Stem Cells: Mice born from eggs created from stem cells!

jtotheizzoe:

Baby Mice Born from Eggs Made from Stem Cells

Let that headline sink in for a minute.

At first glance, these mice look like normal little critters, the standard-issue Mus musculus. And if you looked at their DNA, you probably wouldn’t be able to tell them apart from many other lab mice. Except these are special.

They were created from eggs that came from stem cells. 

Yep, that’s right. For decades now, researchers have been able to turn a specific kind of stem cell, embryonic stem cells, into a full blown mouse. As amazing as it seems, that’s a pretty standard lab procedure. An ES cell gets treated in a particular way to create a “fake embryo”, then implanted into a hormone-treated mouse and develops like a normal baby mouse. While that is important for many experiments, it doesn’t help humans much … especially humans with fertility issues.

But these mice are different. Stem cells, both embryonic versions and stem cells created from skin (skin, I tell you!), were coaxed into becoming eggs and then fertilized by male sperm. They grew up to be those whiskery guys above.

This amazing feat, from Kyoto University’s Katsuhiko Hayashi, could one day help us understand how to help humans who have difficulty conceiving. In vitro fertilization may be about to go to the next level.

Science is just awesome. If we wrote this out, it would look something like:

Skin -> stem cell -> egg + sperm (from male mouse -> BABY MOUSE

Simplified, that’s “skin -> BABY MOUSE”

(via Scientific American)

(via futurecurious)

Data Storage: The next leap forward.

contemplatingmadness:

Soon you’ll be backing up your hard drive using DNA

Think the memory card in your camera is high-capacity? It’s got nothing on DNA. With data accumulating at a faster rate now than any other point in human history, scientists and engineers are looking to genetic code as a form of next-generation digital information storage.

Now, a team of Harvard and Johns Hopkins geneticists has developed a new method of DNA encoding that makes it possible to store more digital information than ever before. We spoke with lead researcher Sriram Kosuri to learn why the future of archival data storage is in genetic code, and why his team’s novel encoding scheme represents such an important step toward harnessing DNA’s vast storage potential.

The Problem

Humanity has a storage problem. Recent surveys conducted by IDC Digital Universesuggest that the perfusion of technology throughout society has triggered an explosion in the volume of information that we as a species produce on a daily basis. Between photos, video, texts, tweets, Facebook updates, unsolicited FarmVille requests, Instagram posts and various other forms of digital data production, the world’s information is doubling every two years, and that raises some important questions, chief among them being: where the hell do we put it all?

“In 2011 we had 1.8 * 10²¹ bytes of information stored and replicated” explains Sriram Kosuri, a Harvard geneticist and member of the Wyss Institute’s synthetic biology platform, in an email to io9. “By 2020 it will be 50 times that. That’s an astounding number; and doesn’t include a much larger set of data that’s thrown away (e.g., video feeds).”

As Kosuri points out, not all of this information needs to be stored, but — being the diligent little hoarders that we are — a good deal of it will be cached away somewhere for posterity; and at the rate we’re generating information, we’ll need to find new storage solutions if we want to have any hope of keeping up with our demand for space. “Our ability to store, manage, and archive such information is being constantly strained already,” notes Kosuri. “Archival storage is also a large problem.”

The (Theoretical) Solution: The Advantages of DNA Storage

Archival storage is where DNA comes in. As storage media go, it’s hard to compete with the universal building blocks of life. In an article published in today’s issue of Science, Kosuri — in co-authorship with geneticistYuan Gao and synthetic biology pioneer George Church — describes a new technique for using DNA to encode digital information in unprecedented quantities. We’ll get to their novel storage method in the next section, but for now let’s look at some numbers that help contextualize what Kosuri identifies as the two major advantages of DNA storage: information density and stability.

At theoretical maximum, one gram of single stranded genetic code can encode 455 exabytes of information. That’s almost half a billion terabytes, or 4.9 * 10¹¹ GB. (As a point of reference, the latest iPad tops out at 64 GB of storage space.) DNA strands also likes to fold over on top of themselves, meaning that, unlike most other digital storage media, data needn’t be restricted to two dimensions; and being able to store data in three-space translates to more free-space.

DNA is also incredibly robust, and is often readable even after being exposed to unfavorable conditions for thousands of years. Every time researchers recover genetic information from a woolly mammoth specimen, or sequence the genome of a 5,300 year-old human mummy, it’s a testament to DNA’s durability and data life. Just try recovering files from a 5,000-year-old CD or DVD. Hell, try it with a 20-year old disc; odds are it just isn’t going to happen.

That being said, DNA has its shortcomings. “It’s not re-writable, it’s not random access, and it is very high latency,” explains Kosuri, “so really the applications are for archival storage (not to downplay the importance of archives).”

The (Practical) Solution

To demonstrate the vast potential of DNA storage, Kosuri and his team used just shy of 55,000 159-nucleotide chunks of single stranded genetic code to encode a 5.27-megabit book, containing 53,426 words, 11 jpg images and one JavaScript program. They then proceeded to use next-generation DNA sequencing techniques to read it back. (For those who need refreshing, nucleotides are the individual building blocks that, when joined together, form strands of DNA.)

5.27-megabits probably doesn’t strike you as a lot (that comes out to roughly 660 kilobytes of information, about what you’d find on a 3.5” floppy from the 80s), but it’s impressive for at least three reasons:

One: It positively crushes the previous DNA-storage record of 7,920 bits.

Two: The novel encoding method employed by Kosuri and his colleagues allowed them to address issues of cost and accuracy, two long-standing technical hurdles facing DNA storage:

The major reason why this would have been difficult in the past is that it is really difficult to construct a large stretch of DNA with exact sequence, and make it cheaply.  We took an approach that allows us to use short stretches of DNA (basically by having an address (19 bits) and data block (96 bits), so each short stretch can be stitched together later after sequencing. Using short stretches allowed us to leverage both next-generation synthesis [for writing data]… and next-generation sequencing [for reading data] technologies to really lower cost and ease.

Three: It offers a compelling proof of concept that DNA can be used to store digital information at remarkable densities. “What we published in terms of scale is… obviously small compared to commercial technologies now,” explains Kosuri, but “using our method, a petabyte of data [one petabyte = 1,024 terabytes] would require about 1.5 mg of DNA.” Since that genetic information can be packaged in three dimensions, that translates to a storage volume of about one cubic millimeter.

The logarithmic plot featured here illustrates how the storage density demonstrated by Kosuri and his team (labeled “This Work”) compares to technologies of today andtomorrow. You should really just reference the graph, but to summarize: DNA wins out by a landslide.

“For example,” explains Kosuri, “we are ~10 orders of magnitude (100 billion fold) more dense than a CD, a million-fold more dense than the best commercial storage technologies, and about ~1000 fold more dense than [other] proof-of-concept work (e.g., position atoms on a surface).” He says the secret to DNA’s superiority harkens back to the fact that it can be stored dry in three dimensions; “thus there is no surface that requires a thickness, which really kills 3D data density.”

The Future

DNA storage has its limitations. As I mentioned earlier, it’s not re-writable, and it’s not random access. Its latency is also too high for it to be practical for anything other than archival storage, but we’ve already established that we’re in dire need of space for archiving, anyway. The only other big limiting factors, at present, are synthesis and sequencing technologies — and those won’t be an issue for much longer.

According to Kosuri, the costs of DNA synthesis and sequencing have been dropping much faster than Moore’s law. In the supplementary information section of their paper, Kosuri and his colleagues imagine what a petabyte of storage would require, from the standpoint of synthesis and sequencing costs, and conclude that they would need a roughly 6 order of magnitude drop in sequencing, and 7-8 in synthesis for storage media of that capacity to become feasible.

“To give perspective,” explains Kosuri, “costs have been dropping for the past 5-10 years at 10x and 5x per year for sequencing and synthesis respectively.” In other words: this tech is right around the corner. Are you ready for your DNA drive?

The researchers’ results are published in the latest issue of Science.

This raises a good question for which an answer should be arrived at before we lose another Lonesome George.

discoverynews:

Should We Have Cloned Lonesome George?

The death of the tortoise raises the question — how can we save our endangered animals before it’s too late?

keep reading

With rewritable digital data in DNA storage capacity becomes almost moot.

emergentfutures:

Rewritable digital data stored in live DNA

“It took us three years and 750 tries to make it work, but we finally did it,” says Jerome Bonnet, a postdoctoral scholar at Stanford University, who worked with graduate student Pakpoom Subsoontorn and assistant professor Drew Endy to reapply natural enzymes adapted from bacteria to flip specific sequences of DNA back and forth at will.

In practical terms, they have devised the genetic equivalent of a binary digit—a “bit” in data parlance. “Essentially, if the DNA section points in one direction, it’s a zero. If it points the other way, it’s a one,”

Full Story: Futurity

I’m not so sure where this one will lead, But It´s a good step forward, however, needs to be monitored, but not chocked with oversight and watchdogs neither.

futurescope:

DARPA, Venter launch assembly line for genetic engineering

DARPA has launched a program called called “Living Foundries,”designed to apply the conventions of manufacturing to living cells, Wired Danger Room reports.

DARPA has awarded seven research grants worth $15.5 million to six different companies and institutions, including the University of Texas at Austin, Cal Tech, and the J. Craig Venter Institute.

“Living Foundries” aspires to streamline genetic engineering for “on-demand production” of whatever bio-product suits the military’s immediate needs, starting with a library of “modular genetic parts.”

The agency wants researchers to come up with a set of “parts, regulators, devices and circuits” that can reliably yield various genetic systems. After that, they’ll also need “test platforms” to quickly evaluate new bio-materials to “compress the biological design-build-test cycle by at least 10X in both time and cost,” while also “increasing the complexity of systems that can be designed and executed.”

[via] [Wired] [image credit: VA]

(via futurescope)

wildcat2030:

You wouldn’t know it from appearances, but a metal cube the size of a toaster, created at the University of Alberta, is capable of performing the same genetic tests as most fully equipped modern laboratories—and in a fraction of the time. At its core is a small plastic chip developed with nanotechnology that holds the key to determining whether a patient is resistant to cancer drugs or has diseases like malaria. The chip can also pinpoint infectious diseases in a herd of cattle. Talk about thinking outside the box. (via Nano nod for lab-on-a-chip - University of Alberta)

scienceyoucanlove:

Synthetic DNA shown to evolve

Scientists from the UK Medical Research Council’s Laboratory of Molecular Biology have developed polymerases for artificial DNA, which not only “unzips” the artificial DNA, but manages to transcribe the genetic code to natural DNA, and back again.

This hints that if there is life beyond Earth, it could be bound to evolution if not the same chemistry for life here. It also shows that life may not solely be restricted to DNA or RNA. 

It should be pointed out that this does not represent a full genetics platform (as it’s still dependent on DNA), and that a self replicating system which does not require DNA still needs to be developed.

This research has implications in many fields, including astrobiology, synthetic genetics and the search into the origins of life (DNA/RNA). It is believed that DNA evolved from RNA, but that RNA in turn evolved from a simpler molecule that performed the same function.

contemplatingmadness:

XNA is synthetic DNA that’s stronger than the real thing

New research has brought us closer than ever to synthesizing entirely new forms of life. An international team of researchers has shown that artificial nucleic acids - called “XNAs” - can replicate and evolve, just like DNA and RNA.

We spoke to one of the researchers who made this breakthrough, to find out how it can affect everything from genetic research to the search for alien life.

The researchers, led by Philipp Holliger and Vitor Pinheiro, synthetic biologists at the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, say their findings have major implications in everything from biotherapeutics, to exobiology, to research into the origins of genetic information itself. This represents a huge breakthrough in the field of synthetic biology.

Read more

(via project-argus)