Hunting for DNA stories at natural history museums

Researchers use a new methods to extract DNA from preserved samples, opening the door to exploring the DNA of millions of preserved specimens housed at museums.

A slice of history

Washington, London, Chicago, Vienna and Beijing are just some of the cities that are home to natural history museums with perfectly preserved biological specimens. In some cases, these samples represent the last remnants of a species long extinct.

This is why being able to access the DNA of these preserved organisms is of such importance. Their DNA story can give us so much insight into the environment, diet and even the microbiome from that exact moment these sample was preserved.

The problem with preserved DNA

Formalin has been our preservative of choice for more than 150 years for fixing biological samples. A disinfectant and an antiseptic, formalin stops parasites from growing on tissue samples keeping them in ‘perfect’ condition.

But, the problem is formalin fixation can damage DNA by breaking it into fragments. Not only that, formalin can interfere with the processes used to recover and analyze DNA, making it very difficult to access the valuable genetic information trapped inside these preserved museum samples.

Schematic of formalin-induced crosslink formation and the removal of crosslinked proteins by treatment with proteinase K.
(A) A protein can attack formaldehyde, which can then react with DNA, RNA, or proteins to form a crosslink. This crosslink reaction is in reversible dynamic equilibrium. (B) Treatment with a protease, proteinase K, allows DNA recovery.

These issues are further compounded by the fact that most current methods for recovering DNA from preserved samples have to be done at high temperatures (49C) and take a long time (>17 hours), increasing the likelihood of further damage to the DNA samples.

The vortex fluidic device

Above are only some of the reasons behind why researchers in this study looked into a recently patented technology called a vortex fluidic device (VFD) for tackling the problem of fragile samples.

This technique first claimed its fame in 2015 with the “unboiling a boiled egg” experiment, introducing the idea that mechanical forces in a thin microfluidic devise can reshape proteins to gain back their original structure.

In this case, researchers predicted that the power of VFD can be used to accelerate the activity of the enzyme used during DNA extractions, reducing the time necessary to recover DNA thereby increasing the yield.

Enter the lobster

They began by preserving an adult male lobster bought from a fishery in Boston in using standard practices. This sample was stored at room temperature for one month, before shipping it to the study location at University of California Irvine. All subsequent experiments were performed using this sample, which was in preservative for 2 years.

Researchers found that compared to conventional methods, using VFD reduced the DNA extraction time from >17 hours to less than 2 hours, which would decrease the amount of damage to DNA. More importantly perhaps, they showed that DNA collected using this new, faster method was amenable to standard DNA sequencing protocols as well as DNA quantifying protocols, opening a whole new world of possibilities for obtaining DNA samples from millions of fixed samples housed in natural history museums around the world.

DNA secrets revealed

Since it’s invention, the vortex fluidics device has made a profound impact on several different biomedical fields. The ability to unravel the genetic stories hidden in samples that date more than 150 years, can now be added to this list of accomplishments.

Scientists postulate that more than 400 million formalin-fixed samples are available at natural history museums from around the world. Having the ability to unravel the DNA stories hidden within these samples will give scientists with an invaluable source of informations, to improve our understanding of the world around us.


Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

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