The Genetic Rescue Foundation Blog

Strike One

As previously mentioned Beth Shapiro and her team at the UCSC Paleogenomics Lab have been performing the initial sample analysis for our attempt to sequence the moa genome. Unfortunately the news is not good for our first batch of samples. Here’s Beth’s report.

We extracted only one sample (and one blank) as a first pass. We sequenced about 4 million reads, of which 99.8% were unique (which means the library was very complex, or that a lot of different DNA sequences were present in the extract). Unfortunately, only 0.04% of these mapped to the Tinamou genome, which is approximately the same proportion that mapped to human. We also attempted to map the reads to the Anomalopteryx didiformis mitochondrial genome, and recovered only a few reads (0.014X coverage). A comparison to all data available online using the software MEGAN indicated that 84% of the recovered reads mapped to bacteria.

In summary, this specimen appears to have a very high bacterial component. It is not really possible to tell at this coverage whether there is also lots of moa DNA, but the enormous complexity of bacterial sequences means that ~99% of the recovered data will have to be thrown away.

If you want us to repeat the process or to sequence the sample more deeply (to see if we can learn whether there are lots of molecules of moa DNA present) we will. However, it might be better to attempt this with a better preserved bone at this point — one where the proportion of moa DNA to bacterial DNA is skewed more in favor of moa.

So unfortunately the first batch of samples appear to contain very little endogenous DNA. Therefore we will be resuming the hunt for better samples and will be repeating the process with the UCSC Paleogenomics Lab.

This result although disappointing was not particularly surprising. Obtaining a sample rich in endogenous DNA is very difficult, and it’s often necessary to process many samples before one of sufficient quality can be found. We will obtain a new batch of samples and repeat the process with the hope of more favorable results in the next round of analysis.

The Earth has 50 billion tons of DNA. What happens when we have the entire biocode?

One of the greatest achievements of the coming century will be the characterization of the Biocode, not just as a list of genomes of different species, but as patterns of interacting communities. Our first guess at its size opens a door. We will start to understand how it has fluctuated in composition in the past and how it will change in the future. We can start to learn how it works.

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Russia has opened a laboratory in Siberia devoted to the study of extinct animal DNA in the hope of creating clones

The new lab in Yakutsk – often called the world’s coldest city – will “seek out live cells with a view to cloning”, says Semen Grigoryev, director of the Mammoth Museum at the city’s Northeastern Federal University. He tells Ogonek magazine that “the priority is to look into bringing back the mammoth”, adding that the Beijing Institute of Genomics and South Korea’s Sooam Biotech company, which has pioneered dog cloning, will be involved in the study.

Earlier this year, researchers at Harvard University announced they had copied 14 woolly mammoth genes into the genome of an Asian elephant. The scientists at Yakutsk’s new facility hope that their own unrivalled collection of 2,000 or so remnants of prehistoric animals, ranging from primitive dogs and horses to mammoths, will help to identify quality cell tissue from which to extract useful DNA.

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Critically endangered species successfully reproduced using frozen sperm from ferret dead for 20 years

Black-footed ferrets, a critically endangered species native to North America, have renewed hope for future survival thanks to successful efforts by a coalition of conservationists, including scientists at Lincoln Park Zoo, to reproduce genetically important offspring using frozen semen from a ferret who has been dead for approximately 20 years.

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UCSC Paleogenomics Lab joins quest for moa genome

ucsc-logo

The Moa Revival Project is excited to announce that the UCSC Paleogenomics Lab will be assisting with the moa genome sequencing attempt.

The Paleogenomics Lab is a joint venture between renowned scientists Beth Shapiro, and Richard (Ed) Green. Their research focuses on a wide range of evolutionary and ecological questions, mostly involving the application of genomics techniques to better understand how species and populations evolve through time.

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Kiwi Genome Sequenced

Researchers of the University of Leipzig and the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have now sequenced the genetic code of this endangered species and have identified several sequence changes that underlie the kiwi’s adaptation to a nocturnal lifestyle.

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Over 5000 base pairs were inserted into mammalian cells using a simplified end joining process

Researchers have shown that a site specific double strand break (DSB) generated both in the genome and the donor plasmid using the CRISPR-Cas9 system can be efficiently used to target ∼5 kb plasmids into mammalian genomes via nonhomologous end joining (NHEJ). They were able to achieve efficiencies of up to 0.17% in HEK293 cells and 0.45% in CHO cells. This technique holds promise for quick and efficient insertion of a large foreign DNA sequence into a predetermined genomic site in mammalian cells.

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