Week¹

Material²

Assignment Due³

Jan   23

Lecture 1: Course Overview and Important Things to Know: Sharing materials (via Dropbox, UVA Box, etc.) throughout the semester. Managing your cells/proteins; you need pure, soluble proteins (WT and mutant). Evaluating purity. Thinking about experimental design. Example of how to devise your own protocol based on the literature (M&M sections; previous work). How to organize your group and execute your experimental design this term.

Reading Material: EnzymeAssays1.pdf (p1-29); LG p 39-45 (buffers) and 105-109 (General cloning methods and transformation; p. 108 – preparing LB medium)

Lab Week 1 : Prepare media, prepare buffers

Jan 30

Lecture 2:  In-class activity I

Reading Material: EnzymeAssays1.pdf (p. 29–44) and POI relevant sections in LabFax4.pdf (Enzyme cofactors) and LabFax5 (Solutions used in enzymology); LG p. 110-119 (protein expression, SDS-PAGE)

Lab Week 2⁴: Protein expression

In-class activity Part I

Feb 6

Lecture 3:  Important Things to Know: More on experimental design: Controls, background signal, how to know when you observe activity; Common mistakes in past years.

Reading Material: EnzymeAssays1.pdf (p. 29–44) and POI relevant sections in LabFax4.pdf (Enzyme cofactors) and LabFax5 (Solutions used in enzymology); LG p. 125-135 (Affinity Chromatography and Dialysis)

Lab Week 3:  Protein purification and dialysis

Due @ 1:00 PM on 2/8/2014: Assignment 1:

POI Proposal re-write

Feb

13

Lecture 4: In-class activity

Reading Material: Literature relevant to your POI; LG p. 147-155 (protein quant), LG p. 52-65 (LDH assays)

Lab Week 4: Protein [ ] determination; progress curves (first kinetics assays)

In-class activity Part II

Feb

20

Lecture 5: In-class activity

Reading Material: Enzyme Assays2.pdf; LG p. 128-138 and 62-80 (LDH assay)

Lab Week 5: Quiz; Kinetics assays, week 2

In-class activity Part III

Feb

27

Lecture 5:  Data-analysis clinic: What is a ‘significant’ result?; processing kinetic data; +/- controls; the ‘blank’ versus baseline subtraction; etc.

Reading Material: Ten Simple Rules for Doing Your Best Research (TSR_best research.pdf)

Lab Week 6: Continue POI kinetic assays (and/or purification, troubleshooting as necessary)

Assignment 2: M&M

Mar

6

Spring Break — No lecture or labs

Mar

13

Lecture 7: POI Group Meeting #1 Student groups will meet during the lecture hour to prepare for their group meeting presentation, which will occur during part of lab session this week. Times/locations will be announced.

Reading Material: POI-relevant literature

Lab Week 7: Continue POI kinetic assays (and/or purification, troubleshooting as necessary);  POI group meetings

Assignment 3: Group Meeting⁶ Presentation I

Mar

20

Lecture 8: Dynamic lecture: Just-In-Time⁵ feedback from Instructors & TAs focusing on questions and problems you submit on-line; POI group discussions

Reading Material:  POI-relevant literature

Lab Week 8: Quiz; Continue POI kinetic assays (and/or purification, troubleshooting as necessary)

Mar

27

Lecture 9:  Dynamic lecture: In class comparison of experimental problems & results.  Two scenarios: (1) We have observed turnover with our POI?  What next?   (2) We have not found enzymatic activity… What next?!?

Reading Material:  POI-relevant literature

Lab Week 9: Quiz; Continue POI kinetic assays (and/or purification, troubleshooting as necessary)

Apr

3

Lecture 10: POI Group Meeting #2  Student groups will meet during the lecture hour to prepare for their group meeting presentation, which will occur during part of lab session this week. Times/locations will be announced.

Reading Material:  POI-relevant literature

Lab Week 10: POI kinetics assays and variations (and/or purification, troubleshooting as necessary);  POI group meetings

Assignment 4: Group Meeting⁶ Presentation II

Apr

10

Lecture 11:  Figure clinic – the good/bad, best practices, common mistakes and pitfalls to avoid in your figures (for poster and manuscript projects)

Reading Material: Ten Simple Rules for Getting Published (TSR_publishing.pdf); POI-relevant literature

Lab Week 11 : Quiz; POI kinetics assays and variations (and/or purification, troubleshooting as necessary)

Assignment 5: Intro, Figures, Future Directions

April

17

Lecture 12: Posters & papers: How to prepare and present a scientific poster and a scientific manuscript (for your final projects 4 and 5).

Reading Material:  POI-relevant literature

Lab Week 12:  Quiz; Final POI kinetics assays and variations; final assays; finalize calculations, plots, etc. with TA input

Prepare posters for local ACS meeting⁷, more details will be given as they become available.

April

24

Lecture 13: Data clinic – Instructors/TAs will help answer questions about synthesizing all your data for a given POI (different partner pairs working on one POI) into a cohesive ‘story’ for the final report and poster.

Reading Material:  —

Lab Week 13: Poster sessions⁷ (to be scheduled in 10-min blocks during this week’s scheduled lab section time)

Assignments 6 and 7: Poster and Presentation by 8:00 AM on April 25 (we need time to print all the posters for presentations starting April 25)

May

1

Lecture 14: Lab clean-up and check-out during lecture time – all sections.  (May 2 is the official last day of classes.)

Assignment 8: Manuscript; 

due by 1:00 pm May 1 (lecture start time; turn in printed copies at labs)