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PBIO 4500/5500: BIOTECHNOLOGY & GENETIC ENGINEERING (3 credits) .... engineering of insect-resistant plants; Genetic engineering of “golden rice” ...

Time & Place: Tuesday & Thursday 12:00-1:20 PM; Irvine 114

Instructor: Allan Showalter Fall 2016

Text: Molecular Biotechnology (4th Edition) ©2010 by Bernard R. Glick, Jack J. Pasternak and Cheryl L. Patten

Course web site:

Prerequisites: PBIO1140 or BIOS 1700

Course Description: The purpose of this course is to introduce students to basic molecular biological concepts and techniques used in the fields of biotechnology and genetic engineering. Current experimentation and progress in these fields as well as ethical considerations of this research will be discussed.

Learning Objectives: • Gain an understanding of basic molecular and cellular biology concepts and techniques. • Gain an understanding of current experimentation in biotechnology and genetic engineering. • Gain an appreciation and knowledge of how to deal with ethical issues relating to science. • Learn how to conduct a comprehensive literature review on a biological topic. • Learn how to read and understand primary publications in the scientific literature. • Learn how to present scientific research data to an audience.

Grades will be based on the following:

1. A midterm exam on the first third of the course (100 points). 2. A midterm exam on the second third of the course (100 points). 3. A comprehensive final exam (100 points). 4. A graded, in-class presentation on a biotechnology or genetic engineering topic, preferably a controversial one, to be approved by the instructor (100 points for PBIO 4500 students and 50 points for PBIO 5500 students). Each student will have to prepare a one-paragraph abstract of his or her presentation and a list of relevant references (including the article titles) for distribution to the class. Graduate students enrolled in the course will additionally have to submit an 8- 10 page double spaced paper (50 points) on their chosen topic following the format of a review paper in Nature Reviews Molecular Cell Biology (, being sure to include complete article titles for all references. 5. Homework (100 points). See assigned homework problems and instructions for completing them on page 5 of the syllabus. Answers will be posted on the course web site after the assignment due date. 6. Pop quizzes (variable point values). The instructor reserves the right to give pop quizzes covering the required reading material and the previous lecture material.

Thus, excluding quizzes, there are 500 points possible. Typically, 93.3% and above will earn an A, 90-93.3% an A-, 86.7-90% a B+, 83.3-86.7% a B, 80- 83.3% a B-, 76.7-80% a C+, 73.3-76.7% a C, 70-73.3% a C-, 66.7-70% a D+, 63.3-66.7% a D, 60-63.3% a D-, and below 60% an F.

Exams will be based upon material covered in class lectures as well as in the assigned readings. Office Hours: By appointment, Porter Hall-Room 504 (phone: 740-593-1135 or email: [email protected])

Academic Conduct/Misconduct: The penalty for course-related academic dishonesty (i.e., cheating on exams, plagiarism, etc.) will be failure of the entire course along with a report of the incident being sent to University Judiciaries. Note that University Judiciaries may impose additional sanctions, and students may appeal academic sanctions through the grade appeal process. Cell phones must be turned off during class; violators will be asked to bring treats for the class.

Attendance Policy: Attendance is highly recommended. Any absences must be well justified and explained to the instructor in advance in order to make up any of the graded material.

Intellectual Property: The lectures, classroom activities, and all materials associated with this class and developed by the instructor are copyrighted in the name of Allan Showalter on August 26, 2016.

Accommodations for Students with a Disability Policy: Any student who suspects s/he may need an accommodation based on the impact of a disability should contact the class instructor privately to discuss the student’s specific needs and provide written documentation from the Office of Student Accessibility Services. If the student is not yet registered as a student with a disability, s/he should contact the Office of Student Accessibility Services.


Instructor: Dr. Allan Showalter


1 Aug. 23 1 Introduction Aug. 25 2 DNA, RNA and protein synthesis

2 Aug. 30 3 Recombinant DNA technology Sept. 1 3 Recombinant DNA technology

3 Sept. 6 3 Recombinant DNA technology Sept. 8 4 DNA synthesis, amplification and sequencing

4 Sept. 13 5 Bioinformatics, genomics and proteomics Sept. 15 5 Bioinformatics, genomics and proteomics

5 Sept. 20 6, 7 Prokaryotic & eukaryotic gene expression Sept. 22 - Exam I

6 Sept. 27 9 Molecular diagnostics Sept. 29 10 Protein therapeutics

7 Oct. 4 11 Nucleic acids as therapeutic agents Oct. 6 12 Vaccines

8 Oct. 11 13 Genetic engineering of microbes Oct. 13 13 Genetic engineering of microbes

9 Oct. 18 14 Bioremediation and biomass utilization Oct. 20 16 Microbial insecticides

10 Oct. 25 - Genetic engineering of plants: methodology Oct. 27 18 Exam II

11 Nov. 1 19 Engineering plants to overcome stress Nov. 3 20 Engineering plant quality and proteins

12 Nov. 8 21 Transgenic animals Nov. 10 21 Transgenic animals

13 Nov. 15 22 Regulating the use of biotechnology Nov. 17 23 Societal issues in biotechnology

14 Nov. 22 - Class presentations Nov. 24 - No Class (Thanksgiving Break)

15 Nov. 29 - Class presentations Dec. 1 - Class presentations

Dec. 8 (Thursday) - Final Exam (10:10 AM)

* Assigned readings are from chapters in your text, Molecular Biotechnology (4th Edition) ©2010 by Bernard R. Glick, Jack J. Pasternak and Cheryl L. Patten. SOME SUGGESTED TOPICS FOR YOUR CLASS PRESENTATIONS (This list is merely a guide for potential topics; please consider other biotechnology/genetic engineering topics that interest you at present or as the course progresses. Note that controversial biotechnology/genetic engineering topics are perhaps the most interesting as you can present the scientific information, the arguments “for” and “against” the technology, and your opinions.)

Finding effective drugs to treat tuberculosis using a genetically engineered luciferase gene Using the polymerase chain reaction to detect disease-causing agents (e.g., HIV) Using restriction fragment length polymorphisms to detect genetic diseases Using genetically modified organisms to clean up the environment Production of human pharmaceuticals in the milk of genetically engineered farm animals Treating human brain tumors by gene therapy with the thymidine kinase gene The production of biodegradable plastics in plants The production of antibodies (i.e., plantibodies) in plants for medical use The production of a particular human pharmaceutical in bacteria Cause, detection, and treatment of a particular genetic disease (e.g., cystic fibrosis) Genetic engineering of transgenic fish (e.g., salmon) with growth hormone genes Production of recombinant tissue plasminogen activator for treating heart attacks Engineering organisms with the jellyfish green fluorescent protein to follow development The human genome project and the ethical considerations associated with it Mammalian cloning (i.e., the cloning of sheep or humans or pets) The use of gene knockouts to determine gene function Enhancer trap experiments to locate tissue-specific promoters Genetic engineering of herbicide-resistant plants Genetic engineering of insect-resistant plants Genetic engineering of “golden rice” Genetically engineering of disease-resistant farm animals Human gene therapy for SCID (Severe Combined Immunodeficiency Disease) Genomics application(s) DNA microarrays and the identification of genes associated with specific pathways Genetic screening for human diseases Proteomics application(s) Embryonic stem cell research and its applications for treating certain human diseases Biology and molecular biology of Bacillus anthracis, causative agent of Anthrax Biology and treatment of H1N1 (swine) influenza Marathon mice

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PRESENTATION FEEDBACK (i.e., comments on the organization and clarity of the talk, the quality of the visual aids, the oral delivery/general "flow" of the talk, the scientific accuracy of the information presented, and whether sufficient background information was presented): ASSIGNED HOMEWORK PROBLEMS Complete and submit the assigned homework problems listed for each chapter on Tuesdays in class (or at the very next class meeting in the case of any holidays). Submit your answers as a printed word document; additional graphical information can be added by hand as needed. Once chapters are covered or introduced in lecture, homework assignments for those chapters will be due on the next Tuesday. Due dates may be adjusted by the instructor if necessary. Each chapter homework assignment is worth 5 points, resulting in 100 possible points for homework. Homework answers will be posted on the course web site after the assignment due date.

Chapter Questions 1 2,5,6,10 2 1,2,3,5,12 3 1,2,3,4,5,8,9,10 4 2,3,4,5,8,9,10,11,12,13,16 5 1,2,3,7,10,11,14,15,17,19 6 1,3,6,8,20 7 1,2,3,7,10,11,13,14 9 1,3,4,5,9,12,15,17,18,21 10 1,5,10,11,12 11 1,2,3,7,8,11 12 1,2,3,4,5,7,15,16 13 1,4,9,10,12,17 14 2,5,12,13 16 3,4,9,15 18 1,2,3,4,5,6,10,11,15,16 19 1,2,4,6,7,8,11,15,16 20 1,3,9,14,17,19 21 1,2,3,4,5,6,8,10,13,15 22 1,2,4,5,6,8,10,13 23 3,4,6,7,9,12,13