tag:theconversation.com,2011:/africa/topics/arabidopsis-42971/articlesArabidopsis – The Conversation2020-08-28T12:21:31Ztag:theconversation.com,2011:article/1438022020-08-28T12:21:31Z2020-08-28T12:21:31ZWhen plants and their microbes are not in sync, the results can be disastrous<figure><img src="https://images.theconversation.com/files/354907/original/file-20200826-7211-8fafms.jpg?ixlib=rb-1.1.0&rect=0%2C5%2C3943%2C2500&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A healthy wild-type _Arabidopsis_ plant (left) and a mutant plant suffering from a microbe imbalance (right).</span> <span class="attribution"><span class="source">Sheng-Yang He</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>Many of us have heard about <a href="https://www.niddk.nih.gov/about-niddk/70th-anniversary/inflammatory-bowel-disease-ibd">inflammatory bowel disease</a>, a debilitating condition that is associated with an abnormal collection of microbes in the human gut – known as the gut microbiome. <a href="http://www.thehelab.org">My lab</a> recently found that, like humans, plants can also develop this condition, known as dysbiosis, with severe consequences. </p>
<p>As part of <a href="https://doi.org/10.1038/s41586-020-2185-0" title="primary research">this study</a>, my colleagues and I discovered that some genes and processes involved in controlling dysbiosis in plants may be similar to those in humans. Discovery of dysbiosis in the plant kingdom opens new possibilities for stimulating innovation in plant health and global food security.</p>
<p><a href="https://doi.org/10.1016/j.cub.2018.02.049">I am a plant microbiologist</a> interested in how plants and microbes interact with each other. Although our research in the past has centered on <a href="https://doi.org/10.1038/nature20166">molecular details of pathogenic infections</a>, this work led my lab into the fascinating world of plant microbiome.</p>
<h2>Do plants have microbiomes?</h2>
<p>When scientists say that human “gut bacteria” should be well balanced, they are referring to the genetic material of all the microbes living in human digestive systems, or the gut microbiome. Do plants have microbiomes as well? The answer is yes.</p>
<p>In fact, the parts of the plant that grow aboveground, called phyllosphere, and those parts that grow below, called rhizosphere, provide one of the largest habitats for microbe colonization on Earth. Both are vital for human life on Earth.</p>
<p>The phyllosphere takes up carbon dioxide for photosynthesis, which is necessary to build biomass and is a primary source of food, fuels, fibers and medicines. Photosynthesis also releases oxygen for animals and humans to breathe, which is why plants are often considered to be the lungs of our planet. The rhizosphere, on the other hand, takes up water and nutrients from soil.</p>
<p><a href="https://doi.org/10.1111/nph.13312">Numerous studies</a> have shown that plant microbes help plants extract nutrients from the soil and cope with drought, pathogens, insects and other stresses. </p>
<p><a href="https://doi.org/10.1038/nature22399">Ecological studies</a> have also noted that the greater diversity of microbes living on plant leaves, the more productive the plants seem to be. </p>
<p>Today, most plant scientists believe global strategies to ensure crop productivity and food security must consider plants’ microbiome. The U.N.’s Food and Agriculture Organization estimates that <a href="http://www.fao.org/plant-health-2020/about/en/">up to 40% of food crops</a> are lost due to plant pests and diseases annually, and the United Nations General Assembly declared 2020 as the International Year of Plant Health.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=672&fit=crop&dpr=1 600w, https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=672&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=672&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=844&fit=crop&dpr=1 754w, https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=844&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/353922/original/file-20200820-22-5xngpc.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=844&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Some microbes are associated with the leaves and shoots, while another distinct set live among the roots.</span>
<span class="attribution"><span class="source">Sheng-Yang He</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<h2>How do plants keep microbiota healthy?</h2>
<p>Given the importance of microbiota – the specific community of microbes living on or near plants – for plant health, we reasoned that plants must have evolved a sophisticated genetic network to select the right mix of microbes. </p>
<p>If that is true, then knowing which plant genes influence the types of microbes surrounding the plant could guide future research to optimize plant microbiomes to help plants grow better, stronger and to produce more biomass and yield.</p>
<p>Indeed, my group has now identified some of these “microbiota-controlling” genes in the model plant <em>Arabidopsis thaliana</em>. </p>
<p><a href="https://doi.org/10.1038/s41586-020-2185-0">We found that several genes</a> involved in plant immunity and water balance are critical for selecting and maintaining a healthy microbiota inside <em>Arabidopsis</em> plant leaves. </p>
<p>When we removed these identified genes from plants, the <em>Arabidopsis</em> plant mutants could not host the correct mix of microbes and displayed symptoms of dysbiosis, including dead or yellowing leaves. As far as we know, this was the <a href="https://doi.org/10.1038/s41586-020-2185-0">first time the negative effects of dysbiosis have been causally documented</a> in the plant kingdom.</p>
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<h2>Interesting features of ‘sick’ plants</h2>
<p>My colleagues and I observed some notable dysbiosis features in our mutant <em>Arabidopsis</em> plants. </p>
<p>First, dysbiosis mutants tend to have an abnormally high level of microbes living inside the leaves. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=420&fit=crop&dpr=1 600w, https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=420&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=420&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=528&fit=crop&dpr=1 754w, https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=528&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/354912/original/file-20200826-7319-1g8b3ca.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=528&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A leaf from a healthy <em>Arabidopsis</em> plant (left) and a leaf from a dysbiosis mutant plant (right).</span>
<span class="attribution"><span class="source">Sheng-Yang He</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>Second, there is a drastic change in the diversity of microbes. For example, in normal <em>Arabidopsis</em> plant leaves, there are all kinds of bacteria living inside the leaf. In contrast, overall diversity of bacteria is greatly reduced in the dysbiotic mutants, suggesting that healthy plants promote microbial diversity, presumably to increase the benefits to plant health.</p>
<p>Third, while bacteria that belong to the phylum <em>Fermicutes</em> are abundant inside wild-type <em>Arabidopsis</em> leaves, the abundance is significantly reduced in our genetic mutants. In addition, we saw a dramatic increase in the number of harmful bacteria inside the dysbiosis mutant leaves. We find it interesting that some of these microbiota changes are also observed in inflammatory bowel disease human patients, suggesting conceptual parallels in the development of dysbiosis in humans and plants.</p>
<h2>What’s next?</h2>
<p>We are excited about our identification of several plant genes and processes involved in preventing dysbiosis. The microbiota-controlling genes we identified in <em>Arabidopsis</em> are found in the genomes of many other plants, suggesting our findings may have broad applicability. </p>
<p>In the future, we could experiment with changing these host genes, which may lead to microbiota-based approaches that improve plant health. For example, gene-editing technologies could be used to create a healthy biome in plant leaves by enhancing expression of specific genes. A synthetic healthy microbiome may be formulated as a probiotic to prevent dysbiosis in plants, much as <a href="https://www.genome.gov/news/news-release/Microbes-in-us-and-their-role-in-human-health-and-disease">probiotics have been promised to improve human gut microbiome health</a>.</p>
<p>Of note, mutations in genes related to a person’s immune system, are a well-known <a href="http://doi.org/10.3389/fimmu.2015.00551">risk factor for the development of inflammatory bowel disease</a> in humans. Perhaps, future research will find more shared characteristics in how plants and humans interact with their respective microbiota in order to prevent disease. </p>
<p>The ease of genetic studies in plants, such as <em>Arabidopsis</em>, also offers the possibility that researchers will be able to identify more genes involved in preserving microbiota health in people and plants.</p><img src="https://counter.theconversation.com/content/143802/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Sheng-Yang He receives funding from Howard Hughes Medical institute, National Institutes of General Medical Sciences, Michigan State University</span></em></p>Just as humans can suffer from an imbalance of microbes in their gut, plants can suffer a similar syndrome in their leaves. This finding opens up new possibilities for improving food security.Sheng-Yang He, University Distinguished Professor, HHMI Investigator, Michigan State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/985952018-07-20T10:45:46Z2018-07-20T10:45:46ZPathogens attack plants like hackers, so my lab thinks about crop protection like cybersecurity<figure><img src="https://images.theconversation.com/files/228509/original/file-20180719-142417-14wj3wh.jpg?ixlib=rb-1.1.0&rect=541%2C44%2C2076%2C1633&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Plant hackers at work: microscopic oomycete spores infiltrating a plant root.</span> <span class="attribution"><span class="source">John Herlihy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Plants feed us. Without them we’re goners. Through thousands of years of genetic modification by selective breeding, humans have developed the crops that keep us alive. We have large kernels of grains, plump fruits and nutritious, toxin-free vegetables. These forms would never be found in nature, but were bred by people to keep us healthy and happy. </p>
<p>Unfortunately, microbes find our wonderfully productive food plants just as delicious as we do. These plant pathogens cause diseases that have changed world history and still affect us today.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/228470/original/file-20180719-142420-gduelt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">On the left, corn and its wild ancestor teosinte. Selective breeding has genetically modified crops to suit human needs. On the right, plant pathogen ergot on corn. We aren’t the only ones to subsist on our crops.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:On_Corn._Ergot_-_Flickr_-_gailhampshire.jpg">Left: Nicolle Rager Fuller, National Science Foundation, Right: gailhampshire</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>These pathogens are plant hackers. Just like computer hackers, they’re specialized infiltrators, adept in stealth and disruption. The methods are the same, too: shut down defenses and access the target’s resources. Once they’re in, plant pathogens eat all they can and reproduce wildly. Computer hackers desire wealth or information, but the plant hackers are after our food. Up to <a href="https://doi.org/10.1094/PHI-I-2001-0425-01">25 percent of crops</a> globally are lost to diseases before they reach market. </p>
<h2>Oomycetes on the attack</h2>
<p>The most infamous and cunning plant hackers are the <a href="https://www.apsnet.org/edcenter/intropp/PathogenGroups/Pages/IntroOomycetes.aspx">oomycetes</a>. The <a href="http://www.bbc.co.uk/history/british/victorians/famine_01.shtml">Irish Potato Famine</a> in the 1840s was caused by the oomycete <a href="https://en.wikipedia.org/wiki/Great_Famine_(Ireland)#Blight_in_Ireland"><em>Phytophthora</em></a>, Greek for “plant destroyer.” This biological disaster led to the emigration of millions of people to the United States, and <a href="http://www1.assumption.edu/ahc/irish/overview.html">changed both countries</a> forever. Even today, oomycetes and the rest of the plant pathogens remain a barrier to <a href="http://www.fao.org/3/a-i6583e.pdf">global food security</a>, contribute to <a href="https://doi.org/10.3390/agriculture2030182">malnutrition</a> and <a href="https://doi.org/10.1016/j.fgb.2014.10.012">cost billions of dollars in losses annually</a>. </p>
<p>The oomycetes are a strange product of evolution. They look and behave like fungi; hence their Greek name “egg-fungus.” It wasn’t until the advent of gene sequencing that researchers correctly identified the oomycetes as a relative of algae, <a href="https://www.apsnet.org/edcenter/intropp/PathogenGroups/Pages/Oomycetes.aspx">not fungi</a>. Oomycetes start as single microscopic spores that infiltrate plant leaves or roots undetected. Once inside, they establish a perverse connection with the host plant’s cells. The hackers gain access and can mess around with anything they want – from switching off the plant’s security systems to breaking into stores of plant nutrients.</p>
<p>Evolution has given the oomycetes a repertoire of toxins and proteins that <a href="https://doi.org/10.1126/science.1203659">converge on hubs of the plant immune system</a> to disable it. Plants can fight back against these attacks if they recognize oomycete-specific chemicals or the hackers’ toxins. But detection is difficult and fleeting. The oomycetes hackers have genomes built for evolution. Core genes for metabolism and growth mutate and change at a normal pace. However, genes for toxins, and those that control infection are positioned to rearrange, combine or be turned off after a single generation. These new forms evolve so quickly that they baffle the slow-to-change plant immune system. This “<a href="https://dx.doi.org/10.1016/j.gde.2015.09.001">two-speed genome</a>” means the oomycetes always have a leg up on plant immune detection. When farmers use genetically identical crops year-to-year, oomycetes <a href="https://doi.org/10.1016/j.meegid.2013.10.017">don’t take long to evolve</a> around plants’ defenses.</p>
<p>So how do researchers and growers stop the plant hackers and help crops? Despite the cost and <a href="https://extension.psu.edu/potential-health-effects-of-pesticides">drawbacks</a>, <a href="https://doi.org/10.2478/v10102-009-0001-7">pesticide</a> has been an <a href="https://ipm.tamu.edu/about/pesticides/">important tool</a>
to control plant disease.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=449&fit=crop&dpr=1 600w, https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=449&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=449&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=565&fit=crop&dpr=1 754w, https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=565&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/228473/original/file-20180719-142432-1wmv2d1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=565&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Cucurbit downy mildew on watermelon.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Downy_mildew_on_watermelon_2.jpg">David B. Langston, University of Georgia</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Farmers try to use minimum effective amounts of fungicide, which helps lower the chance oomycetes will develop resistance. For instance, the <a href="http://cdm.ipmpipe.org/">Cucurbit Downy Mildew Forecast Service</a> in Georgia combines reports of disease with weather forecasts to predict the likely path of disease spread. This allows growers to minimize sprays by sticking to high risk periods.</p>
<p>But it would be nice to have other weapons in the arsenal to fight off these plant hackers.</p>
<h2>Getting rid of exploitable loopholes</h2>
<p>In the <a href="https://fralin.vt.edu/Faculty/JohnMcDowell.html">McDowell lab</a> where I research here at Virginia Tech, we look for new ways to combat oomycete diseases.</p>
<p>Computer hackers rely on exploiting flaws in code to access systems and take what they want. Oomycetes work the same way, using their host to achieve their ends. For instance, <a href="https://doi.org/10.1126/science.1213351">plant diseases activate natural plant pumps</a> to supply sugar for their own growth. Some oomycetes have <a href="https://doi.org/10.1126/science.1195203">lost the capacity</a> to produce critical nutrients, meaning they rely on their plant host to do it for them. Without the plant host susceptibilities, the pathogen would starve before the plant got sick.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/225800/original/file-20180702-116120-v888ys.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Blue-stained omycete pathogen infecting transparent plant root cells.</span>
<span class="attribution"><span class="source">John Herlihy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>My colleagues and I study oomycete disease in the model plant <em>Arabidopsis</em>, more commonly called <a href="https://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp">thale cress</a>. This weed is only grown in laboratories, but, like lab mice for humans, provides a tool to understand what goes on in our fields, orchards and gardens.</p>
<p>We focus on the relationships between plants and pathogens, looking for other ways oomycetes exploit their hosts. If we can identify the mechanisms of plant cell machinery that a pathogen requires to cause disease, we can breed or engineer plants to change, turn off or get rid of those vulnerabilities.</p>
<p>We test plants that have been genetically manipulated to turn off individual genes related to nutrient uptake, transport, storage and regulation. We infect these modified plants and look for any that are more resistant than their normal relatives. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=300&fit=crop&dpr=1 600w, https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=300&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=300&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=377&fit=crop&dpr=1 754w, https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=377&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/228502/original/file-20180719-142428-1pofq5w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=377&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"><em>Arabidopsis</em> seedlings before and after oomycetes infection. The white hairs on the infected plant on the right are spore-producing reproductive structures. The pillowy appearance gave the pathogen its name, downy mildew.</span>
<span class="attribution"><span class="source">John Herlihy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Often the removal of a gene is detrimental to the plant and the disease suffers as well. But occasionally we find a test plant that, despite its inactive gene, does just fine – and is less susceptible to the disease. Potentially, those plants lack a key component the pathogen requires to survive and grow. Finding those susceptibility genes and closing those exploitable holes in plant defense is my goal. </p>
<p>Looking forward, there is hope that research can diminish the impact of plant diseases. Like a computer, no plant defense system is perfect. However, if loopholes can be closed, hackers will have a much tougher time accessing what they’re after. Both breeding and genetic engineering provide paths to close those loopholes that may also exist in the vegetable crops that are most affected by plant hacking.</p>
<p>Even if everyone on Earth had enough to eat, a <a href="http://www.fao.org/3/a-i6583e.pdf">growing population</a>, increased <a href="https://foodsource.org.uk/book/export/html/41">demand for meat</a>, and a need for more <a href="https://avrdc.org/new-strategy-new-logo/">fresh produce</a> necessitates growing more food. This can either come from more farmland or more efficient farms. Strategies that employ <a href="https://insteading.com/blog/why-pesticides-are-actually-important-for-agricultural-sustainability/">limited pesticide</a> use along with plants that are more resilient to the pathogen hackers could make the farms we have more productive.</p><img src="https://counter.theconversation.com/content/98595/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>John Herlihy receives funding from the National Science Foundation. </span></em></p>Oomycete spores hack into plants to get what they need, causing agricultural disease. Can researchers figure out how to close plants’ security loopholes and create more resilient crops?John Herlihy, Ph.D. Student in the School of Plant and Environmental Science, Virginia TechLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/840242017-11-26T23:46:19Z2017-11-26T23:46:19ZStudying circadian rhythms in plants and their pathogens might lead to precision medicine for people<figure><img src="https://images.theconversation.com/files/195885/original/file-20171122-6020-15wox5s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Though not this obvious from the outside, plants are keeping time.</span> <span class="attribution"><span class="source">Hua Lu</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>At dusk, the leaves of the tamarind tree close, waiting for another dawn. Androsthenes, a ship captain serving under Alexander the Great, made the first written account of these leaf movements in the fourth century B.C.</p>
<p>It took centuries longer to discover that he was describing the effects of the circadian clock. This internal time-sensing mechanism allows many living organisms to keep track of time and coordinate their behaviors along 24-hour cycles. It follows the regular day/night and seasonal cycles of Earth’s daily rotation. Circadian research has advanced so far that the <a href="https://www.nobelprize.org/nobel_prizes/medicine/laureates/2017/">2017 Nobel Prize</a> in physiology or medicine was awarded for the groundbreaking work that <a href="https://theconversation.com/nobel-winners-identified-molecular-cogs-in-the-biological-clocks-that-control-our-circadian-rhythms-85061">elucidated the molecular basis underlying circadian rhythms</a>.</p>
<p>Biologists like us are studying the circadian clocks in plants for insights into how they affect the health and well-being of all life on Earth. As researchers continue to untangle more about how these clocks work – including how they influence interactions between hosts and their invading pathogens and pests – new forms of specially timed precision medicine could be on the horizon.</p>
<h2>Our hidden pacemaker</h2>
<p>Organisms from all three domains of life possess an amazing diversity of circadian rhythms. Seemingly simple <em>Cyanobacteria</em> <a href="https://doi.org/10.1038/nrmicro.2016.196">alternate photosynthetic activity between day and night</a>. The fungus <em>Neurospora crassa</em> produces <a href="https://www.ncbi.nlm.nih.gov/pubmed/21707668">spores every morning just before dawn</a>. Migratory monarch butterflies use a delicate <a href="https://doi.org/10.1016/j.celrep.2016.03.057">sun compass in their annual migration</a>. Almost <a href="https://www.nigms.nih.gov/education/pages/Factsheet_CircadianRhythms.aspx">every aspect of human activity</a> is influenced by the circadian clock – you can easily see this in yourself if you fly across time zones or engage in shift work.</p>
<p>The driving force behind circadian rhythms is what scientists call the <a href="https://doi.org/10.1038/nsmb.3327">circadian clock’s central oscillator</a>, an elaborate network of genes that turn each other’s activity on and off. Together, they form complex feedback loops that accurately calibrate time.</p>
<p>Although individual clock genes are not always the same across domains of life, the feedback mechanism of the central oscillator is. This mechanism acts as a switch to synchronize an organism’s daily activities with day and night fluctuations and other environmental changes. Such amazing balancing acts reflect organisms’ abilities to anticipate changing environment throughout the day. </p>
<h2>Precise timekeeping and health</h2>
<p>A well-calibrated circadian clock is critical for growth and fitness, which is why misalignment of the circadian clock with environmental cues causes diverse and far-reaching health issues. Some human diseases, including <a href="https://doi.org/10.1126/scitranslmed.3003200">diabetes</a>, <a href="https://doi.org/10.1073/pnas.1008734107">obesity</a>, <a href="https://doi.org/10.1515/hmbci-2013-0057">cardiovascular disease</a> and <a href="https://doi.org/10.1007/s11920-014-0483-7">some psychiatric disorders</a> such as depression and bipolar disorder, are likely linked to circadian clocks being out of sync with the environment. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=236&fit=crop&dpr=1 600w, https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=236&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=236&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=297&fit=crop&dpr=1 754w, https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=297&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/195917/original/file-20171122-6016-ewil30.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=297&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">After infection by a fungus, plants with a mutant circadian clock (right) showed much more damage than the normal plants (left).</span>
<span class="attribution"><span class="source">Hua Lu</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Increasing evidence also links the circadian clock to plant health. In particular, plant scientists have shown that a properly tuned <a href="https://doi.org/10.1146/annurev-phyto-080516-035451">circadian clock is important for plant disease resistance</a> to arrays of pathogens and pests. Although plants do not produce antibodies or use specialized immune cells to ward off invaders, some aspects of their immune system are similar to ours. Because of how easy it is to grow and genetically manipulate them, some plants, like <em>Arabidopsis</em>, serve as ideal systems to investigate how the circadian clock influences the outcome of diseases in plants once infected.</p>
<h2>Plant-pathogen interactions around the clock</h2>
<p>Plants, being immobile, must strategically allocate their limited energy and resources when faced with pathogens and pests. They have the sophisticated ability to <a href="https://doi.org/10.1146/annurev-phyto-080516-035451">time their defense</a>, which allows them to anticipate likely attacks before they occur and modulate defense responses to real attackers.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=323&fit=crop&dpr=1 600w, https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=323&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=323&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=405&fit=crop&dpr=1 754w, https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=405&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/196307/original/file-20171124-21838-1fowi5t.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=405&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Stomata are little pores on the plant’s surface that can open and close.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-vector/opening-closing-stomata-411951568">Valentina Moraru/Shutterstock.com</a></span>
</figcaption>
</figure>
<p>The forefront of plant defense is on the surface. Physical features like trichomes, little hairs that stick out, protectively cover a plant, and wax coatings deter invaders from clinging onto the surface. The plant surface also has numerous mouth-like pores called stomata. Normally, <a href="https://doi.org/10.1038/nrg3976">stomata rhythmically open in the day and close at night</a>, a process regulated by the circadian clock in anticipation of light and humidity changes. While this process is important for photosynthesis and water exchange, opening stomata can be used by some pathogens as portals to access nutrients and space inside the plant tissue and closing stomata restrict pathogen invasion. </p>
<p>Beyond frontline physical barriers, plants have evolved complex surveillance systems to detect pathogens and pests as intruders. When cell surface receptors recognize a pathogen, the plant immediately closes its stomata at the invasion site. <a href="https://doi.org/10.1371/journal.ppat.1003370">Dysfunctional circadian clocks impair stomatal closure</a>, resulting in more severe disease.</p>
<p>Further pathogen recognition sends alert signals deep into the plant tissue, activating an arsenal of defense responses, including reprogramming of gene expression, production of antimicrobial compounds and enhancement of defense signaling. Even in the absence of pathogens, many of these responses show low but rhythmic changes that are influenced by the circadian clock. When a real attack arrives, the plants’ daily rehearsal of their defense systems ensures a <a href="https://doi.org/10.1146/annurev-phyto-080516-035451">strong and concerted timely defense</a>. Plants with misaligned clocks succumb to the attack. </p>
<p>One excellent example of a plant timing its defense comes from <a href="https://sites.duke.edu/donglab/">Xinnian Dong’s group</a> at Duke University. <em>Hyaloperonospora arabidopsidis</em> is a pathogen that disseminates its virulent spores in the morning and causes disease in <em>Arabidopsis</em> plants. Dong’s group elegantly showed that <em>Arabidopsis</em> anticipates this attack by expressing a set of defense genes at dawn that gives resistance against the pathogen. When the researchers disrupted the <em>Arabidopsis</em> circadian clock, it abolished this <a href="https://doi.org/10.1038/nature09766">morning defense</a> and made the plant more susceptible. </p>
<p>Plants also rely on timely defense to fight off insects. For instance, cabbage loopers have peak feeding activity before dusk. Beautiful work by <a href="http://www.bioc.rice.edu/%7Ebraam/">Janet Braam’s group</a> at Rice University showed that <em>Arabidopsis</em> produces the defense signaling hormone jasmonic acid with a peak at noon in anticipation of this attack. When the insects actually strike, the circadian clock <a href="https://doi.org/10.1073/pnas.1116368109">boosts this noon defense</a>, producing more jasmonic acid to inhibit insect feeding. </p>
<h2>Do clocks dance in pairs?</h2>
<p>As seen from these examples, pathogens and pests have their own circadian clocks and use them to determine the best time to be active. How does this ability affect their invasions of hosts? So far, researchers aren’t sure whether pathogen and pest clocks are coordinated to that of the host. If they are, then how in sync they are could determine the outcome of their interactions.</p>
<p>Current evidence indicates that some eukaryotic microbes, such as <a href="https://doi.org/10.1038/nature09766"><em>Hyaloperonospora arabidopsidis</em></a> and <a href="https://doi.org/10.1105/tpc.112.102046"><em>Botrytis cinerea</em></a>, are able to manipulate the <em>Arabidopsis</em> circadian clock. Even prokaryotic pathogens, like <a href="https://doi.org/10.1371/journal.ppat.1003370"><em>Pseudomonas syringae</em></a>, in spite of lacking a canonical central oscillator, can interfere with plant clocks in various ways.</p>
<p>In humans and mice, <a href="https://doi.org/10.1016/j.cell.2014.09.048">some populations of gut microbiota oscillate daily</a>, depending on the host circadian clock. Interestingly, <a href="https://doi.org/10.1177/0748730417729066">gut microbiota are capable of reprogramming the host clock</a>. How does this transkingdom communication occur? How can it influence the outcome of host and microbe interactions? Research in this area represents a fascinating and unexplored level of host-invader dynamics.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/196308/original/file-20171124-21801-qcc5qi.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Well-timed actions in plants – like the tamarind tree’s closing leaves noticed by Androsthenes millennia ago – could eventually help us design more precise medicines.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/young-tamarind-leaves-blur-background-481065826">oraphan_nan/Shutterstock.com</a></span>
</figcaption>
</figure>
<h2>The clock as healer and helper</h2>
<p>The ability to integrate time cues with development and responses to environmental assaults is an evolutionary adaptation. Plants have taught biologists much about circadian rhythms and their role in modulating everything from development to defense.</p>
<p>Clock research has opened an opportunity to apply this knowledge to other systems, including humans. How can we modify the daily cycling of certain defense features to enhance immunity without causing developmental stress? What times of day are we most susceptible to certain pathogens? What are the most invasive times of day for various pathogens and pests?</p>
<p>Answers to questions like these will help unravel host-pathogen/pest interactions, not just in plants but also in people. Ultimately, this knowledge could contribute to the design of precision medicines that are tailored to boost timely defense in individual people to fight against various pathogens and pests. In addition, our understanding of plant disease resistance will aid agricultural control of pathogens and pests, mitigating the global challenge of crop loss.</p>
<p>Ongoing research continues to reveal how the influence of circadian rhythms extends as boundlessly as the sun’s rays.</p><img src="https://counter.theconversation.com/content/84024/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Hua Lu receives funding from National Science Foundation. </span></em></p><p class="fine-print"><em><span>Linda Wiratan receives funding from the UMBC Undergraduate Research Award.</span></em></p>Precisely calibrated timekeepers are found in organisms from all domains of life. Biologists are studying how they influence plant/pathogen interactions – what they learn could lead to human medicines.Hua Lu, Associate Professor of Biological Sciences, University of Maryland, Baltimore CountyLinda Wiratan, B.S. Student of Biochemistry and Molecular Biology, University of Maryland, Baltimore CountyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/818032017-09-15T10:21:37Z2017-09-15T10:21:37ZSeeds in space – how well can they survive harsh, non-Earth conditions?<figure><img src="https://images.theconversation.com/files/185909/original/file-20170913-18075-165yqah.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Spend many months attached to the ISS and see how well you grow.</span> <span class="attribution"><a class="source" href="https://www.nasa.gov/mission_pages/station/research/experiments/1674.html">NASA</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>Will we someday colonize space? Will our children visit other planets? To achieve goals like these, we’ll need to crack one crucial challenge: how to feed ourselves for long periods away from Earth.</p>
<p>A <a href="http://www.mars-one.com/faq/mission-to-mars/how-long-does-it-take-to-travel-to-mars">trip to Mars would take months</a>, and exploring the depths of the galaxy would take even longer. Provision of nutritious food for travelers is a significant obstacle. While stockpiling food is an option, storing enough to last many months strains weight and space limitations in spacecraft – and missions could easily outlast food shelf life. Growing food in space will be essential.</p>
<p>Essential – and not necessarily easy. The conditions in the vacuum of space are quite harsh compared to Earth. Seeds in space must be able to withstand large doses of ultraviolet and cosmic radiation, low pressure and microgravity. </p>
<p>Believe it or not, the first space travelers were seeds. In 1946, <a href="https://www.nasa.gov/pdf/449089main_White_Sands_Missile_Range_Fact_Sheet.pdf">NASA launched a V-2 rocket carrying maize</a> seeds to observe how they’d be affected by radiation. Since then, the scientific community has learned <a href="https://doi.org/10.1079/SSR200193">a great deal</a> about the effects of the space environment on seed <a href="https://doi.org/10.1016/j.asr.2011.05.017">germination</a>, <a href="https://doi.org/10.1016/0273-1177(86)90076-1">metabolism</a>, <a href="https://doi.org/10.1016/j.asr.2005.06.043">genetics</a>, <a href="http://journal.ashspublications.org/content/130/6/848.short">biochemistry</a> and even <a href="https://doi.org/10.1016/S0273-1177(03)00250-3">seed</a> <a href="https://doi.org/10.1016/j.actaastro.2006.09.009">production</a>. </p>
<p>Astrobiologists David Tepfer and Sydney Leach recently investigated <a href="https://doi.org/10.1089/ast.2015.1457">how seeds would do back on Earth</a> after spending extended periods on the International Space Station. The experiments they conducted on the <a href="https://www.nasa.gov/mission_pages/station/research/experiments/696.html">EXPOSE</a> <a href="https://www.nasa.gov/mission_pages/station/research/experiments/211.html">missions</a> were much longer than many other ISS seed experiments, and placed the seeds on the outside of the station, in the dead of space, rather than inside. The goal was to understand not only the effects of long-term radiation exposure, but a bit about the molecular mechanisms of those effects.</p>
<h2>Seeds have some defenses</h2>
<p>Seeds possess a couple of remarkable traits that Tepfer and Leach hypothesized would give these “model space travelers” a fighting chance.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=575&fit=crop&dpr=1 600w, https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=575&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=575&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=722&fit=crop&dpr=1 754w, https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=722&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/185911/original/file-20170913-20280-41e1zd.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=722&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Seeds protect their important insides with a strong external seed coat.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Dycotyledon_seed_diagram-en.svg">LadyofHats</a></span>
</figcaption>
</figure>
<p>First, they contain multiple copies of important genes – what scientists call redundancy. Genetic redundancy is common in flowering plants, especially food products such as <a href="https://www.sciencedaily.com/releases/2014/09/140930090636.htm">seedless watermelon and strawberries</a>. If one genetic copy is damaged, there’s still another available to do the job.</p>
<p>Secondly, seed coats contain chemicals called flavonoids that act as sunscreens, protecting the seed’s DNA from damage by ultraviolet (UV) light. On Earth, our planet’s atmosphere filters out some harmful UV light before it can reach us. But in space, there is no protective atmosphere.</p>
<p>Would these special features be enough to let the seeds survive or even thrive? To find out, Tepfer and Leach conducted a series of experiments – both outside the International Space Station and back on Earth – with tobacco, <em>Arabidopsis</em> (a flowering plant commonly used in research) and morning glory seeds. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=440&fit=crop&dpr=1 600w, https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=440&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=440&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=553&fit=crop&dpr=1 754w, https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=553&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/185905/original/file-20170913-20310-w6bmrn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=553&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The EXPOSE-R experiment attached to the exterior of the International Space Station.</span>
<span class="attribution"><a class="source" href="https://www.nasa.gov/mission_pages/station/expeditions/expedition26/russian_eva27.html">NASA</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<h2>Bombarded with energy</h2>
<p>Their EXPOSE-E experiment flew to the International Space Station (ISS) in 2008 and lasted 558 days – so just under two years.</p>
<p>They stored the seeds in a single layer on the outside of the ISS behind a special kind of glass that let in ultraviolet radiation only at wavelengths between 110 and 400 nanometers. DNA readily absorbs UV radiation in this wavelength range. A second, identical set of seeds was on the ISS, but shielded completely from UV radiation. The purpose of this experimental design was to observe the effects of UV radiation separately from other types of radiation <a href="https://www.space.com/32644-cosmic-rays.html">like cosmic rays</a> that are everywhere in space.</p>
<p>Tepfer and Leach chose tobacco and <em>Arabidopsis</em> seeds for EXPOSE-E because both have a redundant genome and therefore good odds for survival. They also included a genetically engineered variety of tobacco with an antibiotic resistance gene added; the plan was to later test this gene in bacteria and determine if there was any damage. In addition to normal <em>Arapidopsis</em>, they sent up two genetically modified strains of the plant that contained low and absent UV-protective chemicals in their seed coat. They also sent purified DNA and purified flavonoids. This gave the researchers a wide range of scenarios by which to understand the effects of space on the seeds.</p>
<p>A second ISS mission called EXPOSE-R included only the three types of <em>Arabidopsis</em> seeds. These received a little over double the dose of ultraviolet light because of the longer experiment time, 682 days. Lastly, researchers performed a ground experiment back in the lab that exposed <em>Arabidopsis</em>, tobacco and morning glory seeds to very high doses of UV light for only a month.</p>
<p>After all these various exposure conditions, it was time to see how well the seeds could grow.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=410&fit=crop&dpr=1 600w, https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=410&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=410&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=515&fit=crop&dpr=1 754w, https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=515&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/185907/original/file-20170913-20270-l4me1j.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=515&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The Expose-R experiment was equipped with three trays containing a variety of biological samples – including seeds.</span>
<span class="attribution"><a class="source" href="https://www.nasa.gov/mission_pages/station/multimedia/exp18_eva2.html">NASA</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<h2>What would researchers reap?</h2>
<p><a href="https://doi.org/10.1089/ast.2015.1457">When the seeds returned to Earth</a>, the researchers measured their germination rates – that is, how quickly the root emerged from the seed coat.</p>
<p>The seeds that had been shielded in the lab did the best, with more than 90 percent of them germinating. Next came the seeds that had been exposed to UV radiation for one month in the laboratory, with better than 80 percent germinating. </p>
<p>For the space-traveling seeds, more than 60 percent of the shielded seeds germinated. A mere 3 percent of space UV-exposed seeds did.</p>
<p>The 11 <em>Arabidopsis</em> plants that did grow from both the wild type and genetically engineered seeds did not survive once planted in soil. Tobacco plants, however, showed reduced growth but that growth rate recovered in subsequent generations. Tobacco has a much heartier seed coat and a more redundant genome, which may explain its apparent survival advantage.</p>
<p>When the researchers plugged the antibiotic resistance gene into bacteria, they found it was still functional after its trip to space. That finding suggests it’s not genetic damage that’s making these seeds less viable. Tepfer and Leach attributed the reduced germination rate to damage to other molecules in the seed besides DNA – such as proteins. A redundant genome or built-in DNA repair mechanisms weren’t going to overcome that damage, further explaining why the <em>Arabidopsis</em> plants didn’t survive transplanting.</p>
<p>In the ground experiments, the researchers found that radiation damage is dose-dependent – the more radiation the seeds received, the worse their germination rate.</p>
<p>These discoveries could inform future directions for research in space agriculture. Scientists may consider genetically engineering seeds to have added protection for the cellular machinery critical for protein synthesis, such as ribosomes. Future research will also need to explore further how seeds stored in space germinate in microgravity, rather than on Earth.</p>
<p>As researchers add to the knowledge of how space affects plants and their seeds, we can continue to make the strides necessary toward producing food in space. It will be a crucial step toward sustainable colonies that can survive beyond the comfortable confines of Earth’s biosphere.</p><img src="https://counter.theconversation.com/content/81803/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Gina Riggio is affiliated with Blue Marble Space.</span></em></p>If you want to live on Mars, you’re going to need to grow food. Seeds are naturally equipped to handle challenging Earth environments, but how well can they survive what they’ll encounter off-planet?Gina Misra, Ph.D. Student in Cell and Molecular Biology, University of ArkansasLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/835502017-09-11T00:40:35Z2017-09-11T00:40:35ZCan random bits of DNA lead to safe, new antibiotics and herbicides?<figure><img src="https://images.theconversation.com/files/185339/original/file-20170909-32271-qkj3sf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Plants make proteins based on whatever genetic material you give them.</span> <span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:CSIRO_ScienceImage_3176_Arabidopsis_in_growth_cabinet_at_the_CSIRO_Discovery_Centre_labs_Black_Mountain_ACT.jpg">Carl Davies, CSIRO</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>I was cutting my grass when the battery in my iPod died. Instead of enjoying the distraction of music, my brain switched to its usual nerd mode of thinking about molecules. Within a few passes of cut grass, I was pondering the biggest “Why not?” of my scientific career: Could we discover new drugs and useful agricultural compounds by challenging organisms with clusters of random chemistry?</p>
<p>My background is in molecular biology – the study of DNA, genes and how an organism’s blueprints are decoded and assembled into life. The discipline requires an understanding of how molecular codes are deciphered and turned into functional biology. Anyone in this field is plagued with dreams of dancing molecules, interacting and performing the roles that turn DNA information into our food, the plants in our environment and our families.</p>
<p>Every day in the lab we move genes around. It’s easy. Not meant to generate new products for consumers, moving DNA is used as a research tool that lets us understand how specific genes work. A classic example is <a href="https://doi.org/10.1016/j.tplants.2013.04.004">the NPR1 gene</a> from the model plant <em>Arabidopsis</em>; it’s a defense gene that confers enhanced tolerance to disease when you drop it into almost any plant’s genome. Manipulating genetic information – in plants, microbes and some animals – is commonplace.</p>
<p>On that half-cut lawn it occurred to me – instead of inserting DNA information we understand, what if we introduced a scrambled mess of random DNA code into a plant or bacterium? Could we identify random bits of genetic information that could give rise to small proteins (called peptides) that change an organism’s physiology or development?</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=383&fit=crop&dpr=1 600w, https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=383&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=383&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=482&fit=crop&dpr=1 754w, https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=482&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/185340/original/file-20170909-32321-1ht2o80.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=482&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">In all living things, the ‘words’ in the genetic material code for particular amino acids, so the organism can build the proteins it needs.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Peptide_syn.png">Boumphreyfr</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>Normally DNA encodes instructions that coordinate the order of the amino acid building blocks in a protein. Each amino acid has specific chemical characteristics. Strung together in a peptide chain, they fold into a protein that provides cellular structure or function, based on the complementary chemistries of its amino acid components.</p>
<p>My hypothesis was that a short, scrambled DNA message could give rise to a novel string of amino acids. This would be a small cluster of discrete chemistry that likely never existed before on the planet. The vast majority of the time it would be meaningless and just become cellular rubbish. But maybe on rare occasion it could do something new and desirable.</p>
<p>To test the hypothesis, our research team used randomized templates to synthesize trillions of random DNA fragments using simple DNA amplification techniques. Each was flanked by the genetic instructions to start and stop production of a peptide inside the plant.</p>
<p>Then we used standard genetic engineering techniques to insert a novel DNA sequence into thousands of individual <em>Arabidopsis thaliana</em> plants – and sat back to watch what would happen when the plants turned the random genetic information into little random peptides. We were hoping for cases where specific protein structures might find a connection with biological chemistry and we’d see the result in the plants themselves. </p>
<p>As the plants grew, we were blown away by what we observed.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=612&fit=crop&dpr=1 600w, https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=612&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=612&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=770&fit=crop&dpr=1 754w, https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=770&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/185322/original/file-20170908-3138-symph.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=770&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">In some cases, adding a random ‘gene’ had a big effect on how plants grew… or not.</span>
<span class="attribution"><span class="source">Kevin Folta</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Some plants were flowering early. Others were small and stunted. Others grew larger leaves. Some were loaded with healthy purple pigments. Still others grew up to a point…then died.</p>
<p>We then retrieved the particular random DNA sequence we’d added to each, a simple feat for a molecular biologist, and inserted the same sequence into new plants. Most of the time the random information affected the new generation of plants in exactly the same way, demonstrating that something was indeed happening related to the added, garbled information. We <a href="https://doi.org/10.1104/pp.17.00577">recently published our results</a> in the journal Plant Physiology.</p>
<p>What is this random information doing inside the cell? The small random molecules generated from the inserted DNA instructions could affect a specific process, just by chance. They could bind a needed nutrient. They might inhibit a key enzyme. They could turn on flowering or protect a plant from freezing. Nobody really knows exactly how until the plants are examined in detail one by one. These new proteins may also be good models to design new useful molecules with similar chemical properties, but that are more durable in the cell. Our goal is to produce a compound that may be applied to crops to change the way plants grow and behave, or perhaps stop the growth of invasive or weedy plants.</p>
<p>The process is like throwing monkey wrenches into a complicated machine. Most of the time they clank around and affect nothing; but once in a long while a wrench catches in some critical gears and brings the machine to a halt. Other times the wrench might short-circuit a wasteful process, allowing the machine to run more efficiently. These peptides are molecular monkey wrenches.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/185320/original/file-20170908-32313-35x4f1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Small proteins created through this process might be the future of safe, sustainable and specific weed control.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/kegriver/6145920474">KegRiver</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<p>Some of these peptides must interfere with an important biological process because they kill the plant. These findings bring to light new vulnerabilities in plants that researchers could exploit to develop environmentally friendly and nontoxic herbicides. Agriculture currently relies on a few relatively old chemistries, cultivation (using fossil fuels) or human labor to control the weeds that compete with food plants for resources. Good weed control means that valuable fertilizers, water and sunlight go only to the desired plants, rather than weeds. So new herbicide chemistries would be extremely valuable as farmers work to produce food for growing populations.</p>
<p>But why stop at plants? We are using the same approach to discover the next generation of antibiotics. The goal is to identify random information that affects a single species of problematic bacterium. For instance, we could potentially target <em>S. aureus</em>, the antibiotic-resistant bacteria that causes MRSA. We are hunting for new molecules that could destroy MRSA-related bacteria while leaving the rest of the microbiome unaffected. These experiments are underway in our lab.</p>
<p>Randomness may pinpoint undiscovered vulnerabilities or opportunities in plants, bacteria and other organisms. There even may be applications in solving human disease. The future is exciting as we mine the vast collections of new molecules and study how they integrate with biology to produce important desired outcomes. </p>
<p>Several of the molecules we’ve already identified slow plant growth. Future products from this technology might even be applied to make lawns grow more slowly. While others may find this advance helpful, I’ll have to skip using it. Cutting the grass gets my good ideas flowing.</p><img src="https://counter.theconversation.com/content/83550/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Kevin M. Folta's salary is paid by the University of Florida. His laboratory's research is currently funded by the United States Department of Agriculture/NIFA and the Florida Strawberry Research and Education Foundation. All historical funding, including all support for his outreach programs and reimbursements can be seen at <a href="http://www.kevinfolta.com/transparency">www.kevinfolta.com/transparency</a>.</span></em></p>Inserting a random DNA mishmash into a plant or bacterium directs it to make a novel protein. Sifting through the resulting molecules, researchers may find ones have medical or agricultural uses.Kevin M. Folta, Professor and Chair, Horticultural Sciences Department, Graduate Program in Plant Molecular and Cellular Biology, University of FloridaLicensed as Creative Commons – attribution, no derivatives.