BIO 421 – Advanced Genetics

Fall 2016

Course Syllabus

Instructor and Course Information

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.

 

Course Description: 

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, today’s 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 Brooker’s Genetics, Analysis and Principles is a good source.

Readings for the Course: 

I will assign a number of readings from the primary research literature.  These will include “classic” 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. 

Expectations:           

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!).

Pre-requisites

BIO303 (Genetics) but BIO 310 is also good to have prior to this course.

Blackboard

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.

Exams and Grading

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. 

Tentative Lecture Schedule

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

Powerpoint Images

 

2

Sept. 28

Discovering genes: the importance of Thomas Hunt Morgan and Mutational analysis

Powerpoint Images

Overheads from class

 

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

Morgan, 1911

Fire et al. 1998

Tabara et al. 1999

3

Oct 3

Genetic Mapping and construction of genetic maps

Powerpoint Images

Overheads from class

 

Quiz over Morgan and Bridges, 1916

Morgan and Bridges, 1916 (Part I – pages 5-23)

4

Oct 5

Note that we are a little behind and will not likely get very far into this lecture material….Mapping by 2-factor and 3-factor crosses

Powerpoint Images

Handout for mapping to a chromosome

Overheads from class

 

Brenner, 1974 (particular attention to 3-factor crosses for gene order)

5

Oct  10

Three-factor crosses

Powerpoint Images

Overheads from class

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.

Mapping using molecular markers

Powerpoint Images

Overheads from class

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

Powerpoint Images

Sarin et al. 2008

8

Oct 24

Continue with whole genome sequencing; begin Analysis of Genes

Powerpoint Images

View today’s Prezi

 

9

Oct 26

Continue with Analysis of Genes and begin Reverse Genetics

Powerpoint Images

Center for Biological Sequence Analysis

NCBI BLAST

TM Prediction

InterPro

Blandin et al. 2002

Problem set 2 – Due Wednesday, Nov. 2 at the beginning of class.

Answers to the Problem Set

10

Oct 31

Reverse Genetics

Powerpoint Images

 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

Powerpoint Images

Movie on Engineered Nucleases

Movie on Zinc-Finger Nuclease Technology

Carroll, 2011

Pennisi, 2013

12

Nov 7

Transcriptomes and Proteomes

Quiz over Sardana et al., 2008

Powerpoint Images

Proteomics movie

Reinke et al.  2000;

Pan et al.  2008

Sardana et al. 2008

Feng et al. 2010

Nov 9

Exam 2 - Bring a Scantron form 882

13

Nov 14

Epigenetics, microRNAs

Powerpoint Images

TBA

14

Nov 16

The Human Genome, then begin Quantitative Genetics

Powerpoint Images

International Human Genome Sequencing Consortium.  2001

Chapter on Quantitative Genetics

15

Nov 21

Quantitative Genetics and QTL mapping

Powerpoint Images

Wittenburg et al.  2006

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

Powerpoint Images

Movies shown on Prezi about SNP chip technologies

Agyris et al. 2005

17

Nov 30

Finish Quantitative Genetics – we will finish the outline and Powerpoint Images from last lecture

Quiz over Roach et al., 2010

Roach et al.  2010

Answers to the Problem Set

Answers to the Quz

18

Dec 5

Final Exam – 6:00 – 8:00 pm

 

Readings

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.