Packaging our components into one Oak Wilt detection tool kit:

What is inside:

Hand-held drill, pre-packaged Dipstick reagents, Dipstick reagents handling and mixing tool for extracting the DNA

ddH2O, freeze-dried LAMP reaction mix

Portable heater for amplifying target DNA

This tool kit will be sent to our users to help identify if the oak tree is infected by oak wilt or not, in a timely manner.

Extract DNA from oak tree:

The hardware team 3D prototyped an extraction tool that can collect wood dust of the oak tree. See Hardware page’s Extraction Tool Design section. They successfully extracted some fine sapwood samples that may contain fungus DNA from an oak tree in a local park in Toronto. We learnt from Dr. Loyd and Demian say that, in their usual practice, they obtain a piece of wood in their forest and grind it into fine samples for oak wilt diagnosis.

The Dipstick DNA Extraction kit will be able to isolate DNA from the unwanted materials. If the sample contains fungus DNA, Dipstick should be able to extract it. To prove that, the hardware team tested Dipstick on a related fungal species. See Hardware page’s Dipstick Experiment section.

Activate freeze-dried reagents

See Experiment page’s Step 5 and its associated results. Wet lab tested if the selected LAMP reaction still works well when it is freeze-dried. The result shows a positive amplification on oak wilt DNA template. To reactivate the freeze-dried LAMP reagent (contains primer mix, master mix, and water), our users will need to add ddH2O and the extracted DNA to the freeze-dried LAMP reagent in a PCR tube.

Amplify target DNA

See Hardware page’s Thermistor section. The hardware team built a portable heater that has accurate temperature control using a PID controller. For LavaLAMP master mix, the heater will operate at 71 degree celsius to amplify the DNA isothermally.

Visualize results with naked eyes:

See Experiment page’s Step 3 and its associated results. Currently, iGEM Toronto demonstrated successful primer designs and the ability to observe results through SYBR green fluorophores. Users would need to use a hand-held UV lamp. Wet Lab tried out the NEB colorimetric master mix to demonstrate that it is possible to visualize LAMP results using naked eyes. See Experiment page’s Step 1 and its associated results. Further experiments are required to prepare our own master mix that can be freeze-dried and observed through color change.

So what?

If our users detected positive oak trees on site, actions can be done to contain and control the spread of oak wilt disease.