4. Solid State Sequencer
Solid state gene sequencing machine
Can determine structural sequences of long stretches
of DNA
Cheaper and faster sequences
Oncology particularly could benefit
Nanopore technology is a possible competitor
5. Sequence entire genome
from single cell
Multiple Annealing and Looping-based Amplification
Cycles (MALBAC)
Just one cell to reproduce entire DNA molecule
Can find a single base pair mutation in the entire
genome with 70% accuracy
Duplicates the DNA molecule for study
Amplification is smooth over the genome
Linear rather than exponential amplification
9. Reversing Alzheimer’s
New compound, molecule TFP5
Reverses symptoms and memory loss
Up for clinical trials
Non-toxic
10.
11. Lab rats get sixth sense
Allows rats to see or rather “touch” infrared light
Infrared detector implanted in tactile processing brain
area
Blind could see by similar device implantation in other
areas of brain.
Cross sense interpretation
No loss of normal sense function
15. Breakthrough Prize in Life
Extension
Brin, Zukcerberg, Anne Wojcicki (23and Me)
Rewards for curing diseases
Rewards for life extension
Each year 11 laureates will receive $3 million each
Editor's Notes
http://nextbigfuture.com/2013/02/real-bionic-man-for-1-million.htmlA real-world bionic man has been built. It has a frame of state-of-the-art prosthetic limbs and a functional heart-lung system, complete with artificial blood pumping through a network of pulsating modified-polymer arteries. It has a bionic spleen to clean the blood, and an artificial pancreas to keep his blood sugar on the level. Behind the deep brown irises are a pair of retinal implants, giving him a vista of the crowds of curious humans who meet his gaze.He even has a degree of artificial intelligence: talk to him, and he'll listen (through his cochlear implants), before using a speech generator to respond. Although, like us, he sometimes stumbles over his words, memorably describing his idol Eminem as a "well-known crapper", before quickly correcting himself.
http://nextbigfuture.com/2013/02/printing-human-embryonic-stem-cells.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+blogspot%2Fadvancednano+%28nextbigfuture%29In recent years, the use of a simple inkjet technology for cell printing has triggered tremendous interest and established the field of biofabrication. A key challenge has been the development of printing processes which are both controllable and less harmful, in order to preserve cell and tissue viability and functions. Here, we report on the development of a valve-based cell printer that has been validated to print highly viable cells in programmable patterns from two different bio-inks with independent control of the volume of each droplet (with a lower limit of 2 nL or fewer than five cells per droplet). Human ESCs were used to make spheroids by overprinting two opposing gradients of bio-ink; one of hESCs in medium and the other of medium alone. The resulting array of uniform sized droplets with a gradient of cell concentrations was inverted to allow cells to aggregate and form spheroids via gravity. The resulting aggregates have controllable and repeatable sizes, and consequently they can be made to order for specific applications. Spheroids with between 5 and 140 dissociated cells resulted in spheroids of 0.25–0.6 mm diameter. This work demonstrates that the valve-based printing process is gentle enough to maintain stem cell viability, accurate enough to produce spheroids of uniform size, and that printed cells maintain their pluripotency. This study includes the first analysis of the response of human embryonic stem cells to the printing process using this valve-based printing setup.Tests showed that 80-90% of the embryonic stem cells stayed viable.
http://www.technologyreview.com/news/511311/solid-state-sequencer-debuts-at-genome-conference/Nabsys, a DNA technology startup, showed off today its solid-state gene sequencing machine at the Advances in Genome Biology and Technology conference in Marco Island, Florida. The company says that later this year it will begin selling its machine, which will allow researchers to determine the structural organization of long stretches of DNA. This differs from most existing sequencing methods, which read DNA in short snippets that are later stitched together by software. The new system will, at first, complement existing methods, but it could eventually offer cheaper and faster sequencing than other approaches.Understanding the overall order of DNA sequence on a chromosome is important for studying disease and treating patients, but this big picture can be difficult to get because of the short-snippet approach of most sequencing. Because these methods cannot always figure out how to arrange long repetitive sequences, they can fail to recognize missing sequences, additional sequences, or repeated sequences, all of which can lead to disease.Oncology, in particular, could benefit from Nabsys’s approach because the genomic changes that occur in cancer cells often include large, structural rearrangements. “In a tumor, you need to characterize the mixture of [genetic variation] in your sample at different length scales,” says Barrett Bready, CEO of Nabsys.Groups such as Oxford Nanopore (see “Nanopore Sequencing”), which introduced its technology a year ago at the same conference, and Gundlach’s lab are developing nanopore technologies as another method for getting long sequences, but so far no nanopore technology has made it to the market. These systems use a biological pore as the site of DNA analysis, which limits the speed at which DNA can be read.
http://news.harvard.edu/gazette/story/2013/01/one-cell-is-all-you-need/Uses a method — dubbed MALBAC, short for Multiple Annealing and Looping-based Amplification Cycles — that requires just one cell to reproduce an entire DNA molecule.More than three years in the making, the breakthrough technique offers the potential for early cancer treatment by allowing doctors to obtain a genetic “fingerprint” of a person’s cancer from circulating tumor cells. It also could lead to safer prenatal testing for a host of genetic diseases.“If you give us a single human cell, we report to you 93 percent of the genome that contains three billion base pairs, and if there is a single base mutation, we can identify it with 70 percent detectability, with no false positives detected,” Xie said. “This is a major development.”As its name suggests, Xie said, MALBAC is a type of DNA amplification that allows researchers to duplicate the single DNA molecule present in a cell many times so it can be analyzed in the lab.MALBAC relies on linear amplification, meaning it is able to minimize the sequence-dependent bias.Just as it does with other methods, the amplification process begins by splitting the DNA double helix into two single strands. Xie’s team then adds a random “primer” — tiny fragments of DNA — that binds in dozens of locations along each strand.To extend those primers, Xie’s team used a DNA polymerase, the same cellular “machine” that synthesizes DNA as cells divide. Using that machine, researchers are able to extend the primers from as few as seven bases to as many as 2,000. Upon heating, they break the elongated primers apart from the original DNA, yielding half products.When those half products are then amplified using the same primers, the two ends of the DNA combine, forming a loop that prevents it from being amplified again. The leftover half products and the original DNA are subject to another cycle of amplification. After five cycles of such linear pre-amplification, the full product is amplified by PCR to produce enough material for sequencing.
A new technique developed at MIT can edit DNA in precise locations.GRAPHIC: CHRISTINE DANILOFF/IMOLResearchers at MIT, the Broad Institute and Rockefeller University have developed a new technique for precisely altering the genomes of living cells by adding or deleting genes. The researchers say the technology could offer an easy-to-use, less-expensive way to engineer organisms that produce biofuels; to design animal models to study human disease; and to develop new therapies, among other potential applications.To create their new genome-editing technique, the researchers modified a set of bacterial proteins that normally defend against viral invaders. Using this system, scientists can alter several genome sites simultaneously and can achieve much greater control over where new genes are inserted, says Feng Zhang, an assistant professor of brain and cognitive sciences at MIT and leader of the research team. “Anything that requires engineering of an organism to put in new genes or to modify what’s in the genome will be able to benefit from this,” says Zhang, who is a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research.Zhang and his colleagues describe the new technique in the Jan. 3 online edition of Science. Lead authors of the paper are graduate students Le Cong and Ann Ran.This approach can be used either to disrupt the function of a gene or to replace it with a new one. To replace the gene, the researchers must also add a DNA template for the new gene, which would be copied into the genome after the DNA is cut. Each of the RNA segments can target a different sequence. “That’s the beauty of this — you can easily program a nuclease to target one or more positions in the genome,” Zhang says. The method is also very precise — if there is a single base-pair difference between the RNA targeting sequence and the genome sequence, Cas9 is not activated. This is not the case for zinc fingers or TALEN. The new system also appears to be more efficient than TALEN, and much less expensive.
http://www.news.cornell.edu/stories/Feb13/earPrint.htmlCornell bioengineers and physicians have created an artificial ear that looks and acts like a natural ear, giving new hope to thousands of children born with a congenital deformity called microtia.In a study published online Feb. 20 in PLOS One, Cornell biomedical engineers and Weill Cornell Medical College physicians described how 3-D printing and injectable gels made of living cells can fashion ears that are practically identical to a human ear. Over a three-month period, these flexible ears grew cartilage to replace the collagen that was used to mold them.To make the ears, Bonassar and colleagues started with a digitized 3-D image of a human subject's ear and converted the image into a digitized "solid" ear using a 3-D printer to assemble a mold.They injected the mold with collagen derived from rat tails, and then added 250 million cartilage cells from the ears of cows. This Cornell-developed, high-density gel is similar to the consistency of Jell-O when the mold is removed. The collagen served as a scaffold upon which cartilage could grow.The process is also fast, Bonassar added: "It takes half a day to design the mold, a day or so to print it, 30 minutes to inject the gel, and we can remove the ear 15 minutes later. We trim the ear and then let it culture for several days in nourishing cell culture media before it is implanted."
Injectable gel repairs damage after heart attack in pigs http://blogs.nature.com/spoonful/2013/02/injectable-gel-repairs-damage-after-heart-attack-in-pigs.htmlAs you read this sentence, on average at least one person in the US will have started to clutch her chest. The blood flow to her heart will become blocked and cardiac muscle cells will start to die off and get replaced with scar tissue. This person has just suffered a heart attack and most likely will go on to develop heart failure, a weakening of the heart’s ability to pump blood and oxygen. In five years time, there’s a 50/50 chance she’ll be dead.There are currently no treatments that can repair the damage associated with this so-called ‘myocardial infarction’ (MI), but a potential solution is now showing promise in a large-animal model. Reporting today in Science Translational Medicine, a team of bioengineers at the University of California–San Diego (UCSD) has developed a protein-rich gel that appears to help repair cardiac muscle in a pig model of MI.
http://www.eurekalert.org/pub_releases/2013-01/foas-pcr010213.phpNew research in the FASEB Journal by NIH scientists suggests that a small molecule called TFP5 rescues plaques and tangles by blocking an overactive brain signal, thereby restoring memory in mice with Alzheimer'sA new ray of hope has broken through the clouded outcomes associated with Alzheimer's disease. A new research report published in January 2013 print issue of the FASEB Journal by scientists from the National Institutes of Health shows that when a molecule called TFP5 is injected into mice with disease that is the equivalent of human Alzheimer's, symptoms are reversed and memory is restored—without obvious toxic side effects."We hope that clinical trial studies in AD patients should yield an extended and a better quality of life as observed in mice upon TFP5 treatment," said Harish C. Pant, Ph.D., a senior researcher involved in the work from the Laboratory of Neurochemistry at the National Institute of Neurological Disorders at Stroke at the National Institutes of Health in Bethesda, MD. "Therefore, we suggest that TFP5 should be an effective therapeutic compound."To make this discovery, Pant and colleagues used mice with a disease considered the equivalent of Alzheimer's. One set of these mice were injected with the small molecule TFP5, while the other was injected with saline as placebo. The mice, after a series of intraperitoneal injections of TFP5, displayed a substantial reduction in the various disease symptoms along with restoration of memory loss. In addition, the mice receiving TFP5 injections experienced no weight loss, neurological stress (anxiety) or signs of toxicity. The disease in the placebo mice, however, progressed normally as expected. TFP5 was derived from the regulator of a key brain enzyme, called Cdk5. The over activation of Cdk5 is implicated in the formation of plaques and tangles, the major hallmark of Alzheimer's disease."The next step is to find out if this molecule can have the same effects in people, and if not, to find out which molecule will," said Gerald Weissmann, M.D., Editor-in-Chief of the FASEB Journal. "Now that we know that we can target the basic molecular defects in Alzheimer's disease, we can hope for treatments far better – and more specific – than anything we have today."
http://nextbigfuture.com/2013/02/synthesizing-dna-10000-times-cheaper.htmlProblem: Synthetic biology has the potential to create new organisms that could do an infinite number of things. But the cost of synthesizing DNA is currently prohibitively expensive. Solution: Austen has developed a new technique to synthesize DNA 10,000 times cheaper than existing technology. 1. DNA microarray2. Microbeads capture DNA - separates the sequences3. Beads copy the single strand many times4. Attach beads to glass and read out the sequences for quality control and create a quality score5. Use laser to recover the DNA (Laser pulse catapulting)Print up to 100 strands per second
http://www.bbc.co.uk/news/science-environment-21459745US researchers have effectively given laboratory rats a "sixth sense" using an implant in their brains.An experimental device allowed the rats to "touch" infrared light - which is normally invisible to them.The team at Duke University fitted the rats with an infrared detector wired up to microscopic electrodes that were implanted in the part of their brains that processes tactile information.The results of the study were published in Nature Communications journal.The researchers say that, in theory at least, a human with a damaged visual cortex might be able to regain sight through a device implanted in another part of the brain.Lead author Miguel Nicolelis said this was the first time a brain-machine interface has augmented a sense in adult animals.The experiment also shows that a new sensory input can be interpreted by a region of the brain that normally does something else (without having to "hijack" the function of that brain region)."We could create devices sensitive to any physical energy," said Prof Nicolelis, from the Duke University Medical Center in Durham, North Carolina."It could be magnetic fields, radio waves, or ultrasound. We chose infrared initially because it didn't interfere with our electrophysiological recordings."
Rats Given Telepathy ?!Never mind the lobsters in Accelerando. Look out for the lab rats!Technological telepathy: brain-to-brain communication between rats achievedhttp://www.gizmag.com/brain-brain-communication-rats-duke/26454/Telepathy has long been a subject of controversy in physical and psychological circles, offering the potential for removing the material and sensory walls between individuals, and allowing the direct transmission of information without using any of our known sensory channels or physical interactions. Although true telepathy still appears to be pseudoscience, futurists have long predicted that some form of technologically-based telepathy would eventually emerge ... and, it would appear, it has.Researchers at Duke University Medical Center in Durham, North Carolina in the U.S. report in the February 28, 2013 issue of Scientific Reports the successful wiring together of sensory areas in the brains of two rats. The result of the experiment is that one rat will respond to the experiences to which the other is exposed.Neurobiologist Miguel Nicolelis and his colleagues have been experimenting with direct electrical stimulation of sensory areas in an attempt to extend the reach of our senses. "Our previous studies with brain-machine interfaces had convinced us that the brain was much more plastic than we had thought," said Nicolelis. "In those experiments, the brain was able to adapt easily to accept input from devices outside the body and even learn how to process invisible infrared light detected by an artificial sensor. So, the question we asked was, if the brain could assimilate signals from artificial sensors, could it also assimilate information input from sensors from a different body.”The Duke University group is pushing forward with additional experiments, most notably by trying to interconnect several rats at once. The main question is if emergent properties might come out of such a "brain-net," perhaps leading to mental abilities not possessed by any one rat. Professor Nicolelis even suggests that an "organic computer" capable of solving puzzles in a non-Turing way might emerge from a brain-net, which could avoid many of the limitations of traditional computing systems.Whatever the future holds, what has already been accomplished is worth a certain amount of wonder. Imagine what it might feel like to be a unit in a multiform brain having many bodies. The benefits and potential dangers of such entities deserves contemplation.
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2510.htmlSynthetic circuits integrating logic and memory in living cellsLogic and memory are essential functions of circuits that generate complex, state-dependent responses. Here we describe a strategy for efficiently assembling synthetic genetic circuits that use recombinases to implement Boolean logic functions with stable DNA-encoded memory of events. Application of this strategy allowed us to create all 16 two-input Boolean logic functions in living Escherichia coli cells without requiring cascades comprising multiple logic gates. We demonstrate long-term maintenance of memory for at least 90 cell generations and the ability to interrogate the states of these synthetic devices with fluorescent reporters and PCR. Using this approach we created two-bit digital-to-analog converters, which should be useful in biotechnology applications for encoding multiple stable gene expression outputs using transient inputs of inducers. We envision that this integrated logic and memory system will enable the implementation of complex cellular state machines, behaviors and pathways for therapeutic, diagnostic and basic science applications.Not to mention Brain (and Body) Computer Interface and implanted computer circuitry.
Neural implants are set to be revolutionised by a new type of graphene transistor with a liquid gate, say bio-engineershttp://www.technologyreview.com/view/511141/graphene-and-the-emergingtechnology-of-neural-prostheses/The emerging technology of neural prostheses has the power to change what it means to be human. The ability to implant electrodes into the eyes ears, spine or even the brain has the potential to overcome degenerative disease, mend broken bodies and even enhance our senses with superhuman abilities.But despite numerous trials of electronic devices implanted into the human body, there are still many challenges ahead. The problem is that most of these devices are based on silicon substrates which are hard, rigid and sharp. Those are not normally qualities that sit well with soft tissue.Consequently, any small movement of these devices can damage nearby tissue and in the worst cases, form scar tissue. What’s more, the hot, wet and salty environment inside the body can damage electronic components, limiting their lifespan. What’s needed, of course, is a flexible substrate that is also biocompatible with human tissue. Now Lucas Hess and pals at the TechnischeUniversitätMünchen in Germany say they’ve found the ideal material–graphene. Today, they outline their plans for graphene-based neural prostheses and the experiments they’ve already done to test its biocompatibility.Graphene is ideal because carbon “chicken wire” is only a single atom thick and therefore highly flexible. It is also held together by carbon bonds, which are among the most stable known to chemists. That means it should be relatively stable inside the human body.But graphene has another advantage. Hess and pals have shown how it is possible to use it to make transistors that are gated by the solution in which the transistor sits. In other words, the natural body fluids that surround these prostheses will form an integral part of their operation.So-called solution-gated transistors are much more sensitive to electronic changes in their environment than conventional silicon devices. “[Graphene-based] devices…far outperform current technologies in terms of their gate sensitivity,” say Hess and co.These guys have begun to test graphene interfaces with various cells such as retinal ganglion cells, reporting that graphene has excellent biocompatibility.
http://www.breakthroughprizeinlifesciences.org/http://transhumanity.net/articles/entry/the-breakthrough-prize-in-life-sciences-turning-the-tide-for-life-extensionThe tide of funding for life-extension research has turned. With the announcement of the Breakthrough Prize in Life Sciences – sponsored by such renowned entrepreneurs as Yuri Milner, Sergei Brin, and Mark Zuckerberg, as well as Zuckerberg’s wife Priscilla Chan and Anne Wojcicki of 23andMe – there is now a world-class mechanism for rewarding outstanding scientists whose work contributes to understanding and curing debilitating diseases and extending human life. (You can find out more about this prize from The Guardian and Fast Company.) The first eleven laureates of the prize have already been selected, and every subsequent year eleven more will receive $3 million each. The Breakthrough Prize in Life Sciences is founded by Art Levinson, Sergey Brin, Anne Wojcicki, Mark Zuckerberg and Priscilla Chan, and Yuri Milner to recognize excellence in research aimed at curing intractable diseases and extending human life. The prize is administered by the Breakthrough Prize in Life Sciences Foundation, a not-for-profit corporation dedicated to advancing breakthrough research, celebrating scientists and generating excitement about the pursuit of science as a career.Founding sponsors of the Breakthrough Prize in Life Sciences include Sergey Brin and Anne Wojcicki, Mark Zuckerberg and Priscilla Chan, and Yuri Milner, who collectively have agreed to establish 5 annual prizes, US$3 million each, going forward. These prizes will be awarded for past achievements in the field of life sciences, with the aim of providing the recipients with more freedom and opportunity to pursue even greater future accomplishments.Going forward, each year’s prize winners will join the Selection Committee for future awardees. One of the distinguishing characteristics of the Breakthrough Prize will be a transparent selection process, in which anyone will be able to nominate a candidate online for consideration. Also, the prize can be shared between any number of deserving scientists and can be received more than once. In addition, there are no age restrictions for nominees.All Breakthrough Prize recipients will be invited to present public talks targeting a general audience. These lectures, together with supporting materials, will be made available to the public, allowing everyone to keep abreast of the latest developments in life sciences, guided by contemporary masters of the field.
