Enjoy this festive video, created using imagery from MCB Faculty Labs, and please keep an eye out for our MCB Fall 2017 Newsletter...
A perplexing question in immunology has been, how do immune cells remember an infection or a vaccination so that they can spring into action decades later? Research led by scientists at UC Berkeley, in collaboration with investigators at Emory University, has found an answer: A small pool of the same immune cells that responded to the original invasion remain alive for years, developing unique features that keep them primed and waiting for the same microbe to re-invade the body.
Before this study, scientists were not sure how cells can remember an infection from up to 30 years earlier. To tease apart this mystery, the research team tracked a specific kind of immune cell through the human body in the weeks, months and years following a vaccination that gives long-term protection.
March Hellerstein, professor of nutritional science and toxicology, applied a technique that he developed for his HIV/AIDS research in the 1990s to answer fundamental questions about how the immune system remembers infections decades after the first exposure.
The researchers tracked T cells inside people’s bodies after they were given the long-lasting yellow fever virus vaccine, using a technology developed at Berkeley for monitoring the birth and death of cells in humans over long periods of time. The researchers found that CD8+ T cells, responsible for long-term immunity against yellow fever, proliferate rapidly on exposure to the vaccine but then evolve, beginning about four weeks after the vaccination, into a “memory pool” of cells that live more than 10 times longer than the average T cell.
“This work addressed fundamental questions about the origin and longevity of human memory CD8+ T cells generated after an acute infection,” said Marc Hellerstein, senior coauthor and professor of nutritional science and toxicology at UC Berkeley. “Understanding the basis of effective long-term immune memory may help scientists develop better vaccines, understand differences among diseases and diagnose the quality of an individual person’s immune responses.”
The study was published December 13 in the journal Nature. The work was supported by grants from the National Institutes of Health.
When someone gets a vaccine or is exposed to a new infectious agent, cells that recognize the invader but had never have been called into action before – called naive cells – respond by dividing like crazy and developing infection-fighting functions. This creates a large pool of so-called memory cells, named for their ability to remember the specific infectious agent and respond effectively to repeat threats later. Over time, the large pool shrinks to a small number of long-term memory cells, which are primed to provide late protection. But scientists have debated how these memory cells are maintained and ready to strike for so long after the initial exposure.
This study found that one way the pool is maintained for years after vaccination is through the development of several unique features. On the surface and through the actions of their genes, they look like cells that have never been exposed to an infection, but on their DNA the researchers found a fingerprint, called a methylation pattern, that identifies them as having been through battle as an infection-fighting cell, which are called effector cells.
“These cells are like veteran soldiers, camped in the blood and tissues where they fight their battles, waiting for yellow fever to show up,” said Hellerstein. “They are resting quietly and they wear the clothes of untested new recruits, but they are deeply experienced, ready to spring into action and primed to expand wildly and attack aggressively if invaders return.”
For the study, Hellerstein applied a technique that he developed for his HIV/AIDS research in the 1990s and has used widely since to track the birth and death of cells in the human body. The research team had subjects drink small amounts of water that had deuterium instead of hydrogen. Deuterium is non-toxic, but it is slightly heavier than hydrogen, so scientists can track it by mass spectrometry when it gets incorporated into newly replicated DNA in the body’s cells, which occurs only during cell division. Using this method, scientists can learn if a pool of cells is new or old, because newly born cells will have deuterium in their DNA. Scientists or clinicians monitoring the cells over time will see that the deuterium levels in short-lived cells will be diluted after the patients return to drinking regular water, while the deuterium levels in long-lived cells will remain high. In the new study, people drank the deuterium water at different times after receiving the live yellow fever virus vaccine and researchers isolated T cells from the patients, then analyzed their deuterium content.
Yellow fever virus is not a threat in the United States, which means that all the subjects had not been previously exposed and would not get exposed after the tagging period, making the vaccine ideal for studying what happens to newly generated cells over a long period of time, when there is no longer any infectious agent to fight.
After a first acute exposure to an infectious agent or vaccine, the body has an initial phase with lots of short-lived infection fighting soldiers, called effector-memory cells. Then after the threat is cleared, effector cells go away and small numbers of long-term memory cells are present. One of the central questions in immunology was whether the long-term memory cells went through an effector stage or went on a separate pathway of their own. The research team found that that a subset of the effector-memory pool that had divided extensively during the first two weeks after vaccination stayed alive as long-term memory cells, dividing less frequently than once every year.
The extremely long life-span of the surviving memory cells allows them to specialize over time into a unique, previously unrecognized type of T cell. The long-term memory cells have some molecular markers that make them look like naive cells that have never activated, including a gene expression profile that looks like that in naive cells, yet have other molecular markers on their DNA of having gone through battle as effector cells.
“These results make it clear that true long-term memory cells were once effector cells that have become quiescent,” Hellerstein said. “This apparently keeps them poised to respond rapidly as new effector cells upon re-exposure to the pathogen.”
The research team calculated that the half-life of these long-term memory cells is 450 days, compared to a half-life of about 30 days for the average memory T cell in the body, during which they are in general repeatedly exposed to common antigens in the environment. So when the memory pool goes quiet, these unique cells retain a fingerprint stemming back to the original exposure, and remain primed to respond rapidly if there is re-exposure to the pathogen.
“The combination of molecular evidence of a unique life history with direct measurement of their long life span is what gives this study such power,” Hellerstein said. “The technology to measure the dynamics of the birth and death of cells and advances allowing it to be applied to very small numbers of cells let this study happen.”Wednesday, December 13, 2017 - 12:15 byline: By Brett Israel, UC Berkeley Media Relations Legacy: section header item: Date: Wednesday, December 13, 2017 - 12:15 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
Edward E. Penhoet Distinguished Chair in Global Public Health and Infectious Diseases and Professor of Biochemistry, Biophysics and Structural Biology Daniel Portnoy has been named a fellow of the National Academy of Inventors.
The University of California, Berkeley invites nominations and applications for the position of Dean of the College of Natural Resources. The appointee is expected to join the faculty beginning July 1, 2018. This is an internal system-wide UC campus search restricted to those who have attained the rank of Professor at any UC campus or research field station.
The College comprises four Departments: Agricultural and Resource Economics, Environmental Science, Policy, and Management, Nutritional Sciences and Toxicology, and Plant and Microbial Biology. It also has an interdisciplinary graduate program that functions as a department, the Energy & Resources Group. Additionally, it has several centers of expertise. These programs enroll approximately 1900 undergraduate students and 460 graduate students, and are supported by 140 faculty and 16 environmental and agricultural Cooperative Extension Specialists. The College is part of the Land Grant System, and its faculty have appointments in the Agricultural Experiment Station of the State of California.
Top candidates for this position will present records of academic distinction in fields constituting or related to the environment and use of natural resources from a biological, ecological, economic, or social science perspective. The ideal candidate will have an appreciation of the breadth of the College’s research and education. S/he will have a strong sense of the role of the College with respect to the University of California’s Division of Agriculture and Natural Resources(link is external). S/he must be able to work with faculty, students, staff, administrators, and external constituencies to develop a vision and a strategy for the future, with a focus on fundraising, and possess a record of strong administrative skills. S/he will have a record of supporting diversity and a commitment to promoting equity and inclusion for faculty, students, and staff.
Nominations are also sought: these should include the name of the nominee, and a brief statement of the nominee's qualifications. Nominations must be received by December 15, 2017. Applications must be received by February 1, 2018. Applications should include a curriculum vitae, and a statement of interest. Please send these materials to:
Chair, College of Natural Resources Dean Search Committee
Office of the Vice Provost for the Faculty
Electronic submissions should be sent to:
The University of California is an Equal Opportunity/Affirmative Action Employer. This position is a sensitive position and is subject to a criminal background check. Questions may be referred to Carolyn Capps at (510) 642-6474 or firstname.lastname@example.org.College of Natural Resources Dean Search Committee Roster 2017-18
- Jennifer Wolch, Dean (Committee Chair), College of Environmental Design
- Kathryn Baldwin, Development Officer, College of Natural Resources
- Carrie Maser, Alumni and Advisory Board, College of Natural Resources
- Whendee Silver, Professor, Environmental Science, Policy & Management
- John Coates, Professor, Plant & Microbial Biology
- Sofia Villas-Boas, Professor, Agriculture & Resource Economics
- Hei Sook Sul, Professor, Nutritional Sciences & Toxicology
- Dan Farber, Professor, Energy & Resources Group
- Hector Rodriguez, Professor, School of Public Health
- Nipam Patel, Professor, Integrative Biology
- Sheila Barry, Graduate Student, Range Management, CNR
Scott Silva at Bryce Canyon National Park.
3rd year, Environmental Sciences and Ecosystem Management & Forestry with a minor in Geographic Information Science and Technology
Junior Scott Silva wants to make Cal’s trash one of its reusable treasures. He tells us about his efforts at the Zero Waste Research Center, attending Forestry Camp, and how geocaching led him to study environmental science.
How did you decide to study environmental science and forestry?
I became interested in forestry and environmental sciences when I was young, and enjoying the outdoors was one of the only things I enjoyed doing. In addition to being known for wine tourism, my hometown of Napa has a big hiking culture, and my dad took me for hikes often. I started going geocaching, which is an outdoor scavenger hunt that sometimes involves solving puzzles in order to find hidden "caches" that contain a logbook and small knick knates for trading. I learned a lot about the natural landscape while talking with my father and being outdoors, which made me wonder more about how and why nature does what it does.
In high school, my love of hiking grew when I joined the hiking club. I eventually became president of the club, and loved taking my friends out to places to do trail work, hike, or do clean-ups, which helped me gain outdoor leadership experience. I then got to meet a lot of people in working in the field of environmental science and was amazed at the fact that you could get paid for helping the environment. I made it my goal to be involved with environmental sciences, as I wanted to be a manager of natural resources and have a say in land management decisions. All the while, climate change and other anthropogenic impacts were unfolding around the world, fueling my political drive to fight for something I believed in.
As a student here at UC Berkeley, you attended Forestry Field camp. Could you tell us about your experience in the program?
At Forestry Field Camp, we learn about current forestry industry and how it impacts the world’s natural resources. The summer I spent in the program began by taking Sierra Nevada Ecology with Scott Stephens, in which we studied the ecology and natural systems that exist within the Sierra Nevada. This class was super fun because we got to learn the taxonomy and functions of many of the plants found in the Sierras, which involved hiking and be in the field for class. We were even “poisoned” by professor Joe McBride after he fed us blue elderberry. Then, we took Forest Measurements with Rob York, which focused on how foresters measure and select trees for harvest. We also took part in a class called Silviculture with Kevin O'hara, which took us to multiple industrial and state-owned forests to examine about how the timber industry and forest ecosystems operate hand-in-hand. Finally, we had our Forest Management and Assessment class with Frieder Schurr and Rick Standiford, where we were assigned a 160-acre parcel and were asked to write a management plan about it. This class was a good example of what a professional forester does, and we were given many opportunities to create a project that was something craft on our own and take pride in. After this camp, I feel that I know how a professional forester manages a forest, as well as the ecology and cultural experiences that go along with management.
In addition to school, we had many weekend and extracurricular adventures. Every day after class, all of the people at camp would meet for dinner at the dining hall, where we would just joke and laugh about the day, or hang out with local environmental officials and professors. We would also go camping nearly every weekend, whether it be climbing Mount Lassen, floating at Butt Lake, or just fishing in the Feather River. Finally, nights were filled with recreational activities such as dance parties, "forest" ball (a volleyball variant), and night hikes. Participating in these activities helped us form great and lasting friendships. It’s been great to meet people in my major and get to know my classmates on a personal level.
You're involved in the Student Environmental Resource Center (SERC)—what are your primary responsibilities at the Center?
I work in the Zero Waste Research Center at SERC, which looks for upstream and downstream solutions to waste problems on our campus. I am in charge of researching and implementing zero waste programs on campus that are economically viable, as well as sustainable. I look at social, economic, and political impacts of waste projects, and I try to help combine people and programs in order to maximize the efficacy of the zero waste movement. Since launching in 2012, the Zero Waste Research Center has been awarded a grant from The Green Initiative Fund and started recycling and composing projects across campus. With composting, we are attempting to implement a vermi-composting program with aquaponics on campus. Our current recycling projects involve attempting to create 3D printer filament out of plastic waste, as well as other ways to reuse UC Berkeley’s waste in an effort to transform trash into potential resources. With resources like transforming plastic waste into 3D printer filament, we have the opportunity to create an economic advantage of our waste to benefit the Berkeley community’s sustainability efforts.
Scott Silva on a CHAOS Hike at the annual Gourmet Trip in Henry Coe State Park.
In addition to your work with SERC, you’re the president of the Cal Hiking and Outdoor Society (CHAOS). What are some benefits of being involved in a student organization like CHAOS?
CHAOS is a great club because it is full of diverse people who have one goal: hiking. This brings together unique crowds and creates a very inclusive atmosphere. Our club gives our members a lot of perks such as coupons from various brands, access to outdoor recreational spaces and stores, and free gear rentals from our gear shed. Being involved in a student organization helps students find community, helping them establish a “home away from home” on campus. Being part of a student organization can make campus feel smaller, which helps many people feel less lost.
What advice would you offer to students looking to get involved in the outdoors at Cal?
JUST GO OUTSIDE! Between studying for midterms, school groups, and plain old procrastinating, many of us don’t have the time or energy to go outside. But with proper planning and oversight, it’s easy to find time to go on a hike to relax and enjoy the outdoors. This way, students can foster a deeper connection with their environment, which makes being involved with the outdoors much more meaningful.Image: Date: Tuesday, December 5, 2017 - 09:45 Legacy: section header item: Date: Friday, December 1, 2017 - 09:45 headline_position: Top Left headline_color_style: Normal headline_width: Long caption_color_style: Normal caption_position: Bottom Left News/Story tag(s): Student Spotlights
Scientists from the Department of Plant and Microbiology (PMB) have identified the first natural example of a pathway for carbon dioxide fixation previously thought to be only synthetically derived. This discovery has the potential to lead to applications in developing new methods for carbon capture and conversion for the sustainable storing of electrical energy in liquid fuel form.
The finding was published this week in the Proceedings of the National Academy of Sciences by professor John Coates and researchers from his lab, including the study’s first author, Israel Figueroa, a PMB doctoral alumnus.
Carbon fixation is the process by which living organisms like plants or microorganisms convert inorganic carbon to an organic compound for biomass production. The launch point for Figueroa’s doctoral research was a sole microorganism identified by a laboratory in Germany, which—unlike all other known living organisms—uses phosphite as its energy source to fix carbon dioxide. Very little is known about this metabolism or the underlying biochemical pathway, or even the prevalence of phosphite, so Figueroa set out to search for its occurrence in nature.Israel Figueroa (pictured), the study's first lead author, conducted this research in Professor John Coates's lab. Photo by Natalea Schager.
Figueroa began scouring the Bay Area for potential environments that could host anaerobic microorganisms capable of utilizing phosphite and carbon dioxide simultaneously. After sampling locations that included Strawberry Creek on the UC Berkeley campus and marine sediment along the coast, he finally located a sample from East Bay wastewater treatment sludge capable of CO2 fixation that relies on phosphite as an energy source. Using advanced genetic techniques on this sample, he identified a new microorganism and the existence of the novel CO2 fixation for the first time in nature.
This pathway represents the seventh natural mechanism by which living organisms on Earth can capture carbon dioxide and convert it into organic carbon. UC Berkeley has been integral to research in the area of CO2 fixation pathways. Of the seven natural pathways now known, three were discovered on campus, including the Calvin-Benson Bassham cycle and the Arnon-Buchanan cycle, two of the most widely studied pathways. The Calvin-Benson Bassham cycle pathway is considered the primary mechanism by which all plants on Earth fix CO2 through light-dependent photosynthesis.
Understanding and synthesizing carbon fixation is a potential key to creating a more sustainable future for the planet. The discovery of the seventh pathway in nature is a preliminary finding that could that could lead to further advances toward pulling carbon dioxide out of the environment and converting it into a chemical alternative to petroleum that can be used to generate and store energy.
This discovery is part of a broader research mission in the Coates lab, which is investigating the uses of phosphite as a renewable energy source. “We need to consider a different energy future and landscape,” said Coates. “If we can find ways of harnessing this naturally energy-rich chemical, through either chemistry or biology, to make the materials that we need to create sustainable energy resources, we could be closer to an effective means of powering the world.”Image: Date: Wednesday, November 29, 2017 - 15:15 byline: By Mackenzie Smith Legacy: section header item: Date: Wednesday, November 29, 2017 - 15:15 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
Three CNR researchers have been awarded a grant from the Foundation for Food and Agriculture Research (FFAR) to promote ecological resilience and economic viability for the Bay Area’s urban farms. The research will be led by Jennifer Sowerwine, an assistant Cooperative Extension specialist in the Department of Environmental Science, Policy, and Management (ESPM), as well as ESPM faculty members Timothy Bowles and Céline Pallud, and Charisma Acey from the College of Envrionmental Design.
The team will work to improve the sustainability and resilience of urban farms by building healthier soils, conserving water, and promoting beneficial insects. Researchers will also evaluate the effectiveness of existing urban and peri-urban food access and food distribution methods for meeting food needs of urban low-income, food insecure communities.
FFAR, a nonprofit established in the 2014 Farm Bill with bipartisan congressional support, awarded Sowerwine’s team a $295,000 Seeding Solutions grant. The FFAR grant has been matched with funding from UC Berkeley and other private sources for a total investment of nearly $600,000. Drawing from expertise in soil science, ecological diversity management and urban planning, the team will use the grant to conduct research that studies urban farming from multiple angles, from soil to supply chains and distribution to community access to agricultural products.
“In order to ensure urban agriculture can grow and sustainably feed urban populations into the future, we need to better understand urban agriculture challenges from a policy and systems perspective,” said Sowerwine. “This Foundation for Food and Agriculture Research grant will support both research and a participatory process with the public to co-create solutions that can support ecological sustainability, economically viable livelihoods, and equitable access to fresh, healthy, and affordable foods in culturally acceptable ways.”
Policy recommendations and best practice outcomes will be developed in close collaboration with low-income and culturally diverse communities, community leaders, technology and marketing innovators, policy advocates, food producers, educators and extension specialists. The Berkeley Food Institute is providing coordination in this project and will work with the team to disseminate the results widely to decision makers, community advocates, and urban food producers and distributors.
Research will take place throughout the East Bay and findings will be applicable to other urban communities throughout the United States. Collaborators include several urban farming businesses and nonprofit organizations, including the Multinational Exchange for Sustainable Agriculture and Planting Justice.
This project is supported by FFAR through its Seeding Solutions grant program, which calls for bold, innovative, and potentially transformative research proposals in the Foundation’s seven Challenge Areas. This grant supports the Urban Food Systems Challenge Area, which aims to enhance our ability to feed urban populations through urban and peri-urban agriculture, augmenting the capabilities of our current food system.
“The Foundation for Food and Agriculture Research is pleased to support this integrated approach to improving the economic and environmental strength of urban agriculture systems,” said Sally Rockey, executive director of FFAR. “This project shows exciting potential to improve urban farmer livelihoods and nutrition in food insecure communities.”Wednesday, November 29, 2017 - 10:15 Legacy: section header item: Date: Wednesday, November 29, 2017 - 10:15 headline_position: Top Left headline_color_style: Normal headline_width: Long caption_color_style: Normal caption_position: Bottom Left