Hacking The Wooly Mammoth

September 14, 2021 by Al Williams 19 Comments

In case you can’t get enough Jurassic Park movies, you can look forward to plans a biotech company has to hybridize endangered Asian elephants with long-extinct wooly mammoths using gene splicing and other exotic techniques.

Expect a long movie, the team hopes to have calves after six years and we don’t think a theme park is in the making. The claim is that mammoth traits will help the elephants reclaim the tundra, but we can’t help but think it is just an excuse to reanimate an extinct animal. If you read popular press reports, there is some question if the ecological mission claimed by the company is realistic. However, we can’t deny it would be cool to bring an animal back from extinction — sort of.

We aren’t DNA wizards, so we only partially understand what’s being proposed. Apparently, skin cells from a modern elephant will serve as a base to accept extracted mammoth DNA. This might seem far-fetched but turns out the mammoth lived much more recently than we usually think. When they die in their natural deep-freeze environment, they are often well preserved.

Once the gene splicing is set up, a surrogate elephant will carry the embryo to term. The hope is that the improved breed would be able to further interbreed with natural species, although with the gestation and maturity times of elephants, this will be a very long time to bear fruit.

So how do you feel about it? Will we face a movie-level disaster? Will we get some lab curiosity creatures? Will it save the tundra? Let us know what you think in the comments.

DNA manipulation has gone from moon-shot-level tech to readily accessible in a very short amount of time. In particular, CRISPR, changes everything and is both exciting and scary on what it puts in the hands of nearly anyone.

Emmanuelle Charpentier And Jennifer Doudna Sharpened Mother Nature’s Genetic Scissors And Won The Nobel For It

November 3, 2020 by Kristina Panos 8 Comments

It sounds like science fiction — and until 2012, the ability to cheaply and easily edit strings of DNA was exactly that. But as it turns out, CRISPR/Cas9 gene editing is a completely natural function in which bacteria catalogs its interactions with viruses by taking a snippet of the virus’ genetic material and filing it away for later.

Now, two women have won the 2020 Nobel Prize in Chemistry “for developing a method for genome editing”. Emmanuelle Charpentier and Jennifer Doudna leveraged CRISPR into a pair of genetic scissors and showed how sharp they are by proving that they can edit any string of DNA this way. Since Emmanuelle and Jennifer published their 2012 paper on CRISPR/Cas9, researchers have used these genetic scissors to create drought-resistant plants and look for new gene-based cancer therapies. Researchers are also hoping to use CRISPR/Cas9 to cure inherited diseases like Huntington’s and sickle cell anemia.

The discovery started with Emmanuelle Charpentier’s investigation of the Streptococcus pyogenes bacterium. She was trying to understand how its genes are regulated and was hoping to make an antibiotic. Once she teamed up with Jennifer Doudna, they found a scientific breakthrough instead.

Dr. Emmanuelle Charpentier via Wikimedia Commons

Emmanuelle Charpentier Fights Flesh-Eating Bacteria

Emmanuelle Charpentier was born December 11th, 1968 in Juvisy-sur-Orge, France. She studied biochemistry, microbiology, and genetics at the Pierre and Marie Curie University, which is now known as Sorbonne University. Then she received a research doctorate from Institut Pasteur and worked as a university teaching assistant and research scientist. Dr. Charpentier is currently a director at the Max Planck Institute for Infection Biology in Berlin, and in 2018, she founded an independent research unit.

Upon completion of her doctorate, Dr. Charpentier spent a few years working in the States before winding up at the University of Vienna where she started a research group. Her focus was still on the bacteria Streptococcus pyogenes, which causes millions of people to suffer through infections like tonsillitis and impetigo each year. It also causes sepsis, which officially makes it a flesh-eating bacterium.

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Coronavirus Testing: CRISPR Technology Set To Streamline Viral Testing

May 27, 2020 by Dan Maloney 3 Comments

If we could run back 2020 to its beginning and get a do-over, chances are pretty good that we’d do a lot of things differently. There’s a ton of blame to go around on COVID-19, but it’s safe to say that one of the biggest failures of this whole episode has been the lack of cheap, quick, accurate testing for SARS-CoV-2, the virus behind the current pandemic. It’s not for lack of information; after all, Chinese scientists published the sequence of the viral genome very early in the pandemic, and researchers the world over did the same for all the information they gleaned from the virus as it rampaged around the planet.

But leveraging that information into usable diagnostics has been anything but a smooth process. Initially, the only method of detecting the virus was with reverse transcriptase-polymerase chain reaction (RT-PCR) tests, a fussy process that requires trained technicians and a well-equipped lab, takes days to weeks to return results, and can only tell if the patient has a current infection. Antibody testing has the potential for a quick and easy, no-lab-required test, but can only be used to see if a patient has had an infection at some time in the past.

What’s needed as the COVID-19 crisis continues is a test with the specificity and sensitivity of PCR combined with the rapidity and simplicity of an antibody test. That’s where a new assay, based on the latest in molecular biology methods and dubbed “STOPCovid” comes in, and it could play a major role in diagnostics now and in the future.

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Hackaday Podcast 055: The Most Cyberpunk Synthesizer, Data In Your Cells, Bubbly In Your Printer, And The Dystopian Peepshow

February 21, 2020 by Mike Szczys 2 Comments

Hackaday editors Mike Szczys and Elliot Williams discuss the many great hacks of the past week. Just in case you missed the fact that we’re living in the cyberpunk future, you can now pop off your prosthetic hand and jack directly into a synthesizer. The robot headed for Mars has a flying drone in its belly. Now they’re putting foaming agent in filament to make it light and flexible. And did you ever wonder why those pinouts were so jumbled?

Take a look at the links below if you want to follow along, and as always tell us what you think about this episode in the comments!

Take a look at the links below if you want to follow along, and as always, tell us what you think about this episode in the comments!

Direct download (60 MB or so.)

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Better Beer Through Gene Editing

March 27, 2018 by Kristina Panos 63 Comments

As much as today’s American beer drinker seems to like hoppy IPAs and other pale ales, it’s a shame that hops are so expensive to produce and transport. Did you know that it can take 50 pints of water to grow enough hops to produce one pint of craft beer? While hops aren’t critical to beer brewing, they do add essential oils and aromas that turn otherwise flat-tasting beer into delicious suds.

Using UC Berkley’s own simple and affordable CRISPR-CaS9 gene editing system, researchers [Charles Denby] and [Rachel Li] have edited strains of brewer’s yeast to make it taste like hops. These modified strains both ferment the beer and provide the hoppy flavor notes that beer drinkers crave. The notes come from mint and basil genes, which the researchers spliced in to yeast genes along with the CaS9 protein and promoters that help make the edit successful. It was especially challenging because brewer’s yeast has four sets of chromosomes, so they had to do everything four times. Otherwise, the yeast might reject the donor genes.

So, how does it taste? A group of employees from a nearby brewery participated in a blind taste test and agreed that the genetically modified beer tasted even hoppier than the control beer. That’s something to raise a glass to. Call and cab and drive across the break for a quick video.

Have you always wanted to brew your own beer, but don’t know where to start? If you have a sous vide cooker, you’re in luck.

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Movie Encoded In DNA Is The First Step Toward Datalogging With Living Cells

July 13, 2017 by Sean Boyce 33 Comments

While DNA is a reasonably good storage medium, it’s not particularly fast, cheap, or convenient to read and write to.

What if living cells could simplify that by recording useful data into their own DNA for later analysis? At Harvard Medical School, scientists are working towards this goal by using CRISPR to encode and retrieve a short video in bacterial cells.

CRISPR is part of the immune system of many bacteria, and works by storing sequences of viral DNA in a specific location to identify and eliminate viral infections. As a tool for genetic engineering, it’s cheaper and has fewer drawbacks than previous techniques.

Besides generating living rickrolls and DMCA violations, what is this good for? Cheap, self-replicating sensors. [Seth Shipman], part of the team of scientists at Harvard, explains in an interview below a number of possible applications. His focus is engineering cells to act as a noninvasive data acquisition tool to study neurobiology, for example by using engineered neurons to record their developmental history.

It’s possible to see how this technique can be used more broadly and outside an academic context. Presently, biosensors generally use electric or fluorescent transducers to relay a detection event. By recording data over time in the DNA of living cells, biosensors could become much cheaper and contain intrinsic datalogging. Possible applications could include long-term metabolite (e.g. glucose) monitors, chemical detectors, and quality control.

It’s worth noting that this technique is only at the proof of concept stage. Data was recorded and retrieved manually by the scientists into the bacterial genome with 90% accuracy, demonstrating that if cells can be engineered to record data themselves, accuracy and capacity are high enough for practical applications.

That being said, if anyone is working on a MEncoder or ffmpeg command line option for this, let us know in the comments.

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IndieGoGo Project Offers DNA Editing For The Home

November 8, 2015 by Richard Baguley 17 Comments

CRISPR is the new darling of the genetics world, because it allows you to easily edit DNA. It is far more effective than previous techniques, being both precise and relatively easy to use. According to this IndieGoGo project, it is coming to your home lab soon. Genetic researchers love Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) because it allows you to very precisely edit a DNA strand. Using a protein called CAS9, CRISPR can find a very specific sequence in a DNA sequence and cut it. It occurs naturally in cells as part of the immune system: by finding and remembering parts of virus DNA, a cell can recognize and attack it when infected. For the genetics researcher, this allows them to insert new DNA sequences at specific points in the genes of any living cell.

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