Paul Overvoorde- Macalester College

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Paul Overvoorde & LIbby Shoop - Macalester College

Overview of BIOL353: Advanced Genetics 

BIOL353: Advanced Genetics is a four-credit upper level elective for Biology majors that does not have a "wet-lab" component.  In spring of 2014, the class met 3 times per week for 1 hour.  The course was subdivided into three sections

  1. 2 weeks-  Reading and discussing "classic" manuscripts.   • The discussions about these works serve as a platform to review and deepen students understanding of key genetics terms and concepts they were exposed to in an introductory Genetics course. These manuscripts are available on-line from Electronic Scholarly Publishing.   Examples of papers that have been used include:  Mendel (1866).  Versuche über Plfanzenhybriden [Experiments in Plant Hybridization];  Sturtevant, A.H. (1913).  The Linear Arrangement of Six Sex-linked Factors in Drosophila, as Shown by Their Mode of Association.  Journal of Experimental Zoology  14: 43-59;   Beadle, G.W. and Tatum, E.L. (1941).  Genetic Control of Biochemical Reactions in Neurospora.  P.N.A.S. 27: 499-506;   Nirenberg, M.W. and Matthaei, J.H. (1961).  The Dependence of Cell-free Protein Synthesis in E. coli Upon Naturally Occurring or Synthetic Polyribonucleotides.  P.N.A.S.  47: 1588-1602;  Yanofsky, C., Carlton, B.C., Guest, J.R., Hellinski, D.R., and Henning, U.  (1964).  On the Colinearity of Gene Structure and Protein Structure.  Genetics  51: 266-272.
  2. 5 weeks- Reading and discussing a trail of primary literature related to glucose sensing in yeast.  This approach was inspired by the text Genetic Techniques for biological research: A case study approach written by Corinne A. Michels.  Through this section of the course, students gain an appreciation for the on-going process of science and the way that advances in technolgies influence the way that biological questions are presented and addressed.
  3. 7 weeks- Annotating regions of the D. biarmipes dot andD. ananassae 3L chromosomes.

Use of a GEP Annotation Project

Future Plans



Syllabus for BIOL353: Advanced Genetics


Class Meetings:    MWF 10:50-11:50 ARTCOM214.   
FINAL EXAM:    Take Home: Due 5 p.m. on Friday May 9.

Office Hours:    Normally, M & W 1:45-2:45 p.m. and by appointment.  Posted on my office door is a sign-up sheet with times I am available for meetings during a week.  If none of the listed times fit your schedule, you are welcome to either leave a Post-it note or to send an e-mail with three times that would work for you.  In addition, you are welcome to stop by my office at any time, however, unless we have scheduled an appointment, I might not be available for a long period of time as I could have the time already committed to another person, project, or activity.


Course Overview
A.    My Goals for Your Learning in This Course.
 Upon successful completion of this course, you should be able to:
  1. Efficiently read primary or secondary scientific articles so that you can
     a. summarize, interpret, and evaluate genetic data presented in these papers
     b. explain how data were obtained through the use of a flow chart that summarizes the experimental design
  2. Use examples from the metabolism of sugars in yeast as a basis to describe, or interpret data from other genetic systems, topics such as genetic screens, complementation, epistasis, gene isolation,                 recessive or dominant genetic suppressors, and methods to examine protein-protein interactions.
  3. Provide specific examples of the on-going process of science, highlighting the circumstances that allowed careful observation to turn into questions that could be addressed experimentally.
  4. Choose and describe the appropriate molecular genetic tools that enable a gene of interest to be identified, amplified, and introduced into another organism for expression.
  5. Describe the process of assembling a genome and annotating genes with evidence provided by gene predictions, homology to other species, and RNA-seq data.
  6. Explain the importance of understanding genome organization for regulating gene expression.
  7. Work effectively with a group of peers to summarize and communicate the importance of discoveries in the field of genetics today.

B.    Course Purpose and Format
Purpose: The subject of this course is Advanced Genetics.  In contrast to a “facts” or “survey” approach, this course will emphasize the experimental methods used to develop genetic principles and concepts.  The course will rely heavily on primary literature and will involve in depth discussion of the techniques used in these manuscripts.
    The first portion of the course will include papers from the early literature and will be focused on cementing the connection between Mendelian genetics and DNA structure and organization.  This portion of the course will also serve as a review of previous cell biology and genetics experiences.
    During the second part of the course, we will use a trail of primary literature (aimed at understanding glucose sensing and signaling in yeast) to gain insights into a genetic approach to a biological question.  The question of how yeast cells sense and respond to the presence of glucose has been chosen because of the number of genetic and molecular genetic approaches that have been used to address this topic (e.g. mutant screens, epistasis analysis, suppressor and enhancer screens, synthetic phenotypes, molecular characterization of a gene, pleiotropy, two-hybrid analysis, and genome-wide analyses).
    The final segment of the course will be used to explore topics related to Genome Sequencing and Annotation.


Format: For each class meeting, one to two papers will be assigned.  Background information about the papers and the techniques used will be provided during the last segment of the previous meeting time.  Each person is expected to have read each of the papers that are assigned.  To promote more reflective consideration of a paper, a group of you will be assigned as “primary”, “secondary” or “tertiary” readers.  The “primary” readers will be the first ones called upon to present a summary and/or analysis of the paper or to describe a technique that has been used.  These folks will be responsible for initiating our discussion about a paper.  The secondary and tertiary readers will be expected to contribute to the discussion as well.


Participation and Preparation:  Unlike many of the biology courses you might have had before, the success of this course will depend on your level of participation and active engagement with the material.  The readings and assignments have been chosen with the expectation that you will spend at least 8 hours per week preparing for this class. That means spending 8 hours on a paper when only one has been assigned and 3-4 hours per paper when 2 or more paper have been chosen.  This time might be spent reading, researching background information or terms are new, or reflecting/evaluating the data and interpretations presented. 
    Since non-participants inhibit discussion, please don’t come to class if you haven’t read the papers.  This course requires lots of reading AND reflection.  Because we meet only once a week, the course will also require discipline to manage time and reading assignments effectively.  To encourage you to stay on top of things, you will be asked to turn in journal entries using Moodle.  These will have to be done by midnight on Monday during the weeks in which they are assigned.