Congratulations to Florentine Rutaganira (postdoc in Professor Nicole King's Lab), who has been named an HHMI Hanna Gray Fellow. HHMI’s Hanna H. Gray Fellows Program seeks to encourage talented early career scientists who have the potential to become leaders in academic research. Each of the 15 fellows will get up to $1.4M in funding covering Post-doc and assistant professor transitions.
In the crops and orchards of California’s Central Valley, even the tiniest species can have a big impact. Consider wild bees: these pollinators visit a variety of native plants and agricultural fields, providing an essential role in cultivating our food crops.
A new study from UC Berkeley researchers helps create a clearer understanding of how networks of plants and pollinators form over time to create biotic communities. The results of their research, which could help scientists and conservationists rebuild communities when a species goes locally extinct, are published today in Ecology Letters.Pollinator species, like wild bees, often opportunistically change their plant partners as plant communities shift over time. Photo by Leithen M'Gonigle.
Insect pollinators such as butterflies, bees, and hoverflies are important “ecosystem service providers,” according to Lauren Ponisio, who earned her PhD in 2016 from the Department of Environmental Science, Policy, and Management (ESPM). Many of the foods we eat—almonds, blueberries, tomatoes, and more—depend on insect pollination for reproduction.
“Human activities are degrading our ecosystems at an alarming rate, and we want to know how to restore them,” said Ponisio, who was a postdoctoral fellow in ESPM before recently joining UC Riverside as an assistant professor. “If we understand how communities of pollinators and plants form, we might be able to reassemble communities of locally extinct species in the future.”
Ponisio, along with ESPM professor Claire Kremen and UC Riverside postdoctoral fellow Marilia Gaiarsa, tracked the number of times that common Central Valley pollinators such as wild bees and hoverflies visited selected areas of native plant growth. By studying how often pollinators visited plants, they hoped to better understand how these species assemble to make up the communities of plants, insects, and animals that form the biotic communities in and around food crops.More than 100 field technicians, undergraduate and graduate students, and volunteers worked alongside lab managers and postdoctoral researchers to collect the data that culminated in this study. Photo by Leithen M'Gonigle.
To track the interactions between pollinators and plants, researchers gathered eight years of data that resulted in nearly 20,000 pollinator visitation records. The study was made possible by research that began in Kremen’s lab in 2006. In cooperation with local farmers, Kremen’s team planted hedgerows of native plants in five fields that are home to intensely managed agricultural plots.
Researchers then visited the hedgerows—borders of plants that surround fields—between two and five times each year. During each visit, researchers from Kremen’s lab used nets to capture bees and hoverflies that visited the newly planted hedgerows. More than 100 field technicians, undergraduate and graduate students and volunteers worked alongside lab managers and postdoctoral researchers to collect the data that culminated in this study, as well as many other ecology papers. Kremen’s team followed the same schedule to collect samples from two control locations: a group of older established hedgerows, as well as the overgrown borders of crops that were not replanted with native species.
Over the course of the 8-year study, researchers in Kremen’s lab spent more than 500 hours catching pollinator species. Once Ponisio analyzed the data, she discovered that pollinators’ visitation patterns are different from how ecologists have previously described plant-pollinator relationships. Using a statistical model to chart changes in the type of plant species that pollinators during the eight years, Ponisio and her co-authors found that pollinators’ preferences morph as communities of plants grow. This is known as opportunistic attachment: pollinators shift their preference for a particular plant species over time as different plants become available or go locally extinct.
According to Kremen, this finding is a new development in how ecologists understand biotic community assembly. “Our study shows for the first time that the most persistent and abundant pollinator species often opportunistically change their plant partners as the plant community itself changes in response to restoration,” she said.This study's findings could help scientists and conservationists address how to rebuild plant and animal habitats when a species goes locally extinct. Photo by Leithen M'Gonigle
In an effort to make her results transparent and repeatable, Ponisio has published the computer code she used to create the study’s statistical models on the development platform GitHub. “To reproduce this computationally intensive study, you need a lot of code. I want others to have access to this code so they can evaluate the results for themselves,” she said.
These findings will continue to be valuable as scientists and conservationists address how to rebuild plant and animal habitats. “This study demonstrates that pollinators may be malleable in terms of which plants that they visit and that dynamic shifts are part of the assembling process for a community,” said Ponisio. This could mean that scientists might find ways to maintain and rebuild community functionality even when a plant species goes locally extinct.Image: Date: Monday, September 18, 2017 - 11:00 byline: By Mackenzie Smith Legacy: section header item: Date: Monday, September 18, 2017 - 11:00 headline_position: Top Left headline_color_style: Normal headline_width: Long caption_color_style: Normal caption_position: Bottom Left News/Story tag(s): Research News
Photo by Jim Block.
A University of Illinois research project on which UC Berkeley Professor Krishna Niyogi has been a longtime collaborator announced today that it has received a $45 million, five-year reinvestment to continue research on photosynthetic improvements that could increase yields for farmers worldwide.
The funding for the Realizing Increased Photosynthetic Efficiency (RIPE) research project—which has already demonstrated yield increases of 20 percent—comes from the Bill & Melinda Gates Foundation, the Foundation for Food and Agriculture Research, and the U.K. Department for International Development.
“Today's report on world hunger and nutrition from five UN agencies reinforces our mission to work doggedly to provide new means to eradicate world hunger and malnutrition by 2030 and beyond,” said RIPE Director Stephen Long, the Gutgsell Endowed Professor of Crop Sciences and Plant Biology at the Carl R. Woese Institute for Genomic Biology at Illinois. “This investment is timely. Annual yield gains are stagnating and means to achieve substantial improvement must be developed now if we are to provide sufficient food for a growing and increasingly urban world population when food production must also adapt sustainably to a changing climate.”
Building on half a century of photosynthesis research at Illinois, Berkeley, and other partner institutions, RIPE researchers identified seven potential objectives to improve photosynthesis—and with the support of an initial $25 million, five-year grant from the Gates Foundation—began work in 2012 to try to turn their ideas into sustainable increases in crop production.
Niyogi, chair of the Department of Plant and Microbial Biology, has been involved with RIPE since its inception. He was engaged in securing original funding for RIPE from the Gates Foundation, and his research related to the project focuses on the “Relaxing Photoprotection” objective. In a study published in the journal Science last year, Niyogi, Long, and their collaborators demonstrated that one of their approaches could increase crop productivity by as much as 20 percent—a dramatic increase over typical annual yield gains of one percent or less.
Niyogi hopes this is just the beginning. “We are actively working on optimizing our approach, as well as investigating complementary approaches to improve crop productivity that should be synergistic with the increase we’ve already achieved,” he said.
Two other RIPE objectives have now led to even greater yield improvements in greenhouse and preliminary field trials.
“Our modeling predicts that several of these improvements can be combined to achieve additive yield increases, providing real hope that a 50 percent yield increase in just three decades is possible,” Long said. “With the reinvestment, a central priority will be to move these improved photosynthesis traits into commodity crops of the developed world, like soybeans, as well as crops that matter in the developing world, including cassava and cowpeas.”
RIPE and its funders will ensure that their high-yielding food crops are globally available and affordable for smallholder farmers to help feed the world’s hungriest and reduce poverty, particularly in Sub-Saharan Africa and Southeast Asia.
But we still have a long road ahead of us, Long said.
“It takes about fifteen years from discovery until crops with these transformative biotechnologies are available for farmers,” he said. “It will therefore be well into the 2030s before such superior crops are seen at scale in farmers’ fields.”
Realizing Increased Photosynthetic Efficiency (RIPE) is engineering staple food crops to more efficiently turn the sun’s energy into food to sustainably increase worldwide food productivity, with support from the Bill & Melinda Gates Foundation, the Foundation for Food and Agriculture Research, and the U.K. Department for International Development.
Niyogi’s work in partnership with Long is funded by a subaward from the University of Illinois, which works in partnership with UC Berkeley as well as the USDA/ARS, University of Essex, Lancaster University, Australian National University, Chinese Academy of Sciences, Commonwealth Scientific and Industrial Research Organisation, and Louisiana State University.
- Seeing the Light, Breakthroughs magazine, Spring 2017
- Crop Yield Gets Boost with Modified Genes in Photosynthesis, November 2016
- Improving Photosynthetic Efficiency, September 2016
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Withania somnifera grows in dry pockets across India—Punjab, Gujarat, Kerala, and Rajasthan. Commonly known as Indian winter cherry, the fruiting plant has been cultivated for centuries for use in ayurvedic medicine and is known for its anti-inflammatory properties.
Professor Daniel Nomura co-authored the study with graduate students from his laboratory. Pictured left to right: Jessica Spradlin, Carl Ward, Dan Nomura, and Elizabeth Grossman.
Today UC Berkeley researchers published a study that identifies and maps how a natural chemical found in Indian winter cherry suppresses breast cancer cell growth. The study adds to a growing body of research that examines the effects of natural products on cancer cells in order to develop cancer treatments.
The paper was published Cell Chemical Biology by professor Daniel Nomura and researchers from the Departments of Nutritional Sciences & Toxicology, Chemistry, and Molecular & Cell Biology. The full study is available online, ahead of print publication on September 28.
Natural products have been a source of cancer treatments for decades: the drug paclitaxel was first isolated from Pacific yew tree bark in the 1970s and continues to be a common chemotherapy treatment today. While many other natural products exhibit anticancer activity, they are difficult to synthesize and isolate from their natural sources, a crucial step toward creating reliable therapeutics from natural chemicals.
To understand how the anticancer compound in Indian winter cherry functions, Nomura's lab employed chemical proteomic technologies to identify the protein targets of withaferin A, the active natural chemical found in the leaves of the plant. “Using a chemoproteomic technology called activity-based protein profiling (ABPP) enables us to identify natural product protein targets and even the binding pocket or ‘druggable hotspot’ within the protein target,” said Nomura.
Using this protein profiling technology, Nomura and his team studied how the compound targets proteins that impair breast cancer cell growth. They determined that withaferin A targets a regulatory subunit of a tumor suppressor called protein phosphatase 2A, which inactivates the protein kinase B and prevents breast cancer cells from proliferating. After identifying this druggable hotspot, Nomura’s team developed a covalent ligand—a synthetic molecule that binds to the same site as withaferin A—called JNS 1-40 to create the same anticancer activity in breast cancer cells.
The study was co-authored by graduate students, postdoctoral fellows, and research associates in the Nomura Research Group; these include co-first authors Elizabeth Grossman and Carl Ward, as well as Jessica Spradlin, Leslie Bateman, Tucker Huffman, David Miyamoto, and Jordan Kleinman.
The new research builds on a growing map of druggable hotspots that are being drawn within the field of proteomics, the study of proteins. “We use this general chemoproteomic technology to enable drug discovery against the "undruggable" proteome,” said Nomura. “Most protein targets in our cells are seemingly "undruggable" because they lack known pockets into which drug therapies can bind. This technology helps us develop cancer drugs that are much easier to make that have the same therapeutic action as their more complex natural products.”
The process of identifying protein targets of chemicals found in nature and creating a synthetic equivalent could help researchers develop drug therapies for cancer. “Isolating these natural products and understanding how to translate chemicals like withaferin A into drugs has been difficult,” said Nomura. “But the approach demonstrated in this paper will enable us to rapidly identify new cancer targets and cancer drugs.”Image: Date: Thursday, September 14, 2017 - 14:30 byline: By Mackenzie Smith Legacy: section header item: Date: Thursday, September 14, 2017 - 14:30 headline_position: Top Left headline_color_style: Normal headline_width: Long caption_color_style: Normal caption_position: Bottom Left News/Story tag(s): Research News
This story originally appeared in the UC Division of Agriculture and Natural Resources Green Blog.
On the second Saturday of every month, Tuesday Simmons heads to the downtown Berkeley farmers market. Among the produce stalls and coffee stands, she sits behind a table with a sign that reads “Talk to a scientist!” She and other students spend the day fielding questions from strangers about topics that range from genetically modified foods to climate change and more. “We never know who we'll talk to at our public events, or what kinds of questions we'll be asked,” said Simmons, a graduate student in the UC Berkeley Department of Plant and Microbial Biology (PMB). “This makes the farmers markets fun.”
Tim Jeffers and Tuesday Simmons are ready to answer the public’s science questions at the downtown Berkeley farmers market.
Simmons’ monthly visits to the farmers market are organized by the student group CLEAR (Communication, Literacy, and Education for Agricultural Research). The group aims to mentor the next generation of science communicators by engaging in open, transparent, and active conversations with the public about science and research. Funded through the University of California Global Food Initiative, CLEAR offers a series of scientific outreach events including activities at the farmers market, student-led lectures at libraries, and discussions with the public at local pubs.
The events are aimed at making science accessible. “For members of the public who think scientists are a group of scary, isolated individuals funded by companies with special interests, these brief exchanges can be enough to make them question that assumption,” said Simmons, who also noted that translating her microbiology research for the public has helped improve her communication skills.
Learning to create compelling and impactful science communications is also a draw for Daniel Westcott. As a PMB graduate student who studies a specialized field—photosynthetic energy conversion in algae and plants—Westcott noted that discussing his research with non-scientists felt like a challenging hurdle to overcome.
Students like Westcott practice their communications skills through writing for the CLEAR blog. In their monthly blog posts, group members have tackled the economics of the meat industry, and the science behind the Impossible Burger, and the difficulty in labeling foods as “natural,” as well as highlighting CLEAR’s ongoing outreach efforts.
Westcott understands that sharing his research with the public through the blog and other CLEAR activities is essential. “Nearly two million scientific articles are published each year,” Westcott said. “Today’s successful scientists must be media savvy in order to rise above the noise.”
Launched in 2015, CLEAR began as a project across three UC campuses—Berkeley, Davis, and San Diego. At Berkeley, co-founders Peggy Lemaux and Dawn Chiniquy, a PMB postdoctoral fellow, saw the funding as an opportunity to focus on outreach activities and mentorship opportunities, such as helping graduate students write for and talk to non-scientific audiences.
Lemaux, a PMB faculty member and ANR cooperative extension specialist who studies food crop performance and quality, emphasizes that CLEAR is a student-driven organization. All members of CLEAR are volunteers, and a mix of undergraduates, graduate students and postdoctoral researchers participate in the group’s activities. Many of members are PMB students, but students from other scientific fields also participate in CLEAR’s events and monthly meetings. Student scientists from across campus are welcome.
Student Sonia Chapiro speaks about GMOs as part of the "Popping the Science Bubble" scientific seminar series at the Berkeley Public Library on June 19, 2017.
As the faculty organizer of CLEAR, Lemaux mentors students by providing feedback and guidance on their public presentations and blog posts. Recent student-led lecture topics include pesticide use and genetically modified foods, and as new members join the group, they’ll continue to add new presentations to their calendar of events.
CLEAR also hosts workshops and trainings to foster students’ science communication and writing skills. Last spring, the group invited NPR science writer Joe Palca to present a talk, “Real News or Fake Science.” More recently Brian Dunning of Skeptoid gave a presentation titled “Science Communication in a Minefield of Fiction.” This fall, Sara ElShafie, a graduate student in the Department of Integrative Biology and founder of Science Through Story, will give a science communication workshop for CLEAR students.
In recent years, Lemaux has seen a shift in students’ interest in outreach and science communication. “Today’s generation of scientists understand that they must be scientists in the lab and translate the message of their research—and research in general—for the public,” she said.
Some CLEAR students have pursued careers in public communication after leaving Berkeley. Mikel Shybut, PhD ‘15 Plant Biology, is now a fellow at the California Council on Science and Technology where he provides scientific analyses to state legislators. After arranging a day of informational meetings in Sacramento for a group of CLEAR students, Shybut commented, “It's heartening to see what CLEAR has accomplished in the last two years. The group’s outreach efforts demonstrate that scientists can be effective messengers.”
Visit CLEAR’s calendar to learn more about upcoming events. In September join CLEAR at the following events:
- Downtown Berkeley Farmers Market: Come chat with CLEAR members and check out their science demos at the farmers market. They feature a different science theme each month and are always looking forward to listening to community members’ science questions and concerns.
- Science Cafe with PMB professor John Taylor: Join CLEAR members for a beer, fun fungus exhibits, and Dr. John Taylor's tentatively titled, Felons, Fungi and Rats: California's Valley Fever Epidemic.”
Are you interesting in building relationships with local industry companies looking to engage with the MCB research community? Join us for the next MCB Industrial Affiliates Program (IAP) event on September 22nd. The symposium will feature presentations by industry partners about career opportunities within their companies well as an interactive poster session highlighting the research of MCB students and postdocs. Please contact firstname.lastname@example.org for event details or visit our website to learn more about the program.
Sophomores Nissma Bencheikh (intended MCB major) and Roaya Jannatipour (intended IB major) became fast friends at Berkeley their freshman year. But it turns out they had a lot more in common than their love for biology!
In our first student spotlight of the fall semester, Megan Conner shares her passion for writing and analysis, her favorite CNR class, and her experience as the Cal Energy Corps program.Megan Conner 3rd Year, Environmental Economics & Policy, and English
How do you see your majors working together? Do they share any commonalities in how you approach these fields?
English and environmental economics are drastically different areas of study; one is writing-intensive while the other focuses on developing analytical skills. Initially, I didn’t see these majors as complementary. I had a desire to pursue a career with a sustainable, positive impact. At the same time, I had a knack for writing. While these majors seem to have little overlap, I’ve found that my english background supports my pursuits in the Environmental Economics & Policy realm. The english major pushed me to develop a hypersensitivity to how I communicate with others. This is incredibly helpful when I’m working a job or engaging in research, because my power in words often translates into strong collaboration and articulation in my work.
What is your favorite CNR class or professor and why?
Environmental Economics and Policy 100 with associate professor Ethan Ligon has been my favorite course so far. It was a challenging class that pushed my critical thinking skills to the point of exhaustion, but it was well worth it! I came out of that class with a fresh perspective on how economic theory can translate into practical application, as well as a renewed faith in mathematical modeling. The course definitely gave me insight into what the field of environmental economics can offer. Plus, Professor Ligon is a great teacher who really engages his students in thought-provoking ways.
We heard that you participated in the Cal Energy Corps this summer - can you tell us about your internship experience and the organization that you worked with?
Megan Conner (back row, second from right) at dinner with her Center for Carbon Removal coworkers.
This summer I had the opportunity to participate in the Cal Energy Corps program through the Berkeley Energy and Climate Institute. The program places students in internships at companies that pursue sustainable energy and climate solutions. At the end of the internship, participating students are featured in a research symposium in which we present projects related to our work.
Through this program I interned at the Center for Carbon Removal in Oakland. The Center works to accelerate the widespread cleanup of atmospheric carbon dioxide by collaborating with industry leaders, policymakers, and technical experts to deploy carbon removal techniques. While I was there I worked on many projects, but my main research project focused on strategies for enhancing carbon mineralization and assessing current economic barriers to large-scale implementation. The work proved to be engaging. The people I worked with had such extensive knowledge on everything from business to science to engineering. It definitely was a fruitful experience.
Best study spot on campus?
I like to change up my study spots on a regular basis, but I always find myself circling back to the Rosberg Reading Room in Doe Library and the Maps Library in McCone Hall. Both are tucked away and rather quaint—good locations to ease a stressed mind.
What advice do you have for an incoming CNR student?
There are so many opportunities at Cal—especially in CNR—so take advantage of them! Do research with a professor through SPUR (Sponsored Projects for Undergraduate Research), get involved in a program through the Berkeley Energy and Climate Institute, or join an environmentally-focused student organization. Explore interests that spark your curiosity and stimulate your intellectual growth. In the process, you'll meet some really amazing people.
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The Department of Molecular and Cell Biology (MCB) and the Helen Wills Neuroscience Institute (HWNI) are soliciting applications for an Open-Level (tenure-track or tenured) faculty position in Neurobiology. The position will be at the Assistant, Associate, or Full Professor level and rank will be determined on qualifications and experience. The expected start date is July 1, 2018.
The Department of Molecular and Cell Biology at the University of California, Berkeley, is soliciting applications for a faculty position in the area of Host/Microbe Interactions at the level of Assistant Professor (tenure track). We seek applicants who are studying how interactions with microbes shape the biology (at all levels) of animals and other eukaryotes. The expected start date is July 1, 2018.