BIO 106-05 Wednesday LAB/Monday LECTURE Schedule - Fall 2012

DATE DAY
Module 1: Understanding individual genetic variation
SNPs in Human Cdk3 Gene
5-Sep W
1:30 in Bio lab - Course Overview; Lab Safety; conversions and dilutions;
Readings: Appendix A and B , metric conversions, solutions and dilutions
3 pm - Library data bases w/science librarian
Assignments:1) Exercise #1 metric conversions, Appendix B
2) Vassar data bases & SNP Lit search
10-Sep M
DNA, replication, (concept of central dogma) mutation, SNPs; Introduction to PCR
Readings: Campbell:DNA replication Ch. 16; Central Dogma-Gene to Protein Ch 17, p
325-348; Ch 20, PCR p 403-404; SNPs p411-412.
Assignments: readings for SNP lab #1; SNP pre-lab #1
DUE: Vassar data bases and SNP lit search
12-Sep W
LAB #1 Weighing and Pipetting exercises; Extract cheek cell DNA and PCR
Readings: Lab manual - SNP Lab #1; Review Appendix A and B
DUE: 1) Exercise #1 from lab manual appendix B 2) SNP pre-lab #1 on PCR
SEND PCR SAMPLES FOR SEQUENCING - Sept. 17th
17-Sep M
Discussion of SNPs, restriction enzyme digestion &RFLP analysis; DNA electrophoresis
Readings: Restriction enzymes & Gel electrophoresis, Ch 20 p 405- 406;
Assignments: readings for SNP lab #2; SNP pre-lab #2
19-Sep W
LAB #2 RFLP - Restriction digest with gels
Readings: lab manual for week #2
DUE: SNP pre-lab #2
24-Sep M
Sequencing & Bioinformatics discussion - Analysis of gels
Readings: Campbell:DNA sequencing Ch 20 p407-409; Genomes-evolution-
Bioinformatics-Ch 21 p426-434; & 21.6; Genomes & evolutionary history, Ch 26.4, 548-
549. Microarrays Ch 20 p410-411.
Assignment: 1) analyze your DNA gel in class 2) QUIZ #1 3) SNP pre-lab #3
26-Sep W
LAB #3 DNA sequence analysis software; bioinformatics worksheet
Readings:lab manual for week #3
DUE: 1) QUIZ #1 2) pre-lab handout #3 3) RECORD RFLP & sequence data
Assignment: Complete bioinformatics worksheet (in class); Prepare manuscript figures
1-Oct M
Genetics, Hardy-Weinberg principle, and chi-square.
Readings:Genetics Ch 14 p262-272; Hardy Weinburg Ch 23.2 p473-476.
Assignment: 1) articles on human SNPs 2) pre-lab #4
DUE: Manuscript figures
3-Oct W
LAB #4 - Data Analysis - determine genotype; determine population frequencies of
CDK3 SNPs; compare DNA sequence with RFLP data;
Discussion:SNP articles
DUE: pre-lab handout #4 ( H-W problems)
FINAL 'SNP Lab' ASSIGNMENT DUE: Tuesday OCT. 9
BIO 106-05 Wednesday LAB/Monday LECTURE Schedule - Fall 2012
Module 2:Factors that affect biodiversity - Effects of white tailed deer
8-Oct M Biodiversity Mini Lecture; Discuss Sampling Techniques; Discussion NY times article
Readings:Campbell-Ecology & Biosphere Ch 52: 52.1, 52.2, 52.4; Community Ecology
Ch 54 p 1194-1215; Biodiversity & Conservation Ch 56 p 1238-1244 & 56.3 p1249-
NY Times article-Cute deer go bad
Lab #1- collection of soil and leaf litter; set up Berlese Funnels, soil pH, begin SWC &
SOM (Field sampling techniques; identify vegetation; species accumulation curve)
Readings:lab manual for Biodiversity week #1
DUE: Lab Notebook - 1st half
FALL BREAK - OCT 13 - Oct 21st
22-Oct M
Soil characteristics - mini lecture; Primary research paper discussion
Readings:Campbell-Invertebrates Ch 33 p 666-669; Soil Ch 37 p 785-789;
Ecosystems & Biogeochemistry Ch 55, p 1218-1222 & 55.4;
Research article-Huffman-Vertebrate herbivore effects on arthropods
Assignment: literature search
Lab # 2 - complete soil analysis: SWC & SOM; examine mesofauna & classify to order;
Use of the dissecting microscope. Record all class data
Reading:Lab manual for week #2
DUE: Literature search assignment
29-Oct M
Statistics (normal distributions, t-test); Discuss Diversity Indices
Readings: Lab Manual - Appendix C 'Statistics Primer'; Lab #3, Diversity indices
Campbell - Shannon Index Ch 54 p1204 1205.
Lowry Stats Website (optional reference)
Assignment: Statistics homework w/sample data, t-test w/ JMP.
31-Oct W Lab #3 - DATA Analysis: apply appropriate statistical tests and indices - use of Excel &
JMP: soil pH, SWC, SOM, mesofauna diversity, vegetation data on seedlings from VCEP
- exclosed vs. unexclosed; species accumulation curve;
Readings:Lab manual - Biodiversity week #3
Campbell: Review Shannon Index Ch 54 p1204 1205.
Assignment: data analysis worksheet (in class); Research articles w/questions
5-Nov M
Discuss Primary research articles; Discuss biodiveristy final assignment
Readings: Rooney et al. - effects of white tailed deer; Rand et al. - lyme disease
Assignment: Quiz #2; Draft of BD manuscript introduction
7-Nov W
Lab #4 - Continue with data analysis & discussion of BD results; how to present the data;
design the next experiment; Continued discussion of biodiveristy final assignment
Assignment: Prepare figures of pH, SWC, and biodiversity data w/legends (in class)
DUE: Quiz # 2; Draft of Introduction
FINAL 'Biodiv' ASSIGNMENT DUE: Tuesday, November 13
10-Oct W
24-Oct W
BIO 106-05 Wednesday LAB/Monday LECTURE Schedule - Fall 2012
Module 3:Behavior in the bean beetle, Callosobruchus maculatus
12-Nov M
Evolution & speciation; bean beetle model system;
Readings: Campbell - review concepts on evolution, natural selection & speciation.
Evolution Ch. 22, p 452-467; Ch. 23, p 469-485; Ch. 24-species concept, 24.1 & 24.2, p
488-498;
Assignment:find & read primary article on bean beetle behavior
14-Nov W
LAB #1 - Oviposition preferences in Callsobruchus maculatus-experimental set-up, data
collection
Readings: Lab Manual week #1; Review metric conversions Appendix A
Assignment: Find & read primary article on bean beetle behavior
19-Nov M
Discussion on student primary articles - brief presentations or group discussions
Readings:Student chosen primary articles
DUE: Bean beetle primary literature assignment
21-Nov W
This is scheduled as a Friday (no class)
THANKSGIVING BREAK - NOV. 22 - NOV 25TH
26-Nov M
Discussion of how the data should be analyzed - what stats to use
Readings: review stats notes and readings
Assignment: Zannou et al. Life history of flight morph females
28-Nov W
LAB #2 - Statistical analysis of bean beetle data w/JMP; Chi-square, t-tests, Regression
analysis; Graphing with Excel
Readings: Lab manual for week #2; review stats notes and readings
Assignment:( in class) stats analysis worksheet
3-Dec M
Discussion of research article on Callosobruchus maculatus behavior
Readings:Zannou et al. Life history of flight morph females
5-Dec W
LAB #3 - Ovary dissection and slide preparation; Use of the compound microscope;
Readings: Lab Manual week #3; Appendix B & D on pipetting & use of the microscope.
Assignment: Quiz #3
10-Dec M Discussion of final assignment; Overview of fluorescence microscopy;
12-Dec W
LAB #4 - Fluorescence Microscopy - Observation of ovules in female bean beetles
stained with fluorescent nuclear and actin dyes. Class divided in half, 2 x 1.5 hr sessions:
Readings: Lab manual for week #4;
DUE:QUIZ #3
DUE: LAB NOTEBOOKs - 2nd half
DUE: Final Assignment - Sunday, December 16
FINAL EXAM - Practical and essay exam - As scheduled during finals week