The Genetic Rescue Foundation Blog

CRISPR: gene editing is just the beginning

Much of the conversation about CRISPR–Cas9 has revolved around its potential for treating disease or editing the genes of human embryos, but researchers say that the real revolution right now is in the lab. What CRISPR offers, and biologists desire, is specificity: the ability to target and study particular DNA sequences in the vast expanse of a genome. And editing DNA is just one trick that it can be used for. Scientists are hacking the tools so that they can send proteins to precise DNA targets to toggle genes on or off, and even engineer entire biological circuits — with the long-term goal of understanding cellular systems and disease.

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An Ecomodernist Manifesto

A good Anthropocene demands that humans use their growing social, economic, and technological powers to make life better for people, stabilize the climate, and protect the natural world.

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Strike Two

Moa in the Forest

For those of you following our efforts to sequence the moa genome my apologies for the delay in publishing this update. It took a bit of time for our latest batch of samples to find their way to the UCSC Paleogenomics Lab.

bethShapiro

Dr. Beth Shapiro


Just completed the analysis of the last four samples. These are better preserved than the previous samples, but still pretty poor. The best two samples are only around 1.5% endogenous DNA (so 98.5% environmental DNA), which would make it a very expensive genome sequencing project. My recommendation would be to keep looking for a well preserved bone.
 

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So unfortunately our second batch of samples have yielded only slightly better results than the first. I’ve discussed the sequencing efforts with many of the world’s ancient DNA and moa experts. They all agree that finding a well preserved sample is essential and that there’s not much you can do to guarantee your selected sample is high quality.

Plan C

So what are the next steps?

pyramid-valley

At the moment our next plan is to undertake an excavation. There are many promising sites that have not yet been explored including anaerobic swamp locations that hold great promise for preservation.

We’re still determining the target location for the excavation. Once a site has been selected we will invite anyone who has contributed to the moa genome sequencing campaign to join us as we attempt to excavate a “fresh” specimen. Many of the preservation problems appear to be related to decay post excavation. In other words once the specimens are out of ground they decompose more quickly. We’re hoping that if we can excavate and cryopreserve rapidly then we will succeed in sourcing a sample of sufficient quality to sequence in detail.

Thank you to everyone who has supported the campaign so far. I wish I could have better news to share with you. However an excavation is an exciting proposition that presents a great opportunity to involve the community who have supported this work to-date.

Let me embrace thee, sour adversity, for wise men say it is the wisest course.

Genetically Modified Mosquito May Become Weapon Against Zika Virus

Genetically modified mosquitoes that would help fight the Zika virus are getting urgent attention from U.S. regulators as global health officials raise alarms about the pathogen’s spread.

The U.S. Food and Drug Administration is in the final stages of reviewing an application from Intrexon Corp.’s Oxitec unit to conduct a field trial in the Florida Keys, Oxitec Chief Executive Officer Hadyn Parry said in a phone interview. Parry wasn’t able to provide further details on the timing of an FDA decision.

Oxitec genetically modifies the males in a breed of mosquito known as Aedes aegypti — responsible for transmitting Zika, Dengue, Chikungunya and Yellow Fever — so that their offspring die young. The Zika virus has been spreading “explosively” in South and Central America, the World Health Organization said Thursday. Developing a vaccine could take years, drugmakers and health experts have cautioned.

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Meet the Time-Traveling Scientist Behind Editas, the Biotech Company Going Public With Google’s Help

On March 15, 2013, genetic engineer George Church stood in the middle of a circular red rug onstage at the Gilbert H. Grosvenor Auditorium in Washington, D.C., describing a detailed plan for bringing a six-ton, 10-foot, fur-covered creature back from the dead.

By splicing genes responsible for traits like thicker hair, subcutaneous fat and curving tusks into the DNA of an Asian elephant, Church hopes to revive the long-extinct woolly mammoth, or at least create a version of the modern elephant that really likes the cold.

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The Heroes of CRISPR

It’s hard to recall a revolution that has swept biology more swiftly than CRISPR. Just 3 years ago, scientists reported that the CRISPR system—an adaptive immune system used by microbes to defend themselves against invading viruses by recording and targeting their DNA sequences—could be repurposed into a simple and reliable technique for editing, in living cells, the genomes of mammals and other organisms. CRISPR was soon adapted for a vast range of applications—creating complex animal models of human-inherited diseases and cancers; performing genome-wide screens in human cells to pinpoint the genes underlying biological processes; turning specific genes on or off; and genetically modifying plants—and is being used in thousands of labs worldwide. The prospect that CRISPR might be used to modify the human germline has stimulated international debate.

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A Mummified Moa Helps Paleontologists Reconstruct Feeding Behavior

Let’s say you had a mummy of a giant extinct bird—what would you do with it? Marie Attard and co-authors had a brilliant idea. They stuck it in an MRI scanner to get a detailed look at its jaw muscles and reconstruct the way it ate, even though moas have been extinct for 550 years.

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The Anthropocene: Hard evidence for a human-driven Earth

The evidence for a new geological epoch which marks the impact of human activity on the Earth is now overwhelming according to a recent paper by an international group of geoscientists. The Anthropocene, which is argued to start in the mid-20th Century, is marked by the spread of materials such as aluminium, concrete, plastic, fly ash and fallout from nuclear testing across the planet, coincident with elevated greenhouse gas emissions and unprecedented trans-global species invasions.

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Hunting for DNA in Doggerland, an Ancient Land Beneath the North Sea

IN 1931 A fishing boat trawling the North Sea hauled in a spear point along with its catch. The sharpened piece of antler with barbs carved into one sides was almost 14,000 years old—a remnant of a place called Doggerland, underwater since the end of an ice age raised sea levels.

Today, researchers are embarking on an ambitious project to fully explore Doggerland—using DNA, seafloor sediment, and survey data from oil and gas companies.

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‘Anti-malarial mosquitoes’ created using controversial genetic technology

Crispr-Cas9 used to write anti-malarial genes into the DNA of eggs belonging to Anopheles stephensi mosquitoes. A major carrier of the malaria parasite in Asia, the strain is responsible for more than 10% of malaria cases in India.

In lab tests, the modified mosquitoes passed on their anti-malarial genes to 99.5% of their offspring, suggesting that the procedure was incredibly effective and efficient.

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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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