BIO 421 – Advanced Genetics
Fall 2016
Course Syllabus
Instructor: Dr.
Craig W. LaMunyon
Lectures: M/W 5:00 – 6:50 pm, Bldg. 15,
rm. 1807
Office: Bldg.
8, rm. 119
Phone: (909)
869-2273
Email: cwlamunyon@cpp.edu
Office Hours: M/W/F 10:00
–11:00 am; T/Th 4:00 – 5:00 pm or by
appointment
Text: There
is no text assigned for this course.
However, there are assigned readings.
Modern Genetics resides at the intersection of a
number of disciplines, including molecular and cell biology, genomics and
proteomics, developmental biology, evolutionary biology, agriculture, and
medicine. Whereas classical
geneticists were consumed with the construction of linkage maps to understand
the transmission of traits across generations, todayÕs geneticists are
identifying the DNA sequence of those mutated genes, studying the functions of
the encoded proteins, determining sets of genes that interact on a molecular
basis, and dozens of other fascinating aspects of modern genetics. In fact, genetics today is really a tool
- or set of tools - used in many areas of biology. In this course, we are going to study
these tools. Indeed, Cal Poly
Pomona is an institution that prides itself on practical applications, so we
will be examining how geneticists go about their studies. We will not be studying gene expression,
DNA replication, and the like. You
learned about those topics BIO 303 and BIO 310. With the preparation that you have
received in BIO303 and BIO310, we should be able to make some real
headway. Therefore, I will assume
that you already know the following topics: Mitosis and Meiosis, Mendelian and non-Mendelian
inheritance, recombination, DNA structure and replication, gene expression and
its control, and mutation. If you
feel that you are weak in any of these areas, I recommend that you spend some
time with a Genetics textbook and familiarize yourself with the material. I can make some suggestions for Genetics
textbooks, but BrookerÕs Genetics, Analysis and
Principles is a good source.
I will assign a number of readings from the primary research
literature. These will include
ÒclassicÓ studies that established given areas of genetics. The readings will also include more
contemporary papers that demonstrate current practices/concepts in
genetics. In some cases, the
readings will be difficult for you, perhaps because they were written ~100
years ago in English that is not familiar, or perhaps because they are
technically complex. You may need
to read over a section several times before you gain an understanding. Please work hard on the readings. Given
the central importance of the readings to the course, you should read them in
their entirety. Some will be the
subject of quizzes, and you should expect them to be represented on the
exams.
In
this course, I anticipate that you will learn the following:
1.
Mutational
analysis
2.
Gene
mapping using classical and modern molecular techniques
3.
Whole
genome sequencing
4.
Reverse
genetics
5.
Genome
editing
6.
Genomics
and Proteomics
7.
Epigenetics
8.
Quantitative
trait analysis
9.
Quantitative
trait locus mapping
10. Whole Genome Association studies
To further your learning experience in this course, I encourage you to
interrupt me with questions - either if you cannot follow my arguments or if
you want to challenge them (science requires alternative opinions/hypotheses!).
BIO303
(Genetics) but BIO 310 is also good to have prior to this course.
The lecture schedule will be posted on the
Blackboard. It will be updated for
each lecture, and you will find outlines there for each lecture. Also, I will post images from my PowerPoint
presentations on the website and announcements like upcoming quizzes.
There will be three exams in this course: 2 midterms and a final that is
not comprehensive. Each exam covers
approximately 5 lectures. The exams
are of equal value: 100 points each.
The exams will have both multiple choice and written questions. Please bring a ScanTron
form 882. In addition, there will
be quizzes based on five of the readings.
These quizzes are worth 5 points each for a total of 25 points. We will also have both announced and
unannounced quizzes that will be extra credit. While it is impossible to say at this
time, I anticipate approximately 20 pts of extra
credit quizzes. There will be three
problem sets during the quarter, each worth 10 points, for a total of 30
points. Your grade will be based on
355 points (300 for exams, 25 for quizzes on reading, and 30 for problem sets),
even though you may earn more points due to the extra credit quizzes.
There will be no make-up exams. Arrangements
can be made in extreme cases, but you must alert me before the exam.
Please note: the lecture schedule is highly
tentative. Please refer to the schedule in Blackboard for the future. It will give you the up-to-date topics
and readings as they appear.
|
Lecture |
Date |
Topic |
Reading |
|
1 |
Sept
26 |
Course
Introduction; review of Mendelian and non-Mendelian genetics |
|
|
2 |
Sept.
28 |
Discovering
genes: the importance of Thomas Hunt Morgan and Mutational analysis
Note added 10-3-16: Some of you wondered how RNA
interference works. Here is a
video: https://www.youtube.com/watch?v=cK-OGB1_ELE |
|
|
3 |
Oct
3 |
Genetic Mapping
and construction of genetic maps Quiz over Morgan and
Bridges, 1916 |
|
|
4 |
Oct
5 |
Note that we are a little behind and will not likely get very far
into this lecture materialÉ.Mapping by
2-factor and 3-factor crosses Handout for
mapping to a chromosome |
Brenner,
1974 (particular attention to 3-factor crosses for gene order) |
|
5 |
Oct 10 |
Quiz over Brenner,
1974 |
Brenner,
1974 |
|
Problem set 1
– Due October 17 at the beginning of class. Answers
to the Problem Set |
|||
|
6 |
Oct
12 |
Please note: We will not cover the use of 3-factor crosses
to determine location, which is described in the second half of the outline
for Lecture 5. |
Davis
et al. 2005 (we will concentrate on the introduction and the section
devoted to interval mapping) |
|
Oct
17 |
Exam 1 - Bring a Scantron form 882 Answers
to the written questions |
||
|
7 |
Oct
19 |
We
will finish with the outline from last time, and then move to Mutation
identification by whole genome sequencing |
|
|
8 |
Oct
24 |
Continue with whole
genome sequencing; begin Analysis of Genes View
todayÕs Prezi |
|
|
9 |
Oct
26 |
Continue with
Analysis of Genes and begin Reverse Genetics |
|
|
Problem set 2
– Due Wednesday, Nov. 2 at the beginning of class. Answers
to the Problem Set |
|||
|
10 |
Oct
31 |
Quiz over Blandin et al., 2002 |
Blandin et al. 2002 |
|
11 |
Nov
2 |
Genome editing
by TALENs, Zinc-Finger Nucleases, CRISPRs, and the Cre-lox
systems Movie
on Engineered Nucleases Movie on
Zinc-Finger Nuclease Technology |
|
|
12 |
Nov
7 |
Quiz over Sardana et al., 2008
Proteomics
movie |
|
|
Nov
9 |
Exam
2 - Bring a Scantron form 882 |
||
|
13 |
Nov
14 |
TBA |
|
|
14 |
Nov
16 |
International
Human Genome Sequencing Consortium.
2001 |
|
|
15 |
Nov
21 |
||
|
Nov
23 |
No Class Meeting: Complete
an assigned Problem Set to be posted today. It will be due on Wednesday, Nov. 30 Here
is the Problem
Set |
||
|
16 |
Nov
28 |
Continue
Quantitative Genetics and Whole Genome Approaches Movies
shown on Prezi about SNP chip technologies |
|
|
17 |
Nov
30 |
Finish
Quantitative Genetics – we will finish the outline and Powerpoint Images from last lecture Quiz over Roach et
al., 2010 |
|
|
Answers
to the Problem Set Answers to
the Quz |
|||
|
18 |
Dec
5 |
Final Exam – 6:00 –
8:00 pm |
|
1. Morgan, TH. 1911. The origin of nine wing mutations in Drosophila. Science 33:496-499
2. Morgan, TH, and CB Bridges. 1916. Sex Linked Inheritance in Drosophila. Carnegie Inst. Washington, Publ., No.
237.
3. Brenner, S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 71-94.
4. Davis et al. 2005. Rapid single nucleotide polymorphism
mapping in C. elegans. BMC Genomics
6:118
5. Sarin et al. 2008. Caenorhabditis elegans mutant allele identification by
whole-genome sequencing. Nature
Methods 5: 865-867
6. Blandin et al. 2002.
Reverse genetics in the mosquito Anopheles
gambiae: targeted disruption of the Defensin
gene. EMBO reports 3: 852-856
7. Carroll, D. 2011. Genome engineering with zinc-finger
nucleases. Genetics 188:773-782
8. Pennisi,
E. 2013. The CRISPR craze. Science 341: 833-836
9. International Human Genome
Sequencing Consortium. 2001. Initial sequencing and analysis of the
human genome. Nature 409: 860-921
10. Reinke et al. 2000. A Global Profile of Germline Gene Expression in C. elegans. Molecular
Cell 6: 605-616.
11. Pan et al.
2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics 40: 1413-1415.
12. Sardana
et al. 2008. Proteomic Analysis of Conditioned Media from the PC3, LNCaP, and 22Rv1 Prostate Cancer Cell Lines: Discovery and
Validation of Candidate Prostate Cancer Biomarkers. J. Proteome Res. 7: 3329-3338.
13. Feng
et al. 2010. Epigenetic Reprogramming in Plant and Animal
Development. Science 330: 622-627
14. Wittenburg et
al. 2006. QTL mapping for genetic determinants of
lipoprotein cholesterol levels in combined crosses of inbred mouse
strains. J. Lipid Res. 47: 1780-1790
15. Agyris et al. 2005.
Quantitative trait loci associated with seed and seedling traits in Lactuca.
Theoretical and Applied Genetics 111: 1365–1376.
16. Roach et al. 2010. Analysis of Genetic Inheritance in
a Family Quartet by Whole-Genome Sequencing. Science 328: 636-639.