Collaborators at Rice University and the University of Connecticut further engineered the RNA-editing CRISPR-Cas13 system to boost their power for detecting minute amounts of the SARS-CoV-2 virus in biological samples without the time-consuming RNA extraction and amplification step necessary in gold-standard PCR testing.

The new platform was highly successful compared to PCR, finding 10 out of 11 positives and no false positives for the virus in tests on clinical samples directly from nasal swabs. The researchers showed their technique finds signs of SARS-CoV-2 in attomolar (10^-18) concentrations.

The study led by chemical and biomolecular engineer Xue Sherry Gao at Rice’s George R. Brown School of Engineering and postdoctoral researchers Jie Yang of Rice and Yang Song of Connecticut appears in Nature Chemical Biology.

Cas13, like its better-known cousin Cas9, is part of the system by which bacteria naturally defend themselves against invading phages. Since its discovery, CRISPR-Cas9 has been adapted by scientists to edit living DNA genomes and shows great promise to treat and even cure diseases.

And it can be used in other ways. Cas13 on its own can be enhanced with guide RNA to find and snip target RNA sequences, but also to find “collateral,” in this case the presence of viruses like SARS-CoV-2.

“The engineered Cas13 protein in this work can be readily adapted to other previously established platforms,” Gao said. “The stability and robustness of engineered Cas13 variants make them more suitable for point-of-care diagnostics in low-resource setting areas when expensive PCR machines are not available.”

Yang said wild-type Cas13, drawn from a bacterium, Leptotrichia wadei, cannot detect attomolar level of viral RNA within a time frame of 30 to 60 minutes, but the enhanced version created at Rice does the job in about half an hour and detects SARS-CoV-2 in much lower concentrations than the previous tests.

She said the key is a well-hidden, flexible hairpin loop near Cas13’s active site. “It’s in the middle of the protein near the catalytic site that determines Cas13’s activity,” Yang said. “Since Cas13 is large and dynamic, it was challenging to find a site to insert another functional domain.”

The researchers fused seven different RNA binding domains to the loop, and two of the complexes were clearly superior. When they found their targets, the proteins would fluoresce, revealing the presence of the virus.

“We could see the increased activity was five- or six-fold over wild-type Cas13,” Yang said. “This number seems small, but it’s quite astonishing with a single step of protein engineering.

“But that was still not enough for detection, so we moved the whole assay from a fluorescence plate reader, which is quite large and not available in low-resource settings, to an electrochemical sensor, which has higher sensitivity and can be used for point-of-care diagnostics,” she said.

With the off-the-shelf sensor, Yang said the engineered protein was five orders of magnitude more sensitive in detecting the virus compared to the wild-type protein.

The lab wants to adapt its technology to paper strips like those in home COVID-19 antibody tests, but with much higher sensitivity and accuracy. “We hope that will make testing more convenient and with lower cost for many targets,” Gao said.

The researchers are also investigating improved detection of the Zika, dengue and Ebola viruses and predictive biomarkers for cardiovascular disease. Their work could lead to rapid diagnosis of the severity of COVID-19.

“Different viruses have different sequences,” Yang said. “We can design guide RNA to target a specific sequence that we can then detect, which is the power of the CRISPR-Cas13 system.”

But because the project began just as the pandemic took hold, SARS-CoV-2 was a natural focus. “The technology is quite amenable to all the targets,” she said. “This makes it a very good option to detect all kinds of mutations or different coronaviruses.”

“We are very excited about this work as a combinational effort of structure biology, protein engineering and biomedical device development,” Gao added. “I greatly appreciate all the efforts from my lab members and collaborators.”

Co-authors of the paper are Rice postdoctoral researcher Xiangyu Deng, undergraduate Jeffrey Vanegas and graduate student Zheng You; graduate students Yuxuan Zhang and Zhengyan Weng of the University of Connecticut; microbiology supervisor Lori Avery and Kevin Dieckhaus, a professor of medicine, of UConn Health; Yi Zhang, an assistant professor of biomedical engineering at the University of Connecticut; and Yang Gao, an assistant professor of biosciences at Rice.

Xue Sherry Gao is the Ted N. Law Assistant Professor of Chemical and Biomolecular Engineering at Rice.

The National Science Foundation (2031242, 2103025), the Welch Foundation (C-1952, C-2033-20200401), and the Cancer Prevention and Research Institute of Texas (RR190046) supported the research.

Additionally, the post-COVID brain is associated with movement disorders, from tremors and involuntary muscle contractions to epileptic seizures, hearing and vision abnormalities, and balance and coordination difficulties as well as other symptoms similar to what is experienced with Parkinson’s disease.

The findings are published Sept. 22 in Nature Medicine.

“Our study provides a comprehensive assessment of the long-term neurologic consequences of COVID-19,” said senior author Ziyad Al-Aly, MD, a clinical epidemiologist at Washington University. “Past studies have examined a narrower set of neurological outcomes, mostly in hospitalized patients. We evaluated 44 brain and other neurologic disorders among both nonhospitalized and hospitalized patients, including those admitted to the intensive care unit. The results show the devastating long-term effects of COVID-19. These are part and parcel of long COVID. The virus is not always as benign as some people think it is.”

Overall, COVID-19 has contributed to more than 40 million new cases of neurological disorders worldwide, Al-Aly said.

Other than having a COVID infection, specific risk factors for long-term neurological problems are scarce. “We’re seeing brain problems in previously healthy individuals and those who have had mild infections,” Al-Aly said. “It doesn’t matter if you are young or old, female or male, or what your race is. It doesn’t matter if you smoked or not, or if you had other unhealthy habits or conditions.”

Few people in the study were vaccinated for COVID-19 because the vaccines were not yet widely available during the time span of the study, from March 2020 through early January 2021. The data also predates delta, omicron and other COVID variants.

A previous study in Nature Medicine led by Al-Aly found that vaccines slightly reduce — by about 20% — the risk of long-term brain problems. “It is definitely important to get vaccinated but also important to understand that they do not offer complete protection against these long-term neurologic disorders,” Al-Aly said.

The researchers analyzed about 14 million de-identified medical records in a database maintained by the U.S. Department of Veterans Affairs, the nation’s largest integrated health-care system. Patients included all ages, races and sexes.

They created a controlled data set of 154,000 people who had tested positive for COVID-19 sometime from March 1, 2020, through Jan. 15, 2021, and who had survived the first 30 days after infection. Statistical modeling was used to compare neurological outcomes in the COVID-19 data set with two other groups of people not infected with the virus: a control group of more than 5.6 million patients who did not have COVID-19 during the same time frame; and a control group of more than 5.8 million people from March 2018 to December 31, 2019, long before the virus infected and killed millions across the globe.

The researchers examined brain health over a year-long period. Neurological conditions occurred in 7% more people with COVID-19 compared with those who had not been infected with the virus. Extrapolating this percentage based on the number of COVID-19 cases in the U.S., that translates to roughly 6.6 million people who have suffered brain impairments associated with the virus.

Memory problems — colloquially called brain fog — are one of the most common brain-related, long-COVID symptoms. Compared with those in the control groups, people who contracted the virus were at a 77% increased risk of developing memory problems. “These problems resolve in some people but persist in many others,” Al-Aly said. “At this point, the proportion of people who get better versus those with long-lasting problems is unknown.”

Interestingly, the researchers noted an increased risk of Alzheimer’s disease among those infected with the virus. There were two more cases of Alzheimer’s per 1,000 people with COVID-19 compared with the control groups. “It’s unlikely that someone who has had COVID-19 will just get Alzheimer’s out of the blue,” Al-Aly said. “Alzheimer’s takes years to manifest. But what we suspect is happening is that people who have a predisposition to Alzheimer’s may be pushed over the edge by COVID, meaning they’re on a faster track to develop the disease. It’s rare but concerning.”

Also compared to the control groups, people who had the virus were 50% more likely to suffer from an ischemic stroke, which strikes when a blood clot or other obstruction blocks an artery’s ability to supply blood and oxygen to the brain. Ischemic strokes account for the majority of all strokes, and can lead to difficulty speaking, cognitive confusion, vision problems, the loss of feeling on one side of the body, permanent brain damage, paralysis and death.

“There have been several studies by other researchers that have shown, in mice and humans, that SARS-CoV-2 can attack the lining of the blood vessels and then then trigger a stroke or seizure,” Al-Aly said. “It helps explain how someone with no risk factors could suddenly have a stroke.”

Overall, compared to the uninfected, people who had COVID-19 were 80% more likely to suffer from epilepsy or seizures, 43% more likely to develop mental health disorders such as anxiety or depression, 35% more likely to experience mild to severe headaches, and 42% more likely to encounter movement disorders. The latter includes involuntary muscle contractions, tremors and other Parkinson’s-like symptoms.

COVID-19 sufferers were also 30% more likely to have eye problems such as blurred vision, dryness and retinal inflammation; and they were 22% more likely to develop hearing abnormalities such as tinnitus, or ringing in the ears.

“Our study adds to this growing body of evidence by providing a comprehensive account of the neurologic consequences of COVID-19 one year after infection,” Al-Aly said.

Long COVID’s effects on the brain and other systems emphasize the need for governments and health systems to develop policy, and public health and prevention strategies to manage the ongoing pandemic and devise plans for a post-COVID world, Al-Aly said. “Given the colossal scale of the pandemic, meeting these challenges requires urgent and coordinated — but, so far, absent — global, national and regional response strategies,” he said.

Groundwater — the water contained in porous and fractured rocks underground — is the largest freshwater source on Earth apart from the ice caps and glaciers. It feeds into rivers, lakes, and other surface water bodies and is essential for ecosystems. In addition, groundwater systems are an integral part of agricultural irrigation, especially in regions with scarce surface water resources.

Existing large-scale models tend to oversimplify groundwater flow, often do not adequately integrate human water management, and operate at coarser resolutions than needed for modeling small-scale hydrologic processes. In a new study in Geoscientific Model Development, a team of IIASA researchers coupled the Community Water Model (CWatM) (Burek et al., 2020) with the groundwater flow model MODFLOW, allowing for the reproduction of water tables at very fine spatial resolutions. The integrated model simulates hydrological processes occurring in soil and surface water bodies at the hillslope scale, with grid cells smaller than 1 km. It can be used to model water cycles at various geographical levels, ranging from small basins to entire countries.

By comparing the Austrian Seewinkel region and the Indian Bhima basin, extending over 573 and 46,000 km² respectively, the researchers tested the model’s capacity to adequately reproduce water tables under different climatic, geological, and socioeconomic conditions. The simulated results were validated with observed water table depths and fluctuations over a period of 35 years in Seewinkel and 16 years in Bhima.

“These biophysical models are important because water cycles need to be quantified for proper water management. We can study how local and regional water processes interact by linking models at different scales. In particular, a model like CWatM-MODFLOW is a useful tool to project the impact of future water management plans, land cover changes, or climate change,” says Luca Guillaumot, the study’s lead author and a researcher in the IIASA Water Security Research Group (currently at the French weather research center — CNRM).

Furthermore, the authors used the model to assess the impact of groundwater-based irrigation on the water cycle in the two regions under investigation. They found that irrigation increases the amount of water that moves into the atmosphere through evaporation from soil and transpiration through plant tissues, but reduces groundwater support to rivers and humid areas, especially during dry seasons. The results also indicate that the water table is deeper in areas with intense irrigation pumping.

Despite persistent challenges in reproducing water table depth patterns and calibrating the model at resolutions as fine as possible (~100m), the study represents a significant improvement in large-scale hydrological modeling.

“Humans are transforming the Earth’s water systems. IIASA water models can answer important questions about how we affect regional and global water systems at different spatial and temporal scales. Regional stakeholders, including policymakers, can use this information to construct realistic water management scenarios,” concludes study coauthor and IIASA Biodiversity and Natural Resources Program Director Yoshihide Wada.

Global warming is caused by the emission of greenhouse gases. According to the Intergovernmental Panel on Climate Change (IPCC), by 2019 the temperature had risen by 1.1 degrees Celsius compared to pre-industrial levels. However, at the same time, the combustion of fossil fuels emits aerosols, in the form of pollutant particles such as soot or sulfuric acid, which cool our climate. They reflect sunlight and also increase the reflectivity of clouds. According to the IPCC, the presence of aerosols in the atmosphere caused the climate to be 0.5 degrees Celsius cooler in 2019 than without them. Other effects such as land use change also play a role.

Study documents widespread evidence of this reduced cooling climate effect

In a new international analysis, Professor Johannes Quaas, a meteorologist at Leipzig University, and colleagues from across Europe, China, and the US have now documented robust evidence of this effect on the climate of improved air quality. “We analysed data from NASA’s Terra and Aqua satellites. They have been providing comprehensive satellite observations of the Earth since the year 2000, measuring incoming and outgoing radiation, but also clouds and aerosol pollution. The latter has decreased significantly across North America, Europe and East Asia since 2000,” says Professor Johannes Quaas, lead author of the study, which was initiated in a meeting by the two European research projects CONSTRAIN and FORCES.

Reduction in aerosol-induced cooling increases warming due to CO₂ since 2000 by up to 50 per cent

This has also reduced the cooling effect of aerosols. Compared to the year 2000, it has led to an increase in the warming effect that is up to 50 per cent of the one by CO₂ increases in the same period. This means an acceleration of the drivers of global warming compared to the previous period. “Our study should not be interpreted to mean that we should now be emitting more aerosols to cool the climate. On the contrary: aerosols are harmful to human health and the environment, which is why we need to keep reducing emissions,” Quaas concludes. And it is why air quality legislation has become increasingly stringent since the 1970s and is being implemented by more and more countries. Professor Quaas and his colleagues on the new study stress the ever more urgent need for rapid and strong reductions in greenhouse gas emissions.

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The forecasts come from a model developed by the researchers that combines measures of accumulated annual and perennial grass vegetation that is potential fire fuel with recent weather and climate data. When integrated, this information can be translated into maps showing the likelihood of a large wildfire — greater than 1,000 acres — across the Great Basin. These forecasts also can be scaled down to predict fire risk for counties or even single pastures.

Great Basin rangeland fire probability maps for the rangeland fire season, roughly June through September, are posted on the Rangeland Analysis Platform. Two new research articles discussing details and utility of the new model are part of a special issue of Rangeland Ecology & Management. The first paper used vegetation data from the Rangeland Analysis Platform alongside historical fire data from the Monitoring Trends in Burn Severity dataset to build fire-prediction models for the Great Basin using 32 years of historical weather, vegetation, and fire data. The second paper extends the fire probability work from analysis into how practitioners can use this information to make decisions for the fire season.

“Accurate forecasting of rangeland fires depends, in large part, on our ability to quantify the buildup of grassy fuels from the previous year,” explained rangeland scientist Chad S. Boyd with the ARS Range and Meadow Forage Management Research Unit in Burns, Oregon, and a co-leader in developing the model.

Forest fires commonly only need an ignition event, such as a lightning strike, at most forest locations because they generally have enough vegetative fuels to burn every year.

“But with rangeland fires, whether there is enough fuel to feed a large-scale fire really varies from place to place and year to year across the Great Basin,” Boyd added.

Until recently, rangeland fire forecasting was limited by not having accurate measurements of how much annual and perennial grasses and forbs were produced each year. But satellite technology and remote sensing have made precise data readily accessible.

Joe T. Smith, a research scientist with the University of Montana and model designer co-lead, said, “I was a little surprised that accumulation of herbaceous plants from the previous growing season was the best predictor of large range fires. This gives new emphasis to fighting the spread of fast-growing invasive annual grasses like cheatgrass in the Great Basin.”

While woody shrubs and trees like juniper or pinyon-pine don’t really increase the odds of a large fire occurring, their place in the fire landscape still matters. Shrubs burn hotter, causing more extreme fire behavior that puts lives and property at risk and makes wildfires difficult to suppress.

Unlike weather and topography, which are major influences over rangeland fires, people can directly and preemptively manage available fuel. These new fire probability maps will help land managers prioritize where it makes the most sense to invest in fuel management.

“The maps can be used alongside other planning tools to decide where to focus limited resources before the fire season begins,” Boyd explained. “They also can help target annual efforts to reduce fine fuels like grasses, which can lessen the impacts of fire on the region’s wildlife and working lands.”