Earth and Planetary Science
EPS Near-Surface Geochemistry and Geobiology

Research Spotlights

Richard Allen and Qingkai Kong in front of the green Android character at Google headquarters. (Photo courtesy of Richard Allen)

A UC Berkeley idea to crowdsource every cellphone on the planet to create a global seismic network has been adapted by Google and incorporated into the Android operating system, kicking off an effort to build the world’s largest network of earthquake detectors.

Google announced today (Tuesday, Aug. 11) that Android cellphones — potentially billions of mobile phones around the planet — will automatically record shaking during an earthquake and feed the data into Google’s network. Google will analyze the data in real time and, for now, share online the magnitude, location and estimated area of shaking with anyone searching for “earthquake” or “earthquake near me.”

The technology company’s ultimate goal, like that of UC Berkeley, with its MyShake app, is to provide early warning of impending shaking from a quake to those in areas of the world without seismic or early warning networks, but with lots of personal cellphones that can serve as mini-seismometers.

“Google is building on what we have done with MyShake,” said Richard Allen, director of the Berkeley Seismological Laboratory and professor of earth and planetary science, who led the development of MyShake, which was released to the public last October.

MyShake provides Californians with early warning of ground shaking through the ShakeAlert system, which was rolled out last year by the governor’s Office of Emergency Services in conjunction with the U.S. Geological Survey, UC Berkeley and the California Institute of Technology. But the app also collects shaking data from cellphones and feeds it to UC Berkeley for analysis and research. Currently, MyShake has been downloaded by more than 1 million users around the world.

animation of characters dropping, covering and holding on

Earthquake early warning gives people time to drop, cover and hold on until the shaking stops, preventing injuries. (Animation courtesy of Google)

Google’s new Android OS will also provide Californians with early alerts through the ShakeAlert system, duplicating what MyShake does for iPhones, as well as Android phones.

Earthquake early warnings can come seconds to minutes before the ground begins to shake, giving MyShake users — and now Android users — time to duck, cover and hold on. The ShakeAlert system more broadly gives the state’s businesses, utilities, first responders and others time to secure equipment, pause activities or shut off equipment that could be damaged or incapacitated in a quake — or that could cause injuries.

Allen and UC Berkeley researcher Qingkai Kong consulted with Google over the past year to help the company develop and implement the Android Earthquake Alerts System.

“It’s a great project that allowed academic researchers to participate and help Google build the system,” Kong said. “It’s goal is to make an earthquake early warning system available globally that can benefit a lot of people and reduce a lot of casualties in the future. That is always the ultimate goal, to serve society and reduce earthquake hazards.”

Android’s built-in system works similarly to MyShake: Accelerometers in every phone detect shaking and send the data to Google, which uses massive processing to determine the pattern and estimate the spread of shaking.

In a blog post today, Marc Stogaitis, a principal software engineer with Android at Google, noted, “We’re essentially racing the speed of light (which is roughly the speed at which signals from a phone travel) against the speed of an earthquake. And lucky for us, the speed of light is much faster!”

UC Berkeley seismologists – this guy looks a lot like seismology lab director Richard Allen, complete with a Golden Bear cup – were among the earthquake experts consulted by Google before they incorporated ShakeAlert warnings into the Android operating system. (Video courtesy of Google)

According to Kong, Android will only source ground-shaking data from phones that are plugged in and charging and have not moved for a fixed period of time, in order to weed out shaking due to normal movement or to being carried in a pocket or bag.

Allen is hopeful that what Google learns from its crowdsourced earthquake detection network will be applicable to the MyShake experiment, even if outsiders cannot access the data because of privacy concerns.

“Google has great resources, but they are behind a wall,” he said. “I hope we can continue our partnership, so that we can continue to make advances, some inside Google, from which we can learn and apply these lessons outside Google to improve early warning and also better understand earthquake processes.”

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Robert Sanders, UC Berkeley Media relations

In this video, doctoral student Basem Al-Shayeb (right) discusses a new gene-editing protein, CasΦ, which he and postdoc Patrick Pausch (left) discovered in a virus that attacks bacteria. Because it is very small and compact, the novel Cas protein should be easier to deliver to cells by a viral vector to alter plants or cure disease. (UC Berkeley video by Roxanne Makasdjian)

The DNA-cutting proteins central to CRISPR-Cas9 and related gene-editing tools originally came from bacteria, but a newfound variety of Cas proteins apparently evolved in viruses that infect bacteria.

The new Cas proteins were found in the largest known bacteria-infecting viruses, called bacteriophages, and are the most compact working Cas variants yet discovered — half the size of today’s workhorse, Cas9.

Smaller and more compact Cas proteins are easier to ferry into cells to do genome editing, since they can be packed into small delivery vehicles, including one of the most popular: a deactivated virus called adeno-associated virus (AAV). Hypercompact Cas proteins also leave space inside AAV for additional cargo.

As one of the smallest Cas proteins known to date, the newly discovered CasΦ (Cas-phi) has advantages over current genome-editing tools when they must be delivered into cells to manipulate crop genes or cure human disease.

“Adenoviruses are the perfect Trojan horse for delivering gene editors: You can easily program the viruses to reach almost any part in the body,” said Patrick Pausch, a postdoctoral fellow at the University of California, Berkeley, and in UC Berkeley’s Innovative Genomics Institute (IGI), a joint UC Berkeley/UCSF research group devoted to discovering and studying novel tools for gene editing in agriculture and human diseases. “But you can only pack a really small Cas9 into such a virus to deliver it. If you would have other CRISPR-Cas systems that are really compact, compared to Cas9, that gives you enough space for additional elements: different proteins fused to the Cas protein, DNA repair templates or other factors that regulate the Cas protein and control the gene editing outcome.”

Apparently these “megaphages” use the CasΦ protein  — the Greek letter Φ, or phi, is used as shorthand for bacteriophages — to trick bacteria into fighting off rival viruses, instead of itself.

“The thing that actually made me interested in studying this protein specifically is that all the known CRISPR-Cas systems were originally discovered in bacteria and Archaea to fend off viruses, but this was the only time where a completely new type of CRISPR-Cas system was first found, and so far only found, in viral genomes,” said Basem Al-Shayeb, a doctoral student in the IGI. “That made us think about what could be different about this protein, and with that came a lot of interesting properties that we then found in the lab.”

Among these properties: CasΦ evolved to be streamlined, combining several functions in one protein, so that it can dispense with half the protein segments of Cas9. It is as selective in targeting specific regions of DNA as the original Cas9 enzyme from bacteria, and just as efficient, and it works in bacteria, animal and plants cells, making it a promising, broadly applicable gene editor.

“This study shows that this virus-encoded CRISPR-Cas protein is actually very good at what it does, but it is a lot smaller, about half the size of Cas9,” said IGI executive director Jennifer Doudna, a UC Berkeley professor of molecular and cell biology and of chemistry and a Howard Hughes Medical Institute investigator. “That matters, because it might make it a lot easier to deliver it into cells than what we are finding with Cas9. When we think about how CRISPR will be applied in the future, that is really one of the most important bottlenecks to the field right now: delivery. We think this very tiny virus-encoded CRISPR-Cas system may be one way to break through that barrier.”

Pausch and Al-Shayeb are first authors of a paper describing CasΦ that will appear this week in the journal Science.

Biggiephages carry their own Cas proteins

The CasΦ protein was first discovered last year by Al-Shayeb in the laboratory of Jill Banfield, a a UC Berkeley professor of earth and planetary science and environment science, policy and management. The megaphages containing CasΦ were part of a group they dubbed Biggiephage and were found in a variety of environments, from vernal pools and water-saturated forest floors to cow manure lagoons.

graphic showing how a megaphage injects a Cas gene into a bacterium, turning on the bacteria's defenses against competing viruses

A megaphage (left), a member of a bacteriophage family Biggiephage, injects its DNA — including genes for CasΦ (red) — into bacterial cells to turn the bacteria against the phage’s competitor (top). The reddish Pac-Man-like figures are CasΦ proteins, enzymes that cut up viral DNA. The genome of the bacterium is shown in purple. (UC Berkeley image by Basem Al-Shayeb and Patrick Pausch)

“We use metagenomic sequencing to discover the Bacteria, Archaea and viruses in many different environments and then explore their gene inventories to understand how the organisms function independently and in combination within their communities,” Banfield said. “CRISPR-Cas systems on phage are a particularly interesting aspect of the interplay between viruses and their hosts.”

While metagenomics allowed the researchers to isolate the gene coding for CasΦ, its sequence told them only that it was a Cas protein in the Type V family, though evolutionarily distant from other Type V Cas proteins, such as Cas12a, CasX (Cas12e) and Cas14. They had no idea whether it was functional as an immune system against foreign DNA. The current study showed that, similar to Cas9, CasΦ targets and cleaves foreign genomes in bacterial cells, as well as double-stranded DNA in human embryonic kidney cells and cells of the plant Arabidopsis thaliana. It also can target a broader range of DNA sequences than can Cas9.

The ability of CasΦ to cut double-stranded DNA is a big plus. All other compact Cas proteins preferentially cut single-stranded DNA. So, while they may fit neatly into compact delivery systems like AAV, they are much less useful when editing DNA, which is double-stranded, inside cells.

As was the case after Cas9’s gene-editing prowess was first recognized in 2012, there is a lot of room for optimizing CasΦ for gene editing and discovering the best rules for designing guide RNAs to target specific genes, Pausch said.

Other co-authors of the paper are Ezra Bisom-Rapp, Connor Tsuchida, Brady Cress and Gavin Knott of UC Berkeley and Zheng Li and Steven E. Jacobsen of UCLA. The researchers were funded, in part, by the Paul G. Allen Frontiers Group, National Institutes of Health Somatic Cell Genome Editing consortium (U01AI142817-02) and National Science Foundation (DGE 1752814).

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Sarah Slotznick (former Miller postdoc now an Assistant Professor Dartmouth) had her research with EPS Professor Nick Swanson-Hysell on iron speciation in ancient rocks featured as a Research Spotlight in EOS (https://eos.org/research-spotlights/review-of-go-to-iron-analysis-method...). The spotlight focuses on research recently published in an article entitled: Unraveling the Mineralogical Complexity of Sediment Iron Speciation Using Sequential Extractions (https://doi.org/10.1029/2019GC008666).

 

Text of the research spotlight:

Iron is the most abundant transition metal in Earth’s crust—occurring in a wide variety of minerals and in multiple oxidation states, mainly ferrous, or +2, and ferric, or +3—and its presence in different forms in rocks can tell vivid stories about ancient environmental conditions on the planet, such as past nutrient cycling, geologic activity, and oxygen contents.

In recent decades, scientists have probed iron content and speciation in rock samples with a laboratory technique that uses different chemicals to sequentially dissolve, or extract, specific types of iron. First, acetate is used to dissolve iron in carbonates, then hydroxylamine hydrochloride is used for easily reducible oxyhydroxides, then dithionite for ferric iron (oxyhydr)oxides like goethite, and finally, oxalate for magnetite.

In a new study, Slotznick et al. report on magnetic experiments and X-ray diffraction measurements of samples dating from 1.5 billion years ago in the Precambrian up through the Holocene to check just how accurate the assignment of minerals associated with the sequential extraction process actually is. They found that for some steps, especially the one involving dithionite, the technique worked as expected; in other words, dithionite dissolved the target ferric iron (oxyhydr)oxides efficiently while leaving other forms of iron untouched. For other steps, though—especially the final step in which oxalate is used to dissolve magnetite—the researchers discovered that the process did not work as expected. They suggest that in this last step, oxalate was dissolving iron bound in clays rather than just iron in magnetite.

The researchers say their data indicate that the extraction technique is more complex than previously assumed. Overall, the magnetic and X-ray diffraction analyses suggested that dissolution of iron phases was more gradual than realized, with undissolved portions of minerals from previous steps lingering and with slow dissolution of iron outside the intended targets. Part of the complication, the scientists say, is that rock samples can be extremely heterogeneous and variables like composition, grain size, and crystallinity can create differences that affect how iron dissolves.

The team’s analysis of a large data compilation highlighted that Precambrian sedimentary rocks contain more iron that is dissolved by oxalate (and thus they potentially contain more of certain iron-bearing clays) than Phanerozoic sedimentary rocks. The researchers say this observation suggests that a significant shift in iron cycling occurred between these two time periods. (Geochemistry, Geophysics, Geosystems, https://doi.org/10.1029/2019GC008666, 2020)

Citation: Shultz, D. (2020), Review of go-to iron analysis method reveals its pros and cons, Eos, 101, https://doi.org/10.1029/2020EO141919. Published on 27 March 2020. CC BY-NC-ND 3.0

Doug Hemingway (former Miller postdoc now at Carnegie) published research with Max Rudolph (UC Davis) and EPS Professor Michael Manga about striping effect on Saturn's moon.  Their paper, Cascading parallel fractures on Enceladus, offers an explanation of the unique stripes present on the south pole of Enceladus.

For the press release from Carnegie Institution for Science, click here.  For related coverage by the New York Times, click here.

satellite image showing eruption of ammonia plume on Jupiter

EPS Professor Imke de Pater and graduate student Chris Moeckel study the atmospheric mechanisms that create eruptions of ammonia on Jupiter.  The ammonia plumes affect the visible color banding of Jupiter's atmosphere as the eruptions of white gas displace the other darker, typically brown, lower-level clouds.

 

Click here for the full article published in Astronomical Journal, "First Alma Millimeter Wavelength Maps of Jupiter, with a Multi-Wavelength Study of Convection".

Check out here for an interview Imke de Pater on Space .com, "Ammonia Storms on Jupiter Are Messing Up Its Picture-Perfect Cloud Bands".

Go here for an interview with Chris Moeckel in The Daily Californian about this research, "UC Berkeley study finds ammonia plumes changing Jupiter’s atmosphere".

Image: Scientists on board the R/V Thomas G. Thompson recover a seismometer that had been recording earthquakes on the seafloor off the Pacific Northwest coast. Scientists used this information to confirm the presence of a tear in the Juan de Fuca tectonic plate under central Oregon.  (Photograph by William Hawley)

A hole in a subducted plate, in the mantle beneath North America, may cause volcanism and earthquakes on the surface of the Earth. Volcanism on the surface of North America appears to have been spatially coincident with a known zone of weakness on the slab for the last ~17 million years. We suggest that this hole is caused by tearing along the zone of weakness, a feature that is created when the plate is formed at the ridge. The tearing not only causes volcanism on North America but also causes deformation of the not‐yet‐subducted sections of the oceanic plate offshore. This tearing may eventually cause the plate to fragment, and what is left of the small pieces of the plate will attach to other plates nearby.

William Hawley (EPS graduate student) and Richard Allen (EPS Professor, BSL Director) present a tomographic model of the Pacific Northwest from onshore and offshore seismic data that reveals a hole in the subducted Juan de Fuca plate.

For a write-up in National Geographic about this research, click here.

Click here for the full article, The Fragmented Death of the Farallon Plate, published in Geophysical Research Letters.

 

Robert Sanders, Media relations|June 24, 2019

You might expect that plants hoping to thrive in California’s boom-or-bust rain cycle would choose to set down roots in a place that can store lots of water underground to last through drought years.

But some of the most successful plant communities in the state — and probably in Mediterranean climates worldwide — that are characterized by wet winters and dry summers  have taken a different approach. They’ve learned to thrive in areas with a below-ground water storage capacity barely large enough to hold the water that falls even in lean years.

Surprisingly, these plants do well in both low-water and rainy years precisely because the soil and weathered rock below ground store so little water relative to the rain delivered.

“The key point from our study is that, in many sites on the North Coast, the storage capacity is small relative to how much it rains,” said Jesse Hahm, a graduate student at the University of California, Berkeley, and one of two first authors of the study. “Because the capacity for the subsurface to store water over the wet season is small, it still rains enough, even in the dry years, to replenish the water supply. The limited below-ground storage capacity is the key mechanism that decouples the plants and how much water availability they have in the summer from big swings in winter rainfall.”

As a result, these plants are much more resilient in drought years, as evidenced by California’s relatively unscathed North Coast during recent droughts that killed hundreds of millions of trees in the Sierra Nevada.

researchers investigate spring
David Dralle of Sacramento State investigates water emerging from a spring. Researchers at the Eel River Critical Zone Observatory have used hillslope-scale insights into how water is stored below ground to explain state-wide patterns of plant drought response. (UC Berkeley photo by Jesse Hahm)

“Because the subsurface water gets replenished even in drought years, in the summer these plants feel the same amount of water supply below ground, no matter how much rain fell during the winter,” Hahm said. “They don’t really know if it rained a lot or a little, because they have the same amount of water stored below ground each summer.”

On the flip side, plants growing today on ground that can soak up as much water as the winter rains can provide are hosting plants that will have to deal with the state’s increasingly drier climate, putting them at risk as the climate changes. This may be a problem for Sierra Nevada plant communities that are relying less on a persistent snowpack and increasingly on stored subsurface water to last through the dry summer.

Hahm and David Dralle, the other first author and a former Berkeley graduate student who is an assistant professor at Sacramento State University, describe their findings, along with their colleagues, in a paper recently accepted by the journal Geophysical Research Letters and now posted online.

Rock moisture

While most people think plants rely only on water stored in the topsoil, Berkeley’s William Dietrich, professor of earth and planetary science, and recent graduate Daniella Rempe, an assistant professor at the University of Texas, Austin, recently discovered that water stored in fractured and weathered rock underneath the soil plays an equal or greater role. What Dietrich and Rempe call “rock moisture” can amount to a significant proportion of what plants rely on annually.

Jesse Hahm in the field
Berkeley graduate student Jesse Hahm levels an automated rain gauge deployed as part of an effort to track water fluxes across the landscape in order to measure seasonal subsurface water storage. (UC Berkeley photo by Wendy Baxter)

A major implication of the new study, Dietrich says, is that global climate models need to incorporate rock moisture into their calculations to accurately represent and predict the impacts of drought or heavy rainfall. In recent years, drought- or heat-killed trees have fueled catastrophic wildfires in California, Spain, Greece, Australia and many regions with a dry, Mediterranean climate.

“Understanding how water is stored deep within the weathered bedrock and how variations in that water supply and in rainfall affect plant water supply in that zone is extremely important in a seasonally dry climate,” Hahm said.

In their study, the researchers looked at 26 sites statewide. All were below the snow belt, so that winter rain stored below ground was the dominant source of water for the plants during the summer dry season. Using rainfall data and U.S. Geological Survey stream flow data to calculate the amount of water stored annually underground, they were able to assess the below-ground storage capacity of the soil and the weathered rock.

Of the 26 sites, only seven — all in the Northern Coast Ranges — had limited subsurface water storage capacity and fared well during the state’s recent protracted drought, between 2011 and 2016. These sites ranged from grass and oak savanna and chaparral to dense Douglas fir forests, but all were characterized by low subsurface storage relative to average annual rainfall in the area, which tends to be high. The excess water that the subsurface couldn’t store in the winter ran through the soil and fractured bedrock and ended up in the streams.

The other sites, including most sites in Southern California, suffered in the drought, with vegetation die-offs and less healthy, less green plants. All were characterized by below-ground storage that is sufficient to sop up most of the rainfall that falls yearly, but that had been left depleted in drought years.

winter runoff
Berkeley professor Bill Dietrich surveys saturation overland flow during a winter storm. The storage of water in some landscapes is limited by the extent of weathering in the soil and fractured bedrock. (UC Berkeley photo by Jesse Hahm)

Using satellite images to gauge the productivity and health of the vegetation at each site, the researchers concluded that the sites with high relative storage capacity were the ones that varied the most between wet and dry years in how green the plants were. Sites with low below-ground storage capacity relative to average annual precipitation fared better, remaining similarly green and healthy in drought years and wet years alike.

Hahm noted that many plants in the Sierra Nevada rely on the snowpack to quench their thirst during typical rainless summers. But as temperatures rise with global warming, winter precipitation will increasingly occur as rain.

“In a way, this is a glimpse into the future,” Hahm said. “As the climate warms, and as the snowline elevation increases in these mountain ranges, more and more places will switch from being reliant on snowpack to being reliant on water stored in the subsurface. Understanding how this storage capacity limitation will impact plants across the state in high montane areas needs to be explored more.”

The insights about rock moisture emerged from a long-term project at the Angelo Coast Range Reserve in Northern California, part of the UC Natural Reserve System, where scientists at the Eel River Critical Zone Observatory followed water from the sky through vegetation, soil and rock into the streams and back up into the atmosphere via evaporation and transpiration to chart the life cycle of water in the environment. Primary funding for the observatory, which Dietrich directs, comes from the National Science Foundation (EAR 1331940).

Other co-authors of the study are graduate student Alexander Bryk and Todd Dawson, professor of integrative biology, both from Berkeley, and Sally Thompson of the University of Western Australia.

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In a new paper in the journal Proceedings of the National Academy of Sciences, paleontologist Robert DePalma and his colleagues, including Walter Alvarez a Professor of the Graduate School and Professor Mark Richards from University of California, Berkeley Earth and Planetary Sciences, describe the site, dubbed Tanis, and the evidence connecting it with the asteroid or comet strike off Mexico’s Yucatan Peninsula 66 million years ago. That impact created a huge crater, called Chicxulub, in the ocean floor and sent vaporized rock and cubic miles of asteroid dust into the atmosphere. The cloud eventually enveloped Earth, setting the stage for Earth’s last mass extinction.

“It’s like a museum of the end of the Cretaceous in a layer a meter-and-a-half thick,” said Mark Richards, a UC Berkeley professor emeritus of earth and planetary science who is now provost and professor of earth and space sciences at the University of Washington.

Richards and Walter Alvarez, a UC Berkeley Professor of the Graduate School who 40 years ago first hypothesized that a comet or asteroid impact caused the mass extinction, were called in by DePalma and Dutch scientist Jan Smit to consult on the rain of glass beads and the tsunami-like waves that buried and preserved the fish. The beads, called tektites, formed in the atmosphere from rock melted by the impact.

Read the full article here

(Graphic courtesy of Robert DePalma)

Edwards Lab heads to sea to collect particulate lipid samples from the San Pedro Basin, halfway between Long Beach and Catalina Island. These samples will be used to study the microbial biology of the area and their impacts on ocean biogeochemistry. Learn more at the lab's website, https://www.bethanieedwardslab.com

Photos courtesy of Will Kumler, Edwards Lab Manager.

CIDER is a yearly interdisciplinary research incubator made possible by @BerkeleySeismo's Dr. Barbara Romanowicz, where Earth dynamicists collaborate on interdisciplinary new ideas like this:

https://www.yahoo.com/news/scientists-discovered-quadrillion-diamonds-hidden-184200854.html

 

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