Page 80 - The Economist

80 Science and technology The Economist December 9th 2017
2 sels included nitrogen, bacteria, relatively lograms of nitrogen waste alone by se- pare samples themselves, often because
harmlesstracemetalslikealuminium,cop- questering it into the tissues and shells of by using a MinION they do not have to
per and iron, as well as toxic metals like the animals. But what can be done with wait for a laboratory to send back results.
mercury, lead and arsenic. Five groups of the mussels once harvested? The research- Mars, a large food company, is testing the
organic contaminants, including the insec- ers hope they can be treated and recycled device on production lines in China, look-
ticides chlordane and DDT, also ended up instead of ending up in landfill. Provided ing for particular bacterial pathogens such
accumulatingin the mussels. thelevelsofcontaminantsarenottoohigh, as Salmonella and E. coli. It already scruti-
Based upon these numbers, the team the mussels could be used as animal feed nises its equipment and products closely
estimates an annual harvest ofa single raft or fertiliser. What they will not do, though, for such contamination, but according to
ofmussels would remove more than 62 ki- is end up on someone’s plate. 7 Robert Baker, who is in charge offood safe-
tyatthe firm, the currentarrangements can
take days or weeks to return results. His
DNA sequencing hope isthatonce automated preparation is
available, real-time monitoring will be
A genome in the hand able to spot problems almost instantly. It
will also extend the range of bugs that can
be detected; current tests are for specific
pathogens, whereas sequencing can iden-
tify whatever bug might turn up. Early re-
sults, says MrBaker, are promising.
The provenance of food is also a good
Small, portable devices take genome sequencing outofthe lab
candidate for genomic investigation. Fol-
EVICES for analysing DNA used to be lowing a scandal in some British super-
Dbig, clunky and not very good. Hun- markets, in which meat marked as beef
dredswererequiredfortheinitialsequenc- wasfound to contain material from horses,
ing of the human genome, a project that there isdemand forteststhatcan verify the
started in the late1990s and tookover a de- origin and species of meat products. Cran-
cadetocompleteatacostofatleast$500m. swick, a British supplierofcooked meats, is
Since then, sequencing a human genome working in partnership with the Universi-
has become a routine process; prices have ty of Warwick on the use of the hand-held
fallen to below $1,000. Although the ma- sequencers to analyse samples of DNA ex-
chines that do the job have got better and tracted from packaged meat and confirm
more compact, they still cost several hun- the species from which it hails.
dred thousand dollars. Various groups are The benefits of on-the-spot sequencing
tryingto make them smallerand cheaper. may be greater still in the developing
The first device small enough to put in world. Agricultural researchers in Tanza-
your pocket is already on the market. It nia and Uganda plan to use Oxford Nano-
comes from Oxford Nanopore, a maker of pore’s devices to help identify the viruses
DNA-sequencing equipment based in the thatplague cassava crops. Some 550m peo-
eponymous English city. It is about the size ple, most of them African, rely on cassava
of a chunky mobile phone. Although the as a staple, but scourges such as brown
machine is swathed in patents, other min- streakvirus, spread by whitefly, can reduce
iature devices are bound to follow in time. yieldsbya factorof40. Both the Mikocheni
The MinION, as the device is called, is Agricultural Research Institute (MARI) in
firstpluggedintoalaptop.Itworksbysuck- Decoding in the field Dar es Salaam and the National Crops Re-
ing strands of DNA through a “flow cell”, sources Research Institute in Kampala al-
made up of an array of tiny holes that are ciers in Svalbard or sucked out of stagnant ready gather samples, in an effort to identi-
just a few nanometres (billionths of a me- ponds in the bowels of disused coalmines fy the strains of virus and to help farmers
tre) in diameter. The way that electricity in Wales. The technology was also em- plant resistant crops. But these have to be
flows across the surface of such a hole ployed to profile the virus behind an out- sent abroad to laboratories in Australia,
changes, depending upon the shape ofthe breakofEbola in west Africa in 2015. South Korea or Switzerland for sequenc-
molecule passing through it. As strands of It is not, though, as simple as popping a ing—a processthatcan take months. In a pi-
DNA are composed of four types of sub- sample in one end and getting the answer. lot project in September, Laura Boykin, an
unit, called bases, which have different To provide a truly portable gene-sequenc- agronomist at the University of Western
shapes, nanopore sequencing permits the ing device, it is necessary to miniaturise Australia, and Joseph Ndunguru, MARI’s
orderofthese basesto be determined—and and automate the preparation of samples. director, used hand-held sequencers to re-
with it the message carried by a gene. To extract DNA, biological samples must turn strain data to farmerswithin 48 hours.
Nanopore’s device is not a direct com- have their cells broken open, a process As portable sequencing devices get
petitor to the bigger, more complex ma- called lysing. The extracted DNA needs to even faster and more accurate, Clive
chines able to deliver the high levels of ac- be of sufficient purity that the readings are Brown, Oxford Nanopore’s chief technol-
curacy demanded by busy laboratories. not contaminated. This is a tricky task, and ogy officer, raises the prospect of a device
Rather, the MinION is designed to take one that requires some biochemical train- that anyone can use to understand the ge-
gene-sequencing out into the field. The de- ingand often the use ofcentrifuges and ex- nomic profile of the world around them.
vice itself costs $1,000 and the flow-cell pensive reagents. Although the firm is The user will merely touch the device to
cartridges it uses, each ofwhich lasts a few keeping the details close to its chest, Ox- something, whetherit is blood, spit or a su-
months, cost around $500 if purchased in ford Nanopore is working on a small de- permarket chicken, and get a genomic pro-
bulk. So far, MinIONshave been used to se- vice called Zumbador, which it claims will file in return. Gene sequencing used to be
quence the DNA of microbes scraped out be able to prep samples automatically. the work of years; soon enough it may be
ofthe snow in Antarctica, swabbed off gla- For now, many users are happy to pre- ubiquitous and quotidian. 7