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Author Topic: Testing for Life


Bryan
Europa Astronaut
Posts: 98
Testing for Life
on: March 12, 2014, 23:55

Testing for alien life will be a challenge. Most of our chemical testing kits look for signs of life as we know it: amino acids, specially left handed ones, carbohydrates, lipids, nucleic acids. We identify microorganisms either by culture or by DNA testing. It is unlikely anything will grow on our culture mediums, and we do not know if they even use DNA. Ideally we would have an NMR machine to identify organic compounds, but that is unlikely to fit on the ship. Our best hope for on-site life identification is the simple microscope, and hope that whatever you see is bigger than 200nm, has good contrast, and is plentiful enough that it appears on the slide. (Or is big enough to be seen by the naked eye should be be so lucky.)

This is another reason I believe this mission should result in the crew returning with plenty of samples. Life might be completely unrecognizable to us without extensive testing with expensive and quite heavy (and hard to transport) scientific equipment.



Rex
Europa Dreamer
Posts: 17
Re: Testing for Life
on: March 13, 2014, 15:10

Hi Bryan, there's maybe a simpler option: i.e., to identify genetic information carriers (DNA analogues) not by their chemical but by their general physical properties. Keep tuned, my OE idea is slated to be published in "Astrobiology" in the next few days! šŸ˜‰



Bryan
Europa Astronaut
Posts: 98
Re: Testing for Life
on: March 14, 2014, 01:37

Please post the link when it is published, I would love to see it.

Any teasers on how that would work?



Rex
Europa Dreamer
Posts: 17
Re: Testing for Life
on: March 14, 2014, 08:10

The title of my contribution will be "Nanopore-based instruments as biosensors for future planetary missions". šŸ™‚



Rex
Europa Dreamer
Posts: 17
Re: Testing for Life
on: March 31, 2014, 23:38

Paper is out now (and open access for two weeks)
http://online.liebertpub.com/doi/pdf/10.1089/ast.2013.1120 šŸ˜‰



Bryan
Europa Astronaut
Posts: 98
Re: Testing for Life
on: April 2, 2014, 04:32

Just read the article and think it's a great idea!

First, to your knowledge, have any of the devices (The MinION device for example) been tested in extreme environments, such as Antarctic or deserts, especially in areas where the ambient microbial life is sparse?

Second, if we expand the diameters of the pores to allow for alternative larger nucleic acids, would you expect that to increase the noise level as the pores would also allow some other macromolecules or nano particles to enter the pore and cause interference.

Thirdly, perhaps looking for those large molecules could be a side project. If we found with these pores a large number of objects in the 50 to 3000kDa range, this could be preliminary evidence for biologically derived macromolecules.

This paper gave me quite a bit to think about . Thank you for the contribution and all the hard work.



Bryan
Europa Astronaut
Posts: 98
Re: Testing for Life
on: April 2, 2014, 04:39

Also, how could this process work with unprocessed circular DNA (assuming we will not have the restriction enzymes to perform cuts?)



Rex
Europa Dreamer
Posts: 17
Re: Testing for Life
on: April 2, 2014, 12:29

Hi Bryan, you have very good questions and I'm almost glad you were not among the peer-reviewers of my paper šŸ˜‰

1) The MinION device is undergoing distribution among the first set of "beta-testers" (our lab is among them). To my knowledge it has never been tested yet under extreme conditions and publications on nanopores devices are still restricted to experimental setups. I doubt that biological nanopores would be the best choice anyway due to the specificity of the involved enzymes to Terran nucleic acids (see section 5 of my manuscript "Possible issues"), thus I would prefer solid-state devices. In any case, implementing nanopores on a planetary mission would require further R&D developments. Adequate preparation of the sample in order to maximize the chances of success will definitely be an issue, especially in the case of the extreme dilutions we may expect out there.

2) Yes, probably the noise will increase as more macromolecules or other particles will be able to access the nanopore, but while small and (roughly) spherical analytes will result either in short-lived spikes or in pore clogging (Fig. 4B and C, respectively) the nanopore will still be able to distinguish linear polymers of a size-range corresponding to the pore diameter by the characteristic duration of their signal (Fig. 4D). The key here will be to find adequate (physical) means to slow the translocation of the nucleic acids to a speed enabling the most possible accurate analysis.

3) Check this one out: http://www.nanoscalereslett.com/content/9/1/140/abstract

4) I'm regularly performing DNA extractions from bacteria and I would say it is virtually impossible to get the chromosome out in one piece due to physical stresses which the DNA is undergoing during the procedure (mostly you get 20-50 kb chunks, if you work veeeery carefully) so I won't bother up to much about circularity. This may be at the utmost a problem in case of small plasmid-like structures or viruses with circular genomes, but Iā€™m confident that it can be solved mechanically.



Bryan
Europa Astronaut
Posts: 98
Re: Testing for Life
on: April 2, 2014, 18:04

So I'm guessing there are no commercial graphene nano pores available yet.

What if the linear molecules are highly modified post-transationally? Their secondary structures may have many more covalent bonds than ours between non-adjacent monomers. This may not only apply to polypeptide chains, but also to nucleic acids. I can imagine a system that uses such secondary bonding to supercoil DNA instead of histones or similar proteins in our system. These could even be branched systems similar in structure to glycogen (though I am unsure how a system would replicate consistently.)

How confidant are you that the procedures that you use to extract Terran DNA will work on extraterrestrial cells?

Sorry for the deluge of questions. I'm a grad student right now, so asking a ton of questions is pretty much my job. šŸ™‚



Rex
Europa Dreamer
Posts: 17
Re: Testing for Life
on: April 2, 2014, 21:57

Your guess is right, Bryan, but technology is moving incredibly fast in this field. šŸ˜‰
I'm confident that the charged linear polymer suggested by Steven Benner is the most probable blueprint for informational molecules. As you correctly pointed out, branched molecules are probably too complex for replication to occour and nature tends to keep things simple.
Your suggestion about DNA analogues that use covalent bonds for self-packaging is intriguing, however let me argue with a couple of arguments: (1) not all life forms on Earth have histones (e.g., bacteria do not), thus the same may apply for hypotetical organisms that would use covalent bonds in their "DNA" (2) histones have a great advantage over covalent bonds, that is that the packaging mechanism is largely independent from the DNA sequence itself; covalent bonds instead would require the informational molecule to have a restricted choice in the sequence of its subunits (in the same way that you can not replace a cystein by any other aminoacid in a protein without loosing the associated disulfide bond). Of course one could imagine that the covalent bonds are mediated by the backbone itself, but this raises the question which backbone subunits would be suitable in order to have adequate-spaced bonds and the latter may in turn be incompatible with the backbone's repulsive electrical charge of Benner's model (which is not a problem with histones, since the latter are positively charged).
And if really alien "DNA" is packaged with disulfide bonds ? Well, maybe we may (precautionary) use a reducing agent such as beta-mercaptoethanol or dithiothreitol to unfold it! šŸ™‚
How confident am I that Terran DNA extraction protocols will work on extraterrestrial cells? I am not, but usually boiling cells is sufficient to free some nucleic acids in the supernatant (of course certain ones, like RNA, may be promptly degraded).
Yes, there are some assumptions that have to be made (and this is why my article was submitted as "hypothesis" ... :D), but to sum it up I think that nanopores may offer a quite straightforward approach and, most importantly, would possibly deliver an unambiguous signature that can not be emulated by any known abiotic process.

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