Full schedule

LECTURE AND LAB SCHEDULES FOR FALL 2008

LECTURES
LABS
PREPARATION

Lecture 1: Sept. 8

-Why this course exists

-Introduction to genetic research

-Summary of experiments and assignments for the term

-Mark breakdown

-Principles/Guidelines to ensure fair grading for all students

-Lab safety rules

No lab
No preparation

Lecture 2: Sept. 15

-Restriction Enzymes (Discovery, Properties, Uses)

-Polymerase Chain Reactions (Principles, Uses)

-Visualization of DNA using Agarose Gel Electrophoresis

-Tips on how to do well in this week’s “warm-up” lab

Read Intro Lab

Sept16, 17 ----- Lab 1

-Restriction enzyme digest

-PCR

-Agarose gel

-Gel documentation

Read Intro Lab and work out the volumes for a master mix.

Lecture 3: Sept. 22

-Process of plasmid DNA purification

-Properties of cloning vectors

-Use of vectors

-Expressed Sequence Tags (Properties, Uses)

-How to effectively use NCBI Website
Read Experiment 1 protocol

Sept. 23, 24 -----Lab 2

-DNA purification for EST analysis
Read Experiment 1 protocol

Lecture 4: Sept. 29

-Principles and process of DNA Sequencing

-How to search the Honeybee genome using ESTs

-Question/answer: Article 1
Read Assignment 1, First assigned (Article 1) paper and Experiment 2 protocol. Answer assigned questions.

Sept. 30, Oct. 1 -----Lab 3

-Restriction enzyme digest and agarose gel

-Prepare DNA for DNA sequencing

-Send DNA for sequencing
Read Experiment 1 protocol

Lecture 5: Oct. 6

-Studying DNA polymorphisms through Mouse Murder Mystery

-Genomic DNA isolation from mouse tissue

-Markers to be used in the PCR

-DNA polymorphism (Different types, how to detect them)

-Principles behind polyacrylamide gel electrophoresis

-Discussing mandatory Article 2 (question/answer period)
Read Article 2. Answer assigned questions

Oct. 9, 10 -----Lab 4

-Isolation of mouse DNA

-Agarose gel analysis

-First round of PCR (Sets 1 & 2)

Read Experiment 2 protocol

Those who are doing a PCR with assigned primers must have the volumes of the master mix in their notebook.

Oct. 13

Thanksgiving (No Lecture)

Oct. 14, 15 -----Lab 5

-Second round of PCR (Sets 3&4)

-Polyacrylamide gel and Gel documentation

Read Experiment 2 protocol

Those who are doing a PCR with assigned primers must have the volumes of the master mix in their notebook.

Lecture 6: Oct. 20

-Principles and process of RNA isolation

-Basic subcloning

-Discussing mandatory Article 3 (question/answer period)
Read Experiment 2 protocol and Experiment 3 protocol. Read Article 3. Answer assigned questions

Oct. 21, 22 -----Lab 6

-Polyacrylamide gel and Gel documentation

-Restriction digestion and gel isolation of DNA fragment

-Restriction digestion of vector
Read Experiment 2 protocol and Experiment 3 protocol

Lecture 7: Oct. 27

-Principles and process of RT-PCR

-Det 1

-Discussing mandatory Article 4 (question/answer period)

-Assignment 1 due
Read Article 4. Answer assigned questions

Oct. 28, Oct. 29 ----- Lab 7

-RNA preparation

-Agarose gel

-Pictures of plants

- Set up ligation reactions
Read protocols for experiment 3, 4 and 5.

Lecture 8: Nov. 3

-Yeast experiment

-Genetic screens

-Discussing mandatory Article 5
Read Article 5. Answer assigned questions

Nov. 4, 5 -----Lab 8

-RT-PCR

-pick mutants and restreak

-transform ligation reactions
Read protocols for experiment 3, 4 and 5.

Lecture 9: Nov.10

Yeast Complementation Analysis

-Discussing mandatory Article 6 (question/answer period)

-Assignment 2 due
Read Article 6. Answer assigned questions

Nov. 11, 12----- Lab 9

-Polyacrylamide gel electrophoresis/Gel documentation

-Grid and mate mutants for complementation

-pick transformants for DNA isolation
Read protocols for experiments 3, 4 and 5

Lecture 10: Nov. 17

Critical appraisal of scientific articles

-Discussing mandatory Article 7 (question/answer period)
Read Article 7. Answer assigned questions

Nov. 18, 19 -----Lab 10

-select for complementation analysis

-mini plasmid DNA isolation

Lecture 11: Nov. 24

Critical appraisal of scientific articles (continued)

-Assignment 3 due

Nov. 25, 26 ----- Lab 11

-Last day of Labs

-Complementation analysis

-beta-galactosidase assay

-Restriction digestion of clones
Read protocols for experiments 3 and 5. Have volumes for restriction digests written in your notebook.

Dec. 1

-Review

-Assignment 4 due

-Notebooks due

Biology 3596a/b Home

LECTURES	LABS	PREPARATION
Lecture 1: Sept. 8 -Why this course exists -Introduction to genetic research -Summary of experiments and assignments for the term -Mark breakdown -Principles/Guidelines to ensure fair grading for all students -Lab safety rules	No lab	No preparation
Lecture 2: Sept. 15 -Restriction Enzymes (Discovery, Properties, Uses) -Polymerase Chain Reactions (Principles, Uses) -Visualization of DNA using Agarose Gel Electrophoresis -Tips on how to do well in this week’s “warm-up” lab		Read Intro Lab
	Sept16, 17 ----- Lab 1 -Restriction enzyme digest -PCR -Agarose gel -Gel documentation	Read Intro Lab and work out the volumes for a master mix.
Lecture 3: Sept. 22 -Process of plasmid DNA purification -Properties of cloning vectors -Use of vectors -Expressed Sequence Tags (Properties, Uses) -How to effectively use NCBI Website		Read Experiment 1 protocol
	Sept. 23, 24 -----Lab 2 -DNA purification for EST analysis	Read Experiment 1 protocol
Lecture 4: Sept. 29 -Principles and process of DNA Sequencing -How to search the Honeybee genome using ESTs -Question/answer: Article 1		Read Assignment 1, First assigned (Article 1) paper and Experiment 2 protocol. Answer assigned questions.
	Sept. 30, Oct. 1 -----Lab 3 -Restriction enzyme digest and agarose gel -Prepare DNA for DNA sequencing -Send DNA for sequencing	Read Experiment 1 protocol
Lecture 5: Oct. 6 -Studying DNA polymorphisms through Mouse Murder Mystery -Genomic DNA isolation from mouse tissue -Markers to be used in the PCR -DNA polymorphism (Different types, how to detect them) -Principles behind polyacrylamide gel electrophoresis -Discussing mandatory Article 2 (question/answer period)		Read Article 2. Answer assigned questions
	Oct. 9, 10 -----Lab 4 -Isolation of mouse DNA -Agarose gel analysis -First round of PCR (Sets 1 & 2)	Read Experiment 2 protocol Those who are doing a PCR with assigned primers must have the volumes of the master mix in their notebook.
Oct. 13 Thanksgiving (No Lecture)
	Oct. 14, 15 -----Lab 5 -Second round of PCR (Sets 3&4) -Polyacrylamide gel and Gel documentation	Read Experiment 2 protocol Those who are doing a PCR with assigned primers must have the volumes of the master mix in their notebook.
Lecture 6: Oct. 20 -Principles and process of RNA isolation -Basic subcloning -Discussing mandatory Article 3 (question/answer period)		Read Experiment 2 protocol and Experiment 3 protocol. Read Article 3. Answer assigned questions
	Oct. 21, 22 -----Lab 6 -Polyacrylamide gel and Gel documentation -Restriction digestion and gel isolation of DNA fragment -Restriction digestion of vector	Read Experiment 2 protocol and Experiment 3 protocol
Lecture 7: Oct. 27 -Principles and process of RT-PCR -Det 1 -Discussing mandatory Article 4 (question/answer period) -Assignment 1 due		Read Article 4. Answer assigned questions
	Oct. 28, Oct. 29 ----- Lab 7 -RNA preparation -Agarose gel -Pictures of plants - Set up ligation reactions	Read protocols for experiment 3, 4 and 5.
Lecture 8: Nov. 3 -Yeast experiment -Genetic screens -Discussing mandatory Article 5		Read Article 5. Answer assigned questions
	Nov. 4, 5 -----Lab 8 -RT-PCR -pick mutants and restreak -transform ligation reactions	Read protocols for experiment 3, 4 and 5.
Lecture 9: Nov.10 Yeast Complementation Analysis -Discussing mandatory Article 6 (question/answer period) -Assignment 2 due		Read Article 6. Answer assigned questions
	Nov. 11, 12----- Lab 9 -Polyacrylamide gel electrophoresis/Gel documentation -Grid and mate mutants for complementation -pick transformants for DNA isolation	Read protocols for experiments 3, 4 and 5
Lecture 10: Nov. 17 Critical appraisal of scientific articles -Discussing mandatory Article 7 (question/answer period)		Read Article 7. Answer assigned questions
	Nov. 18, 19 -----Lab 10 -select for complementation analysis -mini plasmid DNA isolation
Lecture 11: Nov. 24 Critical appraisal of scientific articles (continued) -Assignment 3 due
	Nov. 25, 26 ----- Lab 11 -Last day of Labs -Complementation analysis -beta-galactosidase assay -Restriction digestion of clones	Read protocols for experiments 3 and 5. Have volumes for restriction digests written in your notebook.
Dec. 1 -Review -Assignment 4 due -Notebooks due