Earth and Planetary Science
EPS Geophysics

Research Spotlights

Flyer text, white on blue and gold background, Basic Science Lights the Way, Conversations on Current Research, When the Earth Shakes

 

A leading research university atop a seismic fault, Berkeley excels at studying earthquakes and creating early warning tools. What you should know to be informed and prepared.

Watch a recording of the talk given Wednesday, October 13, 2021:
https://www.youtube.com/watch?v=Ut0885199xU

Roland Bürgmann, Garniss H. Curtis Chair of Earth and Planetary Science
Qingkai Kong, Research Scientist, Lawrence Livermore National Laboratory
Sarina Patel, doctoral candidate, Department of Earth and Planetary Science
Moderated by Richard Allen, Interim Dean of Mathematical & Physical Sciences
 
Full listing of talk series Basic Science Lights the Way, Conversations on Current Research:
https://basicscience.berkeley.edu/

west Texas earthquake USGS screenshot

Berkeley Seismological Lab (BSL) and EPS Postdoctoral Researcher Guang Zhai, ASU Professor Manoochehr Shirzaei, and EPS Professor Michael Manga publish a research article which demonstrates the deep seismic effects of shallow wastewater injection from industrial activity in western Texas in the journal Proceedings of the National Academy of Sciences (PNAS): Widespread deep seismicity in the Delaware Basin, Texas, is mainly driven by shallow wastewater injection

photo of collected ostrich shell fragments with handwrittem notation of an alpha numeric code in permanent marker on the shells

Robert Sanders, UC Berkeley Media relations| April 30, 2021

Fragments of ostrich eggshells from the Ysterfontein 1 site near Cape Town, South Africa. Researchers have determined that these eggshells are about 120,000 years old, discarded by early Homo sapiens who lived along the coast and exploiting marine food resources as well as ostrich eggs. The scale bar at lower right is 1 centimeter (0.4 inches). (Photo Elizabeth Niespolo)

Archeologists have learned a lot about our ancestors by rummaging through their garbage piles, which contain evidence of their diet and population levels as the local flora and fauna changed over time.

One common kitchen scrap in Africa — shells of ostrich eggs — is now helping unscramble the mystery of when these changes took place, providing a timeline for some of the earliest Homo sapiens who settled down to utilize marine food resources along the South African coast more than 100,000 years ago.

Geochronologists at the University of California, Berkeley, and the Berkeley Geochronology Center (BGC) have developed a technique that uses these ubiquitous discards to precisely date garbage dumps — politely called middens — that are too old to be dated by radiocarbon or carbon-14 techniques, the standard for materials like bone and wood that are younger than about 50,000 years.

In a paper published this month in the journal Proceedings of the National Academy of Sciences, former UC Berkeley doctoral student Elizabeth Niespolo and geochronologist and BGC and associate director Warren Sharp reported using uranium-thorium dating of ostrich eggshells to establish that a midden outside Cape Town, South Africa, was deposited between 119,900 and 113,100 years ago.

That makes the site, called Ysterfontein 1, the oldest known seashell midden in the world, and implies that early humans were fully adapted to coastal living by about 120,000 years ago. This also establishes that three hominid teeth found at the site are among the oldest Homo sapiens fossils recovered in southern Africa.

The technique is precise enough for the researchers to state convincingly that the 12.5-foot-deep pile of mostly marine shells — mussels, mollusks and limpets — intermixed with animal bones and eggshells may have been deposited over a period of as little as 2,300 years.

The new ages are already revising some of the assumptions archeologists had made about the early Homo sapiens who deposited their garbage at the site, including how their population and foraging strategies changed with changing climate and sea level.

“The reason why this is exciting is that this site wouldn’t have been datable by radiocarbon because it is too old,” Niespolo said, noting that there are a lot more such sites around Africa, in particular the coastal areas of South Africa.

map of coast around Cape Town, South Africa
Ysterfontein 1 (YFT1) is one of many middens along the Cape coast, some from the Middle Stone Age (white dots) and some from the more recent Later Stone Age (orange dots). The new dates for Ysterfontein 1 make it the oldest known midden in the world and helps put it in the context of the other sites as archeologists try to understand how early Homo sapiens lived and changed over the last 120,000 years. (Graphic courtesy of Elizabeth Niespolo)

“Almost all of this sort of site have ostrich eggshells, so now that we have this technique, there is this potential to go and revisit these sites and use this approach to date them more precisely and more accurately, and more importantly, find out if they are the same age as Ysterfontein or older or younger, and what that tells us about foraging and human behavior in the past,” she added.

Because ostrich eggshells are ubiquitous in African middens — the eggs are a rich source of protein, equivalent to about 20 chicken eggs — they have been an attractive target for geochronologists. But applying uranium-thorium dating — also called uranium series — to ostrich shells has been beset by many uncertainties.

“The previous work to date eggshells with uranium series has been really hit and miss, and mostly miss,” Niespolo said.

Precision dating pushed back to 500,000 years ago

Other methods applicable to sites older than 50,000 years, such as luminescence dating, are less precise — often by a factor of 3 or more — and cannot be performed on archival materials available in museums, Sharp said.

Middle Stone Age artifacts from Ysterfontein 1
Middle Stone Age artifacts recovered from the Ysterfontein 1 midden include denticulates, points and red ochre (lower right). (Images courtesy of Richard Klein)

The researchers believe that uranium-thorium dating can provide ages for ostrich eggshells as old as 500,000 years, extending precise dating of middens and other archeological sites approximately 10 times further into the past.

“This is the first published body of data that shows that we can get really coherent results for things well out of radiocarbon range, around 120,000 years ago in this case,” said Sharp, who specializes in using uranium-thorium dating to solve problems in paleoclimate and tectonics as well as archeology. “It is showing that these eggshells maintain their intact uranium-series systems and give reliable ages farther back in time than had been demonstrated before.”

“The new dates on ostrich eggshell and excellent faunal preservation make Ysterfontein 1 the as-yet best dated multi-stratified Middle Stone Age shell midden on the South African west coast,” said co-author Graham Avery, an archeozoologist and retired researcher with the Iziko South African Museum. “Further application of the novel dating method, where ostrich eggshell fragments are available, will strengthen chronological control in nearby Middle Stone Age sites, such as Hoedjiespunt and Sea Harvest, which have similar faunal and lithic assemblages, and others on the southern Cape coast.”

The first human settlements?

Ysterfontein 1 is one of about a dozen shell middens scattered along the western and eastern coasts of Western Cape Province, near Cape Town. Excavated in the early 2000s, it is considered a Middle Stone Age site established around the time that Homo sapiens were developing complex behaviors such as territoriality and intergroup competition, as well as cooperation among non-kin groups. These changes may be due to the fact that these groups were transitioning from hunter-gatherers to settled populations, thanks to stable sources of high-quality protein — shellfish and marine mammals — from the sea.

black and white cross section of the middens, and photos of the pile of marine shells
Photographs of marine shells and a schematic stratigraphy for the Ysterfontein 1 shell midden. The positions of ostrich eggshells used for dating and paleoenvironmental reconstruction are shown as egg symbols in the stratigraphic section. (Graphic courtesy of Elizabeth Niespolo)

Until now, the ages of Middle Stone Age sites like Ysterfontein 1 have been uncertain by about 10%, making comparison among Middle Stone Age sites and with Later Stone Age sites difficult. The new dates, with a precision of about 2% to 3%, place the site in the context of well-documented changes in global climate: it was occupied immediately after the last interglacial period, when sea level was at a high, perhaps 8 meters (26 feet) higher than today. Sea level dropped rapidly during the occupation of the site — the shoreline retreated up to 2 miles during this period — but the accumulation of shells continued steadily, implying that the inhabitants found ways to accommodate the changing distribution of marine food resources to maintain their preferred diet.

The study also shows that the Ysterfontein 1 shell midden accumulated rapidly — perhaps about 1 meter (3 feet) every 1,000 years -— implying that Middle Stone Age people along the southern African coast made extensive use of marine resources, much like people did during the Later Stone Age, and suggesting that effective marine foraging strategies developed early.

For dating, eggshells are better

Ages can be attached to some archeological sites older than 50,000 years through argon-argon (40Ar/39Ar) dating of volcanic ash. But ash isn’t always present. In Africa, however — and before the Holocene, throughout the Middle East and Asia — ostrich eggshells are common. Some sites even contain ostrich eggshell ornaments made by early Homo sapiens.

Elizabeth Niespolo in white lab coat and goggles pipetting under a fume hood
Elizabeth Niespolo, at the time a graduate student in UC Berkeley’s Department of Earth and Planetary Science, separating uranium from thorium in a lab at the Berkeley Geochronology Center. (Photo by Warren Sharp, BGC)

Over the last four years, Sharp and Niespolo, at the time a graduate student in UC Berkeley’s Department of Earth and Planetary Science, conducted a thorough study of ostrich eggshells, including analysis of modern eggshells obtained from an ostrich farm in Solvang, California, and developed a systematic way to avoid the uncertainties of earlier analyses. One key observation was that animals, including ostriches, do not take up and store uranium, even though it is common at parts-per-billion levels in most water. They demonstrated that newly laid ostrich shells contain no uranium, but that it is absorbed after burial in the ground.

The same is true of seashells, but their calcium carbonate structure — a mineral called aragonite — is not as stable when buried in soil as the calcite form of calcium carbonate found in eggshell. Because of this, eggshells retain better the uranium taken up during the first hundred years or so that that they are buried. Bone, consisting mostly of calcium phosphate, has a mineral structure that also does not remain stable in most soil environments nor reliably retains absorbed uranium.

Uranium is ideal for dating because it decays at a constant rate over time to an isotope of thorium that can be measured in minute amounts by mass spectrometry. The ratio of this thorium isotope to the uranium still present tells geochronologists how long the uranium has been sitting in the eggshell.

Uranium-series dating relies on uranium-238, the dominant uranium isotope in nature, which decays to thorium-230. In the protocol developed by Sharp and Niespolo, they used a laser to aerosolize small patches along a cross-section of the shell, and ran the aerosol through a mass spectrometer to determine its composition. They looked for spots high in uranium and not contaminated by a second isotope of thorium, thorium-232, which also invades eggshells after burial, though not as deeply. They collected more material from those areas, dissolved it in acid, and then analyzed it more precisely for uranium-238 and thorium-230 with “solution” mass spectrometry.

cross section through 118,00-year-old eggshell
A cross-section of a fragment of an ancient eggshell from Ysterfontein 1 shows that the eggshell structures are well preserved, even though it was buried about 118,000 years ago. At the center is a pore that served as a pathway for oxygen for the incubating chick. Pitted lines are where the researchers used a laser to ablate portions of the eggshell to track concentrations of uranium and thorium and establish the age. (Image courtesy of Elizabeth Niespolo)

These procedures avoid some of the previous limitations of the technique, giving about the same precision as carbon-14, but over a time range that is 10 times larger.

“The key to this dating technique that we have developed that differs from previous attempts to date ostrich egg shells is the fact that we are explicitly accounting for the fact that ostrich eggshells have no primary uranium in them, so the uranium that we are using to date the eggshells actually comes from the soil pore water and the uranium is being taken up by the eggshells upon deposition,” Niespolo said.

Working with UC Berkeley professor of integrative biology Todd Dawson, Niespolo also analyzed other isotopes in eggshells — stable isotopes of carbon, nitrogen and oxygen — to establish that the climate rapidly became drier and cooler over the period of occupation, consistent with known climate changes at that time.

Niespolo, now a postdoctoral fellow at the California Institute of Technology but soon to be an assistant professor at Princeton University, is working with Sharp to date middens at other sites near Ysterfontein. She also is developing the uranium-series technique to use with other types of eggs, such as those of emus in Australia and rheas in South America, as well as the eggs of now extinct flightless birds, such as the two-meter (6.6-foot) tall Genyornis, which died out some 50,000 years ago in Australia.

The work was supported by the Leakey Foundation, Ann and Gordon Getty Foundation and National Science Foundation (BCS-1727085).

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From the search for Earth-like planets to seeking knowledge of past climates on Earth, Berkeley’s early-career faculty in the physical sciences push the boundaries of basic research and teaching in their fields. Join us tomorrow to hear from professors in four MPS departments about how their work lights the way.

TUESDAY, APRIL 27, 2021
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Rising Stars of Berkeley Mathematical and Physical Sciences
Courtney Dressing, Alexander Paulin, Daniel Stolper, Norman Yao, and moderator Frances Hellman
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For more information, visit basicscience2021.berkeley.edu
Robert Sanders, UC Berkeley Media relations| January 4, 2021
A 2019 eruption of Steamboat Geyser in the Norris Geyser Basin of Yellowstone National Park. The geyser’s first documented activity was in 1878, and it has turned off and on sporadically since, once going for 50 years without erupting. In 2018 it reactivated after a three-and-a-half-year hiatus, for reasons that are still unclear. (UC Berkeley photo by Mara Reed)

When Yellowstone National Park’s Steamboat Geyser — which shoots water higher than any active geyser in the world — reawakened in 2018 after three and a half years of dormancy, some speculated that it was a harbinger of possible explosive volcanic eruptions within the surrounding geyser basin. These so-called hydrothermal explosions can hurl mud, sand and rocks into the air and release hot steam, endangering lives; such an explosion on White Island in New Zealand in December 2019 killed 22 people.

A new study by geoscientists who study geysers throws cold water on that idea, finding few indications of underground magma movement that would be a prerequisite to an eruption. The geysers sit just outside the nation’s largest and most dynamic volcanic caldera, but no major eruptions have occurred in the past 70,000 years.

“Hydrothermal explosions — basically hot water exploding because it comes into contact with hot rock — are one of the biggest hazards in Yellowstone,” said Michael Manga, professor of earth and planetary sciences at the University of California, Berkeley, and the study’s senior author. “The reason that they are problematic is that they are very hard to predict; it is not clear if there are any precursors that would allow you to provide warning.”

He and his team found that, while the ground around the geyser rose and seismicity increased somewhat before the geyser reactivated, and the area currently is radiating slightly more heat into the atmosphere, no other dormant geysers in the basin have restarted. The temperature of the groundwater propelling Steamboat’s eruptions has also not increased, and no sequence of Steamboat eruptions, other than the one that started in 2018, occurred after periods of high seismic activity.

“We don’t find any evidence that there is a big eruption coming. I think that is an important takeaway,” he said.

The study will be published this week in the journal Proceedings of the National Academy of Sciences.

Three simple questions

Manga, who has studied geysers around the world and created some in his own laboratory, set out with his colleagues to answer three main questions about Steamboat Geyser: Why did it reawaken? Why is its period so variable, ranging from three to 17 days? And, why does it spurt so high?

6 members of the Steamboat Geyser team arrayed around a table with their computers
Six members of the science team assembled around a table in McCone Hall at UC Berkeley in the summer of 2019, at work on the Steamboat Geyser project. Clockwise from lower left, Carolina Munoz-Saez, Anna Barth, Sahand Hajimirza, Tarsilo Girona, Sin-Mei Wu and Majid Rasht-Behesht. The three questions and hypotheses the team analyzed are on the greenboard, while the fluid dynamics equations that describe a geyser eruption are on the whiteboard. (UC Berkeley photo by Michael Manga)

The team found answers to two of those questions. By comparing the column heights of 11 different geysers in the United States, Russia, Iceland and Chile with the estimated depth of the reservoir of water from which their eruptions come, they found that the deeper the reservoir, the higher the eruption jet. Steamboat Geyser, with a reservoir about 25 meters (82 feet) below ground, has the highest column — up to 115 meters, or 377 feet — while two geysers that Manga measured in Chile were among the lowest — eruptions about 1 meter (3 feet) high from reservoirs 2 and 5 meters below ground.

“What you are really doing is you are filling a container, it reaches a critical point, you empty it and then you run out of fluid that can erupt until it refills again,” he said. “The deeper you go, the higher the pressure. The higher the pressure, the higher the boiling temperature. And the hotter the water is, the more energy it has and the higher the geyser.”

To explore the reasons for Steamboat Geyser’s variability, the team assembled records related to 109 eruptions going back to its reactivation in 2018. The records included weather and stream flow data, seismometer and ground deformation readings, and observations by geyser enthusiasts (https://geysertimes.org/geyser.php?id=Steamboat). The researchers also looked at Steamboat’s previous active and dormant periods and those of nine other Yellowstone geysers, and at ground surface thermal emission data from the Norris Geyser Basin.

They concluded that variations in rainfall and snow melt were probably responsible for part of the variable period, and possibly for the variable period of other geysers as well. In the spring and early summer, with melting snow and rain, the underground water pressure pushes more water into the underground reservoir, providing more hot water to erupt more frequently. During winter, with less water, lower groundwater pressure refills the reservoir more slowly, leading to longer periods between eruptions. Because the water pushed into the reservoir comes from places even deeper than the reservoir, the water is decades or centuries old before it erupts back to the surface, he said.

In October, Manga’s team members demonstrated the extreme impact that water shortages and drought can have on geysers. They showed that Yellowstone’s iconic Old Faithful Geyser stopped erupting entirely for about 100 years in the 13th and 14th centuries, based on radiocarbon dating of mineralized lodgepole pine trees that grew around the geyser during its dormancy. Normally the water is too alkaline and the temperature too high for trees to grow near active geysers. The dormancy period coincided with a lengthy warm, dry spell across the Western U.S. called the Medieval Climate Anomaly, which may have caused the disappearance of several Native American civilizations in the West.

“Climate change is going to affect geysers in the future,” Manga said.

Geysers could help understand volcanic eruptions

Manga and his team were unable to determine why Steamboat Geyser started up again on March 15, 2018, after three years and 193 days of inactivity, though the geyser is known for being far more variable than Old Faithful, which usually goes off about every 90 minutes. They could find no definitive evidence that new magma rising below the geyser caused its reactivation.

In this 2015 video, volcanologist Michael Manga and student Esther Adelstein describe a laboratory experiment that helps to explain how geysers like Old Faithful work. (Video by Roxanne Makasdjian and Phil Ebiner, with geyser footage by Eric King and Kristen Fauria)
 

The reactivation may have to do with changes in the internal plumbing, he said. Geysers seem to require three ingredients: heat, water and rocks made of silica — silicon dioxide. Because the hot water in geysers continually dissolves and redeposits silica, every time Steamboat Geyser erupts, it brings up about 200 kilograms, or 440 pounds of dissolved silica. Some of this silica is deposited underground and may change the plumbing system underneath the geyser. Such changes could temporarily halt or reactivate eruptions if the pipe gets rerouted, he said.

Manga has experimented with geysers in his lab to understand why they erupt periodically. In these experiments, periodic eruptions appear to be caused by loops or side chambers in the pipe that trap bubbles of steam that slowly dribble out, heating the water column above until all the water boils from the top down, explosively erupting in a column of water and steam.

Studies of water eruptions from geysers could give insight into the eruptions of hot rock from volcanoes, he said.

“What we asked are very simple questions and it is a little bit embarrassing that we can’t answer them, because it means there are fundamental processes on Earth that we don’t quite understand,” Manga said. “One of the reasons (that) we argue we need to study geysers is that if we can’t understand and explain how a geyser erupts, our hope for doing the same thing for magma is much lower.”

The research, led by UC Berkeley graduate student and first author Mara Reed, resulted from a collaboration that started in one of the annual summer workshops put on by the Cooperative Institute for Dynamic Earth Research, or CIDER. Other co-authors are Carolina Munoz-Saez of the University of Chile and Columbia University in New York, Sahand Hajimirza of Rice University in Texas, Sin-Mei Wu of the University of Utah, Anna Barth of Columbia University, Társilo Girona of the University of Alaska, Majid Rasht-Behesht of Brown University in Rhode Island, Erin White of Yellowstone National Park in Wyoming, Marianne Karplus of the University of Texas at El Paso and Shaul Hurwitz of the U.S. Geological Survey in California. The work was supported by the National Science Foundation.

RELATED INFORMATION

photo: Shaul Hurwitz/USGS

Climate change could affect famous Yellowstone geyser, Old Faithful, as paper co-authoured by EPS Chair Michael Manga shows severe drought ~800 years ago dried it up.

For more coverage:

Read article by Inside Science, Around 800 Years Ago, Yellowstone's Old Faithful Stopped Erupting

Read article by Science, Drought once shut down Old Faithful—and might again

Read article by Nature, Famed geyser Old Faithful went quiet in drought’s grip

Watch video by Weather Channel, Could Yellowstone’s Old Faithful Dry Up? Say It Isn’t So

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).

RELATED INFORMATION

 

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.

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