teaching « James and the Giant Corn

February 12, 2010

Easy DNA extractions (with pineapple!)

Filed under: teaching — Tags: dna, teaching — James @ 2:00 pm

First wet lab work I've done in more than a month. Also how often do you see a bottle actually LABELLED as "Strawberry DNA extraction"?

It’s actually quite easy* to extract visible quantities of DNA from fruits and vegetables using nothing less common than dish soap and rubbing alcohol. For our class we chose strawberries, but I also heard of people using kiwis and bananas to great success.

Of course it takes a mere second for someone to say “I don’t eat food with genes in it” and 15 minutes to prove them wrong by extracting DNA from an (organically grown) banana, but that imbalance between the time and effort it takes to repeat piece of false information and the time it takes to refute that same misinformation isn’t going to change. It is something anyone in the habit of going up against misconceptions with nothing but demonstrable facts on their side has to get used to.

The demonstration itself went pretty smoothly. Unfortunately, since it’s a hundred student lecture, we had to do most of the preparation beforehand, so I don’t think most of them realized just how easy DNA extractions can be.

*Note that this recipe calls for the use of meat tenderizer to break down some of the remaining proteins in the solution before extracting DNA, and points out that pineapple juice will make an acceptable alternative (as it also contains enzymes that break down proteins.) I mention this only to reiterate my point, as if you hadn’t heard it before, that pineapples are one of the most awesome fruits known to mankind.

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February 3, 2010

We got to genetics in class today and the story of the shrunken 2 gene

Filed under: biology,Plants,Politics,teaching — Tags: ap1, cal, class assignments, shrunken2, sweet corn — James @ 1:17 am

Arabidopsis that carries broken copies of both the AP1 (apetala1) and CAL (cauliflower) genes. The flower bearing stems have been replaced by these cauliflower-head-like growths. Image from "Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development" by Frank Wellmer et al (in PLOS Genetics a creative commons licensed journal). Article here: http://dx.doi.org/doi:10.1371/journal.pgen.0020117

Just in time for me to put together my worksheet for Thursday! I’ve managed to work in the CAL gene, which I talked about last week in my discussion of Cruciferous vegetables:

Cauliflower plants (and broccoflower plants) have broken copies of the CAL gene, which (when it isn’t broken) is helps the plant decide to switch from producing stems that were bear flowers to the flowers themselves. Without a functional version of CAL, cauliflowers just keep making denser and denser stems, producing the distinctive heads of cauliflower. If you have journal access, you can read more about the CAL gene at this science paper: http://dx.doi.org/10.1126/science.7824951

I also threw in a question that uses the shrunken2 gene (one of the two most common genes that convert normal starchy corn into sweet corn). From the question in question:

Note the shriveling of the yellow kernels that carry two broken copies of the shrunken2 gene, the purple kernels carry either one broken and one working copy of shrunken2, or two working copies. The change in color is controlled by another gene nearby on the same chromosome, shrunken2 itself has no effect on the color of corn kernels. Photo credit goes to MG Neuffer and MaizeGDB.

Corn kernels without a working copy of the shrunken2 gene can’t convert very much of the sugar provided by photosynthesis in the leaves of the corn plant into starch. Instead, sugar itself accumulates in the kernel making the corn taste quite sweet.

When sugary corn kernels are dried, they shrivel up, while starchy ones remain relatively round and smooth. This has to do with the fact that sugars are water soluble while starch is not. So, as I understand it, corn kernels with more sugar are also a greater percentage water than corn kernels that are made mostly of starch.

The mutant form of shrunken2 was identified by John Laughnan, a maize geneticist at the University of Illinois Urbana-Champaign. The story of the discovery as told in Maize Genetics and Breeding in the 20th Century by Peter Peterson and Angelo Bianchi: (more…)

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January 27, 2010

First Day Teaching (epilogue)

Filed under: biology,teaching — Tags: floral development — James @ 2:37 pm

Belated I know. The first section I ever taught could have gone better. Twenty-nine people showed up for a section with an enrolment cap of 25 in a classroom with only 17 desks and no eraser for the chalk board. So that was fun. Still, I made it through a review the parts of a plant (roots, shoots, and leaves), the parts of a flower (sepals, petals, stamens and carpels), and a diagram of why a plant needs both mitochondria and chloroplasts (chloroplasts harvest and store light energy, mitochondria turn stored energy into the form used by the cell, ATP). And the second section I taught, later that same afternoon, went a lot better (In addition to being more sure of the material, I had time to steal back enough desks to bring the room to its rated capacity of 25, hunt down an elusive chalk board eraser, and draw the first set of figures on the board before the students showed up.)

A recreated example (should be familiar to anyone who, like me, took the first two weeks of intro botany):

The basic diagram of four parts of a (eudicot) flower. From the outside in. A: Sepals, small, generally boring green bits that look a fair bit like tiny petals. B. Petals. C. Anthers. The male part of the flower, responsible for producing pollen. D. Carpal(s) The female part of the flower. Pollen lands on the top surface, then grows a tube down into the flower to fertilize the eggs and central cells.

I’ve seen variants of this figure in 3 courses I took as an undergraduate, and now I’m using it myself. I’d be interested to hear if anyone has seen (or can think up) variants that might be easier for people with no background studying plants to grasp. (more…)