Researcher at Iowa State University has discovered how a group of proteins from plant pathogenic bacteria interact with DNA in the plant cell, opening up the possibility for what the scientist calls a "cascade of advances."
dam Bogdanove, associate professor in plant pathology, was researching the molecular basis of bacterial diseases of rice when he and Matthew Moscou, a student in the bioinformatics and computation biology graduate program, discovered that the so-called TAL effector proteins injected into plant cells by strains of the bacterium Xanthomonas attach at specific locations to host DNA molecules.
They found that different proteins of this class bind to different DNA locations, and particular amino acids in each protein determine those locations, called binding sites, in a very straightforward way.
"When we hit on it, we thought, 'Wow, this is so simple, it's ridiculous,'" Bogdanove said. Bogdanove's research will be published in an upcoming issue of the journal Science and is highlighted in last week's Science Express, an early online edition for research the Science editors feel is particularly timely and important. The paper is being published alongside a study from another research team that arrived at the same conclusions independently.
In his research, Bogdanove was examining how Xanthomonas uses TAL effectors to manipulate gene function in plants in ways that benefit the pathogen. Bogdanove was specifically interested in how different TAL effector proteins are able to activate different corresponding plant genes.
Over the past decade, understanding of this unique class of proteins has grown in leaps and bounds, according to Bogdanove.
Researchers in Germany, at Kansas State University, Manhattan; and here at Iowa State (Bing Yang, assistant professor in genetics development and cell biology) had previously shown that these proteins bind host DNA and activate genes important for disease, or in some cases defense against the bacteria. But no one yet understood how different TAL effectors recognized different parts of the DNA in order to attach and turn on the different genes at those locations.
Through computer analyses, Bogdanove and Moscou discovered that pairs of amino acids distributed throughout a TAL effector protein each specify a particular nucleotide, one of the bases in DNA abbreviated as the letters G, A, T, or C. The complete set of these pairs directs the protein to a matching string of Gs, As, Ts, and Cs in the DNA.
"This simple relationship allows us to predict where a TAL effector will bind, and what genes it will activate. It also makes it likely that we can custom engineer TAL effectors to bind to virtually any DNA sequence," says Bogdanove.
According to Bogdanove, being able to predict TAL effector binding sites will lead quickly to the identification of plant genes that are important in disease. Natural variants that lack these binding sites are a potential source of disease resistance.
Another potential application is adding TAL effector binding sites to defense-related genes so they are activated upon infection.
The possibilities for this new technology extend beyond plant disease control, according to Bogdanove.
"We might be able to use TAL effectors to activate genes in non-plant cells, possibly even in human stem cells for gene therapy. Or we might be able to use them to modify DNA at specific locations and help us study gene function. This could apply in many areas, including cancer research, for example," he said.
Bogdanove said the simplicity of the results surprised the research team.
"A predictable and potentially customizable kind of protein-DNA binding has been hard to find in nature. As Matt and I talked about the possibilities, we got excited and one of us said -- I don't remember who -- 'We've got to submit this to Science, dude,'" said Bogdanove.
Moscou investigated TAL effector DNA binding with Bogdanove through his participation in the Bioinformatics and Computation Biology (BCB) Lab, a student-run organization that provides assistance with computational analyses for life science researchers on campus. Moscou is a founding member of the BCB Lab, which is supported by a training grant to the BCB graduate program from the National Science Foundation. Moscou is doing his dissertation research on a plant pathogenic fungus under Roger Wise, professor in plant pathology.
Research in the Bogdanove laboratory is supported by funding from the NSF Plant Genome Research Program and from the United Stated Department of Agriculture -- Agricultural and Food Research Initiative program.
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Iowa State University (2009, November 13). Researcher Discovers Key To Vital DNA, Protein Interaction. ScienceDaily. Retrieved November 14, 2009, from http://www.sciencedaily.com /releases/2009/11/091110171654.htm
Friday
Sunday
Modified Crops Reveal Hidden Cost Of Resistance
Genetically modified squash plants that are resistant to a debilitating viral disease become more vulnerable to a fatal bacterial infection, according to biologists. "Cultivated squash is susceptible to a variety of viral diseases and that is a major problem for farmers," said Andrew Stephenson, Penn State professor of biology. "Infected plants grow more slowly and their fruit becomes misshapen."
In the mid-1990s, the U.S. Department of Agriculture approved genetically modified squash, which are resistant to three of the most important viral diseases in cultivated squash. However, while disease-resistant crops have been a boon to commercial farmers, ecologists worry there might be certain hidden costs associated with the modified crops.
"There is concern in the ecological community that, when the transgenes that confer resistance to these viral diseases escape into wild populations, they will (change) those plants," said Stephenson, whose team's findings appeared Oct. 26 in the Proceedings of the National Academy of Sciences. "That could impact the biodiversity of plant communities where wild squash are native."
Stephenson and his colleagues James A. Winsor, professor of biology; Matthew J. Ferrari, research associate; and Miruna A. Sasu, doctoral student, all at Penn State; and Daolin Du, visiting professor, Jiangsu University, China, crossed the genetically modified squash into wild squash native to the southwestern United States and examined the resulting flower and fruit production.
Unlike a lab experiment, the researchers tried to mimic a real world setting during their three-year study.
The researchers then looked at the effects of the virus-resistant transgenes on prevalence of the three viral diseases, herbivory by cucumber beetles, as well as the occurrence of bacterial wilt disease that is spread by the cucumber beetles.
"When the cucumber beetles start to feed on infected plants they pick up the bacteria through their digestive system," explained Sasu. "This feeding creates open wounds on the leaves and when the bugs' feces falls on these open wounds, the bacteria find their way into the plumbing of the plant."
The researchers discovered that as the viral infection swept the fields containing both genetically modified and wild crops, the damage from cucumber beetles is greater on the genetically modified plants. The modified plants are therefore more susceptible to the fatal bacterial wilt disease.
"Plants that do not have the virus-resistant transgene get the viral disease," explained Stephenson, whose team's work is funded by the National Science Foundation. "However, since cucumber beetles prefer to feed on healthy plants rather than viral infected plants, the beetles become increasingly concentrated on the healthy -- mostly transgenic -- plants."
During a viral epidemic, the transgene provides modified plants with a fitness advantage over the wild plants. But when both the bacterial and viral pathogens are present, the beetles tend to avoid the smaller viral infected plants and concentrate on the healthy transgenic plants. This exposes those plants to the bacterial wilt disease against which they have no defense.
"Wild and transgenic plants had the same amount of damage from beetles before viral diseases were prevalent in our fields," said Stephenson. "Once the virus infected the wild plants, the transgenic plants had significantly greater damage from the beetles."
Results from the study show that over the course of three years, the prevalence of bacterial wilt disease was significantly greater on transgenic plants than on non-transgenic plants.
According to the researchers, their findings suggest that the fitness advantage enjoyed by virus-resistant plants comes at a price. Once the virus infects susceptible plants, cucumber beetles find the genetically modified plants a better source for food and mating.
"Our study has sought to uncover the ecological cost that might be associated with modified plants growing in the full community of organisms, including other insects and other diseases," said Ferrari. "We have shown that while genetic engineering has provided a solution to the problem of viral diseases, there are also these unintended consequences in terms of additional susceptibility to other diseases."
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Adapted from materials provided by Penn State.
Monday
Gene Developed Through Conventional Breeding To Improve Cowpea Aphid Resistance
The cowpea or black-eyed pea, as it is more commonly known, is a New Year’s tradition for good luck. But disease and particularly aphids, which can wreck a crop within a few a days, are especially bad luck for the cowpea, according to scientists. (Credit: Texas AgriLife Research photo by Blair Fannin)The cowpea or black-eyed pea, as it is more commonly known, is a New Year's tradition for good luck. But disease and particularly aphids, which can wreck a crop within a few a days, are especially bad luck for the cowpea, according to scientists. Several new lines of cowpeas with genes that are aphid-resistant and less susceptible to disease are currently being tested by researchers with Texas AgriLife and other Texas A&M System entities.
"The cowpea has been an important and popular food crop throughout the southern U.S.," said Dr. B.B. Singh, a visiting professor in the soil and crop sciences department at Texas A&M. "It's commonly known as the southern pea, field pea, crowder pea, black-eyed pea, purple-hull pea and pinkeye pea widely grown in the southern states."
The researchers' discoveries could yield big rewards. An international food crop, the cowpea was most popular in the southern U.S. from the 1930s through '70s, and East Texas remains a large U.S. cowpea-producing region.
And during times of drought, the cowpea can be a viable alternative forage crop for livestock producers, due to its ability to fix nitrogen, tolerate drought and provide high-quality fodder, Singh said. It is a high-quality forage for cattle producers, with a protein content as high as 28 percent in seeds and 17 percent to 20 percent in the fodder after harvesting the seeds.
However, the aphid is currently the biggest threat to cowpea producers, Singh said.
"(Aphids) like dry weather," explained Singh, who has spent his entire career studying the cowpea. "Immediately after infestation, they start sucking the juice (sap) from cowpea leaves, stem, flowers and pods of the plants reducing their growth and development and causing severe reduction in yield. They also spread viruses. Aphids can ruin a crop within a few days."
Singh, came to the department as a visiting professor following his retirement two years ago from the International Institute of Tropical Agriculture, considered the epicenter of cowpea research.
At Texas A&M, Singh is working with colleagues Dr. J. Creighton Miller, D.C. Sheuring and Dr. Bill Payne using field trials in College Station to find a solution to the aphid problem.
Singh has brought more than 35 lines of cowpeas with drought and aphid tolerance, as well as resistance to other diseases and higher yield potential, to College Station. His work there has involved using conventional breeding methods to cross those lines with six Texas and California varieties in greenhouse and field settings.
"Many of the IITA lines are resistant to aphid, bacterial blight, powdery mildew and drought, whereas most of the U.S. lines are susceptible," Singh said. "A number of crosses were made to transfer the resistance to aphids and drought from the IITA lines to the U.S. lines."
In mid July, an aphid infestation hit the College Station trials, putting the new varieties to the test.
"It's been fairly severe, permitting selection of resistant plants from the F2 and F3 populations," he said. "Due to drought and aphids this crop season, all of the susceptible cowpea varieties and segregating plants have been completely damaged, showing 80 percent to 100 percent yield loss, while the aphid resistant varieties and segregating plants are completely healthy with normal yield. The resistance is simply inherited, very effective and highly stable across environments."
From the segregating populations, the resistant plants with diverse maturity dates, plant type, growth habits and seed types have been selected to meet the need for grain type, fodder-type and pasture-type cowpea varieties, he said.
"These are being advanced to achieve uniformity and multi-location testing for stability of resistance and yield potential," Singh added. The new aphid-resistant, high-yielding varieties could be available to farmers as early as 2011, Singh said.
"The cowpea has worldwide importance as a crop for both human and animal nutrition," said Payne of Texas AgriLife Research, assistant director for research at the Norman Borlaug Institute for International Agriculture. "Introducing improved disease- and drought-resistant and higher-yield varieties could not only have tremendous potential for Texas and U.S. agriculture, it could help provide poor and developing countries with an important alternative source of nutrition."
According to the International Institute of Tropical Agriculture in Africa, the cowpea is an important food crop in many African, Asian and South American countries, especially as an alternative source of protein where people cannot afford meat and fish. The crop typically is grown by subsistence farmers with limited agricultural resources, who use it to feed livestock or sell for additional income.
The international Food and Agriculture Organization estimates more than 7.5 million tons of cowpeas are produced annually worldwide, with sub-Saharan Africa responsible for about 70 percent of that amount.
"We are already involved in international research projects in Africa relating to cowpeas," Payne noted. "It's exciting to think where these new activities in College Station and the research already under way in Africa may lead."
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Texas A&M AgriLife (2009, October 26). Gene Developed Through Conventional Breeding To Improve Cowpea Aphid Resistance.
Loss Of Tumor-suppressor And DNA-maintenance Proteins Causes Tissue Demise
Hair follicle regeneration by undamaged cells (red, left panel) is delayed by the presence of damaged cells (arrows, right panel). Damaged cells are maintained because of the absence of p53 (right panel). (Credit: Yaroslava Ruzankina, PhD; David Schoppy; Eric Brown, PhD, University of Pennsylvania School of Medicine)A study published in the October issue of Nature Genetics demonstrates that loss of the tumor-suppressor protein p53, coupled with elimination of the DNA-maintenance protein ATR, severely disrupts tissue maintenance in mice. As a result, tissues deteriorate rapidly, which is generally fatal in these animals. In addition, the study provides supportive evidence for the use of inhibitors of ATR in cancer therapy.
Essentially, says senior author Eric Brown, PhD, Assistant Professor of Cancer Biology at the University of Pennsylvania School of Medicine, the findings highlight the fact that day-to-day maintenance required to keep proliferative tissues like skin and intestines functional is about more than just regeneration, a stem cell-based process that forms the basis of tissue renewal. It's also about housekeeping, the clearing away of damaged cells.
Whereas loss of ATR causes DNA damage, the job of p53 is to monitor cells for such damage and either stimulate the early demise of such cells or prevent their replication, the housekeeping part of the equation. The findings indicate that as messy as things can become in the absence of a DNA maintenance protein like ATR, failing to remove resulting damaged cells by also deleting p53, is worse. "Because the persistence of damaged cells in the absence of p53 prevents appropriate tissue renewal, these and other studies have underscored the importance not only of maintaining competent stem cells, but also of eliminating what gets in the way of regeneration," explains Brown.
"An analogy to our findings is what happens to trees during the changing seasons," says Brown. "In springtime, leaves are new and undamaged. But as the summer wears on, the effects of various influences - insects, drought, and disease - cause them to lose the pristine qualities they once had. However, the subsequent fall of these leaves presents a unique opportunity for regeneration later on, a chance to rejuvenate from anew without pre-existing obstacles. Similarly, by suppressing the accumulation of damaged cells in tissues, p53 permits more efficient tissue renewal when ATR is deleted."
Cells without ATR that remain uncleared may be block tissue regeneration either by effectively refusing to relinquish space to undamaged cells, or by secreting signals that halt regeneration until they have been removed.
These results came as something of a surprise, says Brown. Previous studies pairing DNA-repair mutations with p53 mutations always led to a partial rescue of the DNA repair mutation "We think this happens because p53 loss helps cells with just a little DNA damage to continue to contribute to the tissue" says Brown. So at a minimum, the team expected nothing to happen.
"But we got the opposite result: Absence of p53 did not rescue the tissue degeneration caused by ATR loss, it made it much worse. This result suggested that allowing mutant cells without ATR to persist is more harmful to tissues than eliminating them in the first place." Brown speculates that could be because the ATR mutation produces much more damage than most other DNA-repair defects.
According to Brown, their findings and those of other laboratories also reinforce the potential of a new therapeutic for cancer. That's because, among their other discoveries, the team noticed that cells missing both ATR and p53 have more DNA damage than those missing either gene alone. As a large fraction of human cancers have p53 mutations, he says, "p53-deficient tumors might be especially susceptible to ATR inhibition." Indeed, clinical trials already are underway involving an ATR partner protein called Chk1. "Our study provides supportive evidence for the potential use of ATR/Chk1 inhibitors in cancer therapy," says Brown
The report was supported by the National Institute on Aging and the Abramson Family Cancer Research Institute.
Laboratory members Yaroslava Ruzankina, PhD and MD/PhD student David Schoppy are lead authors of this study. Amma Asare, Carolyn Clark, and Robert Vonderheide, all from Penn, are co-authors.
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DNA-maintenance Proteins Causes Tissue Demise." ScienceDaily 21 October 2009. 27 October 2009Tuesday
Definition of Biotechnology
What is biotechnology?
Biotechnology are defined as the controlled and deliberate manipulation of biological systems, whether it is the whole living cells or part of the cell components, for the efficient manufacture or processing of useful products. The fact that living organisms’ biological capabilities to evolve in such a vast scale means that we are able to obtain a broad mixture of substances by selecting the suitable organisms. Many of the substances are useful to people as food, fuel and medicines. Over the past three decades, biologists have gradually applied the methods of physics, chemistry and mathematics in order to gain precise knowledge, at the molecular level. Biologists are able to identified and learn how living cells make these substances. By combining this newly-gained knowledge with the methods of engineering and science, what has emerged is the concept of biotechnology which embraces all of the above-mentioned disciplines. One of the examples of biotechnology is the process of fermentation. Fermentation is a process using microbes to produce wine, cheese, beer, bread and yogurt.
How do Biotechnology Influencing the Industry
In actual fact, biotechnology has existed long before the term “biotechnology” came into use. It has changed the traditional industries such as food processing and fermentation. Biotechnology plays a major part in the development of new technology for industrial production of hormones, antibiotics and others chemicals, food and energy sources and processing of waste materials. Thus, it is important that this industry is staffed by trained bio technologists who are equipped with comprehensive biological knowledge and thorough practical training in engineering methods. Some of the major industries involved in biotechnology are agriculture, crop production and pharmaceutical products.
Biotechnology are defined as the controlled and deliberate manipulation of biological systems, whether it is the whole living cells or part of the cell components, for the efficient manufacture or processing of useful products. The fact that living organisms’ biological capabilities to evolve in such a vast scale means that we are able to obtain a broad mixture of substances by selecting the suitable organisms. Many of the substances are useful to people as food, fuel and medicines. Over the past three decades, biologists have gradually applied the methods of physics, chemistry and mathematics in order to gain precise knowledge, at the molecular level. Biologists are able to identified and learn how living cells make these substances. By combining this newly-gained knowledge with the methods of engineering and science, what has emerged is the concept of biotechnology which embraces all of the above-mentioned disciplines. One of the examples of biotechnology is the process of fermentation. Fermentation is a process using microbes to produce wine, cheese, beer, bread and yogurt.
How do Biotechnology Influencing the Industry
In actual fact, biotechnology has existed long before the term “biotechnology” came into use. It has changed the traditional industries such as food processing and fermentation. Biotechnology plays a major part in the development of new technology for industrial production of hormones, antibiotics and others chemicals, food and energy sources and processing of waste materials. Thus, it is important that this industry is staffed by trained bio technologists who are equipped with comprehensive biological knowledge and thorough practical training in engineering methods. Some of the major industries involved in biotechnology are agriculture, crop production and pharmaceutical products.