Molecular Genetics: Biology 700



Syllabus for Fall 2015

Molecular Genetics: Biology 700.4/700.5

Class: Tuesday and Thursday 6:30-8:20 PM (5 credit h) Science Building D346

Contact information:

AM: Dr. Alicia Meléndez (course head)

alicia.melendez@qc.cuny.edu

NSB D-338, phone 718 997-4580

CSD: Cathy Savage-Dunn

mailto:Cathy.SavageDunn@qc.cuny.edu

NSB D-330, phone 718 997-3440

Required Texts:

1. Walker, M. and Hawley, S. (2003) Advanced Genetics Analysis, Blackwell Publishing.

2. WORMBOOK, () a comprehensive collection of original peered reviewed chapters covering topics related to C. elegans biology.

3. Papers from the primary literature: There will also be a series of scientific papers to read, some are announced on the syllabus and others will be announced as needed throughout the semester on Blackboard.

Recommended Texts:

1. Hartwell, L. et al (2008) Genetics: From Genes to Genomes, 5th edition, McGraw This edition no longer includes sections on model organisms for genetic research, but these are available online at the McGraw-Hill web site. Registration is simple. 
Complete Information: 
"Genetics: From Gene to Genomes"
Leland Hartwell, Leroy Hood, Michael Goldberg, Ann Reynolds, Lee Silver, and Ruth Veres.
ISBN: 0072848464 © 2008

McGraw-Hill, the publisher's web site. 
Amazon.

Objectives:

After taking this course, you should

-Understand the basic mechanisms of transmission of genetic traits, as first described by Mendel.

-Understand how genetic research is carried out, how we use genetic techniques to answer biological questions.

-Understand how epistasis analysis is carried on, and how modifying genes may work: suppressors and enhancers.

-Understand and recognize the differences involved using different genetic model organisms.

-Understand how to problem solve and how to analyze data from genetic analyses.

-Be able to read an article from the primary literature and understand the genetics described, and be able to evaluate its conclusions.

Coverage: This course is intended as an advanced course in genetic analysis. The focus is on the basic principles that underlie genetic analysis: the nature of mutations, complementation, suppression, enhancement, recombination, segregation, and gene regulation. Our goal is to provide insights into the process of genetic analysis and how this functions in the study of a biological process. We discuss the basic tools, current techniques of genetic analyses, and the different genetic model organisms: the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and mouse Mus musculus. For each of these species we will consider methods for the identification of informative mutations revealing new genes or new gene functions, and methods for testing the expression of modified genes. Genomics, including applicable genomics resources and practical bioinformatics tools, will also be covered. Articles from the primary literature to better understand new techniques, and possible misunderstandings in genetic analysis are also discussed. The course assumes familiarity with the genetics of eukaryotes, and working knowledge of molecular biology, as for example transcription, splicing, translation, and replication.

Grading for Bio 700 Students

The final grade for will be calculated as follows:

Quizzes 50% (Students have the option of dropping 2 quizzes from the 12 total quizzes)

Presentation 20%

Final Exam 30%

Makeup Policy

There will be no makeup exams given under any circumstances.

Student Disability Services

To receive disability-related academic accommodations students must first be registered with the Center for Student Disability Services. Students who have a documented disability or suspect they may have a disability are invited to set up an appointment with the Director of the Center for Student Disability Services, Ms. Mirian-Detres Hickey at 718-997-5870, or they can walk-in and make an appointment at Frese Hall, room 111. If you have already registered with the Center for Student Disability Services please provide your instructor with the course accommodation form and discuss your specific accommodation with him/her.

University's Policy on Academic Integrity

The faculty and administration of Queens College support an environment free from cheating and plagiarism. Each student is responsible for being aware of what constitutes cheating and plagiarism and for avoiding both. An example would be to use exact words or figures from a source without attributing those words to the author or the source. The complete text of the CUNY Academic Integrity Policy and the Queens College procedure for implementing that policy can be found at this site:

‎ Integrity Memo Fall 2014.pdf

If a faculty member suspects a violation of academic integrity and upon investigation, confirms that violation, or if the student admits the violation, the faculty member MUST report the violation. The penalty for violation will be failure in the course and a report to the Office of Student affairs.

Calendar:

|Date |Lectu |Topic |Hartwell |Hawley |Articles/Other |

| |rer | | | | |

|Th 8/27 |AM |1. Intro: Genes to Genomes |Ch. 4 | | |

|Tue 9/1 |CS |2. DNA manipulation Techniques |Ch. 9 | |Problem Set 1 due (Intro Genetics) |

|Th 9/3 |CS |3. Using Genetics- Mutations |On line Ch. |Ch. 1, p.1-14,| |

| | |Quiz 1: Intro and DNA techniques |C. elegans |and p. 31-50 | |

| | | |Ch. 7, 8 | | |

|Tue 9/8 |CS |4. Genetics- Mutations | | |Problem Set 2 due (Mutations) |

| | |Discussion | | |Article 1 for discussion |

|Th 9/10 | |NO CLASS Mon Schedule | | | |

|Tue 9/22 | |NO CLASS College Closed | | | |

|Fri |CS |7. Chromosome |Ch. 5,6 |Ch. 8 | |

|9/25 | |Quiz 3: Complementation | | | |

|Tue 9/29 |CS |8. Genome Rearrangements |Ch. 12 | |Article 2 for discussion |

|Th 10/1 |CS |9. Recombination |Ch. 6 |Ch. 7 |Article 4 for discussion |

| | |Quiz 4: Chromosome and Genome Rearrangements | | |WB: Transposons in C. elegans |

|Tue |AM | 10. Mapping and Cloning- |Ch. 10 |Ch. 6,7 |WB : Mapping |

|10/6 | |Discussion | | |Article 3 for discussion |

| | | | | |Problem Set 4 due (Mapping |

|Th 10/8 |CS |11. Transposons-Discussion |Ch. 12 | | |

|Tue 10/13 |AM |12. Suppressors |Ch. 12 |Ch. 4 |WB: Genetic Suppression |

| | |Quiz 5: Mapping and Cloning | | |Problem Set 5 due (Transposons) |

|Th 10/15 |AM | 13. Enhancers and Redundancy- | | |WB: Genetic Enhancers |

| | | | | |WB: Gene duplications and Redundancy |

| | | | | |WB: LIN-12/Notch signaling |

| | | | | |Redundancy article |

|Tue 10/20 |AM |14. Suppressors and Enhancers | | |Problem Set 6 due (Suppressors & Enhancers) |

| | |Discussion | | |Article 5 for discussion |

|Th |AM |15. Epistasis | |Ch. 5, p. |WB: Epistasis |

|10/22 | |Quiz 6: Suppressors and Enhancers | |107-118 | |

|Tue |AM |16. Epistasis- Discussion | | |Problem Set 7 due (Epistasis) |

|10/27 | | | | |Article 6 for discussion |

|Th 10/29 |CS |17. Gene Regulation |Ch. 15, 16 | | |

| | |Quiz 7: Epistasis | | | |

|Tue 11/3 |CS |18. Gene Regulation | | |Problem Set 8 due (Gene Regulation) Article 7 for discussion |

| | |Discussion | | | |

|Th 11/5 |AM |19. RNAi and CRISPR/Cas |Ch. 16 | |RNAi articles and CRISPR/Cas articles |

| | |Quiz 8: Gene Regulation | | | |

|Tue |AM |20. RNAi and CRISPR/Cas- Discussion | | |Problem Set 9 due (RNAi) |

|11/10 | | | | |Article 8 and 9 for discussion |

|Th |CS |21. Epigenetics |Ch. 16 | | |

|11/12 | |Quiz 9: RNAi | | | |

|Tue |CS |22. Genetic Model systems-Yeast |On line Ch. |Ch. 7, p. | |

|11/17 | | |Yeast |168-178 | |

| | | |Ch. 5 | | |

|Th 11/19 |CS |23. Yeast- Discussion | | |Problem Set 10 due (Yeast genetics) |

| | | | | |Article 10 for discussion |

|Tue 11/24 |AM |24. Genetic Model systems- Drosophila |On line Ch. |Ch.5, p. |Article 11 for discussion |

| | |Quiz 10: Yeast Genetics |Drosophila |118-126 | |

|Th 11/26 | |NO CLASS THANKSGIVING | | | |

|Th |AM |26. Genetic Mosaics | | |WB: Mosaics |

|12/3 | |Quiz 11: Drosophila Genetics | | |Article 13 for discussion |

|Tue |CS |27. Genetic Model Systems- Mouse |On line Ch. | |Problem Set 12 due (Mosaics) |

|12/8 | | |Mouse | | |

|Th |CS |28. Genetic Model systems- Mouse Discussion | | |Problem Set 13 due (Mouse genetics) |

|12/10 | |Quiz 12: Mosaics | | |Article 14 for discussion |

TBA

Dec 16-23 | |Final exam | | | | |Lecture days have a QUIZ on the material from the week before and the reading of this day.

Articles 1-14 in bold are to be discussed by the students.

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