Genetics (BY 3114) Spring 2013

MWF 10:00-10:50, MS 321 Lab: Thursday 11:55-1:45, 1:55-3:45, 3:55-5:45 MS 302 Instructor: Dr. Beth Conway, Assistant Professor of Biology; Office - McFarland Science 305A Office phone: 615-966-5741 Cell phone: 615-429-4601 (if texting, please identify yourself) E-mail: beth.conway@lipscomb.edu Office hours: Wed 9-10, 3-4:30; Thurs 12-4, Fri 11-2:30 Lab Instructor: Ms. Holly Spencer; holly.spencer@lipscomb.edu Required materials for course: Text book: Genetic Analysis: An Integrated Approach (Sanders and Bowman) Other: - A standard scientific calculator (have with you at all class and lab meetings) - A bound laboratory composition book - Laptops will be needed for research projects in some class and lab sessions; I will try to remind students ahead of time when it is necessary to bring laptops.

Course overview and objectives:

This course is designed to instruct students in basic and advanced genetic principles, including: 1) Inheritance Patterns, including Mendelian and non-Mendelian inheritance; 2) Molecular Genetics, including nucleic acid structure, function, and gene expression and regulation; 3) Modern genetic technologies, 4) Medical Genetics, and 5) Genetic analysis of individuals and populations. Additionally, students will use primary experimentation in the laboratory to predict and test inheritance patterns in organisms. Critical thinking will be emphasized in this course, both in the lecture and the lab. Learning Objectives 1. Identify patterns of genetic inheritance: Mendelian, nonMendelian, and Gene Interactions 2. Determine Gene Linkage; Map genes to chromosomes; understand the concepts of human linkage analysis 3. Perform statistical analyses on genetic data 4. Comprehend Delivery Lecture, major lab project, laboratory exercises, case studies Assessment Quizzes, Lab grades, major lab report grade, exams Goals Minimum Grade: 70%

Lecture, major lab project, laboratory exercises, case studies

Quizzes, Lab Grades, major lab report grade, exams

Minimum Grade: 70%

Lecture, major lab project, laboratory exercises Lecture, class

Quizzes, Lab Grades, major lab report grade, exams Quiz, Exam

Minimum Grade: 70% Minimum Grade:

Genetics at a Molecular level 5. Appreciate the importance of the epigenome to determining traits 5. Learn basic applications of Genetics to biotechnologies 6. Learn the genetic basis of human disease and cancer 7. Learn how genetic inheritance affects development, populations, and quantitative traits 8. Apply genetic concepts to critical thinking skills

discussions Lecture, class discussions, literature, Lab project Lecture, Class project Quiz, Exam, Lab Report

80% Minimum Grade: 70%

Exam, presentation of class project

Minimum Grade: 70%

Lecture, Laboratory exercise, case studies Lecture, laboratory exercises and project, case studies

Exam, Lab Grade, graded assignments Exam, Laboratory report, Graded assignments

Minimum Grade: 70% Minimum Grade: 70%

Major laboratory project: open-ended analysis of gene interactions

Major Lab report grade

Minimum Grade: 80%

Course requirements: Students must demonstrate understanding of the content covered in both class and laboratory. Students are expected to read the assigned chapter prior to coming to class and be prepared to participate in class discussions and exercises, as well as laboratory experiments. Major assignments to be completed throughout the semester include: 1. 3 regular exams (see schedule) 2. 1 comprehensive, final exam 3. Lab reports on 2 major lab projects 4. Laboratory exercises 5. Quizzes and assignments to assess understanding of assigned reading material and lecture content 6. Participation in class discussions Preparation for Class: Students are expected to read the assigned portion of the textbook in preparation for class each day. This will enable us to spend class time applying concepts that are already familiar. Please follow the reading assignment chart to prepare for class each day; failure to do so will diminish your ability to master the concepts we will cover this semester.

Assessment:
The following are predicted points but may be subject to change as needed to fit the course. 1. Pre-test: This 15-point test will be taken on Blackboard during the 2nd week of the semester, and will cover basic foundational concepts to Genetics that I expect students to have mastered upon matriculating into this class. All students that score less than 75% on this pre-test will be required to attend a remedial study session covering these topics, followed by a re-take of the pre-test.

2. Regular Exams: 3 regular-semester exams (50-100 points each) will be given after completion of each major course section (total: 250 pts) 3. Final, comprehensive exam (150 points) 4. Laboratory exercises: 2 formal lab reports/presentations will be due throughout the semester, together totaling approx. 80 points. 5. Quizzes and Assignments may be given throughout the semester (points TBD but not to exceed 30 points) 6. Estimated Total points for the semester = 540 7. The Final grade will be determined as a percentage of the total points possible as follows. Grades will not be rounded up; the instructor reserves the right to make objective judgment calls based on grade distribution patterns. 100-90.0% = A (499 or more out of 555 total points); 89.9-80.0% = B (444-498 out of 555 total points); 79.970.0% = C (389-443 out of 555 total points); 69.9-60.0% = D (333-388 out of 555 total points); less than 60% = F (332 points or less out of 555 total points). 8. Optional Assignments: Occasionally, the entire class will be given the opportunity to attend seminars or complete additional assignments for credit. However, no opportunities will be given to individuals that are not extended to the entire class, and the maximum allotment of extra credit points may not exceed 10 raw points for the semester for any individual.

Exam Policies:
Make-Up Exams: Students are required to be present for exams; make-up exams will NOT be permitted except in the case of school-approved excused absences or emergency situations. For excused absences, the student is responsible for alerting me as far in advance as possible as to his/her absence and scheduling a time to make up the exam. The instructor reserves the right to administer a make-up exam unique from the exam taken by the class. All exams must be made up within 3 days of the originally scheduled exam. Appropriate documentation must be provided for any missed exams. Only illnesses resulting in hospitalization, death of an immediate family member, or school trips are considered excused. Exams missed for all other reasons will result in a grade of 0 for that exam. Time Limits: Students with learning styles requiring additional time to take exams should present signed documentation from the office of academic advising early in the semester. In all other instances, exams must be completed within the regular class meeting time; additional time will not be given.

Attendance:
According to the university policy, missing the equivalent of 3 weeks of class (9 absences in lecture and/or lab combined), either for excused or unexcused reasons, will result in the student being automatically dropped from the class, NO EXCEPTIONS. Students are expected to keep up with their own absences, and may be dropped from the course without warning if the maximum number of absences is exceeded. If the maximum absences are reached or exceeded in the last 2 weeks of the semester, the students final semester grade will be reduced by one letter grade per absence exceeding the maximum . Excused absences should be cleared with the instructor prior to the class meeting, and all work should be made up by the student by the following class period. Tardiness is inconsiderate to both the instructor and to your fellow students and should be avoided at all costs. I reserve the right to penalize any student exhibiting a consistent pattern of

tardiness by lowering their academic average. Students will be given a warning before points are deducted. Lab attendance: Due to the complicated nature and the available of the laboratories, lab makeups will not be allowed, and students should make every effort to attend lab. Assume that labs will go the full 2 hours and do NOT schedule work, appointments, etc. during that time. Excused absences must be approved in advance, and the student should make arrangements to attend the alternate lab section if possible. During the weeks set aside for work on the independent project, times should be agreed by all members of each lab group- lab partners are expected to keep up with and report absences by other members of their groups in the final lab report; grades will be adjusted as necessary. Students Responsibility for Notification of Extended Absence In the case of individual absences, students should contact their professors directly. However, students who find themselves in circumstances which would cause them to miss classes for an extended period of time (e.g., missing a week or more of classes due to illness) should contact Steve Prewitt, Associate Provost for Student Academic Support, (steve.prewitt@lipscomb.edu; 615-966-5804). The Associate Provost for Student Academic Support will communicate the students situation to the appropriate faculty members. Students are expected to provide timely notification to the Associate Provost for Student Academic Support regarding any extended absence and may be required to provide supporting documentation for their absences.

General Information:
Etiquette: Cell phone use and Texting: Cell phone use is not permitted during either class or lab. Cell phones must be turned off or silenced during class and lab, and use of the cell phone during a class or lab session (including texting) will result in being marked absent for that class period. Cell phones must be turned OFF and put away during exams and other assessments. If the instructor observes a student using a cell phone for any reason during an exam, the student will automatically receive a 0". Cell phones may NOT be used in place of calculators during exams. Laptops: Laptops are permitted for taking notes during class and other class-relevant, instructordirected activities only. Please be considerate of those around you and realize that using your laptop for irrelevant purposes is a distraction to your peers. For this reason, I reserve the right to suspend laptop privileges to students who abuse the use of their laptops during class. Other technology: Recorders may be used in class to aid note-taking. No other technology (unless approved by the instructor) is permitted. Food and Beverages: Food or beverages should NEVER be brought into the lab; however, you may bring them into the classroom. Please be thoughtful of those around you and avoid distractions. Lab Safety: Close-toed shoes MUST be worn at all times while working in the laboratory. Food and drink are not permitted in lab. All hazardous waste must be disposed of correctly, and students may not leave the lab until work areas are completely and correctly cleaned. Academic Integrity Policy: As a Christian University, academic integrity is expected at all times. Unless explicitly stated, all work should be done independently and without collaboration with fellow students. Likewise, cheating on exams and outside assignments will not be tolerated and will result in academic consequences. Please see the Universitys Code of Conduct and Academic Integrity Policy in the

Student Handbook. Please be especially careful about plagiarism with any written or verbal assignments. Plagiarism penalties will be enforced whether it is intentional or accidental. Plagiarism will result in a grade deduction, depending on the severity of the case, and all cases will be reported to the academic integrity committee. Students Requiring Accommodations: If you have a diagnosed disability as defined by the ADA and are eligible for accommodations, please contact the Office of Disability Services at 279-1781 or 279-5737 within the first week of classes. Students who qualify for accommodations must provide a letter and a contract outlining and defining the required accommodations from the Office of Disability Services to the professor within the first two weeks of the semester. Dropping Courses: A drop/add form from the Office of the Registrar (Burton Bible Building 226) must be signed by both your course instructor and your advisor, which is then submitted to the registrar. Please check the Lipscomb website for specific deadlines for dropping courses. Class Schedule Disruption Policy Except in the rarest of instances, Lipscomb University does not cancel classes or close offices. However, should an event (weather-related or otherwise) occur that requires disruption of the entire Lipscomb University class schedule, students will be notified via multiple venues including the Lipscomb homepage (www.lipscomb.edu), a text message sent through LU ALERT (http://lualert.lipscomb.edu), and the Lipscomb Weather Information Line (9661836). For information on possible snow-related closures or late starts, students should consult local television stations (2-WKRN, 4-WSMV, 5-WTVF and 6-WZTV, and Channel 9 on campus). Students should look for information regarding Lipscomb University, not David Lipscomb Campus Schools. Instructor Assistance: Please do not hesitate to ask me questions during class or at any other time. I prefer students ask questions in person rather than over email, as explaining concepts over email is not often productive. I will make all efforts to be available to students with any questions or requiring additional help both inside and outside the classroom. However, students are expected to take careful notes during lecture and to study the lecture material regularly, so that questions may be clarified as soon as possible. If it is not possible to come to my office during regular office hours, you may email, call, or text me to set up an appointment at another time. Note: If sending me a text, please sign your name at the end of the message. No, I do not have all 2500 Lipscomb students in my address book.

Projected Course Schedule:

Date Chapter 1/7-1/11 1-2 1/10 Lab 1/11 2 Topic(s) Intro to Genetics; Single Gene Inheritance Introduction to Lab and Drosophila Genetics Genetics Pre-Test on Blackboard must be completed before class on 1/11. A mandatory review session will be held at 3 pm Wednesday 1/16 for all students scoring less than 75%. Independent Assortment, Chi-Square, Pedigrees, Probability Drosophila Inheritance Project (breed mutants) MLK Day; No Class X-linked inheritance Gene Interactions in Drosophila Project Gene Interaction Gene Interaction Gene Interactions in Drosophila Project (phenotype F1; F1xF1 cross) TGF-b/CF paper discussion Reading Assn Ch 1 (review); 2.1-2.2

1/141/18 1/17 1/21 1/23 1/24 1/25 1/28-30 1/31 2/1

2 Lab 3 Lab 4 4 Lab 4

2.3, 2.4 (skim), 2.5-2.6

Review 3.1-3.2; Read 3.3-3.5 4.1 (105-117), 4.2, 4.3 (122-123; 127133), 4.4

Read TGF-b in CF paper, focusing on main concepts

2/4 2/6 2/7 2/8 2/11-13 2/14 2/15 2/18-20 2/21 2/22 2/25-27 2/28 3/1 3/4 3/6 3/7 3/8 3/11-13 3/14

Lab 5 5 Lab 7-9 Lab 10 13 Lab

EXAM #1 (CHAPTERS 1-4) Open/Exam #1, cont Drosophila Inheritance Project Genetic Linkage and Mapping Mapping, Human Linkage and Lod Scores Drosophila Inheritance Project (phenotype F2) CAS Student Scholars Symposium Overview of Molecular Genetics Drosophila Inheritance Project Case Study: Sickle Cell Disease Chromosomal Abnormalities Drosophila Inheritance Project Human Karyotyping Simulation Lab Exam 2(Chapters 5, 7-10, 13) Exam 2, cont. Gene Regulation Drosophila Lab Reports Due Ghost In Your Genes Gene Regulation and Epigenetics Research Assignment: PubMed article search to find updated research on Ghost In Your Genes studies Assignment: Read Cancers Little Helpers and

5.1-5.3 5.5

Skim all chapters as review

13.1-13.4

15 Lab 15 Lab

15.1, 15.2-3

15.2-15.3 (focus on basic terms/concepts)

3/15

15

3/18-22 3/25-27

Complete questions SPRING BREAK Berdasco 2009 Paper Discussion

Read Berdasco 2009 paper before class; have discussion questions prepared 16.2-16.4 16.2-16.4 17.1 (562-567, 575581), 17.3 (586-88), 17.4

3/28 3/29 4/1 4/3-5

Lab 16 16 17

Begin DNA Methylation Project: Treat Cells Recombinant DNA Technology Recombinant DNA Technology Applied DNA Technology

4/4 4/8 4/10

Lab 17 17

DNA Methylation Project: Isolate DNA Ethics of DNA Technology Ethics of DNA Technology: BVVL Case Study

4/11

Lab

4/12 4/15

Part I: DNA Methylation Project: Measure DNA methyl. Part II: Genomics Simulations (bring laptops!) Genomics (continued from lab); bring laptops to class Exam 3 (Ch 15-17)

Read BVVL papers (Tennessean article and skim scientific article) and answer discussion guide Read 18.1-18.3 before lab; prepare for quiz over assigned reading

4/17-19

22

Population Genetics

22.1, 22.2-22.7 (major concepts, not math), 22.8

4/18 4/22 4/24 4/26 5/1

Lab 22

Methylation Reports Due Population Genetics: Bloodtyping Lab Population Genetics, Evolution Preparation for Final Exam STUDY DAY 9-11 AM; FINAL EXAM