Recent News https://biology.ucdavis.edu/articles.rss Recent News for College of Biological Sciences en The Plant-Pathogen Arms Race: Nature Communications Study Reveals Key Player in Plant Immunity https://biology.ucdavis.edu/news/plant-pathogen-arms-race-nature-communications-study-reveals-key-player-plant-immunity <span class="field field--name-title field--type-string field--label-hidden">The Plant-Pathogen Arms Race: Nature Communications Study Reveals Key Player in Plant Immunity</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/5451" typeof="schema:Person" property="schema:name" datatype="">Greg Watry</span> </span> <span class="field field--name-created field--type-created field--label-hidden">July 19, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/Tobacco-mosaic-virus-symptoms-orchid-UC-Davis-College-of-Biological-Sciences.jpg?h=f8bf4c48&amp;itok=CDuq08EI" width="1280" height="720" alt="Orchid leaves with symptoms of tobacco mosaic virus" title="Orchid leaves with symptoms of tobacco mosaic virus. Department of Plant Pathology, North Carolina State University, Bugwood.org " typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary UC Davis researchers have identified the function of a key protein that regulates plant immunity UBR7 is a negative regulator of plant immune responses, meaning it keeps immune receptors in check unless a pathogen invades The research could eventually lead to agricultural practices capable of endowing crops with broad-spectrum resistance against pathogens The co-evolutionary arms race between plants and pathogens is one of biological balance. Plants want to defend themselves from invaders, while pathogens want to infect their hosts without killing them to propagate. Plant biologists are keen to understand the molecular battles occurring in infected plant cell territory. “Our main thrust is to understand how plant immune receptors and their associated proteins react when a pathogen invades plant cells,” said Professor Savithramma Dinesh-Kumar, Department of Plant Biology and The Genome Center. “The first set of plant nucleotide-binding leucine-rich repeat (NLR) class of immune receptors were cloned almost 25 years ago, but we still don’t understand how these receptors are functioning.” In a study appearing in Nature Communications, Dinesh-Kumar and his colleagues from Iowa State University, China Agricultural University, Stanford University and Massachusetts Institute of Technology identified the function of a key protein that regulates plant immunity. The fundamental research could eventually lead to agricultural practices capable of endowing crops with broad-spectrum resistance against pathogens. “How do we engineer these receptors to recognize multiple pathogens?” said Dinesh-Kumar. “Or how can we engineer the downstream signaling steps to activate responses to multiple pathogens?” ID’ing plant cell destruction Using Nicotiana benthamiana, a tobacco plant, as a model system, Dinesh-Kumar and colleagues employed a proximity labeling technique called TurboID to identify proteins that interact with an NLR immune receptor called N. NLR receptors are critical to both plant and animal pathogen defense. The proximity labeling technique allowed Dinesh-Kumar and colleagues to identify the network of proteins that could work in concert to regulate NLR-mediated immune response. Dinesh-Kumar and his colleagues used Nicotiana benthamiana as a model plant system in the study. ChandresIn the study, the team focused on the N NLR immune receptor. This receptor provides resistance to the tobacco mosaic virus, which can infect crops like tomatoes, peppers, potatoes and other important Solanaceae crops. “Using this method, we identified interesting players, but then in order to probe further, we focused on one protein which seemed to be involved in selective protein degradation process in the cell,” said Dinesh-Kumar.  That protein is an UBR-box containing ubiquitin protein ligase E3 component N-recognin 7, otherwise known as UBR7.       “This protein UBR7 is highly conserved from plants to animals, but we know very little about this ligase’s function in any system,” said Dinesh-Kumar. The researchers’ experiments revealed that UBR7 plays a key role in negative regulation of N NLR levels. Basically, UBR7 keeps the NLR immune receptor levels in check unless the cell detects an invading pathogen. “The reason we focused on that is that we don’t know too much about negative regulators of immunity in plants,” said Dinesh-Kumar, noting that research often focuses on positive regulators. Dinesh-Kumar said the presence of UBR7 might prevent NLR receptors from auto-activating and hence inducing autoimmunity. “If you induce autoimmunity (without the presence of a pathogen), it is not good for the plant because the cells will die and growth will be affected,” he said. “But when the pathogen comes, this protein is disassociated from the receptor so the receptor can then activate immune response to contain the pathogen to the infection site.”  Dinesh-Kumar noted that while their study was under review, other research showed that a related protein called UBR2 was shown to activate immune receptors in humans in response to anthrax toxins. Turbo-charging research methods According to Dinesh-Kumar, the research provides the first evidence of the roles the UBR family of proteins play in plant immunity. “For us, the highlight here is the biology,” said Dinesh-Kumar. “The biology of how immune receptors function and recognize pathogens.”   While the highlight is the biology, the methodology Dinesh-Kumar and his colleagues used is also important. The TurboID method, the research team reports, was more efficient than other proximal labeling methods like BioID and BioID2 in plants. “We hope that the methods we describe and the approach we describe will be useful for others who want to use this in plant biology research,” said Dinesh-Kumar. Yongliang Zhang, Ugrappa Nagalakshmi, Neeraj Lal, Wenjie Zheng, Pin-jui Huang and Yuanyuan Li from UC Davis; Gaoyuan Song and Justin Walley from Iowa State University; and Tess Branon and Alice Ting from Stanford University and Massachusetts Institute of Technology were involved in the study. The work was supported by the National Science Foundation, National Institutes of Health, China Scholarship Council and National Natural Science Foundation of China. Stay Informed! Sign up for our monthly email newsletter "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "In a study appearing in Nature Communications, researchers identified the function of a key protein that regulates plant immunity. The fundamental research could eventually lead to agricultural practices capable of endowing crops with broad-spectrum resistance against pathogens. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><em><strong>UC Davis researchers have identified the function of a key protein that regulates plant immunity</strong></em></li> <li><em><strong>UBR7 is a negative regulator of plant immune responses, meaning it keeps immune receptors in check unless a pathogen invades</strong></em></li> <li><em><strong>The research could eventually lead to agricultural practices capable of endowing crops with broad-spectrum resistance against pathogens</strong></em></li> </ul></div> </aside><p><span><span><span><span><span><span>The co-evolutionary arms race between plants and pathogens is one of biological balance. </span></span></span></span></span></span><span><span><span><span><span><span>Plants want to defend themselves from invaders, while pathogens want to infect their hosts without killing them to propagate. Plant biologists are keen to understand the molecular battles occurring in infected plant cell territory.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“Our main thrust is to understand how plant immune receptors and their associated proteins react when a pathogen invades plant cells,” said Professor Savithramma Dinesh-Kumar, Department of Plant Biology and The Genome Center. “The first set of plant nucleotide-binding leucine-rich repeat (NLR) class of immune receptors were cloned almost 25 years ago, but we still don’t understand how these receptors are functioning.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>In a study appearing in<a href="https://www.nature.com/articles/s41467-019-11202-z"> <em>Nature Communications</em></a>, Dinesh-Kumar and his colleagues from Iowa State University, China Agricultural University, Stanford University and Massachusetts Institute of Technology identified the function of a key protein that regulates plant immunity. The fundamental research could eventually lead to agricultural practices capable of endowing crops with broad-spectrum resistance against pathogens.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“How do we engineer these receptors to recognize multiple pathogens?” said Dinesh-Kumar. “Or how can we engineer the downstream signaling steps to activate responses to multiple pathogens?” </span></span></span></span></span></span></p> <h4><span><span><span><strong><span><span><span>ID’ing plant cell destruction</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>Using <em>Nicotiana benthamiana</em>, a tobacco plant, as a model system, Dinesh-Kumar and colleagues employed a proximity labeling technique called TurboID to identify proteins that interact with an NLR immune receptor called N. NLR receptors are critical to both plant and animal pathogen defense. The proximity labeling technique allowed Dinesh-Kumar and colleagues to identify the network of proteins that could work in concert to regulate NLR-mediated immune response.</span></span></span></span></span></span></p> <figure role="group" class="caption caption-img align-right"><img alt="Tobacco plant" data-entity-type="file" data-entity-uuid="8bff4c51-c6cb-4985-8627-a0ff32732e56" height="333" src="/sites/g/files/dgvnsk2646/files/inline-images/UC-Davis-College-of-Biological-Sciences-Tobacco-plant.jpg.png" width="363" /><figcaption><em>Dinesh-Kumar and his colleagues used Nicotiana benthamiana as a model plant system in the study. </em><a href="https://commons.wikimedia.org/wiki/User:Chandres">Chandres</a></figcaption></figure><p><span><span><span><span><span><span>In the study, the team focused on the N NLR immune receptor. This receptor provides resistance to the tobacco mosaic virus, which can infect crops like tomatoes, peppers, potatoes and other important <em>Solanaceae</em> crops. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“Using this method, we identified interesting players, but then in order to probe further, we focused on one protein which seemed to be involved in selective protein degradation process in the cell,” said Dinesh-Kumar. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>That protein is an UBR-box containing ubiquitin protein ligase E3 component N-recognin 7, otherwise known as UBR7.      </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“This protein UBR7 is highly conserved from plants to animals, but we know very little about this ligase’s function in any system,” said Dinesh-Kumar. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>The researchers’ experiments revealed that UBR7 plays a key role in negative regulation of N NLR levels. Basically, UBR7 keeps the NLR immune receptor levels in check unless the cell detects an invading pathogen. “The reason we focused on that is that we don’t know too much about negative regulators of immunity in plants,” said Dinesh-Kumar, noting that research often focuses on positive regulators.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Dinesh-Kumar said the presence of UBR7 might prevent NLR receptors from auto-activating and hence inducing autoimmunity. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“If you induce autoimmunity (without the presence of a pathogen), it is not good for the plant because the cells will die and growth will be affected,” he said. “But when the pathogen comes, this protein is disassociated from the receptor so the receptor can then activate immune response to contain the pathogen to the infection site.”  </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Dinesh-Kumar noted that while their study was under review, other research showed that a related protein called UBR2 was shown to activate immune receptors in humans in response to anthrax toxins. </span></span></span></span></span></span></p> <h4><span><span><span><strong><span><span><span>Turbo-charging research methods</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>According to Dinesh-Kumar, the research provides the first evidence of the roles the UBR family of proteins play in plant immunity. “For us, the highlight here is the biology,” said Dinesh-Kumar. “The biology of how immune receptors function and recognize pathogens.”  </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>While the highlight is the biology, the methodology Dinesh-Kumar and his colleagues used is also important. The TurboID method, the research team reports, was more efficient than other proximal labeling methods like BioID and BioID2 in plants. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“We hope that the methods we describe and the approach we describe will be useful for others who want to use this in plant biology research,” said Dinesh-Kumar. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Yongliang Zhang, Ugrappa Nagalakshmi, Neeraj Lal, <span>Wenjie Zheng, Pin-jui Huang</span> and Yuanyuan Li from UC Davis; Gaoyuan Song and Justin Walley from Iowa State University; and Tess Branon and Alice Ting from Stanford University and </span></span></span><span><span><span><span>Massachusetts Institute of Technology were involved in the study. </span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span>The work was supported by the National Science Foundation, National Institutes of Health, China Scholarship Council and </span></span></span><span><span><span><span>National Natural Science Foundation of China</span></span></span></span><span><span><span>.</span></span></span></span></span></span></p> <p class="text-align-center"><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></p> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/food-agriculture-plants" hreflang="en">Food, Agriculture and Plant Biology</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/plant-biology-0" hreflang="en">Department of Plant Biology</a></div> <div class="field__item"><a href="/tags/plant-biology-graduate-group" hreflang="en">Plant Biology Graduate Group</a></div> <div class="field__item"><a href="/tags/biochemistry-molecular-cellular-and-developmental-biology-graduate-group" hreflang="en">Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group</a></div> <div class="field__item"><a href="/tags/plant-immunity" hreflang="en">plant immunity</a></div> <div class="field__item"><a href="/tags/plant-biology" hreflang="en">plant biology</a></div> <div class="field__item"><a href="/tags/agriculture" hreflang="en">agriculture</a></div> <div class="field__item"><a href="/tags/crops" hreflang="en">crops</a></div> <div class="field__item"><a href="/tags/pathogens" hreflang="en">pathogens</a></div> </div> </div> Fri, 19 Jul 2019 17:11:16 +0000 Greg Watry 3326 at https://biology.ucdavis.edu Discovering Curiosity: Tilling the Fields of Plant Molecular Biology with Professor Savithramma Dinesh-Kumar https://biology.ucdavis.edu/news/discovering-curiosity-tilling-fields-plant-molecular-biology-savithramma-dinesh-kumar <span class="field field--name-title field--type-string field--label-hidden">Discovering Curiosity: Tilling the Fields of Plant Molecular Biology with Professor Savithramma Dinesh-Kumar </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/5451" typeof="schema:Person" property="schema:name" datatype="">Greg Watry</span> </span> <span class="field field--name-created field--type-created field--label-hidden">July 16, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/Savithramma-Dinesh-Kumar-College-of-Biological-Sciences-UC-Davis-2.jpg?h=cc275b66&amp;itok=X6hQxyDg" width="1280" height="720" alt="Savithramma Dinesh-Kumar" title="For his excellence in molecular plant pathology research, Professor Savithramma Dinesh-Kumar recently received the Noel T. Keen Award from The American Phytopathological Society. David Slipher/UC Davis " typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary For his excellence in research, Dinesh-Kumar has received the American Phytopathological Society&#039;s Noel T. Keen Award  His interest in plants goes back to his youth working with his father on his family&#039;s farm in India His well-published research focuses on host-microbe interactions and plant defense tactics Professor Savithramma Dinesh-Kumar, Department of Plant Biology, grew up in Bhadravathi, India. As a kid, he routinely spent time with his father, a high school teacher, on their farm in a nearby village. They grew rice and sugarcane, harvesting the latter crop by night when its sugar content was optimal. “Since I was on the farm, I was always interested in plants, especially why farmers grow so many varieties of rice,” said Dinesh-Kumar. But when it came time for university, Dinesh-Kumar initially decided to study engineering. While good at mathematics, he found the work too abstract. It wasn’t tangible, like the soil and crops in the farm fields of his youth. So Dinesh-Kumar took a different route and enrolled at the University of Agricultural Sciences in Bangalore, India. He started studying genetics, which eventually opened doors to research on plant breeding and plant-pathogen interactions. A storied career followed. Dinesh-Kumar has published more than 100 research papers and reviews and has received many accolades, including being named a fellow of the American Association for the Advancement of Science in 2018. And now, he can add another honor to the list. For his excellence in molecular plant pathology research, Dinesh-Kumar recently received the Noel T. Keen Award from The American Phytopathological Society. “This is a great honor,” said Dinesh-Kumar, who expressed gratitude for the nomination. “I was not expecting this at all actually because Noel Keen is one of the pioneers in the plant pathology field.” “Professor Dinesh-Kumar’s work on host-microbe interactions has helped reveal the fascinating molecular world of plant defense tactics,” said Mark Winey, dean of the College of Biological Sciences. “His continuing research and insights have had significant impact on the field and demonstrate the strength of our stellar Department of Plant Biology.”      Dinesh-Kumar and colleagues found that chloroplasts coordinate with the cell’s nucleus to instigate and execute plant defense responses. Des CallaghanOn the front lines of plant defense After completing a master’s degree in Genetics, Dinesh-Kumar traveled half a world away to the United States. His first stop was the University of Kentucky, where he secured a graduate research position in the Department of Forestry and Natural Resources. There, he worked on a project concerning fungal resistance in poplar trees. Though he enjoyed the work, Dinesh-Kumar wanted to try his hand at molecular biology. “I always had my mind on molecular biology back when I was a master’s student,” said Dinesh-Kumar. “I had a lot of theoretical exposure but not any hands-on experience.” One day, he saw an announcement for a three-week intensive molecular biology training program at the The University of Chicago’s Marine Biological Laboratory, Woods Hole, Mass. It was the perfect opportunity to indulge his molecular biology curiosity. The program solidified Dinesh-Kumar’s sentiment that molecular biology is fundamental to answering basic questions about plant defense tactics. Inspired, Dinesh-Kumar enrolled in a Molecular, Cellular and Developmental Biology Ph.D. program at Iowa State University and joined the lab of W. Allen Miller, a professor of plant pathology and microbiology. Dinesh-Kumar’s dissertation explored the barley yellow dwarf virus (BYDV), which affects cereal crops. His research revealed that the virus uses leaky scanning and translational read-through strategies to produce three different proteins from a single subgenomic RNA.      “My goal was to figure out what sequences in the viral RNA are responsible for making these multi-pronged proteins from a single RNA,” said Dinesh-Kumar, who also constructed the first successful infectious clone of BYDV. Following graduation, Dinesh-Kumar headed further west and joined Professor Barbara Baker’s laboratory at the UC Berkeley Plant Gene Expression Center. He continued studying viral resistance and became part of the team that cloned the first virus resistance gene “that confers resistance to the tobacco mosaic virus,” according to The American Phytopathological Society. The team identified the first plant resistance protein that contained Toll-Interleukin-1 receptor (TIR) homology domain. The work was foundational for the field, and today, these receptors are known to be integral to not only plant immunity but animal immunity as well. “In the last 20 years, the thrust has been to understand how these immune receptors recognize pathogens and how they activate signal transduction in the plant so the ultimate output is resistance,” said Dinesh-Kumar. “We still don’t have a complete understanding of how these resistance proteins are working.” Chlorophyll, pictured here, are green pigments that absorb light, providing the energy for photosynthesis. Ma KelvanContaining plant infections Dinesh-Kumar joined the UC Davis faculty in 2010 following a roughly 10-year stint at Yale University. Today, he’s the chair of the Department of Plant Biology and also holds an appointment with the UC Davis Genome Center. His research focus is still on understanding the molecular basis of host-microbe interactions. “One of the area we’re interested in recently is, how do chloroplasts actually contribute to plant resistance?” said Dinesh-Kumar, noting that chloroplasts produce reactive oxygen species and the salicylic acid hormone. Both are important players in plant defense. What’s more, Dinesh-Kumar and colleagues found that chloroplasts coordinate with the cell’s nucleus to instigate and execute plant defense responses. These actions are incredibly exact. When a plant is infected with a pathogen, its immune receptors activate a cascade of responses leading to cell death that keep the pathogen contained. Dinesh-Kumar and colleagues found that plant cells activate autophagy to keep cell death localized to the infection site. “The idea is that if it contains the pathogen at the infection side, the rest of the plant can be free from the pathogen and it will not be able to spread,” said Dinesh-Kumar. It’s a cellular sacrifice that benefits the whole organism.   “The question the field is interested in is, what causes this cell death and how immune receptors activate this process?” he added. “Why is cell death only occurring in a few cells but not spreading?” The ultimate goal—after figuring out how these biochemicals and organelles work in tandem with one another—is to engineer plant proteins that confer broad-spectrum resistance to a suite of pathogens. Dinesh-Kumar and his team are working hard to identify and further describe the molecules involved in plant defense. “We are optimistic that our research on mechanistic understanding of how immune receptors function could pave the way towards engineering durable resistance against pathogens in important crop plants,” said Dinesh-Kumar. Dinesh-Kumar will receive the Noel T. Keen Award at The American Phytopathological Society annual meeting in August.   Stay Informed! Sign up for our monthly email newsletter Dinesh-Kumar joined the UC Davis faculty in 2010 following a roughly 10-year stint at Yale University. David Slipher/UC Davis"> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "During his career, Savithramma Dinesh-Kumar has published more than 100 research papers and reviews and has received many accolades. For his excellence in molecular plant pathology research, Dinesh-Kumar recently received the Noel T. Keen Award from The American Phytopathological Society " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><strong><em><span><span><span><span><span><span>For his excellence in research, Dinesh-Kumar has received the American Phytopathological Society's Noel T. Keen Award </span></span></span></span></span></span></em></strong></li> <li><em><strong>His interest in plants goes back to his youth working with his father on his family's farm in India</strong></em></li> <li><em><strong>His well-published research focuses on host-microbe interactions and plant defense tactics</strong></em></li> </ul></div> </aside><p><span><span><span><span><span><span>Professor Savithramma Dinesh-Kumar, Department of Plant Biology, grew up in Bhadravathi, </span></span></span></span></span></span><span><span><span><span><span><span>India. As a kid, he routinely spent time with his father, a high school teacher, on their farm in a nearby village. They grew rice and sugarcane, harvesting the latter crop by night when its sugar content was optimal. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“Since I was on the farm, I was always interested in plants, especially why farmers grow so many varieties of rice,” said Dinesh-Kumar. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>But when it came time for university, Dinesh-Kumar initially decided to study engineering. While good at mathematics, he found the work too abstract. It wasn’t tangible, like the soil and crops in the farm fields of his youth. So Dinesh-Kumar took a different route and enrolled at the University of Agricultural Sciences in Bangalore, India. He started studying genetics, which eventually opened doors to research on plant breeding and plant-pathogen interactions. A storied career followed. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Dinesh-Kumar has published more than 100 research papers and reviews and has received many accolades, including being named a fellow of the American Association for the Advancement of Science in 2018. And now, he can add another honor to the list. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>For his excellence in molecular plant pathology research, Dinesh-Kumar recently received the Noel T. Keen Award from The American Phytopathological Society. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“This is a great honor,” said Dinesh-Kumar, who expressed gratitude for the nomination. “I was not expecting this at all actually because Noel Keen is one of the pioneers in the plant pathology field.” </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“Professor Dinesh-Kumar’s work on host-microbe interactions has helped reveal the fascinating molecular world of plant defense tactics,” said Mark Winey, dean of the College of Biological Sciences. “His continuing research and insights have had significant impact on the field and demonstrate the strength of our stellar Department of Plant Biology.”     </span></span></span></span></span></span></p> </blockquote> <figure role="group" class="caption caption-img"><img alt="Chloroplasts" data-entity-type="file" data-entity-uuid="9a51866b-e5f3-41d2-b6fd-087ecd35bafd" src="/sites/g/files/dgvnsk2646/files/inline-images/Chloroplast-College-of-Biological-Sciences-UC-Davis-border.jpg" /><figcaption>Dinesh-Kumar and colleagues found that chloroplasts coordinate with the cell’s nucleus to instigate and execute plant defense responses. Des Callaghan</figcaption></figure><h4><span><span><span><strong><span><span><span>On the front lines of plant defense</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>After completing a master’s degree in Genetics, Dinesh-Kumar traveled half a world away to the United States. His first stop was the University of Kentucky, where he secured a graduate research position in the Department of Forestry and Natural Resources. There, he worked on a project concerning fungal resistance in poplar trees. Though he enjoyed the work, Dinesh-Kumar wanted to try his hand at molecular biology. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“I always had my mind on molecular biology back when I was a master’s student,” said Dinesh-Kumar. “I had a lot of theoretical exposure but not any hands-on experience.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>One day, he saw an announcement for a three-week intensive molecular biology training program at the The University of Chicago’s Marine Biological Laboratory, Woods Hole, Mass. It was the perfect opportunity to indulge his molecular biology curiosity. The program solidified Dinesh-Kumar’s sentiment that molecular biology is fundamental to answering basic questions about plant defense tactics. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Inspired, Dinesh-Kumar enrolled in a Molecular, Cellular and Developmental Biology Ph.D. program at Iowa State University and joined the lab of W. Allen Miller, a professor of plant pathology and microbiology. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Dinesh-Kumar’s dissertation explored the barley yellow dwarf virus (BYDV), which affects cereal crops. His research revealed that the virus uses leaky scanning and translational read-through strategies to produce three different proteins from a single subgenomic RNA.      </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“My goal was to figure out what sequences in the viral RNA are responsible for making these multi-pronged proteins from a single RNA,” said Dinesh-Kumar, who also constructed the first successful infectious clone of BYDV. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Following graduation, Dinesh-Kumar headed further west and joined Professor Barbara Baker’s laboratory at the UC Berkeley Plant Gene Expression Center. He continued studying viral resistance and became part of the team that cloned the first virus resistance gene “that confers resistance to the tobacco mosaic virus,” according to The American Phytopathological Society. The team identified the first plant resistance protein that contained Toll-Interleukin-1 receptor (TIR) homology domain. The work was foundational for the field, and today, these receptors are known to be integral to not only plant immunity but animal immunity as well. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“In the last 20 years, the thrust has been to understand how these immune receptors recognize pathogens and how they activate signal transduction in the plant so the ultimate output is resistance,” said Dinesh-Kumar. “We still don’t have a complete understanding of how these resistance proteins are working.” </span></span></span></span></span></span></p> </blockquote> <figure role="group" class="caption caption-img"><img alt="Chlorophyll" data-entity-type="file" data-entity-uuid="44533413-87a0-4628-b0be-24197057bba2" src="/sites/g/files/dgvnsk2646/files/inline-images/Kelvan-Ma-chlorophyll-College-of-Biological-Sciences-UC-Davis_0.jpg" /><figcaption>Chlorophyll, pictured here, are green pigments that absorb light, providing the energy for photosynthesis. Ma Kelvan</figcaption></figure><h4><span><span><span><strong><span><span><span>Containing plant infections</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>Dinesh-Kumar joined the UC Davis faculty in 2010 following a roughly 10-year stint at Yale University. Today, he’s the chair of the Department of Plant Biology and also holds an appointment with the UC Davis Genome Center. His research focus is still on understanding the molecular basis of host-microbe interactions. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“One of the area we’re interested in recently is, how do chloroplasts actually contribute to plant resistance?” said Dinesh-Kumar, noting that chloroplasts produce reactive oxygen species and the salicylic acid hormone. Both are important players in plant defense.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>What’s more, Dinesh-Kumar and colleagues found that chloroplasts coordinate with the cell’s nucleus to instigate and execute plant defense responses. These actions are incredibly exact. When a plant is infected with a pathogen, its immune receptors activate a cascade of responses leading to cell death that keep the pathogen contained. Dinesh-Kumar and colleagues found that plant cells activate autophagy to keep cell death localized to the infection site.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“The idea is that if it contains the pathogen at the infection side, the rest of the plant can be free from the pathogen and it will not be able to spread,” said Dinesh-Kumar. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>It’s a cellular sacrifice that benefits the whole organism.   </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“The question the field is interested in is, what causes this cell death and how immune receptors activate this process?” he added. “Why is cell death only occurring in a few cells but not spreading?”</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>The ultimate goal—after figuring out how these biochemicals and organelles work in tandem with one another—is to engineer plant proteins that confer broad-spectrum resistance to a suite of pathogens. Dinesh-Kumar and his team are working hard to identify and further describe the molecules involved in plant defense. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“We are optimistic that our research on mechanistic understanding of how immune receptors function could pave the way towards engineering durable resistance against pathogens in important crop plants,” said Dinesh-Kumar. </span></span></span></span></span></span></p> </blockquote> <p><span><span><span><span><span><span>Dinesh-Kumar will receive the Noel T. Keen Award at The American Phytopathological Society annual meeting in August.   </span></span></span></span></span></span></p> <p class="text-align-center"><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></p> <figure role="group" class="caption caption-img"><img alt="Savithramma DInesh-Kumar" data-entity-type="file" data-entity-uuid="ad4e0553-231e-42b9-8887-2a8a08da1ecf" src="/sites/g/files/dgvnsk2646/files/inline-images/Savithramma-Dinesh-Kumar-College-of-Biological-Sciences-UC-Davis-1.jpg" /><figcaption>Dinesh-Kumar joined the UC Davis faculty in 2010 following a roughly 10-year stint at Yale University. David Slipher/UC Davis</figcaption></figure></div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/food-agriculture-plants" hreflang="en">Food, Agriculture and Plant Biology</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/plant-biology-0" hreflang="en">Department of Plant Biology</a></div> <div class="field__item"><a href="/tags/awards" hreflang="en">awards</a></div> <div class="field__item"><a href="/tags/microbes" hreflang="en">microbes</a></div> <div class="field__item"><a href="/tags/plant-biology" hreflang="en">plant biology</a></div> <div class="field__item"><a href="/tags/model-plants" hreflang="en">Model Plants</a></div> <div class="field__item"><a href="/tags/pathogens" hreflang="en">pathogens</a></div> <div class="field__item"><a href="/tags/discovering-curiosity" hreflang="en">Discovering Curiosity</a></div> <div class="field__item"><a href="/tags/plant-biology-graduate-group" hreflang="en">Plant Biology Graduate Group</a></div> <div class="field__item"><a href="/tags/biochemistry-molecular-cellular-and-developmental-biology-graduate-group" hreflang="en">Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group</a></div> </div> </div> Tue, 16 Jul 2019 15:11:54 +0000 Greg Watry 3321 at https://biology.ucdavis.edu The Infection Heist: How Social Viruses Team Up for the Perfect Score https://biology.ucdavis.edu/news/infection-heist-how-social-viruses-team-perfect-score <span class="field field--name-title field--type-string field--label-hidden">The Infection Heist: How Social Viruses Team Up for the Perfect Score</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/16" typeof="schema:Person" property="schema:name" datatype="">David Slipher</span> </span> <span class="field field--name-created field--type-created field--label-hidden">July 11, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/Virus-Bank-Heist-College-of-Biological-Sciences-UC-Davis.png?h=874824da&amp;itok=PxG14Zh_" width="1280" height="720" alt="virus bank heist" title="The safe-cracker, the inside man, the getaway driver. Each member plays a key role in a bank heist. This metaphor helps explain how different viruses interact to co-infect cells. David Slipher/(CC0)" typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary Viruses in competitive environments can interact to co-infect hosts, but these relationships may change once inside the host cell​​​​ Díaz-Muñoz studies the reproductive strategies of multiple viruses, comparing the DNA of parental strains ​The social interactions of viruses may upend many of the established scientific principles of how virology works If you’ve seen any heist movie, you know it takes a team to get the job done. The safe-cracker, the inside man, the getaway driver. Each member plays a key role, without which the group’s success is jeopardized. Viruses in a competitive environment work in a similar way. A perspective paper published in mSystems suggests that interactions between viruses are more complicated than virologists originally thought. Using social evolution theory, Samuel Díaz-Muñoz, assistant professor of microbiology and molecular genetics, hopes to help fight viral and bacterial infections with new treatments that harness interactions between viruses. Díaz-Muñoz sees understanding the social interactions of viruses as a key to help limit viral outbreaks. With fellow researchers Rafael Sanjuán of the University of Valencia and Stuart West of Oxford University, he has coined the term “sociovirology” which aims to develop evolutionary models to help predict virus-virus interactions. Similar models have been developed for bacteria, cancer and many other levels of biology. “We have a new lens to look at viruses that might change some fundamental principles of virology and definitely bring new approaches to treat bacterial and viral diseases,” said Díaz-Muñoz. It’s always better when we’re together An electron micrograph reveals 1918 H1N1 influenza strain virus particles (in green) attacking a cell (in blue). NIH/NIAIDSuccessful virus strains can team up to accomplish their objective of infecting a host cell. One virus strain might have a specialized, lock-pick like protein which is particularly effective at cracking the cell’s vault.  A second virus strain excels at the getaway, exiting the cell and evading antibodies that might pursue it. Together, the two viruses succeed in co-infecting the cell and divvying up the ultimate score—their individual reproductive successes. But as with most good heist scenarios, circumstances change. Cooperation between the team may end once a role is fulfilled. Take out one of the strains and suddenly there’s one less member with which to split the loot. For a virus, it’s always about looking out for yourself ahead of the competition. “Social interaction isn&#039;t always collaborative,” said Díaz-Muñoz. “It can be neutral and it can be detrimental to different extents. When the situation changes, the relationships change.” In the lab, Díaz-Muñoz creates viral environments with different levels of competition to test his theory. In one scenario a virus, called strain A, is all alone. In other scenarios, it’s partnered with a different strain, strain B, or many strains CDEFG, etc., in a competitive environment. “We&#039;re not looking at only strains A and B. We&#039;re trying to look at ABCDEFG down the line and their combinations,” Díaz-Muñoz said. “And so that is why it becomes incredibly complex.” How does Strain A perform in these different scenarios and how do these actions affect the offspring it generates? Predicting the outcomes becomes extremely difficult as more and more variables are added. But denser environments increase the likelihood among different parental strains for interaction—be it cooperation, cheating or something in between. Systems like game theory can help create theoretical models for virus-virus interactions. CDC  What does it mean to be social? While the bank heist scenario illustrates a fun, anthropomorphic overreach, Díaz-Muñoz is quick to point out that social activity doesn’t imply that viruses act with intentional decision making or even conscious awareness. “You don&#039;t need to be sophisticated at all to be social,” said Díaz-Muñoz. “It&#039;s not that they know what they’re doing, it&#039;s just that the behavior happens to be advantageous in that setting.” For virologists, being social simply means that one virus affects the reproduction of another. There’s no learning per se, only reactions. Successful reactions promote survival, while unsuccessful attempts could mean doom. In crowded environments, viruses can “cheat” competing strains out of their reproduction. Coinfection of a cell results in multiple infecting viruses, called parents, combining the genetic material they’ll pass on, much like human parents each contributing an equal part of their genetic code. But cheater viruses have techniques to bias this process to favor their progeny. The complexity of co-reproduction means that offspring strains could include a mish-mash of all parents’ DNA, and if there are cheaters at work, the researchers will be able to spot them by analyzing the genome segments of the offspring strains. Does a segment show preference for promoting one strain at the expense of the other? This digital illustration shows a cell infected with a generic influenza virus. The viral envelope in tan protects the virus&#039; genetic material from a host&#039;s immune cells, and the proteins in blue and red help recognize and bind to a host&#039;s cells. CDC The viral strains the Díaz-Muñoz Lab studies include those responsible for the 1968 and 2009 influenza pandemics, among other epidemic strains. Researchers like to pick these popular strains because their infection rates are well characterized. Together, they represent a diversity of genetic variation and separation in time and geography which makes them valuable models. Gaming the system While viruses aren’t active decision makers and only perform a specific task to exploit an advantage, Díaz-Muñoz uses systems like game theory to help explain scenarios of cooperation and competition. One example is that of the Prisoner’s Dilemma. In this scenario two criminals are imprisoned separately. The authorities don’t have enough evidence to convict them both so each prisoner is given the opportunity to either cooperate and betray his partner, or remain silent to protect each other. It’s a classic example of how two individuals may not cooperate, even if doing so is actually in their best interest. Scenarios like this bring elements of game theory into the virology mix, with applications in logic and computer science, mathematics, and social sciences. This theory has been tested in viruses by Paul Turner (Yale University) and Lin Çhao (University of California, San Diego). Díaz-Muñoz aims to extend the work of his postdoctoral advisors beyond the lab, to see if similar dynamics play out in natural viral infections. Díaz-Muñoz will continue to expand the variety and complexity of his virus environments, eventually introducing combinations of 3-4 parental virus strains to evaluate their social behavior. Sociovirology is shaking down the long-held assumptions of virology, as co-infection can change every stage of the viral lifecycle and can provide better models for how viruses interact in natural environment. Díaz-Muñoz envisions that this emerging field may rewrite the textbook doctrines of how viruses function at the most fundamental level.  “It turns out viruses have been dealing with each other for millions of generations. Maybe we can learn something from them in our own battles with viral diseases,” said Díaz-Muñoz. Stay Informed! Sign up for our monthly email newsletter "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "Much like characters in a bank heist, viruses in competitive environments can collaborate for their share of the &quot;score&quot; of successfully co-infecting hosts. But these relationships may change once inside the host cell, according to Assistant Professor Samuel Díaz-Muñoz​. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><strong><em>Viruses in competitive environments can interact to co-infect hosts, but these relationships may change once inside the host cell</em></strong>​​​​</li> <li><em><strong><span><span><span><span><span><span>Díaz-Muñoz studies the reproductive strategies of multiple viruses, comparing the DNA of parental strains</span></span></span></span></span></span></strong></em></li> <li>​<strong><em>The social interactions of viruses may upend many of the established scientific principles of how virology works</em></strong></li> </ul></div> </aside><p><span><span><span><span><span>If you’ve seen any heist movie, you know it takes a team to get the job done. The safe-cracker, the inside man, the getaway driver. Each member plays a key role, without which the group’s success is jeopardized.</span></span></span></span></span></p> <div> <p><span><span><span><span><span><span>Viruses in a competitive environment work in a similar way. </span></span><span>A perspective paper published in</span> <span><a href="https://msystems.asm.org/content/4/3/e00121-19"><em>mSystems</em></a><em> </em><span>suggests that interactions between viruses are more complicated than virologists originally thought. Using social evolution theory, Samuel Díaz-Muñoz, assistant professor of microbiology and molecular genetics, hopes to help fight viral and bacterial infections with new treatments that harness interactions between viruses.</span></span></span></span></span></span></p> </div> <div> <p><span><span><span><span><span><span>Díaz-Muñoz sees understanding the social interactions of viruses as a key to help limit viral outbreaks. With fellow researchers Rafael Sanjuán of the University of Valencia and Stuart West of Oxford University, <a href="https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(17)30401-8">he has coined the term “sociovirology”</a> which aims to develop evolutionary models to help predict virus-virus interactions. Similar models have been developed for bacteria, cancer and many other levels of biology. </span></span></span></span></span></span></p> </div> <div> <blockquote> <p><span><span><span><span><span><span>“We have a new lens to look at viruses that might change some fundamental principles of virology and definitely bring new approaches to treat bacterial and viral diseases,” said Díaz-Muñoz.</span></span></span></span></span></span></p> </blockquote> <h3><span><span><span><span><strong><span><span>It’s always better when we’re together</span></span></strong></span></span></span></span></h3> <figure role="group" class="caption caption-img align-right"><img alt="H1N1 virus under microscope" data-entity-type="file" data-entity-uuid="4882ee64-bfa4-4356-a20c-d4c2270092ed" height="399" src="/sites/g/files/dgvnsk2646/files/inline-images/H1N1-Virus-College-of-Biological-Sciences-UC-Davis.jpg" width="399" /><figcaption>An electron micrograph reveals 1918 H1N1 influenza strain virus particles (in green) attacking a cell (in blue). NIH/NIAID</figcaption></figure><p><span><span><span><span><span><span>Successful virus strains can team up to accomplish their objective of infecting a host cell. One virus strain might have a specialized, lock-pick like protein which is particularly effective at cracking the cell’s vault. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>A</span></span><span><span> second virus strain excels at the getaway, exiting the cell and evading antibodies that might pursue it. Together, the two viruses succeed in co-infecting the cell and divvying up the ultimate score—their individual reproductive successes.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>But as with most good heist scenarios, circumstances change. Cooperation between the team may end once a role is fulfilled. Take out one of the strains and suddenly there’s one less member with which to split the loot. For a virus, it’s always about looking out for yourself ahead of the competition.</span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“Social interaction isn't always collaborative,” said Díaz-Muñoz. “It can be neutral and it can be detrimental to different extents. When the situation changes, the relationships change.”</span></span></span></span></span></span></p> </blockquote> </div> <div> <p><span><span><span><span><span><span>In the lab, Díaz-Muñoz creates viral environments with different levels of competition to test his theory. In one scenario a virus, called strain A, is all alone. In other scenarios, it’s partnered with a different strain, strain B, or many strains CDEFG, etc., in a competitive environment. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“We're not looking at only strains A and B. We're trying to look at ABCDEFG down the line and their combinations,” Díaz-Muñoz said. “And so that is why it becomes incredibly complex.”</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>How does Strain A perform in these different scenarios and how do these actions affect the <span><span>offspring it generates</span></span>? Predicting the outcomes becomes extremely difficult as more and more variables are added. But denser environments increase the likelihood among different parental strains for interaction—be it cooperation, cheating or something in between. </span></span></span></span></span></span></p> <figure role="group" class="caption caption-img align-center"><img alt="virus microscopy" data-entity-type="file" data-entity-uuid="c816d624-8019-4f40-bc2d-b9ac03ee70ec" src="/sites/g/files/dgvnsk2646/files/inline-images/Virus-College-of-Biological-Sciences-UC-Davis%20-%20crop.jpg" /><figcaption>Systems like game theory can help create theoretical models for virus-virus interactions. CDC</figcaption></figure><p> </p> </div> <div> <h3><span><span><span><span><strong><span><span>What does it mean to be social?</span></span></strong></span></span></span></span></h3> <p><span><span><span><span><span><span>While the bank heist scenario illustrates a fun, anthropomorphic overreach, Díaz-Muñoz is quick to point out that social activity doesn’t imply that viruses act with intentional decision making or even conscious awareness.</span></span></span></span></span></span></p> </div> <div> <blockquote> <p><span><span><span><span><span>“You don't need to be sophisticated at all to be social,”</span><span><span> said Díaz-Muñoz. “It's not that they know what they’re doing, it's just that the behavior happens to be advantageous in that setting.”</span></span></span></span></span></span></p> </blockquote> <p><span><span><span><span><span><span>For virologists, being social simply means that one virus affects the reproduction of another. There’s no learning per se, only reactions. Successful reactions promote survival, while unsuccessful attempts could mean doom.</span></span></span></span></span></span></p> </div> <div> <p><span><span><span><span><span><span>In crowded environments, viruses can “cheat” competing strains out of their reproduction. Coinfection of a cell results in multiple infecting viruses, called parents, combining the genetic material they’ll pass on, much like human parents each contributing an equal part of their genetic code. But cheater viruses have techniques to bias this process to favor their progeny. </span></span></span></span></span></span></p> </div> <div> <p><span><span><span><span><span><span><span>The complexity of co-reproduction means that offspring strains could include a mish-mash of all parents’ DNA, and if there are cheaters at work, the researchers will be able to spot them</span></span></span><span><span> by analyzing the genome segments of the offspring strains. Does a segment show preference for promoting one strain at the expense of the other? </span></span></span></span></span></span></p> </div> <figure role="group" class="caption caption-img align-left"><img alt="virus illustration" data-entity-type="file" data-entity-uuid="74033dd9-8b05-4f2d-a971-e4dadf4c4ed7" height="346" src="/sites/g/files/dgvnsk2646/files/inline-images/Virus-Structure-College-of-Biological-Sciences-UC-Davis.jpg" width="358" /><figcaption>This digital illustration shows a cell infected with a generic influenza virus. The viral envelope in tan protects the virus' genetic material from a host's immune cells, and the proteins in blue and red help recognize and bind to a host's cells. CDC</figcaption></figure><div> <p><span><span><span><span><span><span>The viral strains the Díaz-Muñoz Lab studies include those responsible for the 1968 and 2009 influenza pandemics, among other epidemic strains. Researchers like to pick these popular strains because their infection rates are well characterized. Together, they represent a diversity of genetic variation and separation in time and geography<span><span> </span></span>which makes them valuable models. </span></span></span></span></span></span></p> <h3><span><span><span><span><strong><span>Gaming the system</span></strong></span></span></span></span></h3> <p><span><span><span><span><span><span><span>While viruses aren’t active decision makers and only perform a specific task to exploit an advantage, Díaz-Muñoz uses systems like game theory to help explain scenarios of cooperation and competition. </span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span>One example is that of the Prisoner’s Dilemma. In this scenario two criminals are imprisoned separately. The authorities don’t have enough evidence to convict them both so each prisoner is given the opportunity to either cooperate and betray his partner, or remain silent to protect each other. It’s a classic example of how two individuals may not cooperate, even if doing so is actually in their best interest.<span><span> </span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span>Scenarios like this bring elements of game theory into the virology mix, with applications in logic and computer science, mathematics, and social sciences. This <a href="https://www.nature.com/articles/18913">theory has been tested in viruses</a> by Paul Turner (Yale University) and Lin Çhao (University of California, San Diego). Díaz-Muñoz aims to extend the work of his postdoctoral advisors beyond the lab, to see if similar dynamics play out in natural viral infections.</span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span>Díaz-Muñoz will continue to expand the variety and complexity of his virus environments, eventually introducing combinations of 3-4 parental virus strains to evaluate their social behavior. </span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Sociovirology is shaking down the long-held assumptions of virology, as co-infection can change every stage of the viral lifecycle and can provide better models for how viruses interact in natural environment. Díaz-Muñoz envisions that this emerging field may rewrite the textbook doctrines of how viruses function at the most fundamental level. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span><span> “It turns out viruses have been dealing with each other for millions of generations. Maybe we can learn something from them in our own battles with viral diseases,” </span>said Díaz-Muñoz.</span></span></span></span></span></span></p> </blockquote> <p class="text-align-center"><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></p> <div class="responsive-embed" style="padding-bottom: 56.25%"><iframe width="480" height="270" src="https://www.youtube.com/embed/Rpj0emEGShQ?feature=oembed" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe></div> </div> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/genetics-microbiology" hreflang="en">Cellular and Microbiology</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/microbiology" hreflang="en">microbiology</a></div> <div class="field__item"><a href="/tags/viruses" hreflang="en">viruses</a></div> <div class="field__item"><a href="/tags/influenza" hreflang="en">influenza</a></div> <div class="field__item"><a href="/tags/reproduction" hreflang="en">reproduction</a></div> <div class="field__item"><a href="/tags/infection" hreflang="en">infection</a></div> <div class="field__item"><a href="/tags/model-organisms" hreflang="en">model organisms</a></div> <div class="field__item"><a href="/tags/evolution" hreflang="en">evolution</a></div> </div> </div> Thu, 11 Jul 2019 17:39:33 +0000 David Slipher 3316 at https://biology.ucdavis.edu Finding a Voice in Science: iBioseminars in Cellular and Molecular Biology Encourages Student Engagement https://biology.ucdavis.edu/news/MCB110Y <span class="field field--name-title field--type-string field--label-hidden">Finding a Voice in Science: iBioseminars in Cellular and Molecular Biology Encourages Student Engagement</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/5451" typeof="schema:Person" property="schema:name" datatype="">Greg Watry</span> </span> <span class="field field--name-created field--type-created field--label-hidden">July 09, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/iBiology-MCB110Y-College-of-Biological-Sciences-UC-Davis-3.jpg?h=5bda6110&amp;itok=DYhA9pyJ" width="1280" height="720" alt="iBiology class" title="MCB 110Y &quot;iBioseminars in Cellular and Molecular Biology&quot; combines at-home video lectures, produced by iBiology, with discussion-based classes. David Slipher/UC Davis" typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary MCB 110Y &quot;iBioseminars in Cellular and Molecular Biology&quot; combines at-home video lectures, produced by iBiology, with discussion-based classes Students watch talks from leading experts on topics like the origins of cellular life, cellular mobility and proteins They then prepare presentations on the lectures and discuss them as a group As an undergraduate student at a small liberal arts college, Kassandra Ori-McKenney knew firsthand the difficulty of speaking up during lectures.  “The teacher would ask a question and I would know the answer,” said Ori-McKenney, now an assistant professor of molecular and cellular biology. “I would repeat it in my head over and over, but I would never raise my hand.” Ori-McKenney hadn’t found her voice. But during her senior year at Vassar College in Poughkeepsie, N.Y., she enrolled in a discussion-based course with around a dozen other students. Ori-McKenney and her colleagues read recent research papers, prepared presentations on the papers and then discussed them.    “It was the first time that I actually felt empowered to share my opinion,” said Ori-McKenney. “There was no real right or wrong. It was just a discussion about the work: what you thought about it and where you thought the research was going.” Years later, Ori-McKenney empowers her UC Davis students to speak up and share their thoughts. Teaming up with fellow faculty (and husband) Richard McKenney, assistant professor of molecular and cellular biology, Ori-McKenney and McKenney are spearheading a new iteration of MCB 110Y “iBioseminars in Cellular and Molecular Biology,” a course that combines at-home video lectures, produced by iBiology, with discussion-based classes. This spring the duo taught the course for the first time. MCB 110Y was originally developed by Distinguished Professor Jonathan Scholey, Department of Molecular and Cellular Biology. “Having this kind of intimate discussion section is a unique opportunity for all the students here,” said McKenney. “I hope that we can help change the way that at least a small subset of students may be thinking about how we learn about science.”   A mission to bring science to the world The idea to reintroduce the course to the UC Davis curriculum was prompted by a meeting with Scholey, a mentor to both Ori-McKenney and McKenney. As the three caught up, Ori-McKenney and McKenney realized the class could be a great way to introduce active learning strategies to their students rather than just memorization and regurgitation. McKenney himself was familiar with the shortcomings of the memorization and regurgitation method. As a student, he found it difficult to sit down with a textbook for long hours. The course covers a variety of topics in cellular biology, including cytoskeletal mechanics. David Slipher/UC Davis“Unfortunately, a lot of science is that way because there’s so much information and there’s just no better way to disseminate that information in a short time period,” he said. With the new class, McKenney and Ori-McKenney found they could trust the scientific credibility of content curated by iBiology, which includes talks from leading experts on many biology topics, like the origins of cellular life, cellular mobility and proteins. What’s more, there was a familiar face involved with the iBiology project. McKenney’s postdoctoral advisor, Ronald Vale, a professor of cellular and molecular pharmacology at UC San Francisco, founded iBiology in 2006. His video lecture on molecular motor proteins was part of the spring 2019 syllabus. iBiology has “a mission to bring the world’s top scientists and their research to anyone who has an internet connection,” said Ori-McKenney. Ori-McKenney and McKenney realized the class could be a great way to introduce active learning strategies to their students rather than just memorization and regurgitation. David Slipher/UC DavisTaking the time to think critically Over the course of the spring class, the six students of MCB 110Y learned the basics of cell biology, prepared presentations on the lectures and then discussed them in class with Ori-McKenney and McKenney. Among the class were Samantha Wallace and Madeleine Beans, both seniors majoring in Genetics and Genomics.   “It’s not going and sitting and listening to a teacher or a professor,” said Wallace. “You watch the lectures beforehand online and then we go and we talk about it and we can ask any questions, any curiosities. We can branch off from there in any way we want, which was really great.”   “The ability to discuss research in science is really, really critical,” said Beans. “That’s going to be very useful both in classes, in studying with people but especially in professional life because that’s what you need to be doing,” she added. “You need to work with other people.”  Ori-McKenney and McKenney plan on teaching MCB 110Y again next spring. “This course is really built for people who want to take that next step to make science a full-time commitment or career,” said McKenney. “So we’re looking for students who are…strongly motivated to take that next step into going past the textbook, going past the exam and saying ‘I want to learn what’s going on at the cutting-edge of science.’”  Over the course of the spring class, the six students of MCB 110Y learned the basics of cell biology, prepared presentations on the lectures and then discussed them in class with Ori-McKenney and McKenney.  David Slipher/UC DavisStay Informed! Sign up for our monthly email newsletter "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "Assistant Professors Kassandra Ori-McKenney and Richard McKenney are spearheading a new iteration of MCB 110Y “iBioseminars in Cellular and Molecular Biology,” a course that combines at-home video lectures, produced by iBiology, with discussion-based classes. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><em><strong>MCB 110Y "iBioseminars in Cellular and Molecular Biology" <span><span><span><span><span><span>combines at-home video lectures, produced by </span></span></span><a href="https://www.ibiology.org/"><span><span><span>iBiology</span></span></span></a><span><span><span>, with discussion-based classes</span></span></span></span></span></span></strong></em></li> <li><strong><em>Students watch<span><span><span><span><span><span> talks from leading experts on topics like the origins of cellular life, cellular mobility </span></span></span></span></span></span></em></strong><span><span><span><span><span><span><strong><em>and</em></strong></span></span></span></span></span></span><strong><em><span><span><span><span><span><span> proteins</span></span></span></span></span></span></em></strong></li> <li><strong><em><span><span><span><span><span><span>They then prepare presentations on the lectures and discuss them as a group</span></span></span></span></span></span></em></strong></li> </ul></div> </aside><p><span><span><span><span><span><span>As an undergraduate student at a small liberal arts college, Kassandra Ori-McKenney knew firsthand the difficulty of speaking up during </span></span></span></span></span></span><span><span><span><span><span><span>lectures.  </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“The teacher would ask a question and I would know the answer,” said Ori-McKenney, now an assistant professor of molecular and cellular biology. “I would repeat it in my head over and over, but I would never raise my hand.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Ori-McKenney hadn’t found her voice. But during her senior year at Vassar College in Poughkeepsie, N.Y., she enrolled in a discussion-based course with around a dozen other students. Ori-McKenney and her colleagues read recent research papers, prepared presentations on the papers and then discussed them.   </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“It was the first time that I actually felt empowered to share my opinion,” said Ori-McKenney. “There was no real right or wrong. It was just a discussion about the work: what you thought about it and where you thought the research was going.” </span></span></span></span></span></span></p> </blockquote> <p><span><span><span><span><span><span>Years later, Ori-McKenney empowers her UC Davis students to speak up and share their thoughts. Teaming up with fellow faculty (and husband) Richard McKenney, assistant professor of molecular and cellular biology, Ori-McKenney and McKenney are spearheading a new iteration of MCB 110Y “iBioseminars in Cellular and Molecular Biology,” a course that combines at-home video lectures, produced by </span></span></span><a href="https://www.ibiology.org/"><span><span><span>iBiology</span></span></span></a><span><span><span>, with discussion-based classes. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>This spring the duo taught the course for the first time. MCB 110Y was originally developed by Distinguished Professor Jonathan Scholey, Department of Molecular and Cellular Biology.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“Having this kind of intimate discussion section is a unique opportunity for all the students here,” said McKenney. “I hope that we can help change the way that at least a small subset of students may be thinking about how we learn about science.”  </span></span></span></span></span></span></p> <div class="responsive-embed" style="padding-bottom: 56.25%"><iframe width="480" height="270" src="https://www.youtube.com/embed/TdMzaWjQdmM?feature=oembed" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe></div> <h4><span><span><span><strong><span><span><span>A mission to bring science to the world</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>The idea to reintroduce the course to the UC Davis curriculum was prompted by a meeting with Scholey, a mentor to both Ori-McKenney and McKenney. As the three caught up, Ori-McKenney and McKenney realized the class could be a great way to introduce active learning strategies to their students rather than just memorization and regurgitation. McKenney himself was familiar with the shortcomings of the memorization and regurgitation method. As a student, he found it difficult to sit down with a textbook for long hours. </span></span></span></span></span></span></p> <figure role="group" class="caption caption-img align-right"><img alt="Whiteboard" data-entity-type="file" data-entity-uuid="4cbc9a31-7351-4fcd-87c2-f9e5d395b38b" height="277" src="/sites/g/files/dgvnsk2646/files/inline-images/iBiology-MCB110Y-College-of-Biological-Sciences-UC-Davis-2.jpg" width="416" /><figcaption>The course covers a variety of topics in cellular biology, including cytoskeletal mechanics. David Slipher/UC Davis</figcaption></figure><p><span><span><span><span><span><span>“Unfortunately, a lot of science is that way because there’s so much information and there’s just no better way to disseminate that information in a short time period,” he said. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>With the new class, McKenney and Ori-McKenney found they could trust the scientific credibility of content curated by iBiology, which includes talks from leading experts on many biology topics, like the origins of cellular life, cellular mobility and proteins. What’s more, there was a familiar face involved with the iBiology project. McKenney’s postdoctoral advisor, Ronald Vale, a professor of cellular and molecular pharmacology at UC San Francisco, founded iBiology in 2006. His video lecture on molecular motor proteins was part of the spring 2019 syllabus. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>iBiology has “a mission to bring the world’s top scientists and their research to anyone who has an internet connection,” said Ori-McKenney. </span></span></span></span></span></span></p> <figure role="group" class="caption caption-img"><img alt="The iBiology discusses cell biology outside" data-entity-type="file" data-entity-uuid="720842a1-9441-45be-8bab-63eba7313e26" src="/sites/g/files/dgvnsk2646/files/inline-images/iBiology-MCB110Y-College-of-Biological-Sciences-UC-Davis-1.jpg" /><figcaption>Ori-McKenney and McKenney realized the class could be a great way to introduce active learning strategies to their students rather than just memorization and regurgitation. David Slipher/UC Davis</figcaption></figure><h4><span><span><span><strong><span><span><span>Taking the time to think critically</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>Over the course of the spring class, the six students of MCB 110Y learned the basics of cell biology, prepared presentations on the lectures and then discussed them in class with Ori-McKenney and McKenney. Among the class were Samantha Wallace and Madeleine Beans, both seniors majoring in Genetics and Genomics.  </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“It’s not going and sitting and listening to a teacher or a professor,” said Wallace. “You watch the lectures beforehand online and then we go and we talk about it and we can ask any questions, any curiosities. We can branch off from there in any way we want, which was really great.”   </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“The ability to discuss research in science is really, really critical,” said Beans. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“That’s going to be very useful both in classes, in studying with people but especially in professional life because that’s what you need to be doing,” she added. “You need to work with other people.”  </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Ori-McKenney and McKenney plan on teaching MCB 110Y again next spring. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“This course is really built for people who want to take that next step to make science a full-time commitment or career,” said McKenney. “So we’re looking for students who are…strongly motivated to take that next step into going past the textbook, going past the exam and saying ‘I want to learn what’s going on at the cutting-edge of science.’”  </span></span></span></span></span></span></p> </blockquote> <figure role="group" class="caption caption-img"><img alt="The MCB 110Y class" data-entity-type="file" data-entity-uuid="dfdf23d5-a776-423f-b510-57b23fff45a8" src="/sites/g/files/dgvnsk2646/files/inline-images/MCB110Y-College-of-Biological-Sciences-Full-1.jpg" /><figcaption>Over the course of the spring class, the six students of MCB 110Y learned the basics of cell biology, prepared presentations on the lectures and then discussed them in class with Ori-McKenney and McKenney.  David Slipher/UC Davis</figcaption></figure><p class="text-align-center"><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></p> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/genetics-microbiology" hreflang="en">Cellular and Microbiology</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/molecular-and-cellular-biology" hreflang="en">Department of Molecular and Cellular Biology</a></div> <div class="field__item"><a href="/tags/stem-education" hreflang="en">STEM education</a></div> <div class="field__item"><a href="/tags/teaching" hreflang="en">teaching</a></div> <div class="field__item"><a href="/tags/ibiology" hreflang="en">iBiology</a></div> <div class="field__item"><a href="/tags/cellular-biology" hreflang="en">cellular biology</a></div> <div class="field__item"><a href="/tags/molecular-biology" hreflang="en">molecular biology</a></div> <div class="field__item"><a href="/tags/women-stem" hreflang="en">Women in STEM</a></div> <div class="field__item"><a href="/tags/video" hreflang="en">video</a></div> </div> </div> Tue, 09 Jul 2019 15:16:11 +0000 Greg Watry 3306 at https://biology.ucdavis.edu Nurturing Seeds and Growing Minds: John Harada Steps Down as Executive Associate Dean of Academic Affairs https://biology.ucdavis.edu/news/nurturing-seeds-and-growing-minds-john-harada-steps-down-executive-associate-dean-academic <span class="field field--name-title field--type-string field--label-hidden">Nurturing Seeds and Growing Minds: John Harada Steps Down as Executive Associate Dean of Academic Affairs</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/5451" typeof="schema:Person" property="schema:name" datatype="">Greg Watry</span> </span> <span class="field field--name-created field--type-created field--label-hidden">July 01, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/John-Harada-College-of-Biological-Sciences-UC-Davis-5.jpg?h=d65e4190&amp;itok=2TuVD-2q" width="1280" height="720" alt="John Harada" title="On top of his plant biology research, Professor John Harada has served as the College of Biological Sciences’ Executive Associate Dean of Academic Affairs for the past six years. He stepped down from the post at the end of June. David Slipher/UC Davis" typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary For the past six years, John Harada has served as the College of Biological Sciences&#039; Executive Associate Dean of Academic Affairs During Harada’s term, the campus initiated a new process to advance faculty through the merit and promotion system Harada will return his attention to his lab, where he studies seeds and the gene networks governing their development Following his graduation from Garfield High School in East Los Angeles, John Harada wasn’t sure what to expect from higher-ed. A first-generation college student, he navigated his freshman year at the University of California, Los Angeles without a strong network nor much academic direction. He knew he liked biology and thought the natural route, professionally speaking, was to pursue medicine. He then took his first biochemistry class with Charles West, now a professor emeritus of chemistry and biochemistry. Harada’s life changed. “It dawned on me,” said Harada, “that what this guy is saying is that all of life is just directed chemistry.” With a new outlook, Harada spent the succeeding years completing a B.S. in biochemistry and followed that degree with a Ph.D. in biochemistry from the University of Washington. Along the way, he discovered an affinity for the complexities of biochemistry. Today, Harada focuses his research on seeds and the gene networks governing their development. With his colleagues, he’s using techniques called laser capture microdissection and chromatin immunoprecipitation to understand the underlying genetics of seeds to help make an important food source even more nutritious. “Seeds feed the world,” said Professor Harada, Department of Plant Biology. “It’s been estimated that 75 percent of the calories that are consumed by humans actually come from seeds.” “If you can change the nutritional quality of seeds, or the number of seeds or the size of the seeds that crops are able to produce then you can increase yields,” he added. On top of his research, Harada has served as the College of Biological Sciences’ Executive Associate Dean of Academic Affairs for the past six years. He stepped down from the post at the end of June. “As the primary academic executive officer for the college, John administers faculty personnel matters and provides thought leadership and collaborates across many academic areas,” said College of Biological Sciences Dean Mark Winey. “He’s has been an instrumental force in shaping the vision, direction and outreach of many of our programs.” During Harada’s term, the campus initiated a new process to advance faculty through the merit and promotion system.  Harada said “Implementation of the step plus system has allowed CBS faculty to be rewarded not only for their outstanding research, but also for their excellence in teaching and service.” Like a conductor trying to orchestrate a sublime performance, Harada is trying to figure out the genetic balance that leads to healthy and nutritious seeds. David Slipher/UC DavisSowing the seeds of scientific progress By 1981, the year Harada received a Ph.D. degree, molecular biology was a nascent but budding field. Harada participates in a meeting between UC Davis and Osaka University educators at the launch of a new biotechnology research and training program. David Slipher/UC DavisHarada returned to UCLA and took a postdoctoral position in the lab of Bob Goldberg, now a distinguished professor of molecular, cell and development biology. In the Goldberg Lab, Harada worked on plant genetics, examining the genes responsible for producing a class of storage proteins in soybean seeds. It was “the bad old days of biology,” according to Harada, and while the technology available at the time was making waves, it was cumbersome compared to the later revolution of genomic sequencing in the 1990s. “Now we’re in the age of high-throughput sequencing, so now people just sequence genomes; they sequence transcriptomes,” he said. “It’s really amazing. It tells you that many of the major advances in biology are dictated by technology.” Before, the process of determining what genes are active consisted of taking cloned DNA copies of a messenger RNA, separating their strands and allowing them to reconnect with RNA. Via this process, researchers could measure the level at which a gene is expressed.  In 1984, following his postdoctoral work, Harada joined the UC Davis faculty. He was attracted to the campus for its reputation in plant biology and agriculture. Though he was interested in plants, Harada didn’t actually have any formal training in plant biology. “I wanted to go to a place where if I had questions, I could ask people,” he said. “I found out when I got here, I could ask people specific questions about plant biology and in many cases, the world expert was on the faculty here.” “There were no downsides to coming to UC Davis,” he added. “The faculty here is outstanding.”  Using laser capture microdissection and chromatin immunoprecipitation experiments, Harada and his colleagues peer at the organization of the seed’s gene networks throughout its developmental process, from morphogenesis to maturation. USDAFostering collaboration and exploring seed genetic networks That mentality of collaboration that initially attracted Harada to UC Davis is something he’s helped the college nurture over the years. “Most of graduate education in the U.S. is department-based,” said Harada. “A lot of the reason why I think there’s such great collaboration at UC Davis is because of the graduate group system.” Unlike a department-based system, graduate groups at UC Davis run university-wide, meaning faculty with appointments across many different departments, colleges and schools on campus can participate in graduate curriculum and instruction based on their subject matter expertise. Harada is a member of the Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, the Integrative Genetics and Genomics Graduate Group and the Plant Biology Graduate Group, which each offer specialties and focus areas. “These students are taking different classes, having different experiences and yet, they’re all in the same lab, so they can teach each other,” he said. “This integration often encourages interdisciplinary research.” After stepping down from his post as executive associate dean for academic affairs, Harada will continue his genetic research on seed development. Currently, Harada, his lab members and colleagues with UCLA’s Goldberg Lab are collaborating on a National Science Foundation-funded project to understand the genes underlying the soybean seed. Using laser capture microdissection and chromatin immunoprecipitation experiments, Harada and his colleagues peer at the organization of the seed’s gene networks throughout its developmental process, from morphogenesis to maturation. “We can watch this developmental shift occurring in what genes are turning on and turning off, and where they’re turning on and off in different parts of the seed,” he said. “We’ve been really able to obtain lots of insights into what’s occurring in the seeds that people really didn’t know about before.” Like a conductor trying to orchestrate a sublime performance, Harada is trying to figure out the genetic balance that leads to healthy and nutritious seeds. “It’s been estimated that by the year 2050, we’re going to need to be able to produce anywhere between 70 to 100 percent more food than we produce now,” he said. “We have to do that in the face of global climate change.  Hopefully, the information that we generate will help to meet this challenge.” Stay Informed! Sign up for our monthly email newsletter Harada will continue his genetic research on seed development. David Slipher/UC Davis"> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "After six years serving as the Executive Associate Dean of Academic Affairs for the College of Biological Sciences, Professor John Harada stepped down from the post at the end of June. He&#039;ll continue his research on seeds and the gene networks governing their development. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><em><strong>For the past six years, John Harada has served as the College of Biological Sciences' Executive Associate Dean of Academic Affairs</strong></em></li> <li><strong><em><span><span><span><span><span><span>During Harada’s term, the campus initiated a new process to advance faculty through the merit and promotion system</span></span></span></span></span></span></em></strong></li> <li><strong><em><span><span><span><span><span><span>Harada will return his attention to his lab, where he studies seeds and the gene networks governing their development</span></span></span></span></span></span></em></strong></li> </ul></div> </aside><p><span><span><span><span><span><span>Following his graduation from Garfield High School in East Los Angeles, John Harada wasn’t sure what to expect from higher-ed. A first-</span></span></span></span></span></span><span><span><span><span><span><span>generation college student, he navigated his freshman year at the University of California, Los Angeles without a strong network nor much academic direction. He knew he liked biology and thought the natural route, professionally speaking, was to pursue medicine. He then took his first biochemistry class with Charles West, now a professor emeritus of chemistry and biochemistry. Harada’s life changed. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“It dawned on me,” said Harada, “that what this guy is saying is that all of life is just directed chemistry.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>With a new outlook, Harada spent the succeeding years completing a B.S. in biochemistry and followed that degree with a Ph.D. in biochemistry from the University of Washington. Along the way, he discovered an affinity for the complexities of biochemistry. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Today, Harada focuses his research on seeds and the gene networks governing their development. With his colleagues, he’s using techniques called laser capture microdissection and chromatin immunoprecipitation to understand the underlying genetics of seeds to help make an important food source even more nutritious. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“Seeds feed the world,” said Professor Harada, Department of Plant Biology. “It’s been estimated that 75 percent of the calories that are consumed by humans actually come from seeds.”</span></span></span></span></span></span></p> </blockquote> <p><span><span><span><span><span><span>“If you can change the nutritional quality of seeds, or the number of seeds or the size of the seeds that crops are able to produce then you can increase yields,” he added. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>On top of his research, Harada has served as the College of Biological Sciences’ Executive Associate Dean of Academic Affairs for the past six years. He stepped down from the post at the end of June.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“As the primary academic executive officer for the college, John administers faculty personnel matters and provides thought leadership and collaborates across many academic areas,” said College of Biological Sciences Dean Mark Winey. “He’s has been an instrumental force in shaping the vision, direction and outreach of many of our programs.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>During Harada’s term, the campus initiated a new process to advance faculty through the merit and promotion system.  Harada said “Implementation of the step plus system has allowed CBS faculty to be rewarded not only for their outstanding research, but also for their excellence in teaching and service.”</span></span></span></span></span></span></p> <figure role="group" class="caption caption-img"><img alt="John Harada" data-entity-type="file" data-entity-uuid="af08e9ba-f4c4-43e1-ac6f-85819748492b" src="/sites/g/files/dgvnsk2646/files/inline-images/John-Harada-College-of-Biological-Sciences-UC-Davis-7.jpg" /><figcaption>Like a conductor trying to orchestrate a sublime performance, Harada is trying to figure out the genetic balance that leads to healthy and nutritious seeds. David Slipher/UC Davis</figcaption></figure><h4><span><span><span><strong><span><span><span>Sowing the seeds of scientific progress</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>By 1981, the year Harada received a Ph.D. degree, molecular biology was a nascent but budding field. </span></span></span></span></span></span></p> <figure role="group" class="caption caption-img align-right"><img alt="John Harada" data-entity-type="file" data-entity-uuid="4adb0d3c-ef73-4d6d-b5a6-48e1df42a60d" height="436" src="/sites/g/files/dgvnsk2646/files/inline-images/Harada-College-of-Biological-Sciences-UC-Davis-10-Crop.jpg" width="310" /><figcaption>Harada participates in a meeting between UC Davis and Osaka University educators at the launch of a new <a href="https://biology.ucdavis.edu/news/kirin-osaka-university-uc-davis-exchange-program">biotechnology research and training program</a>. David Slipher/UC Davis</figcaption></figure><p><span><span><span><span><span><span>Harada returned to UCLA and took a postdoctoral position in the lab of Bob Goldberg, now a distinguished professor of molecular, cell and development biology. In the Goldberg Lab, Harada worked on plant genetics, examining the genes responsible for producing a class of storage proteins in soybean seeds. It was “the bad old days of biology,” according to Harada, and while the technology available at the time was making waves, it was cumbersome compared to the later revolution of genomic sequencing in the 1990s. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“Now we’re in the age of high-throughput sequencing, so now people just sequence genomes; they sequence transcriptomes,” he said. “It’s really amazing. It tells you that many of the major advances in biology are dictated by technology.” </span></span></span></span></span></span></p> </blockquote> <p><span><span><span><span><span><span>Before, the process of determining what genes are active consisted of taking cloned DNA copies of a messenger RNA, separating their strands and allowing them to reconnect with RNA. Via this process, researchers could measure the level at which a gene is expressed.  </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>In 1984, following his postdoctoral work, Harada joined the UC Davis faculty. He was attracted to the campus for its reputation in plant biology and agriculture. Though he was interested in plants, Harada didn’t actually have any formal training in plant biology. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“I wanted to go to a place where if I had questions, I could ask people,” he said. “I found out when I got here, I could ask people specific questions about plant biology and in many cases, the world expert was on the faculty here.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“There were no downsides to coming to UC Davis,” he added. “The faculty here is outstanding.”  </span></span></span></span></span></span></p> <figure role="group" class="caption caption-img"><img alt="Seed development" data-entity-type="file" data-entity-uuid="ff477ef3-fea2-4212-a3d6-802414f3b8a8" src="/sites/g/files/dgvnsk2646/files/inline-images/Seed-Development-2-College-of-Biological-Sciences-UC-Davis.jpg" /><figcaption>Using laser capture microdissection and chromatin immunoprecipitation experiments, Harada and his colleagues peer at the organization of the seed’s gene networks throughout its developmental process, from morphogenesis to maturation. USDA</figcaption></figure><h4><span><span><span><strong><span><span><span>Fostering collaboration and exploring seed genetic networks</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>That mentality of collaboration that initially attracted Harada to UC Davis is something he’s helped the college nurture over the years. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“Most of graduate education in the U.S. is department-based,” said Harada. “A lot of the reason why I think there’s such great collaboration at UC Davis is because of the graduate group system.”</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Unlike a department-based system, graduate groups at UC Davis run university-wide, meaning faculty with appointments across many different departments, colleges and schools on campus can participate in graduate curriculum and instruction based on their subject matter expertise. Harada is a member of the Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, the Integrative Genetics and Genomics Graduate Group and the Plant Biology Graduate Group, which each offer specialties and focus areas. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“These students are taking different classes, having different experiences and yet, they’re all in the same lab, so they can teach each other,” he said. “This integration often encourages interdisciplinary research.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>After stepping down from his post as executive associate dean for academic affairs, Harada will continue his genetic research on seed development. Currently, Harada, his lab members and colleagues with UCLA’s Goldberg Lab are collaborating on a National Science Foundation-funded project </span></span></span><a href="http://seedgenenetwork.net/"><span><span><span>to understand the genes underlying the soybean seed</span></span></span></a><span><span><span>.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Using laser capture microdissection and chromatin immunoprecipitation experiments, Harada and his colleagues peer at the organization of the seed’s gene networks throughout its developmental process, from morphogenesis to maturation. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“We can watch this developmental shift occurring in what genes are turning on and turning off, and where they’re turning on and off in different parts of the seed,” he said. “We’ve been really able to obtain lots of insights into what’s occurring in the seeds that people really didn’t know about before.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Like a conductor trying to orchestrate a sublime performance, Harada is trying to figure out the genetic balance that leads to healthy and nutritious seeds.</span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“It’s been estimated that by the year 2050, we’re going to need to be able to produce anywhere between 70 to 100 percent more food than we produce now,” he said. “We have to do that in the face of global climate change.  Hopefully, the information that we generate will help to meet this challenge.”</span></span></span></span></span></span></p> </blockquote> <p class="text-align-center"><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></p> <figure role="group" class="caption caption-img"><img alt="John Harada" data-entity-type="file" data-entity-uuid="abee3282-f33c-4606-b2a9-e5e71a8f048d" src="/sites/g/files/dgvnsk2646/files/inline-images/John-Harada-College-of-Biological-Sciences-UC-Davis-4.jpg" /><figcaption>Harada will continue his genetic research on seed development. David Slipher/UC Davis</figcaption></figure></div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/campus-community" hreflang="en">Campus and Community</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/plant-biology-0" hreflang="en">Department of Plant Biology</a></div> <div class="field__item"><a href="/tags/seeds" hreflang="en">seeds</a></div> <div class="field__item"><a href="/tags/climate-change" hreflang="en">climate change</a></div> <div class="field__item"><a href="/tags/food" hreflang="en">food</a></div> <div class="field__item"><a href="/tags/food-science" hreflang="en">food science</a></div> <div class="field__item"><a href="/tags/agriculture" hreflang="en">agriculture</a></div> </div> </div> Mon, 01 Jul 2019 15:52:21 +0000 Greg Watry 3296 at https://biology.ucdavis.edu Discovering Curiosity: The Cycle of Mentorship with Assistant Professor of Teaching Marina Crowder https://biology.ucdavis.edu/news/discovering-curiosity-cycle-mentorship-assistant-professor-teaching-marina-crowder <span class="field field--name-title field--type-string field--label-hidden">Discovering Curiosity: The Cycle of Mentorship with Assistant Professor of Teaching Marina Crowder</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/5451" typeof="schema:Person" property="schema:name" datatype="">Greg Watry</span> </span> <span class="field field--name-created field--type-created field--label-hidden">June 25, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/UC-Davis-College-of-Biological-Sciences-Marina-Crowder-Teaching.jpg?h=005b3b73&amp;itok=J93xLepd" width="1280" height="720" alt="Marina Crowder" title="An assistant professor of teaching in the Department of Molecular and Cellular Biology, Marina Crowder teaches hundreds of UC Davis students each quarter. Courtesy photo" typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary Assistant Professor of Teaching Marina Crowder was inspired by her own mentors to pursue a career in teaching and mentorship A UC Davis alum, Crowder worked in the labs of Professors JoAnne Engebrecht and Francis McNally as a student Today, she teaches courses like &quot;Genes and Gene Expression&quot; and “Introduction to Human Heredity,” and recently developed the course “History of Cancer” As a freshman at UC Davis, Marina Crowder didn’t have time for undergraduate research. A first-generation college student, Crowder just wanted to get her bearings. She focused her attention on her classes. And when she wasn’t in class, she worked as a restaurant server to support herself. But during the winter break of her sophomore year, Crowder was in a car accident, one so severe she had to withdraw from classes for a quarter. “The car accident kind of switched my thinking in realizing that time is going by fast and I need to get involved in something more than just going to class,” said Crowder. Upon her return to campus, she enrolled in BIS 101 “Genes and Gene Expression,” then taught by Professor JoAnne Engebrecht, Department of Molecular and Cellular Biology. “It was my first upper division genetics class and I absolutely loved it and I absolutely loved the professor,” said Crowder. Encouraged by her friends, Crowder approached Engebrecht and asked if there were any undergraduate research opportunities in her lab. There were. In the Engebrecht Lab, Crowder studied sex-specific differences in the nematode Caenorhabditis elegans with respect to the regulation and timing of meiosis, the division process for producing gametes. The experience led to her first publication in the journal Developmental Biology.      “They really involved me in the project and I got to do my own experiments and really was able to make meaningful contributions,” she said. “It was huge as a first-generation student.” In a cyclical twist of fate, Crowder now occupies the role Engebrecht once held for her, as a mentor and the current instructor for BIS 101. Now an assistant professor of teaching in the Department of Molecular and Cellular Biology, Crowder teaches hundreds of UC Davis students each quarter. “Every day it’s surreal for me when I teach BIS 101 because I identify that course as completely changing my career and my life,” said Crowder. “I really hope that my class can have some kind of impact like that on some of the students I teach.” Wriggling worms and jumping frogs Crowder worked in the lab of Professor Rebecca Heald at UC Berkeley. In this picture, she&#039;s collecting newt eggs in the UC Berkeley Botanical Garden. Courtesy photoBy the time she graduated in 2007 with a B.S. in Genetics, Crowder was more familiar with the research landscape. She stayed at UC Davis for graduate school and joined the lab of Professor Francis McNally, Department of Molecular and Cellular Biology, where she continued her investigations into meiosis in C. elegans. Only this time, she zeroed in on female meiosis, specifically the molecular mechanisms governing the positioning of the meiotic spindle, the scaffolding necessary for proper cell division. As she wrapped up her Ph.D. studies, Crowder looked to her next steps. Where did her passions lie? She liked the workbench but also wanted to explore career options outside the lab. With support from her mentors, she enrolled in a faculty diversity internship program run by the Los Rios Community College District. For six months, Crowder taught an introduction to biology class for non-majors while continuing her Ph.D. studies. “I had TA experience, but it was the first time that I had thought about teaching as a craft,” she said. It “opened my eyes to professional development and the intentional practice that goes into being an effective teacher.” Crowder finished a Ph.D. in Biochemistry, Molecular, Cellular and Developmental Biology, and afterward headed further west for a postdoctoral position in the lab of Professor Rebecca Heald, Department of Molecular and Cellular Biology at UC Berkeley. It was as far as Crowder was willing to move. Her father had recently passed away and she wanted to stay close to her mother. “Moving across the country was just not in the cards for me,” she said. Working in the Heald Lab required Crowder to switch model systems. She no longer dealt in wriggling worms. Instead, she focused on the jumping African clawed frog (Xenopus laevis). “Typically when you do a postdoc, you’re encouraged to either switch to a different subfield or switch to a different model to gain new experiences,” she said. “I switched model systems but continued my interest in meiosis and mitosis and the underlying molecular mechanisms of spindle architecture and function.” When she moved to her postdoctoral position, Crowder switched from studying nematodes to studying the African clawed frog (Xenopus laevis). Brian Gratwicke The tug to teach Again, Crowder felt the draw to teach. While in her postdoctoral role, she found an opportunity to design and teach her own course at Laney College, a community college in Oakland. The course focused on scientific communications in the biomanufacturing and biopharmaceutical fields. “I did not consider myself any type of expert on scientific communication but they gave me this course,” she said. “It was really empowering and I learned that I could do this.” For three years, Crowder worked in the Heald Lab, her work funded by the Ruth L. Kirschstein Postdoctoral Fellowship from the National Institutes of Health. There was about a year or two left in her funding when her alma mater posted a job opening that Crowder couldn’t pass up. “There was a new teaching faculty position that…opened up in the Department of Molecular and Cellular Biology and it just seemed like a perfect fit,” she said. “I couldn’t pass up applying for this job.” Crowder landed the job and returned to Aggieland. As an assistant professor of teaching, Crowder focuses heavily on engaging with undergraduate students at UC Davis. She teaches BIS 101, MCB 10 “Introduction to Human Heredity,” among other courses and recently developed the MCB23 course “History of Cancer.” While her classes tend to be large, numbering in the hundreds, Crowder wants to ensure each student feels the experience is worthwhile. Part of that is creating a space where her students feel comfortable, that they’re heard and that they’re individuals, not just a face among a sea of faces. To accomplish this, Crowder uses the lecture hall space, moving among the rows of students, creating intimate engagement through proximity. “I see my role as facilitating them to engage with the content and think about it in different ways,” she said. “Biology for me is fascinating, and it’s beautiful and I love it because we’re always learning something.” “It’s just fascinating, the way things work,” she added. Stay Informed! Sign up for our monthly email newsletter "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "An assistant professor of teaching in the Department of Molecular and Cellular Biology, Marina Crowder teaches hundreds of UC Davis students each quarter. From BIS 101 &quot;Gene and Gene Expression&quot; to MCB23 &quot;History of Cancer,&quot; Crowder doesn&#039;t just want her students to learn the material from class; she wants them to engage with it. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><em><strong>Assistant Professor of Teaching Marina Crowder was inspired by her own mentors to pursue a career in teaching and mentorship</strong></em></li> <li><em><strong>A UC Davis alum, Crowder worked in the labs of Professors JoAnne Engebrecht and Francis McNally as a student</strong></em></li> <li><em><strong>Today, she teaches courses like <span><span><span><span><span><span>"Genes and Gene Expression" and “Introduction to Human Heredity,” and recently developed the course “History of Cancer” </span></span></span></span></span></span></strong></em></li> </ul></div> </aside><p><span><span><span><span><span><span>As a freshman at UC Davis, Marina Crowder didn’t have time for undergraduate research. A first-generation </span></span></span></span></span></span><span><span><span><span><span><span>college student, Crowder just wanted to get her bearings. She focused her attention on her classes. And when she wasn’t in class, she worked as a restaurant server to support herself. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>But during the winter break of her sophomore year, Crowder was in a car accident, one so severe she had to withdraw from classes for a quarter.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“The car accident kind of switched my thinking in realizing that time is going by fast and I need to get involved in something more than just going to class,” said Crowder. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Upon her return to campus, she enrolled in BIS 101 “Genes and Gene Expression,” then taught by Professor JoAnne Engebrecht, Department of Molecular and Cellular Biology. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“It was my first upper division genetics class and I absolutely loved it and I absolutely loved the professor,” said Crowder. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Encouraged by her friends, Crowder approached Engebrecht and asked if there were any undergraduate research opportunities in her lab. There were.</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>In the </span></span></span><a href="https://jengebre.faculty.ucdavis.edu/"><span><span><span>Engebrecht Lab</span></span></span></a><span><span><span>, Crowder studied sex-specific differences in the nematode <em>Caenorhabditis elegans </em>with respect to the regulation and timing of meiosis, the division process for producing gametes. The experience led to her first publication in the journal </span></span></span><a href="https://www.sciencedirect.com/science/article/pii/S0012160607010433?via%3Dihub"><em><span><span><span>Developmental Biology</span></span></span></em></a><em><span><span><span>. </span></span></span></em><span><span><span> <em> </em>  </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“They really involved me in the project and I got to do my own experiments and really was able to make meaningful contributions,” she said. “It was huge as a first-generation student.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>In a cyclical twist of fate, Crowder now occupies the role Engebrecht once held for her, as a mentor and the current instructor for BIS 101. Now an assistant professor of teaching in the Department of Molecular and Cellular Biology, Crowder teaches hundreds of UC Davis students each quarter. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“Every day it’s surreal for me when I teach BIS 101 because I identify that course as completely changing my career and my life,” said Crowder. “I really hope that my class can have some kind of impact like that on some of the students I teach.” </span></span></span></span></span></span></p> </blockquote> <h4><span><span><span><strong><span><span><span>Wriggling worms and jumping frogs</span></span></span></strong></span></span></span></h4> <figure role="group" class="caption caption-img align-right"><img alt="Marina Crowder" data-entity-type="file" data-entity-uuid="d198d008-18a6-4403-b50f-4d1e28a073f9" height="410" src="/sites/g/files/dgvnsk2646/files/inline-images/UC-Davis-College-of-Biological-Sciences-Marina-Crowder-Postdoctoral.jpg" width="415" /><figcaption>Crowder worked in the lab of Professor Rebecca Heald at UC Berkeley. In this picture, she's collecting newt eggs in the UC Berkeley Botanical Garden. Courtesy photo</figcaption></figure><p><span><span><span><span><span><span>By the time she graduated in 2007 with a B.S. in Genetics, Crowder was more familiar with the research landscape. She stayed at UC Davis for graduate school and joined the lab of Professor Francis McNally, Department of Molecular and Cellular Biology, where she continued her investigations into meiosis in <em>C. elegans. </em>Only this time, she zeroed in on female meiosis, specifically the molecular mechanisms governing the positioning of the meiotic spindle, the scaffolding necessary for proper cell division. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>As she wrapped up her Ph.D. studies, Crowder looked to her next steps. Where did her passions lie? She liked the workbench but also wanted to explore career options outside the lab. With support from her mentors, she enrolled in a faculty diversity internship program run by the Los Rios Community College District. For six months, Crowder taught an introduction to biology class for non-majors while continuing her Ph.D. studies. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“I had TA experience, but it was the first time that I had thought about teaching as a craft,” she said. It “opened my eyes to professional development and the intentional practice that goes into being an effective teacher.”</span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Crowder finished a Ph.D. in Biochemistry, Molecular, Cellular and Developmental Biology, and afterward headed further west for a postdoctoral position in the lab of Professor Rebecca Heald, Department of Molecular and Cellular Biology at UC Berkeley. It was as far as Crowder was willing to move. Her father had recently passed away and she wanted to stay close to her mother. “Moving across the country was just not in the cards for me,” she said. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Working in the Heald Lab required Crowder to switch model systems. She no longer dealt in wriggling worms. Instead, she focused on the jumping African clawed frog (<em>Xenopus laevis</em>). </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“Typically when you do a postdoc, you’re encouraged to either switch to a different subfield or switch to a different model to gain new experiences,” she said. “I switched model systems but continued my interest in meiosis and mitosis and the underlying molecular mechanisms of spindle architecture and function.”</span></span></span></span></span></span></p> </blockquote> <figure role="group" class="caption caption-img"><img alt="Frog" data-entity-type="file" data-entity-uuid="be0e833a-f7e1-404b-9320-9730d7053bbf" src="/sites/g/files/dgvnsk2646/files/inline-images/UC-Davis-College-of-Biological-Sciences-Marina-Crowder-Frog.jpg" /><figcaption>When she moved to her postdoctoral position, Crowder switched from studying nematodes to studying the African clawed frog (<em>Xenopus laevis). Brian Gratwicke </em></figcaption></figure><h4><span><span><span><strong><span><span><span>The tug to teach</span></span></span></strong></span></span></span></h4> <p><span><span><span><span><span><span>Again, Crowder felt the draw to teach. While in her postdoctoral role, she found an opportunity to design and teach her own course at Laney College, a community college in Oakland. The course focused on scientific communications in the biomanufacturing and biopharmaceutical fields. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“I did not consider myself any type of expert on scientific communication but they gave me this course,” she said. “It was really empowering and I learned that I could do this.” </span></span></span></span></span></span></p> </blockquote> <p><span><span><span><span><span><span>For three years, Crowder worked in the Heald Lab, her work funded by the Ruth L. Kirschstein Postdoctoral Fellowship from the National Institutes of Health. There was about a year or two left in her funding when her alma mater posted a job opening that Crowder couldn’t pass up. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>“There was a new teaching faculty position that…opened up in the Department of Molecular and Cellular Biology and it just seemed like a perfect fit,” she said. “I couldn’t pass up applying for this job.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>Crowder landed the job and returned to Aggieland. </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>As an assistant professor of teaching, Crowder focuses heavily on engaging with undergraduate students at UC Davis. She teaches BIS 101, MCB 10 “Introduction to Human Heredity,” among other courses and recently developed the MCB23 course “History of Cancer.” </span></span></span></span></span></span></p> <p><span><span><span><span><span><span>While her classes tend to be large, numbering in the hundreds, Crowder wants to ensure each student feels the experience is worthwhile. Part of that is creating a space where her students feel comfortable, that they’re heard and that they’re individuals, not just a face among a sea of faces. To accomplish this, Crowder uses the lecture hall space, moving among the rows of students, creating intimate engagement through proximity. </span></span></span></span></span></span></p> <blockquote> <p><span><span><span><span><span><span>“I see my role as facilitating them to engage with the content and think about it in different ways,” she said. “Biology for me is fascinating, and it’s beautiful and I love it because we’re always learning something.” </span></span></span></span></span></span></p> </blockquote> <p><span><span><span><span><span><span>“It’s just fascinating, the way things work,” she added. </span></span></span></span></span></span></p> <p class="text-align-center"><em><strong><a class="btn--lg btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></strong></em></p> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/campus-community" hreflang="en">Campus and Community</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/discovering-curiosity" hreflang="en">Discovering Curiosity</a></div> <div class="field__item"><a href="/tags/molecular-and-cellular-biology" hreflang="en">Department of Molecular and Cellular Biology</a></div> <div class="field__item"><a href="/tags/mentorship" hreflang="en">mentorship</a></div> <div class="field__item"><a href="/tags/women-stem" hreflang="en">Women in STEM</a></div> <div class="field__item"><a href="/tags/chromosomes" hreflang="en">chromosomes</a></div> <div class="field__item"><a href="/tags/model-organisms" hreflang="en">model organisms</a></div> <div class="field__item"><a href="/tags/cancer" hreflang="en">cancer</a></div> </div> </div> Tue, 25 Jun 2019 16:50:23 +0000 Greg Watry 3286 at https://biology.ucdavis.edu Kirin Joins Osaka University and UC Davis to Train the Next Generation of Plant Biotechnologists https://biology.ucdavis.edu/news/kirin-osaka-university-uc-davis-exchange-program <span class="field field--name-title field--type-string field--label-hidden">Kirin Joins Osaka University and UC Davis to Train the Next Generation of Plant Biotechnologists</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/16" typeof="schema:Person" property="schema:name" datatype="">David Slipher</span> </span> <span class="field field--name-created field--type-created field--label-hidden">June 24, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/Osaka-Kirin-Exchange-Program-College-of-Biological-Sciences-UC-Davis-3.jpg?h=06ac0d8c&amp;itok=TZDaQDfg" width="1280" height="720" alt="leadership from Osaka University, UC Davis and Kirin" title="Leaders from Kirin, Osaka University and UC Davis gathered on campus Friday, June 21 to formally sign the exchange agreement. From left to right: Professor Eiichiro Fukusaki, Graduate School of Engineering, Osaka University; Takahiro Nagafuchi, manager, Plant Biotechnology Project and Legal Department, Kirin; Professor Emeritus Raymond Rodriguez, Department of Molecular and Cellular Biology, UC Davis; Hiroshi Okawa, plant biotechnology project leader, Kirin; Professor Kazuhito Fujyama, director of the International Center for Biotechnology, Osaka University; Mark Winey, dean of the College of Biological Sciences, UC Davis; Joanna Regulska vice provost and associate chancellor, Global Affairs, UC Davis; Professor Genta Kawahara, vice president of global engagement, Osaka University; and Hiroyuki Naganuma, manager, Project Planning Section, R&amp;D Division, Kirin." typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary The exchange partnership will focus on the research and development of plant-made-pharmaceuticals (PMPs) Graduate students will spend up to a month conducting research alongside faculty at each location The cross-cultural experience will help develop the skills and international mindset needed by a new generation of plant biotechnicians Educators from Osaka University and the University of California, Davis are proud to announce the launch of a new biotechnology research and training program between Japan and the United States. The approximately $23,000 in initial support comes from Kirin Holdings Company, an international food, beverage and pharmaceutical wellness brand. Graduate students from both universities will gain access to world-class research facilities and professional training across many areas of plant biotechnology, with an emphasis on human health. By traveling between Osaka University and UC Davis, graduate students and their faculty mentors will share cross-cultural experiences that grow scientific knowledge—and potential new technologies.  “We are happy to expand our global engagement with the United States,” said Professor Genta Kawahara, vice president of global engagement at Osaka University. “The UC system, especially UC Davis, is Osaka University’s closest and strongest international partner.” Bridging the Pacific Global exposure will help future plant biotechnicians to solve global problems. David Slipher/UC DavisOn Friday, June 21, leadership from Kirin and Osaka University traveled to the UC Davis campus for a ceremonial signing of the international agreement. “The future of biology research will come through international collaboration, mentorship and technology exchange,” said Mark Winey, dean of the UC Davis College of Biological Sciences. “The exchange program, thanks to the generous support of Kirin CEO Yoshinori Isozaki, creates a wonderful opportunity to share, innovate and provide students with an international research experience.” The College of Biological Sciences has pledged $10,000 to support the new partnership. The College of Engineering will also partner in the endeavor. “This partnership is an alliance to solve the difficult, multidisciplinary problems that challenge the global community,” said Ricardo H.R. Castro, executive associate dean of research and graduate studies and professor of materials science and engineering in the College of Engineering. “We are happy to partner with the College of Biological Sciences, Osaka University and Kirin, hoping to bring engineering aspects to support the translation of science for novel plant-based therapeutics.” One goal of the exchange program is to help train the next generation of plant biotechnologists, giving them the perspectives and skills to move seamlessly between countries and cultures to address research problems of global importance. “Given the complexity of today’s global challenges, partnering with other universities and with industry is critical, particularly as we strive to prepare our students for today’s interconnected and multicultural world,” said Joanna Regulska, UC Davis vice provost and associate chancellor, Global Affairs. The exchange partnership between Osaka University and UC Davis will explore new research and applications for plant-made pharmacueticals. David Slipher/UC Davis Promoting global research and multicultural understanding The program will promote student mobility across borders and provide access to the world-class research experiences and international perspectives needed to solve our planet’s toughest challenges. What&#039;s in an identity? The 3 leaves are the program’s scientific themes: plant molecular biology, chemical engineering and human health The helix-like structure underscores the importance of genes, genetics and nucleic acids The 3 outer rings represent the colors of the partners; blue for Osaka University, blue/gold for UC Davis and red for Kirin The rings are ancient symbols representing unity, wholeness and perfection—attributes aspired to by all program participants “Society is currently facing many global threats to human health and wellbeing,” said Raymond Rodriguez, exchange program chairman and UC Davis professor emeritus of molecular and cellular biology. “Whether it be Ebola or global warming, we need a new kind of mission-oriented, interdisciplinary scientist capable of working in diverse teams to quickly address these threats in safe, sustainable and environmentally friendly ways.” “Many students (in Japan) know about US culture, but they have not seen it in reality,” said Professor Kazuhito Fujyama, director of the Osaka University International Center for Biotechnology. “Through these kinds of experiences they learn not only scientific, but cultural differences.” Kirin research scientists will assist both universities in identifying and developing plant-made pharmaceuticals (PMPs) to strengthen the company’s growing pharmaceutical and biotechnology sectors. “Supporting new research in academia is a key role for our company,” said Hiroshi Okawa, plant biotechnology project leader with Kirin. “Each university knows about their own industries, so by joining together we can expand our knowledge of and capacity for global business.” About Osaka University Officially founded 1931, Osaka University is considered one of Japan’s top public research universities and its academic ties go back to 1724. Osaka University is located in the Kansai region of Honshu, Japan’s main island. Researchers from Osaka University and UC Davis have collaborated on more than 185 publications since 2013. About Kirin Holdings Company With a focus on lifestyle and health, Kirin aims to become a global leader in food, beverages and pharmaceuticals. Support for the new exchange program reinforces Kirin’s KV2027 plan, an aspirational vision for the company’s future.  Kirin is a Global Fortune 500 company. Stay Informed! Sign up for our monthly email newsletter The full delegation from Kirin, Osaka University and UC Davis attended the formal signing event on Friday, June 21. David Slipher/UC Davis  "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "Educators from Osaka University and UC Davis are proud to announce the launch of a new biotechnology research and training program between Japan and the United States. Graduate students from both universities will gain access to world-class research facilities and professional training across many areas. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><em><strong>The exchange partnership will focus on the research and development of plant-made-pharmaceuticals (PMPs)</strong></em></li> <li><em><strong>Graduate students will spend up to a month conducting research alongside faculty at each location</strong></em></li> <li><em><strong>The cross-cultural experience will help develop the skills and international mindset needed by a new generation of plant biotechnicians</strong></em></li> </ul></div> </aside><p><span><span><span><span>Educators from Osaka University and the University of California, Davis are proud to announce the launch of a new biotechnology research and training program between Japan and the United States. The approximately $23,000 in initial support comes from Kirin Holdings Company, an international food, beverage and pharmaceutical wellness brand.</span></span></span></span></p> <p><span><span><span><span>Graduate students from both universities will gain access to world-class research facilities and professional training across many areas of plant biotechnology, with an emphasis on human health. By traveling between Osaka University and UC Davis, graduate students and their faculty mentors will share cross-cultural experiences that grow scientific knowledge—and potential new technologies. </span></span></span></span></p> <blockquote> <p><span><span><span><span>“We are happy to expand our global engagement with the United States,” said Professor Genta Kawahara, vice president of global engagement at Osaka University. “The UC system, especially UC Davis, is Osaka University’s closest and strongest international partner.”</span></span></span></span></p> </blockquote> <h3><span><span><span><strong><span>Bridging the Pacific</span></strong></span></span></span></h3> <figure role="group" class="caption caption-img align-right"><img alt="plant samples" data-entity-type="file" data-entity-uuid="6a87b405-39e5-4ca1-913b-78398a172069" height="301" src="/sites/g/files/dgvnsk2646/files/inline-images/plant-samples-College-of-Biological-Sciences-UC-Davis_1.jpg" width="453" /><figcaption>Global exposure will help future plant biotechnicians to solve global problems. David Slipher/UC Davis</figcaption></figure><p><span><span><span>On Friday, June 21, leadership from Kirin and Osaka University traveled to the UC Davis campus for a ceremonial <span>signing of the international agreement.</span></span></span></span></p> <p><span><span><span><span>“The future of biology research will come through international collaboration, mentorship and technology exchange,” said Mark Winey, dean of the UC Davis College of Biological Sciences. “The exchange program, thanks to the generous support of Kirin CEO Yoshinori Isozaki, creates a wonderful </span>opportunity to share, innovate and provide students with an international research experience.” </span></span></span></p> <p><span><span><span>The College of Biological Sciences has pledged $10,000 to support the new partnership. The College of Engineering will also partner in the endeavor.</span></span></span></p> <p><span><span><span><span>“This partnership is an alliance to solve the difficult, multidisciplinary problems that challenge the global community,” said Ricardo H.R. Castro, executive associate dean of research and graduate studies and professor of materials science and engineering in the College of Engineering. “We are</span></span></span></span><span><span><span><span> happy to partner with the College of Biological Sciences, Osaka University and Kirin, hoping to bring engineering aspects to support the translation of science for novel plant-based therapeutics.”</span></span></span></span></p> <p><span><span><span><span>One goal of the exchange program is to help train the next generation of plant biotechnologists, giving them the perspectives and skills to move seamlessly between countries and cultures to address research problems of global importance.</span></span></span></span></p> <blockquote> <p><span><span><span>“Given the complexity of today’s global challenges, partnering with other universities and with industry is critical, particularly as we strive to prepare our students for today’s interconnected and multicultural world,” said Joanna Regulska, UC Davis v</span>ice provost and associate chancellor, Global Affairs<span>. </span></span></span></p> <figure role="group" class="caption caption-img align-center"><img alt="signing documents on table" data-entity-type="file" data-entity-uuid="d101a6bc-b641-43e2-98ec-ab5ec69f64ea" src="/sites/g/files/dgvnsk2646/files/inline-images/Osaka-Kirin-Exchange-Program-College-of-Biological-Sciences-UC-Davis-2.jpg" /><figcaption>The exchange partnership between Osaka University and UC Davis will explore new research and applications for plant-made pharmacueticals. David Slipher/UC Davis</figcaption></figure></blockquote> <h3><span><span><span><strong>Promoting global research and multicultural understanding</strong></span></span></span></h3> <p><span><span><span>The program will promote student mobility across borders and provide access to the world-class research experiences and international perspectives needed to solve our planet’s toughest challenges.</span></span></span></p> <aside class="wysiwyg-feature-block u-width--half u-align--left"><h3 class="wysiwyg-feature-block__title">What's in an identity?</h3> <div class="wysiwyg-feature-block__body"><img alt="logo poster" data-entity-type="file" data-entity-uuid="f0aeb469-97c0-423a-a742-b4ecb2526ef7" height="364" src="/sites/g/files/dgvnsk2646/files/inline-images/Joint-Signing-Ceremony-UC-Davis-1_0.jpg" width="364" class="align-center" /><ol><li><strong><span><span><span>The</span></span></span></strong><strong><span><span><span> 3 leaves are the program’s scientific themes: plant molecular biology, chemical engineering and human health</span></span></span></strong></li> <li><strong><span><span><span>The helix-like structure underscores the importance of genes, genetics and nucleic acids </span></span></span></strong></li> <li><strong><span><span><span>The 3 outer rings represent the colors of the partners; blue for Osaka University, blue/gold for UC Davis and red for Kirin</span></span></span></strong></li> <li><strong><span><span><span>The rings are ancient symbols representing unity, wholeness and perfection—attributes aspired to by all program participants</span></span></span></strong></li> </ol></div> </aside><blockquote> <p><span><span><span><span>“Society is currently facing many global threats to human health and wellbeing,” said Raymond Rodriguez, </span>exchange program chairman<span> and UC Davis professor emeritus of molecular and cellular biology. “Whether it be Ebola or global warming, we need a new kind of mission-oriented, interdisciplinary scientist capable of working in diverse teams to quickly address these threats in safe, sustainable and </span></span>environmentally friendly<span><span> ways.”</span></span></span></span></p> </blockquote> <p><span><span><span>“Many students (in Japan) know about US culture, but they have not seen it in reality,” said Professor Kazuhito Fujyama, director of the Osaka University International Center for Biotechnology.<strong> </strong>“Through these kinds of experiences they learn not only scientific, but cultural differences.”</span></span></span></p> <p><span><span><span><span>Kirin research scientists will assist both universities in identifying and developing plant-made pharmaceuticals (PMPs) to strengthen the company’s growing pharmaceutical and biotechnology sectors.</span></span></span></span></p> <p><span><span><span><span>“Supporting new research in academia is a key role for our company,” said Hiroshi Okawa, plant biotechnology project leader with Kirin. “Each university knows about their own industries, so by joining together we can expand our knowledge of and capacity for global business.”</span></span></span></span></p> <h4><span><span><span><strong><span>About Osaka University</span></strong></span></span></span></h4> <p><span><span><span><span>Officially founded 1931, </span><a href="https://www.osaka-u.ac.jp/en"><span>Osaka University</span></a><span> is considered one of Japan’s top public research universities and its academic ties go back to 1724. Osaka University is located in the Kansai region of Honshu, Japan’s main island. Researchers from Osaka University and UC Davis have collaborated on more than 185 publications since 2013.</span></span></span></span></p> <h4><span><span><span><strong><span>About Kirin Holdings Company</span></strong></span></span></span></h4> <p><span><span><span>With a focus on lifestyle and health, Kirin aims to become a global leader in food, beverages and pharmaceuticals. Support for the new exchange program reinforces Kirin’s <a href="https://www.kirinholdings.co.jp/english/news/2019/0214_01.html">KV2027</a><span><span> plan</span></span>, an aspirational vision for the company’s future. <strong> </strong></span>Kirin is a <a href="http://fortune.com/global500/2013/kirin-holdings-company-limited-496/">Global Fortune 500 company</a>.</span></span></p> <p class="text-align-center"><em><strong><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></strong></em></p> <figure role="group" class="caption caption-img align-center"><img alt="group photo" data-entity-type="file" data-entity-uuid="f4ede293-24b4-42a5-857e-5d08e47b9f2d" src="/sites/g/files/dgvnsk2646/files/inline-images/Osaka-Kirin-Exchange-Program-College-of-Biological-Sciences-UC-Davis-4.jpg" /><figcaption>The full delegation from Kirin, Osaka University and UC Davis attended the formal signing event on Friday, June 21. David Slipher/UC Davis</figcaption></figure><p> </p> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/food-agriculture-plants" hreflang="en">Food, Agriculture and Plant Biology</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/graduate-student-news" hreflang="en">Graduate Student News</a></div> <div class="field__item"><a href="/tags/philanthropy" hreflang="en">philanthropy</a></div> <div class="field__item"><a href="/tags/global-education" hreflang="en">global education</a></div> <div class="field__item"><a href="/tags/exchange-programs" hreflang="en">exchange programs</a></div> <div class="field__item"><a href="/tags/plant-biology" hreflang="en">plant biology</a></div> </div> </div> Mon, 24 Jun 2019 16:54:29 +0000 David Slipher 3281 at https://biology.ucdavis.edu From Sheep and Cattle to Giraffes, Genome Study Reveals Evolution of Ruminants https://biology.ucdavis.edu/news/sheep-and-cattle-giraffes-genome-study-reveals-evolution-ruminants <span class="field field--name-title field--type-string field--label-hidden">From Sheep and Cattle to Giraffes, Genome Study Reveals Evolution of Ruminants</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/5936" typeof="schema:Person" property="schema:name" datatype="">Lisa Howard</span> </span> <span class="field field--name-created field--type-created field--label-hidden">June 21, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/20190319-baby-animals-5584.jpg?h=c07b8def&amp;itok=nJKwtrjK" width="1280" height="720" alt="Sheep" title="A lamb and ewe at the UC Davis Sheep Barn. Ruminants such as sheep, goats, cattle and deer are among the most successful and widespread groups of mammals. A new study of genomes of 44 wild and domesticated ruminants sheds light on their evolution and success, especially their unique digestive system. (UC Davis photo)" typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="Quick Summary Ruminants are among the most successful wild mammals and valuable livestock 40 trillion base pairs went into mapping genomes of 44 species Public database will be valuable resource for science and breeding A team of researchers has carried out a detailed study of the genomes of ruminants, giving new insight into their evolution and success.  Ruminants including deer and antelope, as well as sheep, goats, cattle and their wild relatives, have thrived in many ecosystems around the globe. They range in size from the tiny lesser mouse deer of Malaysia to the towering African giraffe.   The new study published today (June 21) in Science and led by Wen Wang and Guojie Zhang at the Kunming Institute of Zoology, and Rasmus Heller at the University of Copenhagen, Denmark, included Professor Harris Lewin at the UC Davis Department of Evolution and Ecology and Genome Center.  Ruminants form an important part of U.S. and world agricultural systems. Farms and ranches have an estimated 95 million cattle in the U.S. alone, along with an estimated 5.2 million sheep and 2 million goats. “As ecosystems around the world begin to show the impact of climate change, knowing what the genes and their variants are can help with conservation efforts of threatened and endangered ruminant species. It can also provide resources to help mitigate the effects of climate change on agricultural commodities, such as breeding cattle, to be more adapted to warmer, drier climates,” said Lewin. The team generated more than 40 trillion base pairs of raw DNA sequences and assembled them into genomes for 44 species. Based on this data they were able to create a new family tree for ruminants — placing the largest (giraffe) and smallest (lesser mouse deer) on some of the earliest branches after ruminants emerged as a group 32 to 39 million years ago.  “The data produced in this study provides a foundational genomic roadmap for this ecologically and economically important group of mammals,” said Lewin, who also chairs the Earth BioGenome Project, a global effort to sequence the genetic code of all the planet’s eukaryotes — some 1.5 million known species, including all plants, animals, protozoa and fungi. “It is a tremendous resource not only for understanding how evolution has shaped ruminants, but also for understanding the basis of both desirable and undesirable traits, such as inherited diseases.” Genes for a unique digestive system All ruminants have a specialized, multichambered stomach that allows them to ferment the plants they eat using microbes and to bring material up for further chewing, aiding digestion. This highly specialized digestive system allows ruminants to make the most of a diet high in otherwise-indigestible cellulose.   The study showed that, among the 295 newly evolved genes identified in ruminants, many were associated with the digestive system, such as the structure and function of the compartmented stomach — the rumen, omasum and abomasum.  The team also identified a number of genes associated with horns and antlers. Ruminants typically have horns or antlers that can play a role in defense or mating behavior.  The researchers were also able to pinpoint evolutionary changes at the species level. As the tallest terrestrial animal, giraffes have a distinct stature and body shape, which likely are adaptions to their savanna habitat. The researchers found that among the 366 genes related to bone development, 115 genes had giraffe-specific mutations.  The ruminant genomes may also hold evidence of humans’ impact on these animals. When the researchers used a method to infer past population size, they found massive declines for more than half the species from 100,000 to 50,000 years ago — around the time modern humans left Africa and spread around the world.  The researchers have created the Ruminant Genome Database, a public collection of the genomic and transcriptomic data presented in their study. The work was supported by a number of agencies and foundations in China, Europe and the U.S. The UC Davis portion was funded by the U.S. Department of Agriculture and the Robert and Rosabel Osborne Endowment.  This story originally appeared on the UC Davis News website.  Media contact(s) Harris Lewin, Evolution and Ecology, lewin@ucdavis.edu Andy Fell, News and Media Relations, 530-752-4533, ahfell@ucdavis.edu Media Resources Read the paper (Science) Earth BioGenome Project Ruminant Genome Database Stay Informed! Sign up for our monthly email newsletter "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "A team of researchers has carried out a detailed study of the genomes of ruminants, giving new insight into their evolution and success. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><aside class="wysiwyg-feature-block u-width--half u-align--right"><h3 class="wysiwyg-feature-block__title">Quick Summary</h3> <div class="wysiwyg-feature-block__body"> <ul><li><em><strong>Ruminants are among the most successful wild mammals and valuable livestock</strong></em></li> <li><em><strong>40 trillion base pairs went into mapping genomes of 44 species</strong></em></li> <li><em><strong><em>Public</em><em> database will be </em><em>valuable</em> resource for science and breeding</strong></em></li> </ul></div> </aside><div> <div> <div> <div> <div> <p>A team of researchers has carried out a detailed study of the genomes of ruminants, giving new insight into their evolution and success. </p> <p>Ruminants including deer and antelope, as well as sheep, goats, cattle and their wild relatives, have thrived in many ecosystems around the globe. They range in size from the tiny lesser mouse deer of Malaysia to the towering African giraffe.  </p> <p>The new study published today (June 21) in <a href="https://science.sciencemag.org/content/364/6446/eaav6202"><em>Science</em></a> and led by Wen Wang and Guojie Zhang at the Kunming Institute of Zoology, and Rasmus Heller at the University of Copenhagen, Denmark, included Professor Harris Lewin at the UC Davis Department of Evolution and Ecology and Genome Center. </p> <p>Ruminants form an important part of U.S. and world agricultural systems. Farms and ranches have an estimated 95 million cattle in the U.S. alone, along with an estimated 5.2 million sheep and 2 million goats.</p> <p>“As ecosystems around the world begin to show the impact of climate change, knowing what the genes and their variants are can help with conservation efforts of threatened and endangered ruminant species. It can also provide resources to help mitigate the effects of climate change on agricultural commodities, such as breeding cattle, to be more adapted to warmer, drier climates,” said Lewin.</p> <p>The team generated more than 40 trillion base pairs of raw DNA sequences and assembled them into genomes for 44 species. Based on this data they were able to create a new family tree for ruminants — placing the largest (giraffe) and smallest (lesser mouse deer) on some of the earliest branches after ruminants emerged as a group 32 to 39 million years ago. </p> <p>“The data produced in this study provides a foundational genomic roadmap for this ecologically and economically important group of mammals,” said Lewin, who also chairs the <a href="https://www.earthbiogenome.org/">Earth BioGenome Project</a>, a global effort to sequence the genetic code of all the planet’s eukaryotes — some 1.5 million known species, including all plants, animals, protozoa and fungi. “It is a tremendous resource not only for understanding how evolution has shaped ruminants, but also for understanding the basis of both desirable and undesirable traits, such as inherited diseases.”</p> <h4>Genes for a unique digestive system</h4> <p>All ruminants have a specialized, multichambered stomach that allows them to ferment the plants they eat using microbes and to bring material up for further chewing, aiding digestion. This highly specialized digestive system allows ruminants to make the most of a diet high in otherwise-indigestible cellulose.  </p> <p>The study showed that, among the 295 newly evolved genes identified in ruminants, many were associated with the digestive system, such as the structure and function of the compartmented stomach — the rumen, omasum and abomasum. </p> <p>The team also identified a number of genes associated with <a href="https://science.sciencemag.org/content/364/6446/eaav6335">horns and antlers</a>. Ruminants typically have horns or antlers that can play a role in defense or mating behavior. </p> <p>The researchers were also able to pinpoint evolutionary changes at the species level. As the tallest terrestrial animal, giraffes have a distinct stature and body shape, which likely are adaptions to their savanna habitat. The researchers found that among the 366 genes related to bone development, 115 genes had giraffe-specific mutations. </p> <p>The ruminant genomes may also hold evidence of humans’ impact on these animals. When the researchers used a method to infer past population size, they found massive declines for more than half the species from 100,000 to 50,000 years ago — around the time modern humans left Africa and spread around the world. </p> <p>The researchers have created the <a href="http://animal.nwsuaf.edu.cn/code/index.php/Ruminantia">Ruminant Genome Database</a>, a public collection of the genomic and transcriptomic data presented in their study.</p> <p>The work was supported by a number of agencies and foundations in China, Europe and the U.S. The UC Davis portion was funded by the U.S. Department of Agriculture and the Robert and Rosabel Osborne Endowment. </p> <p><em><strong>This story originally appeared on the <a href="https://www.ucdavis.edu/news/sheep-and-cattle-giraffes-genome-study-reveals-evolution-ruminants">UC Davis News website</a>. </strong></em></p> </div> </div> </div> </div> </div> <div> <div> <div> <h4>Media contact(s)</h4> <p class="media-contacts"><a href="https://www.ucdavis.edu/person/articles/1302">Harris Lewin</a>, Evolution and Ecology, lewin@ucdavis.edu</p> <p class="media-contacts"><a href="https://www.ucdavis.edu/person/articles/432">Andy Fell</a>, News and Media Relations, 530-752-4533, ahfell@ucdavis.edu</p> </div> </div> </div> <div> <h4><span>Media</span> Resources</h4> <div> <div> <ul><li><a href="https://science.sciencemag.org/content/364/6446/eaav6202">Read the paper (Science)</a></li> <li><a href="https://www.earthbiogenome.org/">Earth BioGenome Project</a></li> <li><a href="http://animal.nwsuaf.edu.cn/code/index.php/Ruminantia">Ruminant Genome Database</a></li> </ul><p class="text-align-center"><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></p> </div> </div> </div> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/human-animal-health" hreflang="en">Human and Animal Health</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/evolution-and-ecology" hreflang="en">Department of Evolution and Ecology</a></div> <div class="field__item"><a href="/tags/genome-center" hreflang="en">Genome Center</a></div> <div class="field__item"><a href="/tags/genomes" hreflang="en">genomes</a></div> <div class="field__item"><a href="/tags/earth-biogenome-project" hreflang="en">Earth Biogenome Project</a></div> </div> </div> Fri, 21 Jun 2019 16:12:51 +0000 Lisa Howard 3301 at https://biology.ucdavis.edu Meet the 2019-2020 Officers of the Phi Sigma Honor Society, Delta Gamma Chapter https://biology.ucdavis.edu/news/meet-2019-2020-phi-sigma-officers <span class="field field--name-title field--type-string field--label-hidden">Meet the 2019-2020 Officers of the Phi Sigma Honor Society, Delta Gamma Chapter</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/16" typeof="schema:Person" property="schema:name" datatype="">David Slipher</span> </span> <span class="field field--name-created field--type-created field--label-hidden">June 20, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/Phi-Sigma-College-of-Biological-Sciences-UC-Davis-5_0.jpg?h=e5aec6c8&amp;itok=mEw5id_0" width="1280" height="720" alt="Phi Sigma Honor Society Delta Gamma 2019-2020 leadership " title="Meet the Phi Sigma Honor Society Delta Gamma 2019-2020 leadership (from left to right): Shenhav David, Ryan Vinh, Christopher Vo and Andy Yan. David Slipher/UC Davis" typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description="For the 2019-2020 academic year, the Phi Sigma Honor Society, Delta Gamma Chapter is hosting multiple socials during the fall quarter for current and prospective Phi Sigma members. Prospective nominees will receive an invitation to Phi Sigma events via an email from student leadership. The criteria for nomination to the Gamma Delta Chapter are more rigorous than most chapters. At UC Davis, a minimum GPA of 3.5 is mandatory for undergraduates. This GPA requirement is significantly higher than the national requirement of 3.0 and is a reflection of the high caliber of students at UC Davis. “The Phi Sigma board is excited to offer members with more opportunities to connect with College of Biological Sciences faculty,” said Delta Gamma Chapter Co-President Ryan Vinh. “We hope to develop a strong, tight-knit community over the next few years that undergraduates can look to for mentorship and support.” Learn more about the Phi Sigma Honor Society, Delta Gamma Chapter Other events scheduled for the upcoming academic year include the annual Phi Sigma Student Research Showcase, organized to coincide with the university-wide Undergraduate Research Conference, as well as research seminars given by CBS faculty. Phi Sigma will also look to host workshops and more social activities throughout the 2019-2020 year based on member feedback. 2019-2020 Phi Sigma officer profiles   Ryan Vinh. David Slipher/UC DavisRyan Vinh, Co-President Ryan Vinh is a senior neurobiology, physiology and behavior student. He works as an undergraduate research assistant in the lab of Professor Amparo Villablanca, Department of Internal Medicine, which studies vascular determinants of dementia and analyzes the effect of diet on endothelial function. Vihn volunteers at the Knights Landing One Health Center student-run clinic which provides community-centered care for the town of Knights Landing and surrounding areas. Vinh joined Phi Sigma to promote research efficacy among UC Davis undergraduates and to help foster a community of highly-motivated, research-driven students. Vinh believes Phi Sigma can become a pillar of support for the continual growth of undergraduate involvement in research. Christopher Vo. David Slipher/UC DavisChristopher Vo,  Co-President Christopher Vo is a senior studying microbiology. He is a bioengineering research intern in the lab of Cheemang Tan, Department of Biomedical Engineering, working on biomimetic artificial cells and synthetic biological networks in probiotics for biomedical and therapeutic applications. Vo co-author in a peer-reviewed scientific journal regarding his work on engineered cell-adhesion in bacteria for enhanced efficacy. He previously worked as a genetics research intern, researching mutations involved in meiosis and their role in fetal development. Vo is the co-founder and vice-president of the Asian and Pacific Islander American Public Affairs at UC Davis student group. He previously volunteered as supplies and training director and for the Willow Clinic, which serves the Sacramento homeless community through free medical and dental services. Vo hopes to promote not only academic scholarship but also foster connections between students and faculty members. Shenhav David. David Slipher/UC DavisShenhav David, Secretary Shenhav David is a senior microbiology student. She is an undergraduate researcher in the lab of Professor Andreas Bäumler’s, Department of Medical Microbiology and Immunology, which focuses on enteric pathogens, hosts, and gut microbiota. David worked as an undergraduate researcher in the lab of Professor Satya Dandekar, Department of Medical Microbiology and Immunology, studying the effects of HIV and SIV on gastrointestinal mucosal lymphoid tissue. Davis has extensive experience working in the private sector as a research assistant at Applied StemCell. David joined Phi Sigma in hopes of creating a networking opportunity for ambitious students involved in research. Andy Yan. David Slipher/UC DavisAndy Yan, Treasurer Andy Yan is a senior studying neurobiology, physiology, and behavior. He works as an undergraduate researcher in the lab of Associate Professor Dominik Haudenschild, Department of Orthopedic Surgery. He researches the kinematics of SMAD4 proteins in the BMP pathway during osteogenesis. Yan volunteers at the Pantry in the Memorial Union and his favorite hobbies include hiking and going to the ARC. Yan joined Phi Sigma to get more involved with like-minded peers in the College of Biological Science. Stay Informed! Sign up for our monthly email newsletter The Gamma Delta Chapter was established at UC Davis in 1984. The coat of arms banner proclaims &quot;Truth shall spring from the earth.&quot; David Slipher/UC Davis  "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "For the 2019-2020 academic year, the Phi Sigma Honor Society, Delta Gamma Chapter is hosting multiple socials during the fall quarter for current and prospective Phi Sigma members. It&#039;s a great way for students to connect with their peers in the life sciences. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><span><span>For the 2019-2020 academic year, the Phi Sigma Honor Society, Delta Gamma Chapter is hosting multiple socials during the fall quarter for current and prospective Phi Sigma members. Prospective nominees will receive an invitation to Phi Sigma events via an email from student leadership.</span></span></p> <p><span><span>The criteria for nomination to the Gamma Delta Chapter are more rigorous than most chapters. At UC Davis, a minimum GPA of 3.5 is mandatory for undergraduates. This GPA requirement is significantly higher than the national requirement of 3.0 and is a reflection of the high caliber of students at UC Davis.</span></span></p> <blockquote> <p><span><span>“The Phi Sigma board is excited to offer members with more opportunities to connect with College of Biological Sciences faculty,” said Delta Gamma Chapter Co-President Ryan Vinh. “We hope to develop a strong, tight-knit community over the next few years that undergraduates can look to for mentorship and support.”</span></span></p> </blockquote> <p class="text-align-center"><span><span><a class="btn--primary" href="https://biology.ucdavis.edu/about/awards/phi-sigma">Learn more about the Phi Sigma Honor Society, Delta Gamma Chapter</a></span></span></p> <p><span><span>Other events scheduled for the upcoming academic year include the annual Phi Sigma Student Research Showcase, organized to coincide with the university-wide <a href="https://urc.ucdavis.edu/conference">Undergraduate Research Conference</a>, as well as research seminars given by CBS faculty. Phi Sigma will also look to host workshops and more social activities throughout the 2019-2020 year based on member feedback.</span></span></p> <h3><span><span><strong>2019-2020 Phi Sigma officer profiles</strong></span></span><br />  </h3> <figure role="group" class="caption caption-img align-left"><img alt="Ryan Vinh" data-entity-type="file" data-entity-uuid="bb3d10d8-1fa3-4de1-a470-923ebd18fdcd" height="217" src="/sites/g/files/dgvnsk2646/files/inline-images/Phi-Sigma-Honor-Society-College-of-Biological-Sciences-UC-Davis-crop-3.jpg" width="145" /><figcaption>Ryan Vinh. David Slipher/UC Davis</figcaption></figure><h4><span><span><strong>Ryan Vinh, Co-President</strong></span></span></h4> <p><span><span><span>Ryan Vinh is a senior neurobiology, physiology and behavior student. He works as an undergraduate research assistant in the lab of <a href="https://biology.ucdavis.edu/people/amparo-villablanca">Professor Amparo Villablanca, Department of Internal Medicine</a>, which studies vascular determinants of dementia and analyzes the effect of diet on endothelial function. </span></span></span></p> <p><span><span><span>Vihn volunteers at the Knights Landing One Health Center student-run clinic which provides community-centered care for the town of Knights Landing and surrounding areas. Vinh joined Phi Sigma to promote research efficacy among UC Davis undergraduates and to help foster a community of highly-motivated, research-driven students. Vinh believes Phi Sigma can become a pillar of support for the continual growth of undergraduate involvement in research.</span></span></span></p> <figure role="group" class="caption caption-img align-right"><img alt="Christopher Vo" data-entity-type="file" data-entity-uuid="fda4b118-e51e-483a-a588-06580bae512b" height="213" src="/sites/g/files/dgvnsk2646/files/inline-images/Phi-Sigma-Honor-Society-College-of-Biological-Sciences-UC-Davis-Crop.jpg" width="142" /><figcaption>Christopher Vo. David Slipher/UC Davis</figcaption></figure><h4><span><span><strong>Christopher Vo,  Co-President</strong></span></span></h4> <p><span><span><span>Christopher Vo is a senior studying microbiology. He is a bioengineering research intern in the lab of <a href="https://biology.ucdavis.edu/people/cheemeng-tan">Cheemang Tan, Department of Biomedical Engineering</a>, working on biomimetic artificial cells and synthetic biological networks in probiotics for biomedical and therapeutic applications. </span></span></span></p> <p><span><span><span>Vo co-author in a peer-reviewed scientific journal regarding his work on engineered cell-adhesion in bacteria for enhanced efficacy. He previously worked as a genetics research intern, researching mutations involved in meiosis and their role in fetal development. Vo is the co-founder and vice-president of the Asian and Pacific Islander American Public Affairs at UC Davis student group. He previously volunteered as supplies and training director and for the Willow Clinic, which serves the Sacramento homeless community through free medical and dental services. Vo hopes to promote not only academic scholarship but also foster connections between students and faculty members.</span></span></span></p> <figure role="group" class="caption caption-img align-left"><img alt="Shenhav David" data-entity-type="file" data-entity-uuid="32c544cf-558a-44cc-a40d-67a0caeb784c" height="208" src="/sites/g/files/dgvnsk2646/files/inline-images/Phi-Sigma-Honor-Society-College-of-Biological-Sciences-UC-Davis-crop-4.jpg" width="139" /><figcaption>Shenhav David. David Slipher/UC Davis</figcaption></figure><h4><span><span><strong>Shenhav David, Secretary</strong></span></span></h4> <p><span><span><span>Shenhav David is a senior microbiology student. She is an undergraduate researcher in the lab of <a href="https://biology.ucdavis.edu/people/andreas-baumler">Professor Andreas Bäumler’s, Department of Medical Microbiology and Immunology</a>, which focuses on enteric pathogens, hosts, and gut microbiota. David worked as an undergraduate researcher in the lab of <a href="https://biology.ucdavis.edu/people/satya-dandekar">Professor Satya Dandekar, Department of Medical Microbiology and Immunology</a>, studying the effects of HIV and SIV on gastrointestinal mucosal lymphoid tissue. Davis has extensive experience working in the private sector as a research assistant at Applied StemCell. David joined Phi Sigma in hopes of creating a networking opportunity for ambitious students involved in research.</span></span></span></p> <figure role="group" class="caption caption-img align-right"><img alt="Andy Yan" data-entity-type="file" data-entity-uuid="8597a343-6ce0-4a71-9e0e-6252db200f49" height="207" src="/sites/g/files/dgvnsk2646/files/inline-images/Phi-Sigma-Honor-Society-College-of-Biological-Sciences-UC-Davis-crop-2.jpg" width="138" /><figcaption>Andy Yan. David Slipher/UC Davis</figcaption></figure><h4><span><span><span><strong>Andy Yan, Treasurer</strong></span></span></span></h4> <p><span><span><span><span><span>Andy Yan is a senior studying neurobiology, physiology, and behavior. He works as an undergraduate researcher in the lab of <a href="https://biology.ucdavis.edu/people/dominik-haudenschild">Associate Professor Dominik Haudenschild, Department of Orthopedic Surgery</a>. He researches the kinematics of SMAD4 proteins in the BMP pathway during osteogenesis. Yan volunteers at the Pantry in the Memorial Union and his favorite hobbies include hiking and going to the ARC. Yan joined Phi Sigma to get more involved with like-minded peers in the College of Biological Science.</span></span></span></span></span></p> <p class="text-align-center"><em><strong><a class="btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></strong></em></p> <figure role="group" class="caption caption-img align-center"><img alt="Phi Sigma sash and tassel" data-entity-type="file" data-entity-uuid="f28dbe36-2397-40a9-87e7-dca5ea0a313e" src="/sites/g/files/dgvnsk2646/files/inline-images/Phi-Sigma-Sash-College-of-Biological-Sciences-UC-Davis-banner-for-web.jpg" /><figcaption>The Gamma Delta Chapter was established at UC Davis in 1984. The coat of arms banner proclaims "Truth shall spring from the earth." David Slipher/UC Davis</figcaption></figure><p> </p> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/campus-community" hreflang="en">Campus and Community</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/undergraduate-student-news" hreflang="en">Undergraduate Student News</a></div> <div class="field__item"><a href="/tags/women-stem" hreflang="en">Women in STEM</a></div> <div class="field__item"><a href="/tags/phi-sigma-biological-honor-society" hreflang="en">Phi Sigma Biological Honor Society</a></div> </div> </div> Thu, 20 Jun 2019 21:16:52 +0000 David Slipher 3276 at https://biology.ucdavis.edu Dark Centers of Chromosomes Reveal Ancient DNA https://biology.ucdavis.edu/news/dark-centers-chromosomes-reveal-ancient-dna <span class="field field--name-title field--type-string field--label-hidden">Dark Centers of Chromosomes Reveal Ancient DNA </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span lang="" about="/user/5461" typeof="schema:Person" property="schema:name" datatype="">Andy Fell</span> </span> <span class="field field--name-created field--type-created field--label-hidden">June 18, 2019</span> <div class="field field--name-field-sf-primary-image field--type-image field--label-hidden field__item"> <img src="/sites/g/files/dgvnsk2646/files/styles/sf_landscape_16x9/public/images/article/langley_cenhap_image1.jpg?h=7652de0f&amp;itok=LLrIp8qm" width="1280" height="720" alt="Chromosomes" title="The central area of chromosomes, the centromere, contains DNA that has survived largely unchanged for hundreds of thousands of years, researchers at UC Davis and the Lawrence Berkeley Laboratory have found. Some of this DNA comes from Neanderthals or other relatives or ancestors of humans from before modern humans migrated out of Africa. (Sasha and Charles Langley)" typeof="foaf:Image" class="image-style-sf-landscape-16x9" /> </div> <div class="addthis_toolbox addthis_default_style addthis_32x32_style" addthis:url="https://biology.ucdavis.edu/articles.rss" addthis:title="Recent News" addthis:description=" Geneticists exploring the dark heart of the human genome have discovered big chunks of Neanderthal and other ancient DNA. The results open new ways to study both how chromosomes behave during cell division and how they have changed during human evolution.   Centromeres sit in the middle of chromosomes, the pinched-in “waist” in the image of a chromosome from a biology textbook. The centromere anchors the fibers that pull chromosomes apart when cells divide, which means they are really important for understanding what happens when cell division goes wrong, leading to cancer or genetic defects.  But the DNA of centromeres contains lots of repeating sequences, and scientists have been unable to properly map this region.  “It’s the heart of darkness of the genome, we warn students not to go there,” said Charles Langley, professor of evolution and ecology at UC Davis. Langley is senior author on a paper describing the work published June 18 in the journal eLife. Langley and colleagues Sasha Langley and Gary Karpen at the Lawrence Berkeley Laboratory and Karen Miga at UC Santa Cruz reasoned that there could be haplotypes — groups of genes that are inherited together in human evolution — that stretch over vast portions of our genomes, and even across the centromere.  That’s because the centromere does not participate in the “crossover” process that occurs when cells divide to form sperm or eggs. During crossover, paired chromosomes line up next to each other and their limbs cross, sometimes cutting and splicing DNA between them so that genes can be shuffled. But crossovers drop to zero near centromeres. Without that shuffling in every generation, centromeres might preserve very ancient stretches of DNA intact. The researchers looked for inherited single nucleotide polymorphisms — inherited changes in a single letter of DNA — that would allow them to map haplotypes in the centromere.  They first showed that they could identify centromeric haplotypes, or “cenhaps,” in Drosophila fruit flies.   That finding has two implications, Langley said. Firstly, if researchers can distinguish chromosomes from each other by their centromeres, they can start to carry out functional tests to see if these differences have an impact on which piece of DNA is inherited. For example, during egg formation, four chromatids are formed from two chromosomes, but only one makes it into the egg. So scientists want to know: Are certain centromere haplotypes transmitted more often? And are some haplotypes more likely to be involved in errors? Secondly, researchers can use centromeres to look at ancestry and evolutionary descent.  Turning to human DNA, the researchers looked at centromere sequences from the 1000 Genomes Project, a public catalog of human variation. They discovered haplotypes spanning the centromeres in all the human chromosomes.  Haplotypes from half a million years ago In the X chromosome in these genome sequences, they found several major centromeric haplotypes representing lineages stretching back a half a million years. In the genome as a whole, most of the diversity is seen among African genomes consistent with the more recent spread of humans out of the African continent. One of the oldest centromere haplotype lineages was not carried by those early emigrants. In chromosome 11, they found highly diverged haplotypes of Neanderthal DNA in non-African genomes. These haplotypes diverged between 700,000 to a million years ago, around the time the ancestors of Neanderthals split from other human ancestors. The centromere of chromosome 12 also contains an even more ancient, archaic haplotype that appears to be derived from an unknown relative.  This Neanderthal DNA on chromosome 11 could be influencing differences in our sense of smell to this day. The cells that respond to taste and smell carry odorant receptors triggered by specific chemical signatures. Humans have about 400 different genes for odorant receptors. Thirty-four of these genes reside within the chromosome 11 centromere haplotype. The Neanderthal centromeric haplotypes and a second ancient haplotype account for about half of the variation in these odorant receptor proteins.  It’s known from work by others that genetic variation in odorant receptors can influence sense of taste and smell, but the functional effects of the variation found in this study are yet to be discovered and their impact on taste and smell analyzed.  The work was supported by grants from the National Institutes of Health.  Media contact(s) Charles Langley, Evolution and Ecology, 530-752-4085, chlangley@ucdavis.edu Andy Fell, News and Media Relations, 530-752-4533, ahfell@ucdavis.edu Media Resources Read the paper (eLife) This story originally appeared on UC Davis News Stay Informed! Sign up for our monthly email newsletter "> <a class="addthis_button_facebook"></a> <a class="addthis_button_linkedin"></a> <script> var addthis_share = { templates: { twitter: "Geneticists exploring the dark heart of the human genome have discovered big chunks of Neanderthal and other ancient DNA. The results open new ways to study both how chromosomes behave during cell division and how they have changed during human evolution. " } } </script> <a class="addthis_button_twitter"></a> <a class="addthis_button_email"></a> <a class="addthis_button_compact"></a> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div> <div> <div> <div> <div> <p>Geneticists exploring the dark heart of the human genome have discovered big chunks of Neanderthal and other ancient DNA. The results open new ways to study both how chromosomes behave during cell division and how they have changed during human evolution.  </p> <p>Centromeres sit in the middle of chromosomes, the pinched-in “waist” in the image of a chromosome from a biology textbook. The centromere anchors the fibers that pull chromosomes apart when cells divide, which means they are really important for understanding what happens when cell division goes wrong, leading to cancer or genetic defects. </p> <p>But the DNA of centromeres contains lots of repeating sequences, and scientists have been unable to properly map this region. </p> <p>“It’s the heart of darkness of the genome, we warn students not to go there,” said Charles Langley, professor of evolution and ecology at UC Davis. Langley is senior author on a paper describing the work published June 18 in the journal <em><a href="https://doi.org/10.7554/eLife.42989">eLife</a></em>.</p> <p>Langley and colleagues Sasha Langley and Gary Karpen at the Lawrence Berkeley Laboratory and Karen Miga at UC Santa Cruz reasoned that there could be haplotypes — groups of genes that are inherited together in human evolution — that stretch over vast portions of our genomes, and even across the centromere. </p> <p>That’s because the centromere does not participate in the “crossover” process that occurs when cells divide to form sperm or eggs. During crossover, paired chromosomes line up next to each other and their limbs cross, sometimes cutting and splicing DNA between them so that genes can be shuffled. But crossovers drop to zero near centromeres. Without that shuffling in every generation, centromeres might preserve very ancient stretches of DNA intact.</p> <p>The researchers looked for inherited single nucleotide polymorphisms — inherited changes in a single letter of DNA — that would allow them to map haplotypes in the centromere. </p> <p>They first showed that they could identify centromeric haplotypes, or “cenhaps,” in <em>Drosophila</em> fruit flies.  </p> <p>That finding has two implications, Langley said. Firstly, if researchers can distinguish chromosomes from each other by their centromeres, they can start to carry out functional tests to see if these differences have an impact on which piece of DNA is inherited. For example, during egg formation, four chromatids are formed from two chromosomes, but only one makes it into the egg. So scientists want to know: Are certain centromere haplotypes transmitted more often? And are some haplotypes more likely to be involved in errors?</p> <p>Secondly, researchers can use centromeres to look at ancestry and evolutionary descent. </p> <p>Turning to human DNA, the researchers looked at centromere sequences from the 1000 Genomes Project, a public catalog of human variation. They discovered haplotypes spanning the centromeres in all the human chromosomes. </p> <h4>Haplotypes from half a million years ago</h4> <p>In the X chromosome in these genome sequences, they found several major centromeric haplotypes representing lineages stretching back a half a million years. In the genome as a whole, most of the diversity is seen among African genomes consistent with the more recent spread of humans out of the African continent. One of the oldest centromere haplotype lineages was not carried by those early emigrants.</p> <p>In chromosome 11, they found highly diverged haplotypes of Neanderthal DNA in non-African genomes. These haplotypes diverged between 700,000 to a million years ago, around the time the ancestors of Neanderthals split from other human ancestors. The centromere of chromosome 12 also contains an even more ancient, archaic haplotype that appears to be derived from an unknown relative. </p> <p>This Neanderthal DNA on chromosome 11 could be influencing differences in our sense of smell to this day. The cells that respond to taste and smell carry odorant receptors triggered by specific chemical signatures. Humans have about 400 different genes for odorant receptors. Thirty-four of these genes reside within the chromosome 11 centromere haplotype. The Neanderthal centromeric haplotypes and a second ancient haplotype account for about half of the variation in these odorant receptor proteins. </p> <p>It’s known from work by others that genetic variation in odorant receptors can influence sense of taste and smell, but the functional effects of the variation found in this study are yet to be discovered and their impact on taste and smell analyzed. </p> <p>The work was supported by grants from the National Institutes of Health. </p> </div> </div> </div> </div> </div> <div> <div> <div> <h2>Media contact(s)</h2> <p class="media-contacts"><a href="https://www.ucdavis.edu/person/articles/2327">Charles Langley</a>, Evolution and Ecology, 530-752-4085, chlangley@ucdavis.edu</p> <p class="media-contacts"><a href="https://www.ucdavis.edu/person/articles/432">Andy Fell</a>, News and Media Relations, 530-752-4533, ahfell@ucdavis.edu</p> </div> </div> </div> <div> <h2><span>Media</span> Resources</h2> <div> <div> <ul><li><a href="https://doi.org/10.7554/eLife.42989">Read the paper (eLife)</a></li> </ul><p><em><strong>This story originally appeared on <a href="https://www.ucdavis.edu/news/dark-centers-chromosomes-reveal-ancient-dna">UC Davis News</a></strong></em></p> <p class="text-align-center"><em><strong><a class="btn--lg btn--primary" href="https://biology.ucdavis.edu/form/tell-us-more-about-yourself-2">Stay Informed! Sign up for our monthly email newsletter</a></strong></em></p> </div> </div> </div> </div> <div class="field field--name-field-sf-article-category field--type-entity-reference field--label-above"> <div class="field__label">Category</div> <div class="field__item"><a href="/articles/ecology-environment" hreflang="en">Ecology and Environment</a></div> </div> <div class="field field--name-field-sf-tags field--type-entity-reference field--label-above"> <div class="field__label">Tags</div> <div class="field__items"> <div class="field__item"><a href="/tags/center-population-biology" hreflang="en">Center for Population Biology</a></div> <div class="field__item"><a href="/tags/evolution-and-ecology" hreflang="en">Department of Evolution and Ecology</a></div> <div class="field__item"><a href="/tags/dna" hreflang="en">DNA</a></div> <div class="field__item"><a href="/tags/chromosomes" hreflang="en">chromosomes</a></div> <div class="field__item"><a href="/tags/neanderthal" hreflang="en">Neanderthal</a></div> <div class="field__item"><a href="/tags/genetics" hreflang="en">genetics</a></div> <div class="field__item"><a href="/tags/humans" hreflang="en">humans</a></div> <div class="field__item"><a href="/tags/genomes" hreflang="en">genomes</a></div> </div> </div> Tue, 18 Jun 2019 18:08:35 +0000 Andy Fell 3271 at https://biology.ucdavis.edu