“We wanted to provide an unbiased assessment of the technology and protocols available for long read sequencing,” Rivera explained. Along with other plant pathologists, Rivera used the company’s protocols to prepare RNA and DNA libraries from virus-infected plant material and from a plant pathogenic bacterium, respectively. After one hour of data sequencing, scientists had enough data to assemble small genomes.

“Diagnosticians will welcome an objective review of this technology,” Rivera said. Rivera and her colleagues published their findings in Plant Health Progress, presenting a side-by-side comparison of the protocols that will allow the reader to identify which library preparation kit is best suited for their needs.

The ability to quickly obtain the entire genome of an organism has great implications for the plant pathology field. “Having more information readily available facilitates identification of emerging pathogens and of pathogens that are difficult to identify,” explains Rivera. For more information, read “Comparison of Nanopore Sequencing Protocols and Real-Time Analysis for Phytopathogen Diagnostics” published in the March issue of Plant Health Progress.

Disclaimer: Mention of trade names or commercial products in this publication is solely to provide specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

Story Source:

Materials provided by American Phytopathological Society. Note: Content may be edited for style and length.

The research team, led by the University of Cambridge, used a new technique in which laser pulses are transmitted in a fibre-optic cable to obtain highly detailed temperature measurements from the surface of the ice sheet all the way to the base, more than 1000 metres below.

In contrast to previous studies, which measured temperature from separate sensors located tens or even hundreds of metres apart, the new approach allows temperature to be measured along the entire length of a fibre-optic cable installed in a deep borehole. The result is a highly detailed profile of temperature, which controls how fast ice deforms and ultimately how fast the ice sheet flows.

The temperature of ice sheets was thought to vary as a smooth gradient, with the warmest sections on the surface where the sun hits, and at the base where it’s warmed by geothermal energy and friction as the ice sheet grinds across the subglacial landscape toward the ocean.

The new study found instead that the temperature distribution is far more heterogenous, with areas of highly localised deformation warming the ice further. This deformation is concentrated at the boundaries between ice of different ages and types. Although the exact cause of this deformation remains unknown, it may be due to dust in the ice from past volcanic eruptions or large fractures which penetrate several hundred metres below the surface of the ice. The results are reported in the journal Science Advances.

Mass loss from the Greenland Ice Sheet has increased sixfold since the 1980s and is now the single largest contributor to global sea-level rise. Around half of this mass loss is from surface meltwater runoff, while the other half is driven by discharge of ice directly into the ocean by fast flowing glaciers that reach the sea.

In order to determine how the ice is moving and the thermodynamic processes at work within a glacier, accurate ice temperature measurements are essential. Conditions on the surface can be detected by satellites or field observations in a relatively straightforward way. However, determining what is happening at the base of the kilometre thick ice sheet is far more challenging to observe, and a lack of observations is a major cause of uncertainty in projections of global sea-level rise.

The RESPONDER project, funded by the European Research Council, is addressing this problem using hot-water drilling technology to bore through Sermeq Kujalleq (Store Glacier) and directly study the environment at the base of one of Greenland’s largest glaciers.

“We normally take measurements within the ice sheet by attaching sensors to a cable that we lower into a drilled borehole, but the observations we’ve made so far weren’t giving us a complete picture of what’s happening,” said co-author Dr Poul Christoffersen from the Scott Polar Research Institute who leads the RESPONDER project. “The more precise data we are able to gather, the clearer we can make that picture, which in turn will help us make more accurate predictions for the future of the ice sheet.”

“With typical sensing methods, we can only attach about a dozen sensors onto the cable, so the measurements are very spaced out,” said first author Robert Law, a PhD candidate at the Scott Polar Research Institute. “But by using a fibre-optic cable instead, essentially the whole cable becomes a sensor, so we can get precise measurements from the surface all the way to the base.”

To install the cable, the scientists had to first drill through the glacier, a process led by Professor Bryn Hubbard and Dr Samuel Doyle from Aberystwyth University. After lowering the cable into the borehole, the team transmitted laser pulses in the cable, and then recorded the distortions in the scattering of light in the cable, which vary depending on the temperature of the surrounding ice. Engineers at Delft University of Technology in the Netherlands and geophysicists at the University of Leeds assisted with data collection and analysis.

“This technology is a big advance in our ability to record spatial variations in ice temperature over long distances and at really high resolution. With some further adaptations, the technique can also record other properties, such as deformation, at similarly high resolution,” said Hubbard.

“Overall, our readings paint a picture that’s far more varied than what current theory and models predict,” said Christoffersen. “We found temperature to be strongly influenced by the deformation of ice in bands and at the boundaries between different types of ice. And this shows there are limitations in many models, including our own.”

The researchers found three layers of ice in the glacier. The thickest layer consists of cold and stiff ice which formed over the last 10,000 years. Below, they found older ice from the last ice age, which is softer and more deformable due to dust trapped in the ice. What surprised the researchers the most, however, was a layer of warm ice more than 70 metres thick at the bottom of the glacier. “We know this type of warm ice from far warmer Alpine environments, but here the glacier is producing the heat by deforming itself,” said Law.

“With these observations, we are starting to better understand why the Greenland Ice Sheet is losing mass so quickly and why discharge of ice is such a prominent mechanism of ice loss,” said Christoffersen.

One of the major limitations in our understanding of climate change is tied to the behaviour of glaciers and ice sheets. The new data will allow the researchers to improve their models of how the Greenland Ice Sheet is currently moving, how it may move in the future, and what that this will mean for global sea-level rise.

The research was funded in part by the European Union.

The research provides a foundation for overcoming the difficult challenges involved in the creation of hierarchical functional organic-inorganic hybrid materials. Nature provides beautiful examples of hierarchically structured hybrid materials such as bones and teeth. These materials typically showcase a precise atomic arrangement that allows them to achieve many exceptional properties, such as increased strength and toughness.

PNNL materials scientist Chun-Long Chen, corresponding author of this study, and his collaborators created a new material that reflects the structural and functional complexity of natural hybrid materials. This material combines the programmability of a protein-like synthetic molecule with the complexity of a silicate-based nanocluster to create a new class of highly robust nanocrystals. They then programmed this 2D hybrid material to create a highly efficient artificial light-harvesting system.

“The sun is the most important energy source we have,” said Chen. “We wanted to see if we could program our hybrid nanocrystals to harvest light energy — much like natural plants and photosynthetic bacteria can — while achieving a high robustness and processibility seen in synthetic systems.” The results of this study were published May 14, 2021, in Science Advances.

Big dreams, tiny crystals

Though these types of hierarchically structured materials are exceptionally difficult to create, Chen’s multidisciplinary team of scientists combined their expert knowledge to synthesize a sequence-defined molecule capable of forming such an arrangement. The researchers created an altered protein-like structure, called a peptoid, and attached a precise silicate-based cage-like structure (abbreviated POSS) to one end of it. They then found that, under the right conditions, they could induce these molecules to self-assemble into perfectly shaped crystals of 2D nanosheets. This created another layer of cell-membrane-like complexity similar to that seen in natural hierarchical structures while retaining the high stability and enhanced mechanical properties of the individual molecules.

“As a materials scientist, nature provides me with a lot of inspiration” said Chen. “Whenever I want to design a molecule to do something specific, such as act as a drug delivery vehicle, I can almost always find a natural example to model my designs after.”

Designing bio-inspired materials

Once the team successfully created these POSS-peptoid nanocrystals and demonstrated their unique properties including high programmability, they then set out to exploit these properties. They programmed the material to include special functional groups at specific locations and intermolecular distances. Because these nanocrystals combine the strength and stability of POSS with the variability of the peptoid building block, the programming possibilities were endless.

Once again looking to nature for inspiration, the scientists created a system that could capture light energy much in the way pigments found in plants do. They added pairs of special “donor” molecules and cage-like structures that could bind an “acceptor” molecule at precise locations within the nanocrystal. The donor molecules absorb light at a specific wavelength and transfer the light energy to the acceptor molecules. The acceptor molecules then emit light at a different wavelength. This newly created system displayed an energy transfer efficiency of over 96%, making it one of the most efficient aqueous light-harvesting systems of its kind reported thus far.

Demonstrating the uses of POSS-peptoids for light harvesting

To showcase the use of this system, the researchers then inserted the nanocrystals into live human cells as a biocompatible probe for live cell imaging. When light of a certain color shines on the cells and the acceptor molecules are present, the cells emit a light of a different color. When the acceptor molecules are absent, the color change is not observed. Though the team only demonstrated the usefulness of this system for live cell imaging so far, the enhanced properties and high programmability of this 2D hybrid material leads them to believe this is one of many applications.

“Though this research is still in its early stages, the unique structural features and high energy transfer of POSS-peptoid 2D nanocrystals have the potential to be applied to many different systems, from photovoltaics to photocatalysis,” said Chen. He and his colleagues will continue to explore avenues for application of this new hybrid material.

Story Source:

Materials provided by DOE/Pacific Northwest National Laboratory. Original written by Sarah Wong. Note: Content may be edited for style and length.

Analyzing data from participants in the UK Biobank, the researchers estimated that maintaining a healthy lifestyle was associated with a nearly 40% reduction in colorectal cancer risk among those with a high genetic risk of developing the disease. The percentage dropped to only about 25% among people at a low genetic risk for this cancer. People with a high genetic risk and an unhealthy lifestyle were more than three times as likely to be diagnosed with colorectal cancer than those with a low genetic risk and a healthy lifestyle.

“Results from this study could be useful to design personalized prevention strategies for colorectal cancer prevention,” said Wei Zheng, MD, PhD, MPH, Anne Potter Wilson Professor of Medicine and associate director for Population Sciences Research at Vanderbilt-Ingram Cancer Center (VICC).

In the analysis, lifestyle scores of unhealthy, intermediate and healthy were determined according to waist-to-hip ratio, physical activity, sedentary time, processed and red meat intake, vegetable and fruit intake, alcohol consumption and tobacco use. Polygenic risk scores are used to measure genetic susceptibility to colorectal cancer. Vanderbilt researchers constructed polygenic risk scores using genetic variants associated with colorectal cancer risk identified in recent large genetic studies including more than 120,000 study participants. They also constructed polygenetic risk scores for several other common cancers in research that was published last year in JNCI Cancer Spectrum.

The recently published study in The American Journal of Clinical Nutrition is one of the few that quantifies potential interactions of overall lifestyle with genetic susceptibility to colorectal cancer.

Story Source:

Materials provided by Vanderbilt University Medical Center. Original written by Tom Wilemon. Note: Content may be edited for style and length.

Led by BTI faculty member Fay-Wei Li, researchers have discovered a new species of cyanobacteria, Anthocerotibacter panamensis, which could help illuminate how photosynthesis evolved to create the world as we know it. The work was published in Current Biology on May 13.

“We never intended to discover a new species,” said Li. “It was a total accident.”

His lab was working on a project to isolate cyanobacteria from hornwort plants, and noticed something weird in a sample from a rainforest in Panama. The researchers sequenced the cyanobacterium’s DNA, and found that it belonged to a group called Gloeobacteria, which is extremely rare.

“Prior to this discovery, only two species of Gloeobacteria had been isolated,” Li said. “There is also a third group of uncultured species from the Arctic and Antarctic regions, but no one knows how many species are in that group.”

Gloeobacteria diverged from the more commonly studied Phycobacteria about 2 billion years ago. The two groups have many differences, and A. panamensis shares some traits with each.

Similar to other Gloeobacteria, the new species lacks thylakoids — the membrane-bound compartments that are the site of the light-dependent reactions of photosynthesis in Phycobacteria and plants.

“Now we can be pretty sure that the thylakoid evolved in Phycobacteria,” Li said.

On the other hand, A. panamensis makes carotenoids — a group of compounds that help protect an organism from sun damage — in a fashion similar to Phycobacteria and plants, but different from the other Gloeobacteria.

“These results suggest that this particular carotenoid biosynthesis pathway evolved in the ancestor of all cyanobacteria, and then was lost in some Gloeobacteria,” said Li.

Li said one of the more interesting findings is that A. panamensis has very few genes that encode the proteins that perform light-dependent reactions. The researchers found that the new species could still perform photosynthesis, but very slowly, which could be of interest to synthetic biologists.

“If you want to build a complete set of photosynthetic machinery with the fewest necessary components, then this species could inform how to do that,” said Li. “Anthocerotibacter has a minimal set of photosystem subunits, but it still functions.”

Story Source:

Materials provided by Boyce Thompson Institute. Original written by Aaron J. Bouchie. Note: Content may be edited for style and length.

Ordinary mice cannot be infected with HIV, so previous HIV mouse models have used mice that carry human stem cells or CD4 T cells, a type of immune cell that can be infected with HIV. But these models tend to have limited utility because the human cells soon perceive the tissues of their mouse hosts as “foreign,” and attack — making the mice gravely ill.

By contrast, the new mouse model, described in a paper in the Journal of Experimental Medicine on May 14, avoids this problem by using a subset of human CD4 cells that mostly excludes the cells that would attack mouse tissue. The researchers showed that the mice can usefully model the dynamics of long-term HIV infection, including the virus’s response to experimental therapies.

“We expect this to be a valuable and widely used tool for studying the basic science of HIV infection, and for speeding the development of better therapies,” said co-first author Dr. Chase McCann. During the study, Dr. McCann was a Weill Cornell Graduate School student in the laboratory of senior author Dr. Brad Jones, associate professor of immunology in medicine in the Division of Infectious Diseases at Weill Cornell Medicine. Dr. McCann, who was supported at Weill Cornell by a Clinical and Translational Science Center (CTSC) TL1 training award, is now the Cell Therapy Lab Lead in the Center for Cancer and Immunology Research at Children’s National Hospital in Washington, DC. The other co-first authors of the study are Dr. Christiaan van Dorp of Los Alamos National Laboratory and Dr. Ali Danesh, a senior research associate in medicine at Weill Cornell Medicine.

The invention of the new mouse model is part of a wider effort to develop and test cell therapies against HIV infection. Cell therapies, such as those using the patient’s own engineered T cells, are increasingly common in cancer treatment and have achieved some remarkable results. Many researchers hope that a similar strategy can work against HIV and can potentially be curative. But the lack of good mouse models has hampered the development of such therapies.

Drs. Jones and McCann and their colleagues showed in the study that the cell-attacks-host problem found in prior mouse models is chiefly due to so-called “naïve” CD4 cells. These are CD4 cells that have not yet been exposed to targets, and apparently include a population of cells that can attack various mouse proteins. When the researchers excluded naïve CD4 cells and instead used only “memory” CD4 cells, which circulate in the blood as sentinels against infection following exposure to a specific pathogen, the cells survived indefinitely in the mice without causing major damage to their hosts.

The researchers observed that the human CD4 cells also could be infected and killed by HIV, or protected by standard anti-HIV drugs, essentially in the same way that they are in humans. Thus, they showed that the mice, which they termed “participant-derived xenograft” or PDX mice, served as a workable model for long-term HIV infection. This term is akin to the “patient-derived xenograft” PDX models used to study cancer therapies, while recognizing the contributions of people with HIV as active participants in research.

Lastly, the researchers used the new model to study a prospective new T-cell based therapy, very similar to one that is now being tested against cancers. They put memory CD4 T cells from a human donor into the mice to permit HIV infection, and then, after infection was established, treated the mice with another infusion of human T cells, these being CD8-type T cells, also called “killer T cells.”

The killer T cells were from the same human donor and could recognize a vulnerable structure on HIV — so that they attacked the virus wherever they found it within the mice. To boost the killer T cells’ effectiveness, the researchers supercharged them with a T cell-stimulating protein called IL-15.

The treatment powerfully suppressed HIV in the mice. And although, as often seen in human cases, the virus ultimately evolved to escape recognition by the killer T cells, the ease of use of the mouse model allowed the researchers to monitor and study these long-term infection and viral escape dynamics in detail.

“I think that the major impact of this model will be its acceleration of the development of T cell-based therapies that can overcome this problem of viral escape,” Dr. Jones said.

He and his laboratory are continuing to study such therapies using the new mouse model, with engineered T cells from Dr. McCann’s laboratory and others.

New sensors developed by Professor Otto Gregory, of the College of Engineering at the University of Rhode Island, and chemical engineering doctoral student Peter Ricci, are so powerful that they can detect threats at the molecular level, whether it’s explosive materials, particles from a potentially deadly virus or illegal drugs entering the country.

“This is potentially life-saving technology,” said Gregory. “We have detected things at the part-per-quadrillion level. That’s really single molecule detection.”

Broad-Based Applications

Because Gregory’s sensors are so small and so powerful, there is a wide range of applications.

“The platform is broad-based, so you can apply it to lots of different venues, with lots of different end users,” said Gregory.

While his research is largely funded by the Department of Homeland Security, other government agencies have taken notice of Gregory’s sensors.

The Department of Defense may be interested in using it to monitor wounds in soldiers and to detect roadside improvised explosive devices (IEDs).

If a soldier or first responder suffered an open wound from shrapnel, Gregory’s sensors could help determine if the wound became infected.

“Hydrogen peroxide generated by the human body for wounds is an indication of how good or how bad antibiotics are working to fight the wound,” said Ricci. “Our sensor could be used as a wearable device to sniff out peroxide coming from the wound at the part-per-billion level.”

At Miami Heat basketball games, dogs have been used to sniff traces of COVID-19 coming from the pores in people’s skin. In an article published in the prestigious journal Nature, Gregory stated that his sensors could be used for the same purpose.

“Where dogs are detecting it from the skin, our sensors would detect it from biomarkers in people’s breath,” Ricci said, who is from West Warwick.

The Coast Guard has shown an interest in using the technology to “sniff out” illegal drugs being smuggled into the United State aboard ships.

Shrinking the ‘Digital Dog Nose’

“Anything that can typically be sniffed out by a dog we can do,” said Gregory. “That’s why we’ve called it the Digital Dog Nose.”

The Digital Dog Nose was featured on shows such as CBS This Morning in November 2019, but what was once the size of a toolbox has been reduced to a quarter of the size of a pack of cigarettes.

“By decreasing the thermal mass of the sensor, we’ve decreased the amount of power required to run the sensor,” said Gregory. “We started with a thermal mass on the order of grams. Now the thermal mass of our sensor is on the order of micrograms.”

One of the keys to making a device as small and powerful as Gregory’s is to find the right battery.

“We have partnered with a company that makes very thin, low-mass batteries in Colorado called ITN Energy Systems,” Gregory said. “They make lithium batteries that are no thicker than a piece of paper. The process has been about finding the right partners, which helps us improve our catalysts and improve our sensor platform.”

Passing the Test

In March 2021, the Naval Research Laboratory brought its mobile testing unit to URI’s W. Alton Jones Campus to put Gregory’s explosives sensors and others to the test.

“They set up a field test outside using their vapor test bed,” said Ricci. “They were able to select an explosive molecule and deliver it to the sensor system. Knowing what the level was, they wanted to see how our sensor would respond. One of the tests was at the part-per-quadrillion level.”

Staying a Step Ahead

As bad guys have developed new explosives or new ways to improvise on existing explosives, the good guys have tried to stay a step ahead.

“The Department of Homeland Security has asked us to be flexible enough to anticipate and adapt to emerging threats that may come several years down the road,” said Gregory. “We can tweak our catalysts for a specific molecule that is the current threat. That’s what we do with biomarkers. That’s what we do with drugs. What’s nice about this platform is that it’s flexible.”

Coming a Long Way

The sensors Gregory and Ricci have developed have been tested and improved upon over a long period of time. The professor’s research was originally funded 20 years ago by the Defense Advanced Research Projects Agency (DARPA), a research and development agency of the United States Department of Defense that is responsible for the development of emerging technologies for use by the military.

After two years of DARPA funding, the Army funded the project for a year. The Department of Homeland Security has provided funding ever since.

“At the time, this research was very novel and very different,” said Gregory. “DARPA funds projects that are high risk, high reward. We’ve demonstrated that the gamble they took on our concept back then has paid off.”

Michael Silevitch, the Robert D. Black Distinguished Professor of Engineering at Northeastern University, has collaborated with Gregory on his research for more than 10 years.

“This is breakthrough technology,” said Silevitch. “Otto’s work on chemical detectors has evolved to the point of being ready for use in many applications, including the deployment of his sensors on a drone-based platform to help protect soft targets such as schools, shopping malls or places of worship.”

Taking the New Steps

Now that the sensors are very small and lightweight, they could be attached to drones, leading to many new applications.

“We’ve been talking to drone companies about using our sensors on their drones,” said Gregory. “Drones need very lightweight, portable power supplies and you have to tap into their wireless communication. It’s a much different set of engineering conditions than using a robot arm that the Army is looking to use for roadside IEDs.”

Gregory and Ricci are also working on sensor arrays, to differentiate one explosive, or threat, from another.

“We’ll need an array of sensors to detect a specific explosive in the presence of other explosives or precursors,” said Ricci. “If there’s a plume of three different explosives, we may need to identify one from the others.”

Ready to Use

Now that the sensors have proven to be effective, implementing them in real-world situations is just a matter of funding.

“Our sensor is not an off-the-shelf commercial product yet, but we have a potential partner,” Gregory said. “We just need a customer to step up to the plate and say here’s an order for 1,000 of these, can you deliver them?”