9.12 | Fall 2006 | Undergraduate

Experimental Molecular Neurobiology


Course Meeting Times

Lectures: 1 session / week, 2 hours / session

Labs: 1 session / week, 4 hour / session

General Course Information

This course is divided into two main components:

  1. Wet Lab Sessions

    • Labs will progress linearly in order for the class to acquire basic laboratory skills relevant to molecular neurobiology. Our goal in this class is for each student to learn enough molecular skills to be able to perform experiments successfully in future settings.
    • Each week we will begin class with a brief overview of the technique covered that day. We will then employ this experimental technique for the remainder of the class period.
  2. Paper Presentations

    • Each week we will review one paper that elaborates on ideas and techniques that are pertinent to the molecular neuroscience topic of that week.
    • We will randomly select three to four students to each present a specific figure from that paper. In addition students will also utilize these figures to discuss the general molecular technique used to collect the figure data and to explain how this technique applies to the paper overall.
    • Each student will present figures from two papers this semester.


Students will have many opportunities to write this semester, for this course fulfills one of the CI-M requirements for course 9 majors.

  1. Paper Questions - Assigned each Week

    • Professors Lois and Hayashi will provide the class with six to eight specific questions related to a presentation paper. Students will receive these questions after each presentation and will have one week to answer these questions and to submit these answers for grading.
    • Presenters and non-presenters alike will have to submit answers to these questions.
  2. Review Essays - Two per Semester

    • Students will write a three-page summary and critical review of a scientific paper.
    • These essays will be evaluated in two ways. First a scientific writer will analyze the structure, and then the teaching assistant (TA) will analyze the content. The scientific writer will provide feedback that you will use to revise your essay before submitting your paper to the teaching assistant for grading.
  3. Lab Reports - Four per Semester

    • Students will write a brief (two page) lab report using data collected in the wet lab. These papers can use data from one or many lab weeks, depending on the topics covered.
    • Lab reports consist of a few basic components.
      1. Introduction: provides an overview of background related to your experiment, how your experiment fits into this background, and your experimental hypothesis for the paper.
      2. Methods: describes techniques/methods used in an experiment and how one collects data from the experiment.
      3. Results: describes the outcome of the experiment using text and figures.
      4. Discussion: relates the experimental results to the hypothesis and to the overall field of research and explains experiment outcomes, errors, and future directions.

Additional Information

  1. Laboratory Notebooks

    • We will provide students with laboratory notebooks. In the course of performing experiments, you will learn how to properly record methods and data. In general, your lab notebook should be self-explanatory. That is, the notebook should be complete and well organized so that others could use it to accurately repeat your experiments.
    • We will periodically evaluate and grade your notebook for content, presentation and organization in order to help you to learn these record-keeping techniques.
  2. Presentations

    • Each student will have two opportunities to give oral presentations this semester. Figure presentations by each student should last approximately fifteen minutes. We expect students to give computer-based presentations (using Microsoft® PowerPoint®, etc.).

    • We will grade you not only on the information that you present, but also on your ability to convey the information. Some points to remember when giving your presentation:

      • Speak to your audience; make frequent eye contact.
      • Speak slowly, clearly and loudly.
      • Present the information on the screen so that it is large enough for all to see it. Typically one has more slides with less text with this method. Remember the common rule of one slide per minute.
      • Avoid filler words when speaking. Common fillers include, “um”, “ah” and “like”.
    • Feel free to contact the teaching assistants or the lab manager for help with any of these points. Practicing in front of a smaller audience can help you when you face a larger one.

  3. Participation

    • We will grade your participation in both the lab sessions and in the presentation sessions.
    • Participation in the lab means that you have read and understand the protocol for the week, that you perform your experiments to the best of your ability, and that you are actively learning techniques in the lab.
    • Participation in the presentation means that you have read and understand the paper for the week and that you are prepared to answer questions if asked.
  4. End of the Year Quiz

    • In lieu of a paper presentation the last Wednesday of classes, there will be a class quiz. This quiz will consist of approximately 400 questions given orally in a round-robin manner. We will use this tool to show you all how much information you have acquired over the course of the term.
  5. Lab Safety

    • While it is important for you all to learn the molecular techniques that we will teach you this semester, it is equally important that you all are safe while performing these tasks.If you have any questions about lab safety, please contact any of the teaching staff. Additional safety information for this course will not be discussed here, but is placed in the labs section. Please utilize this as a valuable resource.
    • The teaching staff will provide all personal protective equipment for students.

Primrose et al. Principles of Gene Manipulation. Oxford, UK: Blackwell Science, 2006. (DNA Recombinant Technology)

Alberts et al. Molecular Biology of the Cell. Philadelphia, PA: Taylor and Francis, 2002. (Molecular Biology in general)

Martin et al. From Neuron to Brain. Sunderland, MA: Sinauer Associates, Inc., 2000. (Cellular Level Neuroscience in general)

Grading Policy

Your grade for this course will be weighed equally among the following components of the course:

  • Performance in Lab
  • Participation During Lab and During Presentations
  • Lab Notebook
  • Two Presentations
  • Two Essays
  • Paper Questions
  • Four Lab Reports

We will provide you with a grade assessment in the middle of the semester. This assessment will give you an opportunity to view your status in the class prior to the end of the year grades.

If you have any questions about the information found in this overview, please contact any of the teaching staff for this course, especially the faculty.


1 Introduction

2 Julius, David, Amy B. MacDermott, Richard Axel, and Thomas M. Jessel. “Molecular Characterization of a Funcational cDNA Encoding the Serotonin 1c Receptor.” Basic Skills in a Molecular Biology Lab
3 Buck, Linda, and Richard Axel. “A Novel Multigene Family May Encode Odorant Receptors: A Molecular Basis for Odor Recognition.” Sequence Analysis and Vector Design
4 Question and Answer Session PCR and Digestion
5 Shen, Karen, and Tobias Meyer. “Dynamic Control of CaMKII Translocation and Localization in Hippocampal Neurons by NMDA Receptor Stimulation.” DNA Purification and Subcloning
6 Scheiffele, Peter, Jinhong Fan, Jenny Choih, Richard Fetter, and Tito Serafini. “Neuroligin Expressed in Nonneuronal Cells Tiggers Presynaptic Development in Contacting Axons.”

7 Hua, Jackie Yuanyuan, Matthew C. Smear, Herwig Baler, and Stephen J. Smith. “Regulation of Axon Growth In Vivo by Activity-based Competition.” Transformation, Colony pick-up, Miniprep, and Digestion
8 Antoch, Marina P., Eun-Joo Song, Anne-Marie Change, Martha Hotz Vitaterna, Yaliang Zhao, Lisa D. Wilsbacher, Ashvin M. Sangoram, David P. King, Lawrence H. Pinto, and Joseph S. Takahashi. “Functional Identification of the Mouse Circadian Clock Gene by Transgenic BAC Rescue.” Basic Cell Culture
9 Serafini, Tito, Timothy E. Kennedy, Michael J. Galko, Christine Mirzayen, Thomas M. Jessell, and Marie Tessler-Lavigne. “The Netrins Define a Family of Axon Outgrouth-promoting Proteins Homologous to C. elegans UNC-6.” Primary Culture of Neurons from the Brain

Gould, Elizabeth, Alison J. Reeves, Michael S. A. Graziano, and Charles G. Gross. “Neurogenesis in the Neocortex of Adult Primates.”

Kornack, David R., and Pasko Rakic. “Cell Proliferations without Neurogenesis in Adult Primate Neocortex.”

SDS-Polyacrylamide Gel Electrophoresis and Western Blotting
11 MacLauren, R. E., R. A. Pearson, A. MacNeil, R. H. Douglas, T. E. Salt, M. Akimoto, A. Swaroop, J. S. Sowden, and R. R. Ali. “Retinal Repair by Transplantation of Photoreceptor Precursors.” Western Blotting 2: Detection
12 Davis, Graeme W., and Corey S. Goodman. “Synapse Specific control of Synaptic Efficacy at the Terminals of a Single Neuron.” Brain Tissue Processing
13 Brown, Arthur, Paul A. Yates, Patrick Burrola, Dan Ortuno, Ashish Vaidya, Thomas M. Jessell, Samuel L. Pfaff, Dennis D.M. O’Leary, and Greg Lemke. “Topographic Mapping from the Retina to the Midbrain Is Controlled by Relative but not Absolute Levels of EphA Receptor Signaling.”

Course Info

As Taught In
Fall 2006
Learning Resource Types
Presentation Assignments
Written Assignments