4. The Puzzle of Inheritance

2007

October 2007 The Mathematician and the Genome. By Kathleen M. Wong, ScienceMatters@Berkeley.
Excerpt: ...The completion of the Human Genome Project in 2001 was hailed as a major breakthrough in science. For the first time, humans could look at their DNA and discover traits ranging from their propensity to alcohol addiction to the likelihood that their children will have blue eyes.
...Since then, scientists have added the rat, cow, chicken, dog, and even platypus to the list of creatures whose genes have been read like a biochemical book. Each species has shed new light on the structure and function of our own genetic code.
Lior Pachter has been at the forefront of these new genomic analyses. Officially a UC Berkeley professor of mathematics and computer science, Pachter considers himself a mathematical biologist. He uses the power of mathematical modeling and statistics to evaluate the vast quantities of data in DNA.
...Pachter likens genome studies to recreating plans for an existing building. "Until now, we've just been labeling the parts, the doorknobs and windows. Only recently have we started to ask about the function of the parts, and how these functions are related to each other."
...In addition to sequence data, a profusion of other genetic information is now flooding the field. Measurements of gene expression in different tissues, ways to measure gene variations between individuals, and other information can all help make sense of how our DNA makes us who we are. "Mathematics and statistics provides a good means for synthesizing the data in a reasonable way," Pachter says.
Just this year, Pachter began collaborating on the Human Microbiome Project. This new initiative from the National Institutes of Health seeks to analyze the microbial flora that lives in and on the human body. Scientists estimate that each person carries around 10 times more bacterial than human cells, species ranging from helpful gut microbes to pathogens like streptococci. The project will generate a jumble of gene fragments from both known and new species. Pachter's role is to help determine the rough number of creatures represented in the mix.
"It's fun for me that I can combine both mathematics and biology and participate in these major enterprises," Pachter says. "The best thing is, I get to do a lot of beautiful math to go along with it."

26 June 2007. Human DNA, the Ultimate Spot for Secret Messages (Are Some There Now?). The New York Times. ByDennis Overbye. Excerpt: … Using the same code that computer keyboards use, the Japanese group, led by Masaru Tomita of Keio University, wrote four copies of Albert Einstein’s famous formula, E=mc2, along with “1905,” the date that the young Einstein derived it, into the bacterium’s genome, the 4.2-million-long string of A’s, G’s, T’s and C’s that determine everything the little bug is and everything it’s ever going to be. The feat, they said in a paper published in the journal Biotechnology Progress, was a demonstration of DNA as the ultimate information storage material, able to withstand floods, terrorism, time and the changing fashions in technology, not to mention the ability to be imprinted with little unobtrusive trademark labels — little “Made by Monsanto” tags, say. In so doing they have accomplished at least a part of the dream that Jaron Lanier, a computer scientist and musician, and David Sulzer, a biologist at Columbia, enunciated in 1999. To create the ultimate time capsule as part of the millennium festivities at this newspaper, they proposed to encode a year’s worth of the New York Times magazine into the junk DNA of a cockroach. “The archival cockroach will be a robust repository,” Mr. Lanier wrote, “able to survive almost all conceivable scenarios.” …

June 2007. Looking Deep, Deep Into Your Genes. OnEarth, NRDC. by Laura Wright. Excerpt: Discoveries about the impact of the environment on our DNA could revolutionize our concept of illness. ...Although some diseases are inherited through a single genetic mutation -- cystic fibrosis and sickle cell anemia are examples -- the classic "one gene, one disease" model doesn't adequately explain the complex interplay between an individual's unique genetic code and his or her personal history of environmental exposures. That fragile web of interactions, when pulled out of alignment, is probably what causes many chronic diseases: cancer, obesity, asthma, heart disease, autism, and Alzheimer's, to name just a few....
...The completion of the Human Genome Project in 2003 armed scientists with a basic road map of every gene in the human body, allowing them to probe more deeply into the ways our DNA controls who we are and why we get sick, in part by broadening our understanding of how genes respond to external factors.
...In 2001, Jennifer Sass, a neurotoxicologist and senior scientist at the Natural Resources Defense Council (NRDC), who was then a postdoctoral researcher at the University of Maryland, designed an experiment that included the use of microarrays and other molecular tools to figure out how, exactly, mercury was interfering with both our nervous and immune systems. ...The findings of Sass, Silbergeld, and others indicate that mercury might play a role in the development of diseases involving immune system dysfunction. These diseases perhaps include autism ... but also the spate of autoimmune disorders that we can't fully explain, from Graves' disease and rheumatoid arthritis to multiple sclerosis and lupus.
"Do we need to reevaluate our fish advisories?" Silbergeld asks. "Are our regulations actually protecting the most sensitive people?" We target pregnant women and children because we've presumed that mercury's neurotoxic effects are most damaging to those whose brains are still developing. Sass and Silbergeld's findings don't contradict that assumption, but they do suggest that there might be other adults who are far more vulnerable than we'd realized -- who simply can't tolerate the more subtle effect the metal has on their immune system because of a peculiarity in their genetic makeup. Designing fish advisories for those people, whose sensitivities are coded in their DNA, is a challenge we've never tackled before....

23 May 2007. Study: Climate Change Could Harm CropsBy THE ASSOCIATED PRESS. Excerpt: ROME (AP) -- ...During the next 50 years, more than 60 percent of 51 wild peanut species analyzed and 12 percent of 108 wild potato species analyzed could become extinct because of climate change, according to a study released Tuesday by the Consultative Group on International Agricultural Research. Surviving species would be confined to much smaller areas, further eroding their capacity to survive, the report said. The study looked at the distribution of various species and predicted their ability to survive based on current and projected climate data for 2055. Farmers and researchers often depend on wild plants to breed new varieties of crops that contain genes for traits such as pest resistance or drought tolerance, and that reliance is expected to increase as climate changes strain the ability of crops to continue to have the same yields as now, the group said in a statement. In recent years, genes found in wild relatives have helped develop new types of domesticated potatoes that can fight devastating potato blight and new varieties of wheat more likely to survive droughts, the statement said. ''There is an urgent need to collect and store the seeds of wild relatives in crop diversity collections before they disappear,'' said Andy Jarvis, an agricultural geographer who led the study. ''At the moment, existing collections are conserving only a fraction of the diversity of wild species that are out there.'' ....Consultative Group on International Agricultural Research: http://www.cgiar.org

2006

5 September 2006. This Can't Be Love. By CARL ZIMMER. NY Times. Across the eastern United States, a gruesome ritual is in full swing. The praying mantis and its relative, the Chinese mantis, are in their courtship season. A male mantis approaches a female, flapping his wings and swaying his abdomen. Leaping on her back, he begins to mate. And quite often, she tears off his head. The female mantis devours the head of the still-mating male and then moves on to the rest of his body. ...Sexual cannibalism has fascinated biologists ever since Darwin. It is not limited to mantises, but is also found in other invertebrates, including spiders, midges and perhaps horned nudibranchs. Biologists have debated how this behavior has evolved in these species. Some have suggested that sexual cannibalism is just a result of a voracious female appetite. But experiments have also suggested that it is a strategy that females use to select the best fathers for their offspring....

2005

11 October 2005. In the Classification Kingdom, Only the Fittest Survive. By CAROL KAESUK YOON. NY Times. Carolus Linnaeus, the 18th-century botanist and father of scientific naming, enjoyed the unusual status of international scientific hero. Celebrated as the creator of a classification system that ... uses kingdoms of life and two-part Latin names for species, was so complete that it seemed he had forever solved the problem of cataloging the world's living things. So Linnaeus would most likely be shocked - after guessing there were fewer than 15,000 species of animals and plants on earth - to learn that more than 200 years later, scientists are far from finishing the naming of living things and are once again being overwhelmed by an explosion of new species and names. Between 1.5 million and 2 million species have been named, and a deluge of what could be millions more appears imminent. As a result, scientists have once again been seized by 18th-century paroxysms of fear that the field of classification could descend into chaos with precious information lost. For while the Linnaean method for organizing life is still followed and has held up well, no one oversees what has become the rapid and sometimes haphazard proliferation of species names.

19 March 2005. Latest research into the X chromosome brings startling discoveries. The Scotsman. by ROBERT LEE HOTZ. SCIENTISTS have found genetic evidence for what some men have long suspected: it is dangerous to make assumptions about women. The key is the X chromosome, the "female" sex chromosome that all men and women have in common. In a study published this week in the journal Nature, scientists said they had found an unexpectedly large genetic variation in the way parts of women's two X chromosomes are distributed among them. The findings were published in conjunction with the first comprehensive decoding of the chromosome. Females can differ from each other almost as much as they do from males in the way many genes at the heart of sexual identity behave, researchers say. "Literally every one of the females we looked at had a different genetic story," says Duke University genetics expert Huntington Willard, who co-wrote the study. "It is not just a little bit of variation." ...The newly discovered genetic variation between women might help account for differing gender reactions to prescription drugs and the heightened vulnerability of women to some diseases, experts say. ...All told, men and women may differ by as much as 2 per cent of their entire genetic inheritance, greater than the hereditary gap between humankind and its closest relative, the chimpanzee. "In essence," Willard says, "there is not one human genome, but two: male and female." ...The X chromosome contains a larger share of genes linked to disease than any other chromosome. It is implicated in 300 hereditary disorders, including colour blindness, haemophilia and Duchenne muscular dystrophy. Nearly 10 per cent of the genes may belong to a group known to be more active in testicular cancers, melanomas and other cancers, the team reports.

3 May 2005. NASA RELEASE: 05-115. NASA and EPA Team to Improve Crop Management. Can you see the difference between traditional corn and bio-engineered corn? NASA technology is beginning to provide the answer in a snapshot. The technology is called hyperspectral imaging. It uses a special camera to cut one snapshot into 120 color-specific images. Hyperspectral means getting many more images within the spectrum of just one picture. Each image shows a unique characteristic not visible to the human eye. ...The Environmental Protection Agency (EPA) teamed with NASA to use the technology to ensure appropriate management practices are used to avoid the development of resistance in corn pest populations. Pest resistance could severely limit the continued use of these new varieties of corn. With more than 25 million acres of corn planted this year, it is physically and economically infeasible to sample each one. This new technology seeks to provide an active monitoring capability to inform the grower of pest resistance development. Early use of hyperspectral imaging provides the ability to distinguish between the two types of corn and identify pest infestation conditions. Bio-engineered corn has inserted genes to make the plant resistant to insects. ..."This effort will enhance NASA's understanding of image processing techniques to extract knowledge from hyperspectral data sets," said Brian Mitchell of NASA's Space Partnership Development Program at Marshall. "The research being conducted with genetically modified plants and plant growth has the potential to contribute significantly in our ability to grow sustainable and nutritional crops in space. This could prove vital for long duration exploration missions." ...Hyperspectral imaging may be used to treat crew injuries in space. The Institute is working on a portable, handheld camera to take images of a wound site. Using that image to identify wound severity and healing progress will allow doctors to decide the best treatment. The imaging could save precious diagnostic time, which would also improve healing by ensuring timely and proper treatment. Hyperspectral imaging will also detect mold and toxins in spacecraft, a needed tool during long-duration missions to ensure crews have a clean, healthy environment. For info..., visit:
http://www.nasa.gov/home/index.html. For related material on crops and bioengineering, see the Union of Concerned Scientists web page on "Food and Environment"

2004

Summer 2004. Prescription Rice: The Brave New World of Pharma Foods, by Melissa Pamer. Terrain magazine, pp. 10-13. Excerpt: ... Farmers in California's flat, hazy rice fields have worked for years...to please the demanding Japanese palate and gain a toehold in its lucrative market. And it's beginning to work: roughly 40 percent of the rice grown in California goes to Japan. ... Just in the past few years California's rice has finally earned some respect in Japan and other finicky Asian markets, and last year's crop could achieve the best return for farmers in the state's history. But now California farmers worry that the purity of their rice, its hard-won status, and their own livelihood may become casualties of the global debate on genetic modification. At issue is a new kind of rice-a new kind of farm crop, in fact-that is genetically engineered to produce pharmaceuticals. Using the same recombinant DNA techniques that have created GE foods, biotechnology companies are now making plants like rice, corn, and tobacco into "factories" for producing medically useful compounds....Over the past few months, a small Sacramento-based biotechnology company's aim to expand its experimental crop of pharmaceutical rice has caused a shake-up in the normally hermetic California rice industry. In October of last year, Ventria BioScience petitioned the California Rice Commission (CRC) for permission to grow 120 acres of two varieties of rice engineered to produce artificial versions of two human proteins-lysozyme and lactoferrin-which occur naturally in breast milk and tears. ...Ventria's petition set off a review process. ..."One little slip. One slip, that's all it's gonna take. If there's a mistake, the farmer is going to pay-big time," rice farmer Joe Carrancho told the CRC advisory board as it prepared to vote on Ventria's protocol in late March. In work boots and dusty blue overalls, Carrancho held up a chart showing 100 percent opposition to GMO wheat from Japanese consumers. "We are fearful," he said.

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