First Meeting 1/17/06 2:30PM Room E609
|Chung-Ying Daniel Leeemail@example.com|
|Students Mail List|
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|
|1/17||TUE||O'Gorman||Overview||Dudai, 1976 |
|Inbred Strains & Drosophila Crosses||PEDIGREE PROBLEM |
FOR TUE, 1/31
|Linkage & Recombination & Mapping||Zwingman 2001 |
|Presentations - Mapping|
|2/2||THU||Herrup||Determining Site of Gene Action||KIDD |
|Presentations - Site of Gene Action|
|2/9||THU||Lamb||Order of Gene Action||He, 2001 |
Gene Order Problems
|Presentations - Order of Gene Action|
|2/16||THU||O'Gorman||Transgenic vertebrates||ODDO 2003 |
|Presentations - Transgenic vertebrates|
|2/23||THU||Robinson||Transgenic Drosophila||Merek, 2002 |
|Presentations - Transgenic Drosophila|
|3/2||THU||O'Gorman||ES cell mutagenesis||Reading||LECTURE|
|3/7||TUE||Lamb||Bioinformatics||Neurogenomics 2004 |
Molecular Biology Databases 2006
Database Table 2006
NAR 2006 Database Issue
|3/9||THU||DISCUSSION||ES cell mutagenesis||DUPUY SB TRANS |
|3/21||TUE||Robinson||Design of genetic screens||Lee, 1999 |
|Presentations - Genetic screens|
|3/28||TUE||Students||Presentations - Bioinformatics I||Database Group 1 Question |
Database Group 2 Question
|3/30||THU||Students||Presentations - Bioinformatics II||Database Group 3 Question |
Database Group 4 Question
|Friday||3/31||Research proposal (preliminary) topics due|
|4/4||TUE||Herrup||Effects of genetic background||KELLY |
|Tuesday||4/4||Topics approved or revision requested|
|Presentations - Effects of genetic background|
|Friday||4/7||Final Research Topics Due|
|4/11||TUE||Herrup||Imprinting and Inactivation||PLAGGE |
|Presentations - Imprinting and inactivation|
|4/18||TUE||TBA or no class|
|4/20||THU||Research proposals due - no class|
|4/21||FRI||Proposals distributed to student reviewers|
|4/25||TUE||Proposal presentations and critiques|
|4/27||THU||Proposal presentations and critiques|
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.
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:
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.
|Gene/Disease Databases||Entrez Gene||GenAtlas||GeneCards||OMIM||RefSeq||UniGene|
|Gene Expression Databases||ArrayExpress||Brain Atlas||Gene Expression Omnibus||GENSAT||Mouse Gene Expression Database||SAGEmap|
|Gene/Protein Function Databases||Gene Ontology||InterPro||Pfam||PolyPhen||PROSITE|
|Genome Browsers||UCSC Browser||Ensembl Browser||MapView Browser|
|Nucleotide Databases||DDBJ||EMBL||NCBI GenBank|
|Organism Browsers||FlyBase||Mouse Genome Informatics||Rat Genome Database||Saccharomyces Genome Database||WormBase||ZFIN|
|Protein Databases||NCBI Protein||Protein Data Base||Swiss-Prot||UniProt|
|Variation Databases||dbSNP||HapMap||HomoloGene||HGVbase||MGI Mouse SNPs||Wellcome Mouse SNPs|
|Other Resources||Bookshelf||Neuroscience Database Gateway||PubMed|
|ENU Mutagenesis||Baylor ENU||Harwell ENU||Munich ENU||Neuromice ENU||RIKEN ENU|
|Gene Trap Databases||Gene Trap Consortium||Lexicon OmniBank||NAISTrap|
|Tg/KO Databases||CreXMice||Deltagen||Induced Mutant Resource||Int. Mouse Strain Resource||JAX Mice||MMRC|
|Other Resources||Gene Nomenclature||Lee Silver's Mouse Genetics||Jackson Laboratory||Mouse Genome Resources||Mouse Phenome Database||Strain Nomenclature||Whole Mouse Catalog|
|Neurogenetic disorders from NINDS website||DISORDERS.PDF|
|Calculate Chi-square||CHI SQUARE CALCULATION|
|Medical genetics course, UIC||Medical genetics|
|History of Genetics|
|Evolution, historic writings||http://post.queensu.ca/~forsdyke/evolutio.htm#SELECTED%20PAPERS|