Farming

U of T scientists develop custom-engineered protein to battle MERS virus

ullahnor — Tue, 23 May 2017 19:32:47 +0000

U of T scientists develop custom-engineered protein to battle MERS virus

ullahnor Tue, 05/23/2017 - 15:32

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MERS particles attach to the surface of an infected human cell. The engineered protein can paralyze MERS by binding tightly to a key enzyme (image courtesy of the Donnelly Centre for Cellular and Biomolecular Research)

Jovana Drinjakovic

Author legacy

Jovana Drinjakovic

Topic

Breaking Research

Donnelly Centre

Global

Health

Proteins

Farming

Subheadline

Could lead to anti-viral therapeutics for both humans and animals

In 2012, a 60-year-old man with flu-like symptoms died in Saudi Arabia, becoming the first victim of the Middle East Respiratory Syndrome or MERS.

Until now, there has been no vaccine or known treatment. That could change thanks to a new anti-viral tool, developed by ��Ƶ researchers.

Scientists have crafted a custom-engineered protein that can be used to treat MERS and a wide range of pathogens, a potential game-changer in anti-viral therapeutics for both humans and the farming industry.

Writing in the journal PLOS Pathogens, a team led by Professor Sachdev Sidhu of the Donnelly Centre for Cellular and Biomolecular Research and department of molecular genetics, describes how to turn ubiquitin, a staple protein in every cell, into a drug capable of thwarting MERS in cultured human cells.

“Vaccines are important for prevention, but there is a great need for anti-viral medicines to treat people who have become infected,” says Wei Zhang, a postdoctoral researcher in Sidhu’s lab who did most of the work on the study.

“With our tool, we can quickly generate anti-viral medicine, and we hope that our method will inspire other researchers to try it out against diverse pathogens,” says Zhang.

MERS is similar to SARS, the virus that killed almost 800 people in a global epidemic. Both kill upwards of a third of people infected and, like many viruses, emerged from animals – bats and camels in the case of MERS. Although MERS has so far been detected in 27 countries, the outbreak has largely been contained within Saudi Arabia, according to the World Health Organization.

Like many viruses, MERS works by hijacking the ubiquitin system in human cells composed of hundreds of proteins that rely on ubiquitin to keep the cells alive and well. Upon infection, viral enzymes alter ubiquitin pathways in a way that allows the virus to evade the immune defense while multiplying and destroying the host tissue as it spreads in the body.

“Viruses have evolved proteins that allow them to hijack host proteins. We can now devise strategies to prevent this from happening,” says Zhang.

Zhang and colleagues engineered the human ubiquitin protein into a new form that paralyzes a key MERS enzyme, stopping the virus from replicating. These synthetic ubiquitin variants act quickly, completely eliminating MERS from cells in a dish within 24 hours.

The researchers also created UbVs that block the Crimean-Congo virus, the cause of a hemorrhagic fever that kills about 40 per cent of those infected.

And they’re designed to only target only the virus – hopefully minimizing side effects in any future drug.

But before these engineered proteins can be developed into medicine, researchers first must find a way to deliver them into the right part of the body. For this, Zhang and Sidhu are working with Roman Melnyk, an assistant professor at U of T and a biochemist at the Hospital for Sick Children and a world expert in protein delivery.

The team is also investigating the possibility of finding drugs that work in a similar manner but can cross the cell membrane.

It is likely that the proteins will be tested first in plants and animals where regulatory approvals are less strict than they are for human drugs.

“We are also working on an engineered ubiquitin that targets a corn virus responsible for destroying large swaths of corn fields in North America, with colleagues in Manitoba,” says Zhang.

The study was done in collaboration with Marjolein Kikkert of Leiden University Medical Centre in the Netherlands and Brian Mark at the University of Manitoba.

U of T undergrad tests out solar-powered irrigation system in his native South Sudan

ullahnor — Mon, 01 May 2017 16:11:10 +0000

U of T undergrad tests out solar-powered irrigation system in his native South Sudan

ullahnor Mon, 05/01/2017 - 12:11

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James Thuch Madhier, a third-year peace, conflict and justice student at the Munk School of Global Affairs, has launched Rainmaker Enterprise with U of T colleagues (photo by Bibi Veth)

Elaine Smith

Author legacy

Elaine Smith

Topic

Global Lens

Munk School of Global Affairs & Public Policy

Social Entrepreneurship

Undergraduate Students

Subheadline

James Thuch Madhier came to U of T through the Student Refugee Program

James Thuch Madhier fled South Sudan as a teenager, escaping the ravages of civil war and famine.

Next fall, the U of T undergrad and his social entrepreneurship team will be testing out their solar-powered crop irrigation system on 20 acres of land they've acquired in South Sudan.

“I see it as a model that we can scale up across the country and region,” Madhier said. “I believe in a ground-up approach. It’s a way for local farmers to increase production and efficiency so that they are not simply doing subsistence farming.”

Madhier came from South Sudan via Kakuma refugee camp in Kenya through U of T's Student Refugee Program (SRP), which sponsors refugees in collaboration with the World University Service of Canada.

Now a third-year peace, conflict and justice student at U of T's Munk School of Global Affairs, Madhier has worked with his classmates, Mike Hongryul Park, a math and physics student with a passion for sustainable development, and Katie Fettes, a fellow peace, conflict and justice student at Munk, to create a basic, solar-powered crop irrigation system that provides clean drinking water to countries in the developing world.

The team's system, which includes a pump, a holding tank for the seasonal flood waters, solar panels to generate power and drip irrigation, is easy to install and use in South Sudan, where 80 per cent of residents are farmers or raise cattle, only 30 per cent have access to clean drinking water and 5.1 per cent of the population has electricity.

“We’ve adapted the system in a way that will not only irrigate food crops and provide grazing grass for cattle, but will also offer employment to women and youth and address issues of food insecurity,” Madhier said.

In 2016, Madhier, who has long been active with social development programs, was invited by the One Young World organization to attend a global summit for young social changemakers. The summit included a social venture competition, and Madhier and Park decided this was the perfect opportunity to seek assistance with the irrigation project.

Madhier pitched the idea at the summit and won a fellowship award as well as some seed capital and access to professionals who can mentor him.

This past March, the team formally launched Rainmaker Enterprise in partnership with Emmanuel Jal, a former child soldier-turned-musician from South Sudan, and they purchased land in South Sudan to test out the irrigation system during the November dry season.

For the project, the land will be divided so that cows can graze in one area while crops can be grown in another area. It will allow for crop rotation so the land remains productive for both food and grazing. Madhier has a local field manager who will hire a local team to assist him, creating a self-sustaining enterprise.

Madhier says that as a teenager he saw some horrific things during the famine.

“Thiet, my hometown, attracted people from all over the countryside who were suffering,” he said. “In the mornings, you’d see the collection of people who had died of hunger overnight. Sights like these are toxic to the brain.”

After a trip to the Ivory Coast last year to research issues surrounding cocoa farming, Madhier realized that the problems of drought and food insecurity were much more widespread in Africa than he’d realized and decided to do something about it – not a quick fix solution, but something that would effect systemic change.

“Today, I know there has been technological advancement that could be used to lift people out of extreme hunger and food insecurity,” he said.

Rice crops that can save farmers money and cut pollution: new research from U of T

lanthierj — Fri, 22 Jul 2016 15:22:46 +0000

Rice crops that can save farmers money and cut pollution: new research from U of T

lanthierj Fri, 07/22/2016 - 11:22

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Professor Herbert Kronzucker (at left) with grad student Ahmed Hamam (photo by Ken Jones)

Don Campbell

Author legacy

Don Campbell

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Subheadline

“If we can produce more responsible plants that don’t waste fertilizer needlessly, everyone wins”

A new ��Ƶ study has identified “superstar” varieties of rice that can reduce fertilizer loss and cut down on environmental pollution in the process.

The study, authored by U of T Scarborough Professor Herbert Kronzucker in collaboration with a team at the Chinese Academy of Sciences, looked at 19 varieties of rice to see which ones were more efficient at using nitrogen.

“We have this bucolic idea of agriculture – animals grazing or vast fields of majestic crops – but the global reality is it’s one of the biggest drivers of environmental pollution and climate change,” says Kronzucker.

Nitrogen, when applied as fertilizer, is taken up inefficiently by most crops. In tropical rice fields, as much as 50 to 70 per cent can be lost. The problem is that excess nitrogen negatively affects water quality by contaminating nearby watersheds or leaching into ground water. It’s also a significant source of gases such as ammonia and nitrogen oxide, which are not only harmful to aquatic life but also a significant source of greenhouse gas emissions.

While nitrogen is one of three main nutrients required for crops to grow, it also costs the most to produce, adds Kronzucker.

“Anything we can do to reduce demand for nitrogen, both environmentally and for farmers in the developing world struggling to pay for it, is a significant contribution.”

Kronzucker’s study for the first time identifies a novel class of chemicals produced and released by the roots of rice crops that directly influence the metabolism of soil microbes. They found that key microbial reactions that lead to an inefficiency in nitrogen capture can be significantly reduced in certain varieties of rice plants through the action of those specific chemicals released from root cells.

One of the main reasons crops waste so much fertilizer is that they were bred that way. In the past fertilizers were relatively inexpensive to produce because fossil fuels were abundant and cheap. As a result, plant geneticists bred crops that responded to high fertilizer use regardless of how efficient they were at using nitrogen.

“These inefficiencies used to be of little interest, but now, with fluctuating fuel prices and growing concerns over climate change, it’s a much bigger issue,” says Kronzucker, who is the director of the Canadian Centre for World Hunger Research at U of T Scarborough.

There are more than 120,000 varieties of rice stored at the germplasm bank at the International Rice Research Institute (IRRI) in the Philippines, but Kronzucker’s team only focused on varieties that met important criteria. For one they concentrated only on Japonica (the rice used in sushi) and Indica, the world’s most popular rice type commonly grown in China, India and Southeast Asia. The varieties also had to be currently grown by farmers, have a high yield potential, be disease and pest-resistant, grow to the right size and have strong enough roots to withstand monsoon-force winds.

“They had to be proven in the field as viable options. It’s not practical if a rice farmer isn’t going to touch it,” adds Kronzucker.

The hope is for this study to inform rice-growing strategies throughout Asia. One option could be to provide farmers with government incentives like tax credits, to switch to a more nitrogen-friendly variety. Another outcome could be better breeding programs where even better species of crops can be produced.

“There’s no reason a crop can’t result in less pollution while also saving farmers money; the two aren’t incompatible,” says Kronzucker. “If we can produce more responsible plants that don’t waste fertilizer needlessly, everyone wins.”

New origins for farmed rice discovered by U of T, Chinese experts

krisha — Mon, 27 Jun 2016 13:46:55 +0000

New origins for farmed rice discovered by U of T, Chinese experts krisha Mon, 06/27/2016 - 09:46

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(photo by John Isaac/United Nations Photo via flickr)

Sharon Aschaiek

Author legacy

Sharon Aschaiek

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Subheadline

“This gives us another clue about how humans became farmers”

Rice farming is a far older practice than we knew – the oldest evidence of domesticated rice has just been found in China, and it’s about 9,000 years old.

The discovery, made by a team of archaeologists that includes ��Ƶ anthropology professor Gary Crawford, sheds new light on the origins of rice domestication and on the history of human agricultural practices.

“Today, rice is one of most important grains in the world’s economy, yet at one time, it was a wild plant…how did people bring rice into their world? This gives us another clue about how humans became farmers,” says U of T Mississauga's Crawford, an anthropological archaeologist who studies the relationships between people and plants in prehistory.

Working with researchers from the Provincial Institute of Cultural Relics and Archaeology in Zhejiang Province, China and Fudan University in Shanghai, Crawford found the ancient domesticated rice fragments in a probable ditch in the lower Yangtze valley. They observed that about 30 per cent of the rice plant material – primarily bases, husks and leaf epidermis – were not wild, but showed signs of being purposely cultivated to produce rice plants that were durable and suitable for human consumption.

Crawford says this finding indicates that the domestication of rice has been going on for much longer than originally thought. The rice plant remains also had characteristics of japonica rice, the short grain rice used in sushi that today is cultivated in Japan and Korea. Crawford says this finding clarifies the lineage of this specific rice crop, and confirms for the first time that it grew in this region of China.

Crawford (pictured at right) and his colleagues spent about three years exploring the five-hectare archaeological dig site, called Huxi, which is situated in a flat basin about 100 metres above sea level.

Their investigations were supported by other U of T Mississauga participants – anthropology professor David Smith and graduate students Daniel Kwan and Nattha Cheunwattana.

They worked mostly in early spring, fall and winter in order to avoid the late-spring wet season and excruciatingly hot summer months. Digging 1.5 metres below the ground, the team also unearthed artifacts such as sophisticated pottery and stone tools, as well as animal bones, charcoal and other plant seeds.

This study builds on Crawford’s previous research into early agriculture in China, in which he has examined the ancient settlements, tools, and plant and animal management efforts that occurred in different regions of the country. He is interested in better understanding the forces that compelled our human ancestors to transition from hunters and gatherers to farmers.

“The question I ultimately want to answer is, what pushed them to move wholeheartedly into the farming regime? Why did they reduce their emphasis on hunting and expand into crop production?” Crawford says. “People did what they needed to do to make their lives more manageable and sustainable, and the unintended consequence was farming. With this rice discovery, we’re seeing the first stages of that shift.”

Funded by a grant from the Social Sciences and Humanities Research Council, Crawford’s study is published today in Scientific Reports, an online open-access journal from the publishers of Nature.

(Visit flickr to see the original of the photo used at top of article)