Middle and High School … from a Montessori Point of View
Adam Cole has an excellent NPR article on some fascinating researchers who are storing data — text files, web pages, sonnets — on DNA.
This should be a interesting introduction for middle-schoolers to the idea of DNA as a means of storing and transferring information. The question I hope to get is, “How did they do that?”
Peter Eisler has a somewhat scary article on the development of drug resistance in bacteria at the University of Virginia Medical Center. The bacteria were resistant to all of their antibiotics. Everything. And the bacteria were able to pass the genes that gave them their resistance to other bacteria: not just to their offspring, but horizontally to other species of bacteria by exchanging bits of DNA called plasmids.
When genes are passed on from parent to offspring, or even from one microbe to another by cell splitting, it’s called vertical gene transfer. Horizontal transfer, on the other hand, involves different individual organisms passing genes from one to the other. It would be as if two people could exchange genes by shaking hands.
When the doctors began analyzing the bacteria in their first patient, who’d transferred from a hospital in Pennsylvania, they found not one, but two different strains of CRE bacteria. And as more patients turned up sick, lab tests showed that some carried yet another.
“We were really frustrated; we hadn’t seen anything like this in the literature,” says Costi Sifri, the hospital epidemiologist. “The fact that we had different bacteria told us these cases were not related, but the shoe leather epidemiology suggested to us that all these (infections) came from the same patient. … We realized we might be seeing a mobile genetic event.”
In other words, it looked like a single resistance gene was jumping among different bacteria from the Enterobacteriaceae family, creating new bugs before their eyes.
— Eisler 2012: Deadly ‘superbugs’ invade U.S. health care facilities in USA Today.
The really scary part:
There is little chance that an effective drug to kill [drug resistant] CRE bacteria will be produced in the coming years. Manufacturers have no new antibiotics in development that show promise, according to federal officials and industry experts, and there’s little financial incentive because the bacteria adapt quickly to resist new drugs.
Interesting research shows that brass and other copper metal alloy surfaces kill bacteria and degrade their DNA much better than stainless steel or plastic.
Plastic and stainless steel surfaces, which are now widely used in hospitals and public settings, allow bacteria to survive and spread when people touch them.
Even if the bacteria die, DNA that gives them resistance to antibiotics can survive and be passed on to other bacteria on these surfaces. Copper and brass, however, can kill the bacteria and also destroy this DNA.
— Grey (2012): Fit brass fixtures to cut superbugs, say scientists in The Telegraph.
My middle school class tried DNA extractions from dried split peas and cheek cells for a lab this week, and the experiments went rather well.
For the split peas, we followed the Learn.Genetics lab. I blended the peas in some salty water at the front of the class (“Don’t you need a lid for that blender?”), and filtered it. This gave about 120 ml of filtrate. Then I added in 3 tablespoons of dish soap to the filtrate. The soap to breaks down the cell membranes and nuclear membranes because they are made of lipids (fats).
I shared out the resulting green liquid to the four groups. Each student was able to get a fair amount into a test tube so they could complete the lab as individuals.
Disintegrating the cell and nuclear membranes with soap exposed the DNA, but the long DNA molecules tend to be coiled up around proteins. Each student added a pinch (highly quantified I know) of meat tenderizer to their test tube to break down the protein and allow the DNA to uncoil. Enzymes are biological catalysts, large complex molecules that accelerate chemical reactions, the breakdown of proteins in this case, without breaking down themselves, so only a little is needed.
Finally, each student carefully poured rubbing alcohol into the test tube. I had to demonstrate how to tilt the test tube while alcohol was being poured into it so that the alcohol would not mix in with the pea soup but, instead, form a layer at the top, since the alcohol is less dense than the suspension of split peas in salty water.
If it was done carefully enough, the DNA would precipitate at the boundary between the two liquids. If not, the DNA would still precipitate, but it would be mixed in together with the green soup and be harder to distinguish.
Either way, however, students could see the long strands of DNA, and fish them out with glass rods.
The human DNA extraction procedure is well demonstrated by the NOVA video. One student who missed the split pea lab did this experiment instead because it’s faster. It does not require blending to crush the cells, nor does it need the meat tenderizer enzyme.
Although this procedure produces a lot less DNA — after all, you’re only getting a few loose cells from the insides of your cheeks — the strands are still visible. And it’s YOUR DNA.
Since I instructed the class on how to use the microscopes last month, one student wanted to see what his DNA looked like under the microscope. An individual DNA molecule is too small to see, but the strands we have are bunches molecules that are visible. They just don’t look like very much.
From PBS’s DNA The Secret of Life.
It has always strained credibility that the 98% of our DNA not used to code proteins would be useless. But this non-coding DNA picked up the name “junk DNA” because no-one quite knew what it did. In fact, one study (Nóbrega, 2004) found that deleting large chunks of DNA had no discernible effect on mice; the mice born without these pieces of non-coding DNA were viable.
However, a slew of papers from the Encode project indicate that the part of our genome formerly known as junk DNA, regulates the 2% that does the protein coding:
The researchers … have identified more than 10,000 new “genes” that code for components that control how the more familiar protein-coding genes work. Up to 18% of our DNA sequence is involved in regulating the less than 2% of the DNA that codes for proteins. In total, Encode scientists say, about 80% of the DNA sequence can be assigned some sort of biochemical function.
— Jha (2012): Breakthrough study overturns theory of ‘junk DNA’ in genome in The Guardian.
This is more good news for useless bits of biology (see the appendix).
NOVA shows how you can see your own DNA at home. (Learn.Genetics has more details about why it works.)
DNA interactive is another great resource for studying the history of genetics and how we manipulate and use it today (recommended by the indispensable Anna Clarke). They have lesson plans and nice pages on the modern techniques used to work with DNA.
I have not done much with genetic sequencing myself and I found the website interesting and informative. I have, however, written programs to get and work with the GenBank database, which is not that hard since they have some easy tools to work with. I would love to figure out how to get a sample sequenced and then run it through GenBank to identify it. It would so nicely integrate the curriculum, using a practical exercise to solve a problem (like what species are on the nature trail), while using the same tools and resources that scientists use, and tie wonderfully into the short stories in Mirable.
