Chitra Chandrasekaran- Texas Wesleyan University
Genomics at Texas Wesleyan University
Due to the small size of our institution, a stand-alone course in genomics was not possible. Thus, a 4-5 week annotation project was incorporated into a required junior/senior level course in Molecular Biology (Biology 4412, taught by Dr. Chitra Chandrasekaran). This was the first class in which I have used the GEP annotation materials. The class had 6 students enrolled; all were junior and/or senior standing.
Comments Time: The timing of the course and lab worked out very well for us, as students had ample time to each complete their own annotation project. Class meets twice a week, 75 min each, and the lab meets once a week for 3 hours. We used the last 4-5 weeks of the semester for annotation alone.
Projects versus Exercises: The basics of molecular biology had already been covered in the first half of the course. In preparation for the annotation, we started by doing a paper review of the Drosophila genomes paper from the recent issue of Nature, and then we used a modified version of the D. erecta annotation exercise that has been posted on the GEP web site. We did it as a class presentation, as opposed to a homework exercise, and that helped considerably. After that, I basically let them explore on their own using their assigned fosmid.
Outcomes: All the students prepared oral presentations for the class and submitted a written report. Student engagement appeared to be extremely high--I had to chase them out of the computer labs, which is highly unusual! All students were able to resolve issues in their fosmid, and more importantly, identify the ambiguities.
Future: I plan to continue using the annotation projects in the next version of this course (offered Spring 2009). I hope to also incorporate finishing--we were not able to do that because of computer difficulties, which should be resolved this summer.
Biology 4412 Syllabus
'TEXAS WESLEYAN UNIVERSITY
SYLLABUS' Biology 4412-01: Techniques in Molecular Biology
Dr. Chitra Chandrasekaran
Rm113 Schollmeier Science and Technology Building
and by appointment
Biology 4412 is a laboratory-based course designed to familiarize students with the techniques of molecular biology including restriction enzyme analysis, Southern blots, DNA sequencing , the polymerase chain reaction, and cloning. Data interpretation is a strong component of this course. (University Catalog) There is an essential laboratory component where you will perform some of the techniques that are discussed in the course. This is an upper level biology course, and the strongly suggested prerequisites for this course are: Biology 1321, 1322, 2323, 2324 or their equivalent; any Biology 3000 level course, and two years of chemistry. You need to contact me if you do not have these prerequisite courses.
Class meets TTH 9:25-10:40 (SST Rm108) Lab meets W 1:30-4:30 (SST Rm108/McF206). Course web site: http://department.txwes.edu/cchandrasekaran/Biology4412.htm
Students who take this course should achieve: • Competence in laboratory and analytical skills.
• Understanding of principal concepts of the discipline.
• Ability to communicate scientific information in both written and oral forms.
• Ability to read and evaluate the professional literature.
• An understanding of the role of biotechnology in society
• The ability to conceive and design independent laboratory experiments
Pedagogical approaches will include:
• Classroom Lecture
• Laboratory investigations
• Computer applications and investigations
• Inquiry based and problem solving (critical analysis)
• Use of the course Web site
Course requirements You are required to purchase a lab notebook for the lab component of the course (more information will be available on this on the first day of class). There is no assigned textbook for the course; supplementary materials will be assigned for reading and these are required. There will also be information that is required for the class that is not covered in the assigned text. Therefore, regular attendance is critical for successful performance in this course. Since there is a great deal of material that you are expected to know for this course, merely coming to lecture will not ensure a good performance. You need to actively keep up with the material. It is extremely helpful to form study groups with other students to review the material. It is a good idea to obtain the phone numbers of two other classmates whom you can call if you must miss class. If you have any questions about the material, please come by during my office hours or schedule an appointment. Waiting until the week before the exam to cram does not work.
NOTE: Pagers and Cellular phones must be turned off and/or in "quiet" mode in class. iPODs and other portable MP3 players must be turned off while in class. No Bluetooth or other remote communication devices are allowed while in class. If you must leave the room to answer a call, do so quietly.
Grading Midterm Exam I: 20%
Final Exam (comprehensive): 25%
Lab notebook: 15%
(Notebooks will be graded 3 times this semester, unannounced)
Assignments/Problem Sets: 15%
Gene Annotation Project (Genomics): 25% oral presentation: 10% written paper 15%
• No make up exams or assignments will be permitted unless previously arranged with the instructor.
• Grading is based on a standard system (90-100 is A range; 80-90 is B range etc.). Use these ranges to monitor your performance as you progress through this course!
• Assignments are due at the beginning of the class or lab period. Late assignments are treated in the following way: turned in by end of class: 5% deduction turned in by end of day (5 pm): 10% deduction turned in the following day: 30% deduction more than 2 days late: grade of zero for the assignment
•Plagiarism: Please refer to the University Catalog for a definition of plagiarism and the penalties for engaging in plagiarism. For any assignment in this course, the following policy applies: First offense: plagiarized paper will be returned and it must be rewritten within 24 hours. A 15% penalty will be applied to the paper. If the paper is not rewritten within this time, the paper will receive a zero. Second offense: paper will receive a zero.
Regrade policy: If you feel that there has been a grading error on your exam, you will need to submit the ENTIRE exam to me, with a sheet attached to the front detailing the problem you feel has been graded incorrectly. I will regrade the ENTIRE exam, not just the problem in question (so your grade could go up OR down). If there has been an arithmetic error on my part, I will correct it on the spot.
Attendance: In accordance with the attendance policy at Texas Wesleyan University, regular and punctual attendance at all scheduled classes is expected of students. If a student must miss class due to a university-authorized absence, the student must inform the instructor prior to the absence. If this procedure is not followed, the absence will be considered unexcused. If an absence occurs as the result of an unanticipated event (illness, accidents, etc), it is the responsibility of the student to inform the instructor and explain the problem. Failure to clarify the absence immediately upon the student's return will result in the absence counted as unexcused. If possible, you need to contact me or the department secretary by phone within 24 hours of missing the class. If a student decides deliberately not to attend class, the absence is unexcused. If homework or an exam is scheduled on this day, the student will receive a zero for the assignment. Habitual tardiness will not be tolerated and result in a dismissal from class.
Policies Students should read the current Texas Wesleyan University Catalog and Student Handbook to become familiar with University policies. This includes but is not limited to grade appeal, sexual harassment, student access to records, and others; policies specified in the current catalog are applicable unless otherwise stated in this syllabus. Texas Wesleyan University adheres to a disability policy consistent with relevant federal law. The University will provide appropriate accommodation as determined by the Director of the Counseling Center, Dr. Michael Ellison. Students must notify instructors of any permanent or temporary disability and must provide documentation regarding those disabilities prior to the granting of an accommodation. For assistance, students should consult with Dr. Ellison.
Course syllabi are intended to provide students with basic information concerning the course. The syllabus can be viewed as a ‘blueprint’ for the course; changes in the syllabus can be made and students will be informed of any substantive changes concerning examinations, the grading or attendance policies and changes in project assignments.
Safety note :You MUST read the laboratory safety guidelines handed out. Due to the limitless variety of potentially hazardous chemicals which may be found in a scientific or other laboratory environment, students having known, or potential, health-related concerns, such as allergies, asthma, contact dermatitis, pregnancy, or other physiological sensitivities should check with their physician on the advisability of laboratory work. The instructor and/or chair of the teaching department will provide, upon request, a list of the chemicals that will be used in experiments during the semester. More detailed information (that is, Material Data Safety Sheets) will be furnished by the chairpersons upon written request.
Most of the readings for this course will come from an Online Molecular Biology text: http://www.web-books.com/MoBio/. Additionally, I will assign other texts as needed throughout the semester, as well as primary literature resources. The syllabus can be viewed as a ‘blueprint’ for the course; changes in the syllabus can be made and students will be informed of any substantive changes concerning examinations, the grading or attendance policies and changes in project assignments.
1/17-2/12: Introduction to course (1 day), Topics relating to DNA Readings: 1. DNA structure: Chapter 3 in online Molecular Biology text, sections A and B
2. DNA packaging: Chapter 3 in online Molecular Biology text, section D
3. Repetitive DNA: Chapter 3 in online Molecular Biology text, section G
4. DNA replication: Chapter 7 in online Molecular Biology text, sections A and B
2/14-3/4: Start on Topics relating to RNA Readings: 1. RNA structure: Chapter 3 in online Molecular Biology text, section C
2. mRNA and genetic code: Chapter 3 in online Molecular Biology text, section E
3. Gene structure: Chapter 3 in online Molecular Biology text, section F
4. Transcription: Chapter 4 in online Molecular Biology Text, sections A, B, and C
3/5: Midterm I ( DNA and RNA) (midterm is during lab period--note this is a Wed!)
3/10-3/14: Spring Break (no class or lab meetings this week)
3/18-3/19: Topics related to Proteins Readings: 1. Protein Structure: Chapter 2 in online Molecular Biology text, sections A-E 2. Translation: Chapter 5 in online Molecular Biology text, section C
3/24-4/22: Genomes and Annotation: The Drosophila Annotation Project (Washington Univ) Readings: Evolution of genes and genomes on the Drosophila Phylogeny. (2007), Nature 450: 203 Other required material at the course web page (http://department.txwes.edu/cchandrasekaran)--follow the link for Biology 4412
4/23 (Wednesday): Presentation of Oral Annotation Projects (Power Point)
4/29: Review for Final Exam, Final Written Annotation Project Due TODAY
Biology 4412 Laboratory Schedule:
This schedule is subject to change, and students will be informed of any and all changes in a timely fashion. Note that some lab work will be done on lecture days and vice versa. Links on this page will take you to the necessary lab protocols, papers, and worksheets. Please let me know if any of these links are not functional.
January 23: Introduction to the Laboratory Calculations of Solution Concentration (worksheet)
January 30: Laboratory 1: Isolation of Drosophila DNA
January 31: Laboratory 2: Amplification of Drosophila DNA (Thurs)
February 6: Out all week
Feburary 13: Lab 2: Amplification of Drosophila DNA Pour gel for electrophoresis today and store O/N lecture (to make up for absence) February 14: Run gel for PCR (Thursday)
Feburary 20: Laboratory 5: Verification of plasmid inserts
February 26: Laboratory 6: Sequencing plasmid inserts ( preparation) (Tues)
Feburary 27: Laboratory 6: Sequencing plasmid inserts (analysis)
March 5: Exam I (no laboratory assignment)
March 12: Spring Break Holiday
March 19: Lecture (no laboratory assignment--lab will end at 3:00 pm that day)
March 26: Introduction and prep for Laboratory 2 • Laboratory 2: Analysis of Gene Structure by RT-PCR
April 2, 9: Complete Laboratory 2, Work on Genome Annotation Projects
April 16: Open day to work on Genome Annotation Projects in lab
April 23: Presentation of Genome Annotation Projects in lab
- Laboratory Notebooks MUST be turned in on the day of the final in order to receive a grade for the course.