Technology: Gene cloning picks up something nasty on the beach

 作者:池定韪     |      日期:2019-03-03 05:18:02
By ROSIE MESTEL in LOS ANGELES To many Southern Californians life is, as they say, a beach. But when a storm strikes, sewage dumped at sea is often blown back to shore and polluted water pours in from storm drains. This can lead to beaches being closed because of disease-causing bacteria and viruses on the shore. The conventional method for testing water quality is to sample the seawater and wait for bacteria found in sewage to grow on Petri dishes. This process is slow and it can take days to identify if there is a risk and longer to give the all-clear once it is safe to surf again. ‘Essentially you’re closing the beaches today based on what you sampled yesterday morning,’ says Clifford Brunk, a molecular biologist from the University of California at Los Angeles. Now Brunk and his colleague David Chapman, a marine biologist, are developing a faster, better way to monitor bacterial and viral pollution in sea water in just a few hours, using the latest tools in molecular biology. Southern California’s often filthy water is not unique, says Chapman. ‘This technique is applicable to any potentially polluted water.’ The new methods exploit a technique called the polymerase chain reaction (PCR), which revolutionised molecular biology in the 1980s. PCR allows researchers to detect tiny populations of bacteria and viruses without waiting for them to grow, and to distinguish different strains by virtue of differences in the structure of their genetic codes. It can also reveal how much of each type of microorganism is in a sample. Traditional tests for water quality monitor just a few bacteria, notably Escherichia coli, which is abundant in sewage. If E. coli is there, technicians assume that nastier bacteria and viruses could be lurking too. But some pathogens seem to live longer than E. coli, and many living E. coli stubbornly refuse to grow in culture, so information from culture tests is limited. The first step of the new method is to filter the bacteria from the sea water. Then the technicians use enzymes, detergents and freeze-thawing to burst the bacteria open and extract their DNA. Next, they use PCR to produce millions of copies of a precise segment of bacterial DNA, which is common to many bacteria but which has variations unique to particular strains. This is done by adding tiny genetic markers which bind to each end of the key segment. A DNA-synthesising enzyme is then used to copy the marked segment over and over again. The segment of DNA can also be used to identify individual strains of bacteria in the sample. The exact pattern of bases in the segment differs in each strain of bacteria. Technicians then use enzymes to cut the segment into fragments characteristic of different strains of bacteria. The fragments are identified by a technique called electrophoresis. The fragments are drawn through a gel by an electric field and different sized chunks travel different distances. The result – which is analysed by computer – indicates which bacteria are present in the water, and how much there is of each one. The procedure works well in the laboratory for about a dozen types of bacteria, say Chapman and Brunk, and they are now transferring the method to the field. Meanwhile, the nearby Orange County Sanitation Districts are also using PCR to detect dangerous viruses in sewage,