Tuesday October 4, 2005 news@michigandaily.com Jbe ! itldigun ttiI SCIENCE 5 v OGLING OCULAR DISEASES University researchers develop customized DNA chip known as a microarray to diagnose eye disorders By Rossitza lordanova For the Daily E mbedded with DNA molecules, that can screen thrugh thou sands of genetie suences amicrhar;- rays have recently allowed University researchers to diagnose an eye disease that once took several years to detect. In a study published in the September issue of Investiga- tive Ophthalmology and Visual Science, a team of research- ers lead by ophthalmology Prof. Rhada Ayyagari at the University's Kellogg Eye Center successfully tested microar- ray technology's ability to diagnose a specific type of retinitis pigmentosa, also known as RP. With the new technology, ophthalmology Prof. John Heckenlively said, patients with the ocular disease can receive more pre- cise diagnoses that will make treatment "When we have much easier. RP causes pro- treatments we gressive retinal degeneration that would be better can lead to blind- able t tellness. It is passed able to tell down and affects who is eligible one out of 3,500 individuals world- for treatment. wide according to the Kellogg Eye It is basically Center. Currently, the cln- speeding up cal diagnosis of RP the process." is largely based on an individual's electrical activity in the eye, loss of - John Heckenlively, peripheral vision, night blindness and ophthalmology professor retinal changes. and researcher at the But Ayyagari said Kellogg Eye Center the symptoms of RP overlap with those of many other ocu- lar disorders, making it challenging to provide a definite diagnosis. While a clinical diagnosis is only the first step, molecu- lar testing is needed to identify the gene and the mutations involved that cause the disorder. Since there are more than 90 different genetic forms of RP and many forms look alike, manual sequencing techniques to detect the disease are very time consuming and inefficient. Rather than rely on arduous diagnosing processes, Ayya- gari and her team aimed to devise a new technique to detect the disease by directly analyzing the DNA of an individual with a microarray. Chips to Detect Mutations in Retinitis Pigmnentosa Patients hA e; ,w~utgs t~~to k "' a ae #. nk . CC T ~r~4 A A T GC AG CCTC/TT ' .COURTESY OF KELLOGG EYE CENTER Diagram shows the genetic patterns of retinitis pigmentosa the microarray can detect. With a microarraythe DNA of a patient can be screened against multiple genes on a single platform, instead of the traditional sequencing of one gene at a time. There are many different genetic patterns that can indicate the presence of RP. As result, the team used a microarray to siphon through the genetic patterns. Microarrays work by measuring changes in gene expression patterns by comparing one gene pat- tern with another. A normal microarray would not be effective in a disease like RP because of the vast number of mutations that can indicate the disease. However, Ayyagari and her team employed a microarray embedded with the specific gene patterns to detect RP among the hundreds of different varia- tions found within genes. Heckenlively at the Kellogg Eye Center examined the patients who participated in the study. Thirty-five RP patients were screened using the microarray containing 11 genes known to cause RP. The sequences of the genes and mutations the researchers obtained were 99 percent accurate. At the same time, 506 sequence changes associated with RP were detected and 120 of them were not previously reported. Ayyagari said this result emphasizes the usefulness of the technique since it not only provides a definite diagnosis, but also deepens the understanding of the disorder on a molecular level. "We're excited about finding mutations in different genes that would modify other genes," she said. But there are still drawbacks to the technique: inter- pretation of the results is time consuming. Research- ers expect to increase the number of genes that can be included on the microarray chips to make the tech- nique more effective. Still, the use of DNA screening chips is likely to become even more useful in the future because treat- ments currently under development to treat RP will be effective at-treating people with the specific genet- ic mutations. "That in turn means that when we have treatments, we would be better able to tell who is eligible for the treatment. It is basically speeding up the treatment process" Heckenlively said. The Kellogg Eye Center is one of the leading cen- ters for RP research and was among the first centers to set up a certified molecular diagnostics unit for retinal degenerations and glaucoma. Astronomy rapper breaks it down with dark matter mystery Australians win Nobe I Prize for bacteria research Discussion is part of lecture series examining the impact of Einstein on astronomy By Michael Kan Daily Science Editor While astronomers have yet to completely deduce the nature of dark matter after more than seven decades, David Weinberg can break down its history into a 5-minute rap song. "Dark matter. What is it? Do we need it? Where is it?" Weinberg rapped, in the closing minutes of his lecture on dark matter and dark energy. In commemoration of Einstein's contribu- tion to astronomy, the astronomy department's distinguished lecture series this semester will examine Albert Einstein's legacy in the field. Last Friday, Weinberg, an Ohio State Uni- versity astronomy Prof., spoke on the myster- ies of dark matter and dark energy that have dogged astronomers for decades. Weinberg began his lecture by detailing the origins of dark matter, adding that astrono- mers began to notice the phenomenon when examining abnormal galaxy clusters. In 1933 Swiss astrophysicist Fritz Zwicky observed a cluster of galaxies called the Coma Cluster that according to his measure- ments, did not exhibit enough gravity to hold the cluster together. Zwicky concluded the cluster must contain something that would produce enough gravity to hold the galaxies together. "The galaxies were moving so fast that there was not enough gravity to hold them together. So Zwicky decided to call it the missing mass problem." This "missing mass problem" would later become known as dark matter, Not until about the 1970s did the phenom- enon re-emerge into the field of astronomy,. Weinberg said. By then astronomers had observed that the rotational speed of spiral galaxies did not act according to the rules of gravity. Weinberg used the example of a solar sys- +em envna that ac nlnnatc mon na o m the Doctors found that infection, not stress, causes ulcers (AP) - Two Australians won the Nobel Prize in medicine yesterday for a discovery that defied decades of medical dogma and revolutionized the treatment of ulcers. They showed that bacterial infection - not stress - causes ulcers in the stomach and intestine. The 1982 discovery by Drs. Barry Marshall and Robin Warren eventually transformed peptic ulcer disease from a chronic, frequently disabling condition to one that can be cured by a short regimen of antibiotics and other medicines, said the Nobel Assembly of the Karolinska Insti- tute in Stockholm. Marshall, 54, and Warren, 68, discov- ered the bacterium Helicobacter pylori and uncovered its role in causing ulcers and stomach inflammation. The prize, with its $1.3 million check, gives the ultimate vali- dation to an idea that initially drew skepti- cism and derision. The Australians' bacterial theory of ulcers was "very much against prevail- ing knowledge and dogma," Staffan Nor- mark, a member of the Nobel Assembly, said at a news conference in Stockholm. Most doctors believed ulcers came from stress and stomach acid. To make his case, Marshall even delib- erately infected himself by swallowing a culture of H. pylori. "I developed a vomiting illness and had severe inflammation in the stomach for about two weeks," he told The Associ- ated Press. "I didn't actually develop an ulcer, but I did prove that a healthy person could be infected by these bacteria, and that was an advance because the skeptics were saying that people with ulcers somehow had a weakened immune system and that the bacteria were infecting them after the The two researchers began working together in 1981. "After about three years we were pretty convinced that these bac- teria were important in ulcers and it was a frustrating time for the next 10 years though because nobody believed us," said Marshall, a researcher with the University of Western Australia. "The idea of stress and things like that was just so entrenched nobody could really believe that it was bacteria. It had to come from some weird place like Perth, West- ern Australia, because I think nobody else would have even considered it." Dr. David Peura, president of the Ameri- can Gastroenterological Association, said the prize-winning work "revolutionized our understanding of ulcer disease" and "gave millions of people hope." He read about the H. pylori theory in 1983 while serving as a gastroenterologist in the Army, and "I thought it was crazy," he recalled yesterday. But he and a colleague were intrigued, and soon they discovered they could cure ulcers in their own patients with antibiotics targeted at H. pylori. "It was such an intriguing theory that everybody tried to disprove it and couldn't, so we all became believers," said Peura, now a professor of medicine at the Univer- sity of Virginia at Charlottesville. Peura, who met Marshall when both worked at Virginia and considers him a friend, said Marshall's perseverance was responsible for the eventual acceptance of the theory. "Any lesser of a person prob- ably would not have been able to withstand some of the ridicule and scorn that was thrown at him initially," Peura said. As the two Nobel winners celebrated with family over champagne and beer in Perth, the Western Australia state capital, Warren said he was "very excited, also a little overcome. "Obviously, it's the best thing that can ever happen to somebody in medical research. It's just incredible," added Mar- shall in a telephone interview. FOREST CASEY/Daily Ohio State University astronomy Prof. David Weinberg talks about the history of dark matter and dark energy. Since those observations, astronomers wolrlwide have attemnted to shed light on other. This unknown force is called dark ener- 2v and has astronomers even more nuzzled.