Tuesday, 9 April 2013

A walking-dead pidgeon and the return of the can do NGS starting from any source!!!

Here we are again with some surprising data from NGS studies.

Besides provide some interesting (and, why not, funny) scientific stories, the following news clearly demonstrate how, relying on cut of the edge sample preparation, NGS technology allow sequencing from basically any input material. The ability to obtain a good sequence of an entire genome starting from few nanograms, but even picograms, of input DNA open the way to amazing application. From cancer genomics, to prenatal screening, the ability of sequence very little amount of cell-free DNA that is present in circulating blood as already provide really exciting results. This kind of techniques promise great improvements also in epidemic controls and contamination/pathogens detection in foods, water or any other samples.
The topic of sequencing from nanograms or picograms is extensively covered in this post on CoreGenomics, that provides also some examples of recently published papers and dicuss about the new library preparation kits that make NGS sequencing from low input DNA fast and easy!

Now the stories!
We have reported on September 2012 about Revive and Restore (see the our post here), a company founded with the ambitious and controversial aim of sequence and reconstruct the genome of extinct species with the ultimate goal of eventually bring them back to life.
We were not sure how far this initiative would have gone, but the last month they surprised us again with the announcement of an actual project to resurrect the extinct passenger pidgeon.
Ben Novak, a 26-year-old genetics, has received support from the company to achieve the goal of sequencing the entire DNA of this species from a tissue sample received from the Chicago's Field Museum in 2011. Working with evolutionary biologist Beth Shapiro at the University of California, Santa Cruz, they plan to complete the genome of passenger pidgeon and its closest living relative, the band-tailed pidgeon. The extinct DNA will then be aligned to the living one to identify all the differences and finally a massive mutagenesis will be performed on band-tailed pidgeon DNA to re-create the complete sequence of the passenger species.
However the idea not only require hard work, but it could really get dicey. Indeed, according to Shapiro, "because the last common ancestor of the two species flew about 30 million years ago, their genomes will likely differ at millions of locations." Fitting the pieces together will be grueling, if not impossible. GenomeWeb have a post on this and Wired also has covered the story in this article from Kelly Servick.

However one consider this real science or fantasy science, the general topic of de-extinction is getting increasing attention now that the DNA sequencing technology allow to effectively assemble genomes from ancient and degraded samples (remember for example the Neanderthal genome or the Mammoth genome). The collection of DNA from different species is a part of some huge projects intended to preserve and study biodiversity and experts are now discussing if and eventually how we have to deal with species that go extinct over time. If we as human race are responsible for the disappearing of a specific organism and we have the ability to bring it back to life, should we do this? What are the risks of re-introduce extinct species in our ecosystem?

Recently a TEDx event has been organized exploring the topic of de-extinction. and the recent advances in the field have received attention also from the National Geographic and The New York Times (this one dealing with bring an extinct frog back to life). Revive and Restore has a list of candidate organisms waiting for de-exctinction and is searching for collaborators! Looking at their list I may like to see a Dodo walking again in the garden...but want to raise my doubts about a tooth-saber cat!!

The second news is directly from scientific literature. In their paper recently published on Journal of Applied Genetics, Khairat et al. from the University of Tubingen, report the first metagenome analysis on ancient egyptian mummies. Their dataset comprise seven sequencing experiments performed on DNA obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC-124AD) and two unearthed pre-contact Bolivian lowland skeletons. Analyzing the data their were able to identify different genetic materials from bacteria, presumibly due to contamination from mummies conservation procedures, and also from plants, potentially associated with their use in embalming reagents. The paper demonstrates that also DNA from ancient mummies, could be a proper template for NGS sequencing, despite its age and the several treatment performed on the samples in the course of the conservation protocols.

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