Tag Archives: Protocol

Teaching – OA Lesson Plan Development

I’m currently collaborating on tweaking/developing a lesson plan and corresponding curriculum to teach Washington high school students about the chemistry involved in ocean acidification.

This is a project that’s already been in the works and I’m being brought in to assist (or, take over?) with the development. I’m pretty interested and excited by this. The reason for my excitement is that I was in the secondary education program to become a certified secondary education teacher while I was in graduate school. So, this project lets me apply the knowledge I garnered about teaching science during that time.

The current state of the project has a lab protocol, but no real lesson plan for the teachers to utilize. The lab protocol, in my view, is a bit too dense for high schoolers to digest and is a bit too much of “do this, write down the number: that’s ocean acidification!” It currently lacks an important element of science pedagogy: discovery. My goals are to tweak the protocol in such a fashion that it is more engaging and, possibly, hypothesis-(i.e. discovery) driven. This type of teaching has been shown to greatly improve retention and help improve/develop critical thinking skills.

The lesson plan should have sufficient information for teachers to decide if the lesson is appropriate for them to teach (e.g. which Washington state standards are addressed, what learning level(s) does the lesson require, what materials/supplies are needed, etc.), if they have enough time to conduct the lesson, and if they have ample understanding of the topic to feel comfortable teaching it.

I’ve put this project on GitHub. It allows for active collaboration on projects. Although there are some hurdles for those collaborators who have not used the service before, I think there are some good organizational benefits that are worth dealing with the initial headaches that might come for beginning GitHub users.

One benefit to developing this project on GitHub is that all changes are tracked and a description of the changes are required when they are made. This makes it relatively to see what changes were made, by who, and when. Although using something like Google Docs also automatically tracks changes, it does not allow the ability to provide a comment when changes are made. Because of this, it’s not always clear why the change was made in the first place.

An additional benefit, and this is the main reason I think it’s best to develop this project on GitHub, is the Issues tracker (see screenshot):


The Issues section allows for targeted discussion of the project and eliminates the volleys of email that often happen on collaborative projects. It will keep all discussions about this project in a single location and won’t require exhaustive searches of emails that easily get buried during a work week. Additionally, the discussions can remain focused on specific topics without getting lost within a emails attempting to broach multiple topics at once.



Benedict – 4/4/14

Initiated zebrafish infection with M. marinum G13 lux, either with or without the formation of the yellow pigment.

OD600nm of “White” M. marinum G13 lux – Initial 2.45 – Adjusted 0.79. Added 750ul of adjusted cells to 7.5ml of E3 with 50 fish in a 6cm petri dish.
OD600nm of “Yellow” M. marinum G13 lux – Initial 0.64. Adjusted 0.22. Added 1.5ml of adjusted cells to 7.5ml of E3 with 50 fish in a 6cm petri dish.

Note: The pigmented M. marinum appeared to be clumpier when resuspended into E3.

Fish left to get infected at 28oC for 4 days.

2014-04-04 13.56.23

Non-pigmented (Left) and Pigmented M. marinum used for the experiment.

Also infected some fish with Mycobacterium abscessus to see if it will kill the fish.

  • M. abscessus NZRM 4048 was adjusted to an OD600nm of 1 – Initial 1.76, Adjusted 0.66.
  • Use of 24 well plate with 5 fish per well containing 1ml of E3.
  • Infected fish with – 1ul at OD1, 10ul at OD1, 100ul at OD1, 10ul at OD10 and 100ul at OD10. Note: OD10 was cells adjusted to 1 then concentrated 10 fold i.e. resuspend 1ml into 100ul.
  • Fish left to get infected at 28oC.

2014-04-07 14.41.07


Plate used for M. abscessus infections. 5 fish per well. Different concentrations of M. abscessus per column.