Reading the Story in DNA
by Lindell Bromham

ISBN-13: 978-0-19-929091-8

• 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

• Introduction on laboratory techniques (PDF)
  • Lab safety rules
  • Pipetting
  • "Cell management" - sterile technique and plating
  • Biological spectroscopy using a spectrophotometer

• Read the handout

• Introduction on microscopy (PDF)
  • Microscope operation rules
  • Basic microscopy techniques
  • Images on different samples

• 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

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Download and install Matlab (Caltech-only)
• Read the Woods Hole tutorial on basics of Matlab (PDF)
• Assignment 1: Matlab Problems (PDF) with sample code, due on Mon. 4/4 at the beginning of class

• Moran, U., R. Phillips, and R. Milo. SnapShot: Key Numbers in Biology. Cell (2010) vol. 141(7): pp. 1262-1262
• Whitman et al. Prokaryotes: The unseen majority. PNAS (1998) pp. 6578-6583
• Pace NR. Time for a change. Nature (2006) vol. 441: pp. 289

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

• Protocol (PDF)
  • Collect pond water
  • Extract DNA from pond soil

• Read the handout

• Matlab tutorial on Power of Ten (ZIP)

• Group 1: Process DNA from Caltech pond
• Group 2:
  • Estimation exercise on Snapshot
  • Journal club on Whitman paper
  • Matlab tutorial on Powers of Ten project (Need to bring laptop!)

• Group 1:
  • Estimation exercise on Snapshot
  • Journal club on Whitman paper
  • Matlab tutorial on Powers of Ten project (Need to bring laptop!)
• Group 2: Process DNA from Caltech pond

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Assignment 2: Powers of Ten project (PDF) due on Mon. 4/11 at the beginning of class

• Bromham, pp. 104-119
• Lee JB, Hite RK, Hamdan SM, Xie XS, Richardson CC, et al. DNA primase acts as a molecular brake in DNA replication. Nature (2006) vol. 439 pp. 621-624

• 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)

• Introduction on modern biology
• Biology tutorial: Restriction enzymes
• Group 1: Biology tutorial: PCR
• Group 2: Bulk restriction digest

• Group 1:
  • Bulk restriction digest
  • PCR
  • Journal club on Van Oijen paper
• Group 2:
  • Biology tutorial: PCR
  • Journal club on Van Oijen paper
  • PCR

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Assignment 3: PCR and digestion problem (PDF) due on Mon. 4/18 at the beginning of class

• 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 A:
  • Journal club on Van den Broek paper
  • Single molecule digest
• Group B:
  • Gel electrophoresis
  • Biology tutorial: TOPO TA cloning and transformation

• Group A (Meet in the moring):
  • Gel electrophoresis
  • Biology tutorial: TOPO TA cloning and transformation
• Group B (Meet at night):
  • Journal club on Van den Broek paper
  • Single molecule digest

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Assignment 4: Molecular biology write up (PDF) due on Mon. 4/25 at the beginning of class.

• Pushkarev et al. Single-molecule sequencing of an individual human genome. Nature Biotechnology (2009) vol. 27 (9) pp. 847-850

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

• Protocol (PDF)

• Read the journal paper

• Bioinformatics Handout (PDF)

• Group 1: TOPO TA cloning
• Group 2:
  • Bioinformatics (Need to bring laptop!)
  • Final presentation premise
• Journal club on Pushkarev paper

• Group 1:
  • Bioinformatics (Need to bring laptop!)
  • Final presentation premise
• Group 2: TOPO TA cloning
• Matlab tutorial on TPM (ZIP) (Need to bring laptop!)

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Assignment 5: Single molecule restriction assay write up (PDF) due on Mon. 5/2 at the beginning of class. Download the sample data ("TPM_SampleData_2011.zip") for your analysis.
• Final presentation: Each group of four needs to submit a one paragraph (about 10-15 sentences) proposal on the topic of your group's choice. One proposal per group. Due on Mon. 5/2

• Dantas et al. Bacteria Subsisting on Antibiotics. Science (2008) vol. 320 pp. 100-103
• Optional:
  • Dadachova E, et al. Ionizing Radiation Changes the Electronic Properties of Melanin and Enhances the Growth of Melanized Fungi. Plos One (2007) vol. 2(5)
  • Monod. The Growth of Bacterial Cultures. Annual Review Microbiology (1949) pp. 371-385
  • Neidhardt FC. Bacterial growth: Constant obsession with dN/dt. Journal of Bacteriology (1999) vol. 181 pp. 7405-7408

• 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)

• Journal club on Dantas paper
• Group 1: Growth curves and antibiotics
• Group 2: Time-lapse microscopy of growing colonies

• Group 1: Time-lapse microscopy of growing colonies
• Group 2: Growth curves and antibiotics
• Pick colonies for sequencing

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Count colonies from Growth curves and antibiotics during office hours
• Assignment 6: Growth curves and time-lapse microscopy write up (PDF) due on Thursday 5/12 at 5PM in 153 Broad (Turn in a hard copy!)

• Rosenfeld et al. Gene Regulation at the Single-Cell Level. Science (2005) (307) pp. 1962-1965
• Optional:
  • Zenklusen et al. Single-RNA counting reveals alternative modes of gene expression in yeast. Nature Structural and Molecular Biology (2008) vol. 15 (12) pp. 1263-1271

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

• Protocol (PDF)

• Read the handout

• Matlab tutorial on LacI titration curve (ZIP)

• Biology tutorial: gene expression
• Group 1: LacI titration curve
• Group 2::
  • Matlab tutorial on LacI titration curve (Need to bring laptop!)

• Group 1:
  • Matlab tutorial on LacI titration curve (Need to bring laptop!)
• Group 2: LacI titration curve

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Final presentation: discuss with your TA during office hours or by appointment to find 3 reference paper per person and writes 200 words about each paper. Due on Mon. 5/16 at the beginning of class.

• Aligning sequences (Bromham, pp. 185-215)
• Hugenholtz. Exploring prokaryotic diversity in the genomic era. Genome Biology (2002) vol. 3 (2) pp. 1-8
• Optional
  • Takahashi and Yamanaka. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell (2006) vol. 126 pp. 663-676

• Read the handout
• Download and have the softwares mentioned in the tutorial handout installed before arriving in class
• Download your sequencing results before arriving in class

• Aligning sequences tutorial (PDF)
• Bioinformatics lecture 2010 (PPTX | PDF)

• Journal club on Hugenholtz paper
• Sequence analysis Part I (Need to bring laptop!)

• Discussion on evolution
• Final presentation: meet with TAs to make an outline in class or by appointment

• Assignment 7: LacI titration curve questions (ZIP) due on Thursday 5/26 at 5PM in 153 Broad (Turn in a hard copy!).
• Final presentation: Outline on presentation per group due on Mon. 5/23 at the beginning of class.

• Rosenfeld et al. Gene Regulation at the Single-Cell Level. Science (2005) (307) pp. 1962-196
• Optional
  • Qin et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) vol. 464 (7285) pp. 59-65 (Supp. Info.)

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

• Protocol (PDF)

• Plate count anomaly
• Sequence analysis Part II (Need to bring laptop!)

• Journal club on Rosenfeld paper
• Discuss on 16s portfolios including sequence analysis
• Final presentation: start putting slides together (Need to bring laptop!)

• Make sure you have written down in-lab notes following the guidelines in the Grading handout (PDF)
• Check plates from Plate count anomaly and answer questions from handout in your notebook during office hours on Wednesday
• Final presentation: revise slides and meet with your TA to practice presentation by appointment. Each group need to upload their final slides with supporting materials into the corresponding subfolder on the course network drive (http://snowdome.caltech.edu/aph162/Bi1X%202011/Bi1X_FinalPresentation_2011/) no later than 10 PM on Monday 5/30.

• Memorial Day

• 8:30-9am: Each group can check slides format on the presenting computer
• 9am-12pm: Final presentations in class

• Lab notebook is due on Mon. 6/6 at noon in 153 Broad
• 16s Portfolio is due on Mon. 6/6 at noon in 153 Broad (Turn in a hard copy!)

• Lab notebook is due at noon in 153 Broad
• 16s Portfolio is due at noon in 153 Broad (Turn in a hard copy!)

• Enjoy your summer!