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(NEUR/GEN 534)

First Meeting 1/17/06 2:30PM Room E609



Chung-Ying Daniel
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This course is designed for Neurosciences students and others who wish to learn about genetic approaches to neuroscience research.

The class will meet for one and one-half hours twice weekly. Generally there will be one lecture and two student-led presentations and discussions of research articles each week. Occasional problems sets will be assigned to help consolidate understanding of the lecture material. Students are expected to read all the papers assigned for presentation and all students (not just the presenters) will be called upon to answer questions about the papers in class.

At the end of the semester students will write and briefly present a research proposal using genetic approaches to investigate a current question in neurobiology, and will read and critique the proposals of others, acting much as the members of a study section would.

Grading will be based on class participation, which we regard as important, the presentation of research papers, and the final research proposal.


As the semester progresses, the entries under “Reading” and “Notes” will become active links to assigned readings (as pdf's), problem sets, and powerpoints from lectures and possibly also from student presentations.

2006 Tentative 534 Schedule
Date TopicPapersNotes
1/17TUEO'GormanOverviewDudai, 1976
1/19THUO'GormanMendelian InheritanceCh3.2/3/4LECTURE
Inbred Strains & Drosophila CrossesPEDIGREE PROBLEM
FOR TUE, 1/31
Linkage & Recombination & MappingZwingman 2001
Presentations - Mapping
2/2THUHerrupDetermining Site of Gene ActionKIDD
Presentations - Site of Gene Action
2/9THULambOrder of Gene ActionHe, 2001
Richmond, 2001
Gene Order Problems
Presentations - Order of Gene Action
2/16THUO'GormanTransgenic vertebratesODDO 2003
Presentations - Transgenic vertebrates
2/23THURobinsonTransgenic DrosophilaMerek, 2002
Clyne, 2003
Presentations - Transgenic Drosophila
3/2THUO'GormanES cell mutagenesisReadingLECTURE
3/7TUELambBioinformaticsNeurogenomics 2004
Molecular Biology Databases 2006
Database Table 2006
NAR 2006 Database Issue
ZHENG 1999
Spring Break
3/21TUERobinsonDesign of genetic screensLee, 1999
Stowers, 1999
Presentations - Genetic screens
3/28TUEStudentsPresentations - Bioinformatics IDatabase Group 1 Question
Database Group 2 Question
3/30THUStudentsPresentations - Bioinformatics IIDatabase Group 3 Question
Database Group 4 Question
Friday3/31Research proposal (preliminary) topics due
4/4TUEHerrupEffects of genetic backgroundKELLY
Tuesday4/4Topics approved or revision requested
Presentations - Effects of genetic background
Friday4/7Final Research Topics Due
4/11TUEHerrupImprinting and InactivationPLAGGE
Presentations - Imprinting and inactivation
4/18TUE TBA or no class
4/20THUResearch proposals due - no class
4/21FRIProposals distributed to student reviewers
4/25TUEProposal presentations and critiques
4/27THUProposal presentations and critiques
5/13Grades Due


In General:

The intent of this course is to provide Neurosciences students with a foundation in genetic approaches to neuroscience research. The faculty also want to develop students'critical thinking and presentation skills, and to help them to become confident enough to speak up during discussions of diverse topics. While it is unlikely that the faculty will establish fixed office hours, we all will be available for consultation outside of the classroom if students simply ask.

The faculty expects all students to read and have thought about all of the materials assigned. All students will be called upon, at random and with some regularity, to discuss particular points from the readings or to go to the board to, for instance, diagram an experiment. It is not critical to get the “right” answer every time, but evidence of familiarity with the material is essential and will form the basis for a portion of the final grade awarded. While everybody has bad days or weeks, the level of effort students make will become apparent over the course of the semester.

Student Presentations

The students responsible for discussion sessions should present a 15 minute summary of the conceptual background that led to the study reported, and should attempt to place the paper in the context of the corresponding lecture material. While the audience should feel free to ask questions, the faculty will attempt to limit long digressions from the presentation so as to wrap up the presenter's principal responsibility reasonably close to the 15 minute timespan. The faculty member responsible for the corresponding lecture will then lead a discussion that goes into some of the details of the paper and the applicability of the approaches used. During this discussion any member of the class may be called upon to discuss specific points.

It will be helpful if students prepare a CD containing a powerpoint with their introductory material and with a slide for each figure, table, and chart from the paper.

The Research Proposal

The research proposal represents an opportunity to apply what has been learned throughout the semester to the design of novel, informative experiments. We feel that students will derive the greatest benefit from the exercise by writing a proposal on how genetic approaches could be used in their own thesis work or in the investigation of a topic related to work going on in their lab. It would not be appropriate to write about a project that you are currently doing or that you and your advisor have discussed in substantive detail. We recognize that this will be easier for some (i.e. those who are already taking a genetic approach or working in a “genetics” lab) than for others and will adjust our expectations, and grading, accordingly. It is also acceptable for students to decide that they really want to instead write about another, unrelated topic that interests them.

Whatever choice students make, we encourage that they discuss their intentions with the faculty before investing a lot of effort in writing specific aims or the proposal itself. There is no need to wait until the specific aims are due to get feedback.

Description of the specific aims (due 3/31) This should be no more than one, single-spaced page (12pt) with 1” margins. It should include a few sentences on the “big” question being addressed by the proposed research, a few sentences on how the more specific questions addressed experimentally relate to this larger theme, and one or two short paragraphs describing no more than two specific aims. These last should outline the experimental approaches to be used in general terms, and how they will lead to interpretable results, but should not go into great experimental detail.

The Research Proposal (due 4/20) The paper should be no more than 10 pages long. It should be formatted as were the specific aims. It should include the following sections.

(1) Specific Aims. List the broad, long-term objectives and what the specific research proposed in this application is intended to accomplish, e.g., to test a stated hypothesis, create a novel design or solve a specific problem.(one page)

(2) Background and Significance. Briefly sketch the background leading to the present proposal, critically evaluate existing knowledge, and specifically identify the gaps that the project is intended to fill. State the importance and health relevance (if any) of the research described in this application by relating the specific aims to the broad, longterm objectives. (2-3 pages)

(3) Research Design and Methods. Describe the research design and the procedures to be used to accomplish the specific aims of the project. Include how the data will be collected, analyzed, and interpreted. Describe any new methodology and its advantage over existing methodologies. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims.

Presentations (4/23, 4/25) All students will make a brief (5-10 minute) presentation of their proposal to the class. Their proposal will also be distributed to two or three student reviewers before the presentation and these reviewers will be expected to have questions about the proposal to ask during a brief question and answer period that will follow the presentation. Most of the grade for the project will reflect the faculty’s opinion of the written document, but the quality of the presentations and participation in the review of other proposals will also be factored in.

The major criteria that will be used for evaluation will be the clarity, feasibility and discriminative power of the experiments described in the written document. It is fine to propose a highly creative or ambitious project, but you should not propose something that might take many years to complete or that is entirely speculative in nature.


The University's definition of plagiarism, as stated on the academic integrity page of its website is:

  • Plagiarism includes the presentation, without proper attribution, of another's words or ideas from printed or electronic sources. It is also plagiarism to submit, without the instructor's consent, an assignment in one class previously submitted in another.
    Case Academic Integrity Standards

We do not expect anybody to engage in plagiarism, but it sometimes happens because students do not take the time to familiarize themselves about which forms of rephrasing the words and ideas of others are acceptable and which are not, and about how proper attribution should be given. There are many resources on the web that go over this material. It is the student's responsibility to know what plagiarism is and to know how to avoid it.

Drosophila Resources
General Resources
Neurogenetic disorders from NINDS website DISORDERS.PDF
Medical genetics course, UICMedical genetics
courses/neurgen_534/index.txt · Last modified: 2014/11/26 03:33 (external edit)