Researchers Build Complex 3D Nano Structures Out of DNA By Manipulating How Strands Join
“We were amazed that it worked!” said Yan. “Once we saw that it actually worked, it was relatively easy to implement new designs. Now it seems easy in hindsight. If your mindset is limited by the conventional rules, it’s really hard to take the next step. Once you take that step, it becomes so obvious.”
The DNA Gridiron designs are programmed into a viral DNA, where a spaghetti-shaped single strand of DNA is spit out and folded together with the help of small ‘staple’ strands of DNA that help mold the final DNA structure. In a test tube, the mixture is heated, then rapidly cooled, and everything self-assembles and molds into the final shape once cooled.
Next, using sophisticated AFM and TEM imaging technology, they are able to examine the shapes and sizes of the final products and determine that they had formed correctly.
This approach has allowed them to build multilayered, 3-D structures and curved objects for new applications. “Most of our research team is now devoted toward finding new applications for this basic toolkit we are making,” said Yan. “There is still a long way to go and a lot of new ideas to explore. We just need to keep talking to biologists, physicists and engineers to understand and meet their needs.”
Mice Genetically Engineered to be Super-Sensitive to the Smell of TNT, Will Be Used to Clear Landmines
A Belgian organization called APOPO already uses giant African pouched rats as a cheaper way to sniff out landmines. The rats are not genetically modified, but their sense of smell is sharp enough to detect TNT.
…While the furry minesweepers are effective (with two handlers, they can cover a field in one hour that would take two full days for metal detectors), they need nine months of training to become reliable, a process that costs around 6,000 euros per rat.
The genetically engineered mice, however, are so sensitive to TNT that encountering the molecule is likely to change their behavior involuntarily, so they would need little to no training.
[Molecular Neurobiologist} Charlotte D’Hulst… used genetic modification to ensure that the mice have 10,000 to 1,000,000 odor-sensing neurons with a TNT-detecting receptor compared with only 4,000 in a normal animal, “possibly amplifying the detection limit for this odor 500-fold,” she says.
Each odor-sensing neuron in a mouse’s nose is spotted with one kind of odor receptor. Usually, each specific receptor is found in one out of every thousand odor-sensing neurons, but about half the scent-detecting neurons in D’Hulst’s mice have the TNT-detecting receptor.
(via Genetically Modified Mice Could Be Tiny Landmine-Sniffing Heroes | MIT Technology Review)
Researchers Gain ability to Re-Write Gene Sequences in Zebrafish
One of the sequences that Ekker and his colleagues inserted into the zebrafish DNA was one that allows genes to be switched on and off. This could enable researchers to examine the effects of a gene both during early development, by turning the mutation on immediately, or later in life, by turning it on when the fish reaches maturity. It is not usually possible to examine the effects of gene alteration in later life, because fish with deliberately mutated genes that affect development often do not survive into adulthood.
The work “opens up the possibility to do many great experiments using zebrafish”, says Jason Rihel, a developmental biologist who works with zebrafish at University College London. “The ability to directly rewrite native genetic sequences would give us the precise control of genes needed to refine zebrafish models of complex diseases.” Such models could be used to probe “the behavioural functions of specific brain neurons, or to tease apart the network of signals that orchestrate vertebrate development”, he adds.
(via Custom gene editing rewrites zebrafish DNA : Nature News & Comment)
"Biology's Master Programmers:" Technology Review on the State of the Biotech Art
The cost of both decoding DNA and synthesizing new DNA strands… is falling about five times as fast as computing power is increasing under Moore’s Law, which has accurately predicted that chip performance will double roughly every two years. Those involved in synthetic biology, who often favor computer analogies, might say it’s becoming exponentially easier to read from, and write into, the source code of life.
These underlying technology trends, says Church, are leading to an explosion in experimentation of a sort that would have been inconceivable only a few years ago.
Up to now, it’s proved stubbornly difficult to turn synthetic biology into a practical technology that can create products like cheap biofuels. Scientists have found that the “code of life” is far more complex and difficult to crack than anyone might have imagined a decade ago.
What’s more, while rewriting the code is easier than ever, getting it right isn’t. Researchers and entrepreneurs have found ways to coax bacteria or yeast to make many useful compounds, but it has been difficult to optimize such processes so that the microbes produce significant quantities efficiently enough to compete with existing commercial products.
Researchers Hack Sea Sponges to Grow Silica Threads
Traditional genetic engineering involves sticking a foreign gene into bacteria and using the bacteria as tiny factories to make the protein encoded by that gene. This approach wouldn’t work for all silica-forming proteins found in marine sponges. The minerals produced by these proteins, which the researchers want to study, can kill the cells.
So Daniel Morse, of the University of California, Santa Barbara, and his colleagues looked to another protein making strategy: synthetic cells with a tiny plastic bead nucleus surrounded by a bubble of oil that acts as a cell membrane.
The scientists attached a piece of DNA to each of the beads, encoding a unique silica-forming protein, or silicatein. This DNA is a random combination of genes from two related silicateins, interspersed with random mutations.
Then the scientists soaked the beads in watery mixture of the bacterial proteins necessary to turn the DNA into silicateins and covered each bead with a thin layer of oil, trapping water and the enzymes inside. With the artificial cell complete, the interior enzymes made the silicateins, which stuck to antibodies covering the bead’s surface.
Next the scientists triggered a mineral-forming reaction. They broke open the “cells,” soaked them in a solution containing the silicon or titanium molecule used by these proteins, and captured them with a new oil layer.
The silicatein proteins gathered either silicon dioxide or titanium dioxide inside the oil bubble, depending on which mineral precursor they were fed. Then the cells were subjected to two “selection pressures” to weed out non-functional genes and identified those that coded for proteins which made extra strong minerals.
The scientists sorted the beads by size, collecting the largest beads with the thickest mineral layers. Then they shook the beads to break up the mineral coating. Beads that survived this process contained genes for proteins that made minerals of intermediate strength.
(via Artificial cells evolve proteins to structure semiconductors | Ars Technica)
DARPA Launches Program to Industrialize 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.”
What could possibly go wrong?
(via DARPA, Venter launch assembly line for genetic engineering | KurzweilAI)
![Gene Therapy Resets Biological Clock, Slows Aging 24%
Mice treated at the age of one lived longer by 24% on average, and those treated at the age of two, by 13%. The therapy, furthermore, produced an appreciable improvement in the animals’ health, delaying the onset of age-related diseases – like osteoporosis and insulin resistance – and achieving improved readings on ageing indicators like neuromuscular coordination.
The gene therapy utilised consisted of treating the animals with a DNA-modified virus, the viral genes having been replaced by those of the telomerase enzyme, with a key role in aging. Telomerase repairs the extremes of chromosomes, known as telomeres, and in doing so slows the cell’s and therefore the body’s biological clock.
When the animal is infected, the virus acts as a vehicle depositing the telomerase gene in the cells. This study “shows that it is possible to develop a telomerase-based anti-aging gene therapy without increasing the incidence of cancer,” the authors affirm. “Aged organisms accumulate damage in their DNA due to telomere shortening, [this study] finds that a gene therapy based on telomerase production can repair or delay this kind of damage.”
(via Gene therapy for aging-associated decline tested | KurzweilAI)](http://25.media.tumblr.com/tumblr_m44hcuNEqM1qgpcs1o1_500.png)
Gene Therapy Resets Biological Clock, Slows Aging 24%
Mice treated at the age of one lived longer by 24% on average, and those treated at the age of two, by 13%. The therapy, furthermore, produced an appreciable improvement in the animals’ health, delaying the onset of age-related diseases – like osteoporosis and insulin resistance – and achieving improved readings on ageing indicators like neuromuscular coordination.
The gene therapy utilised consisted of treating the animals with a DNA-modified virus, the viral genes having been replaced by those of the telomerase enzyme, with a key role in aging. Telomerase repairs the extremes of chromosomes, known as telomeres, and in doing so slows the cell’s and therefore the body’s biological clock.
When the animal is infected, the virus acts as a vehicle depositing the telomerase gene in the cells. This study “shows that it is possible to develop a telomerase-based anti-aging gene therapy without increasing the incidence of cancer,” the authors affirm. “Aged organisms accumulate damage in their DNA due to telomere shortening, [this study] finds that a gene therapy based on telomerase production can repair or delay this kind of damage.”
(via Gene therapy for aging-associated decline tested | KurzweilAI)
Using Radio Waves to Remotely Trigger Genes in Living Animals:
Rockefeller University researchers have remotely activated genes inside living animals, a proof of concept that could one day lead to medical procedures in which patients’ genes are triggered on demand.
The researchers used radio waves to switch on engineered insulin-producing genes in mice.
Jeffrey Friedman, a molecular geneticist at the Rockefeller University in New York and lead author of the study, says that in the short term, the results will lead to better tools to allow scientists to manipulate cells non-invasively. But with refinement, he thinks, clinical applications could also be possible.
Friedman and his colleagues coated iron oxide nanoparticles with antibodies that bind to a modified version of the temperature-sensitive ion channel TRPV1, which sits on the surface of cells. They injected these particles into tumors grown under the skins of mice, then used low-frequency radio waves to heat the nanoparticles. In turn, the nanoparticles heated the ion channel to its activation temperature of 42 °C. Opening the channel allowed calcium to flow into cells, triggering secondary signals that switched on an engineered calcium-sensitive gene that produces insulin. After 30 minutes of radio-wave exposure, the mice’s insulin levels had increased and their blood sugar levels had dropped.
(via Radio waves switch on genes for non-invasive treatments | KurzweilAI)
Genetically Engineered Viruses Target and Destroy Cancer Cells
To develop JX-594, the therapy in the new study, researchers at Jennerex started with a strain of vaccinia virus, which is adept at evading the immune system. (It was also used in the smallpox vaccine.) They then armed it with a gene encoding a protein called GM-CSF, which triggers an immune attack against cancer cells. They also added a second gene for beta-galactosidase, a marker protein with which they could track the virus’s replication. The effect, says Kirn, was “a product that destroys tumors by multiple, complementary mechanisms.”
(via Engineered Viruses Selectively Kill Cancer Cells - Technology Review)
