Monday, December 20, 2010

Stem Cells in Microgravity

One interesting and recent study on human embryonic stem cells experiencing net microgravity sheds some insight into what may be causing long lasting health problems for astronauts. Researchers at the University of New South Wales in Australia placed stem cells in a rotating machine developed by NASA that introduces a net gravity close to 0g. The stem cells were in the machine for 28 days, while the control group of stem cells was maintained in the exact same nourishing conditions while experiencing normal Earth gravity conditions. After the experiment, the cells showed several differences at the molecular layer. Nearly 64% of proteins in the microgravity group differed from those grown under normal gravity. In the microgravity treated stem cells, there was more expression of proteins that degrade bone and there was less expression of proteins with antioxidant effects. Additionally, proteins involved in cell division, the immune system, the muscle and skeletal systems, calcium levels within cells, and cell motility were also affected in this group.

These results suggest that microgravity conditions directly impact the development of stem cells in the human body. Human embryonic stem cells can develop into any cell type, and they play a role in repair of damaged tissue and in the maintenance of the normal regeneration of organs with the potential to regenerate. With this importance, if experiencing microgravity hinders their development, then long-term space travel poses serious threats to the health of astronauts. Research is currently being done on several differentiated cell types to determine if the molecular changes are more widespread, and these experiments will also take place on future missions into space in order to verify that these results are also seen in true microgravity, as opposed to net microgravity. Another implication of these results is that future research should be directed towards biomedical interventions that prevent these changes in protein expression.

Yet another implication of this study that concerns long-term survival during space travel is the complications that might arise during procreation. If cells do rely on gravity for some sort of mechanical feedback, then the development of an embryo in microgravity could prove to be impossible. Thus, if humans plan to make long distance trips to other planets in our solar system, the issue of genetically engineering human bodies for them to survive procreation in space might be a necessary step in future.

Wednesday, December 15, 2010

Microbialites (One more blog that I forgot to publish...)

A couple weeks ago, I gave a presentation on microbialites for our lesson on extremophiles. I chose to talk about microbialites because I’d never heard of them before, and because there’s been a lot of exciting research going on over the past few years regarding the potential for microbialites to serve as potential biosignatures for life on Mars.

Basically, microbialites are nothing more than organic sedimentary mineral deposits that are covered by a thin layer of microbes that become entombed in the mounds as they grow outwards. The difference between stromatolites and microbialites is that stromatolites are the Earth’s oldest known structure and show no direct evidence of life, whereas microbialites are relatively young in geological terms, as they are only about 12,000 years old. The reason that scientists are getting so excited about them is because they serve as macroscopic evidence of microscopic life. Chris McKay, a scientist with the NASA Astrobiology Institute, regarded microbialites as:

“They are helping us understand one of the big astrobiology questions how early life took hold and began to flourish on Earth, These fossils are like seeing a billion-year-old footprint in the sand and comparing it to a modern foot.”

NASA scientists realized the importance of microbialites over a decade ago, and began studying the ones that are growing in Pavillion Lake in British Columbia in 1998. The microbialites were formed layer after layer with the oldest lying on the bottom, thus the structure provides a record of growth and also yields important clues about the organisms that once lived there. In 2008, NASA researchers reported that the microbialites in Pavillion Lake were composed of calcium carbonate, ranging in size from small bumps just a few centimeters across to enormous structures as large as 12 feet high. Additionally, they came in a variety of vegetable-shapes: some were described as resembling cauliflower, other like broccoli, other like asparagus, and some like carrots.

How these "veggie"-microbialites came to be placed in this lake isn’t completely known. As of last year, scientists are sticking with the hypothesis that bacteria were involved in some way in creating the large structures. However, it's possible that the only role bacteria had was in the formation of the crusts on the surfaces of the structures, but the structures themselves are the products of a purely chemical, rather than biological, process.

Some cyanobacteria excrete calcium carbonate, so one possibility is that the crusts are composed of this bacterial waste. Another is that the bacteria built up an electric charge along their cell walls, which attracted the calcium carbonate in the lake water. Or maybe the cyanobacteria secreted slime that the carbonates bound to.

In other places around the world, Cyanobacteria are famous for building a variety of structures, from thick rubbery mats to the layered dome-like structures we know as stromatolites.Today, though, they are rare, existing only in extreme environments.
The shallow waters of Shark’s Bay, in Western Australia, for example, are home to large fields of dome-shaped stromatolites. But Shark’s Bay is too salty for the tiny worms that like to snack on the bacteria. That’s why the stromatolites can thrive: there’s nothing around to eat them.

Pavilion Lake, however, is “normal.” It has all kinds of larger organisms living in it. It’s even stocked with fish. This is what creates the mystery.

So, researchers are approaching this topic from a variety of different angles. Some of them are looking at the chemistry of the lake water to understand it's topography and underground water sources; and others are doing DNA analysis of the slime that coats the microbialites to figure out which organisms are living there, what they're eating, and what they're excreting. Still other researchers are comparing the carbon in calcium-carbonate samples from the slime layer to carbon from the core of the structures to see if there is a clear biological mark in the core. The basis behind performing this investigation is that living organisms generally use the lighter C-12 isotope, leaving behind the heavier C-13 isotope.

So far the research has been largely inconclusive. The carbonate in the surface communities have a signature of biological activity, however deeper down, the signature doesn't appear to be preserved. This is contradictory to what you would expect since if the structures were built by microorganisms, there should at least be some isotopic evidence of their biological origin. Though, there is a possibility that over time, the structures have dissolved and re-crystallized, and in the process of doing this, changed from one form of calcium carbonate to another, thus losing their biological carbon-isotope signature.

If this avenue of research turns up supportive findings, the results could provide new insight into how biosignatures are modified and preserved over time, which could aid in future efforts to for biosignatures on Mars.

Monday, December 13, 2010

How science fiction can inform Astrobiology: The recap of a discussion with Jeffrey A. Carver

Yesterday we met with science fiction writer, Jeffrey A. Carver. He was extremely welcoming and helpful in explaining to us much about science fiction, writing, and the intersections of these topics with astrobiology. The reason that we felt science fiction would be an interesting topic to discuss in astrobiology is that science fiction deals with the imaginative, which astrobiology lacks. Astrobiology seeks to understand where life could live, what it could look like, and how we could find it, however, this is intentionally limited by our current technology and scientific knowledge. Astrobiologists use science to try to figure out the same things that science fiction writers imagine. While fantasy imagines the impossible, science fiction narrates the possible.

Astrobiologists may say that much of science fiction is unfeasible, however, science fiction does function within the loose (or even strict) boundaries of science. For instance, NASA scientist Geoffrey A Landis, writes with a very strong science background and even works in the cutting edge of space research. There are other authors that are biologists, physicists, etc. and authors who merely have an interest in science and not a degree, that meld their imaginative stories with science.

Science fiction writers focus on the imaginative aspect of extraterrestrial life and space travel down and this perspective is interesting for astrobiology to take into account. There are new technologies and discoveries that have first been described by science fiction writers. A great example is Arthur C Clarke who imagined geostationary satellites, a global library and light rails well before they were developed. In fact, scientists have gone so far as to test the plausibility of space stations and artificial worlds described in science fiction. Clearly there is some overlap in our imagination and the expansion of the limits of science.

The existence of SETI provides evidence of the overlap between science fiction and astrobiology because the use of SETI to ‘find intelligent life’ suggests that there are sentient beings elsewhere in the universe that will be able to communicate in a manner that we understand and whom would want to communicate with us. This is not much more ‘realistic’ than what we find in science fiction. Indeed, some other ideas in science fiction like cloning, cryogenic suspension, and living on the moon are active areas of research (well, living on the moon was at least at some point an active scientific interest). Clearly, science fiction is not totally unfeasible—animals have been cloned and human bodies frozen after death. Science has just not been able to keep up with the imagination and these technologies are not as practical or useful as they appear in science fiction. New areas of research can even be described as ‘science-fiction-y’ such as the creation of a microbe using artificially produced DNA in the spring of 2010.

Scientists in general, are very skeptical and it is not within the discipline of science to imagine things that are far beyond what we already regard as fact or which are beyond what we can understand using current technology. Thus, astrobiologists do not need to believe that the worlds that appear in science fiction are possible, they just need to understand that science is a human endeavor, and because of this, science may be held back by our imagination. There are many topics in astrobiology that would have seemed far-fetched just a couple decades ago, like the idea of a biocentric universe-- that our cosmology and metaphysics cannot ignore the important interplay between conscious observers and quantum effects—and the two-slit experiment. Though science fiction writers may push the boundaries of the feasible at times, the feasible is a human-centric notion bounded by science. We don’t know what is feasible or not and taking a hint from science fiction writers and expanding our imagination of what life could look like and where it could live is an interesting thought experiment for astrobiology.

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.