Culture

Sugarcane is one of the most productive plants on Earth, providing 80 percent of the sugar and 30 percent of the bioethanol produced worldwide. Its size and efficient use of water and light give it tremendous potential for the production of renewable value-added bioproducts and biofuels.

But the highly complex sugarcane genome poses challenges for conventional breeding, requiring more than a decade of trials for the development of an improved cultivar.

Two recently published innovations by University of Florida researchers at the Department of Energy’s Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) demonstrated the first successful precision breeding of sugarcane by using CRISPR/Cas9 genome editing — a far more targeted and efficient way to develop new varieties.

CRISPR/Cas9 allows scientists to introduce precision changes in almost any gene and, depending on the selected approach, to turn the gene off or replace it with a superior version. The latter is technically more challenging and has rarely been reported for crops so far.

In the first report, researchers demonstrated the ability to turn off variable numbers of copies of the magnesium chelatase gene, a key enzyme for chlorophyll biosynthesis in sugarcane, producing rapidly identifiable plants with light green to yellow leaves. Light green plants did not show growth reduction and may require less nitrogen fertilizer to produce the same amount of biomass. That study, published in Frontiers in Genome Editing, was led by CABBI researchers Fredy Altpeter, Professor of Agronomy at the University of Florida’s Institute of Food and Agricultural Sciences (IFAS), and Ayman Eid, a Postdoctoral Research Associate in Altpeter’s lab.

The second study, also published in Frontiers in Genome Editing, achieved efficient and reproducible gene targeting in sugarcane, demonstrating the precise substitution of multiple copies of the target gene with a superior version, conferring herbicide resistance. Scientists co-introduced a repair template together with the gene-editing tool to direct the plant’s own DNA repair process so that one or two of the thousands of building blocks of the gene, called nucleotides, were precisely replaced in the targeted location. The result was that the gene product was still fully functional and could no longer be inhibited by the herbicide. That study was led by Altpeter and former CABBI Postdoc Mehmet Tufan Oz.

Altpeter’s lab, part of CABBI’s groundbreaking project to develop new oil-rich sugarcane varieties, has pioneered research with sugarcane genome editing using the TALEN gene-editing system. But the two recent publications are the first to successfully demonstrate CRISPR gene-editing in sugarcane as well as gene targeting for precision nucleotide substitution in sugarcane using any genome-editing tool.

“Now we have very effective tools to modify sugarcane into a crop with higher productivity or improved sustainability,” Altpeter said. “It’s important since sugarcane is the ideal crop to fuel the emerging bioeconomy.”

Sugarcane is a hybrid of two kinds of parent plants, so it has multiple sets of chromosomes rather than just two, as with humans or “diploid” plants. That creates genetic redundancy — with many sets of genes doing the same job — which may contribute to the plant’s productivity: If one set breaks, there’s a backup. But it makes sugarcane extremely difficult to modify. Crop scientists have to target all the genes and copies that govern a particular trait in order to make improvements.

With conventional breeding, two types of sugarcane are cross-bred to reshuffle the genetic information present in each parent in the hope of enhancing a desirable trait such as disease resistance. The problem is that genes are transferred from the parents to offspring in blocks, and desirable traits are often linked with deleterious genetic material. This means scientists often have to do multiple rounds of backcrossing and screen thousands of plants to restore the elite background, or underlying plant characteristics, in addition to improving one trait they’re attempting to modify. The process is more time-consuming and costly in plants with complex genomes like sugarcane.

Precise gene-editing technologies such as CRISPR-Cas9 offer a much more targeted path to crop improvement because it avoids the reshuffling of genetic information and simply changes inferior gene versions into superior ones. Given the sugarcane genome’s complexity, Altpeter and his team focused initially on genes that control noticeable traits — leaf color and herbicide resistance — so they could determine if the edits worked.

Beyond providing an easily identifiable phenotype, the targeted genes may prove useful in future research. Changing the chlorophyll content of sugarcane has the potential to increase canopy level photosynthesis or reduce the requirement for nitrogen fertilizer, based on previous plant modeling. Sugarcane is a tall, dense plant, with the top leaves getting lots of sun and shading lower foliage. If the upper leaves have less chlorophyll, sunlight can penetrate deeper into the plant, increasing its biomass with the same amount of light and less fertilizer. Herbicide resistance is not only an agronomically desirable trait to facilitate weed management; it will also facilitate future gene-editing efforts by enabling suppression of non-edited plant cells.

At CABBI, Altpeter and his team are already applying the results to develop improved sugarcane lines. Sugarcane has many different gene targets that can translate into more biomass or the production of lipids or specialty fatty acids — all of which would advance CABBI’s goals to produce fuels and other products from plants to replace petroleum. Because the crop is already harvested and processed for sugar extraction, the basic infrastructure to process its raw material into a product on a shelf is essentially in place.

“Adding value streams is relatively inexpensive compared to other crop alternatives,” Altpeter said.

Butterflies and moths have beautiful wings: the bright flare of an orange monarch, the vivid stripes of a swallowtail, the luminous green of a Luna moth. But some butterflies flutter on even more dramatic wings: parts of their wing, or sometimes the entire wing itself, are actually transparent.

Many aquatic organisms, including jellies and fish, are transparent. But transparent butterfly and moth wings are so arresting that merely catching a glimpse of one typically causes a human to lunge for a camera or at least point it out to their friends. These enigmatic, transparent butterfly wings have not been studied comprehensively.

Doris Gomez and Marianne Elias (French National Center for Scientific Research) set out to change that. Last week, along with a multidisciplinary team of ecologists, biologists and physicists, they published a massive survey on the optics and ecological implications of moths and butterflies with transparent wings in the Ecological Society of America's journal Ecological Monographs. They discovered that transparency has evolved in Lepidoptera more than once, and that there are many ways to be transparent.

Gomez, an ecologist who has studied the physics and ecological aspects of iridescence in hummingbird wings and other bird coloration, was intrigued by these so-called "glasswing" butterflies and moths when she met Elias, an evolutionary biologist who worked on the ecology and evolution of the tropical butterflies Ithomiini, which have transparent wings. Gomez was startled to find that almost nothing had been written about transparency in Lepidoptera, nor in any other terrestrial animal.

"This paper is a breakthrough because everything that's been known so far on transparency was about aquatic organisms," Gomez said. "Transparency is so rare in terrestrial organisms that people never bothered to study it comprehensively."

She and her team analyzed 123 species of Lepidoptera from samples in the French Museum of Natural History's collection. They found transparency, or "clearwing" species, in 31 out of 124 families. But not all species accomplish transparency in the same way. They examined the extent to which transparency affects thermoregulation and provides protection against ultraviolet radiation.

Many insects, including wasps, flies and dragonflies, have clear wings. Their wings consist of a transparent membrane made of chitin. Butterfly and moth wings are made of the same kind of transparent membrane, but in most cases moths and butterflies have opaque scales obscuring the membrane. The scales are what are responsible for their mesmerizing patterns and coloration.

Gomez and her team discovered that clearwing species have a number of ways to make their wings transparent. Some transparent moths and butterflies have no scales on their wings at all, leaving the chitin membrane to show through. Many other species do have scales, which can be transparent, upright, narrow or hair-like, allowing light through the wing.

Physicists have studied instances of transparency in individual species or genera, in the hopes of understanding the physics of how to adapt biological concepts to make people, vehicles and even structures invisible or transparent. But before now, no one had appreciated the wealth of approaches lepidopterans can take to achieve transparency, or the fact that it has evolved multiple times in different groups.

"This is the first comparative analysis of transparent butterfly wings," said Elias. "What is notable is that transparency has evolved several times independently. But the way the wings become transparent can be dramatically different, from highly packed transparent scales to the mere absence of scales, through scale reduction in size and density. There are many ways of being transparent. We don't know why this diversity exists."

In some cases, different strategies lead to the same level of transparency, leaving researchers pondering why such diversity exists at all. They theorize that transparency may be beneficial in different ways for different species, including as camouflage or to mimic wasp and bees. Transparency also seems to help moths and butterflies regulate their body temperature, but does not protect them from UV radiation.

Gomez, who has a passion for working with scientists from across other disciplines, included physicists in the study to explore the optical properties of the wings including discerning what birds, their would-be predators, see when they look at a transparent butterfly. They found that the more light that can pass through a wing - i.e., the more transparent it is - the less visible the butterfly is to predators. Transparency acts like the ultimate camouflage.

Like the butterflies themselves, the results are compelling. However, the scientists emphasize that the study has raised more questions and avenues of exploration to continue to uncover the evolutionary role and ecological implications of transparency.

"Butterflies are such iconic organisms," said Gomez. "They're so wonderful to study. I like to study complex concepts, like iridescence and transparency because there is so much to explore - and it's so easy to get everyone excited about them."

Chronic alcohol abuse and hepatitis can injure the liver and lead to fibrosis, the buildup of collagen and scar tissue. As a potential approach to treating liver fibrosis, University of California San Diego School of Medicine researchers and their collaborators are looking for ways to stop liver cells from producing collagen.

"So we thought...what if we take immunotoxins and try to get them to kill collagen-producing cells in the liver," said team lead Tatiana Kisseleva, MD, PhD, associate professor of surgery at UC San Diego School of Medicine. "If these antibodies carrying toxic molecules can find and bind the cells, the cells will eat up the 'gift' and die."

In a study published July 12, 2021 in Proceedings of the National Academy of Sciences, Kisseleva and collaborators provide the first evidence that liver fibrosis might be treatable with immunotoxins designed to bind a protein called mesothelin. Mesothelin is rarely found in the healthy human body. Only cancer cells and collagen-producing liver cells, known as portal fibroblasts, make the protein.

Kisseleva teamed up with co-author Ira Pastan, MD, at the National Cancer Institute, part of the National Institutes of Health (NIH). Pastan is co-discoverer of mesothelin and an expert on using immunotoxins to target the protein on cancer cells. He leads several clinical trials testing the approach to treat patients with ovarian cancer, mesothelioma and pancreatic cancer.

To test Pastan's immunotoxins in the context of liver fibrosis, Kisseleva's team first needed a model. Since the immunotoxins specifically recognize human mesothelin, a traditional mouse model of liver fibrosis wouldn't work. Instead, they transplanted human liver cells isolated from patients to mice and treated them with the anti-mesothelin immunotoxin.

Compared to untreated mice, 60 to 100 percent of human mesothelin-producing cells were killed by the immunotoxins, which also reduced collagen deposition.

Treatment for liver fibrosis is currently very limited. According to the NIH, weight loss is currently the only known method for reducing liver fibrosis associated with non-alcoholic fatty liver disease. Alcoholic liver disease is most commonly treated with corticosteroids, but they are not highly effective. Early liver transplantation is the only proven cure, but it is offered only at select medical centers to a limited number of patients.

"What we want to know now is, can this same strategy be applied to other organs?" Kisseleva said. "Surprisingly enough, the same cells are responsible for fibrosis in the lung and kidneys. This is especially exciting because we already know from Dr. Pasten's cancer clinical trials that anti-mesothelin immunotoxins are safe in humans, potentially speeding up their application in other areas."

Having a home near a busy airport certainly has its perks. It is close to many establishments and alleviates the problem of wading through endless traffic to catch flights. But it does come at a cost -- tolerating the jarring sounds of commercial airplanes during landing and takeoff.

Researchers at Texas A&M University have conducted a computational study that validates using a shape-memory alloy to reduce the unpleasant plane noise produced during landing. They noted that these materials could be inserted as passive, seamless fillers within airplane wings that automatically deploy themselves into the perfect position during descent.

"When landing, aircraft engines are throttled way back, and so they are very quiet. Any other source of noise, like that from the wings, becomes quite noticeable to the people on the ground," said Dr. Darren Hartl, assistant professor in the Department of Aerospace Engineering. "We want to create structures that will not change anything about the flight characteristics of the plane and yet dramatically reduce the noise problem."

The researchers have described their findings in the Journal of Aircraft.

Aircraft noise has been an ongoing public health issue. Airplanes can generate up to 75-80 decibels during landing, which can be damaging to hearing over the long term. For example, studies have shown that people exposed to sustained aircraft noise can experience disturbed sleep and an increased risk of stroke and heart disease compared to those who do not live near airports.

The source of aircraft noise is different during ascent and descent. During takeoff, the engines are the primary source of noise. On the other hand, when airplanes slow down to land, the engines do not need to generate power and are mostly idling. At this time, the wings begin to reconfigure themselves to slow down the airplane and prepare for touchdown. Similar to the opening of Venetian blinds, the front edge of the wing separates from the main body. This change causes air to rush into the space created, circle around quite violently and produce noise.

"The idea is similar to how a sound is generated in a flute," said Hartl. "When a flute is played, air blown over a hole begins to swirl around the hole, and the size, the length and how I cover the holes, produces a resonant sound of a certain frequency. Similarly, the circulating air in the cove created between the front edge of the wing and the main wing resonates and creates a sharp, unpleasant noise."

Earlier work from Hartl's collaborators at NASA showed that fillers used as a membrane in the shape of an elongated "S" within this cove could circumvent the noise-causing air circulation and thereby lessen the jarring sound. However, a systematic analysis of candidate materials that can assume the desired S-shaped geometry during descent and then recess back into the front edge of the wing after landing was lacking.

To address this gap, the researchers performed comprehensive simulations to investigate if a membrane made of a shape-memory alloy could go back and forth, changing shape for every landing. Their analysis considered the geometry, the elastic properties of the shape-memory alloy and the aerodynamic flow of air around the material during descent. As a comparison, the researchers also modeled the motion of a membrane made of a carbon-fiber-reinforced polymer composite under the same airflow conditions.

Hartl said these types of simulations are computationally expensive since the flow of air around the conformal material has to be modeled while analyzing the air-induced motion of the material.

"Every time the air applies some pressure to the material, the material moves. And every time the material moves, the air moves differently around it," he said. "So, the behavior of the airflow changes the structure, and the motion of the structural changes the airflow."

Consequently, the team had to perform calculations hundreds to thousands of times before the motion of the materials was correctly simulated. When they analyzed the outcomes of their simulations, they found that both the shape-memory alloy and the composite could change their shape to reduce air circulation and thereby reduce noise. However, the researchers also found that the composite had a very narrow window of designs that would enable noise canceling.

As a next step, Hartl and his team plan to validate the results of their simulations with experiments. In these tests, the researchers will place scaled-down models of aircraft wings with the shape-memory alloy fillers into wind tunnels. The goal is to check if the fillers can deploy into the correct shape and reduce noise in near real-world situations.

"We would also like to do better," said Hartl. "We might be able to create smaller structures that can reduce noise and do not require the S-shape, which are actually quite large and potentially heavy."

[Points]

319 Tb/s long-haul transmission of wideband (>120 nm) S, C and L-bands signal using 552 PDM-16QAM, wavelength-division multiplexed channels in a 4-core optical fiber

Long-distance transmission over 3,001 km enabled by adoption of both erbium and thulium doped-fiber amplifiers and distributed Raman amplification

Demonstration shows potential of SDM fibers with standard-cladding diameter and compatibility with existing cabling technologies for near-term adoption of high-throughput SDM fiber systems

[Abstract]

Researchers from the National Institute of Information and Communications Technology (NICT, President: TOKUDA Hideyuki, Ph.D.), Network Research Institute, succeeded the first S, C and L-bands transmission over long-haul distances in a 4-core optical fiber with standard outer diameter (0.125 mm). The researchers, lead by Benjamin J. Puttnam, constructed a transmission system that makes full use of wavelength division multiplexing technology by combining different amplifier technologies, to achieve a transmission demonstration with date-rate of 319 terabits per second, over a distance of 3,001 km. Using a common comparison metric of optical fiber transmission the data-rate and distance produce of 957 petabits per second x km, is a world record for optical fibers with standard outer diameter.

In this demonstration, in addition to the C and L-bands, typically used for high-data-rate, long-haul transmission, we utilize the transmission bandwidth of the S-band, which has not yet been used for further than single span transmission. The combined >120nm transmission bandwidth allowed 552 wavelength-division multiplexed channels by adopting 2 kinds of doped-fiber amplifier together with distributed Raman amplification, to enable recirculating transmission of the wideband signal. The standard cladding diameter, 4-core optical fiber can be cabled with existing equipment, and it is hoped that such fibers can enable practical high data-rate transmission in the near-term, contributing to the realization of the backbone communications system, necessary for the spread of new communication services Beyond 5G.

The results of this experiment were accepted as a post-deadline paper presentation at the International Conference on Optical Fiber Communications (OFC 2021).

[Background]

Over the past decade, intensive research has been carried out worldwide to increase the data rates in optical transmission systems using space-division multiplexing as a means to meet the exponentially increasing demand for optical data transmission. More recently, interest in fibers with the same 125 μm cladding diameter as standard single-mode fibers has grown due to their compatibility with conventional cabling infrastructure and concerns over the mechanical reliability of larger fibers. Particularly with multi-core fibers (MCFs), reducing the cladding diameter limits the number of spatial channels, leading to increasing interest in combining such fibers with wider transmission bandwidths in order to meet the expected growth in transmission capacity expected in SDM fibers. Until now, NICT has built various transmission systems that make use of wavelength division multiplexing across the C and L-bands together with state-of-the-art modulation technology to explore high data-rate transmission in a range of new optical fibers. Recently, NICT and research groups around the world have begun to explore S-band transmission, leading to several new records for transmission capacity in optical fibers, but transmission distance has been limited to only a few tens of kilometers.

[Achievements]

NICT has built a long-distance transmission system around a 4-core optical fiber with a standard cladding diameter to exploit wider transmission bandwidth of >120nm across S, C and L-bands. The system exploits wavelength division multiplexing (WDM) and a combination of optical amplification technology to enable long-haul transmission of 552 WDM channels from 1487.8 nm to 1608.33 nm. The system was used to measure achievable transmission throughput with each channel modulated with PDM-16QAM modulation at distances up to 3,001 km, where a data-rate of 319 terabits per second was achieved. This result may be compared to achievements in other SDM fibers and transmission regimes by calculating the product of transmission capacity and distance, often used as a comparison metric. The data-rate x distance product becomes 957 petabits per second x km, which is over 2.7 times larger than previous demonstrations in SDM fibers with standard outer diameter.

Long distance transmission, not previously demonstrated with S-band signals, was enabled by constructing a recirculating transmission loop experimental set-up that combined 2 kinds of rare-earth doped fiber amplifiers with Raman amplification distributed along the transmission fiber itself.

The 4-core MCF with standard cladding diameter is attractive for early adoption of SDM fibers in high-throughput, long-distance links, since it is compatible with conventional cable infrastructure and expected to have mechanical reliability comparable to single-mode fibers. Beyond 5G, an explosive increase from new data services is expected and it is therefore crucial to demonstrate how new fibers can meet this demand. Hence, it is hoped that this result will help the realization of new communication systems that can support new bandwidth hungry services.

[Future Prospects]

NICT will continue to develop wide-band, long-distance transmission systems and explore how to further increase transmission capacity of low-core-count multi-core fibers and other novel SDM fibers. Further, we will work to extend the transmission range to trans-oceanic distances.

The paper containing the results of this experiment was published at the International Conference on Optical Fiber Communication ((OFC2021, June 6 (Sun) to June 11 (Fri)), one of the largest international conferences related to optical fiber communication, this year held virtually due to Corona virus travel restrictions. It was highly evaluated and was presented in the Post Deadline session, known for release of latest important research achievements on June 11 (Fri) 2021 local time.

A research team from the University of Göttingen and the University of British Columbia (Canada) has investigated how people in five different countries react to various usages of genome editing in agriculture. The researchers looked at which uses are accepted and how the risks and benefits of the new breeding technologies are rated by people. The results show only minor differences between the countries studied - Germany, Italy, Canada, Austria and the USA. In all countries, making changes to the genome is more likely to be deemed acceptable when used in crops rather than in livestock. The study was published in Agriculture and Human Values.

Relatively new breeding technologies, such as CRISPR gene editing, have enabled a range of new opportunities for plant and animal breeding. In the EU, the technology falls under genetic engineering legislation and is therefore subject to rigorous restrictions. However, the use of gene technologies remains controversial. Between June and November 2019, the research team collected views on this topic via online surveys from around 3,700 people from five countries. Five different applications of gene editing were evaluated: three relate to disease resistance in people, plants, or animals; and two relate to achieving either better quality of produce or a larger quantity of product from cattle.

"We were able to observe that the purpose of the gene modification plays a major role in how it is rated," says first author Dr Gesa Busch from the University of Göttingen. "If the technology is used to make animals resistant to disease, approval is greater than if the technology is used to increase the output from animals." Overall, however, the respondents reacted very differently to the uses of the new breeding methods. Four different groups can be identified: strong supporters, supporters, neutrals, and opponents of the technology. The opponents (24 per cent) identify high risks and calls for a ban of the technology, regardless of possible benefits. The strong supporters (21 per cent) see few risks and many advantages. The supporters (26 per cent) see many advantages but also risks. Whereas those who were neutral (29 per cent) show no strong opinion on the subject.

A single tree along a city street or in a backyard can provide measurable cooling benefits, according to a new study from American University. The research shows that "distributed" trees, those that are stand-alone and scattered throughout urban neighborhoods, can help to reduce evening heat. The research suggests that planting individual trees can be a strategy to mitigate urban heat, particularly in areas where land for parks can be scarce.

"There are plenty of good reasons to plant trees, but our study shows we shouldn't underestimate the role that individual trees can play in mitigating heat in urban areas," said Michael Alonzo, assistant professor of environmental science and lead author of the new study. "City planners can take advantage of the small spaces that abound in urban areas to plant individual trees." The study is published in Environmental Research Letters.

While urban parks provide important mid-day cooling for residents and visitors, the key to cooling from individual trees happens in the evening. In the new study, which was conducted in Washington, D.C., cooling benefits from distributed trees were found to occur around 6 or 7 p.m. and after sunset. The study revealed lower temperatures in neighborhoods where at least half the area was covered by canopy from distributed trees. Temperatures were 1.4 degrees Celsius cooler in the evening compared with areas with few trees. Even in the predawn hour, areas with only modest distributed canopy cover (about 20 percent of the area) were cooler than those with no trees, showing that on average, afternoon and evening cooling effects last well into the night, Alonzo added.

To arrive at the findings, Alonzo and his colleagues examined air temperature readings. The data was collected over one hot summer day in 2018, across different areas in Washington, D.C. and at multiple times throughout the day, resulting in more than 70,000 air temperature readings. In their analysis, Alonzo and his colleagues examined tree canopy over paved surfaces, over unpaved surfaces, and both patches such as parks, and distributed trees, such as those one might plant in their back or front yards.

The new study confirms that planting individual trees should be considered as part of a strategy to combat rising temperatures in urban areas. In hot summer months many cities across the United States turn into "heat islands." Due to the urban heat island effect, urban areas, with fewer green spaces and higher amounts of impervious surface, get hotter compared to their rural surroundings.

In urban areas, people are more likely to live adjacent to distributed trees rather than parks. In D.C., there are many places to plant individual trees where canopy will shade paved or unpaved surfaces: on streets with single family homes, streets with rowhouses, backyard or small park plantings, Alonzo said. This opens up avenues for increasing the racial and socioeconomic equity of tree planting, but more effort is required to first reduce impervious surface cover in the most built-up residential and commercial districts, Alonzo added. The top five trees along D.C.'s streets include several species of maples, oaks and elms, all of which provide plentiful shade.

Climate studies show that urban temperatures are warming at all times of day including evenings. Yet studying the cooling benefits from individual trees, as well as their benefits during evening hours, has not been widely researched, Alonzo said, and this is an area scientists should continue to explore. More research will be needed in other locations in the United States and under different weather conditions. Alonzo also plans to conduct more research and has collected air temperature readings by bicycle around D.C. during the pandemic.

Though the study was conducted in D.C., Alonzo said the findings are likely applicable along the East Coast or in other cities with a similar climate.

"Evenings are not quite the respite from heat that we once had," Alonzo said. "These distributed trees do help the city cool off in the evening and that's important for human health."

LOWELL, Mass. - Researchers led by a UMass Lowell environmental science professor say mercury measurements in a Massachusetts forest indicate the toxic element is deposited in forests across the globe in much greater quantities than previously understood.

The team's results underscore concern for the health and well-being of people, wildlife and waterways, according to Prof. Daniel Obrist, as mercury accumulating in forests ultimately runs off into streams and rivers, ending up in lakes and oceans.

Mercury is a highly toxic pollutant that threatens fish, birds, mammals and humans. Hundreds of tons of it are released into the atmosphere each year by coal-burning power plants, as well as through gold mining and other industrial processes, and the pollutant is distributed by winds and currents across the globe. Long-term exposure to mercury, or consuming food containing high levels of the pollutant, can lead to reproductive, immune, neurological and cardiovascular problems, according to Obrist, chair of UMass Lowell's Department of Environmental, Earth and Atmospheric Sciences.

Forests constitute the world's most abundant, productive and widespread ecosystems on land, according to Obrist, who said the study is the first that examines a full picture of how mercury in the atmosphere is deposited at any rural forest in the world, including the deposition of mercury in its gaseous form, which most previous studies do not address.

"Trees take up gaseous mercury from the atmosphere through their leaves and as plants shed their leaves or die off, they basically transfer that atmospheric mercury to the ecosystems," he said.

The results of the project, which is supported by a three-year, $873,000 grant from the National Science Foundation (NSF), were published today in an issue of the Proceedings of the National Academy of Sciences. UMass Lowell student Eric Roy, a double-major in meteorology and mathematics from Lowell, is among the study's co-authors.

For the past 16 months, the team has measured how mercury in the atmosphere gets deposited at Harvard Forest in Petersham, a nearly 4,000-acre site that includes hardwood deciduous broadleaf trees such as red oak and red maple that shed their leaves every year. A set of measurement systems placed at various heights on the forest's 100-foot-tall research tower assessed the site's gaseous mercury deposition from the tree canopy to the forest floor.

"Seventy-six percent of the mercury deposition at this forest comes from gaseous atmospheric mercury. It's five times greater than mercury deposited by rain and snow and three times greater than mercury that gets deposited through litterfall, which is mercury transferred by leaves falling to the ground and which has previously been used by other researchers as a proxy for estimating gaseous mercury deposition in forests," Obrist said.

"Our study suggests that mercury loading in forests has been underestimated by a factor of about two and that forests worldwide may be a much larger global absorber and collector of gaseous mercury than currently assumed. This larger-than-anticipated accumulation may explain surprisingly high mercury levels observed in soils across rural forests," he said.

Plants seem to dominate as a source of mercury on land, accounting for 54 to 94 percent of the deposits in soils across North America. The total global amount of mercury deposited to land currently is estimated at about 1,500 to 1,800 metric tons per year, but it may be more than double if other forests show similar levels of deposition, according to Obrist.

The researchers are continuing their work at a second forest in Howland in northern Maine. Howland Forest, a nearly 600-acre research site full of evergreens that retain their leaves year-round, offers a distinctly different habitat than the deciduous forest in Petersham. Assessing both forests will allow researchers to examine differences in mercury accumulation between different forest types, Obrist said.

The work is providing a hands-on research experience for Roy, a UMass Lowell Honors College student who was invited to become a member of the university's Immersive Scholar program in 2019. The initiative enables first-year students with outstanding academic credentials to participate in lab work and research right from the start of their academic studies.

"It's really exciting to be a co-author," Roy said. "This study allowed us to quantify how much mercury is being accumulated in this type of forest. Modelers can use these results to improve their understanding of how mercury cycles through the environment on a global scale and how that might change in the future."

Roy helped analyze the data collected in the field.

"Eric's contributions to the study are tremendous. It's not very common for an undergrad to play such an important role in a major, federally funded research project," Obrist said. "His work is really impressive and he has become more and more active in data analysis and doing complex flux calculations and data processing. He really earned himself second author position in the paper in the Proceedings of the National Academy of Sciences."

COVID-19 outbreaks in French nursing homes almost certainly started in staff - and none of measures put in place stopped the virus from taking hold, new research being presented at the European Congress of Clinical Microbiology & Infectious Diseases (ECCMID), held online this year, shows.

Residents of long-term care facilities represent a small fraction of the general population but account for a disproportionate number of SARS-CoV-2-related deaths in many countries.

In France, 5,203 outbreaks (of 1 case or more) were reported in nursing homes during the first wave of COVID-19. In the Auvergne-Rhône-Alpes region, there were 651 outbreaks, 3,885 residents had confirmed COVID-19 infection and 1,772 (46%) subsequently died.

Little is known, however, about how the COVID-19 virus enters nursing homes nor how it spreads in this complex environment.

Emilie Piet, of the Centre Hospitalier Annecy Geneva, Epagny Metz-Tessy, France and colleagues, carried out a cross-sectional survey in nursing homes in the French Alps from March 1 to May 31 May 2020.

The survey covered cases of COVID-19 among residents and staff during the first lockdown, as well as the staffing during the pandemic, including staffing levels and the use of interim carers.

It also asked about the nursing homes' characteristics (e.g. number of residents, whether these were private or public facilities, if they cared for dementia patients) and hygiene measures implemented (these included wearing face masks, confining residents to their rooms, use of alcohol-based hand sanitiser and bans on visits).

Seventy four (33%) of 225 nursing homes completed the survey. A total of 22 homes, with 1,795 residents in total, had an outbreak of COVID-19 - defined as at least three cases. (See table 1 of abstract).

In the homes with outbreaks, 26% (473/1,795) of the residents had a confirmed or probable case of COVID-19; 19% (341/1,795) of residents were hospitalised and 253 (14%) died of any cause.

In contrast, 0.2% (9/4,096 residents) of residents in the outbreak-free homes had confirmed or probable COVID-19, 6% (247/4,096) were hospitalised and 6% (250/4,096) died of any cause during the period studied.

A total of 19% (250/1,348) of staff in the homes with outbreaks had confirmed or probable cases of COVID-19, compared to 1.4% (46/3,304) in the outbreak-free homes.

The results revealed a strong link between cases in staff and cases in residents.

Further analysis showed that cases of COVID-19 in staff were the only predictor of an outbreak among residents.

In other words, none of the nursing homes' characteristics seemed to have any effect and nor did any of the hygiene measures. However, the homes all employed similar hygiene measures, making it difficult to tease apart their effect, says Dr Piet.

She adds: "This study shows that when strict hygiene measures are implemented in nursing homes, factors such as the number of beds, the ratio of staff to residents and the use of temporary staff do not influence outbreaks.

"We found that apart from staff infections, nothing influenced the occurrence of outbreaks and so, during the national lockdown, staff were the likely source of COVID-19 outbreaks among nursing home residents."

The flu vaccine may provide vital protection against COVID-19, new research being presented at the European Congress of Clinical Microbiology & Infectious Diseases (ECCMID), held online this year, concludes.

An analysis of patient data from around the world strongly suggests that the annual flu shot reduces the risk of stroke, sepsis and DVT in patients with COVID-19. Patients with COVID-19 who had been vaccinated against flu were also less likely to visit the emergency department and be admitted to the intensive care unit (ICU).

Immunising the world against COVID-19 is a daunting challenge and, although production and distribution of vaccines increases daily, some countries are not expected to vaccinate large numbers of their population until the start of 2023.

Recently, several modestly-sized studies suggested that the flu vaccine may provide protection against COVID-19 - meaning it could be a valuable weapon in the fight to halt the pandemic.

Ms Susan Taghioff, of the University of Miami Miller School of Medicine, Miami, USA, and colleagues carried out a retrospective analysis of data on tens of thousands of patients from around the world to find out more.

In the largest study of its kind, the team screened de-identified electronic health records held on the TriNetX research database of more than 70 million patients to identify two groups of 37,377 patients.

The two groups were matched for factors that could affect their risk of severe COVID-19, including age, gender, ethnicity, smoking and health problems such as diabetes, obesity and chronic obstructive pulmonary disease.

Members of the first group had received the flu vaccine between two weeks and six months before being diagnosed with COVID-19. Those in the second group also had COVID-19 but were not vaccinated against flu. The study was conducted using patients from countries including the US, UK, Germany, Italy, Israel and Singapore.

The incidence of 15 adverse outcomes (sepsis; strokes; deep vein thrombosis or DVT; pulmonary embolism; acute respiratory failure; acute respiratory distress syndrome; arthralgia or joint pain; renal failure; anorexia; heart attack; pneumonia; emergency department visits; hospital admission; ICU admission; and death) within 120 days of testing positive for COVID-19 was then compared between the two groups.

The analysis revealed that those who had not had the flu jab were significantly more likely (up to 20% more likely) to have been admitted to ICU.

They were also significantly more likely to visit the Emergency Department (up to 58% more likely), to develop sepsis (up to 45% more likely), to have a stroke (up to 58% more likely) and a DVT (up to 40% more likely). The risk of death was not reduced.

It isn't known exactly how the flu jab provides protection against COVID-19 but most theories centre around it boosting the innate immune system - "general" defences we are born with that are not tailored to any particular illness.

The study authors say their results strongly suggest that the flu vaccine protects against several severe effects of COVID-19. They add that more research is needed to prove and better understand the possible link but, in the future, the flu shot could be used to help provide increased protection in countries where the COVID-19 vaccine is in short supply.

Dr Devinder Singh, the study's senior author and a professor of plastic surgery at the University of Miami Miller School of Medicine, says: "Only a small fraction of the world has been fully vaccinated against COVID-19 to date and, with all the devastation that has occurred due to the pandemic, the global community still needs to find solutions to reduce morbidity and mortality.

"Having access to real-time data of millions of patients is a powerful research tool. Together with asking important questions it has allowed my team to observe an association between the flu vaccine and lower morbidity in COVID-19 patients.

"This finding is particularly significant because the pandemic is straining resources in many parts of the world. Therefore, our research - if validated by prospective randomised clinical trials - has the potential to reduce the worldwide burden of disease."

Ms Taghioff adds: "Influenza vaccination may even benefit individuals hesitant to receive a COVID-19 vaccine due to the newness of the technology.

"Despite this, the influenza vaccine is by no means a replacement for the COVID-19 vaccine and we advocate for everyone to receive their COVID-19 vaccine if able to.

"Continued promotion of the influenza vaccine also has the potential help the global population avoid a possible 'twindemic' - a simultaneous outbreak of both influenza and coronavirus.

"Regardless of the degree of protection afforded by the influenza vaccine against adverse outcomes associated with COVID-19, simply being able to conserve global healthcare resources by keeping the number of influenza cases under control is reason enough to champion continued efforts to promote influenza vaccination."

Nashville, Tenn. (July 10 2021--2:25 EDT)--Patients undergoing hip arthroscopy with high-grade cartilage damage do not see as positive results compared with patients with lower grade cartilage damage, according to research reported today at the American Orthopedic Society of Sports Medicine- Arthroscopy Association of North America Combined 2021 Annual Meeting.

The research was presented by Dominic Carreira, MD, of Peachtree Orthopedics in Atlanta, Ga. Dr. Carreira and his colleagues sought to determine what the impact of acetabular cartilage damage on outcomes following primary repair of acetabular labral tears.

When articular cartilage is damaged, joint pain may result. If the articular cartilage damage becomes diffuse, the term arthritis is used.

To determine this, researchers queried a multi-center hip arthroscopy registry for patients undergoing primary labrum repair from 2014-2017 with documented two-year outcomes. They assigned 472 patients to one of three groups according to severity of articular cartilage damage in the Beck classification system: None, Low Grade (Grade 1 or 2), or High Grade (Grade 3 or 4) Damage.

Patients in all three groups experienced statistically significant improvement in iHOT-12 scores from baseline to final follow-up (p

When accounting for age, BMI, gender, and preoperative iHOT12 scores in logistic regression models for clinically significant outcome thresholds, presence of high grade lesions was a negative predictor for achieving the MCID (odds ratio [95% CI], 0.49 [0.25, 0.91]) and the PASS (0.61 [0.38, 0.98]).Among patients with high grade lesions, there was no significant difference in two-year iHOT-12scores between those undergoing chondroplasty (N = 57) and those undergoing microfracture (N =19) (p = 0.13).

"High grade acetabular articular damage portends inferior patient-reported outcomes two years after primary labral repair," Dr. Carreira reported. "And our results suggest no difference between the efficacy of chondroplasty and microfracture with respect to self-reported outcomes."

New research being presented at the European Congress of Clinical Microbiology & Infectious Diseases (ECCMID), held online this year, reveals raw dog food to be a major source of antibiotic-resistant bacteria, making it an international public health risk.

With some of the multidrug-resistant bacteria in raw dog food identical to those found in hospital patients in several different European countries, the researchers say the trend for feeding dogs raw food may be fuelling the spread of antibiotic resistant-bacteria.

Drug-resistant infections kill an estimated 700,000 people a year globally and, with the figure projected to rise to 10 million by 2050 if no action is taken, the World Health Organisation (WHO) classes antibiotic resistance as one of the greatest public health threats facing humanity.

To find out if pet food is a potential source of spread of antibiotic-resistant bacteria, Dr Ana R. Freitas, Dr Carla Novais, Dr Luísa Peixe and colleagues from UCIBIO, Faculty of Pharmacy, University of Porto, Portugal analysed dog food from supermarkets and pet shops for Enterococci.

Enterococci are opportunistic bacteria. They live harmlessly in the guts of humans and animals but can cause severe infections if they spread to other parts of the body.

A total of 55 samples of dog food (22 wet, 8 dry, 4 semi-wet, 7 treats and 14 raw-frozen) from 25 brands available nationally and internationally were included in the study. The raw-frozen foods included duck, salmon, turkey, chicken, lamb, goose, beef and vegetables.

Thirty samples (54%) contained Enterococci. More than 40% of the Enterococci were resistant to the antibiotics erythromycin, tetracycline, quinupristin-dalfopristin, streptomycin, gentamicin, chloramphenicol, ampicillin or ciprofloxacin. There was also resistance to vancomycin and teicoplanin (2% each) and 23% of the enterococci were resistant to linezolid.

Linezolid is a last-resort antibiotic, used on severe infections when other drugs have failed, and is considered a critically important treatment by the WHO.

All of the raw dog food samples contained multidrug-resistant Enterococci, including bacteria resistant to linezolid. In contrast, only three of the non-raw samples contained multidrug- resistant bacteria.

Genetic sequencing revealed that some of the multi-drug resistant bacteria in the raw dog food were identical to bacteria isolated from hospital patients in the UK, Germany and the Netherlands. Genetically identical bacteria have also been found in farm animals and wastewater in the UK.

In another experiment, the researchers transferred antibiotic resistance genes from the bacteria found in dog food to other, experimental, bacteria - suggesting this can also occur in nature.

The researchers conclude that dog food is a source of bacteria that are resistant to last-resort antibiotics and could potentially spread to humans. Dog food, they add, could be an overlooked driver of antibiotic resistance globally.

Dr Freitas adds: "The close contact of humans with dogs and the commercialisation of the studied brands in different countries poses an international public health risk.

"European authorities must raise awareness about the potential health risks when feeding raw diets to pets and the manufacture of dog food, including ingredient selection and hygiene practices, must be reviewed.

"Dog owners should always wash their hands with soap and water right after handling pet food and after picking up faeces."

Evidence suggests that what happens in one generation--diet, toxin exposure, trauma, fear--can have lasting effects on future generations. Scientists believe these effects result from epigenetic changes that occur in response to the environment and turn genes on or off without altering the genome or DNA sequence.

But how these changes are passed down through generations has not been understood, in part, because scientists have not had a simple way to study the phenomenon. A new study by researchers at the University of Maryland provides a potential tool for unraveling the mystery of how experiences can cause inheritable changes to an animal's biology. By mating nematode worms, they produced permanent epigenetic changes that lasted for more than 300 generations. The research was published on July 9, 2021, in the journal Nature Communications.

"There's a lot of interest in heritable epigenetics," said Antony Jose, associate professor of cell biology and molecular genetics at UMD and senior author of the study. "But getting clear answers is difficult. For instance, if I'm on some diet today, how does that affect my children and grandchildren and so on? No one knows, because so many different variables are involved. But we've found this very simple method, through mating, to turn off a single gene for multiple generations. And that gives us a huge opportunity to study how these stable epigenetic changes occur."

In the new study, Jose and his team found while breeding nematode worms that some matings led to epigenetic changes in offspring that continued to be passed down through as many generations as the scientists continued to breed them. This discovery will enable scientists to explore how epigenetic changes are passed to future generations and what characteristics make genes susceptible to permanent epigenetic changes.

Jose and his team began this work in 2013, while working with nematode worms, Caenorhabditis elegans (C. elegans), a species often used as a model for understanding animal biology. The scientists noticed that worms bred to carry a gene they called T, which produces fluorescent proteins, sometimes glowed and sometimes didn't. This was puzzling because the glowers and the non-glowers had nearly identical DNA.

"Everything began when we stumbled upon a rare gene that underwent permanent change for hundreds of generations just by mating. We could have easily missed it," said Sindhuja Devanapally (Ph.D. '18, biological sciences), a co-lead author of the study who is now a postdoctoral fellow at Columbia University.

To understand the phenomenon better, the researchers conducted breeding experiments in which only the mother or the father carried the fluorescent gene. The team expected that no matter which parent carried the gene, the offspring would glow. Instead, they found that when the mother carried the fluorescent gene, the offspring always glowed, meaning the gene was always turned on. But when the father carried the gene, the offspring usually weakly glowed or did not glow at all.

"We found that there are these RNA-based signals controlling gene expression," Jose said. "Some of these signals silence the gene and some of them are protective signals that prevent silencing. These signals are duking it out as the offspring develop. When the gene comes from the mother, the protective signal always wins, but when the gene comes from the father, the silencing signal almost always wins."

When the silencing signal wins, the gene is silenced for good, or for at least 300 generations, which is how long Jose and his colleagues followed their laboratory-bred worms. Previous examples of epigenetic changes were more complex or they did not last more than a couple of generations. The researchers don't yet know why the silencing signal only wins some of the time, but this new finding puts them in a much better position to explore the details of epigenetic inheritance than ever before.

"While we've found a set of genes that can be silenced almost permanently, most other genes are not affected the same way," said the study's other co-lead author, Pravrutha Raman (Ph.D. '19, biological sciences), who is now a postdoctoral fellow at Fred Hutchinson Cancer Research Center. "After silencing, they bounce back and become expressed in future generations."

With their new findings, the researchers now believe some genes could be more vulnerable to permanent epigenetic change while other genes recover within a few generations. Although studies in worms are not the same as in humans, the research provides a window into biological processes that are likely shared, at least in part, by all animals.

"The two big advantages we now have from this work are that this long-lasting epigenetic change is easy to induce through mating, and that it occurs at the level of a single gene," Jose said. "Now we can manipulate this gene and control everything about it, which will allow us to determine what characteristics make a gene susceptible or resistant to heritable epigenetic change."

Jose and his colleagues expect that future studies may one day help scientists identify human genes that are vulnerable to long-lasting epigenetic changes.

Players of the popular game Red Dead Redemption 2 learn how to identify real American wildlife, new research shows.

The game, set in the American West in 1899, features simulations of about 200 real species of animals.

The new study, by the University of Exeter and Truro and Penwith College, challenged gamers to identify photographs of real animals.

On average, RDR2 players were able to identify 10 of 15 American animals in a multiple-choice quiz - three more than people who had not played the game.

The best performers were players who had completed the game's main storyline (meaning they had played for at least 40-50 hours) or had played more recently.

As well as learning to identify wildlife, some players reported learning about animal behaviour and ecology.

One gamer who participated in the study said RDR2 taught them how to spot a ram that's about to charge, adding: "No joke saved me from breaking a leg in real life."

Dr Sarah Crowley, of the Centre for Geography and Environmental Science at the University of Exeter, said: "The level of detail in Red Dead Redemption 2 is famously high, and that's certainly the case in terms of animals.

"Many of the animals not only look and behave realistically, but interact with each other. Possums play dead, bears bluff charge and eagles hunt snakes."

Co-author Dr Matthew Silk added: "The game features a couple of species that are now much rarer, and one - the Carolina parakeet - that's extinct.

"Hunting played a role in the Carolina parakeet's extinction; if players shoot this species in the game, they are warned of their endangered status. If they continue shooting, the species becomes extinct, highlighting the environmental consequences of players' actions."

The study used real photos of 15 species featured in the game, including the white-tailed deer, jackrabbit, alligator snapping turtle, lake sturgeon, blue jay and roseate spoonbill.

Gamers participating in the study could first enter the name of each animal as text, and were then shown multiple choice options.

The difference in identification skills between players and non-players was generally greatest for animals that are useful in the game, such as fish that can be caught and eaten.

Animals that are rarer in the game, such as the golden eagle, were less commonly identified.

The game also includes an online "naturalist" role that allows players to take up a new life as a protector of the Old West's wildlife - and people who had played this were better still at identifying the real-life animals.

In total, 586 people from 55 countries completed the quiz. 444 had played RDR2.

"We know that many gamers value realism, so game producers might be interested to see these findings, but we realise these games aren't designed to be educational," said Ned Crowley, of Truro and Penwith College.

"We don't expect big-budget games to include messages about conservation, but educators and conservationists can learn from the techniques used in games - such as making things immersive, and having each action mean something in terms of wider progress in the game.

"Being indoors on a computer is often seen as the opposite of engaging with nature, but our findings show that games can teach people about animals without even trying.

"Gaming is very popular, and should be taken seriously by ecologists and conservationists as a force for communication."

Eyewitnesses can identify perpetrators more accurately when they are able to manipulate 3D images of suspects, according to a new study.

A team of researchers in the University of Birmingham's School of Psychology developed and tested new interactive lineup software which enables witnesses to rotate and view lineup faces from different angles.

When the eyewitnesses were able to rotate the image to match the alignment of the face in their memory, they were more likely to accurately pick out the criminal from the lineup.

Lineups are used around the globe to help police identify criminals. Typically these involve witnesses examining an image of the suspect alongside 'fillers' - individuals who look similar, but who weren't involved in the crime.

The ability of the eyewitness to accurately identify guilty from innocent suspects is known as discrimination accuracy. According to the US-based Innocence Project, misidentification is the single greatest cause of wrongful conviction in the US. Since 1989, 365 wrongful convictions have been overturned on the basis of new DNA evidence; reliance on inaccurate eyewitness testimony played a role in securing convictions in many of these cases. Improving discrimination accuracy is therefore clearly important for more reliably identifying criminals.

Professor Heather Flowe, co-lead researcher, said: "We worked closely with law enforcement to develop the interactive lineup procedure to be cost effective and work with current police identification systems. The procedure is a significant advance in improving the accuracy of eyewitness identifications."

In the experimental study, published in Nature's Scientific Reports, researchers recruited more than 3,000 volunteer 'witnesses' to test their discrimination accuracy. The volunteers watched a video of a staged crime being committed. They were then shown images of the perpetrator, alongside filler images of similar faces.

The researchers found that accuracy improved significantly when the volunteers viewed the lineup from the same angle at which they had seen the perpetrator commit the crime. Accuracy was the highest when participants rotated the lineup faces to match the angle of the perpetrator.

Interestingly, the researchers also found that witnesses naturally (without instruction) moved the images into the best position for identification.

Co-author Dr Melissa Colloff said: "There are good reasons to predict that accuracy will be higher if witnesses are able to manipulate images and align them to be similar to the angle of the face in their memory. We know that retrieving memories accurately relies on the context in which they are retrieved being similar to when the memory was formed. The experiments we carried out show this theory in practice. Our participants actively sought out a familiar angle for the lineup image, to help them retrieve information from memory."

The team is now recruiting participants for the next phase of eyewitness memory research. If you are interested in taking part, please sign up here.