Thursday, September 24, 2015

Ice, Ice Baby: Bringing Frozen Viruses Back To “Life”

Back in 2003, a new class of giant, ancient viruses were found that preyed upon unsuspecting amoebas in the Paleolithic.  

Earlier this year, scientists published a study describing how they revived another one of these giant viruses, which has been frozen in Siberian permafrost for 30,000 years! We’ll discuss why they did this in a bit, but let’s first talk about how they did this.

Over the years, lots of cool stuff has been found well-preserved in ice. Otzi, a 5,000 year old “ice man” was a historic find in 1991. He went on to become a spokesperson for the GEICO auto insurance company.
Viruses are minute obligate intracellular parasites. In other words, they cannot replicate outside of a host cell, an attribute that gives them the unflattering distinction of being the worst houseguest ever. That’s right:  viruses storm into your home – unannounced – take off their coat and make themselves right at home. They ransack the place and raid your fridge without even asking. As if that wasn’t bad enough, you come home one day and catch the virus in the act of making babies – lots and lots of babies. Finally, this unruly family blows up your house as they leave, without so much as a “thank you”, and go on their merry way to invade other homes in your neighborhood.

While we can feel the pain that they cause, especially during cold and flu season, we can’t see the culprits. Viruses are really, really tiny - most are smaller than the molecular complex cells use to make proteins.
Many viruses are under 100 nM (0.1 micron), but some (like Ebola) are almost 1.0 micron. Compared to viruses, even a bacterium is enormous. 
So how does one find a virus in thousands of miles of ice? Virus hunters take an approach similar to finding a needle in a haystack. But in this case, instead of a magnet, the scientists use amoebas as “bait” to lure out viruses that might be chilling out in the permafrost.

Amoebas are single-celled organisms called protozoa that, like most cells, fall prey to viruses. By putting permafrost into amoeba cultures, scientists were able to screen samples for those that could kill the amoebas. And they found a “big” surprise.

Thick membrane or no, Pithovirus invades amoebas. Who knows…with this discovery, maybe scientists can devise a new treatment that targets the deadly brain-eating amoeba, Naegleria.
The virus spotted in these infected amoeba cultures resembled a so-called “pandoravirus” or “giant” virus. They are still microscopic of course, but considerably larger than the viruses we know of today (about 1.5 microns in length and 0.5 microns across). Not only are they larger in size, but they contain many more genes. By way of comparison, HIV contains less than 15 genes, but this giant virus has 500 genes. They christened this new giant virus “Pithovirus sibericum”, and it is the oldest virus ever to have been revived to date.

A “huge” find in the world of virology, Pithovirus is now growing in labs again after a 30,000 year slumber. Image taken from Legendre, et al.
Now why on earth would scientists bring a virus back from the dead? Are they mad? Are they trying to facilitate the apocalypse?

Of course not. As climate change continues to melt more and more ice, it is possible that these viruses are going to revive naturally. By resurrecting them in the lab in controlled conditions, researchers can get ahead of this curve by studying the virus. Study of the virus can help determine which one(s) pose a threat and, if so, vaccine and drug development efforts can get underway thanks to our knowledge of the virus. And don’t worry about Pithovirus – it was already found to be incapable of infecting animal cells.

Another reason these viruses are worthy of study is that they can reveal new insights into how cells evolved, since viruses can transfer their DNA to their hosts. They may even shed light on the greatest biological mystery:  the origin of DNA/RNA and how life came to be on Earth.

The same team of scientists isolated yet another ancient giant virus this year from the same permafrost and named it Mollivirus sibericum. You may also be wondering what Siberian virus hunters listen to while exploring those Hoth-like landscapes. I'll take a guess and hope that it is wrong...

Contributed by:  Bill Sullivan, Ph.D.
Follow Bill on Twitter.

Legendre, M., Lartigue, A., Bertaux, L., Jeudy, S., Bartoli, J., Lescot, M., Alempic, J., Ramus, C., Bruley, C., Labadie, K., Shmakova, L., Rivkina, E., Couté, Y., Abergel, C., & Claverie, J. (2015). In-depth study of , a new 30,000-y-old giant virus infecting Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1510795112
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

Thursday, September 17, 2015

The Martian: Getting Home Is Just Half The Problem

"The Martian" movie is coming soon! Starring Matt Damon and based on the bestselling novel by Andy Weir, "The Martian" has a lot of Sci-Fi fans very excited.

"The Martian" is about an astronaut stranded on Mars who is trying to devise a clever way to get back home. But today, we humans here on Earth still have to think of clever ways to survive a trip to the red planet in the first place.

NASA, the ESA, and many other space programs are taking aim at Mars. We have sent probes, rovers, and satellites; now it’s time for humans to make the trip. But this brings big problems along with the big promise. Space is full of cosmic rays, high-energy electrons, high-speed protons and even heavier atoms. They can all kill you over time or fry your equipment.

Radiation in space will make you sick at the least, and don’t underestimate the problem of being sick in space – think about vomiting in a space suit. But it can also damage DNA and most certainly lead to infertility, given enough time and exposure.

All this damage could occur inside the space ship on a long journey to Mars or beyond, not just on space walks. Most high-energy radiation will pass through the hull of a spacecraft and do damage to the occupants. We need protective shields to keep out the bad particles and waves.

Six months on ISS doesn’t give an astronaut anywhere near the 
radiation exposure that six months on Mars, or going to and from 
Mars, would. The reason is that the ISS is still within the Earth’s 
magnetosphere, so it’s protected from most of the dangerous 
radiation. To go to Mars, we’ll have to take 
our own shield along.
Star Trek: Insurrection showed us an example of using a force field to protect the crew. When Picard and mates were observing Ba’ku from a cloaked duckblind, they used a “chromodynamic shield” to deflect or block the metaphasic radiation that inundated the planet. A force field protected the crew, although it was protecting them from rays that would stop their aging and did in fact restore Geordi’s eyesight for a while.

We don’t have a chromodynamic shield, so we've been looking to more conventional mechanisms of shielding. We could always make the walls of a long distance spacecraft thicker. Concrete would work pretty well, if it was dense and about 2 ft thick. A foot or so of aluminum might do just as well. But these are very heavy. Heavy things don’t make for good space gear.

Interestingly, water is a great absorber of radiation. We could put it between the walls of a spacecraft and it could do a pretty good job of protecting the crew and the electronics.  Hydrogen gas might work as well; notice how water is just hydrogen and oxygen. The sleeping quarters on the ISS are lined with impregnated polyethylene as an additional radiation shield. 

But what might work best? – human waste. A privately funded mission to Mars led by Dennis Tito plans to use the astronaut's own excrement as a radiation shield by packing it between the walls of the spacecraft. Organic molecules and water block radiation very nicely, and they’ll be producing more shielding every day. It’s a strange thought that a Mars mission might be jeopardized by constipation.

Dennis Tito is a billionaire investment manager, but first he 
was an engineer. He was the first person to purchase a ride 
into space (Russian rocket) and now he wants to fly 
people around Mars – not to Mars - just a flyby in 2018 
or so. The planets will be aligned to give a 501 day round 
trip then. He wants to use their waste as radiation shielding.
Thank goodness science has kept looking for radiation shields. It's quite the boon that we have natural examples to learn from. The ionosphere of Earth is a great deflector. It’s the reason short wave radio operators can send weak signals very, very far. They bounce off the bottom layers of the ionosphere and back down to Earth, called skywave or skipping. The lower the angle on the way up, the far they will be over the horizon when they bounce back down. 

The ionsophere (80-1000 km altitude) is part of the atmosphere of Earth that protects us from cosmic radiation. It consists of ionized air molecules; the ionization comes from the Sun’s energy. What's an ionized gas called?  – plasma.

So we have a plasma shield around Earth – remember this as it will come up again. The magnetosphere (a 40,000 nanoTesla field goes out hundreds of thousands of km) is produced by the spinning of the Earth’s metallic outer core. It participates in the protection because the ions of plasma in the ionsophere are charged, and electrical charges in a magnetic field produce an electric field.

The magnetosphere, in coordination with the 
plasmasphere, shunts most of the electrons of 
the solar wind and the high energy protons 
around the Earth. Where the magnetic lines 
come out of the Earth at the poles, you have the 
polar cusps. Some radiation can get in there – 
we see them as the auroras.
A new study shows that the plasma interacts with the magnetic field and it becomes more important when there are solar storms that greatly increase the energy of the radiation coming at earth. The plasmasphere, a portion outside the ionosphere, reacts to greater energies coming from the Sun and will plume out to be more protective.  

All this protection comes from the fact that ions in plasma are charged, and the magnetic field is charged – and like charges repel. So the high speed electrons of the solar wind and the protons and heavy ions of cosmic radiation that come close to Earth are repelled by the magnetosphere, the plasma sphere, and most importantly by the electric field produced by the interaction between the plasma and the magnetic field. The vast majority of charged particles and waves are swept around Earth and merge again safely behind us. Now that’s a force field.

Several research groups have begun to think about how this could be mimicked on a small scale to protect astronauts in space. A 2005 project from NASA contemplated using vectran balloons covered in gold that could be charged to positive or negative values. Placed above a moon base and electrified, the balloons might create a magnetic bubble that would shunt radiation away and produce a protected cavity underneath.

No one has thought more about producing a plasma shield than Dr. Ruth Bamford of the Rutherford Appleton Laboratory in England. Since 2008 she has been working on producing mini-magnetospheres that would buffer the small amount of plasma in space; using a magnetic field to hold it in place and build up its density. Together, they would produce an electric field just like the Earth does, and this would shunt radiation and particles away from the protected object.

On the left is the Reiner Gamma lunar swirl. On the right is the 
Reiner crater – no, not for Carl Reiner. We used to think 
the swirls (three on the moon) were dead areas, no magnetic 
field, no water, no nothing. Now we see they are the protected 
areas and are the most interesting places on the Moon.
NASA has also thought about this, using a plasma cloud (probably made from hydrogen gas) on the Sun side of a spacecraft, held in place by a superconducting wire mesh. Unfortunately, superconductors only work to produce a magnetic or electric field if below their transition temperature. And even for the best of materials (YBCO and BSCCO) this is somewhere in the range of -265˚F. If the mesh was exposed to the Sun in space, it would be several hundred degrees at least. Better keep thinking.

A discovery in 2013-2014 brought the thinkers back to Dr. Bamford's mini-magnetospheres. It was discovered that small parts of the moon’s surface are protected from radiation. It turns out that these areas produce weak magnetic fields (few hundred nanaoTesla), and those fields are holding the thin plasma of space in place above them. The field concentrates the plasma, and together they produce a protective electric field to deflect particles and keep the surface of the moon at those spots from being irradiated. Irradiation turns the surface dark, while these “lunar swirls” remain light colored.

This is not a cartoon. The pinkish gas is plasma 
and on top of the middle cylinder is a magnet. The 
magnetic field deflects the plasma and some builds 
up in density on the leading edge. This leading edge 
and the magnetic field form an electric field that 
would shunt more particles. The dark area around 
the magnet is a protected cavity, no cosmic radiation 
gets to that point. It’s a real-life deflector shield.
Bamford’s discovery of the mechanisms behind the swirls made her idea of a mini-magnetosphere plasma shield more attractive, since the protective magnetic forces on the moon are much weaker than previously estimates had thought necessary. Therefore, a smaller (lighter, less energy consuming) superconducting coil could be used to create a magnetic field and hold a thin layer of plasma in a bubble around a spacecraft. Bamford’s group has built such a force field in their lab and predicts that a 1.5 ton apparatus could do the job in space! 

But wait, there’s more. A plasma shield could also protect a ship from high energy weapons. Plasma has the capability to absorb photons of energy like from lasers or phasers!!! And since plasma has to be at a very high temperature to keep the electrons from re-associating with the nuclei, being in space would help since there would be no air to carry the heat away from the plasma. It would stay hot and maintain itself. In fact, incoming weapons fire would reinforce the plasma state by adding energy. 

Contributed by Mark E. Lasbury, MS, MSEd, PhD

Bamford, R., Kellett, B., Bradford, J., Todd, T., Benton, M., Stafford-Allen, R., Alves, E., Silva, L., Collingwood, C., Crawford, I., & Bingham, R. (2014). An exploration of the effectiveness of artificial mini-magnetospheres as a potential solar storm shelter for long term human space missions Acta Astronautica, 105 (2), 385-394 DOI: 10.1016/j.actaastro.2014.10.012

Bamford, R., Gibson, K., Thornton, A., Bradford, J., Bingham, R., Gargate, L., Silva, L., Fonseca, R., Hapgood, M., Norberg, C., Todd, T., & Stamper, R. (2008). The interaction of a flowing plasma with a dipole magnetic field: measurements and modelling of a diamagnetic cavity relevant to spacecraft protection Plasma Physics and Controlled Fusion, 50 (12) DOI: 10.1088/0741-3335/50/12/124025

Walsh, B., Foster, J., Erickson, P., & Sibeck, D. (2014). Simultaneous Ground- and Space-Based Observations of the Plasmaspheric Plume and Reconnection Science, 343 (6175), 1122-1125 DOI: 10.1126/science.1247212