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Isabel

Researchers describe new tubular structures at plant-fungal interface

By | News

For hundreds of millions of years, plants and fungi have formed symbiotic relationships to trade crucial nutrients, such as phosphate and fatty acids. This relationship is extremely important to the growth and survival of both organisms, and solving the mystery of how they transfer molecules to each other could eventually help reduce the use of fertilizer in agriculture.

Now, researchers at the Boyce Thompson Institute (BTI) have uncovered structural networks of tubules at the plant–fungal interface that could shed light on the mechanisms of this natural partnership. Details of the study were published in Nature Plants.

An estimated 80% of vascular plant families form symbioses with a type of soil fungi called arbuscular mycorrhizal fungi. The fungi penetrate the outermost cells of a plant’s roots and grow intricate branch-like structures called arbuscules. Each host plant cell then grows a membrane that envelops an arbuscule, and nutrient exchange takes place within the space between the plant membrane and the fungal cell wall.

In an attempt to understand the fundamental interaction between plants and the fungi, BTI faculty member Maria Harrison and postdoctoral scientist Sergey Ivanov joined forces with R. Howard Berg, director of the Donald Danforth Center’s Integrated Microscopy Facility. They used advanced electron microscopy techniques to image arbuscules present in the roots of the legume Medicago truncatula colonized by the fungus Rhizophagus irregularis, and were surprised by the results.

“Our understanding of the sub-cellular structural basis of the interaction relies on studies performed 30-40 years ago. Many of them indicated that the material around the fungus but inside the plant membrane would be an amorphous matrix of carbohydrate material,” said Harrison, the paper’s corresponding author. Instead, the researchers found a network of round, tubular and dumbbell-shaped structures constructed of lipid membranes, nearly all of which appeared to connect back to the plant cell’s membrane.

The researchers were further surprised to find another network of membrane tubules in the space between the fungal cell membrane and the fungal cell wall. “It was totally unexpected to see such an extensive proliferation of fungal membrane, particularly knowing that the fungus is starving for lipids,” explains Ivanov, the paper’s lead author.

Harrison and Ivanov speculate that the networks are related to the transfer of lipids.

“Somehow lipids are released from the plant cell and fed to the fungus, and we wondered how they move through what we thought was an aqueous matrix between the plant cell membrane and the fungal cell wall,” says Harrison. “But maybe this space isn’t so aqueous after all, and perhaps this membrane-rich environment facilitates the movement of lipids between the organisms.”

Given the plant and fungal membrane networks’ close physical proximity to each other, the fungal network could be involved in lipid absorption in order to optimize the process. The researchers suspect the network is not involved with transferring phosphate to the plant because the membrane networks are more abundant near the larger branches of the arbuscule, whereas phosphate uptake likely occurs near the smaller branches.

Harrison believes that newer technologies are to thank for finding these networks of tubules. “High-pressure freezing fixation of samples gives better membrane preservation than older techniques. I think that is the reason that these extensive membranes were not seen before,” she says. “Plus, 3D electron tomography is very powerful and let us visualize the networks, which didn’t look connected on 2D images.”

Ivanov, worked closely with Berg, who has expertise with cryofixation and electron microscopy, and Jotham Austin II at the University of Chicago, who is an expert in tomography.

Another research group led by Uta Paszkowski of the University of Cambridge in the UK performed similar imaging studies in rice colonized with R. irregularis, and found similar structures. Those results were published in the same issue of Nature Plants.

Read the paper: Nature Plants

Article source:Boyce Thompson Institute

Image credit: Jotham Austin II and R. Howard Berg

Scientists have discovered that grasses are able to short cut evolution by taking genes from their neighbours

By | News

The findings suggest wild grasses are naturally genetically modifying themselves to gain a competitive advantage.

Understanding how this is happening may also help scientists reduce the risk of genes escaping from GM crops and creating so called “super-weeds” – which can happen when genes from GM crops transfer into local wild plants, making them herbicide resistant.

Since Darwin, much of the theory of evolution has been based on common descent, where natural selection acts on the genes passed from parent to offspring. However, researchers from the Department of Animal and Plant Sciences at the University of Sheffield have found that grasses are breaking these rules. Lateral gene transfer allows organisms to bypass evolution and skip to the front of the queue by using genes that they acquire from distantly related species.

“Grasses are simply stealing genes and taking an evolutionary shortcut,” said Dr Luke Dunning.

“They are acting as a sponge, absorbing useful genetic information from their neighbours to out compete their relatives and survive in hostile habitats without putting in the millions of years it usually takes to evolve these adaptations.”

Scientists looked at grasses – some of the most economically and ecologically important plants on Earth including many of the most cultivated crops worldwide such as: wheat, maize, rice, barley, sorghum and sugar cane.

The paper, published in the journal Proceedings of the National Academy of Sciences, explains how scientists sequenced and assembled the genome of the grass Alloteropsis semialata.

Studying the genome of the grass Alloteropsis semialata – which is found across Africa, Asia and Australia – researchers were able to compare it with approximately 150 other grasses including rice, maize, millets, barley and bamboo. They identified genes in Alloteropsis semialata that were laterally acquired by comparing the similarity of the DNA sequences that make up the genes.

“We also collected samples of Alloteropsis semialata from tropical and subtropical places in Asia, Africa and Australia so that we could track down when and where the transfers happened,” said Dr Dunning.

“Counterfeiting genes is giving the grasses huge advantages and helping them to adapt to their surrounding environment and survive – and this research also shows that it is not just restricted to Alloteropsis semialata as we detected it in a wide range of other grass species.”

“This research may make us as a society reconsider how we view GM technology as grasses have naturally exploited a similar process.

“Eventually, this research may also help us to understand how genes can escape from GM crops to wild species or other non-GM crops, and provide solutions to reduce the likelihood of this happening.

“The next step is to understand the biological mechanism behind this phenomenon and we will carry out further studies to answer this.”

Read the paper: PNAS

Article source: University of Sheffield

Image credit: University of Sheffield

Cell division in Plants: How cell walls are assembled

By | News

Plant researchers at Martin Luther University Halle-Wittenberg (MLU)_ are providing new insights into basic cell division in plants. The scientists have succeeded in understanding how processes are coordinated that are pivotal in properly separating daughter cells during cell division. In the renowned scientific publication “The EMBO Journal “, they describe the tasks of certain membrane building blocks and how plants are impacted when these building blocks are disrupted.

For their study, the plant researchers examined the roots of the thale cress plant, Arabidopsis thaliana. They cultivated normal plants and plants in which they artificially switched off certain enzymes that affect the composition of the membranes. “We wanted to find out which membrane building blocks are important for cell division and why,” explains Professor Ingo Heilmann from MLU.

For plants to develop, their cells have to divide. First, the genetic material located in the cell nucleus divides. Two whole new cell nuclei are formed from the duplicated genetic material. The other components of the cell, for example the chloroplasts and mitochondria, are distributed between the two future daughter cells. All this takes place in the parent cell.

Only then the daughter cells will be separated by a new cell wall. The whole process can be compared to a construction site. First, a temporary scaffold made of protein fibres, the so-called phragmoplast, forms in the middle of the cell. Like railway tracks, these fibres guide the building materials needed for the cell wall. Small bubbles gradually transport new cell wall material along the rails. This is assembled together by a complex fusion machinery to form a larger structure: the cell plate. The cell plate continues to grow at its edges from the centre of the cell outwards until a cell wall disc completely separates the daughter cells from one another. “The fusion machinery has to correctly coordinate the protein fibres for everything to function properly, otherwise the freight cars will transport the cell wall material to the wrong spot or at the wrong time and cell plate formation will cease,” explains Heilmann.

Using biochemical and cell biology experiments, his research group was able to show that PI4P, a membrane building block, plays two roles during cell division: PI4P not only controls the activity of the fusion machinery, it also ensures the new material is transported in the right direction. For the first time, the researchers were able to show that PI4P helps to ensure that the protein scaffold of the phragmoplast is assembled and disassembled in the right places. In normal plants, this results in regular cells that fit together perfectly and give the plant its needed stability.

In mutated plants, however, the scientists observed severe defects in cell division: They found enlarged cells containing several cell nuclei as a result of the unsuccessful separation of the daughter cells. Some cells were unable to divide completely, the cell tissue was chaotic, and there were enormous differences in the sizes of the individual cells. “This is not happy tissue. It makes the entire plant more unstable, reduces its size and impacts how it adapts to environmental stimuli,” explains Heilmann.

The results of the research group from Halle help to better understand the dynamics of the plant’s cytoskeleton of microtubules. The cytoskeleton not only determines the direction of cellular transport processes during cell division, but also directs general plant growth. Therefore, the new findings could have far-reaching consequences, for example on the deposition of cellulose in plant cell walls and thus on biomass and cellulose production. However, it must first be determined whether the findings can also be applied to other plants and how the activity of the enzymes investigated here can be specifically regulated.

Read the paper: The EMBO Journal

Article source:Martin-Luther-Universität Halle-Wittenberg

Image credit: Ingo Heilmann (The EMBO Journal)

Genetic blueprint for extraordinary wood-munching fungus

By | News

A relatively unknown fungus, accidentally found growing on an Acacia tree in the Northern Cape, has emerged as a voracious wood-munching organism with enormous potential in industries based on renewable resources.

The first time someone took note of Coniochaeta pulveracea was more than two hundred years ago, when the South African-born mycologist Dr Christiaan Hendrik Persoon mentioned it in his 1797 book on the classification of fungi.

Now C. pulveracea has had its whole genome sequenced by microbiologists at Stellenbosch University (SU) in South Africa, and henceforth made its debut in cyberspace with a few tweets and a hashtag. All because this relatively unknown fungus has an extraordinary ability to degrade wood – hence the descriptor “pulveracea”, meaning powdery.

In the age of biotechnology, biofuels and the usage of renewable raw materials, this is an important fungus to take note of, says Prof Alf Botha, a microbiologist in the Department of Microbiology at SU.

Over the past 25 years, there has been a number of reports on the ability of species in the Coniochaeta genus to rapidly degrade lignocellulose into fermentable simple sugars. But thus far Prof Botha‘s lab is the only one to be working on C. pulveracea.

The work started in 2011, when he quite randomly snapped a brittle twig, covered in lichen, from a decaying Acacia tree. At the time, he was holidaying with family on a farm in the Northern Cape. “At the time we were looking for fungi and yeasts that can break down wood, so I knew this was something special when I decided to keep the twig,” he explains. But to date, despite numerous attempts, they have not been able to find it again.

However, back in the lab there was great excitement when they observed that this species in the Coniochaeta genus was literally munching its way through birchwood toothpicks. Even more astounding was its ability to change form between a filamentous fungus and a yeast, depending on the environment.

“This is highly unusual for a fungus. We’d typically expect this kind of behavior from some fungal pathogens,” explains Botha.

Over the past decade Botha and his postgraduate students focused on unraveling this yeast-like fungus’ behavior. In 2011 Dr Andrea van Heerden found that it produced enzymes that degraded the complex structures of wood into simple sugars, feeding a community of surrounding fungi that do not have the ability to degrade wood. In 2016, she published the results of her investigation into its ability to switch to a yeast-like growth. Understanding this process would be important to the potential use of this fungi in industrial processes.

In the latest study, MSc student CJ Borstlap worked with Dr Heinrich Volschenk, an expert molecular biologist, and Dr Riaan de Witt from the Centre for Bioinformatics and Computational Biology at SU, to produce the first draft genome sequence of C. pulveracea. With a genome size of 30 million nucleotides and over 10 000 genes, this was no easy task. In the process he picked up the necessary coding skills to identify and name all 10 053 genes, and to identify those responsible for the wood-degrading character of the fungus.

Dr Volschenk says the next step is to understand the fungus’ mechanism of breaking down wood and producing sugars on a molecular level: “With the genetic blueprint now available, we can study the network of genes and proteins the fungus employs to convert wood and other similar renewable resources into more valuable products,” he explains.

The sequence data for C. pulveracea have been deposited at the DNA Data Bank of Japan (DDBJ), the European Nucleotide Archive (ENA) at Cambridge, and GenBank in the United States of America, under the accession number QVQW00000000 and is freely available to all researchers in this field.

Read the paper: Microbiology Resource Announcements

Article source: Stellenbosh University

Image credit: Heinrich Volschenk

Plants can skip the middlemen to directly recognize disease-causing fungi

By | News

Scientists at the Max Planck Institute for Plant Breeding Research in Cologne have revealed that direct physical associations between plant immune proteins and fungal molecules are widespread during attempted infection. The authors’ findings run counter to current thinking and may have important implications for engineering disease resistance in crop species.

Fungal diseases collectively termed powdery mildew afflict a broad range of plant species, including agriculturally relevant cereals such as barley, and result in significant reductions in crop yield. Fungi that cause powdery mildew deliver so-called effector molecules inside plant cells where they manipulate the host’s physiology and immune system. In response, some plants have developed Resistance (R) genes, usually intracellular immune receptors, which recognize the infection by detecting the fungus’ effectors, often leading to plant cell death at the site of attempted infection to limit the spread of the fungus. In the prevailing view, direct recognition of effectors by immune receptors is rather a rare event in plant-pathogen interactions, however, and it has been thought instead that in most cases recognition proceeds via other host proteins that are modified by the pathogen.

In barley populations, one of the powdery mildew receptors, designated mildew locus a (Mla), has undergone pronounced diversification, resulting in large numbers of different MLA protein variants with highly similar (>90%) DNA sequences. This suggests co-evolution with powdery mildew effectors, but the nature of the evolutionary relationship and interactions between immune receptor and effectors remained unclear.

To address these questions, Isabel Saur, Saskia Bauer, and colleagues from the department of Paul Schulze-Lefert first isolated several effectors from powdery mildew fungi collected in the field. Except for two, these proteins were all highly divergent from one another. When the authors expressed the effectors together with matching MLA receptors this led to cell death not only in barley but also in distantly related tobacco cells, already suggesting that no other barley proteins are required for recognition. Using bioluminescence as a marker for direct protein-protein interactions, the scientists indeed found specific associations of effector-MLA pairs in extracts of tobacco leaves. Similarly, a protein-protein interaction assay in yeast also revealed interactions only of matching effector-MLA pairs. These results suggest that highly sequence-related MLA receptor variants directly detect unrelated fungal effectors.

Plant disease is a major cause of loss of yield in crops. Transfer of plant R genes between species is a potentially powerful approach to generate disease-resistant crops. The authors’ discovery that multiple variants of the same resistance gene are able to bind dissimilar pathogen proteins, also in distantly related plant species, underlines the potential of this approach and chimes in with the earlier finding that wheat versions of Mla, Sr33 and Sr50, provide disease resistance to the stem rust isolate Ug99, a major threat to global wheat production.

Paul Schulze-Lefert sees further exciting applications on the horizon: “Our discovery that direct receptor-effector interactions are widespread for MLA receptors suggests that it may be feasible to rationally design synthetic receptors to detect pathogen effectors that escape surveillance by the plant immune system.”

Read the paper: eLife

Article source:Max Planck Institute for Plant Breeding Research

Image credit: Takaki Maekawa

World’s biggest terrestrial carbon sinks are found in young forests

By | Climate change, Forestry, News

More than half of the carbon sink in the world’s forests is in areas where the trees are relatively young – under 140 years old – rather than in tropical rainforests, research at the University of Birmingham shows.

These trees have typically ‘regrown’ on land previously used for agriculture, or cleared by fire or harvest and it is their young age that is one of the main drivers of this carbon uptake.

Forests are widely recognised as important carbon sinks – ecosystems capable of capturing and storing large amounts of carbon dioxide – but dense tropical forests, close to the equator have been assumed to be working the hardest to soak up these gases.

Researchers at the Birmingham Institute of Forest Research (BIFoR) have carried out fresh analysis of the global biosphere using a new combination of data and computer modelling in a new study published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS). Drawing on data sets of forest age, they were able to show the amount of carbon uptake between 2001 and 2010 by old, established areas of forest.

They compared this with younger expanses of forest which are re-growing across areas that have formerly experienced human activities such as agriculture or logging or natural disturbances such as fire.

Previously it had been thought that the carbon uptake by forests was overwhelmingly due to fertilisation of tree growth by increasing levels of carbon dioxide in the atmosphere.

However, the researchers found that areas where forests were re-growing sucked up large amounts of carbon not only due to these fertilisation effects, but also as a result of their younger age. The age effect accounted for around 25 per cent of the total carbon dioxide absorbed by forests. Furthermore, this age-driven carbon uptake was primarily situated not in the tropics, but in the middle and high latitude forests.

These forests include, for example, areas of land in America’s eastern states, where settlers established farmlands but then abandoned them to move west towards the end of the 19th century. The abandoned land became part of the US National Forest, along with further tracts abandoned during the Great Depression in the 1930s.

Other significant areas of forest re-growth include boreal forests of Canada, Russia and Europe, which have experienced substantial harvest activity and forest fires. Largescale reforestation programmes in China are also making a major contribution to this carbon sink.

Dr Tom Pugh, of the Birmingham Institute of Forest Research (BIFoR), explained: “It’s important to get a clear sense of where and why this carbon uptake is happening, because this helps us to make targeted and informed decisions about forest management.”

The research highlights the importance of forests in the world’s temperate zone for climate change mitigation, but also shows more clearly how much carbon these re-growing forests can be expected to take up in the future. This is particularly important because of the transient nature of re-growth forest: once the current pulse of forest re-growth works its way through the system this important part of the carbon sink will disappear, unless further reforestation occurs.

“The amount of CO2 that can be taken up by forests is a finite amount: ultimately reforestation programmes will only be effective if we simultaneously work to reduce our emissions,” explains Dr Pugh.

Read the paper: PNAS

Article source:University of Birmingham

Image credit: CCO Public domain

An economist’s perspective on plant sciences: Under-appreciated, over-regulated and under-funded

By | Blog, Future Directions

David Zilberman

Modified crops such as Golden Rice could have major benefits for people in developing nations. Image credit: IRRI Licensed under CC BY 2.0

By David Zilberman, Professor and Robinson Chair, Agriculture and Resource Economics, UC Berkeley

When I started working on agronomical issues in the 1970s, the most exciting technologies were related to water, machinery, and harvesting. Plant genetics seemed to be quite a boring enterprise. But as I became familiar with the Green Revolution, I realized the importance of plant research, and that the golden rule in agriculture is to find the optimal mixture between biotic and abiotic technologies. As an economist working on technology, I started to realize that the past fifty years have drastically changed the way plant sciences are done, and the potential and value of their product.

The discovery of the innerworkings of a cell, combined with the power of computers and precision tools, has changed medicine, but it has perhaps the potential to make an even bigger impact on plant sciences and agriculture. I have been working on the economics and policy aspects of agricultural biotechnology (see also Journal of Economic Perspectives).  Despite the restrictions on genetically modified varieties, they increase yields and make food more affordable for the poor. They also reduce greenhouse gas emissions and actually improved human health (by reducing exposure to chemicals and aflatoxin). But biotechnologies have had limited impact because of regulations that limit their use mostly to feed and fiber crops, and the practical ban on use of GMOs in Europe and parts of Africa.

It’s clear that developing countries can be the major beneficiaries of these technologies. They can save billions of dollars and address severe health and malnourishment problems. Furthermore, applications of biotechnology on food crops can reduce food security problems and increase access to valuable fresh produce throughout the world. Modern biotechnology can provide tools to accelerate adaptation to climate change, and I am surprised that some of the organizations most aware of climate change don’t recognize the value of biotechnology to address it.

Plant science research has already made major achievements using traditional and advanced tools to provide better varieties and improve the global food situation in a world with a fast growing population. There is a large body of literature documenting the rate of return of research, and much of the achievements have been the development of new varieties. The literature suggests that public research that provided much of the benefit has been underfunded, and its funding is declining. Thus, plant research hasn’t reached its potential.

Thus far, applied research in plant sciences at many universities concentrate on grasses, like corn and wheat, but underemphasize trees and algae. One explanation to the emphasis on grasses is the immediate economic benefits they seem to provide. With all the modern tools of biology, the big challenges and some of the most radical and relevant knowledge can come from the study of trees and algae within the context of forest and oceans. Studies of these specimens will enhance our understanding of living systems, is crucially important from a macro-ecological perspective, and from a practical perspective of finding new materials, new foods and efficient sources of energy.

Poplar is one of the most commonly used trees in plant science research. Image credit: Walter Siegmund 

I believe that society tends to underinvest in plant sciences, both because science is underfunded in general and because of the regulations of biotechnology that limit their use, as mentioned above. The contribution of plant scientists to address problems of climate change, deforestation, food security, and environmental quality are under-emphasized and under-recognized. This leads to less investment in this area, less contribution, and less student interest. But more investment in plant sciences may provide better understanding of their impact and how to regulate them, and provide more promising applications. So we are in a vicious cycle of over-regulation and under-funding that mostly hurt regions and populations that are vulnerable, and reduce our capabilities to deal with global changes.

To move forward, we need to have more enlightened regulations that will allow us to take advantage of this incredible science and big jolts in terms of support for research in plant sciences. Enlightened regulations would balance benefits and risks, reduce the cost of access to modern biotechnologies. They also would allow efficient and mutually beneficial transfer of knowledge and genetic materials across locations. Plant sciences is one discipline where the distribution of efforts across locations globally can be especially beneficial as we can learn about the performance of plant systems throughout the world. Therefore, investments in plant sciences should be distributed globally. For example, a major effort to raise funding for 100 Chairs of Plant Sciences around the world, especially in developing countries, will be a good start. It should be associated with support for student research, as well as forums the exchange of new ideas. And finally, new investments in arboretums and greenhouses.

Plant sciences have been providing humanity essential knowledge that enabled the growth and evolution of human civilization without much fanfare. New tools increase its potential and the excitement and value of research in these areas. Society needs to expand their support to plant sciences to enable it to flourish around the world, as well as enlightened regulation to gain benefits from the fruits of this research.

When lipids meet hormones: plants’ answer to complex stresses

By | Blog, Research

This blog has been reposted with permission from the MSU-DOE Plant Research Laboratory.


Unlike animals, plants can’t run away when things get bad. That can be the weather changing or a caterpillar starting to slowly munch on a leaf. Instead, they change themselves inside, using a complex system of  hormones, to adapt to challenges.

Now, MSU-DOE Plant Research Laboratory scientists are connecting two plant defense systems to how these plants do photosynthesis. The study, conducted in the labs of Christoph Benning and Gregg Howeis in the journal, The Plant Cell.

At the heart of this connection is the chloroplast, the engine of photosynthesis. It specializes in producing compounds that plants survive with. But plants have evolved ways to use it for other, completely unrelated purposes.

Their trick is to harvest their own chloroplasts’ protective membranes, made of  lipids, the molecules found in fats and oils. Lipids have many uses, from making up cell boundaries, to being part of plant hormones, to storing energy.

If plants need lipids for some purpose other than serving as membranes, special proteins break down chloroplast membrane lipids. Then, the resulting products go to where they need to be for further processing.

For example, one such protein, breaks down lipids that end up in plant seed oil. Plant seed oil is both a basic food component and a precursor for biodiesel production.

Now, Kun (Kenny) Wang, a former Benning lab grad student, reports two more such chloroplast proteins with different purposes. Their lipid breakdown products help plants turn on their defense system against living pests and other herbivores. In turn, the proteins, PLIP2 and PLIP3, are themselves activated by another defense system against non-living threats.

Playing the telephone game inside plants

In a nutshell, the plant plays a version of the popular children’s game, Telephone, with itself. In the real game, players form a line. The first person whispers a message into the ear of the next person in the line, and so on, until the last player announces the message to the entire group.

In plants, defense systems and chloroplasts also pass along chemical messages down a line. Breaking it down:

  1. The plant senses non-living threats, like cold or drought, and indicates it through one hormone (ABA)
  2. This alarm triggers the two identified proteins to breakdown lipids from the chloroplast membrane
  3. The lipid products turn into another hormone (JA) which takes part in the insect defense system. Plant growth slows to a crawl. Energy goes to producing defensive chemicals.

“The cross-talk between defense systems has a purpose. For example, there is mounting evidence that plants facing drought are more vulnerable to caterpillar attacks,” Kenny says. “One can imagine plants evolving precautionary strategies for varied conditions. And the cross-talk helps plants form a comprehensive defense strategy.”

Kenny adds, “The chloroplast is amazing. We suspect its membrane lipids spur functions other than defense or oil production. That implies more Telephone games leading to different ends we don’t know yet. We have yet to properly examine that area.”

“Those functions could help us better understand plants and engineer them to be more resistant to complex stresses.”

Moving on to Harvard Medical School

Kenny recently got his PhD from the MSU Department of Biochemistry and Molecular Biology. He has just started a post-doc position in the Farese-Walther lab at Harvard Medical School.

“They look at lipid metabolism in mammals and have started a project connecting it with brain disease in humans,” Kenny says. “There is increasing evidence that problems with lipid metabolism in the brain might lead to dementia, Alzheimer’s, etc.”

“I benefited a lot from my time at MSU. The community is very successful here: the people are nice, and you have support from colleagues and facilities. Although we scientists should sometimes be independent in our work, we also need to interact with our communities. No matter how good you are, there is a limit to your impact as an individual. That is one of the lessons I applied when looking for my post-doc.”


Photo of the author, Kun (Kenny) Wang. By Kenny Wang

Read the original article here.

Reflections from the “Feed the Future” conference in Burkina Faso

By | Blog, Research

By Atsuko Kanazawa, Igor Houwat, Cynthia Donovan

This article is reposted with permission from the Michigan State University team. You can find the original post here: MSU-DOE Plant Research Laboratory

By Atsuko Kanazawa

Atsuko Kanazawa is a plant scientist in the lab of David Kramer. Her main focus is on understanding the basics of photosynthesis, the process by which plants capture solar energy to generate our planet’s food supply.

This type of research has implications beyond academia, however, and the Kramer lab is using their knowledge, in addition to new technologies developed in their labs, to help farmers improve land management practices.

One component of the lab’s outreach efforts is its participation in the Legume Innovation Lab (LIL) at Michigan State University, a program which contributes to food security and economic growth in developing countries in Sub-Saharan Africa and Latin America.

Atsuko recently joined a contingent that attended a LIL conference in Burkina Faso to discuss legume management with scientists from West Africa, Central America, Haiti, and the US. The experience was an eye opener, to say the least.

To understand some of the challenges faced by farmers in Africa, take a look at this picture, Atsuko says.

“When we look at corn fields in the Midwest, the corn stalks grow uniformly and are usually about the same height,” Atsuko says. “As you can see in this photo from Burkina Faso, their growth is not even.”

“Soil scientists tell us that much farmland in Africa suffers from poor nutrient content. In fact, farmers sometimes rely on finding a spot of good growth where animals have happened to fertilize the soil.”

Even if local farmers understand their problems, they often find that the appropriate solutions are beyond their reach. For example, items like fertilizer and pesticides are very expensive to buy.

That is where USAID’s Feed the Future and LIL step in, bringing economists, educators, nutritionists, and scientists to work with local universities, institutions, and private organizations towards designing best practices that improve farming and nutrition.

Atsuko says, “LIL works with local populations to select the most suitable crops for local conditions, improve soil quality, and manage pests and diseases in financially and environmentally sustainable ways.”

Unearthing sources of protein

At the Burkina Faso conference, the Kramer lab reported how a team of US and Zambian researchers are mapping bean genes and identifying varieties that can sustainably grow in hot and drought conditions.

The team is relying on a new technology platform, called PhotosynQ, which has been designed and developed in the Kramer labs in Michigan.

PhotosynQ includes a hand-held instrument that can measure plant, soil, water, and environmental parameters. The device is relatively inexpensive and easy to use, which solves accessibility issues for communities with weak purchasing power.

The heart of PhotosynQ, however, is its open-source online platform, where users upload collected data so that it can be collaboratively analyzed among a community of 2400+ researchers, educators, and farmers from over 18 countries. The idea is to solve local problems through global collaboration.

Atsuko notes that the Zambia project’s focus on beans is part of the larger context under which USAID and LIL are functioning.

“From what I was told by other scientists, protein availability in diets tends to be a problem in developing countries, and that particularly affects children’s development,” Atsuko says. “Beans are cheaper than meat, and they are a good source of protein. Introducing high quality beans aims to improve nutrition quality.”

Science alone is sometimes not enough

But, as LIL has found, good science and relationships don’t necessarily translate into new crops being embraced by local communities.

Farmers might be reluctant to try a new variety, because they don’t know how well it will perform or if it will cook well or taste good. They also worry that if a new crop is popular, they won’t have ready access to seed quantities that meet demand.

Sometimes, as Atsuko learned at the conference, the issue goes beyond farming or nutrition considerations. In one instance, local West African communities were reluctant to try out a bean variety suggested by LIL and its partners.

The issue was its color.

“One scientist reported that during a recent famine, West African countries imported cowpeas from their neighbors, and those beans had a similar color to the variety LIL was suggesting. So the reluctance was related to a memory from a bad time.”

This particular story does have a happy ending. LIL and the Burkina Faso governmental research agency, INERA, eventually suggested two varieties of cowpeas that were embraced by farmers. Their given names best translate as, “Hope,” and “Money,” perhaps as anticipation of the good life to come.

Another fruitful, perhaps more direct, approach of working with local communities has been supporting women-run cowpea seed and grain farms. These ventures are partnerships between LIL, the national research institute, private institutions, and Burkina Faso’s state and local governments.

Atsuko and other conference attendees visited two of these farms in person. The Women’s Association Yiye in Lago is a particularly impressive success story. Operating since 2009, it now includes 360 associated producing and processing groups, involving 5642 women and 40 men.

“They have been very active,” Atsuko remarks. “You name it: soil management, bean quality management, pest and disease control, and overall economic management, all these have been implemented by this consortium in a methodical fashion.”

“One of the local farm managers told our visiting group that their crop is wonderful, with high yield and good nutrition quality. Children are growing well, and their families can send them to good schools.”

As the numbers indicate, women are the main force behind the success. The reason is that, usually, men don’t do the fieldwork on cowpeas. “But that local farm manager said that now the farm is very successful, men were going to have to work harder and pitch in!”

Back in Michigan, Atsuko is back to the lab bench to continue her photosynthesis research. She still thinks about her Burkina Faso trip, especially how her participation in LIL’s collaborative framework facilitates the work she and her colleagues pursue in West Africa and other parts of the continent.

“We are very lucky to have technologies and knowledge that can be adapted by working with local populations. We ask them to tell us what they need, because they know what the real problems are, and then we jointly try to come up with tailored solutions.”

“It is a successful model, and I feel we are very privileged to be a part of our collaborators’ lives.”

This article is reposted with permission from the Michigan State University team. You can find the original post here: MSU-DOE Plant Research Laboratory

Putting Big Data to Work with ARPA-E’s TERRA Program

By | Blog, Future Directions, Interviews

This week we spoke to Dr. Joe Cornelius, the Program Director at the Advanced Research Projects Agency – Energy (ARPA-E). His work focusses on bioenergy production and conversion as a renewable and sustainable energy source, transportation fuel, and chemical feedstock, applying innovations in biotechnology, genomics, metabolic engineering, molecular breeding, computational analytics, remote sensing, and precision robotics to improve biomass energy density, production intensity, and environmental impacts.

 

What is ARPA-E? How are programs created?

The Advanced Research Projects Agency-Energy (ARPA-E) is a young government agency in the U.S. Department of Energy. The agency is modeled on a successful Defense Department program, the Defense Advanced Research Projects Agency (DARPA). Both agencies target high-risk, high-reward research in early-stage technologies that are not yet ready for private-sector investment.

Program development is one of the unique characteristics of the agency. ARPA-E projects are in the hands of term-limited program directors, who develop a broad portfolio of concepts that could make a large impact in the agency’s three primary mission areas: energy security, energy efficiency, and emissions reductions. The agency motto is “Changing what’s possible”, and we are always asking ourselves, “if it works, will it matter?”. Getting a program approved is a lot like a doing a PhD; you survey the field, host a workshop, determine key points to research, define aggressive performance metrics, and finally defend the idea to the faculty. If the idea passes muster, the agency makes a targeted investment. This flexibility was recently noticed as one of the great aspects of ARPA-E culture and is an exciting part of the job.

 

What is TERRA and how is it new for agriculture?

TERRA stands for Transportation Energy Resources from Renewable Agriculture, and its impact mission is to accelerate genetic gains in plant breeding. This is an advanced analytics platform for plant breeding. Today, significant scientific progress is possible through the convergence of diverse technologies, and TERRA’s innovation for breeders comes through the integration of remote sensing, computer vision, analytics, and genetics. The teams are using robots to carry cameras to the field and then extracting phenotypes and performing gene linkages. It’s really awesome to see.

 

This is run by the U.S. Department of Energy. How does TERRA tie into energy?

The United States has a great potential to generate biomass for conversion to cellulosic ethanol, but the crops useful for producing this biomass have not seen the improvement that others, such as soybeans or maize, have had. TERRA is focused on sorghum, which is a productive and resilient crop with existing commercial infrastructure that can yield advanced biomass on marginal lands. In addition, sorghum is a key food and feed crop, and the rest of the world will benefit from these advancements.

 

How does TERRA address the challenge of phenotyping in the field?

The real challenges that remain are in calibrating the sensor output and generating biological insight. A colleague from the United Kingdom, Tony Pridmore, captured the thought well, saying “Photography is not phenotying.” It’s generally easy to take the pictures — unless it’s very windy, the aerial platforms can pass over any crop, and the ground platforms are based on proven agricultural equipment. To get biological insights however, each team requires an analytics component, and a team from IBM is contributing their analytics expertise in collaboration with Purdue University.

 

 

What is most exciting about the TERRA program?

We commissioned the world’s biggest agricultural field robot, which phenotypes year-round. The six teams have successfully built other lightweight platforms involving tractors, rovers, mini-bots, and fixed and rotary wing unmanned aerial vehicles. It’s exciting to see some of the most advanced technologies move so quickly into the hands of great geneticists. The amazing thing is how quickly the teams have started generating phenotyping data. I expected it to take years before we got to this point, but the teams are knocking it out of the park, and we are entering into full-blown breeding systems deployment.

 

Who’s on the TERRA teams? How did you build the program?

ARPA-E system teams include large businesses, startups, and university groups. The program was built to have a full portfolio of diverse sensor suites, robotic platform types (ground and aerial), analytics approaches, and geographic breadth. Because breeders are working for a particular target population of environments, different phenotypes are valued differently across the various geographies. For that reason, each group is collecting its own set of phenotypes. Beyond that, we’ve worked very hard to encourage collaboration across the teams and have an exciting GxE (genotype x environment) experiment running, where several teams plant the same germplasm across multiple geographies. By combining this with high-throughput phenotyping, the teams are in a good position to determine key environmental inputs to various traits.

 

Once we achieve rapid-fire field phenotyping, what’s next?

We’re going underground! ARPA-E has made another targeted investment, this time in root phenotyping. We’re really excited about this one. It’s a very similar concept, but the sensing is so much harder. The teams have collaborated with medical, mining, aerospace, and defense communities for technologies that can allow us to observe root and soil systems in the field to allow breeders to improve crops.  Ask us again next year—we will have some cool updates to both programs!