Debunking myths on genetics and DNA

Friday, May 27, 2016

The viruses inside us

Dendogram of endogenous retroviruses. Source: Wikipedia.

Last month I posted a discussion on a PNAS paper that reported the discovery of a new class of viruses, called pithoviruses, found in a layer of Siberian permafrost. In their paper [1], the researchers conclude:
"Our results further substantiate the possibility that infectious viral pathogens might be released from ancient permafrost layers exposed by thawing, mining, or drilling."
I found this possibility intriguing both from a scientific point of view as well as a sci-fi point of view: there are plenty of books out there on zombies and aliens, but what about ancient viruses that thawed from the ice thanks to global warming?

An attentive reader, though, didn't buy the sci-fi "threat" and asked in the comments whether viruses are necessarily bad. Normally we think of viruses as pesky little things. And while most will make us sick for a short time only, some can indeed be deadly, and others can inflict long-term complications.

The reader who asked that question, however, is absolutely right: over the course of evolution, viruses have been beneficial to us. Viruses have driven genetic diversity by transferring genes across species, and in fact, we still carry remnants of viral genes in our DNA, comprising roughly 8-10% of our genome. They are called "endogenous retroviruses", or ERV.

In the rest of this post I will address two questions:

  • What are those viral genes doing in our genome?
  • How did they get there?

What are viral genes doing in our genome?

Most of them are doing nothing. They are "deactivated", meaning they do not code for proteins. Our genome is made of many redundant elements that over the course of evolution were silenced because no longer useful, only to be turned on again later on when a new adaptation happened.

One such example is the placenta, where endogenous retroviruses have been found to be expressed [2-4] and play a role in the growth and implantation of the tissue. We can only speculate on why retroviral genes are expressed in the placenta, but the hypothesis is indeed quite interesting: in order to survive, retroviruses debilitate the immune system. In general, this is not a good thing for the body, except in one very special instance: an embryo is literally a parasite growing inside the mother's body. It carries extraneous DNA and, under normal circumstances, something carrying extraneous DNA would be considered an antigen and attacked by the immune system. Therefore, the expressed viral proteins found in the trophoblasts, the outer layer of the placenta, would have the role of suppressing a possible immune reaction against fetal blood.

Another property viruses have is that of cell fusion: they literally "merge" cells together into one membrane. A second hypothesis is that this property is used during the development of the placenta to build a barrier between the maternal circulation and the fetal circulation.

How did viral genes end up in our genome?

A virus enters the body of a host with the sole purpose of replicating. In order to do so, viruses hijack the cell's own replicating machinery. Retroviruses in particular carry strands of RNA which, once injected inside the cell, are turned into DNA that is then carried inside the cell nucleus and integrated into the cell's genome. This ensures that once the cell replicates, the bit of viral DNA is replicated too.

There is a special set of cells, however, such that when the virus infects them it literally gets stuck. These cells are the gametocytes, a.k.a. oocytes in women, and spermatocytes in men, which do not duplicate unless they get fertilized. But by then the virus is no longer active. It's literally stuck, in the sense that the integrated viral DNA now cannot replicate and cannot escape the host's DNA. It's just a bit of non-functional DNA that gets duplicated along as the embryo grows. The new individual now carries the viral genes in every cell of his/her body, even in the gametocytes, and hence the viral genes will be inherited by future generations as well.

And that's how viruses ended up in our genome a long, long time ago and have literally become "evolutionary fossils." In fact, by looking at these endogenous retroviral sequences, scientists are able to reconstruct the evolution of ancient viruses.


[1] Legendre, M., Bartoli, J., Shmakova, L., Jeudy, S., Labadie, K., Adrait, A., Lescot, M., Poirot, O., Bertaux, L., Bruley, C., Coute, Y., Rivkina, E., Abergel, C., & Claverie, J. (2014). Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology Proceedings of the National Academy of Sciences, 111 (11), 4274-4279 DOI: 10.1073/pnas.1320670111

[2] Emerman M, & Malik HS (2010). Paleovirology--modern consequences of ancient viruses. PLoS biology, 8 (2) PMID: 20161719

[3] Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, Farmer JL, & Spencer TE (2006). Endogenous retroviruses regulate periimplantation placental growth and differentiation. Proceedings of the National Academy of Sciences of the United States of America, 103 (39), 14390-5 PMID: 16980413

[4] Dupressoir A, & Heidmann T (2011). [Syncytins - retroviral envelope genes captured for the benefit of placental development]. Medecine sciences : M/S, 27 (2), 163-9 PMID: 21382324

Sunday, May 15, 2016

To all of you who think New Mexico is all desert ...

... think again! ;-)
The Jemez mountains are covered in ponderosa pines and rivers like Rio Puerco give rise to the beautiful waterfalls we scouted with some photographer friends this past week-end. Enjoy!

© Elena E. Giorgi

© Elena E. Giorgi

© Elena E. Giorgi

© Elena E. Giorgi

Friday, May 13, 2016

Using Supercomputers to Probe the Early Universe

Artist's depiction of the WMAP satellite gathering data to understand the Big Bang. Source: NASA.

For decades physicists have been trying to decipher the first moments after the Big Bang. Using very large telescopes, for example, scientists scan the skies and look at how fast galaxies move. Satellites study the relic radiation left from the Big Bang, called the cosmic microwave background radiation. And finally, particle colliders, like the Large Hadron Collider at CERN, allow researchers to smash protons together and analyze the debris left behind by such collisions.

Physicists at Los Alamos National Laboratory, however, are taking a different approach: they are using computers. In collaboration with colleagues at University of California San Diego, the Los Alamos researchers developed a computer code, called BURST, that can simulate a slice in the life of our young cosmos.

While BURST is not the first computer code to simulate conditions during the first few minutes of cosmological evolution, it can achieve better precision by a few orders of magnitude compared to its predecessors. Furthermore, it will be the only simulation code able to match the precision of the data from the Extremely Large Telescopes currently under construction in Chile. These new telescopes will have primary mirrors that range in aperture from 20 to 40 meters, roughly three times wider than the current very large telescopes, and an overall light-collecting area up to 10 times larger.

A few seconds after the Big Bang, the universe was composed of a thick, 10-billion degree "cosmic soup" of subatomic particles. As the hot universe expanded, these particles' mutual interactions caused the universe to behave as a cooling thermonuclear reactor. This reactor produced light nuclei, such as deuterium, helium, and lithium — all found in the universe today. "Our code, developed with Evan Grohs, who at the time was a graduate student at UCSD, looks at what happened when the universe was about 1/100 of a second old to a few minutes old," says Los Alamos physicist Mark Paris of the Theoretical Division. "By determining the amount of helium, lithium and deuterium at the end of those first few minutes of life, BURST will be able to shed light to some of the existing puzzles of cosmology."

One such puzzle is dark matter: physicists know that such matter exists because of the way galaxies rotate, but they haven't been able to detect it because it does not radiate in any known spectrum. Physicists have theorized that dark matter is made of so-called "sterile neutrinos", which do not interact with any other particle and are responsible for these unobservable interactions. "Once we start getting data from the Extremely Large Telescopes," Paris explains, "we will model sterile neutrinos into the BURST code. If we get a good description, we will be able to prove their existence."

Measurements of the cosmic microwave background radiation have led physicists to theorize "dark radiation," a speculative form of energy that may have acted in the early universe. BURST could possibly reveal whether or not dark radiation is real and caused by sterile neutrinos. "The universe is our laboratory," Paris enthusiastically concludes. "BURST will help us answer questions that are currently very difficult to address with particle colliders like the one at CERN."

Ongoing support for the project is provided by the National Science Foundation at UCSD and the Laboratory Directed Research and Development program through the Center for Space and Earth Sciences at Los Alamos. BURST will be running on the supercomputing platforms at Los Alamos National Laboratory.

Grohs, E., Fuller, G., Kishimoto, C., Paris, M., & Vlasenko, A. (2016). Neutrino energy transport in weak decoupling and big bang nucleosynthesis Physical Review D, 93 (8) DOI: 10.1103/PhysRevD.93.083522

Wednesday, May 4, 2016

May IWSG: Spring is finally here!

This is a monthly event started by the awesome Alex J. Cavanaugh and organized by the Insecure Writer's Support Group. Click here to find out more about the group and sign up for the next event. You can also sign up for the newsletter.

First off a big announcement: the IWSG anthology, titled Parallels: Felix Was Here, is here! Featuring 10 stories from ISWG authors, hand-picked by a panel of agents and writers, you can now get it from Amazon and other retailers. Complete list of purchasing links here.

It's May already, can you believe it? How was your month of April, did you do the A-Z challenge? Already making plans for the summer?

My April wasn't too bad: I'm wrapping up a project at work and I finished a short story which will be the prequel to a new world I'm creating. It's a space opera and I'm very excited about it mostly because... I've never written space opera before! :-) Here's a question for you: would you release a prequel as soon as it's ready or would you wait until the first installment in the series is ready to be released too?

In other news, we've had some very much needed moisture in Northern New Mexico and so I took the chance and shot some droplet macros. :-) Happy May everyone!