Monday, November 15, 2010

Alternatives to RNA from NAI videocon

For this blog entry I wanted to write about one of the talks from the NAI Workshop that I saw on Monday given by Ram Krishnamurty from the Scripps Research Institute on his research into structural alternatives for RNA. The basic motivation of his research is to study the potential of novel oligomer systems to act as informational systems similar to RNA. One of the major goals of Krishnamurty’s team is to systematically synthesize, by chemical methods, potentially self-replicating chemical systems that may have been competitors to RNA in a primordial world. At the conference he presented a system he recently synthesized in which he expected the strands of the molecule to pair well with DNA and RNA as well as with its partner; however, some of the strands failed to bind which led to the discovery an additional criterion for strands that may shed light on why RNA prevailed in the primordial world.

So far this semester, it has come up a lot that before the rise of DNA, RNA acted alone in propagating primitive life. We’ve also explored the idea that, in such an “RNA World”, there would be a fundamental necessity of RNA to act as both a transmitter of information and catalyst of life-sustaining reactions. However, even years of research, the potential for RNA to self-assemble under what are thought to be likely primordial conditions still hasn’t been demonstrated.

In the talk, Krishnamurty presented results they have discovered recently regarding the chemical nature of pre-biotic RNA. The work focused on two pair of oligomers with the diamino and dioxo forms of triazines, and the diamino and dioxo forms of pyrmidines acting as alternative bases. The expectation was that the diamino and dioxo forms of each would exhibit Watson-Crick base pairing, and that the compounds would also bond well with RNA and DNA. It turned out that the diamino triazine paired strongly with RNA and DNA, as expected, but the diaxo triazine paired very weakly. This was strange, but even stranger was that the observations for the pyrmidines was opposite: the dioxo paired strongly, and the diamino paired weakly. This lead to the discovery of a remarkable correlation between whether the base in a synthesized compound bonded will with RNA and DNA or its pair, and the value of its acid dissociation constant (pKa). These results suggest that a base with a pKa value close to that of the base it is to pair with will have weak, if any, bonding, while the team found strong bonding among bases with high differences among their pKa values.

So, the ultimate conclusion of his talk was that the optimal strength of bonding between bases is literally responsible for life as we know it. Bonding that is too weak would prevent self-replication from proceeding, while bonding that was too strong might do the same, because double strands would become too difficult to separate. RNA and DNA exhibit an optimum base pairing strength, and understanding the reasons why are critical to understanding how they arose.

So, Ram and his team initially set out to identify potential RNA alternatives, but what they found was a very interesting new criterion to better understand RNA and DNA and further the search for alternatives or precursors. The pKa itself may not be responsible for the relative bonding strengths of different bases, the results do suggest that pKa differences are a good and relativle convenient indicator for potential bases that will have the proper bonding strength. An interesting time is upon us, where pKa may now be one of the first considerations in work to identify alternative bases.

Saturday, November 13, 2010

Dead on Arrival

By now, we're all familiar with panspermia or more accurately exogenesis--the hypothetical scenario in which life was "deposited" onto Earth by some kind of asteroid or collision early on.

An argument occasionally arises against this idea, supposing that radiation would cause anything but the toughest extremophiles to be damaged beyond repair. There is the emerging idea that genetic material could still be recovered from damaged (read: dead) biological molecules and be used as a sort of springboard for life to develop.

Paul S. Wesson's new paper in Space Science Reviews talks about his theory of "necropanspermia", which isn't nearly as supernatural and awesome as it sounds, but it does bring up a lot of interesting questions about how life gets around in outer space, if it does at all.

Wesson encourages his peers to focus not on the question of "alive or dead" but "the question of genetic information". He argues that "random chemical interactions cannot produce the genetic information" present on Earth right now. He demonstrates by using a model of a prebiotic Earth with a given amount of amino acids. He then goes on to say that the "molecular interactions" that would follow would take 500x10^6 years to create 194 bits of information. For comparison, he gives e. coli: 6x10^6 bits, and a typical virus: 1.2x10^5 bits. So, he posits two possible conclusions. Either, life began on Earth under a directed, not random, sequence of chemical interactions, or it was a large amount of genetic information that was deposited here very early on. Wesson sides with the second camp. "Natural processes do not account for the genomes of observed organisms," he says.

He does, however, admit "that all versions of panspermia suffer from a hole in our knowledge, concerning how to go from an astrophysically-delivered entity which contains substantial information to one which has the characteristics of what we normally regard as life."

So his point is basically that viruses are great candidates to be used as a vessel for genetic information, since that's basically what they are.

One of the biggest detractors is Rocco Mancinelli, who quipped that "once you're dead, you're dead." He studies extremophiles for a living and what needs to go on in an environment to sustain life. I tend to agree with his take on the issue, as he points out that Wesson has missed a few drawbacks to his theory--essentially, that there are more dangers out there than he's led us on to.

Mancinelli mentions potassium decay (over the course of a long period of time in space: very damaging) and dessication, when hydrogen and hydroxyl molecules separate from the cells and form water, which serves to "denature" proteins, forcing them to recombine and lose functionality.


Wednesday, November 10, 2010

Methane on Mars

This is an interesting twist on the view that Mars is a dead planet. A recent six-year study of methane levels in Mars' atmosphere shows the planet is actually far from dead, but whether the activity is merely geological or microbial is still unknown.

A team of researchers based in Italy looked at billions of measurements taken by NASA's Mars Gobal Surveyor to compile seasonal maps of methane gas, which appears in minute quantities in the carbon-dioxide rich atmosphere. The researchers found that methane concentrations are highest in autumn and drop off dramatically in winter. Levels build up again in spring and climb rapidly in summer, which causes the gas to spread across the planet.

Ultraviolet light from the sun breaks methane down, so something is happening either on or in the planet that is replenishing the gas. Also, another mystery is the speed at which methane is being depleted. The seasonal changes are quite unexpected from a planet that is believed to not have much left going on.

Researchers found three regions in the planet's northern hemisphere with consistently higher concentrations of methaneTharsis, Elysium, and Arabia Terrae. The first two are home to the largest volcanoes on Mars, while Arabia Terrae has large quantities of subterranean frozen water.

Lead researcher Sergio Fonti, from Italy's Universita del Salento, says the seasonal nature of the methane levels rules out the possibility of cosmic ray bombardment or meteorite impacts causing the changes. "It could be geology or biology, but it is not coming from another source," claimed Fonti.

On Earth, colonies of bacteria that consume methane have been found living right along species that produce it, and many scientists believe that there could easily be a similar situation on Mars. Still, some skeptics believe that some simple geologic explanation such as the release of methane trapped in frozen water during seasonal melting could help explain the phenomena.

NASA and Europe are planning a joint mission in 2016 to draft more detailed maps of Mars' methane. NASA's Mars Science Laboratory, scheduled for launch next year, also has an instrument that will detect atmospheric methane.


Helping Plants Move onto Land

At the University of Sheffield, a group of scientists is making advances on learning how the Earth's first plants moved onto land over 470 million years ago. Their breakthrough: soil fungi.

The research provides some missing evidence that an ancient plant group formed a partnership with soil-dwelling fungi to help spread green plants across the land nearly 500 million years ago. Several groups provided input to the research, including the Royal Botanical Gardens, Kew, Imperial College London and the University of Sydney. The evidence sheds some light on the evolving relationship between the Earth's land plants and fungi.

It has been suspected that soil fungi played an essential role in assisting early land plants colonize terrestrial environments by forming mutually beneficial relationships, but there has been no evidence demonstrating how this worked. To show exactly how this happened, the team studied a thalloid liverwort plant (below), which is among the most ancient of land plants that still exists and also shares many traits with its original ancestors.

These plants were placed in controlled-environment growth rooms that simulated the conditions of the Palaeozoic era, which is when the plants were believed to have originated. Under these conditions, the benefits of the fungi for the plant's growth were significantly amplified and this favored the early association between the plant and its fungal partners. When the thalloid liverwort was colonized by fungi, its photosynthetic carbon uptake, growth, and asexual reproduction were all significantly enhanced. These factors have a clear beneficial impact on the plant's fitness.

Why does this happen? The fungi provide the plants with essential soil nutrients. This helps them grow and reproduce better, and in exchange, the fungi benefit by receiving carbon from the plants. This symbiotic relationship resulted in each individual plant being colonized by fungi that could take up the area of 1-2 times that of a tennis court.

Again, this idea has been floating around for a while, but this group was the first to provide hard evidence of the process. Professor David Beerling, from the University of Sheffield, said that "[this] shows that plants didn't get a toe-hold on land without teaming up with fungi. ... [This] will require us to think again about the crucial role of cooperation between organisms that drove fundamental changes in the ecology of our planet." This is true, and given that fungi inhabit every type of habitat in the world, it would be interesting to see if there are any other of these associations that may have shaped the Earth as we know it.

Sunday, November 7, 2010

We Had Water the Entire Time?

This isn't an actual entry, but some (very) recent news about the origins of water on Earth before we get too far away from that topic in class.

Apparently, we may have had water from day one. This makes a lot of sense, since I was at one point talking about the discrepancies between the D/H ratio of comets and our ocean (my last presentation, I think).

Friday, November 5, 2010

Zircon Dating: Hadean not so Hadean?

This will include no advice about pursuing a relationship with a mineral.

But it will include some hypotheses on early environmental makeup with the help of half-lives and Australia. In the form of zircons.

So a little bit of background on atmospheric origins: two of the leading theories on how our atmosphere formed that I've found: planetary degassing and comet impact. One of the flaws with the latter are that the D/H (deuterium/hydrogen) ratios of comets that we've studied do not match the D/H of our own planet--Hale-Bopp for one--which reinforces the idea that, while it is possible that some of the responsibility may fall to comets, it can't only come from comets.

What is less known about the atmosphere's formation is the question of when? This is where zircon comes to the rescue.

Deep in the heart of Jack Hills in Western Australia lies some of the oldest pieces of zircon that can give us a hint about the age of our atmosphere. Through measurements utilizing uranium decay (into lead) and the measurements of temperature related to titanium composition, zircons suggest a different Hadean eon.

"For example, oxygen isotope compositions of these ancient zircons suggest the presence of a terrestrial hydrosphere and stable continents only 200 Myr after accretion (Mojzsis et al. 2001)."

The composition of the zircons gives us evidence of the type of environment they were in when they formed, hinting that--since these zircons are in the range of 4.2-4.4 billion years old--the very early Earth had a burgeoning atmosphere.

"Excesses of 129Xe in mantle-derived samples relative to the atmosphere have been interpreted to indicate the presence of live parent 129I in the deep Earth following early degassing of the atmosphere (e.g., Staudacher and Allegre 1982; Allegre et al. 1983) since 129I decays to 129Xe with a half life (t1/2) of only 16 million years. If true, then it is argued that the present atmosphere and hydrosphere must have formed by ~4.4 Gyr (Podosek 1970)."

This posits a different way of dating zircons--not by uranium and lead, but with xenon and iodine, giving further evidence to an earlier-than-though atmosphere.

Lunine textbook

Indestructible Bears

The image to your right might look crazy scary, but that creature is less than a millimeter--and probably poses no threat to humankind whatsoever, which is great, since they're nigh invulnerable.

What this is is the tardigrade, affectionately called "water bears" by some people for their similarities to our mammal friends and their love of water. They find their home on various types of moss, and they're far from uncommon. What is uncommon is their survival mechanism. They need water to stay active, so when it's gone, it is then that they enter a state of "suspended animation" causing them to be able to live without water for over a decade. In this state, they're able to endure intense heat (over 90 degrees celsius) and intense cold (near to absolute zero). Couple that with a strong shield against radiation, and you have a creature that could easily be counted as one of the strongest organisms on Earth.

So, it's pretty great that we've found such a crazy strong organism with a cute name and ironic strengths, but what can we learn from them? Or with them?

Their defense against radiation is particularly interesting, since radiation causes severe damage to DNA. Somehow, these tardigrades don't flinch at this. Proteins will help re-form its integrity, and its own defenses also help. Radiation resistance isn't a tardigrade-exclusive skill. Many extremophiles live in places with extreme radiation levels--caused by uranium-rich granite and radon gas. They've also developed systems in place to repair their DNA and shield a good portion of the radiation.

What is also fascinating about the tardigrades are what scientists have been testing it with, such as acetonitrile, a dissolving chemical present on Titan, as well as possibilities of survival on Mars. Of course, this idea of tardigrades living in these places is slim, since their suspended state would be the only state they could survive in.

Another feat the bears can do is completely dehydrate themselves--a bit confusing considering their name, but altogether astonishing when you consider them as living things literally frozen in this state where they thrive off of nothing.

The creatures are clearly impressive and could hold a lot of clues for human protection against radiation and other forms of astronomical injury--they're able to take a dose of radiation that's 4000 times the strength of a harmful dose for humans. Recent research put them in low Earth orbit, exposed to the extreme conditions of space, and most of them survived, and those that survived could even reproduce.