Science Matters (35 page)

The catch is that sequencing an entire genome for even one person is still an extremely expensive and time-consuming process. And although the cost of sequencing a genome is falling, it will be decades before the cost drops to the point that the process will be cheap enough to be used in the courts. Consequently, the alternative approach of DNA fingerprinting is used. Instead of looking at the whole genome, scientists look at specific genetic landmarks and use them for identification. Think of this process as being analogous to seeing the Eiffel Tower and knowing that you’re in Paris, without having to have a street map of the entire city.

Two different sets of genetic landmarks are now used—one in an old method that has been widely accepted in the courts, the
other in a new method that is being developed in the laboratory. We’ll talk about them separately.

As we pointed out in Chapter 16, only a small portion of human DNA actually codes for proteins. Much of the rest seems to be a jumble of base pairs, some representing genes that are no longer used, some regulating when genes are turned on and off, but most of unknown origin and purpose. In the latter category is a structure known as a variable number tandem repeat, or VNTR. These features are repeating sequences of nonsense DNA located at specific places along the genome. Finding a VNTR in a genome is something like reading a sentence and yabadayabadayabada suddenly some nonsense letters appear before the text resumes. The number of repeats varies from place to place in a single genome and from person to person at a specific location in the DNA. The number of repeats can vary from a few to about 250.

VNTRs are used as landmarks in DNA fingerprinting. The basic idea is that the number of repeats at a specific location varies from one person to the next, and so can be used to identify a specific individual. The procedure used to compare two strands of DNA works like this: Molecules called restriction enzymes are used to cut the DNA at a specific point on both sides of a VNTR. In general, because the number of repeats varies from one person to the next, this procedure will result in two DNA pieces of different lengths for segments taken from the corresponding spots on DNA from different individuals. A small molecule containing a radioactive nucleus is attached to each DNA strand; the strands are then placed in a gel and an electric field is applied. The field causes the strands to move, with the shorter strand moving faster than the longer one. After a specific
amount of time, the field is turned off and a photographic film is laid on top of the system. When the radioactive atoms decay, the film is exposed and the position of the DNA strands detected.

If the two strands are of the same length (as they would be if they came from the same individual), the dark marks on the film will be at the same place, whereas if they are not of the same length they will be at different places. If this process is repeated for several different VNTRs for a given individual, the result will be a kind of bar code, with each bar corresponding to a different VNTR. This bar code, then, becomes the basis for identifying the DNA.

To interpret the results of this sort of test, you have to realize that the chances of any specific VNTR having the same number of repeats in two people is about 1 in 250. In other words, if we look at only one location on the DNA, two people in a large auditorium can be expected to match just by chance. In practice, DNA fingerprinting is done by using five or more locations, a procedure that reduces the probability of a chance match to less than one in a trillion. DNA identification using the VNTR technique is so well developed that it is widely used in criminal investigations, in the identification of bodies in disaster situations, and in establishing paternity.

In addition to having VNTR scattered throughout the genome, our DNA also has many places where there are short sequences of repeating nonsense bases. These segments are called STRs (for short tandem repeats) and pronounced
stars
. Like the VNTR, these short segments of DNA can be used for identification. Typically, there might be up to a dozen or more repeats in an individual STR.

The procedure is similar to what we’ve just described for VNTR. Restriction enzymes are used to cut the DNA on both sides of the STR and a molecular tag is attached. The segments of DNA are then allowed to move through a fluid under the influence of an electric field, and shorter segments will move faster than longer ones. At a specific point downstream, a laser is used to make the molecular tag fluoresce, and the resulting light is recorded, establishing the time of arrival of each segment of DNA. As with the VNTR technique discussed above, these arrival times can be converted into a kind of bar code and used for identification. To get the kind of accuracy now attainable by the VNTR method, scientists typically use a dozen or more STRs in each run.

If you review the mechanism by which genes are expressed in Chapter 16, you will notice that there is nothing in the entire process that depends on whether a specific gene is part of the organism’s original DNA; all that matters is the sequence of base pairs. If, for example, a gene from a different organism (or even one manufactured in the laboratory) had been inserted into a specific organism’s DNA, then the same machinery that produces proteins from ordinary genes would produce the protein coded in the new gene as well. This fact is the basis for the process of genetic engineering.

The process starts with the use of restriction enzymes to cut DNA at places where a specific sequence of base pairs occurs. The cut is made by breaking the bond between a set of base pairs (typically three pairs) so that the DNA is broken into two pieces, each with a string of unattached bases at one end. For example,
if one piece has an exposed set of bases AGT, the complementary piece will have TCA. You can think of these exposed bases as a kind of Velcro patch at the end of a segment of DNA.

If we now bring up another segment of DNA that has a Velcro patch that matches the exposed bases, it will attach itself to the exposed end of the original DNA. This attachment would take place if we brought the other half of the original DNA up and reattached it, of course, but it would also happen if the segment we brought up came from an entirely different source. All that matters is that the base pairs on the new segment match the exposed bases in the original DNA.

And of course if we can do this once for one of the exposed pieces of the original DNA, we can do it twice—once at each end of the new piece of DNA we’re adding. Thus, a new stretch of DNA will have been spliced into the original DNA of the organism. As we pointed out above, once this has been done, the ordinary molecular machinery of the cell will treat the new DNA in exactly the same way as all of the rest, and the cell will start producing the protein encoded in the new gene. This is the end product of genetic engineering.

Let’s look at an example of one of the first uses of this kind of gene splicing. Diabetes is a common and serious disease, and in some cases it must be treated by the injection of insulin. Insulin is a small protein coded for in human DNA, but it is normally produced only by cells in the pancreas. It used to be that the way we got insulin for people suffering from diabetes was to go to a slaughterhouse and collect the pancreases of dead pigs. The material would be ground up, the insulin would be extracted, and after purification, it would be injected into humans. This procedure worked most of the time, but there were often problems with patients exhibiting allergic reactions to the pig insulin.

In the 1980s, a new way of producing insulin was developed.
The gene for insulin from human DNA was spliced into the DNA of a bacterium, which was then allowed to grow and multiply. Each time the cell divided, the new gene was copied along with the rest of the DNA, so that eventually there were large vats of bacteria all excreting human insulin. Today, virtually all of the insulin used in the treatment of diabetes is produced by this process of genetic engineering.

Another place where genetic engineering has seen widespread use is in agriculture. Every major agricultural crop has insect pests that can damage the plants and lower the yield of a farm. Traditionally, farmers have dealt with this problem by spraying their field with insecticides, a process that is expensive and has environmental disadvantages. Genetically engineered plants provide a way around this problem.

Some natural organisms have evolved powerful insecticides and carry the code for those insecticides in their genome. These genes are the organism’s way of protecting itself from predators. If those genes are inserted into the DNA of a crop plant, then that plant will also produce the insecticide and any insect feeding on it will be killed. In such a situation, the spraying of fields with insecticides can be reduced and even in some cases eliminated.

One example of such an organism that has evolved its own insecticide is a bacterium called
Bacillus thuringiensis
, or Bt. The insecticide produced by Bt does not affect mammals or birds, but does a very good job of controlling insects. In the United States, most major crops—soybeans, corn, and cotton, for example—are genetically engineered by the insertion of a Bt gene (or one like it).

Attitudes toward genetically engineered foods vary around the world. When they were first introduced, there was some fear that they would trigger allergic reactions in sensitive individuals,
but that does not seem to have happened. In general, European countries ban them, although genetically engineered crops for ethanol production have been introduced in some places in Europe. When these kinds of crops are introduced elsewhere, it has been found that there is often a 10 to 50 percent increase in yields, which makes them an important weapon in the battle against hunger.

Work is well along on a second generation of genetically engineered plants. Rice, for example, can be modified to include specific vitamins, and scientists are investigating the possibility of inserting genes for antibodies to endemic diseases such as cholera into common foods like bananas. This is a fast-changing field, and we can expect to hear a great deal about it in the future.

Genetic engineering may even play a role in attacking the energy problem. On one level, we can talk about genetically engineering plants to produce more ethanol for fuels. Scientists are also working on engineering bacteria to digest the cellulose in plants, as bacteria in the guts of termites do. The goal is to use crop wastes (cornstalks, for example) to produce natural gas or ethanol. This genetic technology, if successful, would add greatly to our energy supplies without using more fossil fuels or adding net carbon dioxide to the atmosphere.

In 1997, Ian Wilmut at the Roslin Institute in Scotland stunned the world by announcing the birth of Dolly, the first cloned mammal. Countless “Hello, Dolly” headlines greeted the new development, and since that time many other kinds of animals have been cloned.

Cloning begins with a single unfertilized egg. Normally, such an egg has only half of the DNA needed to produce an adult organism. The egg’s DNA is first removed and is then replaced by DNA taken from an adult cell from another animal of the same species. At this point, the egg has a full complement of DNA.

In Chapter 16 we saw that as an organism grows from a single fertilized egg, various stretches of DNA are turned off in each cell as the cell becomes specialized. Thus, the adult DNA that is inserted into the egg has many of its genes switched off. By some process that we do not understand, the egg can undo this switching process, producing DNA in which all genes are functional. Once that has happened, the normal growth process starts and the egg begins to divide. With each division, of course, the DNA is copied, so that all the cells carry the DNA of the animal whose DNA was originally inserted into the egg. The final product will be the birth of an animal whose DNA is identical to that of the donor. This animal is called a clone.

It is important to realize that while the DNA of a clone is identical to the DNA of the donor, it does not mean that the clone is a copy of the original. Human twins, for example, have identical DNA but grow up to be different individuals. Some scientists stress this point by referring to clones as asynchronous twins—twins born at different times. The question of how much human behavior is determined by genetic factors and how much by the environment (the old nature-nurture problem in its modern form) is an important area of research. A complex interplay clearly exists between these factors, and the answer to this question is unlikely to be simple. If pressed, the authors of this book would guess that the result will turn out to be something like a fifty-fifty split.

The first commercial applications of cloning technology were in agriculture. For centuries, farmers have bred livestock to produce
animals with valuable properties—fast growth in hogs, high marbling in beef, and so on. The normal process of gene exchange in reproduction doesn’t guarantee that an animal that has these properties will pass them on to his or her offspring. If a valuable animal is cloned, however, we can be sure that the genes we value will be present in the offspring. Both the U.S. Food and Drug Administration and the European Food Safety Authority have ruled that food products (like meat) from cloned animals could not be differentiated from those same products for non-cloned animals and so is safe for consumption.

At least a dozen different species of domestic animals have been cloned. Such animals are quite expensive—a cloned cow, for example, may cost tens of thousands of dollars and thus is much too valuable to be used for food. The primary use of such animals is in the breeding process itself, where they help to speed up the development of more desirable stock.

Another use of cloning, allied to genetic engineering, involves the use of farm animals to produce pharmaceuticals for human use. The basic idea here is to insert the gene for an important molecule (human growth hormone, for example) into the DNA of a sheep or cow and see if the molecule is present in the animal’s milk. If it is, then cloning the animal will produce a herd that is able to produce that molecule in abundance. This procedure, which has been nicknamed pharming, promises a way to produce drugs that for one reason or another are difficult to produce by ordinary techniques.