• Nurse. The great ideas of biology. Clinical Medicine (2003) vol. 3 (6) pp. 560-568
• Watch IBM's Powers of Ten Movie (youtube)

• Read the handout (PDF)

In lab:

• Introduction on laboratory techniques
  • Lab safety rules
  • Pipetting/Restriction Digest
  • "Cell management" - sterile technique and plating
  • Biological spectroscopy using a spectrophotometer

• Read the handout (PDF)

In lab:

• Introduction on microscopy
  • Microscope operation rules (Micro Manager Manual)
  • Basic microscopy techniques (Kohler Example)
  • Images on different samples

• Read the handouts:
  Digestion background
  Gel

• Matlab handout (ZIP)
• How to connect to FC1 (PDF)

In lab:

• Gel electrophoresis of restriction digests

• Introduction to Bi1x
• Group 1: Logistics and laboratory basics
• Group 2: Microscopy and Powers of Ten

• Journal club on Nurse paper
• Group 1: Microscopy and Powers of Ten
• Group 2: Logistics and laboratory basics

• Meet at the BBB ponds at 7:00PM
• Gel electrophoresis of restriction digests
• Matlab tutorial: bring laptops with Matlab installed

• Assignment 1 (PDF)

• Dantas et al. Bacteria Subsisting on Antibiotics. Science (2008) vol. 320 pp. 100-103

• Read the handout
• Write pre-lab in your notebook following the guidelines in the Grading handout (PDF)

• Handout (PDF)
• Strains List (PDF)

• Read the handout
• Write pre-lab in your notebook following the guidelines in the Grading handout (PDF)

• Handout (PDF)
• Strains List (PDF)

• Group 1:
  • Growth Curves
• Group 2:
• Journal Club
• Growth Movies

• Group 1:
• Journal Club
• Growth Movies
• Group 2:
  • Growth Curves

• Assignment 2 (PDF)

• Van den Broek et al. Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Research (2006) vol. 34 (1) pp. 167-174

• Read the handout
• Write pre-lab in your notebook following the guidelines in the Grading handout (PDF)

• Protocol (PDF)

• Read the handout
• Write pre-lab in your notebook following the guidelines in the Grading handout (PDF)

• Protocol (PDF)

• Group 1:
• Journal club: van den Broek
• Fly crosses
• Group 2:
• Single molecule restriction assay

• Group 1:
• Single molecule restriction assay
• Group 2:
• Journal club: van den Broek
• Fly crosses

• Assignment 3 (PDF)

• In place of a journal article there will be a discussion session following Rob's lecture.

• Read the handout
• Write pre-lab in your notebook following the guidelines in the Grading handout (PDF)

• Handout (PDF)
• Appendix (PDF)

• Read the handout
• Write pre-lab in your notebook following the guidelines in the Grading handout (PDF)

• Protocol (PDF)

• Matlab handout (ZIP)

• Group 1:
  • Luria/Delbrück Lecture
  • Discussion Session
  • Fluctuation test
• Group 2:
  • Mouth swabs (optional)
  • DNA Extraction

• Group 1:
  • Mouth swabs (optional)
  • DNA Extraction
• Group 2:
  • Luria/Delbrück Lecture
  • Discussion Session
  • Fluctuation test

• Everyone:
• Matlab tutorial (growth movies, single cell digest)

• Assignment 4: See Section 6 of Luria-Delbrück Handout

• Pace NR. Time for a change. Nature (2006) vol. 441: pp. 289

• Read the handout
• Write pre-lab in your notebook

• Handout (PDF)

• Write pre-lab in your notebook

• Handout (PDF)

• Everyone:
  • Biology tutorial: PCR, primer design, 16S sequences
  • 16S PCR on purified microbial DNA
  • Journal club

• Everyone:
  • Biology Tutorial: TOPO Reaction/Transformation
  • PCR Purification
  • TOPO Reactions

• Driever and Nüsslein-Volhard. The bicoid Protein Determines Position in the Drosophila Embryo in a Concentration-Dependent Manner. Cell (1988) vol. 54: pp. 95-104

• Read the handout
• Write the pre-lab in your notebook

• Handout (tgz)

• Handout (PDF)

• Lecture: French Flag Model
• Group 1:
• Fly embryo collection
• Embryo mounting and imaging
• Group 2:
• Colony PCR

• Journal club: Driever
• Group 1:
• Colony PCR
• Group 2:
• Fly embryo collection
• Embryo mounting and imaging

• Assignment 5: See Fly Embryo Handout

Week 8

Week 9

Week 10