Stanford/BIOE44:Lab info

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Lab Attendance

Lab attendance is mandatory and there are no make-up labs. A family crisis or severe illness requiring attention from the infirmary and prohibiting you from all your coursework are acceptable reasons for missing lab and every effort will be made to accommodate you in these exceptional circumstances.


Assignment % of Final Grade
Daily Lab Quizzes 15%
Daily Lab Notebook 25%
Research Article Review 30%
Design Project Report & Presentation 30%

Research Article Review

The class will work in groups of 2 or 3 to read and review the following 5 articles:

  1. Ow DW, DE Wet JR, Helinski DR, Howell SH, Wood KV, and Deluca M. Transient and stable expression of the firefly luciferase gene in plant cells and transgenic plants. Science. 1986 Nov 14;234(4778):856-9. DOI:10.1126/science.234.4778.856 | PubMed ID:17758108 | HubMed [Firefly+Plants]
  2. Horstmann V, Huether CM, Jost W, Reski R, and Decker EL. Quantitative promoter analysis in Physcomitrella patens: a set of plant vectors activating gene expression within three orders of magnitude. BMC Biotechnol. 2004 Jul 7;4:13. DOI:10.1186/1472-6750-4-13 | PubMed ID:15239842 | HubMed [MossTransformation]
  3. Gibson DG. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res. 2009 Nov;37(20):6984-90. DOI:10.1093/nar/gkp687 | PubMed ID:19745056 | HubMed [GeneBuildingYeast]
  4. Chan LY, Kosuri S, and Endy D. Refactoring bacteriophage T7. Mol Syst Biol. 2005;1:2005.0018. DOI:10.1038/msb4100025 | PubMed ID:16729053 | HubMed [RefactoringGenomes]
  5. Rutherford SL and Lindquist S. Hsp90 as a capacitor for morphological evolution. Nature. 1998 Nov 26;396(6709):336-42. DOI:10.1038/24550 | PubMed ID:9845070 | HubMed [EvolutionaryCapacitor]
  6. Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, and Heidmann T. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 2006 Dec;16(12):1548-56. DOI:10.1101/gr.5565706 | PubMed ID:17077319 | HubMed [JurassicPark]
All Medline abstracts: PubMed | HubMed
  1. Firefly+Plants: Karina, Alex
  2. Moss Transformation: Drew <-- demo on Tuesday
  3. Gene Building in Yeast: Travis, Aaditya, Daniel
  4. Refactoring A Genome: Sunny, Frank
  5. Evolutionary Capacitance: Claire, Sanjay
  6. Retrovirus Resurrection: Scott, Chris

Each team will need to prepare a 15 minute presentation summarizing your reading and critical assessment of each paper. Your presentation should be 6 slides (not more, not less), following this structure:

  1. Cover slide (authors, title of paper, journal)
  2. Main finding (explain the single most important discovery or new technology presented in the paper)
  3. Primary evidence (how is the main finding supported by the work presented in the paper?)
  4. Main weakness (what is the strongest criticism or weakness that can leveled at the work presented in the paper?)
  5. Future work (given the work presented in the paper, what are the 3 most important questions to be answered, or tools to be developed, next?)
  6. Related reading (list four related research articles that you would like to read next in order to followup on what you've learned from this paper; state your "why" for each paper.

GRADING: Two-thirds of your grade will be on the content and quality of your six slides (please be concise and clear). One-third of your grade will be on your presentation. All readers/presenters should speak during the presentation.

SLIDE DESIGN: Take a look at the advice here, then use or find your own style!


  1. Firefly+Plants: Class/Lab, 13 May
  2. Moss Transformation: Class/Lab, 13 May
  3. Gene Building in Yeast: Class/Lab, 13 May
  4. Refactoring A Genome: Class/Lab, 13 May
  5. Evolutionary Capacitance: Class/Lab, 13 May


Design Projects, Reports & Presentations

[details to be discussed Tuesday 11 May]

Late Work

Late work for major assignments will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week. Daily quizzes and lab notebooks will not be accepted late.

Lab Notebooks