APH 162

General

 

 

Schedule

 

Please note: this schedule is tentative and may change as the term progresses.

Week 1

Session 1: Logistics and laboratory basics
Pre lab:
In lab:
Homework:
  • Brief summary in your lab notebooks of all laboratory exercises.
Session 2: Introduction to microscopy
Reading:
  • Read the Matlab handouts (below) for information on your homework.
In lab:
Homework:

 

Week 2

Session 1: Pond Water Collection
Reading:
In lab:
  • Protocols for Session 1 (PDF)
    • Pond water collection
    • Sample centrifugation & storage
  • Journal club #1
Session 2: DNA Extraction
Reading:
  • Reading:
    • Water sample DNA extraction protocol (PDF)
In lab:
  • Protocols for Session 2 (PDF)
    • DNA Extraction
    • Spectrophotometry of extracted DNA

 

Week 3

Session 1: PCR and Examination of environmental samples
Reading/pre-lab:
In lab
  • Discuss reading and PCR
  • Group 1: Pond water and microscopy
  • Group 2: 16s Journal Club
Session 2: PCR and Examination of environmental samples
In lab
  • Start PCR reactions (PDF)
  • Group 1: 16s Journal Club
  • Group 2: Pond water and microscopy
Homework:  

 

Week 4

Session 1: Single molecule restriction digest
Reading/pre-lab:
In lab:
  • Single molecule restriction digest (docx)
Session 2: Bulk restriction digest
In lab:
  • Lambda Restriction digest (docx)
Homework:
  • TPM Assignment: Due Monday, April 26 (PDF)

 

Week 5

Session 1: Cancelled
Reading/Prelab:
In lab:
  • Cancelled
Session 2: Gel electrophoresis
In lab:
  • Week 5 Lab handout (PDF)
  • Intro to Bioinformatics (PDF)
Homework:
  • Gel Analysis (PDF), Due Monday May 3rd at 7pm.

 

Week 6

Session 1: TOPO Transformation and Plating
Reading/Prelab:
In lab:
  • Journal Club
  • TOPO transformation (PDF)
Session 2: Growth curves and antibiotics
In lab:
Homework:

 

Week 7

Session 1: Video microscopy of growing colonies
Reading:
In lab:
  • Journal Club
  • Video Microsopy of Bacterial Growth (PDF)
  • Pick colonies for sequencing
Session 2: Start final projects
In lab:
  • Journal Club/ Final Topic groups
  • Epifluorescence (PDF)
Homework:
  • Virus analysis, single cell microscopy, Read three papers (PDF)

 

Week 8

Session 1: IPTG Titration curve
Reading:
In lab:
  • IPTG Titration curve (PDF)
Session 2: Plate Count Anomaly
In lab:
  • Matlab Analysis tutorial
  • Plate count anomaly (PDF)
Homework:
  • IPTG Titration curve analysis (PDF)
  • Meet with TAs in final groups to discuss outline for presentation. Split topics between members.
  • Prepare slides for practice presentation next week.

 

Week 9

Session 1: Sequencing Part 1
Reading:
In lab:
  • Bring your computers for analysis. If you don't have a laptop, you may use a computer in the Bi1x lab.
  • Arbel's Presentation on Sequences (PDF)
  • Sequencing exercise (PDF)
Session 2: Sequencing Part 2
In lab:
  • Final presentation meeting: practice presentation
  • Sequencing exercise (PDF) continued
Homework:
  • 16S Portfolio, due June 7th (PDF)
  • Final presentation, on June 7th

 

Week 10

Session 1: Memorial Day (No Class)
Session 2: Open lab time
In lab:
  • Continue on the sequence analysis assignment (included in the 16S Portfolio)
  • Work on 16S portfolio, due June 7th (PDF)
  • Continue refining presentation, on June 7th

 

Week 11

Session 1: Monday June 7th, 11AM- 1PM, Pizza Lunch!
In class:
  • Turn in 16S Portfolio
  • Final presentation
  • Lab notebooks due