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Thursday, August 7, 2008

article : We must Know for Tomorrow’s Salads

Plant Extracts To Conquer Microbes

Research leader of the ARS Processed Foods Research Unit in Albany, California, examines colorful fruit- and vegetable-based edible films: Click here for full photo caption.
Tara McHugh, research leader of the ARS Processed Foods Research Unit in Albany, California, examines colorful fruit- and vegetable-based edible films. Antimicrobial edible films are now being tested against pathogenic bacteria. (K10168-1)

Tender leaves of deep-green, freshly harvested spinach—neatly displayed in sealed bags at the chilled-produce section of your local supermarket—may one day include a powerful new food-safety feature. That added protection might take shape as a five-thousandths-of-an-inch-thick piece of what’s known as “edible film,” made from a purée of spinach itself.

When slipped into the bag, the protective power of this little puréed spinach square or wedge would come from a potent antimicrobial compound chosen from nature’s bounty of botanical bactericides. The antimicrobial would be added in tiny amounts during the puréeing process to provide a safe, effective, natural defense against pathogens like E. coli O157:H7, Salmonella, Listeria, and others.

Carvacrol, the predominant essential oil in oregano, would add a pleasant—and protective—accent to a spinach-purée film, for example. Already shown in lab investigations to be an effective weapon against several major foodborne pathogens, carvacrol currently flavors some popular salad dressings and seasoning mixes. Carvacrol vapors wafting from the wedge into the atmosphere inside the sealed bag would both season and safen the spinach.

Sound too good to be true?

ARS food technologist (right) adds carvacrol, the main active antimicrobial compound in oregano essential oil, to a flavorful tomato-based mixture while technician spreads the mixture to form an antimicrobial edible film: Click here for full photo caption.
ARS food technologist Carl Olsen (right) adds carvacrol, the main active antimicrobial compound in oregano essential oil, to a flavorful tomato-based mixture while technician Rachelle Woods spreads the mixture to form an antimicrobial edible film. Once the film dries, it will be tested against pathogenic bacteria, such as E. coli O157:H7.

Not so, say scientists at the ARS Western Regional Research Center in Albany, California, near San Francisco. The futuristic films they’re developing would complement and supplement other food-safety strategies and tactics on the farm, at the packinghouse, and elsewhere along the way from field to fork.

In pioneering experiments, the California scientists are selecting plant extracts, such as carvacrol, to put in the experimental films and are then pitting the films against pathogenic bacteria such as E. coli O157:H7. Their investigations will help transform edible antimicrobial films from concept to reality.

Though wrinkles remain to be ironed out, their findings from films made with purées of Golden Delicious or Fuji apples provide proof that the concept is sound, that the botanical extracts are powerful, and that practical, affordable films are within technology’s reach.

The experiments are the work of Tara H. McHugh and Wen-Xian Du of the center’s Processed Foods Research Unit; Mendel Friedman of the Produce Safety and Microbiology Research Unit, also at Albany; Roberto J. Avena-Bustillos of the University of California-Davis, and others.

Initial Results Promising

Neither edible films—nor the idea of making them antimicrobial—are new. McHugh’s work that led to the first-ever fruit-purée edible films, for instance, is based on a pending patent that she and coinventors filed in 2004. What is new is research from the Albany lab that shows, for the first time, that those same puréed-apple films—if enhanced with carvacrol—can kill E. coli O157:H7 in laboratory tests. Their suite of apple-purée studies can, the scientists point out, smooth the way to films that could be used to protect fresh-cut leafy greens—spinach, lettuce, and more.

A collaborating researcher from the University of California-Davis uses a micrometer to measure the width of the clear agar zone around one of the two antimicrobial edible film disks: Click here for full photo caption.
Two antimicrobial edible film disks (the top two in the petri dish) repel E. coli O157:H7 growth in the agar surrounding them. Roberto Avena-Bustillos, a collaborating researcher from the University of California-Davis, uses a micrometer to measure the width of the clear agar zone around one of the two disks. The bottom two disks are controls.

Hundreds of Compounds Scrutinized

Carvacrol was one of more than 200 botanical extracts that Friedman, a chemist, analyzed in a globe-spanning study published in 2002. Other studies of the pathogen-fighting prowess of plant oils and oil compounds abound. But the methods used to prepare those compounds for assays vary widely, as do the assays themselves, the strains of any given bacteria that were used, and other scientific variables.

“These earlier studies gave us a wealth of data,” says Friedman, “but there was no common basis of comparison for us to work forward from.”

To remedy that, Friedman and co-researchers used new sample-preparation and assay methods that they invented. For even more consistency, they used the same bacterial strains, from the same suppliers, across the investigation.

Their exhaustive study put plant compounds—from everyday allspice to exotic frankincense—up against four big-time bacterial bad guys: Campylobacter jejuni, E. coli, Salmonella, and Listeria.

A collaborating researcher from the University of California-Davis places an antimicrobial edible film into a small dish within a larger dish of spinach leaves inoculated with E. coli O157:H7: Click here for full photo caption.
Roberto Avena-Bustillos, a collaborating researcher from the University of California-Davis, places an antimicrobial edible film into a small dish within a larger dish of spinach leaves inoculated with E. coli O157:H7. The larger dish is then sealed to evaluate the efficacy of antibacterial vapors released from the film.

The study also delved into the relation of chemical structure to a bactericide’s pathogen-quelling ability. The investigation was, at the time, the most extensive of its kind, according to Friedman.

Many of the compounds examined are already approved for food use—an important bonus in choosing candidates for the experimental films.

Top scores for compounds like oregano’s carvacrol, citral from lemongrass, and cinnamaldehyde from cinnamon earned them a place in the subsequent tests of apple-purée films.

Vapors Go In, Out, Under

Importantly, some of the compounds Friedman studied—including carvacrol—have what’s called a “vapor phase.” Inside the enclosed environment of a packaged salad mix, carvacrol’s protective vapors could find their way into folds and crevices—like those on a crinkly spinach leaf—that other protectants might not reach.

So how do you gauge a film’s ability to fight a foodborne pathogen?

In several studies, extract-enhanced apple films were cut into small disks, each a half-inch in diameter. Then, the disks were put on agar gel teeming with E. coli. The samples, kept chilled, were checked at intervals to see the disks’ effects on the growth and spread of the pathogen.

Graphic: Eight Top E. coli 0157:H7 FightersAs an indicator of bactericidal strength, the researchers measured the zone around the disk in which no living E. coli could be detected. The approach is somewhat like measuring the size of the egg white surrounding the yolk of a fried egg.

The protective zone encircling oregano-impregnated apple purée disks was significantly larger than those of disks containing cinnamon or lemongrass oils, the scientists found.

A related study showed that it took nearly five times as much citral from lemongrass to get the same protective effect as oregano-derived carvacrol.

In their newest work, published in a recent issue of the Journal of Agricultural and Food Chemistry, Du, Friedman, McHugh, and coinvestigators designed a study to answer a key question about making films: Could the manufacturing process—batch or continuous—affect a film’s antimicrobial performance?

For carvacrol, the antibacterial used in the study, the answer is: No. Carvacrol-enhanced apple purée films made with a batch process were about as effective in quelling E. coli as those made with a continuous process, according to preliminary results.

McHugh and Friedman estimate that antimicrobial film inserts for packaged leafy greens—a spinach-purée wedge, a colorful square of carrot-based film, or other innovative options—might be ready within a year or so to test and evaluate at fresh-produce packinghouses. The inserts would add a reassuring new leaf to the history of packaged, ready-to-eat salads in America.—By Marcia Wood, Agricultural Research Service Information Staff.

This research is part of Food Safety (#108) and Quality and Utilization of Agricultural Products (#306), two ARS national programs described on the World Wide Web at

Tara H. McHugh, Wen-Xian Du, and Mendel Friedman are with the USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA 94710; phone (510) 559-5864, fax (510) 559-5851, [McHugh]; phone (510) 559-6148, fax (510) 559-5818, [Du]; phone (510) 559-5615, fax (510) 559-6162, [Friedman].

A biodegradable film made with casein, a milk protein, and glycerol, a byproduct of biodiesel production: Click here for photo caption.
A biodegradable film made with casein, a milk protein, and glycerol, a byproduct of biodiesel production.

Biodegradable Films From Casein

You can’t beat this wrap. At the ARS Eastern Regional Research Center in Wyndmoor, Pennsylvania, scientists have developed biodegradable films that can be used to protect fresh produce and other perishable foods.

Water-resistant, transparent, and edible, the films can protect a range of perishable products from moisture- and oxygen-induced damage.

“Barrier films with low-density polyethylene significantly reduce oxygen permeability,” says research leader Peggy Tomasula, who helped develop the film-production technology. “This can protect the color and shape of a product for a long time and extend shelf life by preventing oxidation of lipids or diffusion of flavor compounds.”

The film-production process combines casein, a byproduct of dairy production, and glycerol, a byproduct of biodiesel production. The ERRC films have not been embedded with antimicrobial materials, Tomasula says, though this is one potential application.

Read more about this research in the May/June 2007 issue of Agricultural Research, online at—By Laura McGinnis, Agricultural Research Service Information Staff.

"For Tomorrow’s Salads: Plant Extracts To Conquer Microbes" was published in the July 2008 issue of Agricultural Research magazine.

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article : Learn more about Outmaneuvering Foodborne Pathogens

Produce and leafy greens in the photo are (clockwise from top): romaine lettuce, cabbage, cilantro in a bed of broccoli sprouts, spinach and other leafy greens, green onions, tomatoes, and green leaf lettuce: Click here for full photo caption.
At various locations, ARS scientists are doing research to make leafy greens and other fresh produce safer for consumers. Produce and leafy greens in the photo are (clockwise from top): romaine lettuce, cabbage, cilantro in a bed of broccoli sprouts, spinach and other leafy greens, green onions, tomatoes, and green leaf lettuce.

If pathogens like E. coli O157:H7 or Salmonella had a motto for survival, it might be: “Find! Bind! Multiply!”

That pretty much sums up what these food-poisoning bacteria do in nature, moving through our environment to find a host they can bind to and use as a staging area for multiplying and spreading.

But ARS food-safety scientists in California are determined to find out how to stop these and other foodborne pathogenic bacteria in their tracks, before the microbes can make their way to leafy greens and other favorite salad ingredients like tomatoes and sprouts.

The research is needed to help prevent the pathogens from turning up in fresh produce that we typically eat uncooked. That’s according to Robert E. Mandrell, who leads the ARS Produce Safety and Microbiology Research Unit. His team is based at the agency’s Western Regional Research Center in Albany, California.

The team is pulling apart the lives of these microbes to uncover the secrets of their success. It’s a complex challenge, in part because the microbes seem to effortlessly switch from one persona to the next. They are perhaps best known as residents of the intestines of warm-blooded animals, including humans. For another role, the pathogens have somehow learned to find, bind, and multiply in the world of green plants.

Sometimes the pathogenic microbes need the help of other microbial species to make the jump from animal inhabitant to plant resident. Surprisingly little is known about these powerful partnerships, Mandrell says. That’s why such alliances among microbes are one of several specific aspects of the pathogens’ lifestyles that the Albany scientists are investigating. In all, knowledge gleaned from these and other laboratory, greenhouse, and outdoor studies should lead to new, effective, environmentally friendly ways to thwart the pathogens before they have a chance to make us ill.

In a greenhouse, a microbiologist examines cilantro that she uses as a model plant to investigate the behavior of foodborne pathogens on leaf surfaces: Click here for full photo caption.
In a greenhouse, microbiologist Maria Brandl examines cilantro that she uses as a model plant to investigate the behavior of foodborne pathogens on leaf surfaces.

A Pathogen Targets Youngest Leaves

Knowing pathogens’ preferences is essential to any well-planned counter-attack. So microbiologist Maria T. Brandl is scrutinizing the little-understood ability of E. coli O157:H7 and Salmonella enterica to contaminate the elongated, slightly sweet leaves of romaine lettuce. With a University of California-Berkeley colleague, Brandl has shown that, if given a choice, E. coli has a strong preference for the young, inner leaves. The researchers exposed romaine lettuce leaves to E. coli and found that the microbe multiplied about 10 times more on the young leaves than on the older, middle ones. One explanation: The young leaves are a better nutrition “buy” for E. coli. “These leaves exude about three times more nitrogen and about one-and-one-half times more carbon than do the middle leaves,” says Brandl.

Scientists have known for decades that plants exude compounds from their leaves and roots that bacteria and fungi can use as food. But the romaine lettuce study, published earlier this year in Applied and Environmental Microbiology, is the first to document the different exudate levels among leaves of the two age classes. It’s also the first to show that E. coli can do more than just bind to lettuce leaves: It can multiply and spread on them.

Research assistant inoculates a lettuce leaf with E. coli O157:H7 in a biological safety cabinet: Click here for full photo caption.
Research assistant Danielle Goudeau inoculates a lettuce leaf with E. coli O157:H7 in a biological safety cabinet to study the biology of the human pathogen on leafy greens.

Adding nitrogen to the middle leaves boosted E. coli growth, Brandl found. “In view of the key role of nitrogen in helping E. coli multiply on young leaves,” she says, “a strategy that minimizes use of nitrogen fertilizer in romaine lettuce fields may be worth investigating.”

In other studies using romaine lettuce and the popular herb cilantro as models, Brandl documented the extent to which E. coli and Salmonella are aided by Erwinia chrysanthemi, an organism that causes fresh produce to rot.

“When compared to plant pathogens, E. coli and Salmonella are not as ‘fit’ on plants,” Brandl says. But the presence of the rot-producing microbe helped E. coli and Salmonella grow on lettuce and cilantro leaves.

“Soft rot promoted formation of large aggregates, called ‘biofilms,’ of E. coli and Salmonella and increased their numbers by up to 100-fold,” she notes.

The study uncovered new details about genes that the food-poisoning pathogens kick into action when teamed up with plant pathogens such as soft rot microbes.

Brandl, in collaboration with Albany microbiologist Craig Parker, used a technique known as “microarray analysis” to spy on the genes. “The assays showed that Salmonella cells—living in soft rot lesions on lettuce and cilantro—had turned on some of the exact same genes that Salmonella uses when it infects humans or colonizes the intestines of animals,” she says. Some of these activated genes were ones that Salmonella uses to get energy from several natural compounds common to both green plants and to the animal intestines that Salmonella calls home.

Using a confocal laser scanning microscope, a microbiologist examines a mixed biofilm of Salmonella enterica (pink) and Erwinia chrysanthemi (green) in soft rot lesions on cilantro leaves (blue): Click here for full photo caption.
Using a confocal laser scanning microscope, microbiologist Maria Brandl examines a mixed biofilm of Salmonella enterica (pink) and Erwinia chrysanthemi (green) in soft rot lesions on cilantro leaves (blue).

A One-Two Punch to Tomatoes

Salmonella also benefits from the presence of another plant pathogen, specifically, Xanthomonas campestris, the culprit in a disease known as “bacterial leaf spot of tomato.” But the relationship between Salmonella and X. campestris may be different than the relation of Salmonella to the soft rot pathogen. Notably, Salmonella benefits even if the bacterial spot pathogen is at very low levels—so low that the plant doesn’t have the disease or any visible symptoms of it.

That’s among the first-of-a-kind findings that microbiologist Jeri D. Barak found in her tests with tomato seeds exposed to the bacterial spot microbe and then planted in soil that had been irrigated with water contaminated with S. enterica.

In a recent article in PLoS ONE, Barak reported that S. enterica populations were significantly higher in tomato plants that had also been colonized by X. campestris. In some cases, Salmonella couldn’t bind to and grow on—or in—tomato plants without the presence of X. campestris, she found.

Listeria monocytogenes on this broccoli sprout shows up as green fluorescence: Click here for full photo caption.
Listeria monocytogenes on this broccoli sprout shows up as green fluorescence. The bacteria are mainly associated with the root hairs.

“We think that X. campestris may disable the plant immune response—a feat that allows both it and Salmonella to multiply,” she says.

The study was the first to report that even as long as 6 weeks after soil was flooded with Salmonella-contaminated water, the microbe was capable of binding to tomato seeds planted in the tainted soil and, later, of spreading to the plant.

“These results suggest that any contamination that introduces Salmonella from any source into the environment—whether that source is irrigation water, improperly composted manure, or even insects—could lead to subsequent crop contamination,” Barak says. “That’s true even if substantial time has passed since the soil was first contaminated.”

Crop debris can also serve as a reservoir of viable Salmonella for at least a week, Barak’s study showed. For her investigation, the debris was composed of mulched, Salmonella-contaminated tomato plants mixed with uncontaminated soil.

“Replanting fields shortly after harvesting the previous crop is a common practice in farming of lettuce and tomatoes,” she says. The schedule allows only a very short time for crop debris to decompose. “Our results suggest that fields known to have been contaminated with S. enterica could benefit from an extended fallow period, perhaps of at least a few weeks.”

Ordinary Microbe Foils E. coli

While the bacterial spot and soft rot microbes make life easier for certain foodborne pathogens, other microbes may make the pathogens’ existence more difficult. Geneticist Michael B. Cooley and microbiologist William G. Miller at Albany have shown the remarkable effects of one such microbe, Enterobacter asburiae. This common, farm-and-garden-friendly microorganism lives peaceably on beans, cotton, and cucumbers.

In one experiment, E. asburiae significantly reduced levels of E. coli and Salmonella when all three species of microbes were inoculated on seeds of thale cress, a small plant often chosen for laboratory tests.

The study, published in Applied and Environmental Microbiology in 2003, led to followup experiments with green leaf lettuce. In that battle of the microbes, another rather ordinary bacterium, Wausteria paucula, turned out to be E. coli’s new best friend, enhancing the pathogen’s survival sixfold on lettuce leaves.

“It was the first clear example of a microbe’s supporting a human pathogen on a plant,” notes Cooley, who documented the findings in the Journal of Food Protection in 2006.

But E. asburiae more than evened the score, decreasing E. coli survival 20- to 30-fold on lettuce leaves exposed to those two species of microbes.

The mechanisms underlying the competition between E. asburiae and E. coli are still a mystery, says Cooley, “especially the competition that takes place on leaves or other plant surfaces.”

Nevertheless, E. asburiae shows initial promise of becoming a notable biological control agent to protect fresh salad greens or other crops from pathogen invaders. With further work, the approach could become one of several science-based solutions that will help keep our salads safe.—By Marcia Wood, Agricultural Research Service Information Staff.

This research is part of Food Safety, an ARS national program (#108) described on the World Wide Web at

To reach scientists mentioned in this article, contact Marcia Wood, USDA-ARS Information Staff, 5601 Sunnyside Ave., Beltsville, MD 20705-5129; phone (301) 504-1662, fax (301) 504-1486.

Listeria monocytogenes on this radish sprout shows up as green fluorescence: Click here for full photo caption.
Listeria monocytogenes on this radish sprout shows up as green fluorescence. The bacteria are mainly associated with the root hairs.

What Genes Help Microbes Invade Leafy Greens?

When unwanted microbes form an attachment, the consequences—for us—can be serious.

That’s if the microbes happen to be human pathogens like Listeria monocytogenes or Salmonella enterica and if the target of their attentions happens to be fresh vegetables often served raw, such as cabbage or the sprouted seeds of alfalfa.

Scientists don’t yet fully understand how the malevolent microbes form colonies that cling stubbornly to and spread across plant surfaces, such as the bumpy leaves of a cabbage or the ultra-fine root hairs of a tender alfalfa sprout.

But food safety researchers at the ARS Western Regional Research Center in Albany, California, are putting together pieces of the pathogen puzzle.

A 1981 food-poisoning incident in Canada, caused by L. monocytogenes in coleslaw, led microbiologist Lisa A. Gorski to study the microbe’s interactions with cabbage. Gorski, with the center’s Produce Safety and Microbiology Research Unit, used advanced techniques not widely available at the time of the cabbage contamination.

“Very little is known about interactions between Listeria and plants,” says Gorski, whose study revealed the genes that Listeria uses during a successful cabbage-patch invasion.

The result was the first-ever documentation of Listeria genes in action on cabbage leaves. Gorski, along with coinvestigator Jeffrey D. Palumbo—now with the center’s Plant Mycotoxin Research Unit—and others, documented the investigation in a 2005 article in Applied and Environmental Microbiology.

Listeria, Behaving Badly

“People had looked at genes that Listeria turns on, or ‘expresses,’ when it’s grown on agar gel in a laboratory,” says Gorski. “But no one had looked at genes that Listeria expresses when it grows on a vegetable.

“We were surprised to find that when invading cabbage, Listeria calls into play some of the same genes routinely used by microbes that are conventionally associated with plants. Listeria is usually thought of as a pathogen of humans. We hadn’t really expected to see it behaving like a traditional, benign inhabitant of a green plant.

“It’s still a relatively new face for Listeria, and requires a whole new way of thinking about it.”

In related work, Gorski is homing in on genetic differences that may explain the widely varying ability of eight different Listeria strains to successfully colonize root hairs of alfalfa sprouts—and to resist being washed off by water.

In a 2004 article in the Journal of Food Protection, Gorski, Palumbo, and former Albany associate Kimanh D. Nguyen reported those differences. Poorly attaching strains formed fewer than 10 Listeria cells per sprout during the lab experiment, while the more adept colonizers formed more than 100,000 cells per sprout.

Salmonella’s Cling Genes

Colleague Jeri D. Barak, a microbiologist at Albany, led another sprout investigation, this time probing the ability of S. enterica to attach to alfalfa sprouts. From a pool of 6,000 genetically different Salmonella samples, Barak, Gorski, and coinvestigators found 20 that were unable to attach strongly to sprouts.

Scientists elsewhere had already identified some genes as necessary for Salmonella to successfully invade and attach to the guts of animals such as cows and chickens. In the Albany experiments, some of those same genes were disrupted in the Salmonella specimens that couldn’t cling to alfalfa sprouts.

Their 2005 article in Applied and Environmental Microbiology helped set the stage for followup studies to tease out other genes that Salmonella uses when it is living on and in plants.

A deeper understanding of those and other genes may lead to sophisticated defense strategies to protect tomorrow’s salad greens—and us.—By Marcia Wood, Agricultural Research Service Information Staff.

Geneticist collects a sediment sample to test for E. coli O157:H7: Click here for full photo caption.
Geneticist Michael Cooley collects a sediment sample to test for E. coli O157:H7. The pathogen was found near fields implicated in the 2006 outbreak of E. coli O157:H7 on baby spinach.

Environmental Surveillance Exposes a Killer

It started as a manhunt for a microbe, but it became one of the nation’s most intensive farmscape searches for the rogue pathogen E. coli O157:H7.

ARS microbiologist Robert E. Mandrell and geneticist Michael B. Cooley of the Produce Safety and Microbiology Research Unit in Albany, California, had already been collaborating in their own small-scale study of potential sources of E. coli O157:H7 in the state’s produce-rich Salinas Valley when, in 2005, they were asked to join another one. The new investigation became a 19-month surveillance—by the two scientists and other federal and state experts—of E. coli in Salinas Valley watersheds.

“It may seem like an obvious concept today,” says Mandrell, “but at the time, there was little proof that E. coli contamination of produce before harvest could be a major cause of food-poisoning outbreaks.”

Mandrell and Cooley aided the California Food Emergency Response Team, as this food-detective squad was named, in tracing movement of E. coli through the fertile valley. This surveillance showed that E. coli O157:H7 can travel long distances in streamwater and floodwater.

In 2006, E. coli O157:H7 strains indistinguishable from those causing human illness associated with baby spinach were discovered in environmental samples—including water—taken from a Salinas Valley ranch.

Wild pigs were added to the list of animal carriers of the pathogen when one of the so-called “outbreak strains” of E. coli O157:H7 was discovered in their dung. The team documented its work in 2007 in PLoS ONE and Emerging Infectious Diseases.

The Albany scientists used a relatively new technique to detect E. coli O157:H7 in water. Developed at the ARS Meat Animal Research Center in Clay Center, Nebraska, for animal hides, the method was adapted by the Albany team for the outdoor reconnaissance.

Because of their colleagues’ work, says Cooley, “We had the right method at the right time.”—By Marcia Wood, Agricultural Research Service Information Staff.

"Outmaneuvering Foodborne Pathogens" was published in the July 2008 issue of Agricultural Research magazine.

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article : The agriculture of Content

The Columbia Encyclopedia, Sixth Edition | Date: 2008

agriculture science and practice of producing crops and livestock from the natural resources of the earth. The primary aim of agriculture is to cause the land to produce more abundantly and at the same time to protect it from deterioration and misuse. The diverse branches of modern agriculture include agronomy , horticulture , economic entomology , animal husbandry , dairying , agricultural engineering, soil chemistry, and agricultural economics.

Early Agriculture

Early people depended for their survival on hunting, fishing, and food gathering. To this day, some groups still pursue this simple way of life, and others have continued as roving herders (see nomad ). However, as various groups of people undertook deliberate cultivation of wild plants and domestication of wild animals, agriculture came into being. Cultivation of crops—notably grains such as wheat, rice, corn, rye, barley, and millet—encouraged settlement of stable farm communities, some of which grew to be towns and city-states in various parts of the world. Early agricultural implements—the digging stick, the hoe , the scythe, and the plow —developed slowly over the centuries, each innovation (e.g., the introduction of iron) causing profound changes in human life. From early times, too, people created ingenious systems of irrigation to control water supply, especially in semiarid areas and regions of periodic rainfall, e.g., the Middle East, the American Southwest and Mexico, the Nile Valley, and S Asia.

Farming was often intimately associated with landholding (see tenure ) and therefore with political organization. Growth of large estates involved the use of slaves (see slavery ) and bound or semifree labor. In the Western Middle Ages the manorial system was the typical organization of more or less isolated units and determined the nature of the agricultural village. In Asia large holdings by the nobles, partly arising from feudalism (especially in China and Japan), produced a similar pattern.

The Rise of Commercial Agriculture

As the Middle Ages waned, increasing communications, the commercial revolution, and the rise of cities in Western Europe tended to turn agriculture away from subsistence farming toward the growing of crops for sale outside the community (commercial agriculture). In Britain the practice of inclosure allowed landlords to set aside plots of land, formerly subject to common rights, for intensive cropping or fenced pasturage, leading to efficient production of single crops.

In the 16th and 17th cent. horticulture was greatly developed and contributed to the so-called agricultural revolution. Exploration and intercontinental trade, as well as scientific investigation, led to the development of horticultural knowledge of various crops and the exchange of farming methods and products, such as the potato, which was introduced from America along with beans and corn (maize) and became almost as common in N Europe as rice is in SE Asia.

The appearance of mechanical devices such as the sugar mill and Eli Whitney's cotton gin helped to support the system of large plantations based on a single crop. The Industrial Revolution after the late 18th cent. swelled the population of towns and cities and increasingly forced agriculture into greater integration with general economic and financial patterns. In the American colonies the independent, more or less self-sufficient family farm became the norm in the North, while the plantation, using slave labor, was dominant (although not universal) in the South. The free farm pushed westward with the frontier.

Modern Agriculture

In the N and W United States the era of mechanized agriculture began with the invention of such farm machines as the reaper , the cultivator , the thresher, and the combine . Other revolutionary innovations, e.g., the tractor , continued to appear over the years, leading to a new type of large-scale agriculture. Modern science has also revolutionized food processing; refrigeration, for example, has made possible the large meatpacking plants and shipment and packaging of perishable foods. Urbanization has fostered the specialties of market gardening and truck farming . Harvesting operations (see harvester ) have been mechanized for almost every plant product grown. Breeding programs have developed highly specialized animal, plant, and poultry varieties, thus increasing production efficiency. The development of genetic engineering has given rise to genetically modified transgenic crops and, to a lesser degree, livestock that possess a gene from an unrelated species that confers a desired quality. Such modification allows livestock to be used as "factories" for the production of growth hormone and other substances (see pharming ). In the United States and other leading food-producing nations agricultural colleges and government agencies attempt to increase output by disseminating knowledge of improved agricultural practices, by the release of new plant and animal types, and by continuous intensive research into basic and applied scientific principles relating to agricultural production and economics.

These changes have, of course, given new aspects to agricultural policies. In the United States and other developed nations, the family farm is disappearing, as industrialized farms, which are organized according to industrial management techniques, can more efficiently and economically adapt to new and ever-improving technology, specialization of crops, and the volatility of farm prices in a global economy. Niche farming, in which specialized crops are raised for a specialized market, e.g., heirloom tomatoes or exotic herbs sold to gourmet food shops and restaurants, revived or encouraged some smaller farms in the latter 20th and early 21st cents., but did little to stop the overall decrease in family farms. In Third World countries, where small farms, using rudimentary techniques, still predominate, the international market has had less effect on the internal economy and the supply of food.

Most of the governments of the world face their own type of farm problem, and the attempted solutions vary as much as does agriculture itself. The modern world includes areas where specialization and conservation have been highly refined, such as Denmark, as well as areas such as N Brazil and parts of Africa, where forest peoples still employ "slash-and-burn" agriculture—cutting down and burning trees, exhausting the ash-enriched soil, and then moving to a new area. In other regions, notably SE Asia, dense population and very small holdings necessitate intensive cultivation, using people and animals but few machines; here the yield is low in relation to energy expenditure. In many countries extensive government programs control the planning, financing, and regulation of agriculture. Agriculture is still the occupation of almost 50% of the world's population, but the numbers vary from less than 3% in industrialized countries to over 60% in Third World countries.

See also agricultural subsidies ; dry farming ; Granger movement ; Green Revolution ; ranch ; range .

See R. Jager, The Fate of Family Farming (2004).

Author not available, AGRICULTURE., The Columbia Encyclopedia, Sixth Edition 2008

The Columbia Encyclopedia, Sixth Edition. Copyright 2008 Columbia University Press

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Tuesday, August 5, 2008

article : Increasing access to antiretroviral drugs would drastically cut AIDS deaths in South Africa

More that 1.2 million deaths could be prevented in South Africa over the next five years by accelerating efforts to provide access to antiretroviral therapy (ART), according to a study released online today by the Journal of Infectious Diseases. Using a sophisticated mathematical model of HIV disease and treatment, a team of researchers led by Rochelle Walensky, MD, MPH of Massachusetts General Hospital (MGH) estimated the number of AIDS-related deaths in South Africa through 2012 under alternative ART scale-up assumptions.

The study results underscore the urgent need for Congress to reauthorize the U.S. President’s Emergency Plan for AIDS Relief (PEPFAR), which has supported the South African government’s effort to increase access to antiretroviral therapy, the researchers note. “If ART is not provided to all who need it, HIV mortality will be enormous,” says Walensky. “Deliberate, purposeful, and expedient scale-up will save millions of lives in South Africa alone.”

South Africa has one of the largest burdens of HIV infection in the world, with 5 to 6 million individuals and 19 percent of adults aged 15 to 49 infected. While government programs supported by PEPFAR and the Global Fund to Fight AIDS, Tuberculosis and Malaria have steadily increased access to antiretrovirals, at the end of 2006 only a third of individuals eligible for the therapy were receiving it.

In order to quantify the potential impact of various strategies for increasing access to ART, the research team projected the number of deaths under five scenarios – ranging from maintaining current access levels, through steady and moderate growth levels, to rapid growth and full access for all patients requiring treatment. Among other factors, calculations were based on the fact that the one-year survival rate for eligible patients who receive antiretroviral therapy is 94 percent, while only 55 percent of those not treated would be expected to survive one year.

Results showed that maintaining current treatment capacity would lead to 2.4 million AIDS-related deaths by 2012. Rapid scale-up, whereby everyone in need would have access by 2011, would reduce the projected number of deaths to 1.2 million during that time period, and immediate full access for all eligible patients would drop deaths to 800,000.

The researchers note that efforts to scale up treatment have resulted in a fivefold increase in access to ART in low and moderate-income countries. “Continued investments in antiretroviral treatment programs worldwide are a public health imperative; the potential loss of life without such support is simply unacceptable,” says Walensky, who is an associate professor of Medicine at Harvard Medical School.

Source : Massachusetts General Hospital

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article : Expansion of monocyte subset could serve as a biomarker for HIV progressions

An increase in the CD163+/CD16+ monocyte subset could be a biomarker for the progression of HIV disease, according to researchers at Temple University.

The researchers reported their findings, “CD163/CD16 Coexpression by Circulating Monocytes/Macrophages in HIV: Potential Biomarkers for HIV Infection and AIDS Progression,” in the March issue of AIDS Research and Human Retroviruses (

A monocyte is a specific white blood cell, a part of the human body’s immune system that protects against blood-borne pathogens and moves quickly to sites of infection within the body’s tissues. As monocytes enter tissue, they undergo a series of changes to become macrophages.

The researchers were investigating alterations in this monocyte subset in patients with HIV infection. As part of this study, they examined a cohort of 18 patients from the Comprehensive HIV Program at Temple University Hospital, under the direction of Ellen Tedaldi, and seven individuals without HIV infection.

“At first, we were just looking at whether or not we saw alterations in this CD163+/CD16+ subset and whether it might be reflective of the amount of virus they have in circulation,” said Tracy Fischer-Smith, an associate scientist in Temple’s Neuroscience Department and the study’s lead author. “We did, indeed, find that patients with detectable virus had an increase of this monocyte subset that correlated with the amount of virus they had in their blood. We were surprised to find that patients with CD4+ T cell counts of less than 450 cells per microliter [200 or less per microliter is defined as AIDS], the increase of this monocyte subset correlates inversely with the number of T cells.”

Fischer-Smith said this finding suggests that as the monocyte cells are increasing, these patients are losing CD4+ T cells, which are critical for the maintenance of immunological competence.

“This may actually provide an earlier window into what is happening with HIV-infected patients where we might be able to see that immune impairment is taking place before we see a dramatic loss of CD4+ T cells,” she said.

“It looks like, based on these correlations, that this particular cell type may be involved in immune impairment and the progression of HIV,” said Jay Rappaport, professor of neuroscience and neurovirology, who oversaw the study. “Is it a good prognostic indicator" If you have a lot of these monocytes, does it mean you are going to progress into AIDS faster" “Right now, all we know is what the correlations are,” he said.

Rappaport added that he believes the CD163+/CD16+ monocyte subset is the first biomarker that correlates with viral load and CD4+ count. “The fact that it actually correlates with both, we think, might make it a key cell type in the pathogenesis of AIDS.” Fischer-Smith said the researchers plan to expand this study by following a cohort of patients longitudinally to see if their findings really can provide doctors with an early warning system and help to design better therapeutic strategies.

“When you are just looking at a single time-point, you don’t know how changes in this monocyte subset might occur over time, and how these changes might relate to the viral load and T cell number in individual patients,” she said. “That is why we want to investigate this further with a longitudinal study of HIV patients.”

Source : Temple University

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article : Clinical trial will test new HIV/AIDS vaccine

A phase 1 clinical trial to test a novel HIV/AIDS vaccine has begun at Brigham and Women’s Hospital (BWH). This new vaccine aims to overcome the problem of preexisting immunity to common vaccine vectors, which is thought to be a major problem in the developing world.

“This study will involve 48 healthy volunteers who will receive either two or three immunizations and who will be followed to assess the safety and immunogenicity of the vaccine,” explains Lindsey R. Baden, MD, Assistant Professor of Medicine at BWH and Harvard Medical School and Protocol Chair for the study.

The vaccine consists of a replication-incompetent, recombinant adenovirus serotype 26 (rAd26) vector encoding an HIV-1 envelope gene.

“The rAd26 vaccine vector was selected for its particularly low seroprevalence in human populations and for its potent immunogenicity and protective efficacy in preclinical studies,” explains Dan H. Barouch, MD, PhD, Associate Professor of Medicine at Beth Israel Deaconess Medical Center (BIDMC) and Harvard Medical School and Principal Investigator of the Integrated Preclinical/Clinical AIDS Vaccine Development (IPCAVD) program that developed the vaccine. This program is sponsored by the Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health.

Manufactured by the Dutch biotechnology company Crucell Holland BV, the rAd26 vaccine is the first HIV-1 vaccine candidate to emerge from the IPCAVD initiative, which brings together investigators from academia and industry in an effort to accelerate the development of promising HIV/AIDS vaccine candidates. The novel strategy used in developing this vaccine enables researchers to circumvent preexisting immunity to the adenovirus serotype 5, the virus responsible for the common cold, which has recently shown limitations as an HIV-1 vaccine vector.

“The rAd26 vector does not regularly occur in the human population and human antibodies to this vector are rare,” explains Jaap Goudsmit, Chief Scientific Officer at Crucell. “The rAd26 vector therefore is efficacious in eliciting good T and B cell responses.”

AIDS remains one of the world’s most devastating health problems, with an estimated 33.2 million people living with HIV/AIDS and 2.5 million new infections reported in 2007 alone.

Source : Beth Israel Deaconess Medical Center

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article : Leading HIV researchers to collaborate on vaccine development

Two global research organizations dedicated to designing a vaccine against HIV – the International AIDS Vaccine Initiative (IAVI), and the Center for HIV/AIDS Vaccine Immunology (CHAVI) – have signed an agreement to work together to address major biological questions that have slowed development of a safe, effective and affordable AIDS vaccine.

“Solving the HIV vaccine puzzle is a scientific challenge that can only be solved through fundamental and applied research, collaboration and transparency. The work that will be done by IAVI, CHAVI and their networks of partners will rapidly enhance our understanding of HIV and help lay the groundwork for new vaccine approaches,” says Dr. Barton Haynes, CHAVI director and professor of medicine at Duke University Medical Center.

There are approximately 33 million people around the world living with HIV, the virus that causes AIDS. Scientists have tested multiple vaccine candidates in early phase trials, but only two have been fully tested in efficacy trials and neither has been found effective in preventing HIV infection or lowering the viral load in patients who subsequently encountered HIV and became infected.

“We are committed to the discovery of an effective vaccine, particularly for regions hardest hit by the epidemic,” says Dr. Wayne Koff, senior vice president of research and development at IAVI. “We are hoping that the synergy of shared investigation will yield insight into novel solutions that will advance AIDS vaccine discovery.”

The shared CHAVI/IAVI research mission will focus on four key areas that will help inform the design of new and improved vaccine candidates:

  • Identification and full-length genetic sequencing of newly transmitted viruses
  • Clarifying the impact of human genetics on the control of HIV infection
  • Collaborative immunological studies that could shed light on why some people who are exposed to HIV do not develop AIDS
  • Development of standardized methods to sample tissues from mucosal surfaces in the body, where HIV initially establishes infection.

Investigators supported by both organizations are especially interested in further understanding what happens in the very earliest post-infection stage of HIV infection, especially within the body’s T cells, a class of white blood cells that normally fight off foreign invaders like bacteria and viruses. One of the goals of this work will be to identify any genetic variations linked to the strength of the immune response at the site of initial infection. CHAVI and IAVI hope that by sharing samples, reagents, databases and laboratories and by launching parallel studies, they will be able to speed up discoveries about this critical phase of the disease.

Each partner to the agreement will contribute unique resources. For example, CHAVI supports high-throughput sequencing technology that can reveal tiny mutations in the ever-changing virus, but which require large numbers of HIV samples in order to identify variations that are meaningful. Through its network of clinical research centers and immunological laboratories around the world, IAVI and its partners have developed a number of tests to evaluate human immune responses to HIV and to potential vaccine candidates, information that can help researchers refine and improve any candidate that shows promise. By pooling technologies, protocols and access to samples, the IAVI/CHAVI collaboration aims to extract maximum information to help accelerate the development of a safe and effective AIDS vaccine.

“As an African clinical investigator and the leader of the scientific steering committee that oversees the IAVI-supported study of acute HIV infection, I am pleased to be collaborating with IAVI and CHAVI. It is critical to investigate the influence of genetic diversity of HIV as well as the variety of human immune responses to HIV among populations that are hardest hit by the epidemic,” said Dr. Pontiano Kaleebu, assistant director and a Principal Investigator at the Uganda Virus Research Institute.

“Now, more than ever, we need to understand the complexities of HIV and the genes that control the human immune response to it,” says Dr. Alan Bernstein, recently appointed as the first executive director of the Global HIV/AIDS Vaccine Enterprise. The Enterprise was established to accelerate development of a safe and effective HIV vaccine through encouraging collaboration within the HIV vaccine research field. “This new collaboration holds great promise in accelerating our basic understanding of HIV and will form the necessary underpinnings needed to develop a vaccine,” Bernstein added.

Source : Duke University Medical Center

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article : The new research findings open new front in fight against AIDS virus

A research group supported by the National Institutes of Health (NIH) has uncovered a new route for attacking the human immunodeficiency virus (HIV) that may offer a way to circumvent problems with drug resistance. In findings published today in the online edition of the Proceedings of the National Academy of Sciences, the researchers report that they have blocked HIV infection in the test tube by inactivating a human protein expressed in key immune cells.

Most of the drugs now used to fight HIV, which is the retrovirus that causes acquired immune deficiency syndrome (AIDS), target the virus’s own proteins. However, because HIV has a high rate of genetic mutation, those viral targets change quickly and lead to the emergence of drug-resistant viral strains. Doctors have tried to outmaneuver the rapidly mutating virus by prescribing multi-drug regimens or switching drugs. But such strategies can increase the risk of toxic side effects, be difficult for patients to follow and are not always successful. Recently, interest has grown in attacking HIV on a new front by developing drugs that target proteins of human cells, which are far less prone to mutations than are viral proteins.

In the new study, Pamela Schwartzberg, M.D., Ph.D., a senior investigator at the National Human Genome Research Institute (NHGRI), part of NIH; Andrew J. Henderson, Ph.D., of Boston University; and their colleagues found that when they interfered with a human protein called interleukin-2-inducible T cell kinase (ITK) they inhibited HIV infection of key human immune cells, called T cells. ITK is a signaling protein that activates T cells as part of the body’s healthy immune response.

“This new insight represents an important contribution to HIV research,” said NHGRI Scientific Director Eric D. Green, M.D., Ph.D. “Finding a cellular target that can be inhibited so as to block HIV validates a novel concept and is an exciting model for deriving potential new HIV therapies.”

When HIV enters the body, it infects T cells and takes over the activities of these white blood cells so that the virus can replicate. Eventually, HIV infection compromises the entire immune system and causes AIDS. The new work shows that without active ITK protein, HIV cannot effectively take advantage of many signaling pathways within T cells, which in turn slows or blocks the spread of the virus.

“We were pleased and excited to realize the outcome of our approach,” Dr. Schwartzberg said. “Suppression of the ITK protein caused many of the pathways that HIV uses to be less active, thereby inhibiting or slowing HIV replication.”

In their laboratory experiments, the researchers used a chemical inhibitor and a type of genetic inhibitor, called RNA interference, to inactivate ITK in human T cells. Then, the T cells were exposed to HIV, and the researchers studied the effects of ITK inactivation upon various stages of HIV’s infection and replication cycle. Suppression of ITK reduced HIV’s ability to enter T cells and have its genetic material transcribed into new virus particles. However, ITK suppression did not interfere significantly with T cells’ normal ability to survive, and mice deficient in ITK were able to ward off other types of viral infection, although antiviral responses were delayed.

“ITK turns out to be a great target to examine,” said Dr. Schwartzberg, noting that researchers had been concerned that blocking other human proteins involved in HIV replication might kill or otherwise impair the normal functions of T cells.

According to Dr. Schwartzberg, ITK already is being investigated as a therapeutic target for asthma and other diseases that affect immune response. In people with asthma, ITK is required to activate T cells, triggering lung inflammation and production of excess mucus.

“There are several companies who have published research about ITK inhibitors as part of their target program,” Schwartzberg said. “We hope that others will extend our findings and that ITK inhibitors will be pursued as HIV therapies.”

Source : NIH/National Human Genome Research Institute

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article : How we know climate change threats to HIV rates

Social factors, including economic pressures caused by climate change, could lead to an increase in HIV infection rates world-wide, warns a leading researcher from the University of New South Wales (UNSW).

Daniel Tarantola, Professor of Health and Human Rights at the School of Public Health and Community Medicine, says that disadvantage in developing countries must be addressed if the world is to prevent a dramatic escalation of the HIV epidemic as well as other health problems.

Professor Tarantola will join a panel of top HIV researchers to address the topic “A Future Free of HIV” at UNSW on Wednesday night. The event will be moderated by the Honourable Justice Michael Kirby AC.

“It was clear soon after the emergence of the HIV epidemic that discrimination, gender inequality and lack of access to essential services have made some populations more vulnerable than others. These problems have not gone away,” Professor Tarantola says.

“Today, additional threats are lurking on the horizon as the global economic situation deteriorates, food scarcity worsens and climate change begins to affect those who were already dependent on survival economies.

“The same is true for climate change. Climate change will trigger a chain of events which is likely to increase the stress on society and result in higher vulnerability to diseases including HIV,” he says.

Professor David Cooper AO, Director of UNSW’s National Centre in HIV Epidemiology and Clinical Research (NCHECR) says: “Science has achieved great strides towards shaping a more effective response to HIV. Yet research has not succeeded in producing the hoped-for ‘magic bullets’ of either a cure or a vaccine.

“We need to escalate our research efforts while sustaining and expanding what we know works: good prevention and access to life-saving antiretroviral therapy and integrated care.”

Source : Research Australia

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As HIV disease progresses in a person infected with the HIV virus, a group of cells in the immune system, the CD8+ T lymphocytes, become “exhausted,” losing many of their abilities to kill other cells infected by the virus. For many years scientists have debated whether this exhaustion of CD8+ T cells is the cause, or the consequence, of persistence of the HIV virus. In a study published this week in PLoS Medicine, Marcus Altfeld and colleagues studied the immune response over time amongst 18 individuals who had very recently become infected with HIV.

These researchers found that the presence of high amounts of HIV in the blood seemed to cause CD8+ T cell exhaustion; when antigen was reduced, either as a result of treatment with antiretroviral drugs, or evolution of viral epitopes to avoid recognition by CD8+ T cells, these epitope-specific CD8+ T cells recovered some of their original functions. These findings suggest that CD8+ T cell exhaustion is the consequence, rather than the cause, of persistent replication of HIV.

In a related article, Sarah Rowland-Jones and Thushan de Silva (from the Medical Research Council in Gambia), who were not involved in the study, discuss approaches to treat HIV efficiently by suppressing the viral load early in infection aimed at preserving HIV-1-specific immune function. They evaluate whether such strategies are likely to be practical.

Citation: Streeck H, Brumme ZL, Anastario M, Cohen KW, Jolin JS, et al. (2008) Antigen load and viral sequence diversification determine the functional profile of HIV-1– specific CD8þ T cells. PLoS Med 5(5):e100.



Sue McGreevey
Public Affairs Office
Massachusetts General Hospital
Boston, MA
+1 617 724-2764

Marcus Altfeld
Massachusetts General Hospital
Partners AIDS Research Center
149 13th Street
Boston, MA 02129
United States of America
+1 617-724-2461
+1 617-724-8586 (fax)

Related PLoS Medicine Research in Translation:

Citation: Rowland-Jones S, de Silva T (2008) Resisting immune exhaustion in

HIV-1 infection. PLoS Med 5(5): e103.


Sarah Rowland-Jones
Weatherall Institute of Molecular Medicine
MRC Human Immunology Unit
Radcliffe Hospital
Headley Way
Oxford, OX3 9DS
United Kingdom
+44 (1865) 222 316
+44 (1865) 222 502 (fax)


Hypofibrinolysis and other risk factors for first venous thrombosis

Frits Rosendaal and colleagues from Leiden University Medical Center
show that the combination of hypofibrinolysis with oral contraceptive use,
immobilization, or factor V Leiden results in a risk of venous thrombosis
that exceeds the sum of the individual risks.

Citation: Meltzer ME, Lisman T, Doggen CJM, de Groot PG, Rosendaal
FR (2008) Synergistic effects of hypofibrinolysis and genetic and acquired risk factors on

the risk of a first venous thrombosis. PLoS Med 5(5): e97.



Frits R. Rosendaal
Leiden University Medical Center
Clinical Epidemiology and Hematology
PO Box 9600
Leiden, 2300 RC
+31 715 264 037

Source : Public Library of Science

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article : Molecular espionage shows a single HIV enzyme's many tasks

Using ingenious molecular espionage, scientists have found how a single key enzyme, seemingly the Swiss army knife in HIV's toolbox, differentiates and dynamically binds both DNA and RNA as part of the virus' fierce attack on host cells. The work is described this week in the journal Nature.

The enzyme, reverse transcriptase (RT), is already the target of two of the three major classes of existing anti-HIV drugs. The new work, using single-molecule fluorescent imaging to trace RT's activity in real time, not only reveals novel insights into how this critical viral enzyme functions, but also clarifies how some of the anti-HIV pharmaceuticals work.

The research team, at Harvard University and the National Cancer Institute, was led by Xiaowei Zhuang at Harvard and Stuart Le Grice at NCI. Elio A. Abbondanzieri at Harvard and Gregory Bokinsky, formerly at Harvard and now at the Lawrence Berkeley National Laboratory, are lead authors.

"Our experiments allowed us, for the first time, a peek at how individual RT molecules interact with the HIV genome," says Zhuang, professor of chemistry and chemical biology and of physics in Harvard's Faculty of Arts and Sciences, as well as an investigator with the Howard Hughes Medical Institute. "We found that RT binds RNA and DNA primers with opposite orientations and that RT's function is dictated by this binding orientation."

HIV begins its assault by injecting its single-stranded RNA into a host cell. Three subsequent steps are all mediated by RT: The viral RNA is converted into single-stranded DNA, the single-stranded DNA is replicated into double-stranded DNA, and the original viral RNA is degraded. Another enzyme mediates the final step of the genome conversion, where the viral double-stranded DNA is inserted into the host's DNA, allowing it to take advantage of the host's genetic machinery to replicate and propagate itself.

Using their molecular probe to spy on this process, Abbondanzieri and colleagues traced RT's multitasking skill to its dynamic active sites, which allow it to bind and process RNA as well as single- or double-stranded DNA.

"Remarkably, RT can spontaneously flip between these two opposite orientations on DNA and RNA to facilitate two distinct catalytic activities," says Abbondanzieri, a postdoctoral researcher in Harvard's Department of Chemistry and Chemical Biology. "These flipping motions, which have never before been seen in a protein-nucleic acid complex, can be likened to a nanoscale version of a gymnastics routine on a pommel horse."

The 180-degree flipping of RT is regulated by nonnucleoside RT inhibitors (NNRTIs), a major class of anti-HIV drugs. Abbondanzieri and coworkers observed NNRTIs inhibiting HIV activity by accelerating RT's flipping between its two active sites, hindering the enzyme's ability to convert single-stranded DNA to double-stranded DNA.

Source : Harvard University

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article : Compound has potential for new class of AIDS drugs

Researchers have developed what they believe is the first new mechanism in nearly 20 years for inhibiting a common target used to treat all HIV patients, which could eventually lead to a new class of AIDS drugs.

Researchers at the University of Michigan used computer models to develop the inhibiting compound, and then confirmed in the lab that the compound does indeed inhibit HIV protease, which is an established target for AIDS treatment. The protease is necessary to replicate the virus, says Heather Carlson, U-M professor of medicinal chemistry in the College of Pharmacy, and principal investigator of the study.

Carlson stresses this is a preliminary step, but still significant.

"It's very easy to make an inhibitor, (but) it's very hard to make a drug," said Carlson, who also has an appointment in chemistry. "This compound is too weak to work in the human body. The key is to find more compounds that will work by the same mechanism."

What's so exciting is how differently that mechanism works from the current drugs used to keep the HIV from maturing and replicating, she says. Current drugs called protease inhibitors work by debilitating the HIV-1 protease. This does the same, but in a different way, Carlson says.

A protease is an enzyme that clips apart proteins, and in the case of HIV drugs, when the HIV-1 protease is inhibited it cannot process the proteins required to assemble an active virus. In existing treatments, a larger molecule binds to the center of the protease, freezing it closed.

The new mechanism targets a different area of the HIV-1 protease, called the flap recognition pocket, and actually holds the protease open. Scientists knew the flaps opened and closed, but didn't know how to target that as a mechanism, Carlson says.

Carlson's group discovered that this flap, when held open by a very small molecule---half the size of the ones used in current drug treatments---also inhibits the protease.

In addition to a new class of drugs, the compound is key because smaller molecules have better drug-like properties and are absorbed much more easily.

"This new class of smaller molecules could have better drug properties (and) could get around current side effects," Carlson said. "HIV dosing regimes are really difficult. You have to take medicine several times in the day. Maybe you wouldn't have to do that with these smaller molecules because they would be absorbed differently."

Kelly Damm, a former student and now at Johnson & Johnson, initially had the idea to target the flaps in this new way, Carlson says.

"In a way, this works like a door jam. If you looked only at the door when it's shut, you'd not know you could put a jam in it," she said. "We saw a spot where we could block the closing event, but because everyone else was working with the closed form, they couldn't see it."

Source : University of Michigan

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article : Dr. Anthony Fauci has reflects on 25 years of HIV

On the 25th anniversary of the first scientific article linking a retrovirus to AIDS, Anthony S. Fauci, M.D., director of the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, reflects in an essay in Nature on his experience treating and studying HIV/AIDS for the past quarter century. Outlining the peaks and valleys of the scientific community’s journey so far, Dr. Fauci writes, “…we must learn from our mis-steps, build on our successes in treatment and prevention, and renew our commitment to developing the truly transforming tools that will one day put this scourge behind us.”

From the outset, AIDS was clearly more menacing than any other novel disease Dr. Fauci and his colleagues had previously encountered, he writes. The period when clinicians lacked the ability to diagnose and treat AIDS was the bleakest of his career. The discovery that HIV causes AIDS stimulated a burst of progress in both the clinic and the laboratory. But the 1987 debut of the first effective drug against HIV, zidovudine (AZT), generated excessive optimism, Dr. Fauci reflects, as the virus quickly and predictably developed drug resistance.

Eight years and thousands of AIDS deaths later, protease inhibitors launched a renaissance of anti-HIV drug development in 1995. Combination therapies dramatically cut the rate of AIDS deaths in the United States—but the developing world has continued to suffer from lack of access to effective treatments for HIV. Even more sobering, Dr. Fauci writes, “Treatment alone will never end the AIDS pandemic…around three people are newly infected for every person put on therapy.”

So what options remain? Dr. Fauci praises research aimed at finding a cure for HIV/AIDS and affirms that this work must continue, but he places considerable hope and energy in preventing HIV infection, most importantly through the development of a vaccine. In retrospect, he writes, the scientific community expected to achieve an HIV vaccine unrealistically quickly. He advises that the steps we must take toward this goal now involve basic research, interdisciplinary research and active fostering of innovation, especially among young investigators. Twenty-five years since the discovery of HIV, Dr. Fauci views the prospect of ending the HIV/AIDS pandemic with cautious optimism.

Source : NIH/National Institute of Allergy and Infectious Diseases

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article : HIV infection stems from few viruses

A new study reveals the genetic identity of human immunodeficiency virus (HIV), the version responsible for sexual transmission, in unprecedented detail.

The finding provides important clues in the ongoing search for an effective HIV/AIDS vaccine, said researchers at the University of Alabama at Birmingham (UAB). The UAB team found that among billions of HIV variants only a few lead to sexual transmission.

Earlier studies have shown that a ‘bottleneck’ effect occurs where few versions of the virus lead to infection while many variants are present in the blood. The UAB study is the first to use genetic analysis and mathematical modeling to identify precisely those viruses responsible for HIV transmission.

George M. Shaw, M.D., Ph.D., professor in the UAB departments of Medicine and Microbiology and senior author on the report, said the research sheds new light on potential vulnerabilities in the virus at a time when science, medicine and society are still reeling from the failure of a major HIV vaccine clinical trial.

“We can now identify unambiguously those viruses that are responsible for sexual transmission of HIV-1. For the first time we can see clearly the face of the enemy,” said Shaw, a project leader with the Center for HIV/AIDS Vaccine Immunology. The center is a National Institutes of Health-sponsored consortium of researchers at UAB, Harvard Medical School in Boston, Oxford University in England, the University of North Carolina in Chapel Hill and Duke University in Durham, N.C.

The new HIV-1 findings are published online in the Proceedings of the National Academy of Sciences.

The new study was performed by sequencing many copies of the HIV envelope gene present in the viruses taken from 102 recently infected patients. The envelope gene encodes for a protein called Env that forms part of the outer covering of the virus, and is responsible for its infectiousness.

The researchers then used sophisticated mathematical models of HIV replication and genetic change to identify the virus or viruses responsible for transmission. In 80 percent of the newly infected patients, a single virus caused transmission, though each virus was different in each patient. In the other 20 percent of patients, two to five unique viruses caused transmission.

“Previously, researchers employed inexact methodologies that prevented precise identification of the virus that initiated infection,” said Brandon Keele, Ph.D., an instructor in UAB’s Department of Medicine and lead study investigator. “Our findings allow us to identify not only the transmitted virus, but also viruses that evolve from it.”

The UAB team said their work would lead to new research on how different HIV genes and proteins work together to make a virus biologically fit for transmission and for growth in the face of mounting immunity.

Statistics show that while the worldwide percentage of people infected with HIV has leveled off, the total number HIV cases is rising. In 2007, 33.2 million people were estimated to be living with HIV, 2.5 million people became newly infected and 2.1 million people died from AIDS, according to the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the World Health Organization.

Source : University of Alabama at Birmingham

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article : The Study finds unique HIV vaccine formula elicits strong immune responses

Today, Advanced BioScience Laboratories, Inc. (ABL) and the University of Massachusetts Medical School (UMMS) report that their unique HIV vaccine formulation was effective in eliciting strong and balanced immune responses in healthy human volunteers. The findings are published in the journal Vaccine (“Cross-subtype antibody and cellular immune responses induced by a polyvalent DNA prime–protein boost HIV-1 vaccine in healthy human volunteers,” Vaccine online, May 22, 2008) In light of these initial findings, additional assays on volunteers’ samples were done by researchers at the University of Alabama at Birmingham, independently confirming the presence of long lasting and high quality T cell responses against HIV antigens. Results from this confirmatory study are currently available online in the Journal of Virology (April 30, 2008).

In this phase I clinical trial, sponsored by the National Institute of Allergy and Infectious Diseases (NIAID), volunteers first received three injections of a DNA vaccine which expresses protective antigens from the HIV virus, followed by two injections of a protein vaccine whose components matched those included in the DNA vaccine. The report in Vaccine is the first scientific article in which a “DNA prime-protein boost” combination vaccination method is tested in humans for HIV vaccine development. Scientists at ABL and UMMS and their collaborators discovered that this combination approach is highly effective in inducing strong antibody and cell-mediated immune responses in human volunteers.

“Given the challenges of developing a vaccine against HIV, scientists have long believed that a final, effective HIV vaccine will require the induction of balanced responses from both arms of human immune system. Our results demonstrate that it is feasible to use this combination approach to achieve this objective,” said Phillip Markham, PhD, of ABL, the Principal Investigator (PI) on this vaccine development effort, performed under contract to the NIAID.

One unique design underlying this combination HIV vaccine formulation is the use of a “cocktail” of five different envelope (Env) proteins collected from HIV viruses circulating in different parts of the world. Env is a key protective antigen and the goal was to elicit broad antibody responses against a wide range of HIV viruses in order to counter the issue of frequent HIV mutations. Indeed, the high titer antibodies found in volunteers’ sera were able to recognize each of a very diverse group of Env antigens that were included in this study. More significantly, the majority of volunteers developed positive neutralizing antibodies against a good portion of the five HIV subtypes included in the assay.

Shan Lu, MD, PhD, professor of medicine and biochemistry & molecular pharmacology at the University of Massachusetts Medical School and the co- Principal Investigator (co-PI) of the vaccine development program, describes the finding of neutralizing antibodies in this study as “a major step forward.”

“Previously, we didn’t know where to start. The neutralizing antibody titers in our study are still relatively low, but, these results are promising and open the door for future efforts to optimize HIV vaccine formulations in order to achieve a protective HIV vaccine,” said Dr. Lu.

The dominant approaches in the current HIV vaccine field rely on viral vector-based delivery systems, an approach that produced disappointing results in a recent efficacy trial. Drs. Markham and Lu believe their HIV vaccine strategy will offer an alternative approach to focus on the induction of protective antibodies for HIV vaccine development, while maintaining strong cell-mediated immune responses. In addition to NIH, the International AIDS Vaccine Initiative (IAVI) also provided funding support to part of the study. Researchers from Duke University Medical School also participated, as did Dr. Paul Goepfert at the University of Alabama-Birmingham.

Source : University of Massachusetts Medical School

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article : Failed HIV drug gets second chance with addition of gold nanoparticles

Researchers at North Carolina State University have discovered that adding tiny bits of gold to a failed HIV drug rekindle the drug’s ability to stop the virus from invading the body’s immune system.

The addition of gold nanoparticles to a modified version of a drug designed in the 1990s to combat HIV – but discarded due to its harmful side effects – creates a compound that prevents the virus from gaining a cellular foothold, say Dr. Christian Melander, assistant professor of chemistry at NC State, and doctoral student T. Eric Ballard.

Their findings appear online in the Journal of the American Chemical Society.

The drug, a compound known as TAK-779, was originally found to bind to a specific location on human T-cells, which blocks the HIV virus’ entry to the body’s immune system. Unfortunately, the portion of the drug’s molecule that made binding possible had unpleasant side effects. When that portion of the molecule – an ammonium salt – was removed, the drug lost its binding ability.

That’s when the researchers turned to gold as the answer. The element is non-reactive in the human body, and would be the perfect “scaffold” to attach molecules of the drug to in the absence of the ammonium salt, holding the drug molecules together and concentrating their effect.

“The idea is that by attaching these individual molecules of the drug with a weak binding ability to the gold nanoparticle, you can magnify their ability to bind,” Melander says.

The researchers’ theory proved correct. They started with a modified version of TAK-779, which didn’t include the harmful ammonium salt. After testing, they found that attaching 12 molecules of the modified drug (SDC-1721) to one nanoparticle of gold restored the drug’s ability to prevent HIV infection in primary cultured patient cells. When only one molecule of the drug was attached to the gold nanoparticle, the compound was unable to prevent HIV infection, indicating that the multivalency of the drug was important for its activity.

“We’ve discovered a non-harmful way to improve the strength and efficacy of an important drug,” Melander says. “There’s no reason to think that this same process can’t be used with similar effect on other existing drugs.”

Source : North Carolina State University

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article : Scientists image a single HIV particle being born

A mapmaker and a mathematician may seem like an unlikely duo, but together they worked out a way to measure longitude – and kept millions of sailors from getting lost at sea. Now, another unlikely duo, a virologist and a biophysicist at Rockefeller University, is making history of their own. By using a specialized microscope that only illuminates the cell’s surface, they have become the first to see, in real time and in plain view, hundreds of thousands of molecules coming together in a living cell to form a single particle of the virus that has, in less than 25 years, claimed more than 25 million lives: HIV.

This work, published in the May 25 advanced online issue of Nature, may not only prove useful in developing treatments for the millions around the globe still living with the lethal virus but the technique created to image its assembly may also change the way scientists think about and approach their own research.

“The use of this technique is almost unlimited,” says Nolwenn Jouvenet, a postdoc who spearheaded this project under the direction of HIV expert Paul Bieniasz and cellular biophysicist Sandy Simon, who has been developing the imaging technique since 1992. “Now that we can actually see a virus being born, it gives us the opportunity to answer previously unanswered questions, not only in virology but in biology in general.”

Unlike a classical microscope, which shines light through a whole cell, the technique called total internal reflection microscopy only illuminates the cell’s surface where HIV assembles. “The result is that you can see, in exquisite detail, only events at the cell surface. You never even illuminate anything inside of the cell so you can focus on what you are interested in seeing the moment it is happening,” says Simon, professor and head of the Laboratory of Cellular Biophysics.

When a beam of light passes through a piece of glass to a cell’s surface, the energy from the light propagates upward, illuminating the entire cell. But when that beam is brought to a steeper angle, the light’s energy reflects off the cell’s surface, illuminating only the events going on at its most outer membrane. By zeroing in at the cell’s surface, the team became the first to document the time it takes for each HIV particle, or virion, to assemble: five to six minutes. “At first, we had no idea whether it would take milliseconds or hours,” says Jouvenet. “We just didn’t know.”

“This is the first time anyone has seen a virus particle being born,” says Bieniasz, who is an associate professor and head of the Laboratory of Retrovirology at Rockefeller and a scientist at the Aaron Diamond AIDS Research Center. “Not just HIV,” he clarifies, “any virus.”

To prove that what they were watching was virus particles assembling at the surface (rather than an already assembled virion coming into their field of view from inside the cell), the group tagged a major viral protein, called the Gag protein, with molecules that fluoresce, but whose color would change as they packed closer together. Although many different components gather to form a single virion, the Gag protein is the only one necessary for assembly. It attaches to the inner face of the cell’s outer membrane and when enough Gag molecules flood an area, they coalesce in a way that spontaneously forms a sphere.

Simon, Bieniasz and Jouvenet found that the Gag molecules are recruited from the inside of the cell and travel to the cell’s surface. When enough Gag molecules get close and start bumping into each other, the cell’s outer membrane starts to bulge outward into a budding virion and then pinches off to form an individual, infectious particle. At this point, the researchers showed that the virion is a lone entity, no longer exchanging resources with the cell. By using tricks from optics and physiology, they were able to watch the steps of viral assembly, budding, and even scission off the cell surface. With such a view they can start to describe the entire lifeline in the birth of the virus.

“I think that you can begin to understand events on a different level if you actually watch them happen instead of inferring that they might occur using other techniques,” says Bieniasz. “This technique and this collaboration made that possible.”

Source : Rockefeller University

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