2013 Project Expectations

Week

Objectives

1

25.02-01.03

• Agree on the course structure
• Meet the partners, and determine how their interests and expertise can feed the project
• Be able to articulate the water problem
• Mind-map to decide on the research path by defining directions to research
• Hello World with an arduino
• Clarify familiarity with biological techniques

ACTION ITEMS for next week:

• Edit and upload video documentation (Sachiko)
• Background research on mapping (Nicolas)
• Background research on Arsenic and E. coli (Jasmina)
• Background research on mobile labs and field compatible labs (Romain)
• Background research on GMOs in Switzerland (Emilie)
• Find out how to collect water samples from Dr. de Alencastro at ENAC (Emilie)
• Access biodesign.cc
• Prepare to discuss your background research findings (all)

2

04.03-08.03

• Exchange feedback on the first class and documentation – how to document your work and research
• Basics of wet-lab research
• How to use github
• Articulate the research direction based on further research
• Set up an action plan and objective for next week
• Evaluate participation using the Group Process Questions

ACTION ITEMS for next week:

• Before 15.03, make an entry to biodesign.cc as discussed (all)
• Research existing coliform bacteria detection methods (Jasmina, Romain)
• GMO legal issues continued (Emilie)
• Contact Prof. van der Meer and learn the type and mechanism of arsenic uptake of the bioreporter (Emilie)
• Research arsenic detection methods minus bioreporter (Nicolas)

3

11.03-15.03

• Logistic discussion on the dates + group self-reflection questions
• Skype session with Bangalore
• update on research from last week + final decision/direction/team making to discuss with Robin on Tuesday

ACTION ITEMS

for next Tuesday 19 March

- Upload any primary literature pdf you found on the wiki.epfl.ch/biodesign-realworld/files section (everyone)

- Update biodesign.cc

• water sampling method for Arsenic/metals (Emilie)
• mobile labs (Romain)
• coliform bacteria presentation (Jasmina)
• PCR primers used in PCR detection of microbes (Sachiko)

- Take the information found, and make a matrix (as drawn on the white board) of all methods found for both arsenic and coliform bacteria.

for next Friday 22 March

• Contact Nina Buffi (Design and construction of a portable whole-cell living bacterial biosensor for the detection of arsenic in water) (Sachiko)
• Find out relevant kits for E. coli detection so we can order them to test (Romain, Jasmina)
• Contact lifepatch for mapping (Nicolas)
• Water sampling method for bacteria (please try to contact someone from here ---there is a group from EPFL http://www.eawag.ch/forschung/wut/schwerpunkte/trinkwasserchemie/index_EN) (Emilie?)

NEW as of Tuesday 19 March

• Upload the matrix (as a pdf) on biodesign.cc, and summarize the motivation for choosing fluorescence as a device
• Take 2 paths arsenic GFP or E. coli/bacteria (fluorescence detection), and write all of the possible steps in designing a sensor

4

18.03-22.03

• Articulate the prototype proposal (arsenic vs coliform detection)and mechanism of how to realize the demonstrable prototype

Action Plan

Before Friday 26 March

• biodesign.cc: (Emilie) Upload the existing matrix (as a pdf) on biodesign.cc, and summarize the motivation for choosing fluorescence as a device

On Friday 26 March

• Meet with Nina Buffi 10am (all)
• Meet with Biosafety officer for setting up a B1 laboratory 14:15 SV cafe (Sachiko)

Before Friday 29 March

• biodesign.cc: (Sachiko) Regulations on setting up a B1 laboratory

5

25.03-29.03

• 29.03 NO in-person feedback - Good Friday
• Email contact with Robin and Sachiko to obtain feedback

ACTION PLAN

Before Tuesday 9 April

• prototype a fluorecence meter
• discuss the direction based on your experience building the fluorescence meter
• biodesign.cc (WHO?) Aresenic GFP reporter on a chip
• biodesign.cc (all) documentation on the process/what went into choosing the components of the fluorescence meter

For Tuesday 9 April
Mid-term presentation

Each person has to present a part of the presentation. (one person per part of presentation? or any other organization welcome)

• Aim of the Project
• Motivation
• Background including other technologies/community usability pros and cons-discuss the direction based on your experience building the fluorescence meter + interview with Nina Buffi
• Design Criteria -what was the design criteria and why?
• Prototype Details

-what was the process in arriving to this prototype?

- can you demonstrate a basic measurement?
- what are the issues for proceeding in this direction?
- which application will you choose and why?

6

01.04-05.04

• 5,6,7.04 Thursday - Sunday hack-a-taq
  DIY PCR hardware and wetware for E. coli detection

ACTION PLAN

Each person has to present a part of the presentation. (one person per part of presentation? or any other organization welcome)

• Aim of the Project
• Motivation
• Background including other technologies/community usability pros and cons-discuss the direction based on your experience building the fluorescence meter + interview with Nina Buffi
• Design Criteria -what was the design criteria and why?
• Prototype Details

-what was the process in arriving to this prototype?

- can you demonstrate a basic measurement?
- what are the issues for proceeding in this direction?
- which application will you choose and why?

7

08.04-12.04

• 09.04 Project proposal presentation and feedback

for Friday 12 April

Dichroic mirror / filter sourcing (Nicolas)
Lens sourcing (Nicolas)
LED sourcing (Nicolas)

Canon powershot CHDK sourcing (Jasmina)
Research CHDK projects relevant to this project (Jasmina)

Generation of waste and relevance to sample holder etc. (Emilie)

Update the process entry on biodesign.cc (Romain)

• Price and purchase necessary items for the next prototype round

8

15.04-19.04

9

22.04-26.04

• Obtain in-person feedback on design direction
• on biodesign.cc
  • the thinking behind selection of filters, and finally how we got them (Nicolas)
  • why we need to search outside of the LED catalogues for the 280nm light source (Romain)
  • add the data analysis on the As eGFP, and eGFP (Jasmina)
  • the references to the literature on the safety (Emilie)
    
    Other action items:
    - count the bacteria plated last week (try using a spot-counting program --- image J should have something like this)
    - look for the rat poison - does it contain As?
    - testing the microscopy grade filter/dichroic mirror set up with bacteria (can the light source be a laser if LED is not strong enough?)
    - play with the CHDK camera set up
    - Schedule the field trip (Romain)
    
    
    Inoculation Monday night (let me know what time)
    TP lab use - Tuesday morning with eGFP bacteria

10

29.04-03.05

11

06.05-10.05

• to decide what kind of experiment we would like to do in Dr. van der Meer's lab, and when
• details on the hiking day/visit to Sion

12

03.05-17.05

• Visit Sion, hiking/collection of water
• contact Dr. van der Meer's lab

13

20.05-24.05

• Arsenic water testing in Prof. van der Meer's lab UNIL
• Final Presentation Preparation

14

27.05-31.05

til 3.06

• Motivate the project and explain the workings of the prototype in a presentation (group)
• Demonstrate the prototype (group)
• Oral exam (individual)