The Year in Science: Genetics

Sunday, January 08, 2006

South Korea Makes Custom Stem Cells

Once again, South Korea took the lead in stem cell research. Woo Suk Hwang, the veterinarian who made headlines when he cloned human stem cells last year, announced in May that he and his colleagues had made stem cells tailored for different patients.

The team produced 11 stem cell lines from 11 men, women, and children with conditions such as diabetes, spinal cord injury, and inherited immune deficiency. The cells were derived from eggs that had been injected with DNA from the patients, so they could eventually be transplanted back to replace or correct the patient's diseased cells without fear of immune rejection. The team is conducting animal studies before beginning human trials.

Hwang is a man on an urgent mission. "I hope that embryonic cells can cure patients in the near future," he says. "Our research opens the door."

Last year, Hwang burst onto the global scene with the first stem cell line created from a cloned human embryo. That line was costly, requiring 242 eggs from 16 women and prompting debates about the ethics of egg donation. Subsequent efforts have averaged one stem cell line from 16.8 embryos. In August Hwang presented the first cloned dog, an Afghan hound named Snuppy.

Scientists in the United States have been trying to find ways around the ban on using federal funds to create stem cells from human embryos. In September Harvard University scientists reported using existing stem cell lines—not eggs—to create more stem cells. The scientists fused stem cells with body cells, creating hybrid cells that had all the characteristics of stem cells. But the cells cannot be used because they have twice the usual amount of genetic material.

The following month, researchers at the Whitehead Institute in Cambridge, Massachusetts, created embryos that lack a gene required for placental growth, potentially appeasing those who object to the creation of viable embryos for research. And a team from Massachusetts-based Advanced Cell Technology extracted a single cell from an embryo and grew stem cells from it without destroying the embryo.

South Korea is offering another alternative. In October, it launched the new World Stem Cell Foundation, which strives to develop stem cells for hundreds of degenerative diseases. Led by Hwang, the center plans to create about 100 new lines each year and distribute them for a fee to scientists around the world. —Apoorva Mandavilli

Chimps' Promiscuity Could Damage DNA

Yes, chimps and humans are remarkably similar, genetically speaking—but new research indicates that the differences are profound. The two species, which split from a common ancestor some 6 million years ago, vary in less than 4 percent of their genetic information, according to the first preliminary draft of the chimpanzee genome, released in August by an international team of researchers. But in a separate study, geneticist David Page of the Whitehead Institute at MIT and his colleagues found that the chimp Y, the male sex chromosome, contains debilitating mutations in a number of genes. In the human Y, those same genes are intact and functional.

Page suspects that chimpanzee sexual behavior explains the damage. Chimps are promiscuous, with females mating in rapid succession with many males. In turn, males fight their bad baby-making odds by producing more and more sperm. And the changes are handed down: While most of the chimp genome's 24 pairs of chromosomes undergo a genetic reshuffling during the production of sperm and eggs, with genes swapped between the two copies, there is only one Y chromosome and thus no mixing—the Y is transmitted intact. The upshot, says Page, is that "if a chimp Y has a genetic variant that enhances sperm count, it will be preferentially passed on, with mutations in other genes dragged along for the ride." Over the last 6 million years, those accumulated mutations have inactivated several genes.

Humans are mostly monogamous, and that has protected our Y. "The human Y is holding its own a lot better than anyone had given it credit for," Page says. "Prior to our paper, the common view was that the human Y was headed for extinction, but we've found that it is not about to crash and burn."  —Kathy A. Svitil

Genes Affect Frequency Of Female Orgasm

In 2005 multiple studies explored the scientific mysteries of female orgasms—why and how women have them, how to tell when they're faking (if you have an MRI machine, that is), and why nearly 30 percent of women in the United States suffer from orgasm inhibition or aren't able to climax at all.

The biggest news came from two independent studies, published in February and May, that revealed a woman's ability (or inability) to orgasm depends in part on genetics. The research teams used data from twin registries in Britain and Australia to compare orgasmic frequency in hundreds of identical and nonidentical female twins. Both studies found the genetic influence differed depending on context: 31 to 34 percent for orgasm through intercourse and 45 to 51 percent for orgasm through masturbation. "What's important to remember is that saying 31 percent of female orgasm that occurs during intercourse depends on genetics is also saying 69 percent isn't genetic," says Khytam Dawood, a behavioral geneticist at the University of Chicago and author of one of the studies.

The findings are no surprise, says Virginia Sadock, director of the New York University Program in Human Sexuality: "People have different athletic abilities, different IQs . . . these things all have genetic components. And so does libido." Although women who have trouble climaxing may have a genetic predisposition, there are many other factors: social, environmental, psychological. "I'm very excited about these studies," she adds, "because women who have difficulty having orgasms can finally stop blaming themselves and thinking, What the hell is wrong with me?!" —Rebecca Skloot

New Secrets Of the Genome Uncovered

Scientists poring over the 3-billion-letter-long genomes of humans and mice made a host of new discoveries in 2005. Highlights include deciphering how individual genes play a role in everything from triggering disease to shaping behavior and appearance.

  • Autism: Statistical geneticist Rita Cantor and her colleagues at UCLA identified a handful of mutations in the middle of chromosome 17, providing the first genetic link to autism that did not involve another chromosomal disorder. In a separate study, researchers from Vanderbilt University Medical Center in Tennessee found mutations on chromosome 17 in the gene for the mood-regulating neurotransmitter serotonin and also reported that 15 of the mutations found in families with autistic members were linked to obsessive-compulsive behavior.
  • Baldness: Markus Nöthen of the Life and Brain Centre of the Bonn University Clinic and Roland Kruse of the Skin Clinic of Düsseldorf University zeroed in on unusual genetic variations on the X chromosome in families with a tendency toward male balding. That section of DNA proved to contain the gene for the androgen receptor, which processes male hormones, or androgens. Researchers suspect that hair growth fails when scalps produce too many androgen receptors or fail to process hormones appropriately. The gene's location on the X chromosome, which is inherited from the mother, helps explain why balding tendencies have long been linked to a man's maternal ancestry. But paternal ancestry may still play a role.
  • Fearlessness: James Olson, a pediatric oncologist at the Fred Hutchinson Cancer Research Center in Seattle, had been probing a gene called neuroD2, which can turn carcinoma cells into neurons. But the study stalled when mice missing a copy of the gene spent their free time fighting instead of breeding. These mice appeared to be oblivious to danger because they had a malformed region in their amygdala, a brain structure involved in regulating fear. "They have an emotional-learning deficit," Olson says. Study of the neuroD2 gene in humans may lead to an improved understanding of thrill-seeking behavior and psychiatric disorders.
  • Ovarian Cancer: Cancer geneticist Tian-Li Wang and pathologist Ie-Ming Shih, both of Johns Hopkins University, found a gene that ignites the most aggressive kind of growth in ovarian cancer. The gene, Rsf-1, not only exists in multiple copies but also increases or decreases the speed at which other genes are read, Wang says. The research could lead to the development of a drug that inhibits the gene. In the meantime, a test for the identified gene could prompt physicians to treat a cancer known to be aggressive in a more forceful manner. —Jessa Forte Netting

Slicing and Dicing RNA Strands May Stop SARS

RNA interference, an immune defense first discovered in plants more than a decade ago, may become a powerful new weapon against SARS and other deadly viruses. In August an international research team reported that they had managed to induce the defense in rhesus monkeys with SARS.

In RNA interference, plants and animals can churn out an enzyme that recognizes double-stranded viral RNA and cuts it up into single strands. The bits, called short interfering RNA, then associate with other enzymes to form a large complex that can silence certain genes and render the virus harmless.

Scientists have begun designing their own short interfering RNA against specific viral targets. In the forefront of this research is Patrick Lu of Intradigm Corporation of Rockville, Maryland. He and his team infected monkeys with the SARS virus by squirting it into their noses. The animals soon began suffering symptoms—fever, loss of appetite, and lung damage. Then the researchers squirted short interfering RNA into their noses. The treatment reduced symptoms and moderately mitigated the impact of the lung damage.

Questions remain about the practicality of using this method in people because it must be delivered just before or just after SARS exposure. Nevertheless, researchers are hopeful. "There are several preclinical studies going on, and some of them may reach the clinical testing stage sometime next year," Lu says. —Nicholas Bakalar

Asian Pathogen Threatens Florida's Citrus Crops

Florida's vital citrus industry is under siege. Federal officials sounded the alarm in early September after sickly pummelo trees turned out to have been infected by a deadly microbe originally from Asia. Huanglongbing, which means "yellow dragon disease" in Chinese, has already devastated citrus groves in Asia, Africa, and South America and now threatens Florida's orange and grapefruit crops. "Wherever the disease has shown up, it's been pretty bad," says Ronald Brlansky, a University of Florida plant pathologist. "They've quit growing citrus in those areas for years until it goes away."

Huanglongbing is one of eight plant pathogens on the U.S. Federal Register's list of "bioterrorism select agents." But the culprit spreading the disease is probably the Asian citrus psyllid, an aphid-size insect first sighted in Florida in 1998. An infected tree may take a few months to several years to show signs of sickness, and by then it's often too late. "The leaves turn yellow and drop, and the fruit becomes bitter and misshapen, making it useless," says Caitlyn Allen, a University of Wisconsin plant pathologist. "Once the tree has it, it's toast."

There is no cure, save a painstaking regime of antibiotic injections that are prohibitively expensive and not certain to work. Most infected trees are simply burned. For now, growers have few options, except to be vigilant. "They try to live with it, try to stay ahead of it," says Brlansky.  —Jessa Forte Netting

Further Adventures Of J. Craig Venter

When last we heard from J. Craig Venter, he was sailing around the world in his 95-foot sloop, Sorcerer II, collecting water samples from the sea and inland lakes. So far the voyage, which started in Nova Scotia and is now in the Caribbean, has more than doubled the number of known microorganisms—and uncovered millions of new genes. In 2005 Venter also began collecting and cataloging the microorganisms of urban air, starting with those floating in Midtown Manhattan. The J. Craig Venter Institute, a not-for-profit research group of more than 200 scientists and staff members, sequences the genes using the same techniques Venter developed to decode the human genome.

At the same time, institute scientists are trying to build new genes that have never existed on Earth. They hope to synthesize genes for specific purposes—the production of hydrogen, for instance. They are also sequencing cancer genes. Meanwhile, the institute is offering a $500,000 prize to anyone who can come up with a technique that would provide a full DNA analysis of a human for $1,000 or less.
In August Venter purchased the Norman Collection of microbiology archives, which contains the papers of genome pioneers like Francis Crick, James Watson, Rosalind Franklin, and Linus Pauling. It will be made available to researchers at the institute's Maryland headquarters. And if that isn't enough, keep an eye out for the institute's mobile education lab, a bus coming soon to a school near you.  —Bruce Stutz

Plants Mend Their Own Faulty DNA

Upending a fundamental tenet of inheritance that has long served as the foundation of genetic theory, a study published in March revealed that plants can correct defective genes inherited from their parents by reverting to an ancestral gene sequence. A Purdue University research team led by Robert Pruitt and Susan Lolle stumbled onto this discovery while working with Arabidopsis, a member of the mustard family that is a favorite experimental model. The parent generation had a mutant version of a gene dubbed hothead, which causes the plants to have fused flowers. Even when each parent carried two mutant versions of the gene, 10 percent of the next generation had normal flowers. Pruitt and his colleagues found that these plants had somehow retrieved ancestral code that allowed them to repair the mutant gene.

Although the discovery was made in plants, Pruitt suspects that animals, including humans, might also use this method to correct faulty genes. "There's another way that genetic information can be inherited, which we've been blissfully unaware of the last 100 years or so," Pruitt says. "To me that just boggles the mind. Then you really start to wonder what else is out there."  —Apoorva Mandavilli

Sequence of X Chromosome Holds Surprises for Men and Women

In March an international team of almost 300 scientists announced the provocative results of sequencing the X chromosome.  Women carry two versions of the chromosome, while men, in addition to the Y chromosome, carry only one.

Researchers hope to use these data to pinpoint genes responsible for more than 100 poorly understood X-linked diseases. Meanwhile, they've found that although the X chromosome contains a meager 1,098 genes, 10 percent of them are turned on in the testes. And in a separate study, researchers have already used the sequence to chart a surprising degree of genetic variation among women.

The project leader, Mark Ross of the Wellcome Trust Sanger Institute in Hinxton, England, speculates that it may not be advantageous for some genes to be on the X chromosome because of its unequal distribution among men and women. On the other hand, gene variants that confer a benefit to males are more likely to accumulate on the X chromosome than on a nonsex chromosome because they will always be expressed on a male's single X chromosome. This might explain why about 10 percent of the genes newly identified on the X chromosome are turned on mainly in the testes, even though little is known about their function.

Inheriting a single X chromosome exposes men to a host of X-linked diseases, such as hemophilia or Duchenne muscular dystrophy, and researchers hope to use the new data to understand more fully the role of genes in other X-linked conditions. Women tend to be protected from diseases related to genes on the X because female cells randomly inactivate one of the X chromosomes, and that leaves some cells with a normal copy up and running.

Using the new data, Laura Carrel, a geneticist at Pennsylvania State College of Medicine in Hershey, and Huntington Willard, a geneticist at Duke University in Durham, North Carolina, discovered that 15 percent of the genes on the inactivated X chromosome are actually not silenced—and most are likely to be expressed at higher levels overall in women than men. Another 10 percent of the genes on the turned-down chromosome vary substantially in the degree of activity from woman to woman. Ross, who wasn't involved in the work, believes the scattershot silencing may prove "a source of considerable genetic variation." What that variation means remains an open question.  —Erik Stokstad

Single Gene Transforms Fish in One Generation

A thumb-size fish has changed the way scientists think about evolution. In a study reported in March, a research team found that a variation in a single gene makes all the difference between ocean-going sticklebacks, which are covered in 35 bony plates to protect them from predators, and the many species of sleeker, minimally plated freshwater sticklebacks. "Evolution in wild populations is thus both simpler than many researchers would have predicted and more reproducible," says vertebrate geneticist David Kingsley of the Stanford University School of Medicine.

Kingsley's laboratory has spearheaded recent research into the little fish. Last year, he and his colleagues found that sticklebacks can lose their spined pelvic fins in one generation after moving from salt water to freshwater, which demonstrates rapid evolution. Both studies show that a collection of minute changes over a long period of time is not required to produce fundamental transformation.  —Jessa Forte Netting

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