Debunking myths on genetics and DNA

Thursday, February 18, 2016

Ice caps melt, prehistoric virus escapes. No, it's not a movie.

Last week I talked about the connection between global warming and the Zika virus. This week I'll discuss another interesting side effect we might observe in the next decade thanks to global warming. The ice caps will melt. Big deal, we already knew that. But have you ever thought of the stuff trapped in that ice that's going to thaw? What if some of that stuff isn't really dead, just dormant, waiting to come back? Sounds like fiction, but it's not.

Up until a few years ago the general notion was that viruses were small. How small? Let's think in terms of genome units: viruses usually carry a handful of genes, either coded into DNA or RNA, and you can think of these as longs strings of four letters: A,C,T (or U if it's RNA), or G. The letters are called nucleotides, and the genome of most common viruses is typically in the order of tens of thousands of nucleotides long. By comparison, the human genome, with its 3 billion nucleotides, is enormous.

The notion of viruses being "small" compared to living cells was turned upside down with the discovery of megaviruses in 2010 (over one million bases) and, in 2013, of the pandoraviruses, a family of viruses that can reach a staggering 2.5 million bases in genome size.

Before you freak out: so far these gigantic viruses have only been found in unicellular organisms called amoebas, not in humans or any other animals. Amoebas acquire their nutrients through phagocytosis and that's also how the gigantic viruses infect them: the cell membrane forms a vesicle around the particle and engulfs it.

The two specimens of pandoraviruses were found in shallow water sediments, one in Chile and the other one in Australia. They were both so big that they could be visible by optical microscopy, reaching 1 μm in length and 0.5 μm in diameter. Now to the interesting bit: the researchers found over 2,000 genes in these pandoraviruses, of which over 90% looked nothing like any other previously known gene. In fact, they appear to be unrelated to the previously discovered megaviruses. So what are they? A fourth domain of life? A completely isolated niche in the tree of life? Or could they be -- as the sci-fi writer in me wants to think -- the remnants of a completely different form of life, one that existed so long ago that these gigantic particles are all there is left of it?

Ok, I thought I was original when I posed that question, but I wasn't. The researchers who'd first discovered the pandoraviruses wondered about the exact same thing and, in order to find an answer, they went digging through fossils. They found a giant virus (which they named pithovirus) in a sample of Siberian permafrost radiocarbon dated to be over 30,000 years old. And I have to say, they beat me in sci-fi imagination because they go as far as to claim that there may be more gigantic viruses frozen out there that could be released from the ice as global warming takes over. *Insert apocalyptic soundtrack here*

The researchers took a sample of Siberian permafrost layer (corresponding to late Pleistocene sediments older than 30,000 years) and used it to inoculate a particular culture of amoebas (called Acanthamoeba castellanii). Lo and behold, they indeed observed particles of a prehistoric giant virus called pithovirus multiplying in the amoeba culture, making it the most ancient eukaryote-infecting DNA virus revived to date! The observed viral particles were amplified and examined through transmission electron microscopy and were found to have many similarities with the pandoraviruses, only they were even bigger. Contrary to pandoraviruses, though, these pithoviruses showed many more similarities to present-day viruses that normally infect humans and animals. This prompted the researchers to raise the alarm:
"Our results further substantiate the possibility that infectious viral pathogens might be released from ancient permafrost layers exposed by thawing, mining, or drilling. Climate change in the Russian Arctic is more evident than in many other regions of the world. Whereas the average global temperature has increased by 0.7 °C during the last 100 y, the average temperatures of the surface layer of Arctic permafrost have increased by 3 °C during the same period."
As the authors themselves put it,
"This work is a reminder that our census of the microbial diversity is far from comprehensive and that some important clues about the fundamental nature of the relationship between the viral and the cellular world might still lie within unexplored environments."
Now, if you'll excuse me, I think I just got an idea for the next bestselling post-apocalyptic thriller.

Philippe, N., Legendre, M., Doutre, G., Coute, Y., Poirot, O., Lescot, M., Arslan, D., Seltzer, V., Bertaux, L., Bruley, C., Garin, J., Claverie, J., & Abergel, C. (2013). Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes Science, 341 (6143), 281-286 DOI: 10.1126/science.1239181

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

Monday, February 15, 2016

Decoding the Dark Matter of the Human Genome

First appeared on my Huffington Post blog on February 15, 2016. 

In 1994, researchers from Harvard and Stanford published a paper in which they described three mice: one was yellow and fat, one mottled and fat, and the last one was brown and lean. An ordinary image, except for one thing: despite being so different, all three mice were genetically identical.

If their genes were exactly the same, what was causing such striking differences in the mice?

Three genetically identical mice that do not look the same. Why?
Photo credit: Nature Publishing, used with permission

At the time, Karissa Sanbonmatsu--staff scientist at Los Alamos National Laboratory--was working on plasma physics, and she had no idea that one day she would tap into this mystery. Even though she started from a completely different field, from the very beginning she was obsessed by one question: What distinguishes life from matter?

"In order to answer that question, the first place to look is the ribosome," Karissa explains. "It's the oldest molecule found in life."

And for a reason: all living cells are made of proteins, and ribosomes are the "factory" inside the cell where these proteins are made.

The breakthrough came in 2003, when the Q Machine, at the time the second fastest supercomputer in the world, was built at Los Alamos National Laboratory. Using the Q Machine, Karissa and colleagues were able to run the largest simulation ever performed until then in biology, allowing them to be the first team to publish an atomic structure of a ribosome in 2004.

This milestone set the foundation for a deeper understanding of the ribosome. Possible future applications, for example, include making new cancer therapies based on how ribosomes differentiate in healthy versus cancerous tissue.

In the meantime, a new, emerging field had been revolutionizing the way we think of genetics and inheritance: epigenetics. The three lab mice from 1994 were one example of how, by switching genes on and off, genetically identical individuals could have different observable characteristics ("phenotypes"). Epigenetics is the field that studies the mechanisms by which the environment can trigger these on/off gene patterns (called gene expression patterns), and how these modifications can be passed on to the next generation.

Both animal and human studies have shown that traits acquired by the parents, such as stress responses or the ability to store fat, can be passed on to their offspring. While DNA remains unaltered, what triggers these changes in phenotype is the activation or deactivation of genes--in other words, whether certain genes produce the proteins they code for.

But how are genes turned on or off? Specific factors regulate whether a gene is expressed (turned on) or silenced (turned off). These factors are recruited by RNA, the single-stranded molecule implicated in numerous cellular processes, from coding and decoding genes to protein synthesis.

When they were first discovered, RNA and DNA molecules that didn't code for proteins were dubbed the "dark matter" of the genome because their function was unknown. Today we know that these molecules can affect gene expression and even change traits by turning on or off certain genes.

That RNA had the power to turn genes off has been known since the early 2000s, when small RNAs were used to create mice whose cells had one particular gene silenced. Larger RNA molecules that don't code for any specific protein can also be found in different sizes inside the cell. Called long non-coding RNAs (lncRNA), they are present in great numbers in stem cells and embryos and are essential in many developmental processes.

"RNA could be the missing link in epigenetics," Karissa explains. "Ribosomes are made of RNA, and so, for me, the leap from ribosomes to lncRNAs was a natural one."

In order to understand how lncRNAs can turn genes on and off, scientists first need to unveil their molecular structure. Can lncRNAs assume different shapes, or 3D structures, and change function accordingly, or are they bidimensional molecules? Karissa and colleagues are determined to solve the puzzle. The same techniques used to resolve the ribosome structure in 2005 can be applied to lncRNAs, but because of their larger size, the team will need faster and better computational tools than the ones they used 10 years ago.

Luckily, next-generation supercomputing is underway at Los Alamos with the construction of Trinity, a machine fast enough to accommodate simulations of 3D atomic structures. This is where Karissa and colleagues are planning to run their lncRNA models.

Revealing the shape of lncRNAs would be a breakthrough. But for Karissa and her team, another even more ambitious project is on the way: "Thanks to the amazing resources offered by Trinity, we will be able to run the first atomistic simulation of human chromatin, the big 'yarn' of DNA and proteins that sits inside the cell nucleus."

Source: National Institutes of Health

This means simulating the 3D structure of three billion base pairs, plus all the proteins the DNA is wrapped around! All genes reside inside the chromatin, and this is where they are activated or deactivated. Therefore, solving the 3D structure of the chromatin will shed new light on the epigenetic mechanisms that regulate gene expression.

Many diseases are characterized by altered gene expression. For example, DNA-repairing genes are turned off in cancer cells, while genes that promote replication are over-expressed. Understanding the mechanisms that lead to these altered on/off patterns and how to reverse them can pave the way to new therapies and more efficient treatments--a bright future indeed for molecules once dismissed as the genome's dark matter.

Elena E. Giorgi is a computational biologist in the Theoretical Division (Theoretical Biology group) at the Los Alamos National Laboratory and the author of the science fiction thrillers Chimeras, Mosaics, and Gene Cards.

Karissa Sanbonmatsu's TEDx talk "How You Know You're in Love: Epigenetics, Stress & Gender Identity."

Duhl DM, Vrieling H, Miller KA, Wolff GL, & Barsh GS (1994). Neomorphic agouti mutations in obese yellow mice. Nature genetics, 8 (1), 59-65 PMID: 7987393

Tung CS, & Sanbonmatsu KY (2004). Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophysical journal, 87 (4), 2714-22 PMID: 15454463

Sanbonmatsu KY, Joseph S, & Tung CS (2005). Simulating movement of tRNA into the ribosome during decoding. Proceedings of the National Academy of Sciences of the United States of America, 102 (44), 15854-9 PMID: 16249344

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Novikova IV1, Hennelly SP, Sanbonmatsu KY. Nucleic Acids Res. 2012 Jun;40(11):5034-51. doi: 10.1093/nar/gks071. Epub 2012 Feb 22. PMID: 22362738
Sanbonmatsu KY (2016). Towards structural classification of long non-coding RNAs. Biochimica et biophysica acta, 1859 (1), 41-5 PMID: 26537437

Friday, February 12, 2016

The Zika outbreak: a wake-up call about climate change?

People are still talking about the Ebola virus and its deadly outbreak in West Africa, and now a new virus is making the headlines: Mostly innocuous and fairly unknown until a few weeks ago, the Zika virus is suddenly dominating the news. Under scrutiny is the virus's putative link with a congenital birth defect called microcephaly, which causes babies to be born with abnormally small heads and undeveloped brains.

Two recent publications [1,2] have documented finding the genome of the Zika virus in the amniotic fluid and brains of fetuses affected by microcephaly from three different mothers. These numbers are still too small to constitute a proof, and in fact, alternative explanations are already cropping up: an organization of Argentinean doctors has published a report in which they claim that it's not the virus, rather the insecticide used against the mosquitos, that causes the birth defect.

But what is Zika and, if the claims about microcephaly turn out to be true, how can it be harmless to most people yet so detrimental to a developing fetus? To answer these questions we have to take a step back and understand how viruses work and why some are endemic in the population, while others seem to come and go in waves.

The Zika virus was first isolated in 1947 from a rhesus monkey and from a pool of mosquitos in the Zika forest in Uganda. It belongs to the same family of viruses as dengue, yellow fever, and West Nile virus. However, unlike its close relatives, Zika was thought to be relatively harmless: most infected people experience no symptoms and a few have just a rash and mild fever. Originally confined to Africa, Zika started expanding to Asia in 2007. Since then the virus has spread exponentially.

Viruses like Zika are similar to Ebola in that they replicate in animal populations, where they are endemic. Ebola, for example, usually infects bats and jumps to humans who consume meat from infected animals. Zika is found in monkeys, and both monkeys and humans contract it through bites from mosquito carriers. To evade the host's immune system, viruses evolve continuously: as organisms build immunity to fight them off, genetic changes enable viruses to escape the newly made defenses.

Most of the people who contract Zika don't even realize they've been infected. They might just notice a pesky mosquito bite. But that pesky bite hints at the virus's covert strength: once inside the mosquito, the virus becomes an invisible enemy, one that hides and migrates through a tiny insect. You can avoid infected people when you see them sniffing and sneezing, but how do you avoid a symptomless agent that spreads through a flying bug?

You don't. In areas where these mosquitos flourish, children get infected early in life, build immunity against the virus, and don't worry about it ever again.

Then why is Zika posing a threat now?

The problem arises when the virus moves to a new geographical area and encounters a population that has never been infected before. Pregnant women are particularly at risk: unless they've been infected earlier in life, in which case their immune system can clear the infection before it reaches the fetus, any disease agent that has the ability to cross the placenta is a potential threat. That's true of Zika. Despite its normally mild symptoms, when it reaches the completely naïve immune system of a fetus in the early stages of pregnancy it can potentially cause permanent damage.

Although the connection between microcephaly and Zika has yet to be confirmed, Los Alamos National Laboratory virologist and epidemiologist Brian Foley does not believe that pesticides are responsible, as hinted by the Argentinean report.

"Of course the insecticide application is slightly correlated," Foley says, "because Zika, dengue, and other similar viruses are spread by mosquitoes. So, wherever you find one, you'll find the other, too. The insecticide mentioned in the Argentinean report has been in use since before 2000 and was heavily tested for mammalian toxicity before being put into use. And it is used all over the world for mosquito control, not just in Argentina and Brazil."

"We can't exclude that Zika is responsible for microcephaly in areas where it has circulated longer. To detect such links takes careful reporting and record keeping, and most countries do not have really accurate reporting to a central database."

The truth is, both the insecticide use and the virus are consequences of a global trend: over the past two decades, vector-borne viruses like Zika and yellow fever have spread globally at an increased rate. Why? That human behavior is once again responsible for this new spread comes as no surprise. Increased traveling between continents, a rapidly growing population and, last but not least, a rise in temperatures have created the perfect conditions for mosquitos--and hence the diseases they carry--to spread virtually unstopped. Humid, densely populated areas riddled with stagnant water become the ideal habitat for these bugs.

The race for a vaccine has started, and several companies have already announced a schedule to begin human trials in the near future. Unlike HIV, for which making a vaccine has turned out much more challenging than originally anticipated, the genome of the Zika virus is not very diverse. However, making any vaccine is regulated by strict government safety rules that require years of testing. "Under normal circumstances, it takes 10-20 years to make a vaccine," Foley explains. "In an emergency situation, they could push it to two to four years. That's still a long time in the event of an outbreak."

It's even longer if you think that Zika may only be the tip of the iceberg of a phenomenon we are bound to see over and over again in the near future.

"The distribution, transmission, and abundance of vectors that bear and transmit diseases are being enhanced by global warming," Foley and colleagues state in a recent publication [3]. "The mean global temperature increased approximately by 1 degree centigrade during the last several hundred years. However, during the next 20 years it is anticipated to increase by 2 to 3 degrees centigrade."

Geographic areas once too cold for mosquito-borne diseases are now seeing an increase in encephalitic viruses, dengue, and West Nile. Similarly, Zimbabwe and Ethiopia are experiencing an increase in typhoid and cholera due to poor hygiene, stagnant water and climate change.

So yes, a vaccine can provide a solution. But if this is only the beginning, we need to think globally. It's not just one virus we're fighting but a global change that's happening too fast for the natural world to adapt on its own.

Elena E. Giorgi is a computational biologist in the Theoretical Division (Theoretical Biology group) at Los Alamos National Laboratory and the author of the science fiction thrillers Chimeras, Mosaics, and Gene Cards. This content was reviewed by Los Alamos National Laboratory and approved for release under LA-UR 16-20983. For more information, please contact the Los Alamos National Laboratory Communication Office.

[1] Mlakar J, Korva M, Tul N, Popović M, Poljšak-Prijatelj M, Mraz J, Kolenc M, Resman Rus K, Vesnaver Vipotnik T, Fabjan Vodušek V, Vizjak A, Pižem J, Petrovec M, Avšič Županc T. N Engl J Med. 2016 Feb 10. Zika Virus Associated with Microcephaly. PMID: 26862926

[2] A. S. Oliveira Melo, G. Malinger, R. Ximenes, P. O. Szejnfeld, S. Alves Sampaio andA. M. Bispo de Filippis. Zika virus intrauterine infection causes fetal brain abnormality and microcephaly: tip of the iceberg? Ultrasound in Obstetrics & Gynecology. Vol 47 Issue 1. DOI: 10.1002/uog.15831

[3] Paul Shapshak , Charurut Somboonwit, Brian T. Foley, Sally F. Alrabaa, Todd Wills, John T. Sinnott (2015). Zika Virus. Global Virology I - Identifying and Investigating Viral Diseases Springer-Verlag

Friday, February 5, 2016


I was supposed to write a great blog post about some great paper a friend sent me. It didn't happen. But I did catch a nice picture of dusk on my way home. So there.

Wednesday, February 3, 2016

February IWSG: what's your outlet when the muse keeps evading you?

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.

Hello to all my IWSG friends. Last time I made a list of new year's preposition, and I have to say the one about taking my time writing is going really, really well. Ha, yes, I'm being sarcastic, because I'm not sue it's a good thing. It took me 2 months to write a 14K-word long novella, and it's taking me forever to draft the third book in my Mayake Chronicle series (ssssh, don't tell anyone, though!).

Is that good or bad? I'm not sure. I like to let characters simmer in my head. At the same time, I have that nagging feeling that I'm not being productive. So, what do I do? I take photos. If there's a thing like cross-training, there's gotta be a cross-inspiration too, right?

What about you? Do you have an outlet when the words get stuck in your head and don't want to come out?