January 2004

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Comparative Genomics National Institutes of Health, National Human Genome Research Institute Sequencing the genomes of the human, the cow and a wide variety of other organisms &endash; from yeast to chimpanzees &endash; is driving the development of an exciting new field of biological research called comparative genomics. By comparing the finished reference sequence of the human genome with genomes of other organisms, researchers can identify regions of similarity and difference. This information can help scientists better understand the structure and function of human genes and thereby develop new strategies to combat human disease. Comparative genomics also provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved among species, as well as genes that give each organism its unique characteristics. Using computer-based analysis to zero in on the genomic features that have been preserved in multiple organisms over millions of years, researchers will be able to pinpoint the signals that control gene function, which in turn should translate into innovative approaches for treating human disease and improving human health. In addition to its implications for human health and well-being, comparative genomics may benefit the animal world as well. As sequencing technology grows easier and less expensive, it will likely find wide applications in agriculture, biotechnology and zoology as a tool to tease apart the often-subtle differences among animal species. Such efforts might also possibly lead to the rearrangement of our understanding of some branches on the evolutionary tree, as well as point to new strategies for conserving rare and endangered species. Although living creatures look and behave in many different ways, all of their genomes consist of DNA, the chemical chain that makes up the genes that code for thousands of different kinds of proteins. Precisely which protein is produced by a given gene is determined by the sequence in which four chemical building blocks &endash; adenine (A), thymine (T), cytosine © and guanine (G) &endash; are laid out along DNA's double-helix structure. In order for researchers to use an organism's genome most efficiently in comparative studies, data about its DNA must be in large, contiguous segments, anchored to chromosomes and, ideally, fully sequenced. Furthermore, the data needs to be organized to allow easy access for researchers using sophisticated computer software to conduct high-speed analyses. The successful completion of the Human Genome Project in April 2003 has demonstrated that large-scale sequencing projects can generate high-quality data at a reasonable cost. As a result, the interest in sequencing the genomes of many other organisms has risen dramatically. In addition to sequencing the 3 billion letters in the human genetic instruction book, researchers involved in the Human Genome Project have already sequenced the genomes of a number of important model organisms that are commonly used as surrogates in studying human biology. These are the chimpanzee, the mouse, the rat, two puffer fish, two fruit flies, two sea squirts, two roundworms, baker's yeast and the bacterium Escherichia coli. Currently, sequencing centers supported by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) are close to completing working drafts of the chicken, the dog, the honeybee, the sea urchin and a set of four fungi. Last summer, the centers also began sequencing the genome of the rhesus macaque monkey, and many other organisms are in the sequencing pipeline. The rapidly emerging field of comparative genomics has already yielded dramatic results. For example, a March 2000 study comparing the fruit fly genome with the human genome discovered that about 60 percent of genes are conserved between fly and human. Or, to put it simply, the two organisms appear to share a core set of genes. Researchers have found that two-thirds of human genes known to be involved in cancer have counterparts in the fruit fly. Even more surprisingly, when scientists inserted a human gene associated with early-onset Parkinson's disease into fruit flies, they displayed symptoms similar to those seen in humans with the disorder, raising the possibility the tiny insects could serve as a new model for testing therapies aimed at Parkinson's. More recently, a comparative genomic analysis of six species of yeast prompted scientists to significantly revise their initial catalog of yeast genes and to predict a new set of functional elements thought to play a role in regulating genome activity. To produce a more comprehensive plan for selecting sequencing targets, NHGRI recently instituted a new process for choosing animals for comparative sequencing. Rather than placing the entire responsibility for advocating for the sequencing of various organisms upon individual researchers, NHGRI has established three working groups comprised of experts from across the research community. Each working group will develop a plan for sequencing organisms that advances knowledge in one of three scientific areas: understanding the human genome, understanding the genomes of major biomedical model systems and evolutionary biology of genomes. Direct requests from researchers will also continue to be accepted. For more on NHGRI's process for selecting sequencing targets, go to: www.genome.gov/Sequencing/OrganismSelection. NHGRI is one of the 27 institutes and centers at the NIH, an agency of the Department of Health and Human Services. Additional information about NHGRI can be found at its Web site, www.genome.gov. Winter Excellent Time To Go Through Saved Garden Seeds By Carol Savonen, Oregon State University Home gardeners are often frugal by nature. They save leftover garden seeds from one year to the next and so forth. There is a certain average number of years that each type of seed remains viable and grows into healthy seedlings. If your seed envelopes date back to the 1980s and 1990s, you'd be better off chucking them and buying new seeds for this spring's planting season. If you want to be absolutely certain they are really too old, you can test their germination with a few seeds placed in a wet paper towel in a warm room. How long garden seeds may last depends on what kind of seeds you have and how you store them, explained Oregon State University vegetable researcher Deborah Kean. If seeds are kept dry, they last longer than in more humid conditions. For example, seed saving on the west side of the Cascades is more difficult than on the east side where it is drier. Some types of seeds are naturally more short-lived than others. Parsnip seeds almost never last more than one growing season, no matter how they are stored, said Kean. Spinach and allium (onions and leeks) seeds are relatively short lived also. The amount of oil in seeds correlates somewhat with how long a seed tends to remain viable. Generally, the higher oil content seeds decline in germination rate more quickly. Seed is best stored through the winter at 40 degrees at 50 percent humidity. A good way to store unused seed packets is to place them in a sealed jar with a desiccant such as powdered milk or rice at the bottom (to absorb moisture). Rice can be reused again as a desiccant if you dry it in the oven at a low temperature. Store your seed jar in the refrigerator or a cool area, such as a basement. Average seed life for common homegrown vegetables and flowers are given below. These seed life spans reflect no special care taken. If you keep your seeds dry and cool, you can expect many of them to last longer than the time periods indicated here, especially beans, peas and corn. • Bush and pole beans&emdash;3 years • Beets&emdash;2 years • Broccoli, Brussels sprouts, cabbage, cauliflower, and kohlrabi&emdash;3 to 5 years • Carrots&emdash;3 years • Collard, Kale&emdash;3 to 5 years • Sweet Corn&emdash;1 year • Cucumbers&emdash;3 years • Leeks, onions&emdash;2 years • Lettuce&emdash;2 years • Melons&emdash;3 years • Oriental greens&emdash;3 years • Parsley&emdash;2 years • Parsnips&emdash;1 year • Peas&emdash;2 years • Peppers&emdash;2 years • Radishes&emdash;4 years • Rutabagas&emdash;3 years • Spinach&emdash;1 season • Squashes&emdash;3 years • Swiss Chard&emdash;2 years • Tomatoes&emdash;3 years • Turnips&emdash;4 years • Flower seed&emdash;annuals are generally good for 1 to 3 years; perennials for 2 to 4 years. First Things First By Brad Vonhof, CPA, Certified Financial Planner, Financial Consultant, Moscow, ID There's more than one person who has commented that during this crazy is-it-up, is-it-down market that investing might better be held off to another day. That's nonsense. Markets will always be going up and going down. The best time to begin protecting your current assets and building your wealth is now. One of the important first steps you should take is to get rid of your consumer debt, especially credit card debt. It doesn't make much sense to grow money at 10 percent per year when a credit card is increasing your expenses by 15 percent or more per year. Even so-called low-interest credit cards can be weights on your wealth-building plan. Once you add up the annual fees, the cash advance charges, the daily interest accrued and any other charges, you can quickly see that it makes good money sense to pay them off. Many people pay their credit card off in full each month. This is better than buying with a credit card and then taking years to pay off what was a small debt. If that's not your situation, I'll help by sharing with you a few debt reduction strategies in a future column. Once you have eliminated your credit card debt, you should start a savings fund. This money is for both those unexpected and expected future expenses, things like insurance premiums, property taxes, back-to-school clothes, planned repairs and guess-what-happened-today fixes. Instead of reaching for your credit card, you'll dip into this saved money. If your credit card debt is so large that you'll need time to zero out the balance, begin building and using this savings fund immediately. Do that instead of increasing the amount owed to your credit card company. But don't&emdash; underscore don't&emdash;stop working on achieving that important goal: eliminating that credit card debt. Money in this savings fund should be liquid. You should be able to get cash fast. Generally, you should put this money into a money market account, preferably one with check-writing or telephone exchange privileges. Given the current interest rate climate, you should shop around for the best rates and accounts. Recently, I've found some of the best rates at credit unions, so if you qualify, look into one of these accounts. But, as I said, before you do anything, do your homework&emdash;look at minimum opening balance requirements, fees, monthly minimums, compounding method, yield rate and options for getting your cash. If you're internet savvy, you can compare money market accounts by visiting BankRate.com at: http://www.bankrate.com/brm/rate/mmmf_home.asp Keep the amount in your savings a set level. If you have a fund of $2,000 and you dip into it, be sure to restore it back to the original level. And don't put this money in a shoe box in your room or tucked away somewhere else! You don't want to be tempted to use it for daily living. There's no magic formula that will tell you how much of a savings fund you need. Look at your annual expenses and fund those planned periodic expenditures. Then allow something for those rainy day expenses. But don't get carried away building such a large fund that you'll never get to Step Three, which is building your short-term savings fund. I'll cover that in my next column. Until next month, your job is to eliminate your credit card debt and begin building your highly liquid, fast cash savings fund. NOTE: Brad Vonhof has been a practicing CPA for 26 years, a Certified Financial Consultant for 18 years and is a Financial Consultant serving Whitman and Latah counties for D.A. Davidson and Co., member SIPC. Heís a member of the American Institute of CPAs, Institute of Certified Financial Planners and has held leadership roles in the Washington Society of CPAs. Brad Vonhof can be reached at 208/883-5396 or 800/808-5396. The above article came to us courtesy of, Growing Your Money, Col. #1-2003: August Column, released: September 2003. Contact: Cynthia (Sunni) Freyer, CFNA PR/Marcom, 509/338-3943, sunni@cfnaonline.com Snow Or Lack Thereof &emdash; Effects On Landscape Plants By Carol Savonen, Oregon State University With snow season upon us, home gardeners should know that the fluffy white stuff can actually benefit plants during freezing winter weather &endash; if you are lucky enough to have much. If you live in Oregon's colder and drier areas, where deep snowfalls are commonly lacking, see below. Snow is an excellent insulator and can protect landscape plants from the devastating effects of repeated freezing and thawing, explained Ross Penhallegon, horticulturist with the Oregon State University Extension Service. Flower bulbs and garden root crops, in particular, will benefit from an insulating layer of snow. Plus, the added moisture when the snow melts is good for plants. For your plants' sake, use snow mulch only where you are sure melting snow will drain away easily and efficiently. Do not pile up a lot of snow in areas around the house where drainage is poor. Too much snow can result in unwanted quagmires around the home. Waterlogged soils in the spring can stress or even kill some plants. Landscape plants under eaves are often drought-stressed. Penhallegon suggests moving some of the snow shoveled off driveways and walkways and pile it around plants under eaves that may have escaped coverage by snowfall. In the drier, colder parts of the state, there may not be enough snowfall to protect plants and provide moisture. Cold weather and desiccating wind combined with sparse snow cover can damage plant root systems. Landscape plants including woody shrubs and perennials in central and eastern Oregon may need supplemental water during extended dry periods in the winter, according to Amy Jo Waldo, central Oregon horticulturist with the OSU Extension Service. As in wetter or snowier parts of the state, shrubs growing under the eaves of a house are particularly susceptible to damage during dry spells. Winter drought-damaged plants are often so weak they do leaf out, but then may die. Others die from drought stress during the winter months. These plants may appear to have been killed by the cold, but more likely the cause is desiccation, said Waldo. During winter dry spells, when there is little or no snow on the ground, a deep watering every six to eight weeks will be enough to keep plants from drying out. Water only when the air temperature is above freezing, and early in the day so the water will have time to soak in before nighttime freezing. Another wintertime concern for eastside gardens is sunscald. Trees with thin bark, such as maples, ash and aspen, are particularly susceptible to sunscald when young, before their bark has thickened. A paper wrap (available at garden stores) can be used during the winter months, but should be removed in early spring when growth resumes. This wrap can be used for two to three years until young trees develop thicker bark.

OSU Offers Newly Revised Home Orchard Publication By Carol Savonen, Oregon State University Think back on this past year's tree fruit harvest. Did your apples rot and drop from the tree before maturing? Did your peach blossoms turn brown and bear no fruit? Did your cherry tree trunk ooze sap? Keeping tree fruit trees pest and disease free and coaxing them into producing bountiful harvests can seem bewildering. The OSU Extension Service recently revised its publication, "Controlling Diseases and Insects in Home Orchards." The10-page booklet is written especially for the home gardener. It is downloadable on the web or printed copies can be ordered by mail. "Controlling Diseases and Insects in Home Orchards" includes cultural, biological and chemical approaches to controlling diseases and insects on apples, pears, cherries, prunes, plums, hazelnuts, walnuts, peaches, nectarines and apricots. Safety tips are given for applying pesticides. "To effectively control diseases and insects in your home orchard, you may need to combine a number of techniques," said Jay Pscheidt, plant pathologist with the Oregon State University Extension Service and coauthor of the publication. "Although pesticides can be used, there are a number of cultural and biological practices which can help keep fruit and nut trees producing and healthy." For more information on "Managing Diseases and Insects in Home Orchards," EC 631, visit our on-line catalog. Our publications and videos catalog at: http://eesc.oregonstate.edu/agcomwebfile/edmat shows which publications are available on the Web and which publications can be ordered as printed publications. Bacteria Discovered In 4,000 Feet Of Rock Fuels Mars Comparison By Mark Floyd, Oregon State University A team of scientists has discovered bacteria in a hole drilled more than 4,000 feet deep in volcanic rock on the island of Hawaii near Hilo, in an environment they say could be analogous to conditions on Mars and other planets. Bacteria are being discovered in some of Earth's most inhospitable places, from miles below the ocean's surface to deep within Arctic glaciers. The latest discovery is one of the deepest drill holes in which scientists have discovered living organisms encased within volcanic rock, said Martin R. Fisk, a professor in the College of Oceanic and Atmospheric Sciences at Oregon State University. Results of the study were published in the December issue of Geochemistry, Geophysics and Geosystems, a journal published by the American Geophysical Union and the Geochemical Society. "We identified the bacteria in a core sample taken at 1,350 meters," said Fisk, who is lead author on the article. "We think there could be bacteria living at the bottom of the hole, some 3,000 meters below the surface. If microorganisms can live in these kinds of conditions on Earth, it is conceivable they could exist below the surface on Mars as well." The study was funded by NASA, the Jet Propulsion Laboratory, California Institute of Technology and Oregon State University, and included researchers from OSU, JPL, the Kinohi Institute in Pasadena, Calif., and the University of Southern California in Los Angeles. The scientists found the bacteria in core samples retrieved during a study done through the Hawaii Scientific Drilling Program, a major scientific undertaking run by the Cal Tech, the University of California-Berkeley and the University of Hawaii, and funded by the National Science Foundation. The 3,000-meter hole began in igneous rock from the Mauna Loa volcano, and eventually encountered lavas from Mauna Kea at 257 meters below the surface. At one thousand meters, the scientists discovered most of the deposits were fractured basalt glass - or hyaloclastites - which are formed when lava flowed down the volcano and spilled into the ocean. "When we looked at some of these hyaloclastite units, we could see they had been altered and the changes were consistent with rock that has been 'eaten' by microorganisms," Fisk said. Proving it was more difficult. Using ultraviolet fluorescence and resonance Raman spectroscopy, the scientists found the building blocks for proteins and DNA present within the basalt. They conducted chemical mapping exercises that showed phosphorus and carbon were enriched at the boundary zones between clay and basaltic glass - another sign of bacterial activity. They then used electron microscopy that revealed tiny (two- to three-micrometer) spheres that looked like microbes in those same parts of the rock that contained the DNA and protein building blocks. There also was a significant difference in the levels of carbon, phosphorous, chloride and magnesium compared to unoccupied neighboring regions of basalt. Finally, they removed DNA from a crushed sample of the rock and found that it had come from novel types of microorganisms. These unusual organisms are similar to ones collected from below the sea floor, from deep-sea hydrothermal vents, and from the deepest part of the ocean - the Mariana Trench. "When you put all of those things together," Fisk said, "it is a very strong indication of the presence of microorganisms. The evidence also points to microbes that were living deep in the Earth, and not just dead microbes that have found their way into the rocks." The study is important, researchers say, because it provides scientists with another theory about where life may be found on other planets. Microorganisms in subsurface environments on our own planet comprise a significant fraction of the Earth's biomass, with estimates ranging from 5 percent to 50 percent, the researchers point out. Bacteria also grow in some rather inhospitable places. Five years ago, in a study published in Science, Fisk and OSU microbiologist Steve Giovannoni described evidence they uncovered of rock-eating microbes living nearly a mile beneath the ocean floor. The microbial fossils they found in miles of core samples came from the Pacific, Atlantic and Indian oceans. Fisk said he became curious about the possibility of life after looking at swirling tracks and trails etched into the basalt. Basalt rocks have all of the elements for life including carbon, phosphorous and nitrogen, and need only water to complete the formula. "Under these conditions, microbes could live beneath any rocky planet," Fisk said. "It would be conceivable to find life inside of Mars, within a moon of Jupiter or Saturn, or even on a comet containing ice crystals that gets warmed up when the comet passes by the sun." Water is a key ingredient, so one key to finding life on other planets is determining how deep the ground is frozen. Dig down deep enough, the scientists say, and that's where you may find life. Such studies are not simple, said Michael Storrie-Lombardi, executive director of the Kinohi Institute. They require expertise in oceanography, astrobiology, geochemistry, microbiology, biochemistry and spectroscopy. "The interplay between life and its surrounding environment is amazingly complex," Storrie-Lombardi said, "and detecting the signatures of living systems in Dr. Fisk's study demanded close cooperation among scientists in multiple disciplines - and resources from multiple institutions. "That same cooperation and communication will be vital as we begin to search for signs of life below the surface of Mars, or on the satellites of Jupiter and Saturn." OSU Publishes New Resource Guide For Organic Farmers By Carol Savonen, Oregon State University "The Organic Farmer's Guide to Oregon State University" is hot off the press. This 24-page guide, published by the OSU Extension Service, lists OSU's analytical laboratories and services and OSU Extension publications of interest to organic and biologically intensive agriculture. This new guide also provides contact information on OSU faculty members with interests in organic and biologically intensive agriculture. Key references and resources for organic growers, such as U.S. Department of Agriculture and State of Oregon programs and accredited organic certifying agents, are listed as well. "The Organic Farmer's Guide to Oregon State University," EM 8835, is available by mail for $1.50 per copy plus $3 shipping and handling. Send your request and check or money order payable to OSU to: Publication Orders, Extension & Station Communications, OSU, 422 Kerr Administration, Corvallis, OR 97331-2119. Or view it on the web at: http://eesc.oregonstate.edu. Select "Publications and Videos," then "Agriculture," then "Business Management and Marketing." How To Buy The Healthiest Indoor Plants By Carol Savonen, Oregon State University Winter is the time we often cheer ourselves up with houseplants and buy gift plants for others. Here's some hints on how to choose a healthy, vigorous houseplant from your local garden center or plant shop, provided by Ross Penhallegon, Oregon State University Extension Service horticulturist. Consider your source. Think about which merchants might likely have the healthiest plants. Does the shop have knowledgeable sales people? Do they specialize in plants, or do they sell everything else too? Beware of discount department stores that get plants in by the truckload and may not know anything about how to care for them. Are the conditions where the plants are found healthy for plants? Is there adequate light and not too much heat? Select a plant that looks healthy and well cared for, with the greenest leaves, unless of course, the foliage is not naturally green. Search for signs of disease, and pest infestations such as white flies, spider mites, aphids or scale, especially on the undersides of the leaves and where the leaves come off the stems. Check the soil for pests too. Avoid plants that look heavily pruned. The store may have cut off diseased or damaged parts. Look for sturdy, compact plants that soon will be blooming, rather than leggy or long plants. Choose plants that have or will have active, healthy new growth. Flower and leaf buds, new leaves or big buds are good signs. Pick out an immature plant over a blooming, mature plant, if there's a choice. Immature plants will stay in their prime longer. Purchase foliage (leafy) plants rather than flowering plants if you have a "black thumb." Foliage plants will survive the winter months better than bloomers. Bloomers will survive better in the spring when the days get longer. Protect the plant from cold shock on the trip home if the plant has been in a warm greenhouse. Surround the plant with a bag or newspaper. If the plant likes humid conditions, spray it with water when you get home. Quarantine your plant for a couple of days once you get it home, to make sure you haven't brought home any unwanted pests. If you have, take the plant back to the store. Ensure the plant is in appropriate soil. If the soil is mostly peat moss, you might want to add some potting mix. Realize that winter is not the optimal time for houseplants. What looks great in a plant shop, may suffer once you bring it home. Allow your houseplants to get as much light as possible. If they look anemic, move them to a sunnier window or under a grow light. OSU Prof Publishes Book On Biological Oceanography By Lisa DeBruyckere, Oregon State University Oregon State University oceanographer Charles Miller has written a new book that provides a comprehensive, up-to-date introduction to ocean ecology. Titled "Biological Oceanography," Miller's book examines the ecology of marine life and covers recent developments that have allowed a re-examination of the ocean's microbial cycling, carbon flow, and climate control. The book, which also covers ocean modeling, fisheries, and habitats, has more than 200 illustrations. It is intended for advanced students in biological oceanography, marine biology, and general marine science courses. Miller, a professor emeritus, taught undergraduate and graduate courses in biological oceanography for 32 years at OSU. During those years, he studied the zooplankton communities of the Oregon upwelling zone and Oregon estuaries, the pelagic ecology of the Gulf of Alaska, the life histories of planktonic copepods, and several varieties of population modeling. Miller has been writing the book for about 20 years as extended notes for his classes. Blackwell Publishers, headquartered in the United Kingdom, proposed a book outline to him that closely resembled those notes, so a deal was struck to revise the notes and publish the book. "I hope the book makes the general content of biological oceanography readily available to students from a wide range of backgrounds," Miller said. "Successive draft completions, the proof corrections and the printed book in hand have all been celebrated with fine champagne." "Biological Oceanography" is available in bookstores and libraries, or can be ordered by contacting the publisher, Blackwell Publishing at www.blackwellpublishing.com. The 402-page book sells for $64.95. Research Creates Plants Resistant To Serious Disease By David Stauth, Oregon State University Researchers at Oregon State University have developed a way to genetically engineer plants that have total resistance to crown gall disease, a pervasive, multi-million dollar problem that for decades has plagued the nursery and horticultural industries around the world. The system has been tested with tobacco plants and apple trees and appears to provide virtually complete protection from this plant disease, which can cause unsightly tumors on plants, usually on their roots, and diminish plant productivity, affect their structural integrity and often force their replacement. OSU scientists believe this genetic technology could be applicable to a wide variety of other fruit, nut, and ornamental trees and plants&emdash;everything from grapes to roses, apple trees and chrysanthemum&emdash;which can suffer impacts from crown gall disease. The findings were just published in two professional journals, Plant Physiology and Molecular Breeding. "Crown gall can be a disaster for nursery owners, and people have been trying to develop ways to address this problem for decades," said Walter Ream, a professor of microbiology at OSU. "The problem is serious enough that it's illegal to sell a plant that has been infected. But this express RNA as the plant begins a biochemical process that would eventually lead to uncontrolled growth of a tumor. But the genetically engineered plants make double-stranded RNA, instead of the single-stranded RNA ordinarily produced. The plant recognizes the double-stranded RNA as a virus, which it has the capacity to destroy with its own natural defense systems. So even though the plant has been infected by crown gall bacteria, the process of tumor formation is interrupted before any damaging effects can occur. "We've already demonstrated the efficacy of this approach with tobacco and apples, and other scientists have used it effectively on walnuts," Ream said. "It appears we can make this system work with most plants, and create varieties that are genetically resistant to the damaging effects of crown gall disease." The commercial use of this technology may be facilitated, Ream said, by its use just on the root stocks of plants, which are often grafted with fruiting wood of various types above the root structure. This would prevent concerns about genetic drift of newly engineered plant characteristics, since the genetically changed part of the plant would play no role in its seed production, pollination or other reproductive systems. This research was supported by the U.S. Department of Agriculture and the OSU Agricultural Research Foundation.

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