Just a SmidgION: Oxford Nanopore announce iPhone-powered sequencing

CTO Clive Brown announces new Oxford Nanopore sequencing and library prep devices during his keynote address to the company’s user group conference

Stop the presses! Not something we call on a regular bases at FLG towers because, well, our work is largely digital. But when the latest news from Oxford Nanopore landed on our desks this afternoon, this old print journalism adage felt rather apt.

Clive Brown, CTO of Oxford Nanopore, talks at the London Calling Conference, via Oxford Nanopore

Yesterday, in his keynote address to the company’s user group conference in London, CTO Clive Brown announced the development of a new smartphone-powered nanopore sequencer, whimsically (and very Britishly) named ‘SmidgION’.

“Even I can’t believe they let me get away with that name,” chuckled Clive during his presentation.

Tiny SmidgION is currently in early-stage development

With 256 channels per flow cell, SmidgION will be smaller than the company’s existing MinION device, and is expected to come to market in 2017. 

MinION has established itself as a versatile field device, and is set to make history later this year as the first device used to sequence DNA in space. With SmidgION Oxford Nanopore are continuing to appeal to the field researcher, with potential applications in monitoring disease outbreaks, and real-time species identification in the fight against wildlife crime. 

Brown also revealed Project Zumbador, also in early development, a combined sample and library prep device that would deliver DNA captured on beads directly into the flow cell. Event attendee and one of our favourite genomics bloggers Keith Robison (Omics! Omics!) shared some images of the early prototype during his twitter coverage.

Zumbador prototype in hand #nanoporeconf pic.twitter.com/oOfzx97lGZ

— Keith Robison (@OmicsOmicsBlog) May 26, 2016

Note – Keith has now written his own coverage of the Oxford Nanopore announcements, including a photo diary in which he takes his personalised MinION device on a bike ride around London.

Interestingly, Brown also announced that Oxford Nanopore are no longer selling devices that contain the R7 nanopore. R7 has given way to R9, the company’s name for a membrane protein derived from Escherichia coli. This development may help the company to side-step a recent legal challenge from Illumina, which claimed that the R7 pore infringed a patent license. Oxford Nanopore licensed the new pore from VIB in Belgium and University College London in March 2016.

ORIGINAL: Front Line Genomics

Liz Harley

27 MAY 16

Scientists develop ‘nanopores’ that inexpensively filter the salt out of seawater

Mohammad Heiranian/University of Illinois

Just think what this could mean.

There’s filtration and then there’s filtration. Engineers in the US have been working on the latter, coming up with a new markedly more energy-efficient way of taking the salt out of seawater, which could deliver huge advantages in terms of providing people with access to drinking water and help combat problems like drought.

The researchers have developed a material that allows high volumes of water to pass through extremely tiny holes called ‘nanopores’ while blocking salt and other contaminants. The material they’re using – a nanometre-thick sheet of molybdenum disulphide (MoS2) riddled with these nanopore holes – is the most efficient of a number of thin-film membranes that the engineers modelled, filtering up to 70 percent more water than graphene.

“Even though we have a lot of water on this planet, there is very little that is drinkable,” said Narayana Aluru, a professor of mechanical science and engineering at the University of Illinois and leader of the study. “If we could find a low-cost, efficient way to purify sea water, we would be making good strides in solving the water crisis."

Molybdenum disulphide coupled with nanopores could be that solution. While desalination isn’t a new concept, the efficiency gains with this kind of new material – both in terms of the energy required to make the filtration work, and also the cost of keeping a desalination system running – could make a world of difference when it comes to processing large amounts of seawater.

“Finding materials for efficient desalination has been a big issue, and I think this work lays the foundation for next-generation materials,” said Aluru. “These materials are efficient in terms of energy usage and fouling, which are issues that have plagued desalination technology for a long time.”

Conventional desalination relies on reverse osmosis to channel seawater through a thin plastic membrane, but the process suffers from a number of bottlenecks. While the membrane appears thin to the eye, from a microscopic perspective it’s more tube- or tunnel-like than a sheet that’s only a nanometre in thickness, which means it requires more pressure (and thus energy) to operate. They’re also susceptible to more clogging, which ramps up operational costs.

In comparison, the extreme thinness of the molybdenum disulphide membrane allows water to pass through with much less resistance, lessening or negating many of the above drawbacks. But the ingenuity behind the system isn’t just in its engineering.

“MoS2 has inherent advantages in that the molybdenum in the centre attracts water, then the sulphur on the other side pushes it away, so we have much higher rate of water going through the pore,” said Mohammad Heiranian, first author of the study. “It’s inherent in the chemistry of MoS2 and the geometry of the pore, so we don’t have to functionalise the pore, which is a very complex process with graphene.”

There you have it, folks – the world’s first thirsty water filter. We love it! The next steps for the researchers are partnering with manufacturers who can bring their modelled desalination technique to life. The first step will be testing, but they’re confident their findings – which are published in Nature Communications – could be applied on an industrial scale for everybody’s benefit.

“I’m in California now, and there’s a lot of talk about the drought and how to tackle it,“ said Amir Barati Farimani, a postdoctoral fellow at Stanford University who worked on the research at Illinois as a graduate student. ”I’m very hopeful that this work can help the designers of desalination plants."

ORIGINAL: Science Alert

PETER DOCKRILL

12 NOV 2015

The Future of Synthetic Biology: Reading and Writing DNA Using Nanopores

Biology is nothing more than a computational system. Granted, it’s far more sophisticated than any other computer available to us today, but we’re slowly beginning to learn how to read and write DNA as we would with code. Thanks to a group of researcher fellows of the Institute of Electrical and Electronics Engineers (IEEE), we’ve now taken one extra step towards a future of synthetic biology.

Published on IEEE Access, researchers used nanopores – a tiny hole inside of a membrane that allows singular molecules of DNA to pass through – in order to read DNA and proteins, and subsequently write new DNA by inserting mini-genes into mammalian cells.

“In conclusion, the future is brilliant, if you think small and do a bit more research. Nanopores can be used to both READ: detect and sequence DNA and sense proteins, and WRITE DNA into cells. These tools will provide methods to explore areas of biology either impractical to reach, or at least logistically intractable.” – IEEE Study

Photo Credit: IEEE / Genetic Literacy Project

Not only is this breakthrough research helping us better understand our own biology, but is equally bringing everyone else along for the ride. By simplifying the methodological ability to sequence single-cell DNA using nanopores, these researchers have provided molecular and sub-molecular analysis within reach for all bench-top scientists and clinical labs outside of the confines of genomics or spectrometry specialists.

But don’t jump off your seats just yet in celebration, because more research is needed for synthetic biology to make a significant impact.

“Prospects for synthetic biology (and manufacturing) using nanopores to program cells (or micelles) and deliver materials are especially alluring. Chemical processing generally becomes more efficient in a microreactor because mass transport limitations are practically eliminated. However, the synthesis, so far, has been focused at a single cell or few nano-reactor level; it needs to be scaled up.” – IEEE Study

FUTURE IMPLICATIONS

The precision of molecular configuration of ions passing through the pores of membranes points to a future of tiny research making extremely large impacts on the health of society. The future of medicine will largely rely on our ability to read and write DNA like code in order to upgrade our bio-computational systems against fatal diseases. By using nanopores as a means of reading and writing DNA, we are steadily revealing the secrets of our own biology, consequently unlocking future possibilities of enhancing our longevity.

ORIGINAL: Serious Wonder
BY B.J. MURPHY

A Superfast DNA Sequencer Based on Motion Detection

Illustration: Alex Smolyanitsky/NIST

For more than 20 years, the practice of using a low-intensity electric current to pull long strands of DNA through nanometer-scale pores in a membraneand measure the electric field variations of the four nucleic acids—A, C, G, T—has been growing as the main approach for DNA sequencers. 

We’ve seen the development of this technology reach the point where U.K.-based Oxford Nanopore has been offering portable DNA sequencers based on this fundamental measurement principle for more than a year. Meanwhile, in the research labs, scientists have been tinkering with better materials for the membrane and have started to work with the “wonder material” graphene to see what benefits it might provide in these types of devices.

Now researchers at the National Institute of Standards and Technology (NIST) may have changed the technology paradigm for DNA sequencers in their proposal for an entirely new material architecture that would represent the first DNA sequencer based on sensing motion in the membrane as the DNA thread passes through it.

In research described in the journal ACS Nano, the NIST researchers proposed a device in which a nanoscale ribbon of molybdenum disulfide is suspended over a metal electrode immersed in water. In this arrangement, the molybdenum disulfide acts as a kind of capacitor, storing an electrical charge. When a single strand of DNA is passed through a pore in the membrane, the membrane only flexes when a DNA base pairs up with and then separates from a complementary base affixed to the hole. It is this flexing that the motion sensor detects as an electrical signal.

In the paper, the NIST researchers performed numerical simulations of how fast and accurate this DNA sequencer could be, and they concluded that the membrane would be 79 to 86 percent accurate in identifying DNA bases in a single measurement at speeds up to about 70 million bases per second. It is this speed and accuracy that the NIST researchers see as a game changer.

“It is the promise of true single-base resolution and the ability to reliably detect repeated DNA motifs at the rates of millions of bases per second,” said Alex Smolyanitsky, a NIST researcher and lead author, in an email interview with IEEE Spectrum. “An array of sensors described in our paper has the potential to accurately sequence DNA at speeds far greater than anything on the current market, while the device itself is envisioned to be portable and low-power.”

In a head-to-head comparison with research darling du jour graphene, the benefits are clear.

“The molybdenum disulfide is much less prone to ‘sticking’ to DNA, compared to graphene,” said Smolyanitsky. “Also, it is expected to be electrically conductive at room temperature.”

Before a complete prototype is built, the NIST researchers will be working on chemical functionalization of the material. But there does seem to be an urgency to the research with a patent already being sought on the design.

“We have immediate plans and expertise to work on the experimental aspects of this technology,” said Smolyanitsky. “In addition, we are open to forming early-stage partnerships with the industry.”

DNA sequencing may be just be a starting application for this design with a wide variety of nanoelectromechanical system and device applications on the NIST researchers’ horizon.

ORIGINAL: IEEE Spectrum
By Dexter Johnson
29 Sep 2016