How Long Do Animals Live? How Can We Live Longer? An infographic exploration of animal longevity, from hare-today-gone-tomorrow to near-eternal-tortoises. What do you think makes some animals live longer than others, predators notwithstanding? Google that and let me know what you find, science detectives. As for what it means for the future longevity of humans, check out these links:  How to achieve massive longevity without overpopulation What synthetic biology and utilizing nature’s genetic tools might mean for tweaking our lifespan. Finally, a thought experiment: If our cells can become somewhat “immortal” in diseases like cancer, what’s to say that we can’t harness some of that biology and apply it to extending human lives without disease? (image via Visual.ly, links via Kirstin Butler)
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How Long Do Animals Live? How Can We Live Longer?

An infographic exploration of animal longevity, from hare-today-gone-tomorrow to near-eternal-tortoises. What do you think makes some animals live longer than others, predators notwithstanding? Google that and let me know what you find, science detectives.

As for what it means for the future longevity of humans, check out these links: 

Finally, a thought experiment: If our cells can become somewhat “immortal” in diseases like cancer, what’s to say that we can’t harness some of that biology and apply it to extending human lives without disease?

(image via Visual.ly, links via Kirstin Butler)

Source: visual.ly

Big Week for “Synthetic” Biology A jellyfish made of silicone, and a bacterium made in silico Synthetic biology is traditionally thought of as repurposing existing or designing new biological parts to do novel things. But in a larger sense, it can be thought of as the ability to create biological systems outside the limitations of pesky things like global and evolutionary time scales. This week marks two really stunning bio accomplishments, each fitting into their own definition of “synthetic”. Whoa, Jellyman: Cal Tech and Harvard biophysicists announced that they had created a sort of “synthetic jellyfish” this week (pictured above left). By taking thin, carefully designed sheets of silicone and layering rat heart muscle cells over them, they were able to make a bell-shaped living device that pulsed and swam just like the bell of a jellyfish. Heart muscle cells, or cardiomyocytes, naturally grow together in sheets and will automatically “beat” in a petri dish (with the help of a little calcium). If you provide an outside voltage (like a pacemaker) they will beat in unison! The rat-heart-silicone “medusoid” shape contracted, with the beating cells pulling on the silicone substrate just as a jellyfish’s own muscle cells act on its bell to swim.  Of course, this isn’t a real jellyfish, but for extra credit you can read Ferris Jabr’s take on what it would actually take to build one. Byte-size Bio: The other big news this week comes from Stanford and the J. Craig Venter Institute (gracing the cover of Cell this week, above right). Not content with making the world’s first synthetic organism and synthetic genome (Venter’s ambition knows no bounds), they decided to build a computer model of an entire bacterium. Well, mostly. They modeled, on a very general scale, the tiny bacterium Mycoplasma genitalium, which only has 525 genes compared to our ~20,000, and all of its internal processes on 128 computers operating for 10 hours. To complete a single cell division, it required half a gigabyte of data. But you have to be careful before you call this a completely “simulated organism”. Normal cells have many, perhaps hundreds, of just different types of genes, and they interact in myriad ways … we have just begun to scratch the surface of those networks. Just look at how complicated even the tiny changes in a cancer cell can be! By simplifying their model down to 28 minimal systems, their computer program matched the bacterium’s biology as we know it. But a more “realistic” model is going to be exponentially more complicated. Here’s some collected reactions at Tree of Life. But, still … wow! Modern biology has done a very good job at describing the function of individual genes and proteins, but our next chapter lies in how these interactions build into systems. The “-omics” era will be one where we map how the thousands of parts that we are made of combine to make us whole.Simulations like this will be at the leading edge of that era. But we have a long way to go … how many computers would it take to model the trillions of cells in the human body?
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Big Week for “Synthetic” Biology A jellyfish made of silicone, and a bacterium made in silico Synthetic biology is traditionally thought of as repurposing existing or designing new biological parts to do novel things. But in a larger sense, it can be thought of as the ability to create biological systems outside the limitations of pesky things like global and evolutionary time scales. This week marks two really stunning bio accomplishments, each fitting into their own definition of “synthetic”. Whoa, Jellyman: Cal Tech and Harvard biophysicists announced that they had created a sort of “synthetic jellyfish” this week (pictured above left). By taking thin, carefully designed sheets of silicone and layering rat heart muscle cells over them, they were able to make a bell-shaped living device that pulsed and swam just like the bell of a jellyfish. Heart muscle cells, or cardiomyocytes, naturally grow together in sheets and will automatically “beat” in a petri dish (with the help of a little calcium). If you provide an outside voltage (like a pacemaker) they will beat in unison! The rat-heart-silicone “medusoid” shape contracted, with the beating cells pulling on the silicone substrate just as a jellyfish’s own muscle cells act on its bell to swim.  Of course, this isn’t a real jellyfish, but for extra credit you can read Ferris Jabr’s take on what it would actually take to build one. Byte-size Bio: The other big news this week comes from Stanford and the J. Craig Venter Institute (gracing the cover of Cell this week, above right). Not content with making the world’s first synthetic organism and synthetic genome (Venter’s ambition knows no bounds), they decided to build a computer model of an entire bacterium. Well, mostly. They modeled, on a very general scale, the tiny bacterium Mycoplasma genitalium, which only has 525 genes compared to our ~20,000, and all of its internal processes on 128 computers operating for 10 hours. To complete a single cell division, it required half a gigabyte of data. But you have to be careful before you call this a completely “simulated organism”. Normal cells have many, perhaps hundreds, of just different types of genes, and they interact in myriad ways … we have just begun to scratch the surface of those networks. Just look at how complicated even the tiny changes in a cancer cell can be! By simplifying their model down to 28 minimal systems, their computer program matched the bacterium’s biology as we know it. But a more “realistic” model is going to be exponentially more complicated. Here’s some collected reactions at Tree of Life. But, still … wow! Modern biology has done a very good job at describing the function of individual genes and proteins, but our next chapter lies in how these interactions build into systems. The “-omics” era will be one where we map how the thousands of parts that we are made of combine to make us whole.Simulations like this will be at the leading edge of that era. But we have a long way to go … how many computers would it take to model the trillions of cells in the human body?
Zoom Info

Big Week for “Synthetic” Biology

A jellyfish made of silicone, and a bacterium made in silico

Synthetic biology is traditionally thought of as repurposing existing or designing new biological parts to do novel things. But in a larger sense, it can be thought of as the ability to create biological systems outside the limitations of pesky things like global and evolutionary time scales. This week marks two really stunning bio accomplishments, each fitting into their own definition of “synthetic”.

Whoa, Jellyman: Cal Tech and Harvard biophysicists announced that they had created a sort of “synthetic jellyfish” this week (pictured above left). By taking thin, carefully designed sheets of silicone and layering rat heart muscle cells over them, they were able to make a bell-shaped living device that pulsed and swam just like the bell of a jellyfish.

Heart muscle cells, or cardiomyocytes, naturally grow together in sheets and will automatically “beat” in a petri dish (with the help of a little calcium). If you provide an outside voltage (like a pacemaker) they will beat in unison! The rat-heart-silicone “medusoid” shape contracted, with the beating cells pulling on the silicone substrate just as a jellyfish’s own muscle cells act on its bell to swim. 

Of course, this isn’t a real jellyfish, but for extra credit you can read Ferris Jabr’s take on what it would actually take to build one.

Byte-size Bio: The other big news this week comes from Stanford and the J. Craig Venter Institute (gracing the cover of Cell this week, above right). Not content with making the world’s first synthetic organism and synthetic genome (Venter’s ambition knows no bounds), they decided to build a computer model of an entire bacterium. Well, mostly.

They modeled, on a very general scale, the tiny bacterium Mycoplasma genitalium, which only has 525 genes compared to our ~20,000, and all of its internal processes on 128 computers operating for 10 hours. To complete a single cell division, it required half a gigabyte of data. But you have to be careful before you call this a completely “simulated organism”. Normal cells have many, perhaps hundreds, of just different types of genes, and they interact in myriad ways … we have just begun to scratch the surface of those networks. Just look at how complicated even the tiny changes in a cancer cell can be!

By simplifying their model down to 28 minimal systems, their computer program matched the bacterium’s biology as we know it. But a more “realistic” model is going to be exponentially more complicated. Here’s some collected reactions at Tree of Life. But, still … wow!

Modern biology has done a very good job at describing the function of individual genes and proteins, but our next chapter lies in how these interactions build into systems. The “-omics” era will be one where we map how the thousands of parts that we are made of combine to make us whole.Simulations like this will be at the leading edge of that era. But we have a long way to go … how many computers would it take to model the trillions of cells in the human body?

Playing God - A BBC Documentary About Genetic Engineering (Watch full online)

With great power comes great responsibility. Join Adam Rutherford in this full-hour exploration (The whole thing! Online!) of the progress and perils of our ability to cut and splice the very fabric of life on command.

“Life itself has become a programmable machine.”

That statement is a bit of an exaggeration, maybe, but certainly genes, DNA, etc. (the stuff that life is made of) can be synthesized, cut and glued back together with such ease these days that a first-week undergrad can do it (even without help from a seasoned veteran biologist such as myself). You could do it in your garage if you wanted. And where the genetic engineering of yesterday was all about putting a gene or two from one organism into another (like this paper, the precursor to Monsanto’s methods), the ease and cheapness of manipulating the tools of synthetic biology create an infinite pool of possibilities for completely human-designed life forms. 

Rest easy, though. When it comes to completely synthetic life, we are still looking at a field in its infancy. Although smart dudes like Craig Venter have succeeded in creating a completely synthetic bacterium, it is an enormously difficult, sensitive and expensive thing to do. I really can’t emphasize how difficult it is, actually. But now is the time, in the early days of meaningful synthetic biology, as prices drop and methods improve, to ask ourselves what is appropriate and what is not.

This will be a global question, and a difficult one. For every drought-resistant strain of wheat that allows us to feed millions of starving children, we can not create another seed monopoly that promotes irresponsible use of herbicides. How do we ensure that the methods used to make plastic-producing bacteria are not the same methods that can produce dangerous bioterrorism strains? How do you feel about having “biohackers” able to order genes and bacteria at will, maybe around the corner from where you live?

Scientists will need to have open discussions. Nonscientists will have to be part of that discussion. This documentary is a must-watch for anyone who wants to know where the future of synthetic biology is headed.

(via EvolutionDocumentary)

Source: youtube.com

fuckyeahmolecularbiology: Lego, Eat Your Heart Out Single-stranded DNA has already proven itself to be a useful addition to the nanotechnologist’s toolbox. Blocks of DNA have been programmed to automatically build themselves into nanoscopic structures; a very long strand can be intricately folded into complex 3D shapes through a process known, appropriately, as DNA origami. Scientists hope that eventually, the DNA programmes could be sophisticated enough to churn out miniscule therapeutic devices that could work inside the body, and even be used to do highly specific tasks, like ferrying drugs to specific sites. Usually, the long, single-stranded DNA required comes from a virus, which raises the possibility that the body could attack the structures - but not anymore. Peng Yin and colleagues at Harvard University have designed a similar technology that relies entirely on synthetic DNA - no viruses allowed. “Our structures could be made to be highly biocompatible,” he says. Instead of folding one long strand of viral DNA, Yin’s team designed short, synthetic DNA strands that can fold into a small tile. (And I mean seriously small - just 7 by 3 nanometres). “Each tile acts like a Lego block,” says Yin. Tiles automatically interlock with neighbouring tiles that carry a complementary DNA sequence. This means that with a bit of forward planning, the team could design a complete set of tiles that lock together to create more than 100 shapes - including any letter of the alphabet.  Scientists hope that synthetic DNA shapes could dodge the immune system, buying them more time to shuttle drugs to the right tissue. Yin believes they could be the future: The body’s own therapeutic system, designed by our cells and for our cells. To read the original article, published in Nature, click here. Image, top: The alphabet generated by Yin and colleagues during their experiment. Image, bottom: Another set of images generated by Yin and colleagues, showing the infinite variety of shapes the DNA can combine into and detailing the advantages for targeted therapeutics. Images, centre line: A computer rendering of how the DNA might fold into the tile structure.
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fuckyeahmolecularbiology: Lego, Eat Your Heart Out Single-stranded DNA has already proven itself to be a useful addition to the nanotechnologist’s toolbox. Blocks of DNA have been programmed to automatically build themselves into nanoscopic structures; a very long strand can be intricately folded into complex 3D shapes through a process known, appropriately, as DNA origami. Scientists hope that eventually, the DNA programmes could be sophisticated enough to churn out miniscule therapeutic devices that could work inside the body, and even be used to do highly specific tasks, like ferrying drugs to specific sites. Usually, the long, single-stranded DNA required comes from a virus, which raises the possibility that the body could attack the structures - but not anymore. Peng Yin and colleagues at Harvard University have designed a similar technology that relies entirely on synthetic DNA - no viruses allowed. “Our structures could be made to be highly biocompatible,” he says. Instead of folding one long strand of viral DNA, Yin’s team designed short, synthetic DNA strands that can fold into a small tile. (And I mean seriously small - just 7 by 3 nanometres). “Each tile acts like a Lego block,” says Yin. Tiles automatically interlock with neighbouring tiles that carry a complementary DNA sequence. This means that with a bit of forward planning, the team could design a complete set of tiles that lock together to create more than 100 shapes - including any letter of the alphabet.  Scientists hope that synthetic DNA shapes could dodge the immune system, buying them more time to shuttle drugs to the right tissue. Yin believes they could be the future: The body’s own therapeutic system, designed by our cells and for our cells. To read the original article, published in Nature, click here. Image, top: The alphabet generated by Yin and colleagues during their experiment. Image, bottom: Another set of images generated by Yin and colleagues, showing the infinite variety of shapes the DNA can combine into and detailing the advantages for targeted therapeutics. Images, centre line: A computer rendering of how the DNA might fold into the tile structure.
Zoom Info
fuckyeahmolecularbiology: Lego, Eat Your Heart Out Single-stranded DNA has already proven itself to be a useful addition to the nanotechnologist’s toolbox. Blocks of DNA have been programmed to automatically build themselves into nanoscopic structures; a very long strand can be intricately folded into complex 3D shapes through a process known, appropriately, as DNA origami. Scientists hope that eventually, the DNA programmes could be sophisticated enough to churn out miniscule therapeutic devices that could work inside the body, and even be used to do highly specific tasks, like ferrying drugs to specific sites. Usually, the long, single-stranded DNA required comes from a virus, which raises the possibility that the body could attack the structures - but not anymore. Peng Yin and colleagues at Harvard University have designed a similar technology that relies entirely on synthetic DNA - no viruses allowed. “Our structures could be made to be highly biocompatible,” he says. Instead of folding one long strand of viral DNA, Yin’s team designed short, synthetic DNA strands that can fold into a small tile. (And I mean seriously small - just 7 by 3 nanometres). “Each tile acts like a Lego block,” says Yin. Tiles automatically interlock with neighbouring tiles that carry a complementary DNA sequence. This means that with a bit of forward planning, the team could design a complete set of tiles that lock together to create more than 100 shapes - including any letter of the alphabet.  Scientists hope that synthetic DNA shapes could dodge the immune system, buying them more time to shuttle drugs to the right tissue. Yin believes they could be the future: The body’s own therapeutic system, designed by our cells and for our cells. To read the original article, published in Nature, click here. Image, top: The alphabet generated by Yin and colleagues during their experiment. Image, bottom: Another set of images generated by Yin and colleagues, showing the infinite variety of shapes the DNA can combine into and detailing the advantages for targeted therapeutics. Images, centre line: A computer rendering of how the DNA might fold into the tile structure.
Zoom Info
fuckyeahmolecularbiology: Lego, Eat Your Heart Out Single-stranded DNA has already proven itself to be a useful addition to the nanotechnologist’s toolbox. Blocks of DNA have been programmed to automatically build themselves into nanoscopic structures; a very long strand can be intricately folded into complex 3D shapes through a process known, appropriately, as DNA origami. Scientists hope that eventually, the DNA programmes could be sophisticated enough to churn out miniscule therapeutic devices that could work inside the body, and even be used to do highly specific tasks, like ferrying drugs to specific sites. Usually, the long, single-stranded DNA required comes from a virus, which raises the possibility that the body could attack the structures - but not anymore. Peng Yin and colleagues at Harvard University have designed a similar technology that relies entirely on synthetic DNA - no viruses allowed. “Our structures could be made to be highly biocompatible,” he says. Instead of folding one long strand of viral DNA, Yin’s team designed short, synthetic DNA strands that can fold into a small tile. (And I mean seriously small - just 7 by 3 nanometres). “Each tile acts like a Lego block,” says Yin. Tiles automatically interlock with neighbouring tiles that carry a complementary DNA sequence. This means that with a bit of forward planning, the team could design a complete set of tiles that lock together to create more than 100 shapes - including any letter of the alphabet.  Scientists hope that synthetic DNA shapes could dodge the immune system, buying them more time to shuttle drugs to the right tissue. Yin believes they could be the future: The body’s own therapeutic system, designed by our cells and for our cells. To read the original article, published in Nature, click here. Image, top: The alphabet generated by Yin and colleagues during their experiment. Image, bottom: Another set of images generated by Yin and colleagues, showing the infinite variety of shapes the DNA can combine into and detailing the advantages for targeted therapeutics. Images, centre line: A computer rendering of how the DNA might fold into the tile structure.
Zoom Info

fuckyeahmolecularbiology:

Lego, Eat Your Heart Out

Single-stranded DNA has already proven itself to be a useful addition to the nanotechnologist’s toolbox. Blocks of DNA have been programmed to automatically build themselves into nanoscopic structures; a very long strand can be intricately folded into complex 3D shapes through a process known, appropriately, as DNA origami. Scientists hope that eventually, the DNA programmes could be sophisticated enough to churn out miniscule therapeutic devices that could work inside the body, and even be used to do highly specific tasks, like ferrying drugs to specific sites.

Usually, the long, single-stranded DNA required comes from a virus, which raises the possibility that the body could attack the structures - but not anymore. Peng Yin and colleagues at Harvard University have designed a similar technology that relies entirely on synthetic DNA - no viruses allowed.

“Our structures could be made to be highly biocompatible,” he says.

Instead of folding one long strand of viral DNA, Yin’s team designed short, synthetic DNA strands that can fold into a small tile. (And I mean seriously small - just 7 by 3 nanometres). “Each tile acts like a Lego block,” says Yin. Tiles automatically interlock with neighbouring tiles that carry a complementary DNA sequence. This means that with a bit of forward planning, the team could design a complete set of tiles that lock together to create more than 100 shapes - including any letter of the alphabet.

 Scientists hope that synthetic DNA shapes could dodge the immune system, buying them more time to shuttle drugs to the right tissue. Yin believes they could be the future: The body’s own therapeutic system, designed by our cells and for our cells.

To read the original article, published in Nature, click here.

Image, top: The alphabet generated by Yin and colleagues during their experiment.

Image, bottom: Another set of images generated by Yin and colleagues, showing the infinite variety of shapes the DNA can combine into and detailing the advantages for targeted therapeutics.

Images, centre line: A computer rendering of how the DNA might fold into the tile structure.

XNA: The Synthetic Super-Cousin of DNA That Can Replicate and Store Information The DNA double helix that we’re all familiar with is a molecular ladder made of three key parts. The backbone of phosphates that tie everything together up and down, the sugar rings (“deoxyribose”) that serve as rungs, and the bases (A, C, G, T) that invisibly bond the two strands of the helix together, head to toe. But that helix can be broken or mutated in nature, leading to mutations. And out of all the compounds in the world that could have evolved to carry our information, why just DNA and its cousin RNA? To answer that question, Vitor Pinheiro’s team created a completely new set of information molecules called XNA. XNA replaces the deoxyribose sugar ring with other chemical rings like threose and cyclohexane. By evolving an enzyme that could read these funny bases, they were able to read DNA into XNA as well as the reverse. Plus it’s super-strong and resistant to breaking or cleaving. Molecules like XNA could expand the information code for synthetic biology as well as help us answer the ultimate question about DNA: Why that, and not something else? Ed Yong has more great detail here. (↬ Not Exactly Rocket Science)
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XNA: The Synthetic Super-Cousin of DNA That Can Replicate and Store Information

The DNA double helix that we’re all familiar with is a molecular ladder made of three key parts. The backbone of phosphates that tie everything together up and down, the sugar rings (“deoxyribose”) that serve as rungs, and the bases (A, C, G, T) that invisibly bond the two strands of the helix together, head to toe.

But that helix can be broken or mutated in nature, leading to mutations. And out of all the compounds in the world that could have evolved to carry our information, why just DNA and its cousin RNA? To answer that question, Vitor Pinheiro’s team created a completely new set of information molecules called XNA.

XNA replaces the deoxyribose sugar ring with other chemical rings like threose and cyclohexane. By evolving an enzyme that could read these funny bases, they were able to read DNA into XNA as well as the reverse. Plus it’s super-strong and resistant to breaking or cleaving.

Molecules like XNA could expand the information code for synthetic biology as well as help us answer the ultimate question about DNA: Why that, and not something else? Ed Yong has more great detail here.

(↬ Not Exactly Rocket Science)

Source: blogs.discovermagazine.com

futurescope: The Potential of Synthetic Biology in Space A lot of proposed synthetic biology applications can seem pretty out there, but some are really out there. NASA is currently advertising open postdoctoral positions in synthetic biology, with particular emphasis on food production in space. Engineered organisms have the potential to do lots of things that would be useful for space colonists, from producing food and fuel to treating wastewater. Because organisms replicate themselves, future astronauts would only have to bring some spores and seeds and empty bioreactors, the organisms would do the rest of the work. […] [via] [Synthetic Biology @ NASA] [photo credit by Matt Mansell] I fully endorse these applications of synthetic biology, and I would love to help develop them. If only we had programs funded that could put them to use …
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futurescope:

The Potential of Synthetic Biology in Space

A lot of proposed synthetic biology applications can seem pretty out there, but some are really out there. NASA is currently advertising open postdoctoral positions in synthetic biology, with particular emphasis on food production in space. Engineered organisms have the potential to do lots of things that would be useful for space colonists, from producing food and fuel to treating wastewater. Because organisms replicate themselves, future astronauts would only have to bring some spores and seeds and empty bioreactors, the organisms would do the rest of the work. […]

[via] [Synthetic Biology @ NASA] [photo credit by Matt Mansell]

I fully endorse these applications of synthetic biology, and I would love to help develop them. If only we had programs funded that could put them to use …

(via futurescope)

curiositycounts:

Scientists create new light source from millions of glowing E.coli. See also the E.chromi project, using “designer” color-coded bacteria for disease detection.

From the toolbox of synthetic biology, this team has assembled a screen where every pixel is an individual bacterium, responsive not to electrical impulse, but to chemical stimulus.