Biology 5666: Evolutionary Genomics Fall 2013

Syllabus

Lecture: M, W 2:00 pm - 3:20 pm in Room 150 Biology Building
Instructor: Dr. Leos Kral (office: Rm. 145A Biology Building)
email address lkral@westga.edu
Note: Best way to contact me is by email. The least efficient way to communicate with me is to leave a phone message and expect me to call you back.
Office Hrs: Monday: 8:00 am to 10:00 am and 3:30 pm to 5:00 pm
Wednesday: 8:00 am to 10:00 am and 3:30 pm to 5:00 pm
Thursday: 8:00 am to 11:00 am
Text: Genomes 3
          by T.A. Brown
Web Site: http://www.westga.edu/~lkral/
This web site contains links to this syllabus and the WebCT site which contains additional course content, a course calendar, grade book and discussion area.

Note: Should any changes be made to this syllabus during the semester (such as changes in due dates, exam dates, or topics), these will be posted on the web site calendar, announcements and/or discussion area. It is your responsibility to log in at least once every  day.

Objectives: To impart an understanding of genomics research.

To impart an understanding of how genomics research is used to elucidate evolutionary processes acting on the genome.

To impart an understanding of how genomics research is used to explore evolutionary relationships between species.
Lecture Topics: Sequential topic listing of text based and other material. Note: this listing is subject to change during the semester.
  1. Introduction (Chapter1)
  2. Studying DNA (Chapter 2)
  3. Mapping Genomes (Chapter 3)
  4. Sequencing Genomes (Chapter 4 and additional material)
  5. Understanding a Genome Sequence (Chapter 5)
  6. Genome Replication (Chapter 15.2 - partial)
  7. Mutations (Chapter 16.1.1 and 16.1.2)
  8. Evolutionary changes due to mutations (gene trees, neutral vs adaptive mutations, identifying adaptive mutations - additional materials)
  9. Genetic Features of Eucaryotic Nuclear Genomes (Chapter 7.2.1 and 7.2.2)
  10. Mobile Genetic Elements (Chapter 9.2 and additional material)
  11. How Many Genes Are There and What Are Their Functions (Chapter 7.2.3)
  12. Origin of New Genes (Chapters 18.2.1 and 7.2.3 and additional materials)
  13. Lateral Gene Transfer (Chapter 18.2 and additional material)
  14. Evolution of Regulation of Gene Transcription (Chapters 6.1 and 11.3.2 and 10.2 and 10.3 and additional materials)
  15. Genome Defense (additional materials)
  16. Molecular Phylogenetics (Chapter 19 and additional materials)
  17. Other topics possible if time permits.
Exam Schedule: Exam 1: Wednesday, September 25
Exam 2: Wednesday, October 30
Final Exam (Exam 3):  Monday, December 9 at 2:00 pm
Writing Assignments: 1) Weekly Homework Questions
Answers due by 5:00 pm each Saturday for each week's homework assignments. Late answer sets will not receive credit.
2) Essay/Short Answer type exams
3) Scientific Literature based writing assignment.
Due dates will be given at the time these exercises are assigned.

Grading: Two hourly exams will be given during assigned class times during the semester and one final exam will be given during finals week. All three exams will cover lecture material from the text, lecture, and any research papers we may discuss. The final exam will only cover material presented after material covered on the second exam, but note that material is cumulative in nature. These exams will be of a "short answer/essay" type format.  Students are expected to take all exams. All exams will only be given at the scheduled times on the scheduled days. Missed exams will be assigned a score of 0 points. It is recognized that emergency situations can occur where missing an exam is unavoidable. What constitutes an emergency situation is at the discretion of the instructor. Therefore, check with the instructor ahead of time to see if your situation qualifies. With proper documentation of the instructor approved emergency situation, a makeup exam can be taken. This option only pertains to the two hourly exams. The final exam can only be made up if the student qualifies for a grade of I (incomplete) under the university guidelines. NOTE: if you miss an exam you must get in contact with the instructor within 24 hours (unless incapacitated) to offer an explanation. No makeups will be given if you delay past that time period.

Each hourly exam (including the final exam) is worth 100 points.

All weekly homework question answer sets will be worth 100 points in total. Each weekly answer set will be worth 100 points/(# of weekly question sets assigned). Note that you can not receive points for answering questions if you were not in class for that lecture on which the questions were based. Each weekly answer set must contain at least 300 words. If answers are too brief, not all points will be assigned. Also note that all answers are due by 5:00 pm each Saturday for each week's homework assignments. Late answer sets will receive 0 points. The answer sets will not be formally graded but answer keys will be provided by the instructor.

The Scientific Literature based writing assignment will be worth 100 points.

Your final grade in this course will be calculated from the exam scores and all writing assignments according to the following formula:

%grade = (Exam1 + Exam2 + Final Exam + Writing Answers points + Scientific Literature based assignment points)/500

Cheating will not be tolerated. Any student caught cheating will receive a grade of 0 points on that exam/assignment and that exam/assignment grade will not be dropped from the calculation of the course average. An F grade for the course may also be assigned at the instructor's discretion. 

There will be no extra credit assignments so donít ask.

Please Note: Grades are assigned on the basis of what you know as evaluated by exams and for writing assignments completed. If you have personal issues which prevent you from coming to class or studying, and subsequently, you do poorly on the exams and/or can not complete writing assignments, you are not entitled to a higher grade than your scores warrant due to hardship. If you can not devote the necessary time to this course, you should reduce your course load. It is better to do well over a longer period of time rather than badly in a shorter period of time.

Grading Scale: Percentage of all possible points:

A = 90% - 100%
B = 80% - 89%
C = 70% - 79%
D = 60% - 69%
F = less than 60%.

Attendance: Mandatory. Absences will result in loss of writing assignment points and thus lower exam grades.
How to Approach this Course:
  1. Come to class and pay attention. Listen for what is being emphasized.

  2. Read the text book, papers, PowerPoint slides and take careful notes of material presented on the black board.

  3. Don't just memorize but strive to understand. As much as possible ask yourself questions such as "why does this work ", "how does this work", "what are the relationships between x and y", etc. Visualize processes understanding their purpose and mode of action. Basically, just keep in mind that "knowing" something means "understanding and comprehending". It does not mean memorizing a bunch of words.

  4. Ask questions. If something is not clear, ask. Utilize office hours, ask during, and/or outside of class (but not before class), utilize the web based discussion area, or send me email (lkral@westga.edu).

  5. Form study groups to explore the material.

  6. Spend time studying and keep up. For best effect you should study at least 2 to 3 hours for each class period within a day of the class period. Studying for a few hours or even all night just before an exam is not sufficient to do well, or perhaps, even to pass the course.

 

Etiquette Rules:

  1. Do not carry on a conversation while lecturing is in progress. This is both rude and disruptive to others.

  2. Do not eat during class - the rustling of wrappers is disruptive to others.

  3. Come to class on time.

  4. Turn off or silence your beepers and cell phones.

  5. Do not bring children to class.

Communication:

  • All official communications from the University and from this instructor will be sent to your MyUWG email address. It is expected that you will access your email through the MyUWG portal on a daily basis. If I need to communicate with you personally about this course, I will do so by sending you email to your MyUWG account. Failure to read my emails will not be an excuse if a lack of response from you results in a lower grade in this course.