Congratulations to Associate Professor of MCB, NST & Chemistry Daniel Nomura for winning an ASPIRE Award from the Mark Foundation for Cancer Research! This award "funds high risk, high reward approaches to solving complex problems in cancer research that tend to fall outside the scope of other funding opportunities."
Nomura's lab is mapping hotspots of binding sites in human proteins that have been traditionally considered "undruggable" and developing novel small molecule drugs that bind to those proteins.
Congratulations to MCB Assistant Professor Priya Moorjani, who has been named a 2019 Sloan Research Fellow! The Alfred P. Sloan Foundation awards this fellowship to outstanding early-career researchers and funds $70,000 over two years to fund their research.
Moorjani's lab studies evolutionary history and its impact on human adaptation and disease.
Climate change has fueled coral reef bleaching throughout the tropics, with negative consequences for reef ecosystems and the people who depend on them. A new study finds that in the Caribbean, independent island nations such as Cuba and Jamaica are less vulnerable to coral bleaching than island territories like Saint Barthélemy.
The study, published today in the Proceedings of the Royal Society B and led by UC Berkeley graduate student Katherine Siegel, uses a compilation of environmental, socioeconomic, and management data from 30 Caribbean islands to assess variation in social and ecological vulnerability to coral bleaching.Coral bleaching is often caused by unusually warm ocean temperatures and impacts the communities that rely on the Caribbean sea for food and tourism. PHOTO: Katherine Siegel.
Coral bleaching—which occurs when corals expel the algae living within their tissues—is often caused by unusually warm ocean temperatures. Corals are the cornerstones of reef ecosystems. If a bleaching event is prolonged and causes enough corals to die, the entire reef ecosystem can become severely compromised. Coral bleaching can have ripple effects for coastal communities that depend on reef ecosystems for benefits such as seafood, tourism, and shoreline protection.
“This study brings together data on 35 biophysical, ecological, socioeconomic, and management variables to create important advances in understanding climate change vulnerability in the Caribbean,” said Siegel, a PhD candidate in the Department of Environmental Science, Policy, and Management.
The study’s interdisciplinary team, with co-authors from Florida State University, UC Santa Barbara, and the University of Vigo, focused on the Caribbean island chain that runs from the Bahamas in the north to Trinidad & Tobago in the south, a region with high socioeconomic diversity, including important differences in economic dependence on reefs.
Following a framework developed by the Intergovernmental Panel on Climate Change, the team divided vulnerability into three separate components: exposure (the likelihood of bleaching events), sensitivity (the effect that bleaching is likely to have on the ecosystem and people), and the ability of the ecosystem and people to adapt to or recover from a bleaching event. Siegel and her collaborators used more than 250 published datasets, survey results, and government reports to assemble indicators for these components on each island, revealing important patterns in vulnerability across the region.The study found that while independent islands are more exposed to environmental conditions that can trigger bleaching events, they are less likely to experience negative socioeconomic consequences because they are less economically dependent on reefs and are better equipped to detect and adapt to environmental changes. PHOTO: Katherine Siegel.
“We were surprised to find that independent islands have lower social-ecological vulnerability than territories,” said Siegel. “Territories—such as the Dutch islands of Sint Maarten and Saba—tend to be left out of global assessments of climate change vulnerability, but our results suggest that they need to invest in improving their ability to adapt to environmental changes.”
The study found that while independent islands are more exposed to environmental conditions that can trigger bleaching events, they are less likely to experience negative socioeconomic consequences because they are less economically dependent on reefs and are better equipped to detect and adapt to environmental changes. In contrast, the French territory Saint Barthélemy has very low exposure but experiences high overall vulnerability due to socioeconomic factors such as an economic dependence on reef tourism.
“Bleaching events have become more common and severe in recent decades, a trend that may only worsen as the world’s oceans continue to warm.” says study co-author Sarah Lester, an assistant professor of geography at Florida State University. “It’s essential that we develop a better understanding of how this disturbance impacts coral reef ecosystems and the people that rely on these ecosystems for their livelihood.”
The study’s findings can help decision-makers and resource managers take actions to reduce the negative impacts of bleaching at the island level. Depending on the causes of an island’s vulnerability, actions could include implementing fishing regulations to protect species that play key roles in reef recovery, enacting land use policies and farming practices to improve the water quality on reefs, establishing environmental monitoring programs, and promoting economic diversification.
- Katherine Siegel, email@example.com
New research published in Nature from Assistant Adjunct Professor Professor Karen Davies and Associate Professor David Savage reveals the structure of NDH, a protein structure necessary for photosynthesis. This new molecular blueprint will allow researchers to directly test hypotheses of how NDH facilitates sugar production.
“This work will lead to a better understanding of how photosynthesis occurs, which could allow us to improve the efficiency of photosynthesis in plants and other green organisms – potentially boosting the amount of food, and thus biomass, they produce,” said lead researcher Davies.
A new paper published in Nature from the lab of MCB Associate Professor Ahmet Yildiz shows how the structure of dynein, a family of cytoskeletal motor proteins, determines its directionality. By engineering variants of dynein with altered stalk angles, the researchers uncover why all dyneins move toward only the minus end of a microtubule during movement.
The research is a collaboration with scientists from the Medical Research Council in the UK and Istanbul Technical University.
Two College of Natural Resources experts have recently been called to Washington DC to testify in front of congress to discuss the maintenance and future of America’s parks and public lands. Last month, Jonathan Jarvis, executive director of the Institute for Parks, People, and Biodiversity, testified on management issues that public lands face during government closures. Yesterday, Patrick Gonzalez, an associate adjunct professor in the Department of Environmental Science, Policy, and Management, testified before the House Subcommittee on National Parks, Forests, and Public Lands about the impacts of human-caused climate change on national parks.
Jonathan Jarvis (second from left) testified before congress on January 12.
On January 12, Jarvis testified at a special hearing of the House Policy and Steering Committee. Jarvis, a former National Park Service (NPS) director, was invited by House Natural Resources committee chairman Raul Grijalva (AZ-D). Jarvis discussed the potentially detrimental effects that a government shutdown can have on national parks and public lands.
In his testimony, Jarvis described his 2013 decision to shutter national parks during a government shutdown and the issues that the parks are now confronted with as they remain open during the current shutdown. He noted that serious management issues crop up as parks remain open during the closure, including the accumulation of trash, overflowing toilets, visitor accidents, and damage to natural resources.
Jarvis concluded that these effects are needlessly harmful and aren’t in the spirit in which the parks were created or are maintained. “The decision [by the president and his administration] to leave the parks open and to furlough the NPS staff is an abdication of their stewardship responsibilities for our national parks,” Jarvis said. His full testimony can be read on the UC Berkeley website.
On February 13, Patrick Gonzalez appeared at House Natural Resources Committee event titled “Climate Change and Public Lands: Examining Impacts and Considering Adaptation Opportunities.”
Yesterday, Gonzalez served as an expert witness during a House Natural Resources Committee event titled “Climate Change and Public Lands: Examining Impacts and Considering Adaptation Opportunities.” Gonzalez is the coordinating lead author for the Southwest for the 2018 US National Climate Assessment and is a lead author on four reports of the Intergovernmental Panel on Climate Change. He is also the lead author of the first comprehensive study of climate change in US national parks, which found that parks are experiencing disproportionate heat and aridity under human-caused climate change.
During his testimony, Gonzalez described the results of his own and and his colleagues’ research and offered adaptation strategies that could help reduce the impacts of climate change in national parks. These resource management tactics include prescribed burning and designating at-risk areas as refugia.
Gonzalez noted that these preventative measures only address the symptoms of climate change and not their cause—human activity, which includes carbon pollution from cars, factories, and farming. “The US national parks protect some of the most irreplaceable natural areas and cultural sites in the world,” he said. “Cutting carbon pollution would reduce human-caused climate change and help save our national parks for future generations.”
The subcommittee’s full hearing can be viewed on YouTube and Gonzalez’s full testimony can be read on the Natural Resources Committee’s website.Image: Date: Thursday, February 14, 2019 - 08:45 Legacy: section header item: Date: Thursday, February 14, 2019 - 08:45 headline_position: Top Left headline_color_style: Normal headline_width: Long caption_color_style: Normal caption_position: Bottom Left
In a mere seven years, Cas9 has shown itself to be a formidable gene editor, employed in humans, plants, animals and bacteria to quickly and accurately cut and splice DNA, transforming biology and opening new avenues for treating disease.
But a new kid on the block, CasX, may give Cas9 a run for its money.
Discovered two years ago by UC Berkeley scientists Jill Banfield and Jennifer Doudna in some of the world’s smallest bacteria, the protein was similar to Cas9, but quite a bit smaller: a big advantage if you’re trying to deliver a gene editor into a cell.
But would it work outside its native bacteria?
According to a study published this week in Nature, CasX is, in fact, a potent and efficient gene editor in both bacteria and human cells. Its design is similar to Cas9 and its well-studied cousin, Cas12, but it is different enough that it appears to have evolved in bacteria independently of the other Cas proteins. It can cut double-stranded DNA like Cas9, can bind to DNA to regulate genes, and it can be targeted to specific DNA sequences like other Cas proteins.
Plus, because it comes from bacteria that are not found in humans — Banfield dredged them from a database of microbes found in groundwater and sediment — the human immune system should accept it more easily than Cas9. Some doctors fear that Cas9 may create an immune reaction in patients treated with CRISPR therapies.
“The immunogenicity, delivery and specificity of a genome-editing tool are all vitally important,” said co-lead author Benjamin Oakes, a former UC Berkeley graduate student and current Entrepreneurial Fellow in the Innovative Genomics Institute. “We’re excited about CasX on all of these fronts.”
Co-lead authors Jun-Jie Liu and Natalia Orlova used a cryo-electron microscope to capture snapshots of the CasX protein going through the motions of editing a gene. Based on the protein’s unique molecular makeup and shape, the researchers concluded that CasX evolved independently of Cas9, sharing no common ancestor.
“The first thing that jumps out is how the highly unique domains accomplish similar roles to what we have seen with other RNA-guided DNA-binding proteins. CasX’s minimal size, with no fat on the bone, helps to clearly demonstrate there is a basic recipe that nature uses,” Oakes said. “Understanding this recipe will help us to better evolve and engineer genome editing tools for our purposes rather than nature’s.”
That’s exactly what he and his colleagues are now doing.
“The culmination of biochemistry, genome editing and structure experiments within this single study is a prime example of the comprehensive efforts that are underway at the IGI,” said Jennifer Doudna, IGI’s executive director, a UC Berkeley professor of molecular and cell biology and of chemistry and a Howard Hughes Medical Institute Investigator. “We aren’t just looking to uncover the next pair of molecular scissors. We want to build the next Swiss Army knife.”
Other authors are Enbo Ma, Hannah B. Spinner, Katherine L.M. Baney, Jonathan Chuck, Dan Tan, Gavin J. Knott, Lucas B. Harrington, Basem Al-Shayeb, Alexander Wagner, Brett T. Staahl, Kian L. Talyor, Julian Brotzman, Eva Nogales and Jennifer Doudna. This research was funded by the Innovative Genomics Institute’s Entrepreneurial Fellows Program, the National Institutes of Health, the Howard Hughes Medical Institute and the National Science Foundation.Wednesday, February 6, 2019 - 10:15 byline: Robert Sanders Legacy: section header item: Date: Wednesday, February 6, 2019 - 10:15 headline_position: Top Left headline_color_style: Normal headline_width: Long caption_color_style: Normal caption_position: Bottom Left
A new paper published in Nature from the labs of MCB Professors Jennifer Doudna and Eva Nogales reveals the power and potential of the CRISPR-CasX gene editing enzyme. Compared to its well-studied cousins Cas9 and Cas12, CasX is much smaller and may be better shaped for more efficient genetic engineering.
Congratulations to MCB & Chemistry Professor Chris Chang, winner of the 2019 Raymond and Beverly Sackler International Prize in Chemistry from Tel Aviv University. This prize is awarded to outstanding young scientists under 45 years of age who exhibit great originality and excellence in their research.
New research from the lab of MCB Professor Marla Feller shows visual stimuli can shape the visual system before eye opening.
These results open up a whole new area of research. “No one has essentially put a mouse in the dark before the eyes open, because they thought it would have no effect,” Feller says. Her next step is to investigate how light exposure before eye opening — which happens in nature for many species of mice — might influence the development of the circuitry within the retina itself.
Cannabis is unlike any other agricultural crop. Because of its circuitous history—once illegal to grow, and now legal but heavily regulated—cannabis has cast a unique footprint on the environment and the communities of farmers who grow it.
UC Berkeley’s new Cannabis Research Center, announced today by a multidisciplinary team of faculty, will explore how cannabis production impacts the environment and society, and how these impacts will evolve under new regulations set in place by legalization.
While other research groups in the University of California are focusing on the individual and public health ramifications of cannabis, the center will be the first in the UC system to explore oft-overlooked dimensions of cannabis growth.
Berkeley News spoke with center co-directors Van Butsic and Ted Grantham, both assistant cooperative extension specialists in the Department of Environmental Science, Policy and Management, to learn more about the state of cannabis production in California and the center’s goals.Berkeley News: What are some of the ecological and community impacts of cannabis production?
Ted Grantham: My research primarily focuses on the impacts of water use. These farms are taking water directly from streams or from groundwater wells connected to streams. Most farms are located in smaller watersheds, so even though the total amount of water taken can be small, it can have a big impact on streams that support sensitive species, such as salmon. Other potential ecological impacts relate to the use of pesticides and fertilizers, and habitat fragmentation from building roads and clearing trees.
The social scientists in the center are also concerned about equity and the sustainability of growing communities. Historically many growers would be characterized as small-scale, and there is concern that through this process of legalization, there is going to be a consolidation of cannabis production following models of industrial agriculture. We are trying to understand if there is a way to have cannabis cultivation continue to sustain local economies and rural communities, while limiting impacts to the environment.
A small cannabis-producing farm in Northern California. (PHOTO: Ted Grantham)How have legalization and associated regulations affected cannabis production so far?
Van Butsic: We’re about a year into the formal legalization of recreational cannabis production and it has been a rocky start. There have been fewer participants in the market — producers — than were anticipated. Some growers appear to have gone out of production, many appear to remain in black market production and a relatively small subset of growers have gone through the process of compliance. And the grower community that has pursued legal production are very vocal about the issues and challenges facing their group. We have been trying to better understand what are the barriers to compliance and, ultimately, if there can be changes made in policies that can really help to catalyze this transition.Cannabis production makes up only a very small percentage of agriculture in California. Why is it important to study its impacts in particular?
Van Butsic: This is a great system to study really big sustainability problems. How do we develop an agricultural system that’s good for the environment and good for farmers? And cannabis is a really interesting spot to look at it because the regulations enforcing cannabis are totally different than in the rest of agriculture, so it would be really interesting to see if we get different outcomes.How do regulations differ between cannabis production and the rest of agriculture?
Van Butsic: Cultivators need to be permitted by the state water board, by local government and by state government to grow cannabis legally, and there are environmental regulations in all three of those levels that they need to comply with that require a higher order of environmental performance than most other agricultural crops.
Tree leaves and needles are removed because they block sunlight needed for marijuana plants. (Pacific Southwest Region 5 photo, via Flickr)So you think that understanding these regulations might help you apply them to other types of agriculture?
Van Butsic: Exactly. Agriculture has been notoriously difficult to regulate in the past, and this is a system where the regulators got the upper hand, and so it will be interesting to see how the producers respond, and if cannabis producers can be profitable and meet these super-high environmental performance measures, then perhaps there is knowledge and technology that can transfer from the cannabis industry to the rest of agriculture that can improve environmental performance of food production.
We are working on a big project right now where we are mapping where all the farms are after the latest regulatory changes. We want to know, if we could take down these barriers and everybody became compliant, what would that mean for local water budgets, environmental health and for the amount of cannabis that would be produced?
Ted Grantham: This is a rapidly changing industry, and no one really knows where it is headed. Everyone is playing catch up to a certain extent, and we believe researchers have an important role in bringing independent scientific information to conversations around cannabis policy.Related Information Tuesday, January 29, 2019 - 09:45 Legacy: section header item: Date: Tuesday, January 29, 2019 - 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): Research News