Schedule Su18

Week 9 (7/11) – Sequence Results – MEET IN MoSE 1201A

Before lab,

In lab,

  • Align sequences & Analyze PCR results
  • Pair PCR results with fluorescence assay results and enter data in class spreadsheet
  • Workshop: Results and Discussion

After lab,

  • Update your lab notebook.
  • Complete the Week 10 pre-lab (open on Friday on Canvas) by Tuesday 7/17
  • Writing Assignment: Complete draft of lab report, upload to Canvas, and bring a print copy to class

Week 7 (6/27) – Sequencing & Fluorescence Results

Before lab,

  • Writing Assignment: Methods, revised to date
  • Complete the Week 7 pre-lab (open on Friday on Canvas) by Tuesday midnight

In lab,

After lab,

  • For review, here’s the video on fluorescence excitation wavelengths and emissions spectra. Time indices 0:10-1:07 and 3:55-5:00 have what you need to know. You’ll need to be logged into GT to view.
  • Update your lab notebook.
  • No lab next week! Happy 4th of July!
  • Complete the Week 8 pre-lab (open on Friday on Canvas) by Tuesday 7/10
  • Writing Assignment: Results and figure for fluorescence assay

Week 6 (6/20) – Choosing Colonies to Genotype and Phenotype

Before lab,

  • You have the option to REVISE your Introduction and Literature Cited. Cite 3 peer reviewed papers in your introduction. Upload your revised assignment to Canvas, being sure to label the file as “revised” at the end of the file name. We will grade only your most recent upload.
  • Read the three protocols for lab this week before you come to class, and bring any questions with you. (This will be available Tuesday). View this Streak Plating video before you come to class to help you visualize and conceptualize this procedure. (Note: we’ll use sterile toothpicks rather than a flamed loop to plate our bacteria.)
  • No Prelab for credit this week, but there is an open prelab if you have specific protocol step inquiries so that we can help you better understand the procedures.

In lab,

After lab,

  • Update your lab notebook, including Video 3 on correct technique for Streak Plating.
  • Complete the pre-lab (open on Monday on Canvas)
  • Writing Assignment: Methods, revised to date

Week 5 (6/13) – Transformation & Plating

Before lab,

  • Writing Assignment: Introduction and Literature Cited. Cite 3 peer reviewed papers in your introduction. Follow the rubric for introduction, literature cite, writing, and formatting sections.
  • Read “Protocol – Transformation.pdf”, available by Monday here and in our inbox.
  • Complete the Pre-lab by Tuesday midnight (pre-lab will be release by Monday).

In lab,

After lab,

  • Update your lab notebook.
  • Complete the pre-lab (open on Monday on Canvas)
  • Writing Assignment: TBD

Week 4 (6/6) – Purification of cut DNA and Ligation; Gels

Before lab,

  • Writing Assignment: Research Topic Sentence & Methodology. Due on Canvas and as a print copy in lab.
  • Skim: Randall et al 2016. For this week, spend 30-45 on this reading to help ground you in the methodology and origin of our strains. Focus on the abstract, the introduction, and the mutagenesis methodology. Plan to revisit this reading again later in the semester.
  • Review “Weeks 3-4 Protocols – Purification & Ligation.pdf” and note the next steps we’ll need to do in week 4.
  • Complete the Pre-lab (due on Canvas by Tuesday midnight)

In lab,

  • Opening discussion on gel electrophoresis and ligation
  • Gel Electrophoresis
  • Peer review of Methods.
  • Visualize gels
  • Purify of “clean up” the PCR digest (the plasmid digestion was cleaned up by the prep lab) and quantify the concentration
  • Set up the Ligation

After lab,

  • Update your lab notebook.
  • Writing Assignment: Introduction and Literature Cited. Cite 3 peer reviewed papers in your introduction (one of these you’ll need to identify by doing a literature search on your own using the library’s resources).
  • Complete the pre-lab (open on Monday on Canvas)

Week 3 (5/30) – PCR Purification and Digestion

Before lab,

  • Writing Assignment:  In your own words write up a ~1 page overview of the Goal, Research question, and Experimental design (gene, strain, number of samples, steps in experiment) we’ll undertake this summer. Due on Canvas and as a print copy in lab.
  • (Note, we’ll wait until next week to read and discuss the Randall et al 2016 paper.)
  • Read “Weeks 3-4 Protocols – Purification & Ligation”. We will provide print copies in lab.
  • Complete the Pre-lab (due TUESDAY by midnight)

In lab,

After lab,

  • Update your lab notebook.
    • Writing Assignment: Research Topic Sentence & Methodology. Due on Canvas and as a print copy in lab.
    • Skim: Randall et al 2016. For this week, spend no more than 30-45 on this reading to help ground you in the methodology and origin of our strains. Focus on the abstract, the introduction, and the mutagenesis methodology. Plan to revisit this reading again later in the semester.
    • Review “Weeks 3-4 Protocols – Purification & Ligation.pdf” and note the next steps we’ll need to do in week 4.
    • Complete the Pre-lab (open Monday in Canvas).

Week 2 (5/23) – Project Overview & Mutagenic PCR

Before lab,

  • Read Shaner et al 2004
  • Writing Assignment: On your own, write up  one paragraph on why you think monomeric fluorescent proteins could be useful for genetics research (Due at start of lab next week on Canvas)
  • Complete the Pre-lab on Canvas
  • Remember to dress appropriately for lab, and bring spare clothes if you want to store them for the semester in the lab.

In lab,

  • Journal Club: Discuss Shaner et al 2004
  • Project Overview & orientation to today’s Protocols
  • Plasmid DNA extraction
  • Nanodrop quantification of DNA extraction
  • Mutagenic PCR

After lab,

  • Update your lab notebook.
  • Read Randall et al 2016 (you’ll need to be logged into your GT account)
  • Writing Assignment: In your own words write up a ~1 page overview of the Goal, Research question, and Experimental design (gene, strain, number of samples, steps in experiment) we’ll undertake this summer.
  • Complete the pre-lab (open on Monday on Canvas).

Week 1 (5/16) – Introduction and Basic Bench Skills

–We will have lab during the first week of summer classes! 

Before lab,

  • Go to the course Canvas site to view and read the course syllabus.
    Please read these two short news reports on genetics research to generate new fluorescence markers for research: “Biologists Discover Gene Behind ‘Plant Sex Mystery” and “Cells Don Festive Holiday Colors”. (Note for later that these are news articles, not peer-reviewed scientific papers.)
  • Please bring:
    • laptops
    • lab coats
    • wear long pants
    • wear close-toed shoes.
      • Details of the dress code are fully explained in the course syllabus.

In lab,

  • Lab Safety talk and contract
  • Micropipette demo and exercise
  • How to read a scientific paper
  • Set up your lab notebook online
  • Record your pipettor video and upload to your notebook and to Canvas.

After lab,

  • Read Shaner et al 2004
  • Writing Assignment: On your own, write up  one paragraph on why you think monomeric fluorescent proteins could be useful for genetics research (Due at start of lab next week on Canvas)
  • Complete the Pre-lab for next week.