Biology 301 lab syllabus

Biology 301: Genetics Lab Syllabus
Fall 2007, Davidson College
Wed. 1:30-4:30 or Thurs. 1:00-4:00 in Dana 256

Dr. Karen Hales, Dana 201A
Phone x2324, email kahales

lab schedule
Go to Aug/Sep, Oct, Nov/Dec

Introduction
Genetic analysis is an extremely precise way of studying biological function. In "forward" genetic analysis, one starts with a desire to understand a particular biological phenomenon. One studies mutant strains that are defective in that process, and then one deduces what genes are altered in those strains. In "reverse" genetic analysis, one starts with a gene of unknown function and defines its biological role by looking to see what happens when it is mutated. In both approaches, a function is connected with a gene. There are many model organisms that scientists use for genetic analysis. Based on the life cycles and biological properties of these organisms, each is an appropriate tool for asking a particular subset of biological questions. We will be doing genetic studies with the fruit fly Drosophila melanogaster to figure out molecular mechanisms of sperm cell development. No one has performed these exact experiments before, and our results will contribute directly to ongoing projects in my research lab. When you do such studies with live organisms, your experimental schedule depends in large part on the generation time of the organism. As a result, just as in the "real world" of genetic research, we will have long-term lab experiments running throughout the course of the semester that will require you to come in to the lab at times other than our scheduled lab period. To compensate, during a few weeks our scheduled lab sessions will include only a brief official meeting. It will be extremely important to keep an organized and thorough lab notebook so that you can keep track of everything that is going on at once. Because this is a semester-long project, we will encounter some concepts in lab before we get to that topic in lecture. You will learn what you need to know at first, but you should expect to develop a deeper conceptual understanding of the project as the semester goes on. This lab course is based upon work supported by the National Science Foundation under Faculty Early Career Development (CAREER) Grant No. 0133335. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).

Lab manual
The lab manual includes background information and specific instructions for all aspects of our project. Click on the links in the schedule below to go directly to the appropriate sections of the lab manual for each week. Access to the lab manual online requires your username and password (same as for email), and the domain name davidson. You should always read through all relevant instructions and protocols before coming to lab.

Lab notebook requirements
You will turn in your neat and organized lab notes, along with an in-class lab summary, each week before you leave lab. Please compile all these records in a loose leaf binder and bring the binder to lab each week.Your notebook will include, among other things,
1) An introductory overview of our main project in your own words. You should complete this shortly after our first two lab meetings. This overview should include a detailed chart of the crosses you will perform, indicating the rationale for choosing the particular progeny classes that you will use in the next step.
2) Records of everything that you and members of your lab group do in the lab. Explain any troubleshooting.
3) All your raw data and your analysis thereof.

Lab report
A final lab report on our main project, incorporating data from all the lab groups will be due on December 7th by email. Each student will write an lab report individually. Please title your file [YourLastName]labreport.doc. Refer closely to the appropriate sections in A Short Guide to Writing about Biology for guidance on how to organize and format the report. There is no minimum or maximum length requirement; please be complete but concise. You should find at least three additional background sources for your introduction beyond the lab manual. Also include an assessment of the relative breakdown of work/effort among all members of your lab group. Your assessment will be kept confidential..

Lab grade: Lab counts 20% of the overall course grade, broken down as follows:

Pre-lab quizzes and weekly lab records	Effort, care, and accuracy with which you perform your experiments	End-of the semester lab report	Total lab grade
6%	6%	8%	20% of overall course grade

return to top

Lab schedule NOTE: You must always wear closed-toed shoes to lab. People wearing sandals will be sent home to change shoes.
Week	Date	Topic/Activity	Pre-lab assignment (some links under construction)
1	August 29/30	Lab safety discussion Background information on Drosophila as a model organism, spermatogenesis, mitochondrial morphogenesis. How to handle and breed flies On your own: Manipulating flies under the stereomicroscope and distinguishing males from females	Safety: read gas cylinder safety Read the following sections in the lab manual: 1 Introduction to Drosophila 2 Spermatogenesis and mitochondrial morphogenesis 3 Fly husbandry
2	September 5/6	Discussion: --previous research on the mitoshell mutant strain and the hunt for the mitoshell gene --the CG7795 gene as a candidate --P elements --making deficiencies near CG7795 --taking laboratory notes On your own: With your lab group, talk through the steps of the project. Make a plan, including A) when each cross will be set up; B) when offspring will be collected; C) how you will distinguish which offspring you want; 4) what you will do with those offspring; and D) what flies need to be collected in advance for later steps, and when to start those collections. I must approve your plan. You will be given vials of Cross 1 in which the offspring will have just been born, along with virgin flies of genotype w;Kr/CyO. You must identify the appropriate offspring from Cross 1 and set up twelve individual vials of Cross 2 today.	Read the following section in the lab manual: 4 This year's experiment: the mitoshell gene, P elements, and making deficiency alleles Read Pechenik chapter 8, pages 143-149, on how to take laboratory notes
3	September 12/13 return to top	Discussion: Review of our project. Tricks for keeping your fruit flies happy and productive. Online activities to analyze CG7795 and other candidate genes. On your own: Monitor your Cross 2 vials. Collect the appropriate virgin females in preparation for Cross 3 (need to do this on your own time in order to get enough.) Between this week and next, each lab group needs to meet with me separately to discuss your progress.	Read section 6 Using Drosophila online resources. When you arrive, boot up the computer and go to that page.
4	September 19/20	We will meet only briefly this week. Afterwards, if you have already set up your Cross 3 vials, you can write your short lab summary and then leave. Otherwise, you must stay until Cross 3 is fully set up. Be sure to number your Cross 3 vials so you know which Cross 2 each one came from. You will need many virgin females for your fertility tests in the next step of your experiment. You should be collecting them now. It is crucial that the females truly be virgins; otherwise, we will miss any newly-generated CG7795 mutations that may have been generated (and defeat the whole purpose). Therefore, all virgins that you collect must be kept by themselves for four days before you use them, to confirm that no larvae are present.
5	September 26/27	Side activity: Workshop on mapping human genetic disorders On your own: continue collecting virgin flies and monitoring Cross 3 vials.	Print out section 7A Human genetic disorder mapping worksheet and bring a copy to lab.
6	October 3/4	We will meet briefly this week to discuss progress. Afterwards, if you have already set up your fertility tests, you can write your short lab summary and then leave. Otherwise, you must stay until fertility tests are fully set up. During the next week, let me know immediately if you suspect that there is sterility in one of your fertility tests.
7	October 10/11	Discussion: Results! Did we get a new CG7795 allele? How do we make a pure stock of this new strain? Recombinant DNA lecture (rescheduled from class time on Fri Oct 12) Side activity: Karyotyping exercises	Read section 7B Karyotyping exercises section of the lab manual.
8	October 17/18 return to top	No lab (week of fall break). On your own, finish up any fly work left to do.
9	October 24/25	Genomic DNA isolation from wild type flies and any new mutant strains.	Read section 5A DNA isolation protocol and bring a copy to lab.
10	October 31/November 1	PCR amplification of CG7795.	Read section 5B PCR protocol and bring a copy to lab.
11	November 7/8	Gel electrophoresis of PCR products. Discussion (while gels are running): --status of the project --lab report expectations --assigning lab groups to week 12 or 14 for testis dissections	Read section 5C Gel electrophoresis Read Pechenik Chapter 8 in its entirety (Writing Laboratory and Other Research Reports)
12	November 14/15	Observation of wild type and mutant Drosophila spermatogenesis by phase contrast microscopy. (Two of the four lab groups)	Review 2 Spermatogenesis and mitochondrial morphogenesis
13	November 21/22	THANKSGIVING BREAK
14	November 28/29	Observation of wild type and mutant Drosophila spermatogenesis by phase contrast microscopy. (Other two of the four lab groups)	Review 2 Spermatogenesis and mitochondrial morphogenesis
15	December 5/6	No official lab meeting...work on lab reports. LAB REPORTS ARE DUE AT CLASS TIME ON FRIDAY DECEMBER 7th. Please email me the file. Remember to title your file [YourLastName]labreport.doc.

return to top

Davidson Biology

Dr. Hales's home page