Illumina, Inc. announced Tuesday that its new HiSeq X Ten Sequencing System has broken the “sound barrier” of human genomics by enabling the $1,000 genome. “This platform includes dramatic technology breakthroughs that enable researchers to undertake studies of unprecedented scale by providing the throughput to sequence tens of thousands of human whole genomes in a single year in a single lab,” Illumina stated.
Initial customers for the HiSeq X Ten System, which will ship in Q1 2014, include Macrogen, based in Seoul, South Korea and its CLIA laboratory in Rockville, Maryland, the Broad Institute in Cambridge, Massachusetts, and the Garvan Institute of Medical Research in Sydney, Australia.
“For the first time, it looks like it will be possible to deliver the $1,000 genome, which is tremendously exciting,” said Eric Lander, founding director of the Broad Institute and a professor of biology at MIT. “The HiSeq X Ten should give us the ability to analyze complete genomic information from huge sample populations. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”
“The HiSeq X Ten is an ideal platform for scientists and institutions focused on the discovery of genotypic variation to enable a deeper understanding of human biology and genetic disease,” Illumina stated. “It can sequence tens of thousands of samples annually with high-quality, high-coverage sequencing, delivering a comprehensive catalog of human variation within and outside coding regions.”
HiSeq X Ten utilizes a number of advanced design features to generate massive throughput. Patterned flow cells, which contain billions of nanowells at fixed locations, combined with a new clustering chemistry deliver a significant increase in data density (6 billion clusters per run). Using state-of-the art optics and faster chemistry, HiSeq X Ten can process sequencing flow cells more quickly than ever before — generating a 10x increase in daily throughput when compared to current HiSeq 2500 performance.
The HiSeq X Ten is sold as a set of 10 or more ultra-high throughput sequencing systems, each generating up to 1.8 terabases (Tb) of sequencing data in less than three days or up to 600 gigabases (Gb) per day, per system, providing the throughput to sequence tens of thousands of high-quality, high-coverage genomes per year.
Illumina Introduces the HiSeq X™ Ten Sequencing System
Any areas of water could be off-limits to all but the cleanest spacecraft.
Dark streaks that hint at seasonally flowing water have been spotted near the equator of Mars1. The potentially habitable oases are enticing targets for research. But spacecraft will probably have to steer clear of them unless the craft are carefully sterilized — a costly safeguard against interplanetary contamination that may rule out the sites for exploration.
River-like valleys attest to the flow of water on ancient Mars, but today the planet is dry and has an atmosphere that is too thin to support liquid water on the surface for long. However, intriguing clues suggest that water may still run across the surface from time to time.
In 2011, for example, researchers who analysed images from NASA's Mars Reconnaissance Orbiter (MRO) spacecraft observed dark streaks a few metres wide that appeared and lengthened at the warmest time of the year, then faded in cooler seasons, reappearing in subsequent years2. "This behaviour is easy to understand if these are seeps of water," says planetary scientist Alfred McEwen of the University of Arizona in Tucson, who led that study. "Water will darken most soils."
The streaks, known as recurring slope lineae, initially were found at seven sites in Mars's southern mid-latitudes. The water may have come from ice trapped about a metre below the surface; indeed, the MRO has spotted such ice in fresh impact craters at those latitudes.
McEwen and his colleagues have now found the reappearing streaks near the equator, including in the gargantuan Valles Marineris canyon that lies just south of it. The MRO has turned up 12 new sites — each of which has hundreds or thousands of streaks — within 25 degrees of the equator. The temperatures there are relatively warm throughout the year, says McEwen, and without a mechanism for replenishment, any subsurface ice would probably already have sublimated.
The possibility of running water could put the sites off-limits for future spacecraft unless they are carefully sterilized. The international guidelines of the Committee on Space Research (COSPAR) of the Paris-based International Council for Science say that sites that may host life, called 'special regions', should only be visited by probes that have been thoroughly treated to prevent microbes from hitching a ride from Earth. "You wouldn't want to send a dirty spacecraft to these places because you'd have the potential to not discover what you're looking for, but what you took with you," says John Rummel, chair of COSPAR's panel on planetary protection.
This blog post was written with Roy Ronen from UCSD (@roy_ronen). We thank Dina Zielinski (@dinazielinski) for super helpful comments! [See our previous blog post about the chemistry of MinION] Oxford...
"As the industrial age is drawing to a close, I think that we're witnessing the dawn of the era of biological design. DNA, as digitized information, is accumulating in computer databases. Thanks to genetic engineering, and now the field of synthetic biology, we can manipulate DNA to an unprecedented extent, just as we can edit software in a computer. We can also transmit it as an electromagnetic wave at or near the speed of light and, via a "biological teleporter", use it to recreate proteins, viruses and living cells at another location, changing forever how we view life."
"At this point in time we are limited to making protein molecules, viruses, phages and single microbial cells, but the field will move to more complex living systems. I am confident that we will be able to convert digitised information into living cells that will become complex multicellular organisms or functioning tissues."
"We could send sequence information to a digital-biological converter on Mars in as little as 4.3 minutes, that's at the closest approach of the red planet, to provide colonists with personalised drugs. Or, if Nasa's Mars Curiosity rover were equipped with a DNA-sequencing device, it could transmit the digital code of a Martian microbe back to Earth, where we could recreate the organism in the laboratory. We can rebuild the Martians in a P4 spacesuit lab -- that is, a maximum-containment lab -- instead of risking them crash-landing on the surface. I am assuming that Martian life is, like life on Earth, based on DNA. I think that because we know that Earth and Mars have continually exchanged material, in the order of 100kg a year, making it likely that Earth microbes have travelled to and populated Martian oceans long ago and that Martian microbes have survived to thrive on Earth. Simple calculations indicate that there is as much biology and biomass in the subsurface of our Earth as in the entire visible world on the planet's surface. The same could be true for Mars."
"If the life-digitalizing technology works, then we will have a new means of exploring the universe and the Earth-sized exoplanets and super Earths. To get a sequencer to them soon is out of the question with present-day rocket technology -- the planets orbiting the red dwarf Gliese 581 are "only" about 22 light-years away -- but it would take only 22 years to get the beamed data back. And that if advanced DNA-based life does exist in that system, perhaps it has already been broadcasting sequence information."
"Creating life at the speed of light is part of a new industrial revolution. Manufacturing will shift from centralised factories to a distributed, domestic manufacturing future, thanks to the rise of 3D printer technology. Since my own genome was sequenced, my software has been broadcast into space in the form of electromagnetic waves, carrying my genetic information far beyond Earth. Whether there is any creature out there capable of making sense of the instructions in my genome, well, that's another question."
Scientists from Yale and Harvard have recoded the entire genome of an organism and improved a bacterium’s ability to resist viruses, a dramatic demonstration of the potential of rewriting an organism’s genetic code.
“This is the first time the genetic code has been fundamentally changed,” said Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale and co-senior author of the research published Oct. 18 in the journal Science. “Creating an organism with a new genetic code has allowed us to expand the scope of biological function in a number of powerful ways.”
The creation of a genomically recoded organism raises the possibility that researchers might be able to retool nature and create potent new forms of proteins to accomplish a myriad purposes — from combating disease to generating new classes of materials.
The research — headed by Isaacs and co-author George Church of Harvard Medical School — is a product of years of studies in the emerging field of synthetic biology, which seeks to re-design natural biological systems for useful purposes.
In this case, the researchers changed fundamental rules of biology.
Proteins, which are encoded by DNA’s instructional manual and are made up of 20 amino acids, carry out many important functional roles in the cell. Amino acids are encoded by the full set of 64 triplet combinations of the four nucleic acids that comprise the backbone of DNA. These triplets (sets of three nucleotides) are called codons and are the genetic alphabet of life.
Isaacs, Jesse Rinehart of Yale, and the Harvard researchers explored whether they could expand upon nature’s handywork by substituting different codons or letters throughout the genome and then reintroducing entirely new letters to create amino acids not found in nature. This work marks the first time that the genetic code has been completely changed across an organism’s genome.
In the new study, the researchers working with E. coli swapped a codon and eliminated its natural stop sign that terminates protein production. The new genome enabled the bacteria to resist viral infection by limiting production of natural proteins used by viruses to infect cells. Isaacs — working with Marc Lajoie of Harvard, Alexis Rovner of Yale, and colleagues — then converted the “stop” codon into one that encodes new amino acids and inserted it into the genome in a plug-and-play fashion.
The work now sets the stage to convert the recoded bacterium into a living foundry, capable of biomanufacturing new classes of “exotic” proteins and polymers. These new molecules could lay the foundation for a new generation of materials, nanostructures, therapeutics, and drug delivery vehicles, Isaacs said.
“Since the genetic code is universal, it raises the prospect of recoding genomes of other organisms,” Isaacs said. “This has tremendous implications in the biotechnology industry and could open entirely new avenues of research and applications.”
A mutation in one gene means that a girl is unable to sense pain – a discovery that could hold clues for the development of new drugs.
A girl who does not feel physical pain has helped researchers identify a gene mutation that disrupts pain perception. The discovery may spur the development of new painkillers that will block pain signals in the same way.
People with congenital analgesia cannot feel physical pain and often injure themselves as a result – they might badly scald their skin, for example, through being unaware that they are touching something hot.
By comparing the gene sequence of a girl with the disorder against those of her parents, who do not, Ingo Kurth at Jena University Hospital in Germany and his colleagues identified a mutation in a gene called SCN11A.
This gene controls the development of channels on pain-sensing neurons. Sodium ions travel through these channels, creating electrical nerve impulses that are sent to the brain, which registers pain.
Overactivity in the mutated version of SCN11A prevents the build-up of the charge that the neurons need to transmit an electrical impulse, numbing the body to pain. "The outcome is blocked transmission of pain signals," says Kurth.
To confirm their findings, the team inserted a mutated version of SCN11A into mice and tested their ability to perceive pain. They found that 11 per cent of the mice with the modified gene developed injuries similar to those seen in people with congenital analgesia, such as bone fractures and skin wounds. They also tested a control group of mice with the normal SCN11A gene, none of which developed such injuries.
The altered mice also took 2.5 times longer on average than the control group to react to the "tail flick" pain test, which measures how long it takes for mice to flick their tails when exposed to a hot light beam. "What became clear from our experiments is that although there are similarities between mice and men with the mutation, the degree of pain insensitivity is more prominent in humans," says Kurth.
The team has now begun the search for drugs that block the SCN11Achannel. "It would require drugs that selectively block this but not other sodium channels, which is far from simple," says Kurth.
"This is great science," says Geoffrey Wood of the University of Cambridge, whose team discovered in 2006 that mutations in another, closely related ion channel gene can cause insensitivity to pain. "It's completely unexpected and not what people had been looking for," he says.
Wood says that there are three ion channels, called SCN9A, 10A and 11A, on pain-sensing neurons. People experience no pain when either of the first two don't work, and agonising pain when they're overactive. "With this new gene, it's the opposite: when it's overactive, they feel no pain. So maybe it's some kind of gatekeeper that stops neurons from firing too often, but cancels pain signals completely when it's overactive," he says. "If you could get a drug that made SCN11A overactive, it should be a fantastic analgesic."
"It's fascinating that SCN11A appears to work the other way, and that could really advance our knowledge of the role of sodium channels in pain perception, which is a very hot topic," says Jeffrey Mogil at McGill University in Canada, who was not involved in the new study.
Allie and Bailey knew each other when they both lived in Florida. More than 20 years later, Allie lives near Chicago and Bailey lives in Bermuda, but Allie’s name still rings a bell for Bailey. That would not be breaking news, except that Allie and Bailey are not people: they are dolphins.
Bailey’s recollection of Allie’s name — or more precisely, of her 'signature whistle', which functions as a name among dolphins — is the most durable social memory ever recorded for a non-human. Yet it is only one of many data points in a study that found that it is the rule, not the exception, for bottlenose dolphins (Tursiops truncatus) to recognize whistles from their distant past. “We can’t tell yet what the upper limit is time-wise, or even if there is one,” says Jason Bruck, a biologist at the University of Chicago who published the results today in Proceedings of the Royal Society B. “We just know it’s at least 20 years.”
Last month, Journal of National Cancer Institute reported on a surprising result. The surprise was on two fronts – (i) the unexpectedness of the finding, (ii) not a single major media channel chose to report on it. That is quite odd, because you would expect media to be extra happy to report any puzzling finding.
A drawback for the use of stem cells in medical treatment is their limited supply due to slow rate of growth in conventional laboratories. Dr Abba Zubair of the Cell Therapy Laboratory at Mayo Clinic in Florida believes this problem could be overcome and stem cell generation sped up by conducting the process in space. He will now have the opportunity to put his hypothesis to the test, courtesy of a US$30,000 grant that will see Zubair send human stem cells to the International Space Station (ISS) to observe whether they do in fact grow at a greater rate than on terra firma.
According to the Mayo Clinic, experiments conducted on Earth using microgravity (replication of gravitational field about 250 miles (402.3 km) from Earth’s surface) have shown that these conditions are more conducive to stem cell growth than conventional laboratories.
UC Berkeley and University of Hawaii astronomers analyzed all four years of Kepler data in search of Earth-size planets in the habitable zones of sun-like stars, and then rigorously tested how many planets they may have missed.
A major question is whether planets suitable for biochemistry are common or rare in the universe. Small rocky planets with liquid water enjoy key ingredients for biology. Astronomers now used the National Aeronautics and Space Administration Kepler telescope to survey 42,000 Sun-like stars for periodic dimmings that occur when a planet crosses in front of its host star. They found 603 planets, 10 of which are Earth size and orbit in the habitable zone, where conditions permit surface liquid water. They measured the detectability of these planets by injecting synthetic planet-caused dimmings into Kepler brightness measurements. They find that 22% of Sun-like stars harbor Earth-size planets orbiting in their habitable zones. The nearest such planet may be within 12 light-years.
"It's been nearly 20 years since the discovery of the first extrasolar planet around a normal star. Since then we have learned that most stars have planets of some size and that Earth-size planets are relatively common in close-in orbits that are too hot for life," said Andrew Howard, a former UC Berkeley post-doctoral fellow who is now on the faculty of the Institute for Astronomy at the University of Hawaii. "With this result we've come home, in a sense, by showing that planets like our Earth are relatively common throughout the Milky Way galaxy."
Just found this interesting short reply in the thread:
"Bioinformatics is very broadly defined. Depending on who you are talking to, it could mean anything from interpreting high throughput experimental results, running programs and canned analyses, some scripting to pipeline things, or software and algorithm development. As you move from the first to last item in the list I gave you, biology becomes a bit less important and computer science more so. In general, a biology program will concentrate on the first 2-3 and the computer science program will concentrate on the last."
The top Science blogs in the Technorati Blog Directory seem to never run dry of interesting content.
The concept of science represents a collection of efforts put forth to expand the knowledge base of mankind, through research made in the fields of natural, formal, social, and applied sciences. The scientific method is at the core of these pursuits, with a general structure involving questions formulated leading to conducted experiments, followed by the results being analyzed and published for all to see. The future of our understanding is based on this research, and resulting scientific discoveries are communicated through the blogosphere in a speedy fashion.
The rate of discovery increases daily, with various blogs reporting on items such as the condition of the Large Hadron Collider experiment, the expanded usage of stem cells for the benefits of living organisms, and the continued development of nanotechnology for the medical and electronic advances it provides.