Biology 201: Genetics
Spring 2016, Davidson College

This is the public version of the syllabus. Enrolled students should go here for the complete version (login required)

MWF 9:30-10:20 in Chambers 1062
Lab Mon 1:30 or Tues 1:40 in Dana 256

Dr. Karen Hales
Dana 201A, x2324


Course schedule  go to Jan, Feb, Mar, Apr, May
Genetics news:
Science Daily Genetics
Genetics Literacy Project
The Scientist
New Scientist

Learning outcomes
By the end of the course, students will be able to explain, verbally and in writing, answers to the questions below. Students will be able to apply their knowledge toward formulating and articulating ethical arguments based on scientific evidence, as well as assessing the accuracy and plausibility of genetic descriptions in the news and in popular culture. In the laboratory students will be able to design and execute experiments that combine classical and molecular genetics of the fruit fly Drosophila melanogaster.

Resources and textbooks
We will use digital resources only for this class, with links in the course schedule below.
While no print book is required, you may benefit from having access to a recent Genetics text as background reference. Good options include Hartwell, Griffiths, Hartl, Hyde, Brooker, and Sanders and Bowman

Office hours
Mondays 11:00-12:00, Wednesdays 12:50-1:50 PM, and Tuesday Common Hours when I don't have other meetings. I can meet with you at other times if necessary--stop by if my door is open, or email to make an appointment (list three possible dates/time ranges).

Email: You are responsible for all information I send by email, so check your messages each day.

Grading: Your final course grade will be calculated as follows:

Two reviews
Daily quizzes
Two in-class presentations 
Lab presentation
Lab assignments
Lab report/poster
Final exam
Participation, effort, initiative
30% (15% each)
5%
15% (7.5% each)
7.5%
5%
10%
20%
7.5%

%
94-100
90-93.9
87-89.9
83-86.9
80-82.9
77-79.9
73-76.9
70-72.9
67-69.9
60-66.9
0-59.9
Course grade
A
A-
B+
B
B-
C+
C
C-
D+
D
F

Attendance and participation
In class I do not record attendance. However, if you are not there to participate, your participation grade is affected. Laboratory sessions are mandatory. An unexcused absence from lab will result in a full letter grade deduction from your course grade.

Honor Code
You are to affirm your respect for and compliance with the Davidson Honor Code on every assignment. The full Honor Pledge reads as follows: "On my honor I have neither given nor received unauthorized information regarding this work, I have followed and will continue to observe all regulations regarding it, and I am unaware of any violation of the Honor Code by others." Plagiarism is an Honor Code violation and is defined as representing another person's words and ideas as one's own. Please carefully read the Davidson Department of Biology statement on plagiarism for comprehensive information on what constitutes plagiarism and how to avoid it.

Classroom etiquette and use of electronic devices
Do not leave the classroom in the middle of class unless it is a true emergency (in lab it's fine to step out briefly at appropriate stopping points). Set cell phones to silent/no vibration so that they do not disturb or distract you or others. Take handwritten notes unless you have received my permission to use a laptop. Laptops, tablets, and cell phones must be closed or face down on your desk unless I have assigned you to investigate something on the internet during class.

Policy on recording of class
Davidson College policy prohibits audio and video recording of classes by students without permission of the instructor. I will consider permission requests on a case-by-case basis. For students with a disability, permission will always be granted when the accommodations authorized by the Dean of Students Office include recording. Authorized recordings are for the sole use of the individual student and may not be reproduced, sold, posted online, or otherwise distributed.

Disabilities
I will do my best to provide accommodations for students with learning or physical disabilities. If you have a learning disability documented by Davidson College, please let me know during the first week of class so that arrangements can be made. I encourage students with other disabilities to self-identify (confidentiality guaranteed) so that we may explore ways to enhance your learning.

Class materials
PowerPoint files used in class will be posted online by the previous evening. I use PowerPoint only to provide illustrations and outline some topics; viewing a PowerPoint file does **not** substitute for attending class. Click the link from the schedule below to download; log in with email credentials. To print, please first set options to include multiple slides per page.

Reading/listening/viewing assignments and study questions
Assignments on the syllabus relate to the topic of that day--you must read/listen/view and take notes on material before coming to class. Study questions are provided; it's to your benefit to write out answers, but they will not be collected.

Quizzes
There will be regular short written quizzes on the material assigned for that day. You may have two "pass" days for which your written quiz grade does not count.

Reviews
Reviews will be take-home, closed book, and closed notes, and typically due on the second class meeting after being made available. You may view the review only when you are ready to start it, and there is a two hour time limit. The final exam (also take home) will be designed to take two to three hours.

Presentations
Assigned groups of 3-4 students will collaborate on presentations twice during the semester in class, as well as once in lab. Each group must send me their powerpoint file by the beginning of the class session when they will present. The grading rubric varies by type of presentation and is explained in the schedule below in the entries for the relevant days.

Lab assignments
In lab you will turn in a short write-up or other assignment at the end of most lab sessions. The formal lab report at the end of the semester will be in the form of a research poster. See lab syllabus for details.

Penalty for late assignments
Ten percent per day or part thereof. The full ten percent penalty applies starting at the beginning of each day that the assignment is late; for example, an assignment that is one hour late will have a ten percent penalty applied.

Math and Science Center
The Math & Science Center (MSC) offers free assistance to students in all areas of math and science, with a focus on the introductory courses. Trained and highly qualified peers hold one-on-one and small-group tutoring sessions on a drop-in basis or by appointment, as well as timely recap sessions ahead of scheduled reviews. Emphasis is placed on thinking critically, understanding concepts, making connections, and communicating effectively, not just getting correct answers. In addition, students can start or join a study group and use the MSC as a group or individual study space. Located in the Center for Teaching & Learning (CTL) on the first floor of the College Library, drop-in hours are Sunday through Thursday, 8-11 PM, and Sunday, Tuesday, Thursday, 4-6 PM, beginning Sunday, August 30. Appointments are available at other times. For more information, visit http://sites.davidson.edu/ctl, or contact Dr. Mark Barsoum (mabarsoum or ext. 2796).

 

return to top

Course schedule
Go to Feb, Mar, Apr, May

Date

Topic

Links become active by the evening before class (use email credentials). If you print, conserve by printing double-sided with multiple slides per page.

Ppt links only available from the student version of the syllabus.

Assignments

Do the reading before class.
Be ready to explain the material.
Take initiative to look up terms and follow links within the sources for supplementary information.

Assignments and links are listed only in the student version of the syllabus. 

Study questions and additional resources

Study questions guide you toward the most relevant concepts in the assignments. I strongly recommend that you write out answers in your notes before coming to class, though they won't be collected.

Study questions are available only in the student version of the syllabus.

M 1/11

DNA structure

Read the whole syllabus. You are responsible for all the information and requirements detailed therein.

How do we know DNA is important?

DNA structure

Special assignment to be fulfilled by Wed January 20 at 4 PM: come see me in my office for five minutes. Make an appointment via Slotted. The purpose is to familiarize you with the location of my office and to help me get to know you. A visit must take place for me to record your grade on the first review.


W 1/13

RNA structure and protein structure

RNA structure

Protein structure


F 1/15 Transcription, RNA processing, and translation Transcription and mRNA processing

Translation


M 1/18

NO CLASS--Dr. Martin Luther King, Jr. holiday




W 1/20

DNA replication, mitotic cell division, and packaging of the genome

DNA replication

Mitosis

DNA packaging and coiling in the nucleus

Special assignment (office visit) due today.

Tomorrow night Thurs 1/21, plan to attend the Smith Lecture, details TBA
Two optional features on the lecturer, Dr. Leslie Vosshall:
The Sweet Smell of Success
Avant Garde Scientist



F 1/22

Genome projects

Human Genome Project

The many non-human genome projects


DNA sequencing by the Sanger method

M 1/25

How genomes are sequenced now Next generation DNA sequencing

Assembling whole genomes from short fragment reads

The $1000 genome and individual sequencing


W 1/27

Features and organization of genomes: how are we different and the same?

Techniques for typing genomes
Landscape of genomes

Important techniques for analyzing genomes

F 1/29

DNA fingerprinting

Surprises when typing someone--mosaicism and chimerism
DNA fingerprinting: typing STRs and analyzing allele frequencies

Mosaicism and chimerism


M 2/1

Intro to gene regulation: where, when, and why?

3D genome structure in the nucleus

Epigenetics: DNA and histone chemical modifications

Gene expression differences in time and space

3D genome structure in the nucleus

Epigenetics intro: DNA and histone modifications

W 2/3

Gene regulation: more on epigenetics

Epigenetic regulation that most genes undergo during development

For just a handful of a genes: imprinting

Epigenetics and X chromosome inactivation

Epigenetic changes from environmental effects

Example of epigenetics in other organisms

F 2/5

Gene regulation: transcriptional activation/repression, RNA editing

Transcriptional regulation

RNA editing

M 2/8

Gene regulation: RNA splicing and RNA interference Alternative splicing of RNA

RNA stability and degradation via RNA interference

W 2/10


Gene regulation: RNA localization, translation, and post-translational modifications

RNA localization within a cell

Translational regulation

Post translational modifications of proteins

F 2/12

Mutations--where, when, and how do they originally occur? How do we classify mutations at different levels?

Mutation mechanisms and DNA repair
Mutations 

DNA repair

M 2/15

How can mutations affect gene activity? Case study vignettes part I

Many genes can be associated with one disorder;
One gene can be associated with many disorders;
Extra or missing stop codons have unexpected effects


Effects of mutations affecting epigenetic regulation

W 2/17

How can mutations affect gene activity? Case study vignettes part II Disorders from defects affecting various gene regulation steps
Do not read these papers in their entirety. Read the abstract and introduction to get the big picture, and then figure out just the indicated specific data figures.

*Each group of students will be assigned a paper to focus on; in class you will explain the data. Everyone is ultimately responsible for understanding all four paper excerpts.


F 2/19

Meiosis

Larger scale mutations at the level of chromosome number

Meiosis

Chromosome number mutations

Take home review #1 on material through 2/17 (mutations and their effects on gene activity), available today and due W 2/24 at class time


M 2/22 Larger scale mutations at the level of chromosome structure Inversions

Translocations

W 2/24

Inheritance of mutations: Mendel's observations connect to meiosis and chromosome segregation

Chromosome segregation and allele frequencies in a population over time
Take home review #1 due today at 9:30 AM

Mendel and basic inheritance patterns

Connecting Mendel's observations to chromosome behavior

Extending Mendelian patterns to a population level

F 2/26

More on population genetics

The folly of the eugenics movement

Effects of selection on H-W equilibrium

Early 20th century eugenics movement


M 2/29

SPRING BREAK    

W 3/2

SPRING BREAK



F 3/4

SPRING BREAK



M 3/7

return to top

Probability assessment for single gene disorders in an affected family and in a population

Pedigree analysis

W 3/9

Interactions among alleles of a single gene; variations on dominance and recessivity

Penetrance and expressivity

Dominance and recessiveness; also lethal alleles


F 3/11

Linkage and independent assortment
Linkage and independent assortment


M 3/14

Early gene hunts: linkage mapping
Linkage mapping

Variation on recombination: Mitotic recombination


W 3/16

Newer gene hunt techniques Genome wide association studies (GWAS)

Exome or full genome sequencing

F 3/18

Genetic studies in model organisms are essential for understanding how human disease genes work

New gene editing techniques
Model organisms

CRISPR gene editing techniques

M 3/21

Quantitative genetics:
Multiple genes and the environment interact to govern complex traits like behavior

What is "heritability"?

Twin studies and controversies

Dissecting behavioral traits: OCD and autism


W 3/23

More on quantitative genetics and the genetics of behavior

Dissecting complex traits: artistic ability and sexual orientation
Follow some of the links within these stories to learn more about the data.

Take home review #2 on material through quantitative genetics distributed today and due W 3/30 at 4 PM.


F 3/25

Transgenerational epigenetic inheritance

How can epigenetic gene regulation pass through generations?


M 3/28

NO CLASS--holiday break



 

W 3/30

DNA testing: what happens at the doctor or at the online commercial service? Take home review #2 due today at 4 PM

Testing for disorders in adults and IVF embryos


Genetic tests during typical pregnancies

Direct-to-consumer DNA testing

In class we will plan ahead for presentations April 6-10


F 4/1

return to top

Genetic therapies for single gene disorders and cancer; pharmacogenomics

Therapies via gene addition, splice modulation, RNAi, or CRISPR

Pharmacogenomics


M 4/4

Cloning as a reproductive or therapeutic option; link to stem cells.

Cloning organisms; therapeutic cloning and stem cell connection

Cloning pets? Can scientists bring back a mammoth?


W 4/6

Amazing genetic adaptations in non-human organisms (group presentations)

Group presentations on curious genetic adaptations
Over the next three classes, each group delivers a 12 minute presentation on an assigned paper. Tell a story. Give brief background, explain in detail the most crucial data (be very selective so that you can be thorough), focusing on genetic mechanisms, and propose a future experiment.
Each group must email me their powerpoint by 9 AM on the day of the presentation.

Articles (group assignments will be listed here once determined):

Grading rubric:

Background info clear, relevant, concise, and complete: 10 pts
Most important data selected for highlighting: 10 pts
Experimental setup explained: 10 pts
Results and meaning thereof made logical and intuitive: 10 pts
Conclusion placing phenomenon in evolutionary big picture: 10 pts
Effective use of powerpoint (including annotating data figures): 10 pts
Public speaking and presence in front of an audience: 10 pts
Answering questions: 5 pts

Total possible: 75 points

F 4/8

Amazing genetic adaptations in non-human organisms (group presentations) Group presentations on curious genetic adaptations
Each group presenting today must email me their powerpoint by 9 AM.

M 4/11

Amazing genetic adaptations in non-human organisms (group presentations)

Group presentations on curious genetic adaptations
Each group presenting today must email me their powerpoint by 9 AM.

Afterwards we will plan ahead for film presentations April 25-26 (see below). See me by M 4/18 if your group cannot obtain or access your film through the library or other method.

W 4/13

Bacteria and our microbiome

Horizontal gene transfer

Bacteria and our microbiome

Horizontal gene transfer (HGT) in bacteria

HGT beyond bacteria

F 4/15

Genetic modification of microorganisms Recombinant DNA technology


What was the public discourse when genetic modification first began
?

Uses for genetically engineered microbes

M 4/18  

Genetic modification of animals Transgenic animals for human health applications

Transgenic animals for food

Do gene-edited organisms count as transgenic?

W 4/20

Genetic modification of plants

How food has been modified genetically in traditional agriculture

Current more precise technologies

***Focus on the * items below and skim the rest for the main ideas

Engineering for pest/pathogen resistance

Engineering for other agricultural reasons

Engineering for human health benefits


F 4/22

Genetic modification of plants

Taking a science-based approach on a fraught topic


M 4/25

Genetics in pop culture I (group presentations)

Film presentations
Over the next two class periods, each group delivers a 10 minute presentation on depictions of genetics in an assigned film. Your presentation must include short relevant clips plus analysis of the genetics portrayals and their plausibility or not.

By 9 AM on the day of your presentation, email me a document with a detailed outline of your presentation and bibliography of any additional sources you used. List the exact coordinates of the film clips you will include.

Films (group assignments will be listed here once determined):

 Grading rubric for presentations:

Very brief overall summary of film: 5 pts
Framing of the context for genetic concepts in film: 15 pts
Selection of appropriate clips (in terms of content and length): 10 pts
Analysis of portrayal of genetic concepts: 15 pts
Discussion of effect of portrayal on public understanding of genetics: 15 pts
Public speaking and presence in front of an audience: 10 pts
Answering questions: 5 pts

Total possible 75 points

W 4/27

Genetics in pop culture II (group presentations) Film presentations
By 9AM on the day of your presentation, email me a document with an outline of your presentation and bibliography of any additional sources. List the exact coordinates of the clips you will include.
 
F 4/29 Dr. H is out of town, but you will meet to discuss ethics, film portrayals, and other assigned topics.
In class meet in your lettered groups from 9:30-9:55, then numbered groups 9:55-10:20. Be ready to report back on Monday.

M 5/2
return to top
Genetics into the future. Course evaluations.


W 5/4 Question and answer session in preparation for final.

F 5/6- Th 5/12

Take home final exam, due at 3:00 PM on Thursday May 11th.


 

return to top


Davidson Biology

Davidson logo
Dr. Hales's home page

Copyright 2015-2016 Department of Biology, Davidson College, Davidson NC 28035