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  • richardmitnick 12:39 pm on June 8, 2016 Permalink | Reply
    Tags: , , Rice, Rice study details stress-diabetes link   

    From Rice: “Rice study details stress-diabetes link” 

    Rice U bloc

    Rice University

    June 6, 2016
    Mike Williams

    Connection established between anxiety control, inflammation, Type 2 diabetes

    A Rice University study has found a link between emotional stress and diabetes, with roots in the brain’s ability to control anxiety.

    1
    Illustration by Andrea Lugo/Rice University

    That control lies with the brain’s executive functions, processes that handle attention, inhibition, working memory and cognitive flexibility and are also involved in reasoning, problem-solving and planning.

    The study published in Psychoneuroendocrinology establishes a metabolic chain reaction that starts with low inhibition, aka attention control, which leaves a person vulnerable to tempting or distracting information, objects, thoughts or activities. Previous studies have shown that such vulnerability can lead to more frequent anxiety, and anxiety is known to activate a metabolic pathway responsible for the production of pro-inflammatory cytokines, signaling proteins that include interleukin-6 (IL-6).

    Along with cognitive tests that measured attention control, the Rice study measured levels of both blood glucose and IL-6 in more than 800 adults. IL-6 is a protein the body produces to stimulate immune response and healing. It is a biomarker of acute and chronic stress that also has been associated with a greater likelihood of diabetes and high blood glucose.

    The research showed individuals with low inhibition were more likely to have diabetes than those with high inhibition due to the pathway from high anxiety to IL-6. The results were the same no matter how subjects performed on other cognitive tests, like those for memory and problem-solving.

    Researchers have suspected a link between anxiety and poor health, including diabetes, for many years but none have detailed the biological pathway responsible, said lead author Kyle Murdock, a postdoctoral research fellow in psychology. He said the Rice study takes a deeper look at how inflammation bridges the two.

    “The literature shows individuals with poor inhibition are more likely to experience stressful thoughts and have a harder time breaking their attention away from them,” Murdock said. “That made me wonder if there’s a stress-induced pathway that could link inhibition with inflammation and the diseases we’re interested in, such as diabetes.

    “Plenty of research shows that when individuals are stressed or anxious or depressed, inflammation goes up,” he said. “The novel part of our study was establishing the pathway from inhibition to anxiety to inflammation to diabetes.”

    Murdock works in the Rice lab of Christopher Fagundes, assistant professor of psychology. The Fagundes lab investigates processes that happen along the border of psychology and physiology, and how those processes affect overall health and potential treatments.

    The data came from a Midlife Development in the United States study of 1,255 middle-aged adults whose cognitive abilities were tested two years apart. More than 800 of those also underwent blood tests to check IL-6 and glucose levels. The Rice researchers found not only the positive link between inhibition and diabetes, but the absence of a link between other cognitive functions and the disease. They also determined that the pathway only went in one direction: Inflammation never appeared to affect inhibition.

    Murdock said a year as a clinical psychology intern at the Oregon Health and Science University, where he studied with co-author and psychologist Danny Duke, led the researchers to think there could also be a feedback loop at play in those with diabetes. “Individuals who are anxious are more likely to avoid treatment and use maladaptive strategies (like smoking or unhealthy diets) that enhance their blood glucose, which is problematic. It’s a snowball effect: The further they go, the worse it gets,” he said.

    “We also know that extremely high blood glucose can impact cognition as well. We talked about how, if we’re going to treat these individuals appropriately, it won’t be by sitting them down in a room and saying, ‘Hey, you need to eat better,’ or ‘You need to use your insulin on time.’”

    The researchers listed several possible interventions, including mindfulness therapy, stimulant or anti-inflammatory medications and cognitive behavioral therapy. “Research shows that people who practice mindfulness do better on the inhibition tests over time,” Murdock said, suggesting that shifting one’s attention away from stressful thoughts may affect physiological responses.

    “I’m a firm believer that mindfulness-based approaches to treatment are a great idea, for a lot of reasons,” Fagundes said. “That doesn’t mean medicines that promote inhibition, such as stimulants, shouldn’t be considered, but a combination of the two could be really helpful.”

    Co-authors of the paper are Angie LeRoy, a Rice staff member and a graduate student at the University of Houston; and Tamara Lacourt, a postdoctoral researcher, and Cobi Heijnen, a professor of symptom research at the University of Texas MD Anderson Cancer Center.

    The National Institute on Aging and the National Heart, Lung and Blood Institute supported the research.

    See the full article here .

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    Rice U campus

    In his 1912 inaugural address, Rice University president Edgar Odell Lovett set forth an ambitious vision for a great research university in Houston, Texas; one dedicated to excellence across the range of human endeavor. With this bold beginning in mind, and with Rice’s centennial approaching, it is time to ask again what we aspire to in a dynamic and shrinking world in which education and the production of knowledge will play an even greater role. What shall our vision be for Rice as we prepare for its second century, and how ought we to advance over the next decade?

    This was the fundamental question posed in the Call to Conversation, a document released to the Rice community in summer 2005. The Call to Conversation asked us to reexamine many aspects of our enterprise, from our fundamental mission and aspirations to the manner in which we define and achieve excellence. It identified the pressures of a constantly changing and increasingly competitive landscape; it asked us to assess honestly Rice’s comparative strengths and weaknesses; and it called on us to define strategic priorities for the future, an effort that will be a focus of the next phase of this process.

     
  • richardmitnick 11:07 am on March 25, 2016 Permalink | Reply
    Tags: , , , Rice   

    From Rice: “New tool probes deep into minerals and more” 

    Rice U bloc

    Rice University

    March 25, 2016
    David Ruth
    713-348-6327
    david@rice.edu

    Mike Williams
    713-348-6728
    mikewilliams@rice.edu

    1
    Rice University geologist Gelu Costin monitors an experiment at the Electron Probe MicroAnalyzer. (Credit: Jeff Fitlow/Rice University)

    Rice University installs sophisticated microprobe for fine analysis of metals, minerals

    Rice Earth scientists have many ways to see deep into the planet, from drilling to seismic models to simulations, and now they have a way to see deep into what comes from the depths.

    The Department of Earth Science brought a powerful new instrument online earlier this year that lets researchers view the fine structures and composition of inorganic samples. The tool has also been of use to local industries and other academic institutions.

    The field emission Electron Probe MicroAnalyzer combines the abilities of an electron microscope and sophisticated spectrometers. Installed at Keith-Wiess Geological Laboratories, it allows for the precise quantitative chemical analysis of samples for almost all of the elements on the periodic table, from beryllium to uranium. New spectroscopic capabilities will allow for the identification of very light elements like lithium in the near future, but analyses are already underway for nitrogen and carbon in crystals and glasses.

    Installation of the new microprobe, a state-of-the-art JEOL JXA 8530F Hyperprobe, drew geologist Gelu Costin to Rice last year.

    2
    EOL JXA 8530F Hyperprobe

    Costin joined the department as a staff scientist to manage the scope, which he said is the only one of its kind at a university in the southwest United States.

    “This is a new invention, field emission on a microprobe,” Costin said.

    The instrument bombards samples of rock or other inorganic materials with electrons focused into a tight beam by a series of electromagnetic lenses. The beam interacts with the sample to reveal nanoscale compositional patterns as small as hundreds of nanometers, while allowing the spectrometers to quantify the object’s constituent elements.

    The probe is fitted with four spectrometers to analyze elements that respond to different wavelengths and an energy-dispersive X-ray spectrometer, all of which work in a high-vacuum environment to image and provide fine analysis of samples. Soon the instrument will be fitted with a fifth spectrometer that will allow quantification of trace elements as well.

    “There are not many analytical techniques that allow major- and minor-element chemistry determination down to micron and submicron scales,” said geologist Rajdeep Dasgupta, a Rice professor of Earth sciences whose experimental petrology lab simulates pressures deep in the planet to produce samples of what might be found there. “This new generation of electron microprobe gives the type of spatial resolution required to characterize some of the high-pressure experiments.

    “We can now determine many minor elements, all the major elements and even some of the trace elements in solid phases and quenched glasses from high-pressure experiments,” he said.

    Dasgupta said the instrument expands the range of research the university’s Earth scientists can take on. “In my group we perform experiments to figure out the behavior of minerals and rocks at extreme pressures and how they exchange elements between different phases,” he said. In the past, researchers would take samples to microprobes at Texas A&M and NASA’s Johnson Space Center to analyze them.

    “We weren’t able to tackle projects that required us to do an experiment and analyze it in detail before designing the next step,” he said. “It wasn’t practically feasible to go to another institution to get one sample analyzed. Now we’re taking on more challenging projects, and we are pushing the analytical capabilities.”

    The microprobe is open to all Rice researchers as well as clients from industry and other academic institutions, Costin said. “We’ve already had a few users from outside geology,” he said. “People are coming over from chemistry to study the quality of nanometer-thin silver films deposited on graphite. With our machine, they can easily check the consistency of its thickness because we know that if the composition changes on the surface, the thickness changes as well.

    “People from metallurgy companies around Houston have used our facility to check the microtextures and composition of micron-scaled phases in metallurgical slugs,” he said. “And people working in the repair and testing of metallic tools in the Houston area have come to check the composition of fillings inside microcracks produced during welding. We are open to all varieties of microprobe applications, from geology to planetary, chemistry, material science and more.”

    3
    The Electron Probe MicroAnalyzer uses spectrometers to quantify elements in rocks or other inorganic samples. These wavelength dispersive spectrometry quantitative maps show the distribution of elements in metallurgical slag. Clockwise from top left: a backscattered electron image that shows differences in average atomic weight of the phases, and atomic weight maps of aluminum, carbon and oxygen. Courtesy of the EPMA Laboratory. (Credit: EMPA Laboratory/Rice University)

    3
    A magnetite sample magnified 5,500 times shows fine details that are invisible to the naked eye but can be clearly captured by the new Electron Probe MicroAnalyzer at Rice University. (Credit: EMPA Laboratory/Rice University)

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Rice U campus

    In his 1912 inaugural address, Rice University president Edgar Odell Lovett set forth an ambitious vision for a great research university in Houston, Texas; one dedicated to excellence across the range of human endeavor. With this bold beginning in mind, and with Rice’s centennial approaching, it is time to ask again what we aspire to in a dynamic and shrinking world in which education and the production of knowledge will play an even greater role. What shall our vision be for Rice as we prepare for its second century, and how ought we to advance over the next decade?

    This was the fundamental question posed in the Call to Conversation, a document released to the Rice community in summer 2005. The Call to Conversation asked us to reexamine many aspects of our enterprise, from our fundamental mission and aspirations to the manner in which we define and achieve excellence. It identified the pressures of a constantly changing and increasingly competitive landscape; it asked us to assess honestly Rice’s comparative strengths and weaknesses; and it called on us to define strategic priorities for the future, an effort that will be a focus of the next phase of this process.

     
  • richardmitnick 10:25 pm on January 11, 2016 Permalink | Reply
    Tags: , Rice, Self-healing material   

    From Rice: “Self-adaptive material heals itself, stays tough” 

    Rice U bloc

    Rice University

    January 11, 2016
    Mike Williams

    Rice University scientists mix up a new type of flexible composite.

    An adaptive material invented at Rice University combines self-healing and reversible self-stiffening properties.

    The Rice material called SAC (for self-adaptive composite) consists of what amounts to sticky, micron-scale rubber balls that form a solid matrix. The researchers made SAC by mixing two polymers and a solvent that evaporates when heated, leaving a porous mass of gooey spheres. When cracked, the matrix quickly heals, over and over. And like a sponge, it returns to its original form after compression.


    watch and download the mp4 video here .

    The labs of Rice materials scientists Pulickel Ajayan and Jun Lou led the study that appears in the American Chemical Society journal ACS Applied Materials and Interfaces. They suggested SAC may be a useful biocompatible material for tissue engineering or a lightweight, defect-tolerant structural component.

    Other “self-healing” materials encapsulate liquid in solid shells that leak their healing contents when cracked. “Those are very cool, but we wanted to introduce more flexibility,” said Pei Dong, a postdoctoral researcher who co-led the study with Rice graduate student Alin Cristian Chipara. “We wanted a biomimetic material that could change itself, or its inner structure, to adapt to external stimulation and thought introducing more liquid would be a way. But we wanted the liquid to be stable instead of flowing everywhere.”

    1
    Rice postdoctoral researcher Pei Dong holds a sample of SAC, a new form of self-adapting composite. The material has the ability to heal itself and to regain its original shape after extraordinary compression. Photo by Jeff Fitlow

    In SAC, tiny spheres of polyvinylidene fluoride (PVDF) encapsulate much of the liquid. The viscous polydimethylsiloxane (PDMS) further coats the entire surface. The spheres are extremely resilient, Lou said, as their thin shells deform easily. Their liquid contents enhance their viscoelasticity, a measure of their ability to absorb the strain and return to their original state, while the coatings keep the spheres together. The spheres also have the freedom to slide past each other when compressed, but remain attached.

    “The sample doesn’t give you the impression that it contains any liquid,” Lou said. “That’s very different from a gel. This is not really squishy; it’s more like a sugar cube that you can compress quite a lot. The nice thing is that it recovers.”

    Ajayan said making SAC is simple, and the process can be tuned – a little more liquid or a little more solid — to regulate the product’s mechanical behavior.

    “Gels have lots of liquid encapsulated in solids, but they’re too much on the very soft side,” he said. “We wanted something that was mechanically robust as well. What we ended up with is probably an extreme gel in which the liquid phase is only 50 percent or so.”

    3
    Graduate student Alin Cristian Chipara and postdoctoral researcher Pei Dong show a sample of their self-adaptive composite, which they say shows potential for tissue engineering or lightweight structural applications. Photo by Jeff Fitlow

    The polymer components begin as powder and viscous liquid, said Dong. With the addition of a solvent and controlled heating, the PDMS stabilizes into solid spheres that provide the reconfigurable internal structure. In tests, Rice scientists found a maximum of 683 percent increase in the material’s storage modulus – a size-independent parameter used to characterize self-stiffening behavior. This is much larger than that reported for solid composites and other materials, they said.

    Dong said sample sizes of the putty-like material are limited only by the container they’re made in. “Right now, we’re making it in a 150-milliliter beaker, but it can be scaled up. We have a design for that.”

    Co-authors are Rice postdoctoral researchers Bo Li, Yingchao Yang, Hua Guo, Liehui Ge and Liang Hong; graduate student Sidong Lei; undergraduate students Bilan Yang and Qizhong Wang; alumnus Phillip Loya; Emilie Ringe, an assistant professor of materials science and nanoengineering and of chemistry; Robert Vajtai, a senior faculty fellow in materials science and nanoengineering, and Ming Tang, an assistant professor of materials science and nanoengineering; Mircea Chipara, an assistant professor of physics and geology at the University of Texas-Pan American, and postdoctoral researchers Gustavo Brunetto and Leonardo Machado and Douglas Galvao, a professor at the State University of Campinas, Brazil.

    Ajayan is chair of Rice’s Department of Materials Science and NanoEngineering, the Benjamin M. and Mary Greenwood Anderson Professor in Engineering and a professor of chemistry. Lou is a professor of materials science and nanoengineering and of chemistry and associate chair of the Department of Materials Science and NanoEngineering.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Rice U campus

    In his 1912 inaugural address, Rice University president Edgar Odell Lovett set forth an ambitious vision for a great research university in Houston, Texas; one dedicated to excellence across the range of human endeavor. With this bold beginning in mind, and with Rice’s centennial approaching, it is time to ask again what we aspire to in a dynamic and shrinking world in which education and the production of knowledge will play an even greater role. What shall our vision be for Rice as we prepare for its second century, and how ought we to advance over the next decade?

    This was the fundamental question posed in the Call to Conversation, a document released to the Rice community in summer 2005. The Call to Conversation asked us to reexamine many aspects of our enterprise, from our fundamental mission and aspirations to the manner in which we define and achieve excellence. It identified the pressures of a constantly changing and increasingly competitive landscape; it asked us to assess honestly Rice’s comparative strengths and weaknesses; and it called on us to define strategic priorities for the future, an effort that will be a focus of the next phase of this process.

     
  • richardmitnick 5:44 pm on November 12, 2015 Permalink | Reply
    Tags: , , Rice   

    From MIT: “Rice Experiment Yields Results” 


    MIT

    MIT Spectrum

    1
    Tavneet Suri conducted an experiment and found that the hunger season could potentially be shortened and yields increased. Photo: Courtesy Tavneet Suri

    Every summer in Sierra Leone, people face two months of hunger when stocks of rice run dry and prices escalate. Professor Tavneet Suri conducted a randomized experiment on the economics of a new high-yield rice to learn more about addressing this glaring issue. She found the hunger season could potentially be shortened, and yields increased for the adopters of this technology, mitigating the adverse effects of this lengthy period of starvation.

    Suri, a development economist and the Maurice F. Strong Career Development Professor in Applied Economics at MIT Sloan, serves as scientific director for Africa in the Abdul Latif Jameel Poverty Action Lab (J-PAL) and co-chair of the J-PAL Agriculture program. She and J-PAL executive director Rachel Glennerster conducted an experiment—designed like a clinical trial in medicine—which tested the adoption and impact of a new kind of rice known as NERICA (New Rice for Africa). NERICA combines the high-yield properties of Asian rice with the resilience of African rice, which is known for resistance to drought and disease. The experiment tested mechanisms that could encourage farmers to try NERICA, such as subsidies to purchase seed, training in new cultivation methods, and information about how its adoption might affect agricultural and health outcomes.

    “Initially we thought NERICA’s shorter growing season could produce two rice harvests, or that a higher yield would give farmers more rice to sell and increase their overall economic situation,” Suri says. “But that was not quite the case. We found instead a profoundly simple outcome. The duration from planting to harvest decreased from 130 days for traditional rice, to 100 days for NERICA. By coming in four weeks earlier and producing a higher yield, the hunger season was reduced. Families had more food, they could eat more consistently through the year, and their children’s nutrition improved.

    “The effects were striking. As an economist, I look for causality. This is one of the first studies of its kind, using a randomized control trial to quantitatively show how an agricultural technology affects child nutrition.”

    Suri’s research takes her across Africa, from Sierra Leone to Rwanda and Kenya. A fourth- generation Kenyan, Suri returned to her home country to conduct a credit experiment there, exploring creative ways to help dairy farmers obtain credit to purchase water storage tanks.

    Storing rainwater in tanks is the best way to have a reliable supply of fresh, clean water for dairy cows during the dry season. But the storage tanks are expensive and farmers cannot afford them without a loan. Pondering new ways to provide credit, Suri had a eureka moment: she would test an asset-collateralized loan, using the tank itself as collateral. If a farmer falls behind on payments, the tank is repossessed. While this credit model is common in the US, for car loans and mortgages, it is almost unheard of in Kenya.

    “Many more farmers purchased tanks; only one tank out of almost 1,000 was repossessed,” reports Suri. “With a more consistent water supply, cows did not get dehydrated and were healthier. But the effects did not end there. We saw an increase in school enrollment for girls, as they no longer had to spend long days fetching water for the household.

    “Most of my ideas come from my travels through Africa,” she says. “It’s hard to imagine having that eureka moment sitting in my office staring at my laptop.”

    See the full article here .

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    MIT Seal

    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

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  • richardmitnick 8:23 pm on August 5, 2015 Permalink | Reply
    Tags: , , Rice   

    From Rice: “Cancer treatment models get real” 

    Rice U bloc

    Rice University

    August 5, 2015
    Mike Williams

    1
    Bone cancer cells populate the surface of a bioscaffold in an electron microscope image. Rice University scientists ran tests to show how realistic environments affect the growth of cancer tumors. The bioscaffolds were placed in a flow perfusion bioreactor to evaluate the cells’ response to the mechanical forces they experience in the body. Courtesy of the Mikos Research Group

    Researchers at Rice University and University of Texas MD Anderson Cancer Center have developed a way to mimic the conditions under which cancer tumors grow in bones.

    By placing cancer cells in a three-dimensional scaffold and subjecting them to the forces that push, pull and continually flow through the body, the researchers are better able to test the efficiency of cancer-fighting drugs.

    The scientists discovered that bone tumors exposed to normal forces express more of a protein, insulin-like growth factor-1 (IGF-1), than detected in static cultures. The IGF-1 signaling pathway plays a critical role in resistance to current chemotherapy. The experiments were performed in a custom-made bioreactor by the Rice lab of bioengineer Antonios Mikos in collaboration with the MD Anderson lab of Joseph Ludwig.

    The study detailed this week in the Proceedings of the National Academy of Sciences shows the value of incorporating mechanical forces when modeling tumors and treatments as opposed to analyzing tumor growth statically, said lead author Marco Santoro, a chemical and biomolecular engineering graduate student of Mikos.

    “Mechanical forces are present in our bodies even though we are not always aware of them,” he said. “Our cells are sensitive to the forces around them and change their behavior accordingly. Tumor cells behave the same way, changing their function depending on the forces they sense.”

    Mikos and his team specialize in materials and strategies for tissue engineering and regenerative medicine. As part of that work, they have created foam-like materials that serve as scaffolds for cells to inhabit and grow into as they become new bone or tissue.

    That material provided an opportunity for the latest experiments at Rice’s BioScience Research Collaborative on bone tumor samples called sarcomas provided by MD Anderson. Sarcoma tumors, also a focus of the Mikos lab, are most often found in the bones of adolescents and young adults.

    The researchers placed sarcoma cells in their porous, biologically inert scaffold and put the scaffold inside a flow perfusion bioreactor to mimic the stimulation those cells would experience amid the tissue inside real bone. They subjected the cells to biomechanical stimuli, including shear stress, by changing the fluid viscosity and flow rate.

    2
    Rice graduate student Marco Santoro led the study to test the spread of bone cancer cells in realistic environments. Photo by Jeff Fitlow

    Over 10 days they found the steady flow of fluid through the scaffold prompted the sarcoma cells to proliferate throughout the structure. The higher shear stress helped the cells significantly increase their production of the IGF-1 protein and also down-regulated the production of two other cancer-related proteins, c-KIT and HER2, compared with static tests.

    They also discovered that adjusting parameters in the bioreactor influenced the cells’ sensitivity to Dalotuzumab, a drug that disrupts the IGF-1 pathway. Higher shear stress appeared to decrease the drug’s effectiveness due to the associated increase in IGF-1 production.

    “For the first time, we showed how the effect of the drug changes according to the forces experienced by the cells,” Santoro said. “IGF-1 is crucial for this kind of sarcoma, which relies on this mechanism for growth. We show that the higher the mechanical stimulation, the more pronounced the secretion of this particular protein.”

    Mikos said the experiments should set a good example for cancer studies. “These experiments have to be tailored for each cancer, because the forces that cells experience vary in different parts of the body,” he said. “In the lungs, they wouldn’t be the same as in the bones. But they give researchers a far more realistic way to mimic the tumor’s local environment.”

    Co-authors of the paper are senior research scientist Salah-Eddine Lamhamedi-Cherradi and researcher Brian Menegaz, both at the University of Texas MD Anderson Cancer Center. Mikos is the Louis Calder Professor of Bioengineering and Chemical and Biomolecular Engineering at Rice. Ludwig is an associate professor of sarcoma medical oncology at MD Anderson.

    MD Anderson Cancer Center and the National Institutes of Health supported the research.

    See the full article here.

    Please help promote STEM in your local schools.

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    Rice U campus

    In his 1912 inaugural address, Rice University president Edgar Odell Lovett set forth an ambitious vision for a great research university in Houston, Texas; one dedicated to excellence across the range of human endeavor. With this bold beginning in mind, and with Rice’s centennial approaching, it is time to ask again what we aspire to in a dynamic and shrinking world in which education and the production of knowledge will play an even greater role. What shall our vision be for Rice as we prepare for its second century, and how ought we to advance over the next decade?

    This was the fundamental question posed in the Call to Conversation, a document released to the Rice community in summer 2005. The Call to Conversation asked us to reexamine many aspects of our enterprise, from our fundamental mission and aspirations to the manner in which we define and achieve excellence. It identified the pressures of a constantly changing and increasingly competitive landscape; it asked us to assess honestly Rice’s comparative strengths and weaknesses; and it called on us to define strategic priorities for the future, an effort that will be a focus of the next phase of this process.

     
  • richardmitnick 1:04 pm on July 28, 2015 Permalink | Reply
    Tags: , , , Rice   

    From PNNL: “Tiny grains of rice hold big promise for greenhouse gas reductions, bioenergy” 


    PNNL Lab

    July 28, 2015
    Dawn Zimmerman

    Rice serves as the staple food for more than half of the world’s population, but it’s also the one of the largest manmade sources of atmospheric methane, a potent greenhouse gas. Now, with the addition of a single gene, rice can be cultivated to emit virtually no methane from its paddies during growth. It also packs much more of the plant’s desired properties, such as starch for a richer food source and biomass for energy production, according to a study in Nature.

    1
    In addition to a near elimination of greenhouse gases associated with its growth, SUSIBA2 rice produces substantially more grains for a richer food source. The new strain is shown here (right) compared to the study’s control.
    Image courtesy of Swedish University of Agricultural Sciences

    With their warm, waterlogged soils, rice paddies contribute up to 17 percent of global methane emissions, the equivalent of about 100 million tons each year. While this represents a much smaller percentage of overall greenhouse gases than carbon dioxide, methane is about 20 times more effective at trapping heat. SUSIBA2 rice, as the new strain is dubbed, is the first high-starch, low-methane rice that could offer a significant and sustainable solution.

    Researchers created SUSIBA2 rice by introducing a single gene from barley into common rice, resulting in a plant that can better feed its grains, stems and leaves while starving off methane-producing microbes in the soil.

    The results, which appear in the July 30 print edition of Nature and online, represent a culmination of more than a decade of work by researchers in three countries, including Christer Jansson, director of plant sciences at the Department of Energy’s Pacific Northwest National Laboratory and EMSL, DOE’s Environmental Molecular Sciences Laboratory. Jansson and colleagues hypothesized the concept while at the Swedish University of Agricultural Sciences and carried out ongoing studies at the university and with colleagues at China’s Fujian Academy of Agricultural Sciences and Hunan Agricultural University.

    “The need to increase starch content and lower methane emissions from rice production is widely recognized, but the ability to do both simultaneously has eluded researchers,” Jansson said. “As the world’s population grows, so will rice production. And as the Earth warms, so will rice paddies, resulting in even more methane emissions. It’s an issue that must be addressed.”
    Channeling carbon

    During photosynthesis, carbon dioxide is absorbed and converts to sugars to feed or be stored in various parts of the plant. Researchers have long sought to better understand and control this process to coax out desired characteristics of the plant. Funneling more carbon to the seeds in rice results in a plumper, starchier grain. Similarly, carbon and resulting sugars channeled to stems and leaves increases their mass and creates more plant biomass, a bioenergy feedstock.

    In early work in Sweden, Jansson and his team investigated how distribution of sugars in plants could be controlled by a special protein called a transcription factor, which binds to certain genes and turns them on or off.

    “By controlling where the transcription factor is produced, we can then dictate where in a plant the carbon — and resulting sugars — accumulate,” Jansson said.

    To narrow down the mass of gene contenders, the team started with grains of barley that were high in starch, then identified genes within that were highly active. The activity of each gene then was analyzed in an attempt to find the specific transcription factor responsible for regulating the conversion of sugar to starch in the above-ground portions of the plant, primarily the grains.

    The master plan

    Upon discovery of the transcription factor SUSIBA2, for SUgar SIgnaling in BArley 2, further investigation revealed it was a type known as a master regulator. Master regulators control several genes and processes in metabolic or regulatory pathways. As such, SUSIBA2 had the ability to direct the majority of carbon to the grains and leaves, and essentially cut off the supply to the roots and soil where certain microbes consume and convert it to methane.

    Researchers introduced SUSIBA2 into a common variety of rice and tested its performance against a non-modified version of the same strain. Over three years of field studies in China, researchers consistently demonstrated that SUSIBA2 delivered increased crop yields and a near elimination of methane emissions.

    Next steps

    Jansson will continue his work with SUSIBA2 this fall to further investigate the mechanisms involved with the allocation of carbon using mass spectrometry and imaging capabilities at EMSL. Jansson and collaborators also want to analyze how roots and microbial communities interact to gain a more holistic understanding of any impacts a decrease in methane-producing bacteria may have.

    Funding for this research was provided by The Swedish University of Agricultural Sciences, the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, the National Natural Science Foundation of China and the Carl Tryggers Foundation.

    See the full article here.

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    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

    i1

     
  • richardmitnick 2:41 pm on July 24, 2015 Permalink | Reply
    Tags: , , Rice   

    From LBL: “Unlocking the Rice Immune System” 

    Berkeley Logo

    Berkeley Lab

    July 24, 2015
    Lynn Yarris (510) 486-5375

    1
    Rice is a staple for half the world’s population and the model plant for grass-type biofuel feedstocks (Photo by Roy Kaltschmidt, Berkeley Lab

    A bacterial signal that when recognized by rice plants enables the plants to resist a devastating blight disease has been identified by a multi-national team of researchers led by scientists with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) and the University of California (UC) Davis.

    The research team discovered that a tyrosine-sulfated bacterial protein called “RaxX,” activates the rice immune receptor protein called “XA21.” This activation triggers an immune response against Xanthomonas oryzaepv.oryzae (Xoo), a pathogen that causes bacterial blight, a serious disease of rice crops.

    “Our results show that RaxX, a small, previously undescribed bacterial protein, is required for activation of XA21-mediated immunity to Xoo,” says Pamela Ronald, a plant geneticist for both JBEI and UC Davis who led this study. “XA21 can detect RaxX and quickly mobilize its defenses to mount a potent immune response against Xoo. Rice plants that do not carry the XA21 immune receptor or other related immune receptors are virtually defenseless against bacterial blight.”

    Ronald, who directs JBEI’s grass genetics program and is a professor in the UC Davis Department of Plant Pathology, is one of two corresponding authors of a paper describing this research in Science Advances, along with Benjamin Schwessinger, a grass geneticist with JBEI’s Feedstocks Division at the time of this study and now with the Australian National University. The paper is titled The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium. (See end of story for a complete list of authors.)

    2
    Pamela Ronald is a leading authority on plant genetics who holds joint appointments with the Joint BioEnergy Institute and the University of California at Davis. (Photo by John Stumbos, UC Davis)

    Rice is a staple food for half the world’s population and a model plant for perennial grasses, such as Miscanthus and switchgrass, which are prime feedstock candidates for the production of clean, green and renewable cellulosic biofuels. Just as bacterial blight poses a major threat to rice crops, bacterial infections of grass-type fuel plants could present major problems for the future production of advanced biofuels. However, the mechanisms by which bacteria infect such grasses is poorly understood.

    “Pathogens of grass-type biofuel crops that would reduce the yield of fuel-producing biomass likely use similar infection mechanisms to Xoo,” says Schwessinger. “Having identified the activator of XA21, we will be able to study the rice immune system in far greater detail than ever before. As rice is the model for grass-type biofuel feedstocks, this might help in the future engineering of more disease-resistant grass-type biofuel crops.”

    Most plants and many animals can only defend themselves against a given disease if they carry specialized immune receptors that sense the invading pathogen behind the disease. In 2009, Ronald and her group identified a small bacterial protein they named “Ax21” as the molecular key that binds to the XA21 receptor to activate a rice plant’s immune response. Diligent follow-up research by her group led to Ronald retracting these results and continuing the search for the true key.

    “We were ecstatic with our results in 2009 because identifying the molecule that XA21 recognizes provides an important piece to the puzzle of how the rice plant is able to respond to infection,” Ronald says, “but then it was back to the drawing board. Now we have the real XA21 activator.”

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    Benjamin Schwessinger and Rory Pruitt were co-lead authors of a Science Advances paper that described the identification of a bacterial signaling molecule which triggers immunity response in rice. (Photo by Daniel Caddell)

    To uncover the true XA21 activator, Ronald and her collaborators studied mutations around an operon known as “RaxSTAB.” Operons are small groups of genes with related functions that are co-transcribed in a single strand of messenger RNA.

    “We hypothesized that the activator of XA21 might be encoded in the proximity of the molecular machinery that we already knew was involved in production of the activator,” says Rory Pruitt, a member of Ronald’s research group and a co-lead author with Schwessinger of the Science Advances paper. “One of these bacterial mutants had a deletion of a then unknown gene, now called raxX.”

    Adds Schwessinger, “When we looked more closely in this operon region we identified raxX as a potentially expressed gene. This small gene stuck out as it was very well conserved in other Xanthomonas that encode RaxSTAB but not conserved in any other bacteria that miss this operon.”

    In addition to its implications for future grass-type biofuel feedstocks, the revelation of RaxX as the bacterial molecule that triggers the XA21-mediated immune response also holds important implications for the worldwide supply of rice. The research team has shown that a number of strains of the blight bacteria can evade XA21-mediated immunity because they encode a variant of raxX alleles.

    “Like prescribing the best vaccination for the flu each season by monitoring which flu strains are going to be the most prevalent, it should be possible to screen wild Xoo populations in the rice-growing regions of Asia and Africa for whether they encode RaxX alleles that are recognized by XA21,” says Schwessinger. “We can then inform farmers which rice varieties will be resistant to those bacterial populations.”

    Schwessinger also notes that several major human diseases involve tyrosine-sulfated proteins, including HIV. However the precise role of tyrosine sulfation in receptor binding and cell invasion is not understood.

    “Understanding the RaxX/XA21 ligand-receptor pair might help medical researchers better understand the role of tyrosine sulfation for receptor binding in human disease,” Schwessinger says. “This could lead to the development of novel components that block the binding of specific tyrosine-sulfated proteins.”

    This research was supported by both the DOE Office of Science, the National Institutes of Health, and the Human Frontier Science Program.

    In addition to Ronald, Schwessinger and Pruitt, other co-authors of the Science Advances paper were Anna Joe, Nicholas Thomas, Furong Liu, Markus Albert, Michelle Robinson, Leanne Chan, Dee Dee Luu, Huamin Chen, Ofir Bahar, Arsalan Daudi, David De Vleesschauwer, Daniel Caddell,Weiguo Zhang, Xiuxiang Zhao, Xiang Li, Joshua Heazlewood, Deling Ruan, Dipali Majumder, Mawsheng Chern, Hubert Kalbacher, Samriti Midha, Prabhu Patil, Ramesh Sonti, Christopher Petzold, Chang Liu, Jennifer Brodbelt and Georg Felix.

    See the full article here.

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