Tag: genetics

Horizontal Gene Transfer: Plasmids

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.

One bacteria cell passes a piece of DNA (called a plasmid) to another. From USA Today — Image links to more complete information.

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.

Anti-biotic Brass

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.

DNA Extraction Labs

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.

Strands of DNA rising from the interface between crushed split pea “sludge” and rubbing alcohol. Bubbles trapped beneath the strands make for interesting convective-like patterns.

Split Pea DNA

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).

Split pea residue left behind after filtering.

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.

When the DNA is mixed in with the split pea filtrate (right) it becomes a little harder to distinguish. On the left you can see that the clear rubbing alcohol floats on top of the denser split pea/water/salt mixture.

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.

Strands of DNA on a glass rod.

Human DNA

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.

A few strands of human DNA (belonging to an individual who asked to be referred to as “Suzanne”) in a test tube. The rubbing alcohol is dyed blue for visual contrast.

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.

DNA strands under the microscope.

Why Diversity is Important

Diversity has been a recurring theme this semester. It started with the diversity conference our middle schoolers attended earlier this year, which, unfortunately, I’m not sure they got a lot out of. As a result, I’ve been making a little bit of a point to bring up the subject when it intersects with our work. This week were were talking about evolution and natural selection, as was able to talk about the practical advantages of both genetic and social diversity.

When the environment changes, species don’t usually have time to adapt. Instead, individuals who already have the genes for beneficial existing traits — traits that work well under the new conditions, like the ability to survive warming climates — will tend to breed more, and over the generations, more and more of the population will have the advantageous trait.

Therefore, to ensure the continuation of the species, we’ll want to have the maximum amount of genetic diversity.

Then I tacked. I asked if anyone was not interested in seeing the continuity of humanity, and the usual wags piped up to say that they could take homo sapiens or leave it. So I showed them the Voluntary Human Extinction Movement website. VHEMT advocates that people voluntarily stop having kids so that humanity eventually will become extinct, restoring the Earth’s environment to a healthy state. Their motto is, “May we live long and die out.”

The class was pretty uniformly aghast.

I particularly like the VHEMT website because it’s really hard to tell if they’re serious or not; which drove my students a little bit crazy. And I eventually got the key question I was angling for, “How could anyone want humans to go extinct?”

My response was, for them at least, quite unsatisfactory, because I chose to answer with a different question: “Do you think that diversity of thought is good?”

For some, their answer was no. However, I then reminded them of that first amendment to the U.S. constitution has to do with freedom of expression, which does seem to suggest that the founders thought diversity of ideas was a good thing. Just like species, countries with greater diversity of ideas are more likely to be able to adapt to changing conditions and succeed.

The application of evolutionary theory to social situations has, historically, been fraught with abuse (see the eugenics movement in particular). I also did not have time to bring the conversation back to why we might want to protect biodiversity. However, this particular lesson gets the point across that diversity has some important practical benefits that might not always be obvious.

Notes

An interview with VHMET on the Discovery Channel:

Genetics: Tracing the Gypsies back to India

A recent genetic study has confirmed that gypsies (Romani) probably originated in India. Dean Nelson summarizes.

Scientists from Hyderabad’s Centre for Cellular and Molecular Biology collaborated with colleagues in Estonia and Switzerland to compare more than 10,000 samples, including from members of 214 different Indian ethnic groups. They were analysed to match a South Asian Y chromosome type known as “haplogroup H1a1a-M82”, which passes down male bloodlines, with samples from Roma men in Europe.

While there were matches with samples from men throughout the Indian sub-continent, the closest match and the least genetic variation occurred with those from north-west India.

When the researchers overlaid the closest matches onto a genetic map of India, the highest density was in areas dominated by India’s “doma”, “scheduled tribes and castes” – the low caste dalits or untouchables who suffer widespread and generational discrimination and usually do society’s dirtiest jobs.

The researchers believe the descendants of today’s Roma gypsies in Europe began their westward exodus first to fight in wars in what is today Punjab between 1001 and 1026 on the promise of a promotion in caste status.

— Nelson, 2012: European Roma descended from Indian ‘untouchables’, genetic study shows in The Telegraph.

This type of genetic study looks at sections of the DNA sequence, specifically a certain group of genes that is slightly different in people from India compared to everyone else.

A gene is a section of DNA that does a certain job, such as producing a specific protein that results in a certain physical characteristic like eye color. Everyone has the gene for eye color, but some people have a version that gives blue eyes, while others might have a green eye version. The different versions of genes are called alleles, so you can say that some people have the allele for blue eyes while others have the green eye allele. Groups of alleles are passed on from parent to child, which is why children look like their parents, and why different ethnic groups from around the world look different from each other.

So if we take a group genes (call it a haplogroup) and compare the versions characteristic of Indians to those of Gypsies, we can see how similar the two groups are. This study (Gresham et al., 2001) found that Romani and Asians share 45% of the alleles within this haplogroup, which is pretty high. They also looked at another haplogroup in the mitochondrial DNA (mtDNA) that is only passed on from mothers to their children (it’s matrilineal) and found a 26% match.

Making the assumption that mutations in genes occur at a constant rate, the new study estimates that the Roma emigrated out of India somewhere around 1000 years ago.

The relatively recent ages determined for haplogroup VI-68 and M in this study suggest that the ethnogenesis of the Roma can be understood as a profound bottleneck event. Although identification of the parental population of the proto-Roma has to await better understanding of genetic diversity in the Indian subcontinent, our results suggest a limited number of related founders, compatible with a small group of migrants splitting from a distinct caste or tribal group.

–Gresham et al., 2001: Origins and Divergence of the Roma (Gypsies) in The American Journal of Human Genetics.

This is however, not the only evidence of an Indian origin. There are also significant similarities between the Romani and Indian languages that were noted long before. In fact, there is a fascinating, and my modern sensibilities, quite politically incorrect article on the topic of the origin of the Gypsies in the February, 1880 issue of Popular Science Monthly.

“Junk” DNA: Not so much

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).

Sections of non-junk DNA transcribe messenger RNA which code proteins. Image from Talking Glossary of Genetics via Wikipedia.