Team:Stanford/Notebook/Lab Work/Week 3

Spring: Brainstorming | Spring Meetings

Summer: Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Summaries

7/5 Monday

Planning Meeting Notes

Agenda

• Design Updates
  • Analog Comparator (Chris & Alex)
  • Redundancy between the two proposals
  • Degree of phosporylation
  • Dynamic range and mechanisms

• • Digital Comparator (Francisco & Karina)
  • RSID; standardizing the design
  • Introducing a PoPs signal output

• Characteristics between the two Comparators
  • What makes the two different?

• Applications
  • Vaginal Infections/Preterm Birth

• is it really a ratio?
• Other ideas: Targeting Cancer Cells, oscillators

• Administrative Details
  • Ordering Stuff: Oligos ordering sheet, Digestion and Gel Extraction Kits?
  • Stipend?
  • Sponsorship Updates
  • MDV Presentation

Goals For the Week

• Chris & Alex
  • need to make 50x TAE
  • complete plasmids as far can get w/o kinase and phosphotase
  • order DNA sometime this week
• Francisco & Karina
  • Run orginal and new designs by Christina
  • design standard sRNA designs and place order by the end of the week

7/6 Tuesday

Greg

• During weekly meeting got up to speed with what the team’s been doing while I was away
• Used heat-shock transformation protocol for DH5alpha to transform with the following genetic material, left to culture overnight:

7/8 Thursday

Christopher

Running a Gel of F2620, pBAD, and psb4A5:

• Make a 0.8% agarose gel (0.4 g of agarose in 50 ml of TAE)
• Heat in microwave until agarose is completely dissolved
• Add 10.0 ul of EtBr to mix (5000x for a 50 ml solution)
• let run for approximately 1 hr
• refer below for bands

      4A5     E/P 3395 bp
      I0500   E/S (on psb2K3) 1210 bp
      F2620   E/S (on pSB1A2) 1061 bp

Gel Extract the Fragments Running a Gel of PCR Product:

• first need to PCR cleanup
• then run on 1.4% agarose gel (0.7 g of agarose in 50 ml of TAE)
• this is necessary because of the 800 bp size of the fragment

Miniprep Ligations

• F2620+E0240+psb1A2
• pBAD+E0240+psb1A2

Restriction Digests PCR product F2620

Laura miniprepped Alex's/Chris' liquid cultures, using Promega kit

• 2 each of:
  • psb1K3
  • J23107
  • B0032
• eluted in 100 uL H2O

7/9 Friday