Using light to describe the ancient world

Archive for the ‘Emission spectroscopy’ Category

#Fluorescent DNA in moa eggshells

 

Researchers labelled DNA in moa eggshells with a fluorescent dye. Moa didn't have green fluorescent bones - this is just a fun picture.

Researchers labelled DNA in moa eggshells with a fluorescent dye. Moa didn’t have green fluorescent bones – this is just a fun picture.

Many researchers use genetic information to study relationships between species. This works because there are tiny differences between the genetic code of a parent and an offspring – over many generations, these small changes eventually produce new species. Closely related species that shared a recent common ancestor will have the most similar genetic code (i.e. most similar DNA sequences). So, by figuring out similarities and differences between the genetic codes, researchers can understand evolutionary relationships between species.

This works really well for modern animals because researchers can easily collect DNA from living tissues. This is a little more challenging if researchers want to use DNA to learn the relationships of extinct animals. DNA degrades over time, so even if you find a fossil that is only a few hundred years old, it may no longer contain DNA. This was the challenge that Charlotte Oskam and colleagues faced when they studied ancient moa eggshells (Oskam et al. 2010). How could they know if DNA was present in the ancient eggshells? One method they explored was confocal fluorescence microscopy.

I will let these two clips explain:

To find out if ancient moa and elephant bird eggshells contained DNA, Oskam and colleagues immersed the shell fragments in a solution of fluorescent dye. The dye is colourless and it binds to DNA. When the dye-labelled DNA is irradiated with a blue laser it appears green. Sure enough, the ancient moa eggshells lit up green in the laser microscope.

“…Confocal imaging of elephant bird (Aepyornis) eggshell in cross section clearly demonstrated that DNA is distributed through the eggshell matrix as evidenced by the presence of fluorescent ‘hot-spots’. Imaging of the inner surface of moa eggshell (Dinornis) also shows foci of DNA…”

This is great, and a real time saver if it stops the researchers from analysing ancient egg shells that don’t have DNA in them. Imagine, though, how amazing it would be if we could find the ancient DNA without the need for a fluorescent dye….

Oskam CL, Haile J, McLay E, Rigby P, Allentoft ME, Olsen ME, Bengtsson C, Miller GH, Schwenninger J-L, Jacomb C, Walter R, Baynes A, Dortch J, Parker-Pearson M, Gilbert MTP, Holdaway RN, Willerslev E and Bunce, M. 2010. Fossil avian eggshell preserves ancient DNA. Proceedings of the Royal Society B: DOI: 10.1098/rspb.2009.2019

Fossil spectroscopy on Mars

Artists impression of the Mars rover ‘Curiosity’ using its LIBS system to analyse rocks.

The next Mars Rover in the launch schedule is a mobile laboratory called ‘Curiosity’. One of the aspirations for Curiosity’s mission is to study the habitability of Mars, with a view towards ancient life. From the Mars Science Laboratory website, “…The rover will analyze dozens of samples scooped from the soil and drilled from rocks. The record of the planet’s climate and geology is essentially “written in the rocks and soil” — in their formation, structure, and chemical composition. The rover’s onboard laboratory will study rocks, soils, and the local geologic setting in order to detect chemical building blocks of life (e.g., forms of carbon) on Mars and will assess what the martian environment was like in the past…”. So, Curiosity will be a Martian paleontologist.

The instrument suite onboard the SUV-sized Curiosity would happily replace the analytical facilities of most geochemistry labs. Curiosity is not carrying vibrational spectroscopic instrumentation (…that will have to wait for ExoMars), but it does have something equally awesome: LIBS. Light-induced breakdown spectroscopy uses a laser (in this case, a neodymium:potassium gadolinium tungstate solid state laser) to atomise a sample. Think Death Star vs. Alderaan. The atomised samples become highly excited, which means electrons jump to higher energy levels. Vacancies in electron shells are eventually refilled: electrons at higher energy levels lose energy and slot into lower energy levels. The energy that is lost during this transition is a photon, with a wavelength characteristic of the atom where all of this is taking place. So, if you collect the photons that are emitted when you atomise your sample, you can assess the composition of the sample you atomised. Think Grand Moff Tarkin with a Polaroid. What makes this particularly awesome, however, is that Curiosity can use its LIBS system on samples that are up to 7m away.

How does this make Curiosity a paleontologist? The fossil remains of life on Earth have very distinct chemistries covering lighter (hydrogen, carbon, oxygen, nitrogen) and heavier elements (calcium, iron). The LIBS system onboard Curiosity can detect most elements, and might give us our first hard evidence for extraterrestrial life.

Image from NASA

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