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Tracing evolution of chicken flu virus yields insight into origins of deadly H7N9 strain

An international research team has shown how changes in a flu virus that has plagued Chinese poultry farms for decades helped create the novel avian H7N9 influenza A virus that has sickened more than 375 people since 2013. The research appears in the current online early edition of the scientific journal Proceedings of the National Academy of Sciences.

The results underscore the need for continued surveillance of flu viruses circulating on poultry farms and identified changes in the H9N2 virus that could serve as an early warning sign of emerging flu viruses with the potential to trigger a pandemic and global health emergency. The work focused on the H9N2 chicken virus, which causes egg production to drop and leaves chickens vulnerable to deadly co-infections. Scientists at St. Jude Children’s Research Hospital and the China Agricultural University, Beijing, led the study.

Researchers used whole genome sequencing to track the evolution of the H9N2 chicken virus between 1994 and 2013. The analysis involved thousands of viral sequences and showed that the genetic diversity of H9N2 viruses fell sharply in 2009. From 2010 through 2013 an H9N2 virus emerged as the predominant subtype thanks to its genetic makeup that allowed it to flourish despite widespread vaccination of chickens against H9N2 viruses.

Evidence in this study suggests the eruptions set the stage for the emergence of the H7N9 avian virus that has caused two outbreaks in humans since 2013, with 115 confirmed deaths. The H9N2 infected chickens likely served as the mixing vessel where H9N2 and other avian flu viruses from migratory birds and domestic ducks swapped genes, researchers noted. The resulting H7N9 virus included six genes from the H9N2.

“Sequencing the viral genome allowed us to track how H9N2 evolved across time and geography to contribute to the H7N9 virus that emerged as a threat to human health in 2013,” said Robert Webster, Ph.D., a member of the St. Jude Department of Infectious Diseases. He and Jinhua Liu, Ph.D., of the College of Veterinary Medicine at the China Agricultural University, are co-corresponding authors.

“The insights gained from this collaboration suggest that tracking genetic diversity of H9N2 on poultry farms could provide an early warning of emerging viruses with the potential to spark a pandemic,” Webster said.

The analysis also provided insight into the creation of the H9N2 virus that emerged as the predominant subtype in 2010. Factors included widespread use of poultry vaccines and the natural tendency of flu to mutate, mix and swap genes.

Beginning in 1998, vaccinating poultry against H9N2 prevented flu outbreak for more than a decade. Vaccines work by recognizing and attaching to the spike-shaped hemagglutinin (HA) protein on the surface of the flu virus. That blocks the virus from infecting healthy cells. Changes in the HA gene that change the shape of the HA protein can reduce vaccine effectiveness and result in disease outbreaks. HA mutations occur naturally over time. Vaccines increase pressure for HA mutations that help the virus escape vaccine detection and cause infection.

Researchers at the China Agricultural University checked H9N2 vaccine effectiveness against the predominant H9N2 virus from 2010-11. Working in vaccinated and unvaccinated chickens, investigators found the vaccine neither protected vaccinated chickens from infection nor prevented spread of the virus in vaccinated chickens. Those failures suggest that due to HA mutations vaccines were less able to recognize the virus.

The tendency of flu viruses to swap genes also contributed to the enhanced ability of the predominant H9N2 subtype to spread. Researchers found that prior to the virus’ emergence as the predominant H9N2 the virus had swapped genes with quail and duck influenza viruses.

The combination fueled the recent outbreaks of H9N2 on chicken farms by helping the virus escape vaccine detection and spread rapidly in vaccinated and unvaccinated poultry, said co-first author Juan Pu, Ph.D., a St. Jude visiting scientist from the China Agricultural University. The other first authors are Shuoguo Wang, Ph.D., of the St. Jude Department of Computational Biology, and Yanbo Yin, Ph.D., of Qingdao Agricultural University, Qingdao, China.

“The emergence of this dominant H9N2 virus was the first step in the genesis of the H7N9 viruses because it greatly increased the likelihood of reassortment between H9N2 and other flu subtypes,” Liu said. Reassortment refers to the tendency of flu viruses to swap genes.

Story Source:

The above story is based on materials provided by St. Jude Children’s Research Hospital. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Tracing evolution of chicken flu virus yields insight into origins of deadly H7N9 strain

An international research team has shown how changes in a flu virus that has plagued Chinese poultry farms for decades helped create the novel avian H7N9 influenza A virus that has sickened more than 375 people since 2013. The research appears in the current online early edition of the scientific journal Proceedings of the National Academy of Sciences.

The results underscore the need for continued surveillance of flu viruses circulating on poultry farms and identified changes in the H9N2 virus that could serve as an early warning sign of emerging flu viruses with the potential to trigger a pandemic and global health emergency. The work focused on the H9N2 chicken virus, which causes egg production to drop and leaves chickens vulnerable to deadly co-infections. Scientists at St. Jude Children’s Research Hospital and the China Agricultural University, Beijing, led the study.

Researchers used whole genome sequencing to track the evolution of the H9N2 chicken virus between 1994 and 2013. The analysis involved thousands of viral sequences and showed that the genetic diversity of H9N2 viruses fell sharply in 2009. From 2010 through 2013 an H9N2 virus emerged as the predominant subtype thanks to its genetic makeup that allowed it to flourish despite widespread vaccination of chickens against H9N2 viruses.

Evidence in this study suggests the eruptions set the stage for the emergence of the H7N9 avian virus that has caused two outbreaks in humans since 2013, with 115 confirmed deaths. The H9N2 infected chickens likely served as the mixing vessel where H9N2 and other avian flu viruses from migratory birds and domestic ducks swapped genes, researchers noted. The resulting H7N9 virus included six genes from the H9N2.

“Sequencing the viral genome allowed us to track how H9N2 evolved across time and geography to contribute to the H7N9 virus that emerged as a threat to human health in 2013,” said Robert Webster, Ph.D., a member of the St. Jude Department of Infectious Diseases. He and Jinhua Liu, Ph.D., of the College of Veterinary Medicine at the China Agricultural University, are co-corresponding authors.

“The insights gained from this collaboration suggest that tracking genetic diversity of H9N2 on poultry farms could provide an early warning of emerging viruses with the potential to spark a pandemic,” Webster said.

The analysis also provided insight into the creation of the H9N2 virus that emerged as the predominant subtype in 2010. Factors included widespread use of poultry vaccines and the natural tendency of flu to mutate, mix and swap genes.

Beginning in 1998, vaccinating poultry against H9N2 prevented flu outbreak for more than a decade. Vaccines work by recognizing and attaching to the spike-shaped hemagglutinin (HA) protein on the surface of the flu virus. That blocks the virus from infecting healthy cells. Changes in the HA gene that change the shape of the HA protein can reduce vaccine effectiveness and result in disease outbreaks. HA mutations occur naturally over time. Vaccines increase pressure for HA mutations that help the virus escape vaccine detection and cause infection.

Researchers at the China Agricultural University checked H9N2 vaccine effectiveness against the predominant H9N2 virus from 2010-11. Working in vaccinated and unvaccinated chickens, investigators found the vaccine neither protected vaccinated chickens from infection nor prevented spread of the virus in vaccinated chickens. Those failures suggest that due to HA mutations vaccines were less able to recognize the virus.

The tendency of flu viruses to swap genes also contributed to the enhanced ability of the predominant H9N2 subtype to spread. Researchers found that prior to the virus’ emergence as the predominant H9N2 the virus had swapped genes with quail and duck influenza viruses.

The combination fueled the recent outbreaks of H9N2 on chicken farms by helping the virus escape vaccine detection and spread rapidly in vaccinated and unvaccinated poultry, said co-first author Juan Pu, Ph.D., a St. Jude visiting scientist from the China Agricultural University. The other first authors are Shuoguo Wang, Ph.D., of the St. Jude Department of Computational Biology, and Yanbo Yin, Ph.D., of Qingdao Agricultural University, Qingdao, China.

“The emergence of this dominant H9N2 virus was the first step in the genesis of the H7N9 viruses because it greatly increased the likelihood of reassortment between H9N2 and other flu subtypes,” Liu said. Reassortment refers to the tendency of flu viruses to swap genes.

Story Source:

The above story is based on materials provided by St. Jude Children’s Research Hospital. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Coffee genome sheds light on the evolution of caffeine

The newly sequenced genome of the coffee plant reveals secrets about the evolution of man’s best chemical friend: caffeine.

The scientists who completed the project say the sequences and positions of genes in the coffee plant show that they evolved independently from genes with similar functions in tea and chocolate, which also make caffeine.

In other words, coffee did not inherit caffeine-linked genes from a common ancestor, but instead developed the genes on its own.

The findings will appear on Sept. 5 in the journal Science.

Why Coffee?

With more than 2.25 billion cups consumed daily worldwide, coffee is the principal agricultural product of many tropical countries. According to estimates by the International Coffee Organization, more than 8.7 million tons of coffee were produced in 2013, revenue from exports amounted to $ 15.4 billion in 2009-2010, and the sector employed nearly 26 million people in 52 countries during 2010.

“Coffee is as important to everyday early risers as it is to the global economy. Accordingly, a genome sequence could be a significant step toward improving coffee,” said Philippe Lashermes, a researcher at the French Institute of Research for Development (IRD). “By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special.”

Lashermes, along with Patrick Wincker and France Denoeud, genome scientists at the French National Sequencing Center (CEA-Genoscope), and Victor Albert, professor of biological sciences at the University at Buffalo, are the principal authors of the study.

Scientists from other organizations, particularly the Agricultural Research Center for International Development in France, also contributed, along with researchers from public and private organizations in the U.S., France, Italy, Canada, Germany, China, Spain, Indonesia, Brazil, Australia and India.

The team created a high-quality draft of the genome of Coffea canephora, which accounts for about 30 percent of the world’s coffee production, according to the Manhattan-based National Coffee Association.

Next, the scientists looked at how coffee’s genetic make-up is distinct from other species.

Compared to several other plant species including the grape and tomato, coffee harbors larger families of genes that relate to the production of alkaloid and flavonoid compounds, which contribute to qualities such as coffee aroma and the bitterness of beans.

Coffee also has an expanded collection of N-methyltransferases, enzymes that are involved in making caffeine.

Upon taking a closer look, the researchers found that coffee’s caffeine enzymes are more closely related to other genes within the coffee plant than to caffeine enzymes in tea and chocolate.

This finding suggests that caffeine production developed independently in coffee. If this trait had been inherited from a common ancestor, the enzymes would have been more similar between species.

“The coffee genome helps us understand what’s exciting about coffee — other than that it wakes me up in the morning,” Albert said. “By looking at which families of genes expanded in the plant, and the relationship between the genome structure of coffee and other species, we were able to learn about coffee’s independent pathway in evolution, including — excitingly — the story of caffeine.”

Why caffeine is so important in nature is another question. Scientists theorize that the chemical may help plants repel insects or stunt competitors’ growth. One recent paper showed that pollinators — like humans — may develop caffeine habits. Insects that visited caffeine-producing plants often returned to get another taste.

The new Science study doesn’t offer new ideas about the evolutionary role of caffeine, but it does reinforce the idea that the compound is a valuable asset. It also provides the opportunity to better understand the evolution of coffee’s genome structure.

“It turns out that, over evolutionary time, the coffee genome wasn’t triplicated as in its relatives: the tomato and chile pepper,” Wincker said. “Instead it maintained a structure similar to the grape’s. As such, evolutionary diversification of the coffee genome was likely more driven by duplications in particular gene families as opposed to en masse, when all genes in the genome duplicate.”

This stands in contrast to what’s been suggested for several other large plant families, where other investigators have noted correlations between high species diversity in a group and the presence of whole genome doublings or triplings.

“Coffee lies in the plant family Rubiaceae, which has about 13,000 species and is the world’s fourth largest; thus, with no genome duplication at its root, it appears to break the mold of a genome duplication link to high biodiversity,” Denoeud said.

Agriculture and Food News — ScienceDaily

Grazers, pollinators shape plant evolution

Oct. 21, 2013 — It has long been known that the characteristics of many plants with wide ranges can vary geographically, depending on differences in climate. But changes in grazing pressure and pollination can also affect the genetic composition of natural plant populations, according to a new study.

Researchers at Uppsala University and Stockholm University are presenting the new study this week in the journal Proceedings of the National Academy of Sciences, PNAS.

It is known that a prominent floral display increases attractiveness to pollinators, but also increases the risk of damage from grazing animals and seed-eating insects. To investigate how pollinators and grazing animals affect the characteristics of natural plant populations, these researchers studied bird’s eye primrose populations in alvar grasslands on the Baltic island of Öland. Two distinct morphs of primrose occur there: a short morph that produces its flowers close to the ground and a tall morph that displays its flowers well above the ground. The tall morph is better at attracting pollinators, but, on the other hand, it is more frequently damaged by grazing animals and seed predators.

In field experiments the scientists have shown that grazing pressure and pollination intensity determine whether the short or the tall primrose morph reproduces more successfully. The difference in plant height has a genetic basis, and over time differences in reproductive success affect the genetic composition of plant populations. For a period of eight years, the researchers documented changes in the proportion of short plants in natural populations and field experiments. The results show that altered grazing pressure leads to rapid changes in the genetic composition of the primrose populations, specifically in the proportion of short plants.

The Agricultural Landscape of Southern Öland has been a World Heritage Site since 2000. The grazing pressure on the alvar grasslands of Öland has increased dramatically in the last fifteen years as a result of measures taken to keep the landscape open.

The study shows that grazing pressure impacts not only which plants dominate but also the genetic composition of the plant populations. These findings help us understand how differences in environmental conditions influence the evolution of genetic differentiation among plant populations, says Professor Jon Ågren at the Evolutionary Biology Centre.

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Story Source:

The above story is based on materials provided by Uppsala University, via AlphaGalileo.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Journal Reference:

  1. Jon Ågren et al. Mutualists and antagonists drive among-population variation in selection and evolution of floral display in a perennial herb. PNAS, October 2013

Note: If no author is given, the source is cited instead.

ScienceDaily: Agriculture and Food News

Evolution shapes new rules for ant behavior, research finds

TGF-FruitImageMay 15, 2013 — In ancient Greece, the city-states that waited until their own harvest was in before attacking and destroying a rival community’s crops often experienced better long-term success.

It turns out that ant colonies that show similar selectivity when gathering food yield a similar result. The latest findings from Stanford biology Professor Deborah M. Gordon’s long-term study of harvester ants reveal that the colonies that restrain their foraging except in prime conditions also experience improved rates of reproductive success.

Importantly, the study provides the first evidence of natural selection shaping collective behavior, said Gordon, who is also a senior fellow at the Stanford Woods Institute for the Environment.

A long-held belief in biology has posited that the amount of food an animal acquires can serve as a proxy for its reproductive success. The hummingbirds that drink the most nectar, for example, stand the best chance of surviving to reproduce.

But the math isn’t always so straightforward. The harvester ants that Gordon studies in the desert in southeast Arizona, for instance, have to spend water to obtain water: an ant loses water while foraging, and obtains water from the fats in the seeds it eats.

The ants use simple positive feedback interactions to regulate foraging activity. Foragers wait near the opening of the nest, and bump antennae with ants returning with food. The faster outgoing foragers meet ants returning with seeds, the more ants go out to forage. (Last year, Gordon, Katie Dektar, an undergraduate, and Balaji Prabhakar, a professor of computer science and of electrical engineering at Stanford, showed that the ants’ “Anternet” algorithm follows the same rules as the protocols that regulate data traffic congestion in the Internet).

Colonies differ, however, in how they use these interactions to regulate foraging. Some colonies are likely to forage less when conditions are dry. These same, more successful colonies are also more likely to forage more steadily when conditions are good.

Gordon found that it’s more important for the ants to not waste water than to forage for every last piece of food. There’s no survival cost to this strategy, even though the colonies sometimes forgo foraging for an entire day. Instead, not only do the colonies that hunker down on the bad days live just as long as those that go all out, they also have more offspring colonies.

“Natural selection is not favoring the behavior that sends out the most ants to get the most food, but instead regulating foraging to hold back when conditions are bad,” Gordon said. “This is natural selection shaping a collective behavior exhibited by the entire colony.”

Gordon’s group is still investigating how the ants gauge humidity, but they have determined that the collective response of the colony to conditions is heritable from parent colony to offspring colony. Even though a daughter queen will establish her new colony so far from the parent colony that the two colonies will never interact, the offspring colonies resemble parent colonies in their sensitivity to conditions.

Although the foraging activity of the offspring colonies and the parent colony didn’t entirely match up on all days, they were similar on extreme days: parent and offspring colonies made similar judgments about when to lie low or take advantage of ideal conditions.

While the region has experienced 10 to 15 years of protracted drought, and the more restrained colonies will most likely fare better reproductively as that trend continues, Gordon can’t yet say whether the emphasis on sustainability evolved in response to climate change pressures.

“What’s evolving here are simple rules for how ants participate in a network that regulates the collective behavior of the colony,” she said.

The work is published in the May 16 issue of the journal Nature.

ScienceDaily: Agriculture and Food News