Study challenges reports of low fatality rate for COVID-19

by Robert Sanders, University of California - Berkeley

Credit: CC0 Public Domain

A comparison of daily deaths in Italy since January 2020 with those over the previous five years there indicates that the fatality rate in that country for those infected with the new coronavirus is at least 0.8%, far higher than that of the seasonal flu and higher than some recent estimates.

Extrapolating from the Italian data, University of California, Berkeley, and Lawrence Berkeley National Laboratory data scientists estimate that the fatality rate in New York City and Santa Clara County in California can be no less than 0.5%, or one of every 200 people infected.

These conclusions contrast with those of a study posted online last week by Stanford University epidemiologists, who pegged the fatality rate at between 0.1% and 0.2%. An affiliated team from the University of Southern California (USC) this week reported a similar fatality rate in Los Angeles.

"Their final number is much lower than our estimate," said senior author Uros Seljak, a UC Berkeley professor of physics, faculty scientist at Berkeley Lab and member of the Berkeley Institute for Data Science. He also is co-director of the Berkeley Center for Cosmological Physics (BCCP).

Seljak says that getting COVID-19 doubles your chance of dying this year.

"If you want to know what are the chances of dying from COVID-19 if you get infected, we observed that a very simple answer seems to fit a lot of data: It is the same as the chance of you dying over the next 12 months from normal causes," said Seljak.

Current uncertainties can push this number down to 10 months or up to 20 months, he added. His team discovered that this simple relation holds not only for the overall fatality rate, but also for the age stratified fatality rate, and it agrees with the data both in Italy and in the U.S.

"Our observation suggests COVID-19 kills the weakest segments of the population," Seljak said.

The paper was posted online Monday on MedRxiv in advance of peer review and submission to a journal.

Italy's deaths twice the official count

The study by Seljak and his colleagues predicts that the true number of deaths in Italy from COVID-19 is more than twice the official figure: around 50,000 people, as of April 18. The country's official statistics listed more than 150,000 confirmed cases, as of that date, and more than 20,000 attributed deaths.

The difference, the researchers say, is likely due to many deaths among older people that have not been counted in the official Italian statistics. The team found a much higher fatality rate for those over 70 years of age: In Lombardy, a region hit hard by the pandemic, those between 70 and 79 had a 2.3% infection fatality rate, while those 80 to 89 had an almost 6% fatality rate. Nearly 13% of those over 90 died.

In comparison, those 40 to 49 had a 0.04% fatality rate.

These differing fatality rates can explain the observed higher number of deaths among younger people in New York City. Because the population there is younger than in Italy, more deaths among young people are expected, despite their lower fatality rate. The researchers predict that about 26% of all deaths from COVID-19 in New York City will be among those younger than 65.

The population of Italy, on the other hand, is older, yielding a higher overall fatality rate for the country's population: 0.8%, versus 0.5% for New York. Only 10% of Italian deaths will be younger than 65.

The team also estimated, based on the predicted fatality rate for those infected with the new coronavirus and the positivity rate for those tested for COVID-19 in New York City, that about one-quarter of that city's population has been infected with the virus. This agrees with the recent announcement by New York Gov. Andrew Cuomo of 21% infection.

The team's predicted infection rate for Santa Clara is around 1%, while that for Los Angeles is around 2%, based on current mortality rates.

Given known infection and fatality rates on the Diamond Princess cruise ship, the team also calculated an upper limit on the fatality rate for those infected: about twice the lower limit, or 1%, for New York City and Santa Clara County.

Uncertainty fueled by lack of diagnostic tests

Uncertainty about the fatality rate for those infected by the new virus, dubbed SARS-CoV-2, resulted from delays in testing, due to a shortage of test kits and testing labs. This left public health officials in the dark about the true rate of infection in the general population, which is needed to calculate what percentage of infected people die.

The Stanford study estimated an infection rate in Santa Clara County of between 2.5% and 4.2% of residents, whereas the USC study estimated an infection rate in Los Angeles between 2.8% and 5.6%. Both are much higher than previous estimates, which means the number of confirmed COVID-positive deaths relative to those infected dropped to a low of 0.2%.

Based on these studies, some of the Stanford authors have argued that COVID-19 is little worse than the seasonal flu, casting doubt on decisions to mandate shelter-in-place and the closing of many businesses.

"Of course, it (the infection fatality rate) matters, for policy decisions," Seljak said. "Is this just a bad case of flu, as they would like to claim, or is it something much more serious?"

To answer that question, Seljak and his colleagues mined a previously untapped source of data: the daily death rate for 1,688 towns in Italy between Jan. 1 and April 4 for the years 2015 through 2020, provided by the Italian Institute of Statistics. The excess deaths between January and April of this year, presumably due to COVID-19, can be used to calculate a lower limit for the death rate from the virus.

"The dataset is a treasure trove for statistical analysis of COVID-19 mortality," Seljak said. "For example, it can give mortality rate as a function of age better than any other data out there, a sad consequence of tens of thousands of deaths from COVID-19 in Italy. With this data, we established that if one gets infected and is above 90 years of age, the probability of dying is at least 10%, because that is the fraction of the entire population of Bergamo province in this age group that died. In contrast, the corresponding number for ages 40 to 49 is 0.04%, far lower than previous estimates."

The Lombardy region of Italy, for example, was a viral hotspot, with the province of Bergamo hardest hit: The infection spread to so many people in Bergamo—likely two-thirds of the population, if not the entire population—that it is possible that so-called herd immunity has set in, Seljak said. That means that enough people are immune, at least temporarily, to stanch the spread of the virus among the the uninfected.

With essentially everyone in Bergamo infected, and the known deaths since January—predicted to be more than 6,000 out of a population of 1 million—it was easy to calculate the lowest possible infected fatality rate: 0.56%.

For Lombardy, the researchers estimated that the lowest possible fatality rate was even higher: about 0.84%. They also estimated that 23% of the population of Lombardy was infected, as of April 18—on average, 35 times the number of positive tests in the province.

The team conducted an analysis for all Italian towns that reported daily death data and for all age groups, using a counterfactual analysis: estimating the expected number of deaths daily between January and April 2020, based on the previous five years, and comparing those numbers with reported deaths. The excess is assumed to be due to COVID-19. The researchers employed statistical methods often used in analyzing large sets of data: the Conditional Mean with a Gaussian process (CGP) and a Synthetic Control Method (SCM).

In nearly all towns, the excess deaths in early 2020 exceeded the official count attributed to COVID-19.

The numbers the team came up with are lower limits, the researchers emphasize, since deaths in many Italian towns are not fully up to date.

"Some of my colleagues think that we have been overly conservative, which might be true," Seljak said. "We have just accounted for the people who have died up until today, but people are still dying."

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More information: Chirag Modi et al. Total COVID-19 Mortality in Italy: Excess Mortality and Age Dependence through Time-Series Analysis, (2020). DOI: 10.1101/2020.04.15.20067074

Provided by University of California - Berkeley 

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Engineers develop precision injection system for plants

by David L. Chandler, Massachusetts Institute of Technology

A microinjection device (red) is attached to a citrus tree, providing a way of injecting pesticide or other materials directly into the plant's circulatory system. Credit: Massachusetts Institute of Technology

While the human world is reeling from one pandemic, there are several ongoing epidemics that affect crops and put global food production at risk. Oranges, olives, and bananas are already under threat in many areas due to diseases that affect plants' circulatory systems and that cannot be treated by applying pesticides.

A new method developed by engineers at MIT may offer a starting point for delivering life-saving treatments to plants ravaged by such diseases.

These diseases are difficult to detect early and to treat, given the lack of precision tools to access plant vasculature to treat pathogens and to sample biomarkers. The MIT team decided to take some of the principles involved in precision medicine for humans and adapt them to develop plant-specific biomaterials and drug-delivery devices.

The method uses an array of microneedles made of a silk-based biomaterial to deliver nutrients, drugs, or other molecules to specific parts of the plant. The findings are described in the journal Advanced Science, in a paper by MIT professors Benedetto Marelli and Jing-Ke-Weng, graduate student Yunteng Cao, postdoc Eugene Lim at MIT, and postdoc Menglong Xu at the Whitehead Institute for Biomedical Research.

The microneedles, which the researchers call phytoinjectors, can be made in a variety of sizes and shapes, and can deliver material specifically to a plant's roots, stems, or leaves, or into its xylem (the vascular tissue involved in water transportation from roots to canopy) or phloem (the vascular tissue that circulates metabolites throughout the plant). In lab tests, the team used tomato and tobacco plants, but the system could be adapted to almost any crop, they say. The microneedles can not only deliver targeted payloads of molecules into the plant, but they can also be used to take samples from the plants for lab analysis.

The work started in response to a request from the U.S. Department of Agriculture for ideas on how to address the citrus greening crisis, which is threatening the collapse of a $9 billion industry, Marelli says. The disease is spread by an insect called the Asian citrus psyllid that carries a bacterium into the plant. There is as yet no cure for it, and millions of acres of U.S. orchards have already been devastated. In response, Marelli's lab swung into gear to develop the novel microneedle technology, led by Cao as his thesis project.

The disease infects the phloem of the whole plant, including roots, which are very difficult to reach with any conventional treatment, Marelli explains. Most pesticides are simply sprayed or painted onto a plant's leaves or stems, and little if any penetrates to the root system. Such treatments may appear to work for a short while, but then the bacteria bounce back and do their damage. What is needed is something that can target the phloem circulating through a plant's tissues, which could carry an antibacterial compound down into the roots. That's just what some version of the new microneedles could potentially accomplish, he says.

"We wanted to solve the technical problem of how you can have a precise access to the plant vasculature," Cao adds. This would allow researchers to inject pesticides, for example, that would be transported between the root system and the leaves. Present approaches use "needles that are very large and very invasive, and that results in damaging the plant," he says. To find a substitute, they built on previous work that had produced microneedles using silk-based material for injecting human vaccines.

"We found that adaptations of a material designed for drug delivery in humans to plants was not straightforward, due to differences not only in tissue vasculature, but also in fluid composition," Lim says. The microneedles designed for human use were intended to biodegrade naturally in the body's moisture, but plants have far less available water, so the material didn't dissolve and was not useful for delivering the pesticide or other macromolecules into the phloem. The researchers had to design a new material, but they decided to stick with silk as its basis. That's because of silk's strength, its inertness in plants (preventing undesirable side effects), and the fact that it degrades into tiny particles that don't risk clogging the plant's internal vasculature systems.

They used biotechnology tools to increase silk's hydrophilicity (making it attract water), while keeping the material strong enough to penetrate the plant's epidermis and degradable enough to then get out of the way.

Sure enough, they tested the material on their lab tomato and tobacco plants, and were able to observe injected materials, in this case fluorescent molecules, moving all they way through the plant, from roots to leaves.

"We think this is a new tool that can be used by plant biologists and bioengineers to better understand transport phenomena in plants," Cao says. In addition, it can be used "to deliver payloads into plants, and this can solve several problems. For example, you can think about delivering micronutrients, or you can think about delivering genes, to change the gene expression of the plant or to basically engineer a plant."

"Now, the interests of the lab for the phytoinjectors have expanded beyond antibiotic delivery to genetic engineering and point-of-care diagnostics," Lim adds.

For example, in their experiments with tobacco plants, they were able to inject an organism called Agrobacterium to alter the plant's DNA—a typical bioengineering tool, but delivered in a new and precise way.

So far, this is a lab technique using precision equipment, so in its present form it would not be useful for agricultural-scale applications, but the hope is that it can be used, for example, to bioengineer disease-resistant varieties of important crop plants. The team has also done tests using a modified toy dart gun mounted to a small drone, which was able to fire microneedles into plants in the field. Ultimately, such a process might be automated using autonomous vehicles, Marelli says, for agricultural-scale use.

Meanwhile, the team continues to work on adapting the system to the varied needs and conditions of different kinds of plants and their tissues. "There's a lot of variation among them, really," Marelli says, so you need to think about having devices that are plant-specific. For the future, our research interests will go beyond antibiotic delivery to genetic engineering and point-of-care diagnostics based on metabolite sampling."


Explore further

Hormone produced in starved leaves stimulates roots to take up nitrogen

More information: Yunteng Cao et al. Precision Delivery of Multiscale Payloads to Tissue‐Specific Targets in Plants, Advanced Science (2020). DOI: 10.1002/advs.201903551

Provided by Massachusetts Institute of Tech

New study finds connection between fault roughness and the magnitude of earthquakes

by McGill University

Credit: McGill University

A new study led by McGill University has found that tectonic plates beneath the Earth's surface can show varying degrees of roughness and could help explain why certain earthquakes are stronger than others.


Earthquakes happen when the rocks beneath the Earth's surface break along geological fault lines and slide past each other. The properties of these faults—such as the roughness of their surface—can have an influence on the size of seismic events, however their study has been challenging because they are buried deep beneath the Earth's surface.

In order to have a better understanding of the characteristics of these faults, researchers from McGill University, the University of California Santa Cruz and Ruhr University Bochum in Germany used high-resolution seismic reflection data to map and measure the roughness of 350 km2 of a plate boundary fault located off the Pacific coast of Costa Rica.

"We already knew that the roughness of a fault was an important factor, but we did not know how rough faults in the subsurface truly are, nor how variable the roughness is for a single fault," says James Kirkpatrick, a professor in McGill's Department of Earth and Planetary Sciences.

Rougher surfaces of faults may explain earthquake magnitude

In a recently published study in Nature Geoscience, Kirkpatrick and his colleagues were able to show that some parts of the studied fault have a rougher surface than others.

Historically, the earthquakes that have occurred in this part of the world have been moderately large (M7) and Kirkpatrick, who is also the study's first author, believes the rough patches they found might be the reason why.

"These rough patches are stronger and more resistant to earthquake slip," he says. "The historical record of earthquakes is relatively short, so we can't say with certainty that larger ones have not occurred. Future seismic events in the area, which will be recorded with modern equipment, should help us determine if they show the same limited magnitude."

Kirkpatrick and his colleagues also hope to apply their methods to other subduction zones where similar geophysical data is available to start to evaluate whether their conclusions are generally applicable.

"This connection between the fault roughness and earthquake magnitude might one day help us understand the size and style of earthquakes most likely to occur a given fault."


Explore further

Seismic biomarkers in Japan Trench fault zone reveal history of large earthquakes
More information: James D. Kirkpatrick et al, Subduction megathrust heterogeneity characterized from 3D seismic data, Nature Geoscience (2020). DOI: 10.1038/s41561-020-0562-9

Journal information: Nature Geoscience 

Provided by McGill University

North Atlantic right whales are in much poorer condition than Southern right whales

by Woods Hole Oceanographic Institution

A female North Atlantic right whale with her calf. Credit: Public Domain

New research by an international team of scientists reveals that endangered North Atlantic right whales are in much poorer body condition than their counterparts in the southern hemisphere.

This alarming research, led by Dr. Fredrik Christiansen from Aarhus University in Denmark, was published this week in the journal Marine Ecology Progress Series. The study is the result of a collaborative effort by scientist from 12 institutions across 5 nations. Among the coauthors are Senior Scientist Peter Corkeron and Associate Scientist Heather Pettis of the Anderson Cabot Center for Ocean Life at the New England Aquarium and Michael Moore and Carolyn Miller of the Woods Hole Oceanographic Institution.

The analyses revealed that individual North Atlantic right whales—juveniles, adults and mothers—were all in poorer body condition than individual whales from the three populations of Southern right whales. This is alarming, since poor body condition for North Atlantic right whales helps explain why too many of them are dying and why they are not giving birth to enough calves. It could also be affecting their growth and delaying juveniles reaching sexual maturity. These combined impacts on individuals help explain why the species is in decline.

Since the cessation of large-scale commercial whaling in the last century, most populations of southern right whales have recovered well. Now there are about 10,000-15,000 southern right whales. Unfortunately, the same cannot be said for the North Atlantic right whales, found today mostly off the east coast of North America. There are now around 410 individuals left, and the species is heading to extinction. Lethal vessel strikes and entanglement in fishing gear continue to kill these whales. Individual North Atlantic right whales also have to cope with the energetic expense and other costs that are caused by frequent entanglements in fishing gear, in particular lobster and crab pots. These burdens, along with a change in the abundance and distribution of the rice-sized plankton that they eat, have left these whales thin and unhealthy, which makes them less likely to have a calf. This, in turn, contributes to the current overall decline of the species. To quantify "thin and unhealthy," Dr. Christiansen and his colleagues investigated the body condition of individual North Atlantic right whales and compared their condition with individuals from three increasing populations of Southern right whales: off Argentina, Australia and New Zealand.

"Good body condition and abundant fat reserves are crucial for the reproduction of large whales, including right whales, as the animals rely on these energy stores during the breeding season when they are mostly fasting," said Dr. Christiansen. Stored fat reserves are particularly important for mothers, who need the extra energy to support the growth of their newly born calf while they are nursing.

The study is the largest assessment of the body condition of baleen whales in the world. The international research team used drones and a method called aerial photogrammetry to measure the body length and width of individual right whales in these four regions around the world. From aerial photographs, the researchers estimated the body volume of individual whales, which they then used to derive an index of body condition or relative fatness.

"This started out as a conversation between a few of us over dinner at a conference in 2015. Now that the results are out, they're quite shocking," said Peter Corkeron of the Anderson Cabot Center for Ocean Life at the New England Aquarium. "We know that North Atlantic right whales as a species are doing poorly, but this work brings home that as individuals, they're also doing poorly. Their decline has been so rapid that we know it's not simply because not enough calves are being born—too many whales are also dying from human-caused injuries. But this study also shows that their decline isn't solely due to these deaths. Their problems are more insidious, and we need to find a way to ensure that the health of all individual whales improves."

"For North Atlantic right whales as individuals, and as a species, things are going terribly wrong. This comparison with their southern hemisphere relatives shows that most individual North Atlantic right whales are in much worse condition than they should be," said Michael Moore from the Woods Hole Oceanographic Institution. "As a veterinarian, I've long been concerned about how entanglements affect the welfare of these whales. Now we are starting to draw the linkages from welfare to this species' decline. Sub-lethal entanglement trauma, along with changing food supplies is making them too skinny to reproduce well, and lethal entanglement and vessel trauma are killing them. To reverse these changes, we must: redirect vessels away from, and reduce their speed in, right whale habitat; retrieve crab and lobster traps without rope in the water column using available technologies; and minimize ocean noise from its many sources."

This work was supported by funding from NOAA, US Office of Naval Research Marine Mammals Program, World Wildlife Fund for Nature Australia, Murdoch University School of Veterinary and Life Sciences, New Zealand Antarctic Research institute, Otago University and New Zealand Whale and Dolphin Trust and Argentina National Geographic Society.

For 40 years, the New England Aquarium's right whale team has extensively researched and tracked individual right whales and curates the North Atlantic Right Whale Catalog. The scientific team monitors the whales' arrival at breeding and feeding grounds, registering new calves, death rates, and also measuring changes in stress and reproductive hormones.

The Woods Hole Oceanographic Institution is dedicated to advancing knowledge of the ocean and its connection with the Earth system through a sustained commitment to excellence in science, engineering and education, and to the application of this knowledge to problems facing society

Lobstering gear could be reduced, changed to save whales

More information: F Christiansen et al. Population comparison of right whale body condition reveals poor state of the North Atlantic right whale, Marine Ecology Progress Series (2020). DOI: 10.3354/meps13299

Journal information: Marine Ecology Progress Series 

New research explores the impact of cover crop residues on weed control

by Cambridge University Press

Credit: CC0 Public Domain

Cover crops have a well-documented role to play in suppressing troublesome weeds. But what happens as those cover crops degrade?

A new study featured in the journal Weed Science explores whether cover-crop residues help to suppress summer annual weeds and promote greater crop yields. Researchers planted single cover-crop treatments of cereal rye, hairy vetch, crimson clover and forage radish in the fall, as well as two-way and three-way mixtures. Each was followed by corn and soybean crops.

The team tracked the biomass of each cover crop and the residual components produced—uncovering several key trends. They found that cover-crop biomass and the ratio of carbon to nitrogen influenced weed suppression and its duration. For example, a 9 to 1 ratio of carbon to nitrogen suppressed pigweed by 50 percent at four weeks after treatment, while a 20 to 1 ratio delivered the same level of control eight weeks after treatment.

Similarly, a cover-crop biomass of 2,800 kg per hectare was needed for 50 percent suppression four weeks after treatment, while a biomass of 6,610 kg per hectare was needed for the same level of suppression at eight weeks after treatment.

In fields where the cover crop was the only weed control measure used, corn and soybean yields increased as both cover crop biomass and carbon to nitrogen ratios increased.

Researchers found that most mixtures of cover crops produced more biomass than individual cover crops alone. Carbon to nitrogen ratios produced by cereal rye and a cereal rye-forage radish mixture were 36 to 1—greater than all the other cover crop treatments. Hairy vetch and crimson clover had ratios of 12 to 1 and 17 to 1, which were the lowest ratios produced by any of the cover crops.

"Our study shows that the biomass of the cover crop isn't all that matters," says Kara Pittman of Virginia Tech, lead researcher for the study. "The composition of the residues the cover crop leaves behind are also important to weed control."

Impacts of cover crop planting dates on soil properties after 4 years

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More information: Kara B. Pittman et al, Cover crop residue components and their effect on summer annual weed suppression in corn and soybean, Weed Science (2020). DOI: 10.1017/wsc.2020.16

The basis of glyphosate resistance in amaranth

by American Society of Plant Biologists

Glyphosate-resistant Palmer amaranth in a cotton field. Credit: William T. Molin

William T. Molin (U.S. Department of Agriculture-Agricultural Research Service, Stoneville, MS) teamed up with Allison Yaguchi, Mark Blenner, and Christopher A. Saski (Clemson University, SC) to sequence and dissect the structure of the extrachromosomal DNA replicon that underlies the molecular and biochemical basis of resistance to the herbicide glyphosate in Palmer amaranth (Amaranthus palmeri). This work aids our understanding of adaptive evolution in plants and has implications for optimizing pesticide use in the environment.

Glyphosate is a widely used broad-spectrum herbicide that targets both broadleaf plants and grasses (dicots and monocots). It kills plants by inhibiting the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), found only in plants and in some bacteria. EPSPS is a key enzyme for the biosynthesis of essential amino acids and is an ideal target for herbicides because animals and humans use another enzyme that is insensitive to glyphosate to fulfill the same function. Some plants, including A. palmeri, can develop resistance to glyphosate toxicity by massively raising the expression of the EPSPS gene during glyphosate stress, essentially flooding the system with extra EPSPS enzyme and thereby counteracting the effects of the herbicide.

Making more copies of a gene is one possible means to increase gene expression: the phenomenon of amplification of genes or gene clusters is a common stress-avoidance mechanism in animals, plants, and microorganisms and is at play here. The amplified genes are often contained within extrachromosomal circular DNA (eccDNA) fragments known as replicons, circles of DNA that are maintained and replicated outside of the normal linear chromosomes in an organism. In humans, eccDNA is a prevalent feature of many cancers and a variety of diseases associated with developmental defects and premature aging. In such cases, eccDNAs carry oncogenes and other genes that may boost the survival and proliferation of diseased cells.

Molin et al. provide the complete sequence of the eccDNA replicon responsible for glyphosate resistance in A. palmeri, reveal its structural organization and genomic content, and examine some of the features that enable it to replicate and persist in the genome through multiple generations. The eccDNA replicon was found to contain 59 genes, a subset of which (including the EPSPS gene) show higher expression after treatment of the resistant plants with glyphosate. In addition to the presence of amplified genes, the eccDNA structure consists of a complex arrangement of repeated sequences and mobile genetic elements—so-called transposable elements—that might play a role in its maintenance and replication based on analogy with other eccDNAs. Author Christopher Saski noted that "the DNA content of the eccDNA replicon is sophisticated. Sequencing this element was difficult, and this complete assembly became possible only when DNA sequencing technology advanced to the single-molecule level, such as developed by Pacific Biosciences" (the biotechnology company that pioneered these methods, based in Menlo Park, CA).

Since the introduction of glyphosate in the 1970s, the rise of glyphosate-resistant weeds has been a growing problem in agricultural settings. The original glyphosate-resistant amaranth weedy plant that started this project was collected from a soybean field that had been routinely sprayed with the herbicide for a decade. The origin of this eccDNA replicon is unknown but is likely a result of transposable element activation and genomic shuffling that might have been pushed along by the use of glyphosate. That is, plants like A. palmeri that contain the eccDNA are able to survive and propagate where glyphosate is used frequently; additionally, glyphosate stress might contribute to the activation of the transposable elements that influence eccDNA formation and activity. Understanding the complete genomic structure and function of the eccDNA replicon will aid our knowledge of how glyphosate resistance develops and evolves in plants and help to further refine herbicide treatment strategies and combat the rise of resistant weeds.

The authors also identified structural features consistent with tethering of the eccDNA to chromosomes, which may facilitate maintenance of the fragment during normal cellular mitosis. Future work will focus on how the eccDNA self-replicates in plant cells, and identifying the essential functional elements of the replicon. This discovery could lead to "new approaches to genome engineering and the possibility of expressing useful agronomic traits outside of the nuclear genome," said Saski.Researchers make breakthrough in glyphosate resistance in pigweeds

More information: Plant Cell, DOI: 10.1105/tpc.20.00099

Journal information: Plan Cell 

Provided by American Society of Plant Biologists

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Supreme Court rejects EPA's narrow view of Clean Water Act

by Mark Sherman

In this March 16, 2020, file photo, a tree blooms outside the Supreme Court in Washington. The Supreme Court ruled Thursday, April 23, that sewage plants and other industries cannot avoid environmental requirements under landmark clean-water protections when they send dirty water on an indirect route to rivers, oceans and other navigable waterways. (AP Photo/Patrick Semansky, File)

The Supreme Court ruled Thursday that sewage plants and other industries cannot avoid environmental requirements under landmark clean-water protections when they send dirty water on an indirect route to rivers, oceans and other navigable waterways.

Rejecting the Trump administration's views, the justices held by a 6-3 vote that the discharge of polluted water into the ground, rather than directly into nearby waterways, does not relieve an industry of complying with the Clean Water Act.

"We hold that the statute requires a permit when there is a direct discharge from a point source into navigable waters or when there is the functional equivalent of a direct discharge," Justice Stephen Breyer wrote for the court.

The decision came in a closely watched case from Hawaii about whether a sewage treatment plant needs a federal permit when it sends wastewater deep underground, instead of discharging the treated flow directly into the Pacific Ocean. Studies have found the wastewater soon reaches the ocean and has damaged a coral reef near a Maui beach.

The Environmental Protection Agency under President Donald Trump reversed the agency's position that Breyer noted has appeared to work well for more than 30 years. That's among many actions the administration has taken to change course on environmental regulations, including making official just days ago a sweeping rollback of the Clean Water Act that would end federal protection for many of the nation's millions of miles of streams, arroyos and wetlands. Public health and environmental groups and some Western states, among other opponents, say the rollback would leave the waterways more vulnerable to pollution from development, industry and farms, and they have promised court fights.

In the Hawaii case, Justices Samuel Alito, Neil Gorsuch and Clarence Thomas dissented. "Based on the statutory text and structure, I would hold that a permit is required only when a point source discharges pollutants directly into navigable waters," Thomas wrote.

David Henkin, a lawyer for the environmental group Earthjustice who argued the case in the high court, said, "This is unquestionably a win for people who are concerned about protecting clean water in the United States."

Sewage plants and other polluters must get a permit under the Clean Water Act when pollutants go through a pipe from their source to a body of water. The question in this case was whether a permit is needed when the pollutant first passes through the soil or groundwater.

Maui injects 3 million to 5 million gallons a day of treated wastewater into wells beneath the Lahaina Wastewater Reclamation Facility, which sits about a half-mile from the Pacific shoreline. Environmental groups in Hawaii sued Maui after studies using dyes to trace the flow showed more than half the discharge from two wells was entering the ocean in a narrow area. They won a ruling from the federal appeals court based in San Francisco.

Breyer raised concerns during arguments in November that a ruling for Maui would provide a "road map" for polluters to evade federal permit requirements.

Still, the court did not go as far as the federal appeals court, which adopted a standard that would have brought even more groundwater discharges under the clean water law.

© 2020 The Associated Press. 

Learn from past to protect oceans

by University of Exeter

Oyster fishing in the eastern US. Image shows oyster fishery, cannery of Pearson & Co., Baltimore. Credit: NOAA Photo Library

History holds valuable lessons—and stark warnings—about how to manage fisheries and other ocean resources, a new study says.

Researchers examined 20 historical examples of fisheries and aquaculture (fish farming), dating from 40 to 800 years ago.The study, led by the universities of Exeter, Hull and Boston, found consistent patterns that resulted in so-called "blue growth"—the development of sustainable ocean economies that benefitted whole communities.

It also noted common "recipes for failure"—and the authors say these offer grave warnings for today.

"Our aim was to see if we could learn from past successes and failures," said Dr. Ruth Thurstan, of the Centre for Ecology and Conservation at the University of Exeter's Penryn Campus in Cornwall.

"We often assume our problems are new, but a look at the past shows societies have faced similar issues before—though many of our challenges today are on a bigger scale.

"Some past societies ultimately failed at blue growth, while others succeeded in balancing economic growth, social equity and sustainability for varying lengths of time."

Dr. Thurstan added: "In basic terms, success came when societies managed to achieve fair—rather than unlimited or open—access to resources, and when they were responsive to change.

"Basing decisions on evidence, getting all parties involved and planning for the long-term were also key.

"Failure occurred when short-term gains were prioritised over long-term sustainability."

Dr. Bryony Caswell, of the School of Geography, Geology and the Environment at the University of Hull said: "Worryingly, the recipes for success that we discovered are rarely included in even the most advanced blue growth agendas today.

"The seas are destined to play an ever-more vital role in food security. If we don't take this chance to learn from history, we may be condemning ourselves to repeating past mistakes."

The study, by an international team of 28 historians, environmental scientists and marine ecologists, looked at examples from around the world.

These included:

• Galway Bay in Ireland where, before the 1850s, community-based management led to equitable access and sustainable management of fish stocks. In the 1850s, trawlers from England arrived. Locally agreed rules were ignored and fish stocks were over-exploited.
• In the Lagoon of Venice, Italy, local regulations achieved a "balance" between the economic freedom of citizens and the protection of shared resources, lasting from the 12th to the 18th Century. After that, political instability and growing demand for food led to regulations being scrapped, resulting in over-exploitation.
• In Japan, access to seaweed resources that benefitted the majority rather than a minority of people, use of traditional knowledge systems and enhanced seaweed cultivation techniques, helped achieve a balance between market demand and ecological sustainability from the 1600s onwards.
• In the east USA, two centuries of over-exploitation and worsening water quality led to a 20th Century collapse of once-widespread oyster reefs. While oyster production today is still far lower than historical levels, a growing appreciation of their benefits to coastal ecosystems has led to large-scale efforts by local communities to restore oyster reefs.

"The question is, can our modern societies achieve blue growth rather than exploiting and depleting our oceans?" said Dr. Emily Klein, of the Frederick S. Pardee Center for the Study of the Longer-Range Future, Boston University.

"History shows us that there are ways to balance sustainability, social equity and economic growth.

"It is difficult, but we believe there are opportunities to make it happen—especially if we can learn from the past."

The paper, published in the journal Fish and Fisheries, is entitled: "Something old, something new: Historical perspectives provide lessons for blue growth agendas."

East African fish in need of recovery

More information: Bryony A. Caswell et al, Something old, something new: Historical perspectives provide lessons for blue growth agendas, Fish and Fisheries (2020). DOI: 10.1111/faf.12460

Journal information: Fish and Fisheries 

No time to waste to avoid future food shortages

by ARC Centre of Excellence for Translational Photosynthesis

Professor Robert Furbank, CoETP Director and Professor John Evans, CoETP Chief investigator at the ANU glasshouses in Canberra, Australia Credit: Natalia Bateman, ARC Centre of Excellence for Translational Photosynthesis

During the past few weeks, empty supermarket shelves, without pasta, rice and flour due to panic buying, has caused public concerns about the possibility of running out of food. Australian farmers have reassured consumers saying that the country produces enough food to feed three times its population. However, will this statement remain true in ten to twenty years in a country severely affected by climate change? The answer is yes, if we are prepared for this and if there is continuous funding towards creating solutions to increase crop production.


"Plant scientists are punching above their weight by participating in global, interdisciplinary efforts to find ways to increase crop production under future climate change conditions. We essentially need to double the production of major cereals before 2050 to secure food availability for the rapidly growing world population," says ANU Professor Robert Furbank from the ARC Centre of Excellence for Translational Photosynthesis (CoETP).

"It is similar to finding a virus vaccine to solve a pandemic, it doesn't happen overnight. We know that Australia's agriculture is going to be one area of the world that is most affected by climate extremes, so we are preparing to have a toolbox of plant innovations ready to ensure global food security in a decade or so, but to do this we need research funding to continue," Professor Furbank says.

Several examples of these innovative solutions were published recently in a special issue on Food Security Innovations in Agriculture in the Journal of Experimental Botany, including five reviews and five research articles.

Co-editor of the Special Issue, ANU Professor John Evans, says that this publication highlights the now widely accepted view that improving photosynthesis—the process by which plants convert sunlight, water and CO2 into organic matter—is a new way to increase crop production that is being developed.

"We are working on improving photosynthesis on different fronts, as the articles included in this special issue show, from finding crop varieties that need less water, to tweaking parts of the process in order to capture more carbon dioxide and sunlight. We know that there is a delay of at least a decade to get these solutions to the breeders and farmers, so we need to start developing new opportunities now before we run out of options," says Professor Evans, CoETP Chief Investigator.

The special issue includes research solutions that range from traditional breeding approaches to ambitious genetic engineering projects using completely different ends of the technological spectrum; from robot tractors, to synthetic biology. All these efforts are focused on finding ways to make crops more resistant to drought and extreme climate conditions and being more efficient in the use of land and fertilisers.

"Our research is contributing to providing food security in a global context, and people often ask what that has to do with Australian farmers and my answer is everything. Aside from the fact that economy and agriculture are globally inter-connected, if Australian farmers have a more productive resilient and stable crop variety, they are able to plan for the future, which turns into a better agribusiness and at the same time, ensures global security across the world," says Professor Furbank.

Too much sugar doesn't put the brakes on turbocharged crops



















































































































More information: John R Evans et al, From green to gold: agricultural revolution for food security, Journal of Experimental Botany (2020). DOI: 10.1093/jxb/eraa110
Provided by ARC Centre of Excellence for Translational Photosynthesis

Zero-emissions Boston could save 288 lives and $2.4 billion annually

by Boston University School of Medicine

Credit: CC0 Public Domain

Air pollution from just the City of Boston contributes to nearly as many deaths across the wider region as car crashes do, as well as non-fatal cardiovascular and respiratory disease and days of missed work.

With much of the City of Boston shut down by COVID-19, the region is enjoying better air quality than it has seen in decades, a preview of the reduced emissions that will come as part of the city's ambitious "Carbon Free Boston" goals.

But what if Boston eliminated all emissions—and not just because of a pandemic, but for good? That is the question asked by a new Boston University School of Public Health (BUSPH) study published in the journal Environmental Research Letters.

The study estimates that a zero-emissions Boston would mean over 200 deaths avoided in the city (and the rest of Suffolk County) each year, with reductions in fatal and non-fatal cardiovascular and respiratory illness extending all the way from Worcester to Barnstable and into southern New Hampshire and northern Rhode Island, with 6 deaths avoided per 100,000 people in the whole region—which the researchers note is roughly equivalent to the Massachusetts motor vehicle crash fatality rate.

"Public health and climate policymaking are intertwined," says study lead author Matthew Raifman, a doctoral student in environmental health at BUSPH. "While Boston's climate policies are focused on reducing greenhouse gas emissions, these actions will also likely reduce deaths and improve the quality of life of residents of Boston and the surrounding region."

The researchers also estimated that the resulting decrease in medical costs and lost/reduced work could save $1.7 billion in Suffolk County, and $2.4 billion for the entire 75-square-mile zone modeled in the study.

"In showing the substantial health and economic benefits that clean air can bring to Boston area residents, this study demonstrates that climate action isn't just about saving the planet; it's also about making us healthier," says study senior author Dr. Patrick Kinney, Beverly Brown Professor of Urban Health and professor of environmental health at BUSPH.

Raifman, Kinney, and colleagues used the US Environmental Protection Agency's Community Multiscale Air Quality model to estimate the 2011 emissions and air quality status quo for Boston and the surrounding 75 square miles, focusing on air pollutants known to harm health: PM2.5 (particulates with a diameter of less than 2.5 micrometers, or 3 percent of the diameter of a human hair) and O3 (ozone). They then set the model's human-made emissions—including motor vehicles, generators, rail, industry, all oil- and gas-burning, shipping and boating, and residential wood fire—from within Boston's city limits to zero.

They found that a zero-emissions Boston would halve PM2.5 concentrations in the city itself, and slightly decrease concentrations for the rest of the modeled zone. Concentrations of ozone would also decrease across much of zone, although Boston and areas west of the city would actually see an increase in ozone during warmer months—which the researchers explain is because of the reduction in nitrogen oxide emissions that would normally transform ozone into other compounds.

The researchers then used the EPA's Environmental Benefits Mapping and Analysis Program (BenMAP) Community Edition v1.5 to estimate how these changes in PM2.5 and ozone would affect health at the county level. The health benefits from the decrease in PM2.5 would mainly override the health harms of increased ozone, resulting in 288 fewer deaths per year across the 75-square-mile area, mainly in Boston and the Greater Boston area. A zero-emissions Boston would also prevent 116 non-fatal heart attacks, 46 cardiovascular hospitalizations, 117 cases of chronic bronchitis, and over 17,000 asthma attacks across the zone, again mainly in Boston. However, the high ozone levels would increase emergency room visits for asthma and respiratory hospitalizations.

Looking at the effects by race and ethnicity, the researchers found that the greatest reduction in deaths and non-fatal health issues relative to population size would be in black residents, who the researchers note currently bear the greatest burden of environmental injustice and are more likely to live in Boston than any other area in the larger modeled zone.

The researchers estimated that the decrease in deaths, hospitalizations, days of missed work, and other benefits of a zero-emission Boston would translate to savings of $1.7 billion for Suffolk County, $182 million for Norfolk County, $159 million for Middlesex County, and tens of millions of dollars in savings for other surrounding counties in eastern Massachusetts and bordering states.

"In this study, we focused only on the City of Boston's climate action plan, but it's important to note that Boston's actions will not occur in a vacuum," Raifman says. "Many cities across the region are pursuing similar climate goals. The sum may be different from the parts."Health effects of China's climate policy extend across Pacific

More information: Matthew Raifman et al. Environ. Res. Lett. 2020 in press https://doi.org/10.1088/1748-9326/ab842b

Journal information: Environmental Research Letters