Topics in Advanced Genetics

(Example from Fall 2012)

This course is designed to follow an introductory course in genetics and molecular biology
(BZ350, LS201 or SC330), for advanced undergraduates or beginning graduate students wishing
to pursue advanced topics in genetics. Gene systems in diverse model organisms will be
covered, including those of prokaryotes, fungi, plants and animals. The course is not intended to
be comprehensive– rather, a number of topics will be covered in some depth. Reading materials
for this course will be made available electronically on RamCT. We will also be using material
from textbooks that are available on line. We will note which textbook a figure is taken from, you
can access the relevant portion at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books
One goal of this course is to demonstrate the range of biological problems that can be addressed
using classical and molecular genetics. Another goal is to have students critically evaluate and
present a scientific paper from a leading journal on a topic in genetics. Grades will be based on a
total of 500 points. In Dr. Bedinger’s half of the course, one 10 point pre-quiz, three problem sets
(10 points each), and two 80 point exams will be given. Dr. Garrity’s half will involve four
problem sets (10 pts each) and two 80 point exams. In-class activities will be worth 20 points.
Students will also make a PowerPoint presentation of a recent journal paper, worth 80 points.

COURSE TOPICS

  • Molecular techniques: Analyzing DNA (including genomes), RNA and proteins
  • Genetic techniques: Identifying and analyzing mutants, forward and reverse genetics
  • Bacteria, not as simple as you think
  • Advantages of prokaryotic systems
  • Chemotaxis, a simple signal transduction pathway
  • Saccharomyces cerevisiae (budding yeast), a unicellular eukaryote
  • Gene replacement and artificial chromosomes
  • Dissection of the cell cycle
  • Arabidopsis thaliana, a plant model
  • Plant strategies in development
  • How does an organ know what it is? Floral organ development
  • Development and disease: using genetics to dissect developmental processes
  • Caenorhabditis elegans, a simple multicellular organism
  • Building a genetic pathway: vulva development
  • Drosophila melanogaster, genetic tools extraordinaire
  • Genes that interact: eye development
  • Zebrafish (Danio rerio), new insights into vertebrate development
  • Is organogenesis modular?
  • Mouse, models for human disease
  • The power of targeted mutagenesis: Hox genes and body plan
  • Stem cells, the potential and the problems, Cancer and genetics

Lectures

  • Introduction to model organisms
  • Analyzing DNA and cloning
  • Genomic
  • Analyzing gene expression – RNA
  • Microarrays, Review quiz on genetics and molecular biology
  • Analyzing gene expression – Proteins [Problem set #1 due]
  • Forward genetics: mutagenesis and analyzing mutants
  • Making transgenic organisms
  • Reverse genetics [Problem set #2 due]
  • EXAM 1 – molecular and genetic techniques
  • Bacteria as a genetic system
  • Bacterial chemotaxis I
  • Bacterial chemotaxis II
  • Yeast as a genetic system
  • Genetics of the cell cycle I
  • Genetics of the cell cycle II
  • Arabidopsis, a model for plant developmental genetics
  •  Floral organ formation I [Problem set #3 due]
  • Floral organ formation II
  • 5 EXAM 2
  • C elegans: a simple multicellular organis
  • Identifying essential genes
  • Vulva development: Ordering genes into a pathway
  • Drosophila: genetics extraordinaire [Problem set #4 due]
  • Genetic mosaics
  •  Eye development: suppressor and enhancer screens
  • Genomics: the Drosophila genome project [Problem set #5 due]
  •  EXAM 3 [Selection of scientific paper approved by this date]
  • Zebrafish: new insights into vertebrate development
  • Approaches to genetic screens in vertebrates
  • The genetic basis of organogenesis I
  • The genetic basis of organogenesis II
  •  Mouse as a premier vertebrate model [Problem set #6 due]
  •  Using transgenic tools [talk outline and reference list due]
  •  Mouse body plan – revelations of Hox gene mutants
  •  Mouse models of human disease
  •  Stem cells [Problem set #7 due]
  • 16 EXAM 4
  •  Regenerative medicine – recent advances
  •  Special topics

Last 4 class periods- Student Presentations

Grading.

1. Review quiz (10 points):
A list of genetic and molecular biology terms and basic problems from introductory genetics will
be presented the first day of class. An in-class quiz on this material will be conducted on
September 3, based on short definitions of a selection of terms and problems. This exercise is an
opportunity to refresh your memory and will allow the class to proceed at an advanced level.

2. Exams (4 X 80 points = 320 points)

Exams will be a combination of fill-in-the-blank, short answer, essay and problem-solving. You
will be expected to not only know definitions, but also to be able to apply your knowledge to
answering questions using genetic approaches

3. Problem sets (7@ 10 pts each)

Problem sets will consist of 4-6 questions covering the essential concepts of the previous week.
The idea is to get you thinking about how you could apply the material we cover in a new context.
The problems will focus on: 1) molecular techniques – which one to use when? 2) genetics of the
organism – what are the progeny and where did they come from? 3) genomics – what
information is out there and how do you get it?
Problems are due at the **beginning of class** on the due dates as listed on the schedule:

PLEASE NOTE: Once problem sets are turned in, we will go over the answers briefly in class.
Therefore, late submissions will not be accepted (whether you attend class or not.)

4. In-class exercises (20 points)

Part of our time in class will be devoted to problem solving, thought questions, or other active
learning exercises. Over the course, these are worth 20 points in total. You must be present in
class – and participating – in order to earn the points. We are not offering make-up for these
points.

5. Presentations (80 points):

Each of you will select a paper from a recent (2011-2012) Nature or Science or similar journal
that needs to be approved by Dr. Garrity or Dr. Bedinger by October 24. The paper needs to be
focused on a gene or set of genes. You will need to identify and READ at least three “support
papers” including review articles, previous work etc. A one-page outline of your talk, including
list of references, is due November 7. Each presentation should be 15 minutes in length.
Practice, and time yourself (it may be helpful to get together with other class members for this).
You should be using about 15 slides per presentation. Slides should be legible, interesting and tothe-
point (don’t make them overly complex). Drs. Garrity and Bedinger will be happy to offer
suggestions on drafts of talks, so long as you make appointments at least a week in advance of
your talk.

6. EXTRA CREDIT OPPORTUNITY- Genetics in the News

A total of 10 extra credit points is possible for students presenting news articles about genetics
(must include a genetic trait or gene or genome) to the class on Fridays (2 extra credit points for
each presentation). Articles should have been published in the popular press (not technical
journals) within the past 6 months, preferably even more recently. Presentations should not
exceed 2 minutes each, and there will be a maximum of five presentations each Friday.