Agricultural Sciences

Plant Community A Weak Predictor Of Bee Community

2011-06-23T05:49:00.000-07:00

Native bees -- often small, stingless, solitary and unnoticed in the flashier world of stinging honeybees -- are quite discriminating about where they live, according to U.S. Geological Survey research.

The study found that, overall, composition of a plant community is a weak predictor of the composition of a bee community, which may seem counterintuitive at first, said USGS scientist and study lead Ralph Grundel. This may be because specialized plant-bee interactions, in which a given bee species only pollinates one plant species and that plant species is only pollinated by that bee species are not common. More common is for a plant species to be pollinated by many pollinator species and each pollinator species pollinating many species of plants.

Given this complex network of interaction between plants and their pollinators, it is not surprising that knowing which plants occur in an area does not necessarily allow us to predict which bees will occur in that area, Grundel said.

Unraveling such mysteries surrounding how native bees inhabit and use different habitats is especially essential now -- the National Academy of Sciences has reported that not only is there direct evidence for decline of some pollinator species in North America, but also very little is known about the status and health of most of the world's wild pollinators. Yet without them, the ability of agricultural crops and wild plants to produce food products and seeds is jeopardized.

"The issues facing honeybees introduced pollinators whose populations are spiraling downward, means that it is even more vital to understand the role of native bees as pollinators and how they divide up and use a landscape," said Grundel.

Many studies have been conducted to determine how a variety of animals -- birds, mammals, and reptiles, for example -- use their native landscapes, but few such studies have been undertaken for native bees. "That's why this type of study is fundamental for enhancing our understanding of native bee distribution," Grundel said. "Our research findings clearly reveal that maintenance of a diverse and abundant bee community requires that managers consider a suite of local and landscape characteristics and management actions."

Grundel and his colleagues wanted to find out if the kinds of plants that live in different habitats can predict what kinds of bees will be there or if other factors -- such as soil type, tree density or even fire -- are more important. To do this, the team surveyed landscapes and collected and identified nearly 5,000 native bees representing at least 175 species in five kinds of habitats at Indiana Dunes National Lakeshore and nearby natural areas around northwestern Indiana. These habitats ranged from dense forests to open fields.

"We had suspected that the closer our collecting sites were to each other the more similar the bees communities we found would be -- but we were wrong," Grundel said. "In fact, mere physical proximity wasn't a very good predictor of how similar bee communities at different sites would be to each other. Instead, local factors -- and even the micro-habitats that we often ignore -- are really important in determining what kinds of bees use an area."

Because many native bees are ground- and cavity-nesters, the scientists weren't surprised to find that an abundant supply of dead wood, such as woody debris and dead tree limbs, was essential in determining what kinds of bees lived where. They were surprised, however, at how important other factors were, including bee preferences for specific soil characteristics and for areas that had burned in the previous two years.

Bee abundance -- how many bees were captured at a site -- was lower in areas with a dense tree canopy and higher if a fire had occurred recently in the area. Bee diversity -- the number of different kinds of bees -- was higher in areas with less tree canopy, but with a higher diversity of flowering plants and an abundance of nesting resources, such as woody debris.

The presence of suitable nesting material was at least as important in determining how many types of bees might use a site as was diversity of plants, which provide nectar and pollen to the bees. The composition of an entire bee community was linked to higher plant variety, less canopy cover and soil characteristics that may be best-suited for nesting.

The study found that specialist bees -- those picky native bees that gather pollen from only a few kinds of plants -- were more likely to live in open areas than areas with a higher density of trees.

"Specialist bees, not surprisingly, were also more associated with the presence of native plants in the areas, but a lot of these native plants were more likely to occur in disturbed areas, including areas that had recently been burned and, somewhat to our surprise, residential areas where soil disturbance is commonplace," Grundel said.

However, specialist bees were often rarer and mainly used open habitats, such as grasslands and savannas. According to a 2005 study, said Grundel, such open Midwest habitats are today perhaps the most poorly conserved habitats on the planet, causing concern about long-term conservation of such bee species.

"At several locations around the world, specialist bumblebees living in plant rich areas, such as these open habitats, have declined significantly," Grundel said. "Similar bumblebee declines have been documented in the Midwest U.S. Documenting how diet breadth, rarity and habitat use are related is important for understanding such patterns of decline and was one of the main objectives of our study. We collected six bumblebee species in our study while a 1930s study in this area collected twelve species. Four of the species we did not find in our study have been identified as bumblebees of special concern due to their disappearance from sites across the Midwest."

USGS researchers in Indiana and Maryland are following up on this research with a recently initiated study examining how native bee populations across the national park system might be affected by climatic variation.

Ralph Grundel, Robert P. Jean, Krystalynn J. Frohnapple, Gary A. Glowacki, Peter E. Scott, Noel B. Pavlovic. Floral and nesting resources, habitat structure, and fire influence bee distribution across an open-forest gradient. Ecological Applications, 2010; 20 (6): 1678 DOI: 10.1890/08-1792.1

Source: United States Geological Survey.

Optimizing Biogas Production From Livestock Manure

2011-06-22T06:27:00.000-07:00

A team of researchers from the Institute for Animal Science and Technology of the Universitat Politècnica de València (Spain) has developed a project that combines pig slurry and agricultural by-products to optimize biogas production. Thus, it manages to add value to farms' excess slurry and offers a sustainable use to some of the by-products from the fruit and vegetable processing industry.

The project's main researchers María Cambra-López, Verónica Moset and Pablo Ferrer are agronomists coordinated by Prof. Antonio Torres. They explain that pig farms generate large amounts of slurry, consisting mainly of animal excreta, cleaning water and feed residues, the management of which normally consists of storing it in pools and then using it as fertilizer in agricultural fields.

However, because of the manure's properties, rich in nutrients -such as nitrogen and phosphorus- and organic matter, it can cause pollution to soil, water and atmosphere as a result of excessive accumulation of these nutrients in soil and water and the emissions of greenhouse gases and ammonia.

In areas such as the north of Castellón and inland Valencia where there is a high concentration of pig production, there is not enough agricultural land to absorb the large volume of slurry produced on local farms. Furthermore, the transport of this slurry to other areas involves extra costs -because of its high water content- that farmers are not willing to accept, says María Cambra-López.

Therefore, the team of Spanish researchers has studied the combined processing of pig slurry and agricultural by-products to produce biogas, in order to provide a sustainable use for these products. Moreover, this combination can avoid undesirable environmental side-effects and the project offers to turn pig slurry into a valuable product: energy.

Verónica Moset explains that slurry on its own does not produce much energy, and therefore a biogas plant is not a profitable business for farmers. However, if we combine it with certain fruit and vegetables from the region that are not good enough to sell, we can increase the methane level and this way produce biogas cost-effectively.

So far, researchers have tested in vitro the combination of pig slurry with peppers, tomatoes, peaches and kaki to study their potential to produce biogas and the optimal combination of both substrates. The engineers found that peppers increased by 44% methane production compared with slurry-only; tomatoes, by 41%; peaches, by 28%, and they did not observe any difference in methane production using kaki.

With this encouraging data, Pablo Ferrer says that they will carry out trials in large-scale digesters and simulate the real biogas production process using peppers, tomatoes and peaches. Researchers believe that in another year they will be able to offer results and could transfer the technology to real-scale centralized biogas plants.

Thus, the benefit of this project is extensive and varied. On the one hand, it reduces the emission of methane during slurry storage, a highly polluting gas that has a higher greenhouse effect than CO2. On the other, it provides farmers with an alternative use for pig slurry as well as an additional income.

The researchers are also working closely with the Centre for Animal Research and Technology of the Valencian Institute for Agricultural Research (IVIA) to evaluate the effect of addition of agricultural by-products such as rapeseed oil, orange pulp or rice husk in pig feed, on methane emissions from manure which could therefore increase biogas production.

This project is funded by the Foundation Agroalimed of the Regional Department of Agriculture, Fisheries and Food.

Source: Asociación RUVID, via AlphaGalileo.

Lyme Disease In Central Illinois: Well Adapted

2011-06-22T06:03:00.000-07:00

A new study offers a detailed look at the status of Lyme disease in Central Illinois and suggests that deer ticks and the Lyme disease bacteria they host are more adaptable to new habitats than previously appreciated.

Led by researchers at the University of Illinois, the study gives an up-close view of one region affected by the steady march of deer ticks across the upper Midwest. Their advance began in Wisconsin and Minnesota and is moving at a pace of up to two counties a year in Illinois and Indiana.

Today the deer tick is established in 26 Illinois counties, up from just eight in 1998, said Illinois Department of Public Health entomologist Linn Haramis. Reports of human Lyme disease cases in the state have more than tripled in the same period, he said.

"We've had several years in a row where we've had over 100 cases, up from about 30 per year more than 10 years ago," Haramis said. "It's not a huge increase, but it's been steady and there's an upward trend."

Deer ticks are known to do best in forested areas, where they can readily move from small mammals (which provide their first meal) to moist leaf litter on the forest floor, and then to deer, on which they mate. Deer ticks do not pick up the Lyme infection from deer, said Jennifer Rydzewski, who completed her master's degree with the study in the department of natural resources and environmental sciences at the University of Illinois.

"The deer tick will feed on a variety of mammals, birds and even reptiles," she said. "But Borrelia burgdorferi, the bacterium that causes Lyme disease, replicates really well within white-footed mice, so white-footed mice are the main reservoir that passes that bacterium on to the immature ticks that are feeding on it."

White-footed mice also are forest dwellers. Prior to the new study, little was known about whether, or how, Lyme disease persists in other habitat types.

To determine if Lyme disease had gained a foothold in the patchwork of forests, farms and prairies of Central Illinois, researchers trapped small mammals in Allerton Park, a 1,500-acre (600-hectare) natural area in Piatt County. They focused on four habitat types: young forest, mature forest, a flood plain and a 30-acre (12-hectare) patch of prairie surrounded by woods and agricultural fields.

The researchers removed deer ticks from the mammals they trapped and tested the ticks for Lyme disease.

They found that the immature forest and the prairie hosted the highest percentage of deer-tick-infested mammals, the highest number of ticks per mammal trapped and the highest rates of ticks infected with Lyme disease of the four habitat types evaluated.

"The highest prevalence of B. burgdorferi infection was found (in deer tick larvae) from the prairie (27 percent) followed by the young forest (15 percent), the mature forest (6 percent) and the flood plain (6 percent)," the researchers wrote.

"Interestingly, all of the positive ticks from the prairie were from prairie voles, not the typical white-footed mouse," Rydzewski said. There also were many more ticks per animal on the prairie voles than on the white-footed mice of the forest, she said.

This is the first study to report evidence that the prairie vole may potentially serve as a competent reservoir host for the Lyme disease bacterium, B. burgdorferi, said Nohra Mateus-Pinilla, a wildlife veterinary epidemiologist at the Illinois Natural History Survey who led the study with Rydzewski and natural resources and environmental sciences emeritus professor Richard Warner. (The Survey is a unit of the Prairie Research Institute at Illinois.)

"The fact that we found tick larvae feeding so prominently on prairie voles and those ticks were infected and hadn't had a chance to feed on anything else is a very strong indicator that we are dealing with a different reservoir of Lyme disease that deserves more attention," Mateus-Pinilla said.

The researchers hypothesize that when newly hatched ticks find themselves on the prairie, they latch on to the first small mammal that comes along, which in most cases is a prairie vole (white-footed mice prefer the forest). The abundance of prairie voles in the prairie is much lower than that of the white-footed mice in the forest, so more tick larvae and nymphs end up on the same few prairie voles. Since the number of ticks per animal is higher on the prairie, the likelihood of infection is higher there as well.

"The landscape of Illinois, especially the northern and central area, is very fragmented with agricultural and other development, so there aren't really big continuous areas that are forested," Rydzewski said. "And so maybe these ticks are finding new habitats to establish themselves in because of the lack of previous habitats."

"What's exciting about the new findings is that we are dealing with potentially new mechanisms of disease transmission that we just have not explored and perhaps we do not understand," Mateus-Pinilla said. "We need to think outside of what we already know about Lyme disease transmission."

The new study appears in the journal Vector-Borne and Zoonotic Diseases.

Researchers from the U. of I. department of pathobiology and Michigan State University also contributed to this study.

Source: University of Illinois at Urbana-Champaign.

What Humans Should Learn From Plants Disease Fighting Mechanisms

2011-06-21T06:17:00.000-07:00

Avoiding germs to prevent sickness is commonplace for people. Wash hands often. Sneeze into your elbow. Those are among the tips humans learn.

But plants, which are also vulnerable to pathogens, have to fend it alone. They grow where planted, in an environment teeming with microbes and other substances ready to attack, scientists note.

Now, researchers are learning from plants' immune response new information that could help them understand more about humans' ability to ward off sickness and avoid autoimmune diseases.

In the latest issue of the journal Science, Texas AgriLife Research scientists report their findings of a "unique regulatory circuit" that controls how a plant turns on and off its immune sensor.

"Plants and animals live out their lives mostly in good health, though they may have been subjected to a lot of pathogenic microbes," said Dr. Libo Shan, AgriLife Research plant molecular biologist and lead author for the journal article. "Scientists all around the world have been interested in how a healthy host can fend off invasions of pathogens and turn off the defense responses promptly once the intruder risk factors are decreasing."

The research team found a "unique regulatory circuit" in which BAK1, a protein involved with cell death control and growth hormone regulation, recruits two enzymes -- PUB12 and PUB13 -- to the immune sensory complex and fine-tunes immune responses.

Basically, the surface of plant cells has sensors that sense microbial invasion. One of the best understood plant receptors is FLS2, found in the common laboratory plant Arabidopsis.

FLS2 could sense the bacterial flagellin, which is a part of the flagellum, or tail-like projection on cells which help it to move. When FLS2 perceives flagellin, a series of "evolutionary conserved immune responses" is activated to fend off bacterial attack, Shan said.

But the immune response can not stay activated or the plant will stop growing and producing.

"To avoid detrimental effects of long-lasting immune activation, plant and animal hosts need a way to switch the activation off," she noted. "How that can be has been a mystery to scientists."

The team discovered that the flagellin perception recruited PUB12 and PUB13 to the receptor FLS2 complex.

Those two enzymes could add a biochemical signature tag, ubiquitin, to the FLS2 receptors which inform sells to degrade the immune senors, she added. As a result of these actions, immune signaling decreased.

Knowing how immune signaling works may help researchers devise ways to help plants and animals -- including humans -- regulate their immune systems. Shan said the mechanism her lab discovered is very broad in that it can be found in both plants and animals.

"We needed to understand the mechanism so that we can regulate it better," she said. "The host needs to know when the signal is triggered (to fight off a pathogen). Then the immune response needs to go quickly up and then back down when it is no longer needed."

Shan believes that this ability could lead to cures, rather than medical relief, from an assortment of ailments including allergies and autoimmune diseases.

"Plants have figured out how to survive in terms of disease and pest resistance," she added. "And what we learn from them at the molecular level might help us understand animal pathogens better."

Dongping Lu, Wenwei Lin, Xiquan Gao, Shujing Wu, Cheng Cheng, Julian Avila, Antje Heese, Timothy P. Devarenne, Ping He, Libo Shan. Direct Ubiquitination of Pattern Recognition Receptor FLS2 Attenuates Plant Innate Immunity. Science, 2011; 332 (6036): 1439-1442 DOI: 10.1126/science.1204903

Source: Texas A&M AgriLife Communications.

New Finding In Plant Cell Membranes Signaling

2011-06-21T06:07:00.000-07:00

Every living plant cell and animal cell is surrounded by a membrane. These cellular membranes contain receptor molecules that serve as the cell's eyes and ears, and help it communicate with other cells and with the outside world.

The receptor molecules accomplish three basic things in the communication process: 1) recognize an outside signal, 2) transport that signal across the cell's membrane and 3) initiate the reading of the signal inside the cell and then initiate the cell's response to that signal. These steps are collectively known as transmembrane signaling.

Transmembrane signaling in animal cells has been significantly more studied and observed than that in plant cells. But now, with support from the National Science Foundation, researchers from Joanne Chory's laboratory at the Salk Institute have published new observations about transmembrane signaling in plants; their paper appears in the June 12, 2011, advanced online edition of Nature.

Transmembrane signaling in a plant cell aided by a steroid. (Credit: Zina Deretsky, National Science Foundation).

According to the study, transmembrane signaling mechanisms used by plants differ from those used by animals. Specifically, Michael Hothorn of the Salk Institute reports that a small steroid molecule on the outside of the plant cell assists in the transmembrane signaling process. By contrast, this sort of molecule and its receptor is generally located inside the nuclei of animal cells.

While studying transmembrane signaling in plants, Hothorn and colleagues observed the steroid, shown in yellow, attach to a membrane-bound receptor, shown in blue. This attachment enabled the steroid's counterpart--a co-receptor protein, shown in orange--to bind to the blue receptor. Once bound, the orange co-receptor and the blue receptor become glued together by the yellow steroid, allowing their intracellular domains to touch and initiate communication.

In the case observed by Hothorn, transmembrane signaling initiated plant growth.

Michael Hothorn, Youssef Belkhadir, Marlene Dreux, Tsegaye Dabi, Joseph. P. Noel, Ian A. Wilson, Joanne Chory. Structural basis of steroid hormone perception by the receptor kinase BRI1. Nature, 2011; DOI: 10.1038/nature10153

Source: National Science Foundation.

Top Dirty And Clean Foods To Buy

2011-06-14T06:19:00.000-07:00

The list of clean and dirty foods, percentage of pesticides in them, is out as published by Environmental group.

Four New Viruses Affecting Bees Identified

2011-06-14T06:02:00.000-07:00

A 10-month study of healthy honey bees by University of California, San Francisco scientists has identified four new viruses that infect bees, while revealing that each of the viruses or bacteria previously linked to colony collapse is present in healthy hives as well.

The study followed 20 colonies in a commercial beekeeping operation of more than 70,000 hives as they were transported across the country pollinating crops, to answer one basic question: what viruses and bacteria exist in a normal colony throughout the year?

The results depict a distinct pattern of infections through the seasons and provide a normal baseline for researchers studying a colony -- the bee population within a hive -- that has collapsed. Findings are reported in the June 7 issue of the online journal PLoS ONE, published by the Public Library of Science.

The study tracked 27 unique viruses that afflict honey bees, including four that previously were unknown and others proposed as causes of the Colony Collapse Disorder that has been wiping out colonies for the past five years, according to senior author Joe DeRisi, PhD, a Howard Hughes Medical Institute investigator and professor of biochemistry and biophysics at UCSF.

"We brought a quantitative view of what real migrating populations look like in terms of disease," DeRisi said. "You can't begin to understand colony die-off without understanding what normal is."

Because the colonies in this study remained healthy despite these pathogens, the research supports the theory that colony collapse may be caused by factors working alone or in combination, said Michelle Flenniken, PhD, who jointly led the research.

Working in the lab, from left, are Michelle Flenniken, a postdoctoral scholar, Joseph DeRisi, PhD, a Howard Hughes Medical Institute investigator and professor of biochemistry and biophysics at UCSF, and Charles Runckel, a graduate student. (Credit: Lab photo by Cindy Chew).

"Clearly, there is more than just exposure involved," said Flenniken, a postdoctoral scholar in the laboratory of UCSF microbiologist Raul Andino, PhD. "We noticed that specific viruses dominated in some seasons, but also found that not all of the colonies tested positively for a virus at the same time, even after long-distance transport in close proximity."

Honey bees are critical to U.S. agriculture, which depends upon them to pollinate 130 different crops, representing more than $15 billion in crop value each year and roughly one-third of the human diet, according to the U.S. Department of Agriculture.

For the California almond crop to be successfully pollinated, DeRisi said, roughly half of the honeybees in the country -- about 1.3 million honeybee colonies -- must be in the Central Valley by the first week in February, when the trees begin to bloom. That need is echoed throughout the country, as different crops come due for pollination, resulting in semis traversing the nation for most of the year, each bearing hundreds of hives.

Since 2006, however, the bee industry has reported a mysterious phenomenon involving the sudden disappearance of most of a hive's worker bees, which leaves the queen and young bees without enough workers to support them. The disorder is one factor in the growing decline of U.S. honey bees -- an estimated 30 percent of the population is lost each year and some beekeeping operations cite 90 percent losses, the USDA reports.

Researchers nationwide have identified various possible causes of that collapse, mainly based on pathogens found in the affected hives. While this study did not identify the cause of colony collapse, it did offer a measurement of the normal levels of pathogens.

In addition to viruses, the research revealed six species each of bacteria and fungi, four types of mites and a parasitic fly called a phorid, which had not been seen in honey bees outside California. One of the new viruses, a strain of the Lake Sinai virus, turned out to be the primary element of the honey bee biome, or community of bacteria and viruses.

"Here's a virus that's the single most abundant component of the bee biome and no one knew it was there," DeRisi said, noting that hundreds of millions of these viral cells were found in each bee in otherwise healthy colonies at certain times of the year.

Flenniken jointly led the work with doctoral student Charles Runckel, in DeRisi's lab. The team used a broad range of molecular detection tools for the study, including gene sequencing and a custom-designed microarray to detect insect pathogens. The microarray was designed using the same principles used for detecting human viruses, which DeRisi pioneered with UCSF professor Donald Ganem, MD. It was built in the Center for Advanced Technology on the UCSF Mission Bay campus.

The research was primarily funded by Project Apis m., which includes members of the American Honey Producers Association, the American Beekeeping Federation, the National Honey Board, California State Beekeepers Association and California almond farmers. DeRisi is supported by the Howard Hughes Medical Institute. Flenniken's research was supported by the Häagen Dazs post-doctoral fellowship in honey bee biology, through University of California, Davis. Other funding sources and data can be found in the full paper.

Co-authors include Andino, in the UCSF Department of Microbiology and Immunology; Juan C. Engel, in the UCSF Sandler Center for Drug Discovery and UCSF Department of Pathology; and J. Graham Ruby and Donald Ganem, in the Howard Hughes Medical Institute and UCSF departments of Biochemistry & Biophysics, and Microbiology.

Charles Runckel, Michelle L. Flenniken, Juan C. Engel, J. Graham Ruby, Donald Ganem, Raul Andino, Joseph L. DeRisi. Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia. PLoS ONE, 2011; 6 (6): e20656 DOI: 10.1371/journal.pone.0020656

Source: UCSF.

How Fungal Diseases Evading Wheats Defences

2011-06-13T20:01:00.000-07:00

Research published in PLoS Genetics on June 9 provides insights into how an important fungal disease is able to evade wheat's defences. The researchers hope that the study, which reveals the fungus' complete genome sequence, will enable them to breed resistant crop plants or improve the use of pesticides.

The genome sequence was produced by an international consortium of researchers including scientists at Rothamsted Research in the UK. The scientists, who were funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and others, are already using the fungus' genome sequence to find ways to control the disease in order to help meet the challenges of ensuring global food security.

The consortium has sequenced the genome of a fungus called Mycosphaerella graminicola which causes leaf blotch disease in wheat. The disease kills cells in the plants leaves leaving large dead blotches which are unable to absorb energy from the sun. This significantly reduces yields and takes a serious toll on wheat crops globally and in the UK; annually a 5-15% reduction in grain yield is incurred in each wheat field solely as a result these infections.

Professor Kim Hammond-Kosack of Rothamsted Research who led the study in the UK said "M. graminicola attacks wheat plants by stealth. There is normally a period of about a week between when a plant first becomes infected and when the characteristic blotches of the disease appear on its leaves. During this time it appears that the plant fails to recognise it has become infected and so is unable to activate its defences to fight back. Studying the fungus' genome will help us to understand how the pathogen is able to go undetected and maybe reveal a chink in its armour that we can exploit."

The genome sequence reveals that M. graminicola has very few genes which produce enzymes able to break-down plant cell walls compared with other fungi which specialise in infecting plants. Plants often use the presence of the sugars and proteins released when a cell is broken down as cue for turning on their immune responses, so the researchers think that the unusually low numbers of genes producing enzymes for breaking down plant cells may be crucial to the fungus' stealth approach.

The team from Rothamsted have already started on work using the genome to look for potential weaknesses in the fungus' defences. Collaborating with researchers at Wageningen University in the Netherlands they have identified a protein in the fungus which is important in keeping it hidden. This research was published recently in Plant Physiology.

Dr Jason Rudd who worked on the project at Rothamsted Research said "We were able to use the information in the genome sequence almost immediately to look for a potential Achilles' heel. We singled out a protein which helps keep the fungus camouflaged and protects it from the plant's defences. When we generated a mutant strain of the fungus which didn't contain the gene for this protein, the infected wheat plants produced strong immune responses and didn't develop the characteristic leaf blotches. Our next step is to use these and similar findings to help farmers combat this disease out in the field in order to reduce wheat losses."

Professor Maurice Moloney, Director and Chief Executive of Rothamsted Research commented "Rothamsted Research is proud to be part of the team that has sequenced and analysed the M. graminicola genome. This fungal pathogen causes one of the most pernicious plant diseases and accounts for significant losses annually in wheat yields throughout the world. This work illustrates the power of sequencing the genomes of plant pathogens in identifying key targets for efficient plant protection."

Professor Douglas Kell, Chief Executive of the Biotechnology and Biological Sciences Research Council, said "Genome sequencing is an important tool in the fight to ensure global food security. Determining the sequence of a destructive crop disease like this is now so quick and affordable that it can be viewed as a research tool rather than a project in itself. This is especially true when the complementary talents of researchers in different countries can be brought to bear. As in this project, this information can be put to immediate use in finding new ways to combat plant disease."

Journal References:

Stephen B. Goodwin et al. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis. PLoS Genetics, 09 Jun 2011 DOI: 10.1371/journal.pgen.1002070

R. Marshall, A. Kombrink, J. Motteram, E. Loza-Reyes, J. Lucas, K. Hammond-Kosack, B. Thomma, J. Rudd. Analysis of two in planta expressed LysM effector homologues from the fungus Mycosphaerella graminicola reveals novel functional properties and varying contributions to virulence on wheat. Plant Physiology, 2011; DOI: 10.1104/pp.111.176347

Fight Aging With Poplar Tree Extract

2011-06-13T19:50:00.000-07:00

Antioxidants are popular anti-aging ingredients in skin creams, and now scientists are reporting a new source of these healthful substances -- leaf buds of poplar trees. Their study appears in the ACS' Journal of Agricultural and Food Chemistry.

Xavier Vitrac and colleagues note that there's a long history of using poplar buds to treat various health problems, such as colds, sinusitis, sunburn and arthritis. A substance found in beehives that is made from poplar buds (called propolis) also appears to have similar disease-fighting benefits. Propolis' effects seem to be due to poplar bud compounds, but very little is known about these substances. To see whether poplar buds are a good source of antioxidants for skin creams, the researchers decided to test an extract from the buds.

The group found that poplar bud extract had moderate antioxidant activity, and it demonstrated anti-aging effects on cells in the laboratory. "The collective antioxidant properties and transcriptional effect of this extract suggest potential anti-aging properties which could be utilized in cosmetic and nutraceutical formulations," the scientists say.

The authors acknowledge support from Conseil Regional d'Aquitaine and the Association Nationale de la Recherche Technique.

Journal Reference:

Stéphanie Dudonné, Pascal Poupard, Philippe Coutière, Marion Woillez, Tristan Richard, Jean-Michel Mérillon, Xavier Vitrac. Phenolic Composition and Antioxidant Properties of Poplar Bud (Populus nigra) Extract: Individual Antioxidant Contribution of Phenolics and Transcriptional Effect on Skin Aging. Journal of Agricultural and Food Chemistry, 2011; 59 (9): 4527 DOI: 10.1021/jf104791t

Researchers Counteract Biofuel Toxicity in Microbes

2011-06-06T09:01:00.000-07:00

Advanced biofuels -- liquid transportation fuels derived from the cellulosic biomass of perennial grasses and other non-food plants, as well as from agricultural waste -- are highly touted as potential replacements for gasoline, diesel and jet fuels. Equally touted is the synthesis of these fuels through the use of microbes. However, many of the best candidate compounds for advanced biofuels are toxic to microbes, which presents a "production versus survival" conundrum.

Researchers at the U.S. Department of Energy (DOE)'s Joint BioEnergy Institute (JBEI) have provided a solution to this problem by developing a library of microbial efflux pumps that were shown to significantly reduce the toxicity of seven representative biofuels in engineered strains of Escherichia coli.

"Working with all available microbial genome sequence data, we generated a library of largely uncharacterized genes and were able to devise a simple but highly effective strategy to identify efflux pumps that could alleviate biofuel toxicity in E. coli and, as a consequence, help improve biofuel production," says Aindrila Mukhopadhyay, a chemist with JBEI's Fuels Synthesis Division, who led this research.

Mukhopadhyay, who also holds an appointment with the Lawrence Berkeley National Laboratory (Berkeley Lab)'s Physical Biosciences Division, is the corresponding author on a paper published in the journal Molecular Systems Biology. Co-authoring the paper with Mukhopadhyay were Mary Dunlop, Zain Dossani, Heather Szmidt, Hou-Cheng Chu, Taek Soon Lee, Jay Keasling and Masood Hadi.

Aindrila Mukhopadhyay, a Berkeley Lab chemist with the Joint BioEnergy Institute, led the creation of a library of microbial efflux pumps that reduce toxicity and boost production of biofuels in engineered strains of microbes. (Credit: Photo by Roy Kaltschmidt, Berkeley Lab Public Affairs).

Research efforts are underway at JBEI and elsewhere to engineer microorganisms, such as E. coli, to produce advanced biofuels in a cost effective manner. These fuels, which encompass short-to-medium carbon-chain alcohols, such as butanol, isopentanol and geraniol, can replace gasoline on a gallon-for-gallon basis and be used in today's infrastructures and engines, unlike ethanol. Biofuels made from branched carbon-chain compounds, such as geranyl acetate and farnesyl hexanoate, would also be superior to today's biodiesel, which is made from esters of linear fatty acids. Cyclic alkenes, such as limonene and pinene, could serve as precursors to jet fuel. Although biosynthetic pathways to the production of these carbon compounds in microbes have been identified, product toxicity to microbes is a common problem in strain engineering for biofuels and other biotechnology applications.

"In order for microbial biofuel production to be cost effective, yields must exceed native microbial tolerance levels, necessitating the development of stress-tolerant microbe strains," Mukhopadhyay says. "It is crucial that we improve tolerance in parallel with the development of metabolic pathways for the production of next-generation biofuels."

Microbes employ various strategies for addressing cell toxicity but perhaps the most effective are efflux pumps, proteins in the cytoplasmic membrane of cells whose function is to transport toxic substances out of the cell. This is done actively, using proton motive force. However, to date very few of these have been characterized for efficacy against biofuel like compounds.

"Sequenced bacterial genomes include many efflux pumps but remain a largely unexplored resource for use in engineering fuel tolerance," Mukhopadhyay says. "We took a systematic approach to screen a library of primarily uncharacterized heterologous pumps for engineering biofuel tolerant host strains. We were then able to demonstrate that expression of a heterologous pump can increase the yield of a biofuel in the production strain."

Since all known solvent-resistant efflux pumps in Gram-negative bacteria fall into the hydrophobe/amphiphile efflux (HAE1) family, Mukhopadhyay and her colleagues constructed a datab

ase of all HAE1 pumps from sequenced bacterial genomes. They then performed a bioinformatics screen to compare regions predicted to be responsible for substrate specificity to those of TtgB, a well-characterized solvent-resistant efflux pump.

"This metric allowed us to rank the complete set of pumps and select a subset that represented a uniform distribution of candidate genes," says Mukhopadhyay. "To construct the library, we amplified efflux pump operons from the genomic DNA of the selected bacteria, cloned them into a vector, and transformed the vector into an E. coli host strain."

In a series of survival competitions, the two microbial efflux pumps that performed best were the native E. coli pump AcrAB and a previously uncharacterized pump from a marine microbe Alcanivorax borkumensis.

"We focused on the A. borkumensis pump and tested it in a strain of host microbe engineered to produce the limonene jet fuel precursor," Mukhopadhyay says. "Microbes expressing the pump produced significantly more limonene than those with no pump, providing an important proof of principle demonstration that efflux pumps that increase tolerance to exogenous biofuel can also improve the yield of a production host."

Mukhopadhyay and her JBEI colleagues have begun evaluating microbial efflux pumps for other important compounds as well as inhibitors present in the carbon source from lignocellulose. They are also looking to improve the A. borkumensis pump and other high performers in their current library, and to optimize the systems by which pump genes are expressed in engineered biofuel-producing microbial strains.

"We believe our bioprospecting strategy for biofuel tolerance mechanisms is going to be a valuable and widely applicable tool in the biotechnology field for engineering new microbial production strains," Mukhopadhyay says.

This research was supported by JBEI through the DOE Office of Science.

Mary J Dunlop, Zain Y Dossani, Heather L Szmidt, Hou Cheng Chu, Taek Soon Lee, Jay D Keasling, Masood Z Hadi, Aindrila Mukhopadhyay. Engineering microbial biofuel tolerance and export using efflux pumps. Molecular Systems Biology, 2011; 7 DOI: 10.1038/msb.2011.21

Source: DOE/Lawrence Berkeley National Laboratory.

Tobacco, A Perfect Pesticide Alternative

2010-10-30T07:35:00.000-07:00

Tobacco, used on a small scale as a natural organic pesticide for hundreds of years, is getting new scientific attention as a potential mass-produced alternative to traditional commercial pesticides.

That's the topic of a report in ACS' bi-weekly journal Industrial & Engineering Chemistry Research.

Cedric Briens and colleagues note that concerns about the health risks of tobacco have reduced demand and hurt tobacco farmers in some parts of the world. Scientists are looking for new uses for tobacco. One potential use is as a natural pesticide, due to tobacco's content of toxic nicotine. For centuries, gardeners have used home-made mixtures of tobacco and water as a natural pesticide to kill insect pests. A "green" pesticide industry based on tobacco could provide additional income for farmers, and as well as a new eco-friendly pest-control agent, the scientists say.

They describe a promising way to convert tobacco leaves into pesticides with pyrolysis. That process involves heating tobacco leaves to about 900 degrees Fahrenheit in a vacuum, to produce an unrefined substance called bio-oil. The scientists tested tobacco bio-oil against a wide variety of insect pests, including 11 different fungi, four bacteria, and the Colorado potato beetle, a major agricultural pest that is increasingly resistant to current insecticides. The oil killed all of the beetles and blocked the growth of two types of bacteria and one fungus.

Even after removal of the nicotine, the oil remained a very effective pesticide. Its ability of the oil to block some but not all of the microorganisms suggests that tobacco bio-oil may have additional value as a more selective pesticide than those currently in use, the report indicates.

Source: American Chemical Society, via EurekAlert!.

Environmental Labeling of Food Needs Robust Scientific Principles

2010-10-30T07:28:00.000-07:00

Environmental labeling of food needs to be based on robust, scientific principles if it is to be effective, says a University of Hertfordshire researcher.

Dr Kathy Lewis, one of the authors of the report, Effective Approaches to Environmental Labeling of Food Products, which explored the effectiveness of environmental labeling, claims that more work is needed on current practices for environmental labeling to bring it up to an adequate scientific level.

"We need a joined-up approach and an industry standard based on robust scientific principles," said Dr Lewis.

The report, which was commissioned by the Department for Environmental, Food and Rural Affairs (DEFRA) and carried out by researchers at the University of Hertfordshire's Agricultural and Environmental Research Unit, in collaboration with the Policy Studies Institute (PSI) and the Food Ethics Council (FEC), explored the effectiveness of current environmental labeling of food as a means of encouraging people to work towards reducing the negative environmental impacts of food production and consumption.

It compared the pros and cons of different existing schemes for environmental labeling of food on industry, consumers and the environment.

It found that a label for industry would have a limited role to play compared with other policy options including regulation; and investigated the potential consequences for industry of launching such a label.

The researchers also found that existing consumer 'eco-labels' need a considerable amount of scientific development before a true "omni-label," designed to give customers a complete overview of a product's environmental and social impact could be a reality.

They also found that at the moment the majority of these labels do not directly infer that any environmental benefits have been achieved.. Dr Kathy Lewis at the University of Hertfordshire's Agricultural and Environmental Research Unit said: "The majority of food 'eco-labels' that are currently in use are based on the promotion of best-practice and do not measure emissions or impacts in any way, mainly due to cost and the scientific practicality.

"A true 'omni-label' would give detailed information about highly scientific topics such as air emissions, water quality and biodiversity; we need to find a standard, simpler way of communicating this to the consumer. We have made these recommendations to DEFRA and we expect these findings will be used to inform Government policy."

Source: University of Hertfordshire, via AlphaGalileo.

Distinguishing between all eight tuna species

2009-10-27T17:45:00.000-07:00

A new paper published October 27 in PLoS One unveils for the first time a method to accurately distinguish between all eight tuna species from any kind of processed tissue using genetic sequencing. Tunas are among the most economically valuable and yet the most endangered commercially exploited fish in the world.

Identification of these species in traded forms, which are typically dressed, gilled and gutted, or loin and belly meat, and either fresh or frozen, is a highly complex process -- which may hamper conservation efforts on trade controls.

The paper, co-authored by Dr Jordi Viñas, a fish genetics specialist at Girona University in Spain and Dr Sergi Tudela, Head of Fisheries of WWF Mediterranean, proposes for the first time ever a genetic method for the precise identification of all eight recognized species of tuna.

The analysis of the DNA sequence variability of two unlinked genetic markers, one a hypervariable segment of the mitochondrial genome and the other a nuclear gene, enables full discrimination between all eight tuna species.

"This methodology will allow the identification of tuna species of any kind of tissue or type or presentation -- including sushi and sashimi," said Dr Jordi Viñas of Girona University. "The differentiation between different tunas, even those with highly similar genes, is now possible."

"Our findings are particularly relevant for the highly overfished, overtraded -- and hence endangered Atlantic bluefin tuna, for which there is a growing campaign to impose a temporary ban on international trade," added co-author Dr Sergi Tudela of WWF. "There will now be no trace of doubt when seeking to identify chilled or frozen tuna flesh at port or point of sale."

Funding: This work was done thanks to funding from OAK Foundation and Prince Albert II of Monaco Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Source: Public Library of Science.

Natural Ways of cleaning contaminated soils

2009-09-24T06:30:00.001-07:00

Researchers at North Carolina State University are working to demonstrate that trees can be used to degrade or capture fuels that leak into soil and ground water. Through a process called phytoremediation – literally a “green” technology – plants and trees remove pollutants from the environment or render them harmless. Through a partnership with state and federal government agencies, the military and industry, Dr. Elizabeth Nichols, environmental technology professor in NC State’s Department of Forestry and Environmental Resources, and her team are using phytoremediation to clean up a contaminated site in Elizabeth City, N.C.

Phytoremediation uses plants to absorb heavy metals from the soil into their roots. The process is an attractive alternative to the standard clean-up methods currently used, which are very expensive and energy intensive. At appropriate sites, phytoremediation can be a cost-effective and sustainable technology, Nichols says.

The Coast Guard site before trees were planted. Bottom -- July 2009: The same view in 2009. Some trees are now more than 30 feet tall. Bare spots indicate where bunkers were located and contamination is greatest. (Credit: Image courtesy of North Carolina State University).

The Coast Guard site was planted with a mixture of fast-growing trees such as hybrid poplars and willows to prevent residual fuel waste from entering the Pasquotank River by ground water discharge. About 3,000 trees were planted on the five-acre site, which stored aircraft fuel for the Coast Guard base from 1942 until 1991. Fuels had been released into the soil and ground water over time. Efforts to recover easily extractable fuel using a free product recovery system – also called “oil skimmers” – had stalled so other remedial options were considered before choosing phytoremediation. “We knew that tree growth would be difficult on portions of the site due to the levels of fuels in the soil and ground water, but, overall, we thought the trees could keep this contamination from moving toward the river by slowing ground water flow,” Nichols said. “Trees need water for photosynthesis so they absorb water from the ground; that process can slow the amount of ground water flowing toward the river.” In the process of absorbing water from the ground, trees can take up fuel contaminants. Some contaminants will be degraded by trees during this process while others will be released into the air by tree leaves and stems. “We wanted to demonstrate that the trees would first slow the movement of fuel toward the river,” Nichols said.

Trees can also increase the abundance and diversity of soil microorganisms around their roots. Some of these soil microorganisms will degrade the fuel still remaining in the ground. “This can be a slower process, but we also want to show that trees will remove the remaining fuel footprint over time,” Nichols continued.

Initially, 500 hybrid poplar and willow trees were planted in 2006. Another 2,500 trees were planted in 2007. “Our initial results are very encouraging, and amounts of fuel in the ground have decreased much faster than anticipated,” Nichols said, “but there is still much to learn about how trees can impact residual, weathered fuels over time. There are two areas on the site where trees do not do well, but, overall, tree growth and survival are impressive.” The Coast Guard has recognized the value of phytoremediation from this study, and has established two additional phytoremediation systems at different locations on base.

The project received a $240,584 grant from the U.S. Environmental Protection Agency and the N.C. Department of Environment and Natural Resources’s (NCDENR) Division of Water Quality 319 program, and an additional $15,000 grant from British Petroleum North America to establish the demonstration site. Nichols worked with Brad Atkinson (NCDENR), Dr. James Landmeyer (U.S. Geological Survey), J.P. Messier (U.S. Coast Guard), and Rachel Cook, a graduate student at NC State, to design and implement the phyto-demonstration site. NC State was recently awarded an additional EPA/NCDENR 319 grant to continue monitoring the site for tree growth and fuel reduction, tree toxicity to fuels, changes to ground water levels and flow, and how fuel contamination is actually removed by trees.

Source: North Carolina State University.

Mosquito repellents from plant essential oils

2009-09-22T11:15:00.000-07:00

Agricultural Research Service (ARS) scientists have teamed up with researchers from a company in American Samoa to investigate the chemical makeup of a mosquito- and ant-repellent essential oil from a native Samoan plant. The ARS scientists and researchers at Agro Research, Inc., in Pago Pago, American Samoa, discovered that the oil from a local plant repelled mosquitoes and pest ants in preliminary studies, which were conducted under a material transfer agreement. The isolation and identification of the active component (or components) will be done as part of a recently established one-year cooperative research and development agreement.

The plant is one of the 540 native species of flowering plants in American Samoa, a U.S. island territory in the South Pacific.

ARS chemists Robert Vander Meer and Ulrich Bernier at the agency’s Center for Medical, Agricultural and Veterinary Entomology in Gainesville, Fla., are working with Agro Research, Inc.’s Pemerika Tauiliili to identify the active ingredients in the plant essential oil.

Two mosquito species—Aedes aegypti and Anopheles albimanus—were used to evaluate the essential oil’s repellency. A. aegypti transmits viruses that cause yellow fever, dengue and chikungunya. A. albimanus transmits malaria parasites and is not as susceptible to repellents as many other mosquito species.

The essential oil was also tested on the red imported fire ant, Solenopsis invicta. Significant repellency was observed with concentrations diluted more than 100-fold, and the active components are likely a small fraction of the total oil.

While American Samoa is malaria-free, mosquitoes pose significant problems for the Samoan population due to transmission of dengue virus.

Exploration for new active ingredients among botanical extracts has value because it can lead to the discovery of new synthetic analogs with unique and useful properties.

Source: USDA/Agricultural Research Service.

Controlling soybean aphids without chemical pesticides

2009-09-21T21:02:00.000-07:00

Two Iowa State University researchers are examining a new method of controlling soybean aphids without the use of chemical pesticides. Bryony Bonning, professor of entomology, and Allen Miller, professor of plant pathology and director of the Center for Plant Responses to Environmental Stresses, are looking at a way to genetically modify soybeans to prevent damage from aphids.

If the research is successful, soybeans will carry in-plant protection from aphids, similar to the way genetically modified corn now keeps the European Corn Borer from destroying corn yields, but using a different molecular tool. Modified corn technology has been in use for about 12 years.

The study is being funded by a Grow Iowa Values Fund Grant. The goal of the grant program is to support development of technologies with commercial potential and to support the growth of companies using those technologies.

The researchers are working with Pioneer Hi-Bred, a DuPont business, as their corporate partner.

Previous research at Iowa State University indicated that if major soybean aphid outbreaks were left untreated, the loss in yield could exceed $250 million in Iowa. The annual cost to prevent the yield loss with insecticides can reach $64 million for Iowa soybean growers.

Soybean aphid outbreaks have become an annual phenomenon in Iowa, according to Miller.

The current research focuses on introducing a gene into soybeans that is harmless to mammals, but creates a toxin that is lethal to aphids that feed on soybean plants.

In order to be effective, the toxin needs to be taken intact into the body cavity of the aphid, not broken down by the digestive system in the bug.

Miller and Bonning identified a plant virus coat protein eaten by soybean aphids that doesn't break down and goes into the aphid body cavity intact.

They know the virus coat protein remains intact because the aphids often spread the virus from plant to plant while they are feeding.

Coat proteins make up the outer shell of a virus particle.

The researchers devised a method to use virus coat proteins to their advantage. The researchers have fused their toxin to the virus' protein coat. Since the protein coat is only part of the virus to be used, there is no risk of an infectious virus. Also, the coat protein is from a virus that normally doesn't infect soybeans.

When the hybrid toxin coat protein is eaten by the aphid, the fatal toxin should get into the aphid body cavity intact.

"What we thought was, if this (virus) protein has this ability to be taken up into the aphid (intact), let's take advantage of that specialization and fuse that to other proteins that are toxic," said Miller.

In addition to possibly curbing the aphid problem and the yield loss it causes, there are other benefits to the farmers and the ecosystems.

"The (potential) economic impact overall is huge," said Bonning. "There will be less insecticide use, and also less fossil fuel used to apply the insecticides."

Also, spraying soybeans with insecticides doesn't just control the aphids, according to Bonning.

"When you spray, you also control beneficial insects," said Bonning. "Lady beetles are affected, for example, and they are a natural enemy of the aphids. So when the aphids come back to a field after spraying, there won't be any lady beetles to naturally control the aphid populations."

Miller adds that if growers spray for aphids and don't eliminate them all, the aphids simply disperse to other fields, making the problem worse.

"There are many reasons not to spray, but you can't tell the growers to stop spraying until you give them an alternative for soybean aphid management," said Bonning.

Source: Iowa State University.

Intelligent hormonal defense in plants

2009-09-17T19:23:00.000-07:00

Plants are not as defenceless as they may seem. Various plant hormones work together to specifically fend off attacks. Dutch-sponsored researcher Antonio Leon-Reyes has now shown how these hormones cooperate. By 'consulting' with each other plant hormones determine which defence mechanism they shall set in motion.

Leon-Reyes investigated how three plant hormones - salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) - cooperate with each other to initiate the correct defence response. The biologist used the model plant Arabidopsis thalania (thale cress) to analyse the communication lines between hormones. He discovered that JA is under the control of SA but if JA and ET cooperate then JA no longer 'listens' to SA.

The right defense

Plants are confronted with various external attacks. Fungi, bacteria, viruses and insects, such as caterpillars and aphids, can inflict serious damage on a plant. The three different hormones all respond to these attacks in their own way. SA ensures that pathogens feeding on living plant tissue are tackled, whereas JA and ET tackle pathogens that live on dead tissue and suppress feeding by insects.

Switching on the defence mechanism requires a lot of energy from the plant and can go to the cost of growth and reproduction. It is therefore vital that the plant only initiates the defence mechanisms required. Leon-Reyes discovered that if the SA response was activated just before or at the same time as the JA response, the defence mechanisms regulated by JA are suppressed. Yet if the JA response was activated at the same time as the ET response then SA could no longer suppress JA.

Each year billions of euros are spent on chemical pesticides to control diseases and plagues. Leon-Reyes's discoveries could make an important contribution to new crop protection methods. His research was part of Corné Pieterse's research project. Pieterse received a Vici grant in 2004 from NWO's Innovational Research Incentives Scheme for his research into the self-defence mechanisms of plants.

Mechanism enabling plants survive dangerous gene alterations

2009-09-11T22:09:00.000-07:00

Unlike animals and humans, plants can't run and hide when exposed to stressful environmental conditions. So how do plants survive? A new Université de Montréal study, published in the journal Proceedings of the National Academy of Sciences, has found a key mechanism that enables plants to keep dangerous gene alterations in check to ensure their continued existence."We've discovered a new pathway that plants use to protect their genes against dangerous alterations that could also allow some useful mutations to occur," says Normand Brisson, a Université de Montréal biochemistry professor who made his discovery with graduate students Alexandre Maréchal and Jean-Sébastien Parent.

"Such mutations played an important role in the evolution of plants with high nutritional value, resistance to disease and harsh climate that are so important to modern agriculture," adds Dr. Brisson. "Our results open new research avenues for the study of similar mechanisms of gene repair in humans that might be important for human evolution, our responses to stress and the prevention of devastating diseases."

How do plant genes mutate?

All living things are constantly exposed to stressors that can provoke gene mutations, yet if uncorrected such mutations can have disastrous consequences such as the development of cancers in humans or cell resistance to cancer-fighting drugs.

Cells have evolved a battery of mechanisms to correct mutations, including recently discovered strategies that can also modify the number of copies of individual genes. These corrective mechanisms have attracted a lot of scientific interest since they could play a key role in species evolution. For example, while chimps and humans have almost identical genes, differences present in the number of copies of individual genes could account for distinctions between these species.

Dr Brisson suspected that a protein family he has studied for years, called the "Whirlies" (because of their peculiar structure similar to a whirligig) might be important to protect against mutations in plant cells – specifically in the chloroplast – the engine of photosynthesis that allows plants to transform carbon dioxide into sugar and expel the oxygen we breathe.

Working with his students and Biochemistry Professor Franz Lang, they showed that Whirlies are key to preventing major rearrangements of genes that could result in the creation of multiple gene copies. The discovery is important, since the number of copies of a gene must be kept scrupulously in balance with other genes so they can function correctly together.

Even though gene multiplication can be thought of as detrimental, such multiplication can be an important adaptation to stressors and so keeping such mutations in check must be balanced against creating mutations that may actually help living things survive in changing conditions.

"As the effects of climate change and industrial pollution cause increasing concern for human health, we might overlook how increases in temperature and pollutants affect the plants we depend on for our survival,'' stresses Dr. Brisson. "These rapid changes in environmental conditions all cause great stress on crops, trees and wild plants and could have further unforeseen effects on their genes."
Source: University of Montreal.

Researchers found a reliable marker of colony collapse disorder

2009-08-25T08:35:00.000-07:00

Researchers report this week that they have found a surprising but reliable marker of colony collapse disorder, a baffling malady that in 2007-2008 killed off more than a third of commercial honey bees in the U.S. Their study, in the Proceedings of the National Academy of Sciences, is the first to identify a single, objective molecular marker of the disorder, and to propose a data-driven hypothesis to explain the mysterious disappearance of American honey bees. The team included researchers from the University of Illinois and the U.S. Department of Agriculture.

U. of I. researchers spearheaded the honey bee genome project, which was completed in October 2006, less than a month before the first reports of colony collapse disorder (CCD) began to circulate. The new study made use of the genome and a genome-based tool, the microarray, to look for differences in gene expression in the guts of healthy honey bees and in those from hives afflicted by CCD.

Such microarray analyses normally identify only active genes – those that have been transcribed into messenger RNA in the first stage of building proteins. But Reed Johnson, a University of Illinois doctoral student in entomology and first author on the study, noticed that the microarrays were turning up large quantities of fragmented ribosomal RNA (rRNA) in the bees affected by CCD. Ribosomes are the factories in which proteins are made, but Johnson observed that this rRNA contained adenosine-rich sequences not seen in normal ribosomes. Such "polyadenylation" is believed to be a sign of ribosome degradation.

"Microarrays for other organisms also contain these mysterious pieces of ribosomal RNA, for reasons that are not yet altogether clear," said entomology and neuroscience professor Gene Robinson, a co-principal investigator on the study with entomology professor and department head May Berenbaum. But comparisons of healthy bees and bees from hives afflicted with CCD showed that the fragments were present at a much higher frequency in the CCD bees, he said.

"They are overrepresented in the CCD bees, significantly overrepresented," Berenbaum said. "The one consistent indicator of CCD across samples collected at multiple times and in multiple places was the overabundance of ribosomal fragments."

When the team looked at the pathogens of healthy bees and bees from hives affected by CCD, they saw that the CCD bees suffered "more than their share" of infections with viruses that attack the ribosome, Berenbaum said. These so-called picorna-like viruses "hijack the ribosome," she said, taking over the cellular machinery to manufacture only viral proteins. The list of picorna-like viruses that afflict honey bees is long and includes Israeli acute paralysis virus, which was once suspected of being the primary cause of CCD.

Numerous suspects have been identified in the hunt for a cause of CCD, from nutritional deficiencies to exposure to genetically modified plants or pesticides. Researchers in Spain recently pointed to a parasitic fungus, Nosema ceranae, which afflicts many CCD bees in Spain.

The loss of ribosomal function would explain many of the phenomena associated with CCD, Berenbaum said.

"If your ribosome is compromised, then you can't respond to pesticides, you can't respond to fungal infections or bacteria or inadequate nutrition because the ribosome is central to the survival of any organism. You need proteins to survive," she said.

The varroa mite, which is believed to have killed off a significant number of honey bees after it was accidentally introduced to the U.S. in 1986, is a carrier of picorna-like viruses, and is likely a significant contributor to the high viral pathogen load that afflicts U.S. bees. The mite may act as a tipping factor leading to ribosome breakdown, the researchers said.

All of these influences, along with the practice of carting bees around the country for pollination services, are significant stressors on the bees, a heavy burden that would be amplified by a loss of ribosomal function, Robinson said.

This study was supported by the USDA. Berenbaum is also an affiliate of the Institute for Genomic Biology at Illinois. Robinson directs the Neuroscience Program at Illinois and is a faculty member of IGB.
Source: University of Illinois at Urbana-Champaign.

Craig Venter and ExxonMobil join hands in biofuel venture

2009-08-20T20:50:00.000-07:00

In these days we all know that regular gas is no more a cheaper ingredient in our lives. Not just the price of the gas in terms of per gallon, but the cost we cannot pay in terms of global warming and melting ice caps. Almost all of the Universities around the world are concentrating on how to make cheaper biofuel. I know that most of the post docs from my circle are working in biofuel related research. There are many alternatives in coming up with good quality biofuel, but petroleum giant Exxonmobil has decided to go with algea. This is the first time that such a big company is investing in biofuels.

Why is that I am writing about it here? Obviously biofuel is my interest, but this is not the right place to talk about it. The reason for mentioning about it here is due to involvement of one of the biggest institutes in human genomics research, The Craig Venter's company, Synthetic Genomics (SGI), is helping ExxonMobil in developing algae based biofuels. In this $600 million contract,SGI
will develop fuels for cars and planes without a need for engine modifications. The scientific team will be testing different cocktails as they are developed at the new facility that will be built in San Diego that includes ponds and bioreactors for the algae to grow. We will be seeing more companies of this type that will follow the suit of biofuels in the coming future.

Airborne soot in combination with particulate pollution not good for global warming

2009-06-30T18:21:00.000-07:00

Particulate pollution thought to be holding climate change in check by reflecting sunlight instead enhances warming when combined with airborne soot, a new study has found. Like a black car on a bright summer day, soot absorbs solar energy. Recent atmospheric models have ranked soot, also called black carbon, second only to carbon dioxide in potential for atmospheric warming. But particles, or aerosols, such as soot mix with other chemicals in the atmosphere, complicating estimates of their role in changing climate.

Los Angeles. Particulate pollution thought to be holding climate change in check by reflecting sunlight instead enhances warming when combined with airborne soot, a new study has found. "Until now, scientists have had to assume how soot is mixed with other chemical species in individual particles and estimate how that ultimately impacts their warming potential," said Kimberly Prather, professor in the Department of Chemistry and Biochemistry and the Scripps Institution of Oceanography at the University of California, San Diego. "Our measurements show that soot is most commonly mixed with other chemicals such as sulfate and this mixing happens very quickly in the atmosphere. These are the first direct measurements of the optical properties of atmospheric soot and allow us to better understand the role of soot in climate change."

Prather and Ryan Moffet, a former graduate student at UC San Diego who is now at the Lawrence Berkeley National Laboratory, measured atmospheric aerosols over Riverside, California and Mexico City. Using an instrument that measures the size, chemical composition and optical properties of aerosols in real time, they showed that jagged bits of fresh soot quickly become coated with a spherical shell of other chemicals, particularly sulfate, nitrate, and organic carbon, through light-driven chemical reactions.

Within several hours of sunrise, most of the atmospheric carbon they measured had been altered in this way, they report in the Proceedings of the National Academy of Sciences online the week of June 29.

Particles of sulfate or nitrate alone reflect light, and some have proposed pumping sulfate aerosols into the atmosphere to slow climate change. But these chemicals play a different role when they mix with soot.

"The coating acts like a lens and focuses the light into the center of the particle, enhancing warming," Prather said. "Many people think sulfate aerosols are a good thing because they are highly reflective and cool our planet. However we are seeing that sulfate is commonly mixed with soot in the same particles, which means in some regions sulfate could lead to more warming as opposed to more cooling as one would expect for a pure sulfate aerosol."

Their measurements showed that in the atmosphere the lens-like shell of sufate and nitrate enhances absorption of light by coated soot particles 1.6 times over pure soot particles.

Soot comes from fires, including those used to cook food and clear agricultural fields, as well as burning of diesel fuel in trucks and ships. Simple measures such as providing better cook stoves with more complete combustion to those in developing countries would help reduce atmospheric soot levels.

Efforts to reduce soot would pay off soon. Unlike carbon dioxide, which lingers in the atmosphere for centuries, soot falls from the sky in a matter of days to weeks, making the reduction of soot a quicker option for slowing down climate change.

"While reducing CO2 concentrations is extremely important, changes we make today will not be felt for quite a while, whereas changes we make today on soot and sulfate could affect our planet on timescales of months," Prather said. "This could buy us time while we grapple with the problems of reducing carbon dioxide and other greenhouse gases." via University of California - San Diego.

Talk to my right ear if you need something

2009-06-24T18:44:00.000-07:00

We humans prefer to be addressed in our right ear and are more likely to perform a task when we receive the request in our right ear rather than our left. In a series of three studies, looking at ear preference in communication between humans, Dr. Luca Tommasi and Daniele Marzoli from the University "Gabriele d'Annunzio" in Chieti, Italy, show that a natural side bias, depending on hemispheric asymmetry in the brain, manifests itself in everyday human behavior.

One of the best known asymmetries in humans is the right ear dominance for listening to verbal stimuli, which is believed to reflect the brain's left hemisphere superiority for processing verbal information. However, until now, the majority of studies looking at ear preference in human communication have been controlled laboratory studies and there is very little published observational evidence of spontaneous ear dominance in everyday human behavior.

Tommasi and Marzoli's three studies specifically observed ear preference during social interactions in noisy night club environments. In the first study, 286 clubbers were observed while they were talking, with loud music in the background. In total, 72 percent of interactions occurred on the right side of the listener. These results are consistent with the right ear preference found in both laboratory studies and questionnaires and they demonstrate that the side bias is spontaneously displayed outside the laboratory.

In the second study, the researchers approached 160 clubbers and mumbled an inaudible, meaningless utterance and waited for the subjects to turn their head and offer either their left of their right ear. They then asked them for a cigarette. Overall, 58 percent offered their right ear for listening and 42 percent their left. Only women showed a consistent right-ear preference. In this study, there was no link between the number of cigarettes obtained and the ear receiving the request.

In the third study, the researchers intentionally addressed 176 clubbers in either their right or their left ear when asking for a cigarette. They obtained significantly more cigarettes when they spoke to the clubbers' right ear compared with their left.

According to the authors, taken together, these results confirm a right ear/left hemisphere advantage for verbal communication and distinctive specialization of the two halves of the brain for approach and avoidance behavior.

They conclude: "Our studies corroborate the idea of a common ancestry - in humans and other species - of lateralized behavior during social interactions, not only for species-specific vocal communication, but also for affective responses." via Springer Science

Obtaining drinking water from air humidity

2009-06-08T20:59:00.000-07:00

Not a plant to be seen, the desert ground is too dry. But the air contains water, and research scientists have found a way of obtaining drinking water from air humidity. The system is based completely on renewable energy and is therefore autonomous. Cracks permeate the dried-out desert ground, the landscape bears testimony to the lack of water. But even here, where there are no lakes, rivers or groundwater, considerable quantities of water are stored in the air. In the Negev desert in Israel, for example, annual average relative air humidity is 64 percent – in every cubic meter of air there are 11.5 milliliters of water.

Research scientists at the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB in Stuttgart working in conjunction with their colleagues from the company Logos Innovationen have found a way of converting this air humidity autonomously and decentrally into drinkable water. “The process we have developed is based exclusively on renewable energy sources such as thermal solar collectors and photovoltaic cells, which makes this method completely energy-autonomous. It will therefore function in regions where there is no electrical infrastructure,” says Siegfried Egner, head of department at the IGB. The principle of the process is as follows: hygroscopic brine – saline solution which absorbs moisture – runs down a tower-shaped unit and absorbs water from the air. It is then sucked into a tank a few meters off the ground in which a vacuum prevails. Energy from solar collectors heats up the brine, which is diluted by the water it has absorbed.

Because of the vacuum, the boiling point of the liquid is lower than it would be under normal atmospheric pressure. This effect is known from the mountains: as the atmospheric pressure there is lower than in the valley, water boils at temperatures distinctly below 100 degrees Celsius. The evaporated, non-saline water is condensed and runs down through a completely filled tube in a controlled manner. The gravity of this water column continuously produces the vacuum and so a vacuum pump is not needed. The reconcentrated brine runs down the tower surface again to absorb moisture from the air.

“The concept is suitable for various sizes of installation. Single-person units and plants supplying water to entire hotels are conceivable,” says Egner. Prototypes have been built for both system components – air moisture absorption and vacuum evaporation – and the research scientists have already tested their interplay on a laboratory scale. In a further step the researchers intend to develop a demonstration facility.via Fraunhofer-Gesellschaft.

Predict future periods of drought more accurately

2009-06-03T21:03:00.000-07:00

Using new data and reconstructions of the “Dust Bowl” drought in America during the 1930s, climatologists at the ETH have shown for the first time a three-dimensional picture of the atmospheric circulation that led to the drought. This will enable climate models to be evaluated and further improved. The scientists hope this work will make it possible to predict future periods of drought more accurately.

In the 1930s, a drought that lasted almost ten years wrought havoc on the Midwest region of North America. The enormous dust storms accompanying it gave the “Dust Bowl” drought its name. This drought had devastating socio-economic consequences for America. John Steinbeck immortalised the tragic story of farmers already impoverished by the economic crisis of the time in his novel “The Grapes of Wrath”. And the legendary “Route 66”, along which the farmers fled towards California, was made famous in part by the Dust Bowl.
The city of Stratford in Texas is engulfed by a dust storm on 18 April 1935. A common event during the "Dust Bowl" drought. (Credit: NOAA George E. Marsh Album).

Digitalised historical data improve model
Scientists have been studying the Dust Bowl phenomenon for decades, and until now the mechanisms that caused this exceptionally long period of drought have not been fully understood, as little information has been available on the atmospheric circulation. Stefan Brönnimann, Professor at the Institute for Atmospheric and Climate Science at ETH Zurich, and his team have now used historical data to reconstruct and analyse the three-dimensional circulation during the Dust Bowl drought. At the time of the drought, wind and temperature readings were already being taken using balloons and aircraft, initially at altitudes of three to eight kilometres, and later at much higher altitudes. These data have now been digitalised as part of a US project and a project undertaken by the Swiss National Science Foundation. Based on these data, Brönnimann’s team used statistical methods to reconstruct the upper air circulation at an altitude of up to 15 kilometres.

Based on computer models, researchers have up to now conjectured that unusual sea surface temperatures in the Pacific and Atlantic Oceans would have altered the wind systems, thereby triggering the drought. At the same time, the dying vegetation, the parched soil and the dust created by these conditions could have further intensified the drought. However, according to Brönnimann, observations to date have offered insufficient confirmation of these hypotheses based on simulated models.

Exceptionally cold Pacific
In their study, the scientists focused on three known circulation patterns which characterise the basic wind conditions of the region and the wider area. Using the new data, they were able to show that a specific wind flow, the Great Plains Low-Level Jet, was shallower at the time of the Dust Bowl. This air current usually carries moist air from the tropical Atlantic far into the region, which covers approximately two million square kilometres. In addition, the Jet did not penetrate as far north as usual, as it was deflected too early towards the east.

The researchers believe this was caused by a high-pressure system that built up over the Plains and was associated with an abnormal upper air flow extending from the Pacific across North America to the Atlantic.

“Overall, these features are clearly consistent with the flow conditions that climate models predict as the effect of a cold Pacific coinciding with a warm Atlantic”, explains Brönnimann. Because the temperatures of the tropical oceans can to a certain degree be predicted, the scientists see here the possibility of predicting periods of drought as well. However, the study also shows up some remaining shortcomings in the models: for the most part, they would not correctly depict the spatial shift of the Low-Level Jet, and in many models the drought is located too far to the south. via ETH Zurich.

Cotton hydromulch "spray-on blanket" from USDA

2009-05-31T20:01:00.000-07:00

Agricultural Research Service (ARS) agricultural engineer Greg Holt helped develop the erosion control industry's first cotton hydromulch "spray-on blanket." Holt is at the ARS Cotton Production and Processing Research Unit in Lubbock, Texas.

Hydromulch is the bright-green mulch used in spray-on slurries that cover bare lands at construction sites and roadside projects, to prevent erosion until vegetation can be established. In the past, hydromulches were made mostly from wood and paper byproducts.
Summit Seed, Inc., employee Dan Pralle sprays a test plot with one of the cotton-based hydromulches developed during the research study on value-added processing of cotton gin byproducts. (Credit: Photo by Greg Holt). GeoSkin® Cotton Hydromulch is made from cotton gin byproducts. It is a combination hydromulch/spray-on erosion-control blanket that performs better than conventional roll-on blankets and requires significantly less labor. Holt and colleagues tested the prototype against commercial erosion control blankets made of straw, wood and coconut.

The total runoff from these four mulches, including soil and mulch ingredients, was: cotton, 222 pounds per acre; straw, 7,832 pounds per acre; wood, 7,474 pounds per acre; and coconut, 3,719 pounds per acre.

The cotton hydromulch was produced using technology developed from cooperative research efforts between ARS; Cotton Incorporated of Cary, N.C.; Summit Seed, Inc., of Manteno, Ill.; and Mulch & Seed Innovations, LLC, of Centre, Ala. ARS has applied for a patent on the process.

The technology has served as a foundation for developing a broader line of cotton hydromulches for erosion control, including a premium hydromulch for steep slopes, and more recently, a midgrade product for flat- to mid-slope terrain.

One of Holt's studies showed that cotton-based hydromulches established a good stand of grass, compared to other hydromulches and a straw blanket which didn't do as well.

Cotton Incorporated is the research and marketing organization representing upland cotton. The organization partially funded some of Holt's studies, which also involved a farm consultant, ARS colleague Ken Potter in Temple, Texas, and a colleague at Auburn University in Auburn, Ala. via USDA/Agricultural Research Service.