time cannot be changed. A small part of the final exam may be cumulative.


Academic Honesty
Students are expected to be honest in their work and to abide by the Saint Mary's College Academic Honesty Policy. The policy may be found in your Student Handbook or on the Registrars Office Homepage under Academic Regulations and Policies of the College. Students found cheating on exams will lose the exam grade. A second incidence of cheating will result in an F in the class. Because of the temptations offered by cell phones, no cell phones will be allowed in class during an exam and the appearance of a cell phone is cause for a grade of zero on the exam. Plagiarism will be considered a reason for severely lowering the grade and will result in a zero on the assignment if it continues. If you do not understand the concept of plagiarism, it would be good to discuss this with me prior to writing your paper. You may also see the following guide from the University of Toronto for more information on plagiarism: (http://www.utoronto.ca/writing/plagsep.html).

Class and Lab Attendance
Attendance in class is expected for the first section and mandatory for the genomics and presentation sections. Please contact me if you need to miss class for any reason. For an excused absence, you are expected to get notes from your lab partner/class mate and you are responsible for the material. If you do not understand the lecture/lab, be sure to make an appointment to see me.

Unexcused class absence will result in a lowering of your grade using the following scale:
First four weeks: 2 missed classes = 25 point loss (~ ½ of a letter grade).
Genomics 8 weeks: 1 missed class = 25 point loss.
Presentation weeks: 1 missed class = 25 point loss.
Lab: 1 missed lab = 25 point loss.

Course Cancellation Policy
I will make every effort to be in class on time, as I expect the same effort will be made by you. If the situation arises so that I must cancel class, I will ask Mrs. Kosek leave a note on the board and contact you through email.

Lecture and Lab Schedule (Tentative)
Week     Date         Lecture Topic                                                                 Readings                                         Assignment Dates
Week 1  Aug 25      Introduction, History, Microbial Biotech                             Chapter 1, 2, 5                                Ethanol Plant Assigned
             Aug 27      Microbial Biotech                                                            Chapter 5
Week 2  Sept 1       Recombinant DNA Technology, Sequencing                     Chapter 3
             Sept 3       Microbial Biotech                                                            Chapter 5
Week 3  Sept 8       Plant Biotech                                                                 Chapter 6
             Sept 10     Plant Biotech                                                                 Chapter 6                                         Ethanol Plant Essay Due
Week 4  Sept 15    Animal Biotech                                                                Chapter 7
             Sept 17    Animal Biotech                                                                Chapter 7
Week 5  Sept 22    Exam 1                                                                                                                                  Exam 1
             Sept 24    Genomics                                                                       Chapter 9 and extra readings.
Week 6  Sept 29    Genomics                                                                                                                              Assignment Dates announced in class.
             Oct 1       Genomics                                                                             
Week 7  Oct 6       Genomics
             Oct 8       Genomics
Week 8  Oct 13     Genomics
             Oct 15     Genomics                                                                                                                               Present. 2- Topic Due
Week 9  Oct 20     Fall Break- NO LAB Oct 19-23
Week 10 Oct 27    Genomics
              Oct 29    Genomics
Week 11 Nov 3      Genomics
              Nov 5      Genomics
Week 12 Nov 10    Genomics
              Nov 12    Genomics
Week 13 Nov 17    Genomics
              Nov 19    Genomics
Week 14 Nov 24    Presentation I
              Nov 26    THANKSGIVING – NO CLASS/LAB
Week 15 Dec 1     Presentation II                                                                                                                            TBA
              Dec 3     Presentation III                                                                                                                           South Bend Med. F.
Week 16 Dec 8     Presentation IV                                                                                                                          Wrap Up/Review
              Dec 10   Presentation V