By Date

Martin Lab: Santiago Yori Restrepo named 2020 Gilliam Fellow

Department of Molecular and Cell Biology - Fri, 07/31/2020 - 09:59

Congratulations to MCB graduate student Santiago Yori Restrepo on being selected as one of the 45 doctoral students and their advisors to received a 2020 Gilliam Fellowship!

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Vlassakis receives Burroughs Wellcome Fund award

Department of Bioengineering - Thu, 07/30/2020 - 15:40
Congratulations to recent BioE PhD Julea Vlassakis, now a postdoctoral scholar in Amy Herr’s lab, one of eight US scholars receiving a 2020 Burroughs Wellcome Fund Career Award at the Scientific Interface. Scholars receive $500,000 over five years to bridge advanced postdoctoral training and the first three years of faculty service.
Categories: Science News

Doudna Lab: New Understanding of CRISPR-Cas9 Tool Could Improve Genome Editing

Department of Molecular and Cell Biology - Thu, 07/30/2020 - 14:54

Out today in Science Magazine, a recent collaboration between MCB Professor of Biochemistry, Biophysics and Structural Biology Jennifer Doudna and David Liu of the Broad Institute could lead to improved gene editing. Read the Berkeley News story here.

Researchers and community-based organizations release COVID-19 Farmworker Study

College of Natural Resources - Wed, 07/29/2020 - 11:08

During the pandemic, Californian farmworkers are particularly vulnerable to a double threat: the risk of COVID-19 infection and unemployment. The California Institute for Rural Studies found that agricultural workers in Monterey County were three times more likely to become infected than those working in non-agricultural industries. Due to a collapse of foodservice demand, the county also experienced a decrease of almost 40 percent in agricultural employment from April to June. 

The COVID-19 Farmworker Study (COFS) Team, which included Cooperative Extension Specialist Susana Matias in the Department of Nutritional Sciences & Toxicology, surveyed over 900 farmworkers in California to better understand how the current pandemic has impacted farmworkers and their families as they continue frontline work.

Through partnerships with organizations such as Alianza Ecologista, Líderes Campesinas, and The Farmworker Care Coalition, the team directed study support and other resources to both grassroots movements and individual workers. Together, the collective of farmworker organizations, researchers, and advocates were able to highlight how the pandemic amplifies existing inequities that California farmworkers have faced for years. 

“Farmworkers play an essential role in the California food system,” says Matias, who studies nutrition and health among farmworkers in California. “Protecting this vulnerable population during the COVID-19 pandemic is critical for all of us.”

The COVID-19 Farmworker Study uplifted voices of farmworkers through phone-based surveys. Six community-based organizations managed 60 surveyors in farmworker communities, inviting individuals in 21 counties to participate while ensuring that interviews were conducted in the language preferred by the respondent. Surveyors asked participants about COVID-19 prevention at the workplace, housing conditions, and transportation methods, among other topics.

The COFS Team published six preliminary findings from the surveys:

  1. Farmworkers experience dramatic loss of work and income during the COVID-19 pandemic. Forty-six percent of the respondents reported decreased work time and subsequent income loss. Reasons for lost work time included employer-based decisions given decreased market demand and worker concerns about health risks. 
  2. Farmworkers lack healthcare access and experience fear about using medical services. Medical costs, lack of insurance, and lack of sick leave were reported to be significant barriers to accessing healthcare. Another reported factor was a mistrust of government agencies and the healthcare system.
  3. Farmworkers are vigilant about COVID-19 prevention practices outside of the workplace. Ninety  percent take action to protect their families from the virus when they return home from work. In addition to washing hands, changing clothes, and showering, some farmworkers take the additional steps to physically distance themselves from family members and their community.
  4. Farmworkers report low numbers of employers providing masks and face coverings. Fifty-four percent of worksites provide face coverings, forcing many farmworkers to purchase or make their own to wear in the workplace. 
  5. Farmworkers have valuable suggestions to improve workplace COVID-19 prevention efforts. Suggestions included improving workflow to maximize physical distancing, providing personal protective equipment, and disseminating useful information on COVID-19 to workers. 
  6. Farmworkers are systematically excluded from important safety-net programs, which heightens their vulnerabilities and those of family members. Many are unable to meet basic needs including child care, food security, and financial assistance. 

The collaboration with community-based organizers provided critical connections to farmworkers, as well as on the ground information that will be relevant in crafting local and regional policies. In close consultation with farmworkers and their communities, the team urges county and industry leaders to provide resources such as expanded income, health care access, and culturally-relevant education to farmworkers.

Find the COFS data here.

Image:  Farmer planting something in soil. Date:  Wednesday, July 29, 2020 - 10:45 Byline:  Anjika Pai Legacy:  section header item:  Date:  Wednesday, July 29, 2020 - 10:45 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 Expose in main "News river"?:  yes Keyword tag(s):  COVID-19

MCB Celebrates 2020 PhD Graduates Online

Department of Molecular and Cell Biology - Tue, 07/28/2020 - 12:32


We sent our MCB PhD class of 2020 off in style last week with an online celebration to mark the occasion. 

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Klinman Lab: Unlocking the health benefits of the PQQ vitamin

Department of Molecular and Cell Biology - Fri, 07/24/2020 - 12:53

Researchers in the lab of Judith Klinman are exploring how PQQ is made in bacteria to understand and unlock the potential health benefits of PQQ in the foods we eat. 

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Desert mosses use quartz rocks as sun shades

UC Berkeley Science News - Thu, 07/23/2020 - 13:30
A UC Berkeley doctoral student discovered that some desert mosses crawl under milky quartz to escape the sun, using the translucent rock as a sunshade
Categories: Science News

New technique to capture CO2 could reduce power plant greenhouse gases

UC Berkeley Science News - Thu, 07/23/2020 - 11:00
Metal-organic frameworks with added nitrogen compounds efficiently trap carbon dioxide from emissions, allowing them to be sequestered underground
Categories: Science News

Research on predictive modeling informs mangrove conservation

College of Natural Resources - Wed, 07/22/2020 - 14:29
Jungle with water on the floor. [image caption]

Photo credit by Jacob J. Bukoski.

Mangroves store high amounts of carbon in soil and vegetation. To better manage these carbon-rich ecosystems, scientists must accurately map where and how much carbon is stored within such coastal wetlands. However, it is unclear how accurate maps are relative to other forms of data, presenting a crucial information gap in the design of forest carbon programs. 

Now, new research describes the importance of novel maps in guiding mangrove managers and policy-makers. The authors of a study, published in the journal Environmental Research Letters on July 23, 2020, compare estimates of mangrove carbon produced through predictive modeling, a technique using statistics and data science, against traditional approaches such as field-based measurements. 

Trees and water in a mangrove. [image caption]

Mangrove forests are known to be among the most carbon-rich ecosystems globally. Consequently, they are attractive candidates for carbon forestry programs. Photo credit by Jacob J. Bukoski.

“We wanted to better understand the spatial scales at which global models of mangrove carbon align—or fail to align—with common methods for estimating carbon such as forest inventories,” explains study lead author Jacob Bukoski, a PhD candidate in the Department of Environmental Science, Policy and Management. “These modeled data are publicly available and are produced at relatively high spatial resolutions, which can be really valuable for people designing climate change mitigation programs in mangroves.”

Guidelines for the traditional measurement approaches are delineated by the Intergovernmental Panel on Climate Change (IPCC), the leading authority on carbon stock estimation. But because IPCC instructions on the use of modeled data are somewhat ambiguous, Bukoski and his team wanted to compare carbon stock estimates and assess the accuracy of the IPCC map data.

Using three different traditional methodological approaches from the IPCC, the authors estimated ecosystem level carbon stocks for mangrove sites in Brazil, the United Arab Emirates, and Thailand. The researchers then compared the values against model estimates for the same sites, and the modeled data out-performed the simplest IPCC methods. However, the predictive models were not definitively better than one IPCC method, which requires boots-on-the-ground measurements of trees and soil.

"Modeled data can improve your accuracy for very little cost."

The findings have implications for carbon stock assessments. “Modeled data can improve your accuracy for very little cost. In fact, the data are free,” said Bukoski. “Whereas field inventories can be expensive to implement, using geographic information systems (GIS) software to analyze the model data can get you close to site-level estimates.” 

Though both methods produce estimates rather than measurements, inherently subject to some uncertainty, the authors argue that the modeled data of mangrove carbon stocks are valuable. “Our hope is that the research will support NGOs and other programs which are working to conserve and restore mangroves,” according to Bukoski. “These programs often do not have the resources to run expensive field inventories, and our goal was to help provide guidance on how modeled datasets might help.”

The study, which can be found on the Environmental Research Letters website, was conducted with research from Angie Elwin, Rich A. Mackenzie, Sahadev Sharma, Joko Purbopuspito, Benjamin Kopania, Maybeleen Apwong, Roongreang Poolsiri, and Matthew D. Potts.

Research News

2020 Rausser College Faculty Retirements

College of Natural Resources - Tue, 07/21/2020 - 10:51

The Rausser College of Natural Resources congratulates the following faculty members on their retirement this year. The College is deeply grateful for their outstanding contributions to the Berkeley community and wishes them the best in all future endeavors.

Gordon Frankie

Professor, Environmental Science, Policy and Management

Gordon Frankie’s research focuses on the behavioral ecology and community organization of solitary bee species in California and Costa Rica. During the past 21 years, the Frankie lab has documented bee diversity, seasonality, and host plant preferences at various sites in northern California and Costa Rica. In Costa Rica, his work was foundational in understanding the floral behavior of dry forest plants, as well as bees’ plant preferences. He conducts comparative bee studies in both wildlands and urban landscapes, ran an experimental floral resource garden at the UC Berkeley Oxford Tract, and manages roughly 120,000 bee specimens that have been collected from field studies, which are currently being curated for deposit in the Berkeley Essig Museum of Entomology. He has surveyed gardens for native species in 15 California cities over a 15 year period, recording roughly 500 bee species in garden habitats—about 30 percent of all known bee species in California.

As honey bee populations decline nationwide, Frankie's research has implications for adapting the agricultural sector. In creating special pollinator habitat gardens, his work has demonstrated a method to supplement both native bees habitat and pollination services on croplands. His outreach and policy work has been extensive, in collaboration with numerous Bay Area schools, museums, and authors to develop public information on pollinators and their habitat. Frankie is first author of the field guide California Bees & Blooms: A Guide for Gardeners and Naturalists, and he is co-author of two forthcoming books on the native bees of Costa Rican gardens and their blooms.

Keith Gilless Keith J. Gilless

Dean Emeritus & Professor Emeritus of Forest Economics

J. Keith Gilless joined the Berkeley faculty as a professor of forest economics in 1983. A member of both the Department of Environmental Science, Policy, and Management and the Department of Agricultural and Resource Economics, he served as Dean of the College from 2007 to 2018 and as the S.J. Hall Chair in Forest Economics from 1996 to 2006. His research covers many areas, including large urban-wildland conflagrations, simulation modeling of fire behavior, the effects of climate change on fire management, natural hazards impacts and planning, and forest harvesting. He serves as the Secretary of the Berkeley Division of the Academic Senate, a member of the Board of Directors of the Faculty Club, a member of the Council of Friends of the Bancroft Library, and as Faculty Advisor for the undergraduate major in Ecosystems Management and Forestry. Off campus, Gilless is chair of the California Board of Forestry and Fire Protection and served for two terms on the US Department of Agriculture’s Forest Research Advisory Council. His accolades include the 2006 ESPM Award for Undergraduate Teaching Excellence, the 1998 Academic Senate Distinguished Teaching Award, and others. He is the co-author of two textbooks on forest resource management and economics.

Terry Norman Norman Terry

Professor, Plant and Microbial Biology

Professor Norman Terry’s research career embraced the physiology and biochemistry of environmental stresses on plants, as associated with water, salinity, mineral nutrients, and toxic heavy metals. Since 1990, his studies focused on phytoremediation, the use of plants to clean up contaminated soil and water. Terry developed methods for using constructed wetlands to remove selenium and toxic heavy metals from agricultural and industrial wastewater and pioneered research into the development of genetically engineered plants for phytoremediation. Terry authored over 265 research publications, obtained three patents, and co-edited the book Phytoremediation of Contaminated Soil and Water, published by Lewis Publishers, New York. Terry taught Plant Biology 180, Environmental Plant Biology, and co-taught Plant Biology 135, Physiology and Biochemistry of Plants, along with other courses.

Patricia Zambryski

Professor, Plant and Microbial Biology

Pat Zambryski joined Berkeley in 1986 as an associate professor of the Division of Molecular Plant Biology, which was soon incorporated into the Department of Plant and Microbial Biology (PMB). Her laboratory conducts research in microbial biology and plant biology. Her research in microbial biology investigates the molecular mechanisms utilized by Agrobacterium that lead to the genetic transformation of plant cells, focusing on the transference of DNA out of bacterial cells and into plant cells. In plant biology, she uses genetics and cell biology to investigate how plant cells communicate via plant specific intercellular structures called plasmodesmata. Zambryski has received numerous accolades throughout her career, including election as an AAAS Fellow in 2010, International Francqui Chair at the University of Gent, Belgium, in 2009, the Miller Research Professorship in 2004, Fellow of the American Society for Microbiology in 2001, and elected Member of the National Academy of Sciences in 2001. Deeply invested in PMB graduate students, she was the department's Head Graduate Student Advisor from 1996 to 2018. Zambryski also developed a class for non-science majors called “The Secret Life of Plants” in 1996, which has grown exceedingly popular and is now required for majors in the College. While Zambryski officially retires this month, she will continue to teach the class for the next several spring semesters.

Image:  Date:  Tuesday, July 21, 2020 - 10:45 Legacy:  section header item:  Date:  Tuesday, July 21, 2020 - 10:45 headline_position:  Top Left headline_color_style:  Normal headline_width:  Long caption_color_style:  Normal caption_position:  Bottom Left News/Story tag(s):  Honors and Awards Expose in main "News river"?:  yes

UC Berkeley to lead $25 million quantum computing center

UC Berkeley Science News - Tue, 07/21/2020 - 10:00
Funded by NSF, the Quantum Leap Challenge Institute for Present and Future Quantum Computing will focus on how best to use evolving quantum computers and training a quantum-smart workforce
Categories: Science News

Congratulations to Britt Koskella on your Promotion to Professor

Department of Integrative Biology - Mon, 07/20/2020 - 16:46

Professor Koskella is an evolutionary biologist seeking to understand how interactions among species generate and maintain much of the diversity you see on earth. She is interested in how species interactions influence genetic diversity within populations, diversity between populations, and species diversity at the community level. By combining evolutionary theory on coevolution, population dynamics, and infection genetics, she directly tests the underlying assumptions and predicted outcomes of host-pathogen and microbial interactions through the

Categories: Science News

MCB COVID-19 News

Department of Molecular and Cell Biology - Mon, 07/20/2020 - 09:03


Over the past several months, our scientific community has united to find ways to slow the spread of the SARS-CoV-2 virus and end the COVID-19 pandemic. We've created a dedicated COVID-19 news page with the latest efforts from the MCB community.

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Emirates launches first Mars probe with help from UC Berkeley

UC Berkeley Science News - Sun, 07/19/2020 - 16:30
The United Arab Emirates leads the Arab world into interplanetary space with the launch of the Hope Probe to study the atmosphere of Mars
Categories: Science News

Pesticides speed the spread of deadly waterborne pathogens

UC Berkeley Science News - Fri, 07/17/2020 - 06:17
UC Berkeley researchers show how agricultural chemicals can increase transmission of the schistosome parasite
Categories: Science News

Doudna lab: It's Tiny But It's Mighty: New CRISPR-CasΦ System

Department of Molecular and Cell Biology - Thu, 07/16/2020 - 12:03

Researchers Patrick Pausch and Basem Al-Shayeb are first authors of a paper describing CasPhi that will appear this week in the journal Science

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Megaphages harbor mini-Cas proteins ideal for gene editing

UC Berkeley Science News - Thu, 07/16/2020 - 11:00
A hypercompact Cas protein similar to CRISPR-Cas9, the revolutionary gene-editing tool, should allow easier viral delivery for gene therapy in humans and crops
Categories: Science News

Using CRISPR genome editing to make cassava safer to eat

UC Berkeley Science News - Tue, 07/14/2020 - 10:36
UC Berkeley researchers in the Innovative Genomics Institute are using CRISPR to remove poisonous cyanide compounds from the staple crop cassava
Categories: Science News

Vision scientists discover why humans literally don’t see eye to eye

UC Berkeley Science News - Mon, 07/13/2020 - 11:32
Study shows that visual precision varies from one person to the next
Categories: Science News

Investigation into fungi food choices yields crucial insights

College of Natural Resources - Fri, 07/10/2020 - 13:33
Neurospora fungus growing on dead wood

Neurospora growing on dead wood at a controlled burn site in North Carolina. Photo by John Taylor.

When you hear the word “fungi” there is a good chance that it conjures an image of an idyllic toadstool, or perhaps a cluster of capped mushrooms, growing out of a fallen log or pile of leaves. Though there are amazingly diverse types of fungi across the planet, fungi that decay plant matter like these iconic forest inhabitants are of particular interest to scientists because the enzymes that they use to break down tough plant cell walls into simple sugars can be mass-produced and used in industrial processes that generate valuable carbohydrate-based compounds, such as biofuels.

Interestingly, these fungi are capable of tailoring which plant cell wall-degrading enzymes they secrete based on the composition of the food sources available. To investigate how the fungi sense and respond in this manner, a team of scientists led by UC Berkeley used multiple techniques to study the genes, gene products, and gene regulation processes in the fungus Neurospora crassa. The recently published work – a collaboration of N. Louise Glass’ Berkeley Lab team, researchers from the U.S. Department of Energy Joint Genome Institute (JGI), and the Technical University of Munich – adds to a rich array of studies seeking to improve our understanding of fungal genomes.

“This paper explored how ascomycete fungi – the largest phylum within the fungal kingdom – choose what things to eat in an environment of many food choices,” explained first author Vincent Wu. “Curiosity aside, these fungi are currently being utilized to produce enzymes, proteins, and other chemicals in mass quantities, so understanding how they decide what to eat can lead to novel ways of engineering these organisms to more efficiently and sustainably assemble these products. Furthermore, this research included a massive transcriptomics analysis with the use of DAP-seq, a powerful new genetic analysis tool implemented at the JGI.”

Read more about this research on the JGI website. This press release originally appeared on the Lawrence Berkeley National Laboratory website.

Image:  Neurospora fungus growing on dead wood Date:  Tuesday, July 14, 2020 - 13:45 Legacy:  section header item:  Date:  Friday, July 10, 2020 - 13:15 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 Expose in main "News river"?:  yes