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BIOL 422

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Biology 422 Advanced Genetics
Genome Structure, Function, and Evolution
Fall 2013

 

Tuesdays and Thursdays: 

9:45am- 11:00am

Location: See attached schedule

 

Instructor:

Dr. Gwilym Haynes

Office: 510 Mueller Laboratories

Email: gdh14@psu.edu

Office Hours: 10:00-11:00 AM Wednesdays, and by appointment

 

Course Objectives:

Biology 422 is a three-credit lecture and computer-based practical course that covers the mechanisms of genome evolution, chromosomal mechanisms of heredity, cytoplasmic and polygenic inheritance, genomics, and evolutionary genetics.

1. The overall goal is to be able to explain more advanced genetic phenomena at the phenotypic and genotypic level, and the historical discovery of these processes.

2. Students will be able to solve genetic problems associated with the phenomena discussed in the course.

3. Students will be able analyze ethical dilemmas in the field of genetics using the seven step method.

 

Course Components and Assessment:

The course will consist of four components, each with its own assessments.  Details of each assessment will be provided in class.

 

Section 1: GWAS and Next-generation sequencing

Students will learn about the new developments in next-generation DNA sequencing technology; and how the genomic data generated through such technologies is applied to identifying the genes and genomic regions underpinning traits of interest. Such traits include genetic disease, behavior and traits relevant to agriculture.   

Assessments:

GWAS assignment

Transcription and translation practical assignment 

Annotation of transcriptome practicals and assignments

Quiz #1

 

Section 2: Chromosome evolution

Students will learn about the various types of mutation that underpin chromosome evolution, how such mutations can spread through populations, and how these mutations can be used in the study of genetics. The section will also include the origin of sex chromosomes.  

Assessments:

Quiz #2

 

Section 3: Population genetics, speciation and the genetics of invasive species

Students will learn about the all-encompassing role that evolution plays in shaping genomes. This section will include chromosome evolution, population genetics, and the effects of selection on the genome. 

Assessments:

Selection detection practical and assignment

        Genetics of invasive species practical and assignment

        Quiz #3

 

Section 4: Human genetics and disease

Students will learn about then genetic basis of hereditary and infectious diseases, and some of the ethical issues surrounding the ever advancing genomic technologies. 

Assessments:

Ethics Assignment

Quiz #4

 

Material covered in this syllabus including due dates of assignments are subject to change.  Notification of any changes will be given in advance. 

 

Supporting Materials:

Text (optional): King, R. C., W. D. Stansfield, P. K. Mulligan 2006 A Dictionary of Genetics.  Oxford University Press, New York, NY.

National Library of Medicine's Genetic Home Reference website: http://ghr.nlm.nih.gov/

Wikipedia (http://www.wikipedia.org) is also a good starting point to get information on a new topic or a subject that you need to revise. Students, however, should never cite Wikipedia in any publication or report. Rather, they should use and cite primary literature sources (which are sometimes cited in Wikipedia articles).  

Course Web site: The online course materials for Advanced Genetics will be available on the ANGEL Site.  At this URL you can link to all materials for the course including the lecture schedules, lecture handouts, associated journal articles, and exam schedules.

Handouts: Handouts for the lectures in the course will be posted on the ANGEL site.  I will make every effort to post the handouts prior to lecture with adequate time for you to print the materials before class.  These handouts are provided as a supplement and should not be viewed as a replacement for coming to lecture or as full notes for the lecture.  The handouts will include figures that are difficult to reproduce as you are taking notes in class.  It is the student’s responsibility to take good notes that emphasize the important points raised by the instructor.

 

Grading:

 

The graded material for BIO422 is listed in the table below.

Assessment

Percent of final grade

GWAS practical and assignment

5%

Translation/Transcription Assignment

5%

Annotation of transcriptome (3 smaller assignments)

25%

Ethics assignment

15%

Detecting natural selection assignment

5%

Genetics of invasive species assignment

5%

Quiz #1

10%

Quiz #2

10%

Quiz #3

10%

Quiz #4

10%

Total

100%

 

 

Extra Credit (25 points): You may do additional summaries of journal articles or seminars for extra credit.  For each additional summary that you do, you will receive 5 points for a maximum of 25 points.

 

Makeup Examination Policy:  Attendance at examinations is mandatory and absence during the scheduled examination time will result in a grade of zero unless prior notification (i.e., telephone call, voice mail, email, etc.) has been made with the course instructor. 

The following are the only legitimate excuses accepted:

- a University sponsored event (with a note from the sponsor)

- an interview for a job or professional school

- a religious holiday recognized by PSU

- verifiable death in the family (e.g., obituary, funeral card - with a date)

- illness, As adults, it is your responsibility to provide reasonable verification; each situation is unique, and we are flexible. We STRONGLY recommend that you notify your instructor prior to the examination.  Note that Ritenour Health center will not provide you with a note for minor illnesses.

 

Make-up exams: A student will only be allowed to make up one regular semester examination.  The makeup examination must be done within a week of the originally scheduled examination.  Requests for multiple makeup examinations suggests a chronic problem.  Historically, most students who take make-up examinations do not perform as well as students who take the regularly scheduled examination.  I strongly encourage students to take the examinations at the regularly scheduled time.

 

Final Grade Assignment

Final grades will be assigned based on the total  points accrued from all assessed material in the course, as detailed in the table below. Note that point totals, not percentages, will be used in assigning the final grade.

 

 

Points

Percentage

Grade*

930-1000.0

93 – 100 %

900-  929.9

90 - 92.9 %

 A-

870-  899.9

87 - 89.9 %

  B+

830-  869.9

83 - 86.9 %

B

800-  829.9

80 - 82.9 %

 B-

770-  799.9

77 - 79.9 %

  C+

700-  769.9

70 - 76.9 %

C

600-  699.9

60 - 69.9 %

D

0-  599.9

0 - 59.9 %

F

*I reserve the right to adjust the grade cutoffs once all grades have been determined.  Major adjustments will only be made if the mean of the class falls below 70%.

 

Expectations:

Time commitment: 2.5 hours of lecture and/or computer practical classes each week (see class schedule), plus 6 hours per week outside of class for reading and solving practice problems.

 

Use of e-mail: 

E-mail is an effective way to handle brief communications, but it is not an effective means to communicate concepts, major ideas, or to discuss a student's performance in the course. Thus:

 

E-mail should be used by students to:

Point out any errors or oversights made by the instructor during lectures.

Set up an appointment to talk with the instructor if you cannot meet during regularly scheduled office hours.

Ask questions about lecture material that can be answered in one to two brief sentences.

 

E-mail should NOT be used by students to:

Ask for explanations about concepts, ideas, theories, laws, processes, or any other information that requires more than two short sentences of explanation. We can explain things and answer major questions much better by talking with you in person than via e-mail.

Ask about your points or grade -- if you feel that a grading mistake has been made, and then bring the graded exam or assignment to us so that we can discuss your concerns in person.

Provide final documentation for a missed exam or assignment. See the course policy regarding how to request a makeup exam.

 

Academic Integrity:

Each student is responsible for completing his or her own work except when directed otherwise by the instructor. Appropriate citations for work derived from the published literature must be included in papers. Plagiarism from other students, published books, articles or web pages (excessive use, or use or quotation without citation to the source) is unethical and will not be tolerated. Academic dishonesty is defined in the "PSU Faculty Senate Policies for Students" activities including but not limited to, “cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students.”. Failure to comply with these policies will lead to sanctions against the student in accordance with the Policy on Academic Integrity in the Department of Biology (http://www.science.psu.edu/academic/Integrity/Policy.htm )

 

Statement Regarding Disabilities:

As part of Penn State’s settlement with the National Federation of the Blind, all Penn State course syllabi going forward must include a statement regarding disabilities. 

Penn State welcomes students with disabilities into the University's educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact the Office for Disability Services (ODS) at 814-863-1807 (V/TTY). For further information regarding ODS, please visit the Office for Disability Services Web site at http://equity.psu.edu/ods/.

 

In order to receive consideration for course accommodations, you must contact ODS and provide documentation (see the documentation guidelines at http://equity.psu.edu/ods/guidelines/documentation-guidelines). If the documentation supports the need for academic adjustments, ODS will provide a letter identifying appropriate academic adjustments. Please share this letter and discuss the adjustments with your instructor as early in the course as possible. You must contact ODS and request academic adjustment letters at the beginning of each semester.

 

BIO422 Fall Semester 2013 Syllabus

 

Week

Day

Date

Location

Activity

Assessment

1

Tue

8/27/2013

216 Thomas

Lecture 1 - Introduction

NA

1

Thurs

8/29/2013

114 IST Building

Lecture 2 - DNA and genome sequencing methods and applications

NA

2

Tue

9/3/2013

216 Thomas

Lecture 3 - Recombination and genome wide association studies (GWAS)

NA

2

Thurs

9/5/2013

114 IST Building

Practical 2  - Transcription and translation

Practical Assignment - Transcription and Translation, due Mon 9/23/2013

3

Tue

9/10/2013

216 Thomas

Lecture 4 - Gene annotation and expression

NA

3

Thurs

9/12/2013

114 IST Building

Practical 1  - GWAS

Practical Assignment - GWAS, due Mon 9/23/2013

4

Tue

9/17/2013

216 Thomas

Lecture 5 - Genetic mutation and chromosome evolution (insertions, deletions and inversions)

NA

4

Thurs

9/19/2013

114 IST Building

Quiz #1 - NG Sequencing, gene annotation and GWAS

Quiz #1

5

Tue

9/24/2013

216 Thomas

Lecture 6 - Chromosome evolution (changes in ploidy)

NA

5

Thurs

9/26/2013

114 IST Building

Practical 3 - Transcriptome Annotation #1

Practical Assignment - Transcriptome Annotation #1, due Mon 10/14/2013

6

Tue

10/1/2013

216 Thomas

Lecture 7 - Chromosome evolution (translocation)

NA

6

Thurs

10/3/2013

114 IST Building

Practical 4 - Transcriptome Annotation #2

Practical Assignment - Transcriptome Annotation #2, due Mon 10/14/2013

7

Tue

10/8/2013

216 Thomas

Lecture 8 - Evolution of sex chromosomes

NA

7

Thurs

10/10/2013

114 IST Building

Practical 5 - Transcriptome Annotation #3

Practical Assignment - Transcriptome Annotation #3, due Mon 10/21/2013

8

Tue

10/15/2013

216 Thomas

Lecture 9 - Population genetics

NA

8

Thurs

10/17/2013

114 IST Building

Quiz #2 - Chromosome evolution

Quiz #2

9

Tue

10/22/2013

216 Thomas

Lecture 10 - The genetics of speciation

NA

9

Thurs

10/24/2013

114 IST Building

Practical 6 - Detecting natural selection in the genome (population genetics)

Practical Assignment - Population Genetics, due Mon 11/18/2013

10

Tue

10/29/2013

216 Thomas

Lecture 11  - The genetics of invasive species

NA

10

Thurs

10/31/2013

114 IST Building

Practical 7 - Genetics of invasive species

Practical Assignment - Invasive Species, due Mon 11/25/2013

11

Tue

11/5/2013

216 Thomas

Lecture 12 - Ethics and genetic information

NA

11

Thurs

11/7/2013

114 IST Building

Discussion - Ethics and genetic information

Essay assignment - ethics and genetics, due Fri 11/22/2013

12

Tue

11/12/2013

216 Thomas

Lecture 13 - Model organisms and their use in genetics studies

NA

12

Thurs

11/14/2013

114 IST Building

Quiz #3 -Genetics of populations, speciation and invasive species

Quiz #3

13

Tue

11/19/2013

216 Thomas

Lecture 14 - Epigenetics and parental imprinting

NA

13

Thurs

11/21/2013

114 IST Building

Lecture 15 - Human evolution and genetics

NA

14

Tue

11/26/2013

NA

Thanksgiving Break

NA

14

Thurs

11/28/2013

NA

Thanksgiving Break

NA

15

Tue

12/3/2013

216 Thomas

Lecture 16 - Genetics of the immune system

NA

15

Thurs

12/5/2013

114 IST Building

Lecture 17 - Genetics of HIV

NA

16

Tue

12/10/2013

216 Thomas

Tutorial - Practice questions for quiz #4

NA

16

Thurs

12/12/2013

114 IST Building

Quiz #4 - Model organisms, epigenetics, human genetics and disease

Quiz #4