Climate change accelerates maturing of grape in wine production

                             Johann Martínez-Lüscher , Nafarroako Unibertsitatea

The increase in temperatures and of CO2 levels – the consequences of climate change – accelerates the maturing of grapes in wine production, affecting colour and possibly aromas”. This was the conclusion of the PhD thesis defended by Johann Martínez-Lüscher, undertaken jointly by the University of Navarra and the University of Bordeaux.

The biologist explained that if the forecasts by the Intergovernmental Panel on Climate Change of a level of 700ppm of carbon dioxide and a temperature increase of 4ºC are proved correct, “the accumulation of sugars could be so rapid that the rest of these processes that depend on this will not be capable of keeping up. This will mean that, on comparing grapes with the same concentration of sugars or degree of alcohol, the crops under climate change conditions will have poorer colouration and this will be noticed in the wine”.

In fact, “it is increasingly more frequent to find wines with a higher alcoholic degree due to the over maturing of the grape”. Nonetheless, in the framework of climate change, the consequences can vary. “For example, the changes in levels of ultraviolet radiation or the decrease in rainfall may have antagonistic effects to those caused by an increase in temperature or CO2 levels. Thus, there are many unknowns about what the future holds”, he added.

Wine in a new scenario

In this way wine production will have to find solutions in order to confront environmental challenges. “The use of slower maturing ‘clones’ (sub-varieties) could be one of the possible strategies. It would also be very tempting to substitute the varieties planted in each location by others better adapted to warmer climates, but this would to a great extent mean giving up the typical characteristics of each variety of our wines – something unthinkable to date”.

Nevertheless, as this expert pointed out, climate change can provide new opportunities: for example, the production of a type of wine in cooler climes where it was not possible before. “This is the case of the incipient wine industry in the United Kingdom where I intend to continue working”, stated the researcher.

Mr. Martínez-Lüscher’s research has been financed by the University of Navarra, the Navarre-Aquitane Cross-Border Cooperation Programme, the Spanish Ministry of Science and Innovation, and the 7th European Union Framework Programme.

Source: Elhuyar Fundazioa

Drug combo supresses growth of late-stage prostate cancer turmors

By Natalie van Hoose

Low doses of metformin, a widely used diabetes medication, and a gene inhibitor known as BI2536 can successfully halt the growth of late-stage prostate cancer tumors, a Purdue University study finds.

Prostate cancer causes the second-highest number of cancer-related deaths in men in the U.S., and methods of treating advanced prostate cancer are limited.

Xiaoqi Liu (pronounced zhow-CHEE' LEE'-oo), associate professor of biochemistry and cancer research, and fellow researchers found that the drugs metformin and BI2536 can work together to suppress the spread of prostate cancer that resists all other available treatments, potentially prolonging patients' lives.

"We've found a promising way to treat late-stage prostate cancer," Liu said. "By combining low levels of two well-tolerated drugs, the progression of this disease could be significantly delayed. Completely curing the cancer at the advanced stage is pretty much impossible, but this treatment might manage it for a while - that's exciting."

A number of treatments exist for the earlier stages of prostate cancer, which grows slowly compared with many other cancers. Because prostate cancer cells need the male sex hormone androgen to develop, one way to treat the disease is to suppress androgen - a process known as castration. If the cancer continues to spread, the patient often undergoes chemotherapy. As a last resort, drugs that block the synthesis of androgen by prostate cancer cells can be used, but these medications only extend a patient's lifespan for several months.

New approaches to treating the most persistent forms of prostate cancer are "urgently needed," Liu said.

Adding to the challenge is the fact that castration treatment can inadvertently encourage the cancer to get tougher. It can heighten oxidative stress on the prostate gland, which increases the expression of Plk1, a gene that has been linked to many cancers. Over-expression of Plk1 can also trigger the synthesis of androgen.

"The goal of castration is to block androgen synthesis," Liu said. "But cancer cells eventually become 'smart' enough to make androgen anyhow, which is why the cancer continues to grow."

Additionally, castration can disrupt the body's metabolism and lead to insulin resistance, which also can stimulate the production of androgen. The cancer will spread until both of these side effects are stopped, Liu said.

Previous studies showed that metformin - an inexpensive, antidiabetic drug that has been commonly used for more than 40 years - is particularly potent to prostate cancer tumors.

Working with fellow researchers from Purdue, the University of Wisconsin-Madison and the Indiana University School of Medicine, Liu found that a combination of low levels of metformin and BI2536, a drug that stifles the activity of Plk1, could work in tandem to slow the growth of prostate tumors too advanced for current treatments by promoting the self-destruction of cancer cells and preventing androgen synthesis.

The drugs did not impact healthy prostate cells, a "key finding," Liu said. "Ideally, cancer therapy will have minimal effects on normal cells."

Because metformin helps regulate metabolism, it may reverse some of the metabolic damage caused by castration, he said.

The researchers tested the drugs in a classical cell culture assay of prostate cancer cells and in advanced prostate tumors in mice. Low concentrations of the drugs significantly slowed the development of cancer in both trials. The mice tumors were grown from the tumor cells of a late-stage prostate cancer patient, suggesting that the treatment would prove effective in humans.

"Those results were amazing," Liu said. "These are the first data we've generated from a real patient, so I was almost jumping in the air when I saw that it worked."

Liu said that the next step in the research is to test the combination of drugs in clinical trials. Further research is also needed to understand the underlying mechanism of metformin and why it is effective at suppressing prostate cancer

Source: Purdue Univesity

Together, humans and computers can figure out plant world

A Web-based system was built for palynologists to interact with stored data and search for pollen images. This screen shows search capabilities by morphology semantics. From Han et al., part of the special issue 'Bioinformatic and Biometric Methods in Plant Morphology' in Applications in Plant Sciences. Credit: Image credit Han et al. Han, J. G., H. Cao, A. Barb, S. W. Punyasena, C. Jaramillo, and C.-R. Shyu. 2014. A neotropical Miocene pollen database employing image-based search and semantic modeling. Applications in Plant Sciences 2(8): 1400030. doi:10.3732/apps.1400030.

As technology advances, science has become increasingly about data -- how to gather it, organize it, and analyze it. The creation of key databases to analyze and share data lies at the heart of bioinformatics, or the collection, classification, storage, and analysis of biochemical and biological information using computers and software. The tools and methods used in bioinformatics have been instrumental in the development of fields such as molecular genetics and genomics. But, in the plant sciences, bioinformatics and biometrics are employed in all fields -- not just genomics -- to enable researchers to grapple with the rich and varied data sources at their disposal.

In July 2013, Surangi Punyasena of the University of Illinois at Urbana-Champaign and Selena Smith of the University of Michigan organized a special session at Botany 2013, the annual meeting of the Botanical Society of America in New Orleans, Louisiana. They invited plant morphologists, systematists, and paleobotanists, as well as computer scientists, applied mathematicians, and informaticians -- all of whom were united in their interest in developing or applying novel biometric or bioinformatic methods to the form and function of plants. The goal: to provide a forum for a cross-disciplinary exchange of ideas and methods on the theme of the quantitative analysis of plant morphology.

As Punyasena explains, "The quantitative analysis of morphology is the next frontier of bioinformatics. Humans are very good at learning to recognize shape and texture, but there are many problems where accuracy and consistency are difficult to achieve with only expert-derived, qualitative data, and in many fields there are often a limited number of experts trained in these visual assessments."

The results of that session, along with invited papers, are published in the August issue of Applications in Plant Sciences as a special issue on Bioinformatic and Biometric Methods in Plant Morphology. Morphology is, of course, the study of form, and form as represented in this collection of articles has a broad scope -- from microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems. The methods presented in the issue, both recent and emerging, are varied as well, including automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment.

Three articles in the issue look at the application of biometric and bioinformatic methods in palynology: Han et al. (2014) introduce an online Miocene pollen database with semantic image search capabilities; Holt and Bebbington (2014) test the applications of an automated pollen classifier; and Mander et al. (2014) analyze differences in human and automated classification of grass pollen based on surface textures. Other papers highlight how biometric and bioinformatic methods apply to plants more broadly, including using skeleton networks to examine plant morphology such as roots (Bucksch, 2014), improving the quantification of geometric leaf shape metrics with a new protocol to measure leaf circularity (Krieger, 2014), comparing human and automated methods of quantifying aspects of leaf venation (Green et al., 2014), and applying morphometrics to charcoalified plant remains (Crawford and Belcher, 2014).

Taken as a whole, the issue presents a compelling argument for the importance of both computational and morphometric approaches.

"I think that there's been a renaissance in morphometric approaches," notes Punyasena. 

"New techniques are using easy access to high-quality digital imaging, powerful computers, and advances in computational analyses like machine learning to rethink the way we gather and analyze morphological data."

As advances in technology allow researchers to gather more and more morphological and image-based data, it has become increasingly important to be able to analyze and interpret those data quickly, accurately, consistently, and objectively. Biometric and bioinformatic methods make this possible, and reveal the potential of data collected from the shape and form of plants to be as rich of a data source as genetic data.

Access to specific articles can be found online at: http://www.bioone.org/toc/apps/2/8

Source: American Journal of Botany

Plants return to Earth after growing in space

Astronaut Reid Wiseman injected a fixative solution onto the seedlings. Credit: NASA

Researchers at Simon Gilroy's lab in the Department of Botany at the University of Wisconsin-Madison this afternoon greeted a truck carrying small containers holding more than 1,000 frozen plants that germinated and grew aboard the International Space Station.

On Tuesday, when Gilroy's team inspected the plants at the Kennedy Space Center in Florida, they saw exactly what they wanted: Petri dishes holding seedlings that sprouted and grew in weightlessness.

After their arrival in Madison, the plants went directly into a deep freeze. After being thawed in a few months, they will donate their RNA to an instrument that will measure the activity of all of their approximately 30,000 genes.

Half of the plants will become subjects in Gilroy's longstanding exploration of the genetic control of the proteins that enable plants to grow in zero gravity. "Gravity is a fantastically pervasive force that affects all biology," says Gilroy. "One astronaut observed that plants get lazy in a weightless environment; they grow long and thin, and don't lay down strong material, just like people lose bone mass in space because it isn't needed for supporting weight."

The other half of the experiment represents a departure for Gilroy, and for NASA, the agency supporting this area of space research. After these plants undergo a similar genetic analysis at UW-Madison's Biotech Center, the data will get an initial check-over from Gilroy's group. And then a treasure trove of digital data on plant genetic activity in microgravity will be made available to any researcher interested in mining it.

"Access to space is very rare," Gilroy says. "Traditionally, a research group will put an experiment in space, get the results and publish. But NASA is trying a new mode, called geneLAB, where the research group will put organisms in space, then, as soon as possible, release the raw data to anyone who wants to analyze it. They hope it will speed up major advances on these tiny samples that we can afford to place in space. I see this as open-source science."

Through the process called transcription, genes produce RNA that becomes the template for proteins, and in both sets of experiments, the RNA data will show which genes become more or less active in microgravity, when compared to an identical set of plants grown on Earth.

While Gilroy plans to focus on structural proteins, the geneLAB experiment compares four variants of Arabidopsis called ecotypes. "This data should provide a broad field of investigation -- far more than one lab can handle," Gilroy says. "We are going to end up with an enormous amount of transcription data. We will do some initial work to check the major genes which go up or down, but there's tremendous potential for further analysis by other labs around the world."

But while the geneLab approach sounds promising, Gilroy concedes that it carries no guarantees. "This may be a path forward in crowd-sourcing science. At the least, as a single lab we could never analyze this data as fully as many labs around the world all working with it."

The "Biological Research in Canister" containers that held these experiments on board the space station were designed, tested and operated according to NASA's rigorous approach, Gilroy says. "Each project represents an enormous investment, and you really want everything to go perfectly. You become one of the most careful scientists in the world. You test everything, make duplicates, and are always considering what may go wrong so you can do another test."

NASA is an unfamiliar world to most botanists, but Gilroy seems to be enjoying every step of the way, and has even learned the organization's peculiar parlance. "At first, talking in acronyms is very strange," he says, "and you can't understand anything when NASA people start going into NASA-speak. But once you get into it, you catch yourself doing the exact same thing."

In the microgravity experiments, Gilroy is exploring the genetic basis of a phenomenon known to gardeners and horticulturalists for many years. Plants that grow up without mechanical stresses -- due to wind, rain or other disturbances -- "are much more susceptible to pests, are not as robust," Gilroy says, "but if you go into a greenhouse and shake the plants, they grow up more compact, strong, and resistant to stress. They are even more resistant to plant diseases."

It turns out that the same signaling system used to detect mechanical stresses like gravity is also used to defend against pathogens. That may explain why plants in space appear more susceptible to disease.

That overlap raises the stakes for understanding the impact of gravity on plants beyond the notion of building stronger crops that can stand up in the field. Understanding the signals could help in the never ending battle against plant disease.

Likewise, NASA has its own practical interest in the research: Plants will supply food and oxygen for long-distance space travel, and keeping them healthy will be a matter of life and death. "If you are growing plants as part of a human life support system," Gilroy says, "you'd rather not have them suddenly die."

Source: University of Wisconsin-Madison

Father-son research team discovers cheatgrass seeds survive wash cycle

Professor Hugh Lefcort and son Caleb examine the cheatgrass in Spokane, Washington. Credit: Gonzaga University

Not many sixth-graders can say they have been published in an academic journal, but Caleb Lefcort can cross that distinction off his list. Caleb got into a discussion with his father, Hugh Lefcort, professor of biology at Gonzaga University, as to whether the seed burrs from cheatgrass would survive the laundry cycle. Hugh believed the seeds would not survive. Instead of simply taking his father's word for it, Caleb -- who was in fourth grade at the time -- suggested the scientific method: an experiment.

The father and son duo set out to determine whether the seeds would survive the wash.
The experiment

Finding cheatgrass seeds was easy. Bromus tectorum (the scientific name for cheatgrass) is nearly ubiquitous in the Inland Northwest and has become an increasing concern throughout North America -- spreading rapidly through the western United States both through natural means and unintended ways, like getting stuck in people's socks and shoes.

"We hypothesized that laundering would impact water potential, and we, therefore, predicted that seeds would exhibit poorer germination and emergence after being laundered," said Hugh. "We also predicted that the effect of laundering would be stronger if bleach was used."

To collect the cheatgrass seeds, Hugh and Caleb walked through a nearby field wearing only socks on their feet. They divided the socks into three different treatments: 1. Not washed or dried; 2. Washed with detergent but not bleach and subsequently dried; and 3. Washed with detergent and bleach and then dried.

The socks that were to be laundered were divided into three different washing machines/detergent/dryer combinations:
1. A Whirlpool washing machine using All brand detergent and Whirlpool dryer;
2. A Samsung washer using Tide brand detergent and a General Electric dryer; and
3. A Maytag machine using Era brand detergent and a Maytag dryer.

Findings

The results of the experiment surprised both Hugh and Caleb.

"There was no significant effect of the different washing machines and their associated laundry detergents and dryers on the number of seeds that sprouted, nor did we find a significant effect of laundry treatments in the number of seeds that germinated," said Hugh.

There was, however, an effect on the seeds that were treated with bleach; they germinated at a slightly slower rate than the other seeds that were tested without bleach. The height of the plants that sprouted from these bleached seeds differed from the height of the plants that experienced the no-bleach-wash treatment.

The research that Hugh and Caleb conducted revealed that cheatgrass seeds and their germination processes are sturdy enough to survive the soaking, soap and agitation of washing machines, the heat of dryers, and often even bleach. Though they designed the study to make it difficult for cheatgrass seeds to germinate, they were surprised at how easily the treated seeds sprouted into plants. Government agencies may consider adding these findings to their public service announcements.

Caleb Lefcort is now a sixth-grader Moran Prairie Elementary School.

Source: Gonzaga University

'Probiotics' for plants boost detox abilities; untreated plants overdose and die

The Doty lab conducts work to see how plants treated with naturally occurring endophytes might handle soils contaminated with a variety of pollutants. Graduate student Robert Tournay, for example, is interested in how the plants handle arsenic. Credit: M Levin/U of Washington

Scientists using a microbe that occurs naturally in eastern cottonwood trees have boosted the ability of two other plants -- willow and lawn grass -- to withstand the withering effects of the nasty industrial pollutant phenanthrene and take up 25 to 40 percent more of the pollutant than untreated plants.

The approach could avoid the regulatory hurdles imposed on transgenic plants -- plants with genes inserted from or exchanged with other plant or animal species -- that have shown promise in phytoremediation, the process of using plants to remove toxins from contaminated sites, according to Sharon Doty, associate professor of environmental and forestry sciences and corresponding author on a paper about the new work in Environmental Science & Technology.

"Our approach is much like when humans take probiotic pills or eat yogurt with probiotics to supplement the 'good' microbes in their guts," she said.

The microbe from the cottonwood was encouraged to colonize the roots of willows simply by dipping rooted and trimmed cuttings in solutions with the microbe. Grasses were treated with microbes in solution as seeds sprouted in soil. Once integrated into the plants, the microbe supplemented their own microbial defenses.

Microbes that take up residence in the inner tissue of plants and don't cause negative symptoms are called endophytes. In nature, endophytes have a welcomed, symbiotic relationship with plants. In polluted soil, for instance, if the right endophytes are present they consume toxins coming up through plant roots. The endophytes get fed and the plant gets help neutralizing pollutants that could kill it.

That's been one challenge of phytoremediation: plants removing pollutants can, all too quickly, succumb to the toxins.

"When the endophyte in these experiments was given to willow and grasses, it reduced the phytotoxic effects of phenanthrene compared to the control plants that did not receive the endophyte and died," said lead author Zareen Khan, a UW research scientist in environmental and forest sciences.

Phenanthrene is carcinogenic, on the Environmental Protection Agency's priority pollutants list and belongs to a class of polycyclic aromatic hydrocarbons that get deposited into the environment via fossil fuel combustion, waste incineration or as byproducts of industrial processes. Soils that become contaminated can be capped with layers of uncontaminated soil or dug up and removed for cleaning at soil remediation facilities or storage at waste disposal facilities.

In their search, UW researchers tested six different endophytes from cottonwood and willow varieties and found one -- lab name PD1 -- from the eastern cottonwood to be superior at breaking down phenanthrene.

They introduced this endophyte into willow cuttings and lawn grass. Willows were chosen because some varieties have already proven adept at removing toxins and the shrubs have extensive root systems, take up a lot of water and grow rapidly. Lawn grass was included because it also grows fast and could be useful in parks and open-space areas.

In lab experiments, the willow cuttings with added endophyte protection continued to grow, kept their leaves and had denser root systems. Untreated plants wilted, lost leaves and their roots turned brown. When soils were analyzed, the treated willows took up 65 percent of the phenanthrene compared with untreated plants that removed 40 percent, an improvement of 25 percent.

Grass seed planted in contaminated soils and watered with solutions containing the PD1 endophyte germinated five days quicker, grew taller and had 100 more tillers, or new offshoots, after 13 days. Treated grass removed 50 percent of the phenanthrene from the soil, compared with untreated grass that removed 10 percent, an improvement of 40 percent.

In phytoremediation, plants that take up pollutants but don't degrade them have to be removed and treated as hazardous waste or otherwise disposed of safely. The willows treated in the UW experiment appear to have degraded some 90 percent of the phenanthrene to harmless components. The researchers said they'd like to determine if that promising finding holds up in mass-balance studies and want to examine the possible effects on bugs or animals that might bite the plants processing the toxins and other environmental considerations. Interestingly, other studies have shown that bugs can smell similar semi-volatile pollutants and avoid eating the plants containing them, Doty said.

The work was funded by a Small Business Innovation Research grant from the National Institute of Environmental Health Sciences and by funds provided through the Byron and Alice Lockwood Endowed Professorship that Doty holds. The other four co-authors on the paper were undergraduate volunteers: David Roman and Trent Kintz have since graduated while May delas Alas and Raymond Yap are still working on their bachelor's degrees.
Just down the road from UW is Seattle's Gas Works Park, a site Doty thinks is a prime candidate for the approach her lab reported. Contaminants in the soil, including phenanthrene, are from a now-dismantled gasification plant. Soils have been covered with uncontaminated soil.

"The idea of leaving a known carcinogen in a public place is not right," she said. "What about problems of erosion? We should do what we can to remove it. We spend so much money treating cancer, I'd like us to take steps to prevent it instead."

Source: University of Washington

Potential biological control for avocado-ravaging disease

University of Florida scientists think they’ve found the first potential biological control strategy against laurel wilt, a disease that threatens Florida’s avocado industry. The redbay ambrosia beetle, see here, bores holes into avocado trees, bringing the disease that causes laurel wilt. Credit: Lyle Buss, UF/IFAS

University of Florida scientists believe they've found what could be the first biological control strategy against laurel wilt, a disease that threatens the state's $54 million-a-year avocado industry.

Red ambrosia beetles bore holes into healthy avocado trees, bringing with them the pathogen that causes laurel wilt. Growers control the beetles that carry and spread laurel wilt by spraying insecticides on the trees, said Daniel Carrillo, an entomology research assistant professor at the Tropical Research and Education Center in Homestead.

But a team of researchers from the Tropical REC and the Indian River Research and Education Center in Fort Pierce have identified a potential biological control to use against redbay ambrosia beetles that could help growers use less insecticide.

First, they exposed beetles to three commercially available fungi, and all of the beetles died. Then they sprayed the fungi on avocado tree trunks, and beetles got infected while boring into the trunk. About 75 percent of those beetles died, said Carrillo, an Institute of Food and Agricultural Sciences faculty member.

Ideally, the fungal treatments could prevent beetles from boring into the trees, eliminating the risk that the pathogen would enter the trees, the study said. But tests showed female beetles bored into the trees and built tunnels regardless of the treatment. Still, researchers say their treatment can prevent the female beetles from laying eggs.

UF/IFAS scientists don't know yet how much less chemical spray will be needed to control the redbay ambrosia beetle. But Carrillo sees this study as the first step toward controlling the beetle in a sustainable way.

"When you want to manage a pest, you want an integrated pest management approach," Carrillo said. "This provides an alternative that we would use in combination with chemical control."

The redbay ambrosia beetle -- native to India, Japan, Myanmar and Taiwan -- was first detected in 2002 in southeast Georgia. It was presumably introduced in wood crates and pallets, and its rapid spread has killed 6,000 avocado trees in Florida, or about 1 percent of the 655,000 commercial trees in Florida. The beetle was first discovered in South Florida in 2010.

Most American-grown avocados come from California, with the rest coming from Florida and Hawaii. The domestic avocado market is worth $429 million, according to Edward Evans, a UF associate professor of food and resource economics, also at the Tropical REC. Florida's avocados are valued at about $23 million, or about 5 percent of the national market.

The redbay ambrosia beetle is not an issue with California avocados, so the new tactic found by Florida scientists wouldn't apply to this pest in the Golden State, said Mark Hoddle, a biological control Extension specialist with the University of California-Riverside. Hoddle studies biological pest control for California avocados. Scientists there are exploring ways to control a different ambrosia beetle, he said, and bug-killing fungi may be useful for the new California pest.

More than 95 percent of Florida's commercial avocados grow in Miami-Dade County, although many Floridians have avocado trees in their yard.
The redbay ambrosia beetle feeds and reproduces on a very wide variety of host plants, native oaks, sycamores, and of course it is very detrimental to avocados.

Source:University of Florida Institute of Food and Agricultural Sciences

Tree diseases can help forests

A healthy seedling of the tree Castilla elastica is on the left, while a dying seedling, attacked by a plant pathogen, is on the right. A study in the Journal of Ecology by University of Utah biologists shows that such tree diseases, while killing individual seedlings, can increase forest biodiversity. Credit: Erin Spear, University of Utah.

Plant diseases attack trees and crops and can hurt lumber and food production, but University of Utah biologists found that pathogens that kill tree seedlings actually can make forests more diverse.

While low rainfall has been blamed for a lack of drought-sensitive trees near the Pacific side of the Panama Canal, the new study answers a mystery about what keeps drought-tolerant trees from that area from living along the wetter Caribbean side of the canal. The answer: disease-causing plant pathogens, the researchers report in their study, published online Wednesday, Nov. 12 by the Journal of Ecology.

"Because seedlings of disease-sensitive tree species can't survive in the wetter forests and drought-sensitive tree species cannot survive in the drier forests, different tree species inhabit the wetter and drier forests even though they are only 30 miles apart" in Panama, says Phyllis Coley, a senior author of the study and a distinguished professor of biology.
In other words, tree pathogens contribute to the staggering diversity of trees in Panama's tropical forests, she adds.

The study's first author, biology doctoral student Erin Spear, says that is important because "conservation planning and predictions about how tree species distributions may shift with climate change require an understanding of the factors currently influencing where species can and cannot survive."

That is particularly important in tropical forests and other forests that are under elevated threat of deforestation.

Funding for the study came from Sigma Xi -- The Scientific Research Society, the Smithsonian Institution and the National Science Foundation.

Of Forests and Pathogens

Tropical forests are threatened, and dry tropical forests are even more threatened because sunnier, drier climates are better for growing crops and are favored by people. Some 90 percent of Panama's residents live on the nation's drier Pacific slope.

Forests are essential for feeding and sheltering animals, providing important medicines, storing carbon and water, and reducing erosion by holding soil in place. These functions are influenced by different species inhabiting a forest, so it is essential to understand why certain tree species can survive in certain areas but not others.

Panama's forests also are important economically because tree roots limit how much soil erodes into the Panama Canal, ensuring that huge container ships can pass. Researchers also believe the forests help maintain water levels in the canal because forest soil stores water, slowly releasing it into streams feeding the canal during the dry season.

Diversity is high in tropical forests. A 930-square-mile area bordering the Panama Canal has more than 800 tree species. By comparison, about half the state of Rhode Island -- or some 610 square miles -- is forested, and that area has only 51 tree species.

Part of the reason Panama's forests have more species is because the Pacific end of the canal receives less annual rainfall -- about 5.9 feet -- than the Caribbean end, where 9.8 feet of rain falls annually.

"While there is considerable evidence that less rain in the drier, Pacific forests means that drought-sensitive tree species can't survive there, it has been unclear what prevents the drought-tolerant species of the drier forests from living in the wetter forests," says University of Utah biology professor Tom Kursar, the study's other senior author. "Our study tackled that unanswered question."

So Spear braved mud, rain, insects and snakes to monitor seedlings of a variety of tree species in the wetter and drier forests of central Panama for pathogen-caused damage and death. Plant pathogens that make plants sick include bacteria, viruses and fungi.

Spear says the researchers' findings suggest that "all seedlings are at a greater risk of being injured and killed by pathogens in the wetter forests than in the drier forests." This could be because the damp environment of the wetter forests helps pathogens survive, and more rainfall helps pathogens move from one seedling to another.

But that's only half the story. Coley says that their study indicates "pathogens are implicated in the absence of the dry-forest tree species from the wetter forests, where they might otherwise be able to live. That is because dry-forest tree species are more likely to die from pathogen attack than wet-forest species."

Diagnosing Sick Seedlings

Spear collected the seeds for the study by hiking for miles, kayaking in the canal to collect fruit from overhanging branches, and even riding a crane-carried gondola more than 100 feet upward into the forest canopy.

She conducted the study at two forest sites in central Panama: one at the large Metropolitan Natural Park in Panama City on the drier Pacific side, and one on private property in the Santa Rita Ridge area on the wetter Caribbean side. She planted "gardens" of tree seeds -- including species typical of wetter and drier forests -- in 30 locations at each site. More than 1,000 seeds were planted; 725 of them sprouted.

Once the seeds were planted, the researchers covered them with wire mesh to protect the seeds and seedlings from being crushed by tree branches or eaten by animals.

Spear visited both sites weekly and took notes on the 725 seedlings. Weekly visits were essential because, diseased seedlings can be dead and decomposing within days.

"We monitored when the seeds germinated, the occurrence of and date when symptoms of pathogen attack were observed, if and when a seedling died, and we ascribed a cause of death," Spear says. Pathogen symptoms included patches of black, dead tissue in the leaves or stem. "In some cases, we could actually see the pathogen growing on the seedling," she says.

Of the 725 seedlings that germinated, 38 percent suffered pathogen-caused damage, including 11 percent of seedlings killed by pathogens.

Compared with seedlings in the drier forest, seedlings in the wetter forest were 74 percent more likely to suffer pathogen-caused damage and 65 percent more likely to be killed by pathogens.

"But what was really striking was that pathogen-caused damage was five times more likely to be lethal for seedlings of dry-forest species than for wet-forest species," suggesting dry- and wet-forest species differ in their ability to halt or slow infection, Spear says.

The researchers next plan to identify specific fungi, bacteria and other pathogens and whether they differ in wetter and drier forests.

During her study at the drier park site in Panama City, Spear discussed her research with tourists and other park visitors.

"I'd emerge from the tangles of vines sweaty, muddy and generally disheveled and people couldn't help but ask what I was doing," Spear recalls. "It was heartening to hear how the forest had touched these very different people."

A brief time-lapse video of a seedling dying from pathogen attack during a period of several days can be seen at: http://vimeo.com/58026978 Video by Erin Spear, University of Utah.


Source: University of Utah

Flu virus key machine: First complete view of structure revealed

The complete structure allows researchers to understand how the polymerase uses host cell RNA (red) to kick-start the production of viral messenger RNA. Credit: © EMBL/P.Riedinger

Scientists looking to understand -- and potentially thwart -- the influenza virus now have a much more encompassing view, thanks to the first complete structure of one of the flu virus' key machines. The structure, obtained by scientists at EMBL Grenoble, allows researchers to finally understand how the machine works as a whole, and could prove instrumental in designing new drugs to treat serious flu infections and combat flu pandemics.

If you planned to sabotage a factory, a recon trip through the premises would probably be much more useful than just peeping in at the windows. Scientists looking to understand -- and potentially thwart -- the influenza virus have now gone from a similar window-based view to the full factory tour, thanks to the first complete structure of one of the flu virus' key machines. The structure, obtained by scientists at the European Molecular Biology Laboratory (EMBL) in Grenoble, France, allows researchers to finally understand how the machine works as a whole. Published in two papers in Nature, the work could prove instrumental in designing new drugs to treat serious flu infections and combat flu pandemics.

The machine in question, the influenza virus polymerase, carries out two vital tasks for the virus. It makes copies of the virus' genetic material -- the viral RNA -- to package into new viruses that can infect other cells; and it reads out the instructions in that genetic material to make viral messenger RNA, which directs the infected cell to produce the proteins the virus needs. Scientists -- including Cusack and collaborators -- had been able to determine the structure of several parts of the polymerase in the past. But how those parts came together to function as a whole, and how viral RNA being fed in to the polymerase could be treated in two different ways remained a mystery.

"The flu polymerase was discovered 40 years ago, so there are hundreds of papers out there trying to fathom how it works. But only now that we have the complete structure can we really begin to understand it," says Stephen Cusack, head of EMBL Grenoble, who led the work.

Using X-ray crystallography, performed at the European Synchrotron Radiation Facility (ESRF) in Grenoble, Cusack and colleagues were able to determine the atomic structure of the whole polymerase from two strains of influenza: influenza B, one of the strains that cause seasonal flu in humans, but which evolves slowly and therefore isn't considered a pandemic threat; and the strain of influenza A -- the fast-evolving strain that affects humans, birds and other animals and can cause pandemics -- that infects bats.

"The high-intensity X-ray beamlines at the ESRF, equipped with state-of-the-art Dectris detectors, were crucial for getting high quality crystallographic data from the weakly diffracting and radiation sensitive crystals of the large polymerase complex," says Cusack. "We couldn't have got the data at such a good resolution without them."

The structures reveal how the polymerase specifically recognises and binds to the viral RNA, rather than just any available RNA, and how that binding activates the machine. They also show that the three component proteins that make up the polymerase are very intertwined, which explains why it has been very difficult to piece together how this machine works based on structures of individual parts.

Although the structures of both viruses' polymerases were very similar, the scientists found one key difference, which showed that one part of the machine can swivel around to a large degree. That ability to swivel explains exactly how the polymerase uses host cell RNA to kick-start the production of viral proteins. The swivelling component takes the necessary piece of host cell RNA and directs it into a slot leading to the machine's heart, where it triggers the production of viral messenger RNA.

Now that they know exactly where each atom fits in this key viral machine, researchers aiming to design drugs to stop influenza in its tracks have a much wider range of potential targets at their disposal -- like would-be saboteurs who gain access to the whole production plant instead of just sneaking looks through the windows. And because this is such a fundamental piece of the viral machinery, not only are the versions in the different influenza strains very similar to each other, but they also hold many similarities to their counterparts in related viruses such as lassa, hanta, rabies or ebola.

The EMBL scientists aim to explore the new insights this structure provides for drug design, as well as continuing to try to determine the structure of the human version of influenza A, because although the bat version is close enough that it already provides remarkable insights, ultimately fine-tuning drugs for treating people would benefit from/require knowledge of the version of the virus that infects humans. And, since this viral machine has to be flexible and change shape to carry out its different tasks, Cusack and colleagues also want to get further snapshots of the polymerase in different states.

"This doesn't mean we now have all the answers," says Cusack, "In fact, we have as many new questions as answers, but at least now we have a solid basis on which to probe further."

Source: European Molecular Biology Laboratory (EMBL)

Three new ornamental dogwoods introduced

'Empire', one of the new dogwood varieties, is shown in the photo at 20 years old. 'Empire' features brilliant white bracts and exfoliated bark. Credit: Phillip Wadl

In the nursery and landscape industries, flowering dogwood (Cornus florida), kousa dogwood (Cornus kousa), and their hybrids are the most popular and economically significant members of the genus Cornus. The deciduous trees are highly valued for their spring display of pink, red, or white bracts, brilliant red fall foliage, and exfoliating bark. In the United States alone, retail and wholesale sales of dogwoods account for more than $30 million dollars annually.

In the past, flowering dogwoods were severely affected by dogwood anthracnose and powdery mildew. A program initiated more than 20 years ago at the University of Tennessee resulted in the release of 'Appalachian Spring', the first flowering dogwood cultivar with resistance to dogwood anthracnose, and four powdery mildew resistant cultivars. "We have found that Cornus kousa is more tolerant to anthracnose and powdery mildew than Cornus florida," explained Phillip Wadl, lead author of report published in HortScience. "Hybrids between these two species are generally more vigorous than typical plants of either parent species, and have resistance or tolerance to dogwood anthracnose and powdery mildew."

Wadl and colleagues Mark Windham, Richard Evans, and Robert Trigiano evaluated 400 seedlings of C. kousa for disease resistance and traits such as color, degree of overlap, size of bracts, tree form, and bark and leaf characteristics. The scientists selected three cultivars they named 'Empire', 'Pam's Mountain Bouquet' and 'Red Steeple' for development and eventual release. 'Empire' is a brilliant, white-bracted kousa dogwood that has a columnar form and exfoliating bark. 'Pam's Mountain Bouquet' (patent pending) is a kousa dogwood with a spreading form that features a prolific fused bract display. 'Red Steeple' is a kousa dogwood that features a columnar-shaped canopy with red foliage that fades to green with high temperature and white bracts that have a red tint along the margins.

The authors noted that dogwood anthracnose and powdery mildew were not observed on any of these trees. Analyses showed that 'Empire', 'Pam's Mountain Bouquet', and 'Red Steeple' are genetically distinct from the 26 cultivars and unnamed accessions of Cornus kousa that are maintained in the University of Tennessee's kousa dogwood collection.

The program has applied for a plant patent for 'Pam's Mountain Bouquet'. A limited quantity of budwood has been distributed to wholesale nurseries in Tennessee and Japan, and selected nurseries have been identified to propagate the cultivars.

Source: American Society for Horticultural Science

This image shows a panda eating in China's Wolong Nature Reserve. Pandas habitat choices center around the ready availability of bamboo -- lots of bamboo. Credit: Sue Nichols, Michigan State University

Walter Dodds, university distinguished professor of biology (pictured), and Allison Veach, doctoral student in biology, are researching grassland streams and the expansion of nearby woody vegetation. They have studied 25 years of data on the Konza Prairie Biological Station and found that increasing fire frequency reduces the rate of woody vegetation expansion. Credit: Image courtesy of Kansas State University

Two Kansas State University biologists are studying streams to prevent tallgrass prairies from turning into shrublands and forests.

By looking at 25 years of data on the Konza Prairie Biological Station, Allison Veach, doctoral student in biology, Muncie, Indiana, and Walter Dodds, university distinguished professor of biology, are researching grassland streams and the expansion of nearby woody vegetation, such as trees and shrubs. They have found that burn intervals may predict the rate of woody vegetation expansion along streams.

Their latest research appears in the peer-reviewed journal PLOS ONE in an article "Fire and Grazing Influences on Rates of Riparian Woody Plant Expansion along Grassland Streams."

Grasslands in North America and across the globe are rapidly disappearing, Veach said, and woody plants are expanding and converting grasslands into forest ecosystems. This change in environment can affect stream hydrology and biogeochemistry, said Dodds, who has studied streams and watersheds on the Konza prairie for more than 20 years.

"This is an important issue regionally, because as trees expand into these grassland areas, people who are using grassland for cattle production have less grass for animals, too," Dodds said.

In their latest research, the biologists studied 25 years of aerial photography on Konza and observed the expansion of trees and shrubs in riparian areas, which include areas within 30 meters of streambeds. The researchers focused on three factors that affect grassland streams: burn intervals; grazers, such as bison; and the historical presence of woody vegetation.

Their analysis revealed an important finding: Burn intervals predicted the rate of woody vegetation expansion. Burning every one to two years slowed the growth of trees and shrubs, Veach said.

"Although we can reduce woody expansion by burning more frequently, we can't prevent it from occurring over time," Veach said. "Woody plant encroachment may not be prevented by fire alone."

The research shows the importance of burning to maintain the tallgrass prairie, Dodds said. While burning can help to slow the expansion of trees and shrubs, additional actions are need to maintain quickly disappearing grassland ecosystems.

"It's clear from this research that if you don't burn at all, these grassland streams basically are going to switch to forests and will not be grassland streams anymore," Dodds said.

Dodds and Veach also found that bison do not significantly affect woody vegetation expansion along streams. Previous Konza research has shown that bison do not spend significant time near stream areas, so they may not influence the growth of nearby trees and shrubs, Veach said.

Woody vegetation also may be expanding in grasslands because of more carbon dioxide in the atmosphere, Dodds said. Grasses and trees compete for carbon dioxide, and grasses are much better at conserving water and efficiently using carbon dioxide. As atmospheric carbon dioxide levels increase, it becomes easier for trees to gather carbon dioxide and gives them a growing advantage over grasses.

"The tallgrass prairie is almost nonexistent on the globe," Veach said. "In order for us to preserve tallgrass prairie, we need to look at woody encroachment because it has been an issue. Things like no fire or differences in climate change may allow woody plant species to competitively take over grasslands."

The biologists plan to continue studying water quality and quantity issues at Konza. Konza is an 8,600-acre tallgrass prairie ecological research site jointly owned by the university and The Nature Conservancy.

Source:  Kansas State University

Expect higher grass pollen, allergen exposure in coming century

A study provides the first evidence that pollen production is significantly stimulated by elevated carbon dioxide in a grass species as a result of climate change, which may have significant impact on human health. Credit: UMass Amherst

Results of a new study by scientists at the University of Massachusetts Amherst strongly suggest that there will be notable increases in grass pollen production and allergen exposure up to 202 percent in the next 100 years, leading to a significant, worldwide impact on human health due to predicted rises in carbon dioxide (CO2) and ozone (O3) due to climate change.

While CO2 stimulates reproduction and growth in plants, ozone has a negative impact on plant growth, the authors point out. In this study in Timothy grass, researchers led by environmental health scientist Christine Rogers of the UMass Amherst School of Public Health and Health Sciences (SPHHS) determined the interactive effects of CO2 and ozone at projected higher levels on pollen production and concentrations of a Timothy grass pollen protein that is a major human allergen. Findings are reported in the current issue of PLOS ONE.

Rogers and plant science colleagues at UMass Amherst, with postdoctoral researcher and first author Jennifer Albertine, write, "The implications of increasing CO2 for human health are clear. Stimulation of grass pollen production by elevated CO2 will increase airborne concentrations and increase exposure and suffering in grass pollen-allergic individuals."

Rogers notes that, "This is the first evidence that pollen production is significantly stimulated by elevated carbon dioxide in a grass species and has worldwide implications due to the ubiquitous presence of grasses in all biomes and high prevalence of grass pollen allergy. These results are similar to our other studies performed in other highly allergenic taxa such as ragweed but with more extreme outcomes and wider impacts."

For these experiments, the researchers exposed grass plants in specially designed continuously stirred tank reactor chambers that allow researchers to expose plants to different atmospheric gas concentrations. They established four experimental atmospheric treatments:

• control, current atmosphere (30 ppb O3 and 400 ppm CO2)
• elevated O3, current CO2 (80 ppb O3, 400 ppm CO2)
• current O3, elevated CO2 (30 ppb O3, 800 ppm CO2)
• elevated O3, elevated CO2 (80 ppb O3, 800ppm CO2)

At the appropriate plant development stage, Albertine and colleagues bagged flowers, captured and measured pollen amounts and extracted the allergen protein Phl p 5 from pollen samples for measurement by enzyme-linked immunosorbent assay (ELISA).

They found that elevated CO2 of 800 ppm, increased pollen production per flower by 53 percent while the different ozone levels had no effect on the amount of pollen produced. There was also a trend of increased number of plants flowering in response to elevated CO2 further increasing pollen production up to 200 percent. While elevated ozone did decrease the Phl p 5 allergen content in pollen, "the strong CO2-stimulation of pollen production suggests increased exposure to Timothy grass allergen overall," even if O3 projections are realized, the authors note.

They add that the health implications of increased ozone are "more complex" because higher levels of this greenhouse gas irritate mucous membranes and worsen the allergic airway response. Projected ozone increases "would likely elicit negative respiratory health effects independent of any health effects as a result of increased pollen by elevated CO2."

Source:  University of Massachusetts at Amherst

Silver gone astray: What concentration of silver ions disrupts biological processes in aquatic life?

Silver ions disrupt cellular metabolism in the green alga Chlamydomonas reinhardtii (photo),
 inhibiting functions such as photosynthesis.
Credit: Image courtesy of EAWAG: Swiss Federal Institute of Aquatic Science and Technology

It has long been known that, in the form of free ions, silver particles can be highly toxic to aquatic organisms. Yet to this day, there is a lack of detailed knowledge about the doses required to trigger a response and how the organisms deal with this kind of stress. To learn more about the cellular processes that occur in the cells, scientists from the Aquatic Research Institute, Eawag, subjected algae to a range of silver concentrations.

In the past, silver mostly found its way into the environment in the vicinity of silver mines or via wastewater emanating from the photo industry. More recently, silver nanoparticles have become commonplace in many applications – as ingredients in cosmetics, food packaging, disinfectants, and functional clothing. Though a recent study conducted by the Swiss National Science Foundation revealed that the bulk of silver nanoparticles is retained in wastewater treatment plants, only little is known about the persistence and the impact of the residual nano-silver in the environment.

Infiltrating the energy metabolism undercover

Smitha Pillai from the Eawag Department of Environmental Toxicology and her colleagues from EPF Lausanne and ETH Zürich studied the impact of various concentrations of waterborne silver ions on the cells of the green algae Chlamydomonas reinhardtii. Silver is chemically very similar to copper, an essential metal due to its importance in several enzymes. Because of that, silver can exploit the cells’ copper transport mechanisms and sneak into them undercover. This explains why, already after a short time, concentrations of silver in the intracellular fluid can reach up to one thousand times those in the surrounding environment.

A prompt response

Because silver damages key enzymes involved in energy metabolism, even low concentrations can cut photosynthesis and growth rates by a half in just 15 minutes. Over the same time period, the researchers also detected changes in the activity of about 1000 other genes and proteins, which they interpreted as a response to the stressor – an attempt to repair silver-induced damage. At low concentrations, the cells’ photosynthesis apparatus recovered within five hours, and recovery mechanisms were sufficient to deal with all but the highest concentrations tested.

A number of unanswered questions

At first glance, the results are reassuring because the silver concentrations that the algae are subject to in the environment are rarely as high as those applied in the lab, which allows them to recover quickly – at least externally. But the experiments also showed that even low silver concentrations have a significant effect on intracellular processes and that the algae divert their energy to repairing damage incurred. This can pose a problem when other stressors act in parallel, such as increased UV-radiation or other chemical compounds. Moreover, it remains unknown to this day whether the cells have an active mechanism to shuttle out the silver. Lacking such a mechanism, the silver could have adverse effects on higher organisms, given that algae are at the bottom of the food chain.

Source:  EAWAG: Swiss Federal Institute of Aquatic Science and Technology.