Allies and Enemies: How the World Depends on Bacteria (20 page)

bones

Pulmozyme for breaking down mucous

secretions in cystic fibrosis patients

Streptokinase as an anticoagulant to

reduce blood clots

Serum albumin as a blood supplement

Taxol ovarian cancer chemotherapy

drug

Tumor necrosis factor to disintegrate

tumor cells

Biotech companies manufacture their products in fermentation

vessels of 300 to 3,000 gallons. Technicians at biotech companies scale up bacterial cultures from small volumes of less than a gallon to fermenters of several gallons. After this modest scaling up of the culturing process, workers in a manufacturing plant increase the production size more by growing the GMO in vessels of 300 to 3,000

gallons. All of the actions leading up to large-scale production comprise upstream processing. A different team of technicians monitors downstream processing, which encompasses all the steps from fermentation to the packaging of a clean, pure final product. Genentech and Amgen, both in California, became the first two biotech companies to reach this large-scale level of production.

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In 1996, scientists at Scotland’s Roslin Institute created Dolly, the

first mammal (a sheep) made by cloning DNA from an adult animal.

The public and many scientists reacted to this news with concern that

humans would be the next organism to be cloned. Renee Reijo Pera,

stem cell researcher at the University of California-San Francisco, remarked, “You can almost divide science into two segments: Before Dolly and After Dolly.” But cloning higher organisms had little in common with bacterial cloning for making GMOs. Dolly’s clone came about by transferring the nucleus—containing an animal’s entire

genome—from an adult sheep’s cell into mammary tissue where the

genome replicated as the tissue reproduced. Cows, goats, pigs, rats,

mice, cats, dogs, horses, and mules have since been similarly cloned.

The goal of animal cloning is to produce a new animal identical in

every way possible to the original animal. Animal cloning thus seeks

to repeat an entire genome in a new animal. Gene cloning in bacteria,

by contrast, serves as a simple way to make many copies of one or more genes in a short period of time. In short, animal cloning makes new animal copies, and bacterial cloning makes new gene copies. By

inserting one or more genes into a bacterial cell’s DNA and then growing the cells through several generations, a microbiologist can produce millions of copies of the “new” DNA overnight because of bacteria’s fast growth rate.

A chain reaction

One spring evening in 1983, biochemist Kary Mullis drove from his

job at Cetus Corporation near San Francisco to his cabin in California’s quiet Anderson Valley. The San Francisco Bay Area had just begun to plant the seeds for the new science called biotechnology.

Molecular biologists had learned how to open DNA molecules with

enzymes and insert genes from an unrelated organism. But cloning

bacteria to make each new batch of genes required considerable labor, and the bacterial cultures produced only miniscule amounts of desired DNA. Mullis pondered this problem as he drove Route 128.

He recalled reading of a bacterium living in hot springs and containing enzymes active at high temperatures that melted most other enzymes. Before reaching his cabin, Kary Mullis had developed an idea that would revolutionize biology.

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In 1966, famed microbial ecologist Thomas Brock and graduate

assistant Hudson Freeze had discovered a bacterium surviving the blistering conditions of Mushroom Spring in Yellowstone National Park. They named the species Thermus aquaticus, Taq for short, and sent a culture to a national repository for microbes near Washington.

DC. Various microbiologists studied the thermophile and its

enzymes, but Taq seemed to offer little in the way of useful attributes.

Mullis suspected that Taq in fact held a crucial attribute.

At a temperature approaching 200°F, DNA becomes unstable

and separates, or denatures, into two single strands instead of its normal double stranded confirmation. Back in his lab, Mullis raised the temperature of a DNA mixture to denature the molecule and then added DNA fragments called primers plus the enzyme DNA polymerase he had extracted from Taq. Next, Mullis lowered the temperature to about 154°F wherein the polymerase began building new DNA copies from the old strands and the primers. By repeatedly heating and cooling the mixture, Mullis could produce about one million copies of the new DNA in 20 minutes and a billion copies in 30

minutes. Molecular biologists call this production of millions of DNA

copies from a small, single piece of DNA, amplification. Taq’s DNA polymerase provided the key to Mullis’s invention because it withstands repeated heating to very high temperatures and then carries out the DNA synthesis step at the cooler (but still high) temperature.

The new process called polymerase chain reaction (PCR) made

any snippet of microbial DNA analyzable. Michael Crichton capitalized on PCR’s extraordinary potential in the 1990 book Jurassic Park, in which scientists amplify dinosaur DNA preserved in ancient amber. Although PCR can amplify pieces of DNA that had been dormant in nature for years, Jurassic Park’s re-creation of an entire extinct genome seemed implausible when the movie was released because closing missing gaps was error-prone. Today, computer programs calculate the likely base sequences of missing pieces of DNA to fill in gaps in damaged DNA. As the power of these programs increases, scientists will reconstruct extinct DNA with increasing accuracy.

When a character on a television crime show says, “We need a rush on the DNA,” a harried lab technician produces within minutes

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the name (accompanied by an up-to-date photo) of the bad guy on a

computer screen. These scenes depict the power of PCR for analyzing biological matter, but the entire PCR process actually takes much longer. A technician first prepares the DNA-primer-polymerase mixture. A heating-cooling machine called a thermocycler requires at least 2 hours to amplify the bits of DNA. Next, the scientist must determine the sequence of the DNA’s subunits or bases, which takes another 24 hours if using an automatic sequencer instrument. Lacking such an machine, manual methods can take up to 3 weeks.

The Food and Drug Administration (FDA) and other government

agencies have put PCR to use in crime-solving. In early 2009, the FDA began a food product recall that would encompass 3,900 peanut butter products as suspect causes of a nationwide Salmonella outbreak that sickened 700 people and killed nine. Microbiologists used PCR to amplify the DNA from bacteria in the products and determine the pathogen’s unique sequence. This so-called DNA fingerprint led CDC investigators to a Blakely, Georgia, manufacturing plant. A leaky roof had allowed rain contaminated with Salmonella-

laced bird droppings to land directly on food processing equipment

and perhaps directly into peanut butter paste as well. Microbiologists

can now trace a single pathogen strain from a person’s stool sample to

an individual farm, a certain shift on the packing line, and even a specific agricultural field.

Real-time PCR has come on the scene as a faster way to analyze

samples to prevent crimes from growing cold. In real-time PCR, a detector monitors the formation of increasing amounts of DNA in the thermocycler as it occurs, unlike traditional PCR that takes extra days to analyze the final products from the thermocycler step. Real-time RCR has helped fight the global poaching industry that trades hides,

pelts, internal organs, horns, feathers, and shells of endangered animals, as well as caviar. Microscopic drops of an animal’s blood on a suspected poacher’s clothes can solve a case. Analysis of ivory sold on the black market has traced the ivory to specific elephant herds in Africa and sometimes to individual families.

Kary Mullis received the 1993 Nobel Prize in chemistry for developing PCR technology. Shortly afterward, the enigmatic Mullis joined a campaign to question the idea that HIV causes AIDS.

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Bacteria on the street

Biotech has developed into a science of contradictions. For instance,

few graduate students in microbiology complete their studies without doing some sort of gene sequencing or gene engineering. The majority of these students have no exposure at all to culturing whole bacterial cells except E. coli, and they spend more time with the dis-assembled bacterium than the whole living cell. The biotech business has a similar dichotomy. The earliest biotech advocates touted gene cloning as a step toward curing humanity’s worst diseases while antibiotech groups predicted the end of nature as we know it. Government leaders recognized the upside for the United States as a world leader in the emerging technology, but they also worried about the need to contain the frightening creatures about to emerge.

A conflicted Wall Street put a modicum of trust in the new industry but did not leap into the biotech pool with both feet. The public’s worry over safety did not make for attractive investments. Biotechnology’s proteins and cells rather than widgets also presented a new business model. What is a marketable product from a biotech company? Is it the cells that produce a hormone, the gene that encodes for the hormone, or the hormone itself? The U.S. Supreme Court helped clear up some of the confusion by ruling in 1980 that bioengineered bacteria could be patented.

At the start of the 1990s, biotech stocks rode the high-tech wave on

Wall Street. By the mid-nineties, however, meager returns turned off

the investors, and their interest in biotech cooled. Biotech-produced

drugs were not easy to make. The manufacture of genetically altered

organisms could produce surprises for even seasoned microbiologists.

Mutant cells, contamination, and the capability of bacteria to shift their metabolic pathways slowed the early progress. Biotech’s biggest draw—back resided in the fact that people could not make up their minds if

the new technology was about to save them or kill them.

Warren Buffett described the perfect product, cigarettes, when he

said, “It cost a penny to make. Sell it for a dollar. It’s addictive.” The dot-com industry grew based on this very philosophy. Biotechnology has not come near matching Buffett’s three criteria. Like conventional drugs, biotech products require large amounts of research cash and lengthy

clinical testing on human subjects. Some drugs, such as new antibiotics,

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have become too expensive to develop. If people cannot imagine how

they would exist without computer technology, they certainly can and

do imagine a world without biotech products. In fact, an increasing number of people in the United States prefer a world without GMOs.

Do we need GMOs? Bioengineered tomatoes taste fine, but so do organic, non-GMO varieties. Bioengineered bacteria clean up oil spills, but so do bacteria native to the waves and sands slickened with oil.

Biotechnology received a golden opportunity on March 24, 1989,

to show the world the value of GMOs released into the environment

for a purpose. The Exxon Valdez oil tanker hit a reef that day in Alaska’s Prince William Sound and spilled an estimated 11 million gallons of crude oil. Whipped by winds, about four million gallons of foamy crude washed ashore, coating 1,300 miles of coastal habitat for

marine organisms, terrestrial animals, and birds. Marine bacteria at

the spill burst into rapid growth in response to the influx of nutrients; crude oil provides a digestible carbon source for bacteria as opposed to refined oils. The United States did not permit the release of GMOs

into the environment in an uncontrolled manner, so microbiologists

could not put to work fast-growing bacteria engineered for oil degradation. They turned instead to bioaugmentation to carry out the largest microbe-based pollution cleanup project in history.

The Environmental Protection Agency’s John Skinner pointed

out shortly after the spill, “Essentially, all the microorganisms needed to degrade the oil are already on the beaches.” Microbiologists accelerated the bacteria’s growth rate by adding nitrogen and phosphorus to the soils. Like bacteria fed a nutrient-rich broth in a laboratory test tube, the native bacteria responded to the augmentation of their environment with added nutrients. The bioaugmentation of the shore’s native bacteria (mainly Bacillus) is believed to have increased by at least sixfold the rate of oil decomposition.