Tech

Coastal fog linked to high levels of mercury found in mountain lions, study finds

image: At least one lion studied had mercury levels known to be toxic to species like mink and otters, and two others had "sublethal" levels that reduce fertility and reproductive success.

Image: 
Sebastian Kennerknecht

Marine fog brings more than cooler temperatures to coastal areas. Researchers at UC Santa Cruz have discovered elevated levels of mercury in mountain lions, the latest indication that the neurotoxin is being carried in fog, deposited on the land, and making its way up the food chain.

Concentrations of mercury in pumas in the Santa Cruz Mountains were three times higher than lions who live outside the fog zone. Similarly, mercury levels in lichen and deer were significantly higher inside the fog belt than beyond it.

Mercury levels found in pumas are approaching toxic thresholds that could jeopardize reproduction and even survival, according to the researchers, whose findings appear in an article that is available free online at http://www.nature.com/articles.

Led by Peter Weiss-Penzias, an environmental toxicologist who has pioneered the study of pollutants in coastal fog, the study is the first to trace the atmospheric source of super-toxic methylmercury in the terrestrial food web up to a top predator.

"Lichen don't have any roots so the presence of elevated methylmercury in lichen must come from the atmosphere," said Weiss-Penzias. "Mercury becomes increasingly concentrated in organisms higher up the food chain."

Although mercury levels in fog present no health risk to humans, the risk to terrestrial mammals may be significant. With each step up the food chain, from lichen to deer to mountain lions, mercury concentrations can increase by at least 1,000 times, said Weiss-Penzias.

The study included fur and whisker samples from 94 coastal mountain lions and 18 noncoastal lions. Mercury concentrations in the coastal samples averaged about 1,500 parts per billion (ppb), compared to nearly 500 ppb in the noncoastal group. At least one lion studied had mercury levels known to be toxic to species like mink and otters, and two others had "sublethal" levels that reduce fertility and reproductive success.

Elevated concentrations of mercury present an additional potential threat to a top predator that is already coping with habitat loss and other risks posed by humans, said senior author Chris Wilmers, a professor of environmental studies and the director of the Puma Project.

"These mercury levels might compound the impacts of trying to make it in an environment like the Santa Cruz Mountains, where there is already so much human influence, but we don't really know," said Wilmers. "Levels will be higher 100 years from now, when the Earth's mercury budget is higher because of all the coal we're pumping into the atmosphere."

The source of fog-borne mercury

Mercury, a naturally occurring element, is released into the environment through a variety of natural processes and human activities, including mining and coal-fired power plants. "Mercury is a global pollutant," said Weiss-Penzias. "What's emitted in China can affect the United States just as much as what's emitted in the United States."

As atmospheric mercury rains down on oceans, it is converted by anaerobic bacteria in deep waters to methylmercury, the most toxic form of mercury. Upwelling brings some methylmercury to the surface, where it is released back into the atmosphere and carried by fog. At high concentrations, methylmercury can cause neurological damage, including memory loss and reduced motor coordination, and it can decrease the viability of offspring.

"Fog is a stabilizing medium for methylmercury," said Weiss-Penzias. "Fog drifts inland and rains down in microdroplets, collecting on vegetation and dripping to the ground, where the slow process of bioaccumulation begins."

Top predators, an international treaty, and a foggy bike ride

Fog is present in coastal areas that border oceans, environmental "hotspots" that are also home to high concentrations of humans. Weiss-Penzias is eager to investigate mercury levels in coastal Chile, where the top predator is a lizard, while Wilmers is curious about mercury levels in coyotes, bobcats, and birds in coastal areas.

"We need to protect the top predators in the environment," said Weiss-Penzias. "They're keystone species. They perform ecosystem services. When you change one thing, it has cascading effects through the system."

As an example of cascade effects, Wilmers cited the removal of wolves from many states in the eastern United States, which resulted in more coyotes, who preyed on foxes that had historically kept the rodent population in check. The loss of foxes ultimately made way for more rodents, which help transmit Lyme disease, said Wilmers, who added, "Locally, potentially, mountain lions keep deer and small predators in check, which could reduce Lyme disease."

The global effort to protect humans and the environment from mercury includes the Minamata Convention on Mercury, an international treaty that was adopted in 2013. Named after a Japanese city that endured a dire incident of mercury poisoning, the treaty is broad in scope, encompassing the entire life cycle of mercury.

"It's important for the future of that treaty to understand all the different ways that mercury impacts the environment," said Weiss-Penzias.

As an atmospheric chemist, Weiss-Penzias said he first became curious about fog-borne pollutants about a decade ago while riding his bike to work. "I was riding through this absolute fogstorm, with water dripping off my glasses, and I just wondered, 'What's in this stuff?'" he recalled. Hypothesizing that mercury might de-gas out of the ocean and end up in fog, he collected samples and sent them to a lab.

"The lab called me, saying they'd have to re-run the tests, because they didn't believe the numbers," said Weiss-Penzias.

Credit: 
University of California - Santa Cruz

New migraine medications could endanger patients with high blood pressure

The neuropeptide αCGRP (α calcitonin gene-related peptide) works in two different ways. It leads to inflammation and dilates the blood vessels right at the release point of the nerve cells, for example in the meninges, which can trigger migraine attacks. However, it has a completely different effect on the heart, as has now been discovered by a team of researchers at the University of Zurich (UZH).

Bad for the meninges, good for the heart

As demonstrated by the scientists through studies on mice, αCGRP is also released from active skeletal muscles. It is transported via the blood from the muscle to the heart where it inhibits the pathological heart remodeling caused by chronic high blood pressure. "It is exactly the same for humans as it is for mice," says study leader Johannes Vogel, professor at the UZH Institute of Veterinary Physiology. "Physical activity and sport increase the blood plasma levels of αCGRP, which has a positive effect on the heart in patients with high blood pressure."

Treatment option for certain patients with high blood pressure

The work carried out by the researchers involved comparing normal mice with others having chronic high blood pressure, which were either sedentary or repeatedly and voluntarily ran in a running wheel. The study revealed that having normal concentrations of αCGRP in the blood plasma is vital and that the peptide is crucial for the positive effects of physical activity on the heart. αCGRP also provides the heart with extra protection, regardless of its antihypertensive properties in high doses. "In the future, substances that activate the release of αCGRP or mimic its action could be used in hypertensive patients who can only be physically active to a very limited extent or in whom antihypertensive medications have little or no effect," explains Johannes Vogel.

Caution required with migraine medications and chronic high blood pressure

The research work also brought another finding to light - long-term administration of αCGRP blockers in mice with chronic high blood pressure resulted in life-threatening cardiac dysfunction. Medications of this kind, which take a targeted approach to blocking the neuropeptide, have recently been approved for migraine prophylaxis. As the neuropeptide αCGRP in species from zebrafish to humans is very similar, it must be part of a key biological mechanism that works in the same way in different organisms. According to cardiovascular specialist Vogel, the results are therefore also relevant to humans: "αCGRP blockers should only be used for migraine prevention with the proviso that patients' blood pressure is monitored regularly. Chronic high blood pressure should be added to the list of contraindications for the long-term use of αCGRP blockers."

Credit: 
University of Zurich

Skiers had lower incidence of depression and vascular dementia -- but not Alzheimer's

Half as many diagnosed with depression, a delayed manifestation of Parkinson's, a reduced risk of developing vascular dementia - but not Alzheimer's. These connections were discovered by researchers when they compared 200 000 people who had participated in a long-distance cross-country ski race between 1989 and 2010 with a matched cohort of the general population. The results of the population register study, led by researchers at Lund University in Sweden together with Uppsala University, were recently published in three scientific articles.

"As brain researchers, we have had the unique opportunity to analyse an exceptionally large group of very physically active people over two decades, and we have unravelled some interesting results", says Tomas Deierborg, research team leader and associate professor at Lund University.

It has been previously shown that the skiers of Vasaloppet, a popular cross-country skiing race in Sweden, have a reduced risk of suffering a heart attack, but not what the situation looked like for brain diseases.

In the group of Vasaloppet skiers (a total of 197 685 people) there were 50 per cent fewer people affected by vascular dementia than in the control group (a total of 197 684 people). On the other hand, researchers discovered that the risk of developing Alzheimer's disease was not reduced, something that contradicts previous studies in the field which show that physical activity has an impact on Alzheimer's.

Two decades after the skiers had competed in the Vasaloppet ski race, 233 had developed dementia (incl. vascular and Alzheimer's dementia), 40 of these people had been diagnosed with vascular dementia and 86 people with Alzheimer 's disease. In the general population, 319 had developed dementia, 72 had developed vascular dementia and 95 had developed Alzheimer's dementia.

"The results indicate that physical activity does not affect the molecular processes that cause Alzheimer's disease, such as the accumulation of the amyloid protein. Nonetheless, physical activity reduces the risk of vascular damage to the brain, as well as to the rest of the body", says memory researcher Oskar Hansson, professor of neurology at Lund University.

The researchers saw similar results when they studied 20 000 subjects in the population study called Malmö Diet and Cancer. The participants who were most physically active had a lower risk of developing vascular dementia, in line with the results found in the Vasaloppet cohort. On the other hand, there were no significant differences in developing Alzheimer's disease between the group that was most physically active and the group with the lowest physical activity.

The researchers also studied whether Vasaloppet skiers had a reduced risk over time of developing Parkinson's disease. Two decades (21 years) after they had participated in the Vasaloppet ski race, 119 people had been diagnosed with Parkinson's. In the general population, 164 people had received the diagnosis. However, the difference between those who are physically active (the Vasaloppet skiers) and the general population appears to diminish over time.

"The mechanisms behind this still need to be investigated, but it seems that those who are physically active have a 'motor reserve' that postpones the onset of the disease. If a person trains a lot it may be possible to maintain mobility for longer, despite the pathological changes in the brain", speculates Tomas Olsson, doctoral student and author of the study.

When the researchers studied how many Vasaloppet skiers suffered from depression compared to the general population, they found that the risk was halved in those who had participated in Vasaloppet.

Following two decades of follow-up, a total of 3 075 people had been diagnosed with depression, of whom 1 030 were Vasaloppet skiers and 2 045 people were from the general population.

Researchers also studied the differences between men and women. The risk of suffering from depression was further reduced in men who were part of the group with the fastest finishing times. This did not apply to the fastest female Vasaloppet skiers, though.

"However, the fastest women still had a lower risk of suffering from depression than those who were not active in the general population", says Martina Svensson, doctoral student at Lund University and author of the scientific articles.

Credit: 
Lund University

A novel pathway to target colorectal cancer

image: Dr. Raymond N. Dubois, noted cancer researcher and dean of the College of Medicine at the Medical University of South Carolina, is senior author on the Gastroenterology article.

Image: 
Sarah Pack, Medical University of South Carolina

While the emergence of precision medicine and immunotherapy has greatly improved outcomes for patients with colorectal cancer, new approaches are still needed for patients with late-stage disease who do not respond to these therapies. According to the American Cancer Society, patients who present with stage 4 colorectal cancer have a five-year survival rate of only 14%. Therefore, researchers are interested in finding new ways to try to inhibit colorectal tumor growth.

Prostaglandin E2, or PGE2, promotes metastasis of colorectal cancer through a microRNA, MIR675, report researchers at the Medical University of South Carolina (MUSC) in an article published online in November by Gastroenterology.

In the study funded by the National Institutes of Health, the MUSC researchers showed that mice treated with PGE2 in a preclinical model of colorectal cancer had vastly more metastatic lesions in the liver and lung than untreated mice. This preclinical evidence suggests that targeting the microRNA could have some therapeutic potential.

"We're still learning more about some of the pathways involved in the development and progression of colorectal cancer," said Raymond N. DuBois, M.D., Ph.D., a noted cancer researcher, dean of the College of Medicine at MUSC and senior author on the article. "I think this is one example where a microRNA could be targeted in a therapeutic way in a subset of patients."

PGE2 is thought to promote tumor cell proliferation, survival and migration. To investigate how PGE2 does this in colorectal cancer, DuBois and the other MUSC investigators, who included first author Bo Cen, Ph.D., a research assistant professor in the DuBois laboratory, performed a screen on colorectal cancer cells treated with PGE2 to detect if there were any changes following treatment. Voucher funding from the South Carolina Clinical & Translational Research Institute paid for a portion of this project.

"We found that many microRNAs changed in response to treatment," explained Cen. "We focused on MIR675-5p because its levels increased more than any other in response to PGE2 treatment."

A microRNA is a small RNA molecule that can silence the expression of certain genes. In this case, MIR675-5p can suppress the expression of p53. P53 is one of the most well-known genes in cancer because it enables production of a protein that can put the brakes on cell division. However, cancer can be clever and find ways to suppress p53 so that cells can continue to divide uncontrollably.

The researchers next identified a potential site on p53 to which MIR675-5p could bind. Then, investigators confirmed that MIR675-5p suppresses p53 to promote metastasis. In a preclinical colorectal cancer model, mice were treated with PGE2 or a vehicle control. Mice treated with PGE2 were found to have more metastases compared to the control.

Further, tumor cells in the group of mice treated with PGE2 had increased expression of MIR675-5p and decreased expression of p53, confirming that PGE2 promotes tumor progression through MIR675-5p and p53.

"We found that PGE2 was able to decrease the expression of p53, which is a very well-known tumor suppressor, and we found it was able to do this by increasing the expression of MIR675-5p," said Cen.

Next, the researchers plan to analyze samples from patients with different stages of colorectal cancer and investigate how levels of PGE2 and MIR675-5p correlate with prognosis or response to therapy.

"Ultimately, we discovered a key mechanism by which PGE2 promotes tumor development and progression," said DuBois. "These findings provide important preclinical evidence that microRNA could possibly be targeted in a therapeutic way to treat a subset of patients."

Credit: 
Medical University of South Carolina

Successful alcohol, drug recovery hampered by discrimination

BOSTON - Even after resolving a problem with alcohol and other drugs, adults in recovery report experiencing both minor or "micro" forms of discrimination such as personal slights, and major or "macro" discrimination such as violation of their personal rights. These experiences are associated with increased distress and lead to both diminished quality of life and a decrease in resources needed to successfully sustain recovery, investigators from the Recovery Research Institute and Center for Addiction Medicine at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) report.

The findings, which have important implications for both substance use disorder treatment and public policy, are published in the journal Drug and Alcohol Dependence.

Although previous studies of persons with substance use disorder found evidence of discrimination while symptomatic, or when incarcerated, or in other stigmatized situations, this is believed to be the first study to look at the prevalence and types of discrimination experienced among those who report that they have resolved a problem and are in recovery, says lead author Corrie L. Vilsaint, PhD, a research fellow at MGH.

She and her colleagues surveyed a nationally representative sample of 2,002 US adults who reported resolving an alcohol or other drug problem and asked, "Since resolving your problem with alcohol or drugs, how frequently have the following occurred because someone knew about your alcohol or drug history?"

The questions solicited information about micro discrimination such as "people assumed I was likely to relapse" and "people said I looked like an alcoholic or addict" and macro discrimination such as job loss, denial of a loan or housing, denial of the right to vote, or insurance refusals.

"In general, we found that nearly 50 percent of the people said that others 'assumed I would relapse', and 38 percent said they felt like at times they were being held to a higher standard than other people. We also captured that about 18 percent reported that they felt like they had been treated unfairly by the police," she says.

In addition 16.2 percent of respondents said they were denied employment, 7.7 percent said they were denied the right to vote, 15.2 percent said that it was hard for them to get medical insurance, 11.2 percent said that insurance would not cover some of their medical costs, and 9.4percent said that they were denied housing, all because someone knew of their prior history of alcohol or other drug problems.

After adjusting for the severity of addiction and years since resolution of the problem, the investigators found that respondents who reported greater levels of discrimination were significantly more likely to suffer from higher psychological distress, lower quality of life, and decreased "recovery capital" - the sum total of resources needed for successful recovery.

"These findings have social and policy implications" Vilsaint says. "It is tough enough struggling with the physical and psychological demands of recovery without having to contend with the kinds of discrimination reported fairly frequently here. Some of these residual tolls that you see in these people's lives from past drug history or past criminal history related to their drug use can block them from seeking addiction recovery, block them from seeking treatment and block them from disclosing that they need help."

The investigators note that additional study is needed to determine which discriminatory experiences are most likely to have a negative effect on recovery efforts.

Credit: 
Massachusetts General Hospital

December's SLAS technology feature article now available

image: This is the cover of SLAS Technology.

Image: 
David James Group

December's SLAS Technology Cover Article Features University of Wisconsin Research, "Automated System for Small-Population Single-Particle Processing Enabled by Exclusive Liquid Repellency"

Oak Brook, IL - Next month's SLAS Technology features the cover article, "Automated System for Small-Population Single-Particle Processing Enabled by Exclusive Liquid Repellency," outlining research led by Chao Li, Ph.D., (University of Wisconsin-Madison, USA). In the article, Li and his team describe how they combined a robotic liquid handler, an automated microscopic imaging system and real-time image-processing software for single-particle identification to create an automated platform using exclusive liquid repellency (ELR) microdrops for single-particle isolation, identification and retrieval.

As the use of single-cell applications have become important to the study of cancer heterogeneity, developmental biology, neurobiology and immunology, there is also an increased interest in identifying and isolating specific single cells from a heterogeneous biological sample to discover its unique traits and heterogeneity. However, this isolation remains challenging due to the large sample volume and cell numbers needed, which could impede the isolation of single cells and make them unsuitable for rare-cell applications like circulating tumor cell (CTC) research.

As single-cell printing techniques that handle smaller sample sizes have developed over time, sample loss is still an issue due to the difficulty of using traditional single-liquid phase liquid-handling and storage equipment such as multiwell plates. Although a variety of specialized multi-liquid phase platforms have been developed for efficiently manipulating small amounts of cell samples without significant liquid loss, they are usually based on a closed-system design which makes external access for individual cell manipulation and retrieval difficult and remains extremely costly.

Li, along with David J. Niles, Ph.D., Duane S. Juang, Ph.D., Joshua M. Lang, Ph.D., and David J. Beebe, Ph.D., (University of Wisconsin-Madison, USA), developed an automated platform using ELR microdrops for lossless single-cell isolation, identification and retrieval. It combines the use of a robotic liquid handler, an automated microscopic imaging system and real-time image-processing software for single-particle identification and enables rapid, hands-free and robust isolation of microdrop-encapsulated rare cellular samples and further on-chip cell culture or down-stream analysis. This application is distinct from other liquid repellent systems and showed no compromise of liquid adhesion on solid surfaces enabling unique applications.

Chao Li received his Ph.D. in physical chemistry from the National Center for Nanoscience and Technology (China) in 2010. His postdoctoral research has included microfluidic systems and applications in biomedicine, including single-cell sample processing, in vitro organotypic model, biofilm dynamics, antimicrobial pharmacodynamics, multispecies microbial communities and host-microbe interactions.

Credit: 
SLAS (Society for Laboratory Automation and Screening)

NASA finds heavy rain potential in Tropical Storm Rita

image: On Nov. 26 at 0224 UTC (Nov. 25 at 9:24 p.m. EST) NASA's Aqua satellite analyzed Tropical Storm Rita's clouds using the AIRS instrument. AIRS showed the strongest storms southeast of the center where the coldest cloud top temperatures as cold as or colder than 210 Kelvin (purple) minus 81 degrees Fahrenheit (minus 63.1 degrees Celsius) around the center.

Image: 
NASA JPL/Heidar Thrastarson

NASA analyzed the cloud top temperatures in Tropical Storm Rita using infrared light to determine the strength of the storm. Rita has triggered warnings in the island nation of Vanuatu.

One of the ways NASA researches tropical cyclones is using infrared data that provides temperature information. Cloud top temperatures identify where the strongest storms are located. The stronger the storms, the higher they extend into the troposphere, and the colder the cloud top temperatures.

On Nov. 26 at 0224 UTC (Nov. 25 at 9:24 p.m. EST) NASA's Aqua satellite analyzed the storm using the Atmospheric Infrared Sounder or AIRS instrument. The AIRS imagery showed the strongest storms were southeast of the center. In those areas, AIRS found coldest cloud top temperatures as cold as or colder 210 Kelvin minus 81 degrees Fahrenheit (minus 63.1 degrees Celsius). NASA research has shown that cloud top temperatures that cold indicate strong storms that have the capability to create heavy rain.

Animated enhanced infrared satellite imagery shows that convection (rising air that forms the thunderstorms that make up a tropical cyclone) is rapidly decaying. That means that thunderstorms cannot form easily. The bulk of the clouds and showers are being pushed to the southeast of the low-level center of circulation by northwesterly winds.

Tropical cyclones do not always have uniform strength, and some sides have stronger sides than others, so knowing where the strongest sides of the storms are located helps forecasters. NASA then provides data to tropical cyclone meteorologists so they can incorporate it in their forecasts.

At 10 a.m. EST (1500 UTC), the Joint Typhoon Warning Center (JTWC) noted that Rita was located near latitude 14.4 degrees south and longitude 169.6 degrees east, about 212 nautical miles north-northeast of Port Vila, Vanuatu. Rita was moving to the south-southwest and had maximum sustained winds of 35 knots (40 mph/65 kph). Rita was moving to the southeast and away from the islands of Vanuatu.

The National Disaster Management Office (NDMO) advises that a Yellow Alert is in effect for people in Penama and Malampa provinces.  Strong to gale force winds may be expected to the east of Penama, Malampa and Shefa Provinces.

On Wednesday, Nov. 27, 2019, the Vanuatu Meteorology and Geo-Hazards Department (VMGD), Port Vila, Vanuatu, said, "Heavy rainfalls are expected over the eastern parts of Penama, Malampa and Shefa province tonight and continuing tomorrow. A Marine strong wind warning for all coastal waters is current. High Seas warning is also current for open waters of Vanuatu close to the system."

The JTWC expects Rita will dissipate over the next day.

Typhoons and hurricanes are the most powerful weather event on Earth. NASA's expertise in space and scientific exploration contributes to essential services provided to the American people by other federal agencies, such as hurricane weather forecasting.

The AIRS instrument is one of six instruments flying on board NASA's Aqua satellite, launched on May 4, 2002.

For updated forecasts from the VMGD website: http://www.vmgd.gov.vu

Credit: 
NASA/Goddard Space Flight Center

Swiss army knife for genome research

image: Three steps to complete enhancer analysis with CRUP: First, an algorithm identifies the active enhancers. Then, it reveals epigenetic differences between data sets and at last, assigns differential enhancers to their respective target genes.

Image: 
C-BY 4.0, Ramisch A et al. (2019), doi: 10.1186/s13059-019-1860-7

It is the the dream of every molecular geneticist: an easy-to-use program that compares data sets from different cellular conditions, identifies enhancer regions and then assigns them to their target genes. A research team led by Martin Vingron at the Max Planck Institute for Molecular Genetics in Berlin has now developed a program that masters all of this.

"DNA is pretty boring, since it is practically the same in every cell," says Martin Vingron, Director and Head of the Department of Bioinformatics at the Max Planck Institute for Molecular Genetics in Berlin. "When the genome is like the book of life, I am most interested in the side notes." These "notes" are small chemical marks attached to the DNA molecule that do not alter the genetic information itself, but influence what happens to the DNA at the respective site. In other words, these marks have an epigenetic effect. They serve as regulators of genomic regions that are responsible for the activation and deactivation of genes, such as promoters and enhancers.

In many complex diseases, the epigenetic control of genes does not work correctly and is of great interest for scientists. The analysis of these regions in the lab, however, is often cumbersome, time-consuming and complicated. That's why Vingron and his team decided to develop a new program package called Condition-specific Regulatory Units Prediction (CRUP) which simplifies analysis and solves several practical problems.

"We wanted to combine the common steps in the process of enhancer prediction in a simple, universal program," says bioinformatician Verena Heinrich who developed the package. CRUP simplifies the analysis in many regards. The machine learning algorithm is not limited to specific cell- or tissue-types. It does not need to be recalibrated prior to each analysis of a data set and allows comparative study of several data series. The tool, which was developed by Heinrich and doctoral student Anna Ramisch, is still easy to use.

The enhancer's stimulating activity

CRUP specifically identifies and characterizes enhancers - DNA segments that stimulate or "enhance" the transcription of genes. These regions attract proteins that attach to promoter sequences which function as a switch for each gene. However, which enhancer controls the right genes at correct time often remains a mystery. "Enhancers and their associated genes can be located far away from each other," says Heinrich. "This makes it difficult for us to assign the regulatory sequences to their respective targets."

The genome contains hundreds of thousands of enhancers which are active in different phases in the life of a cell like during growth, maintenance, or disease. When the DNA is tightly packed like a wool thread on spools of carrier proteins called histones, the regulatory sequences are in a "resting" state. They only become active by chemical modifications to the histone proteins. Then, sections unwrap from the DNA clusters, get exposed, and become accessible to molecules that activate genes. The analysis of histone proteins by chromatin immunoprecipitation (ChIP) in tandem with DNA sequencing then reveals which enhancers are active and which are not.

In three steps to a complete analysis

These ChIP data are the input for the newly developed program. CRUP first examines all sequences and then decides whether it is an enhancer or not. The classification algorithm is based on artificial intelligence, which is trained with information from mouse embryonic stem cells. It detects enhancer regions in many other animal species or tissues, as Heinrich and her colleagues demonstrated on a diverse set of data provided by the German Epigenome Program (DEEP).

In the second step, CRUP can be fed multiple data sets and the program finds where they differ. This makes it possible to interpret a series of measurements or pinpoint differences between tissues. Epigenetic changes to enhancers become apparent - over time, or when comparing healthy and diseased tissues. The third and final step of the analysis is the mapping of genes to their respective enhancers. "We asked: What part of the genome is active at the same time in the same place?" explains Heinrich. To achieve this, CRUP links the enhancer analysis with transcription data that reveal which genes are active, and experiments that tell which parts of the DNA strand are close to each other.

Finally, the researchers tested their program in a practical setting. They analyzed the tissue of mice with the immune disease rheumatoid arthritis and compared it with data from healthy animals. CRUP identified more than 200 differences in enhancer regions, some of which had already been associated with the disease in other studies. The genes that CRUP assigned to these enhancers have also been shown to play a role in disease.

A catalyst for research

"Our program reliably identifies candidates for disease-associated enhancers and links them to their target genes," says Vingron. His team hopes the new tool will make the field more accessible as well as accelerate research to help identify the causes of complex human diseases. "CRUP should be particularly useful for all the research groups that do not have a team of bioinformaticians at hand."

Credit: 
Max-Planck-Gesellschaft

Satellite tracking Guam's Tropical Storm Kammuri

image: NOAA-20 provided a visible image of Kammuri on Nov. 26 at 0354 UTC (Nov. 25 at 10:54 p.m. EST) that shows it is consolidating and strengthening. The image showed bands of thunderstorms wrapping into its low level center.

Image: 
NOAA /NRL

The National Weather Service in Guam has posted warnings as Tropical Storm Kammuri lingers nearby. The NOAA-20 satellite provided forecasters with an image of the storm.

Tropical Depression 29W formed on Nov. 25, and when it strengthened into a tropical storm on Nov. 26 it was renamed Kammuri.

Visible imagery from NASA satellites help forecasters understand if a storm is organizing or weakening. The Visible Infrared Imaging Radiometer Suite (VIIRS) instrument aboard NOAA-20 provided a visible image of Kammuri on Nov. 26 at 0354 UTC (Nov. 25 at 10:54 p.m. EST) that shows it is consolidating and strengthening.  The image showed bands of thunderstorms wrapping into its low level center.

On Nov. 26 (and Nov. 27 local time), a tropical storm warning remains in effect for Guam, Rota, Tinian and Saipan. Tropical storm conditions, including winds of 39 mph or more, are occurring and will persist through noon (local time on Nov. 27) today.

On Nov. 26 at 10 a.m. EST (1500 UTC/1 a.m. CHST on Nov. 27) The National Weather Service in Tiyan, Guam noted that the "center of Tropical Storm Kammuri was located near latitude 11.4 degrees north and longitude 144.4 degrees east. Kammuri is moving west at 24 mph. Kammuri will maintain this motion through tonight [Wed. Nov. 27 local time], then turn toward the northwest on Thursday. Kammuri will decrease in forward speed tonight. Maximum sustained winds have increased to 45 mph. Kammuri is forecast to intensify in the next few days and could become a typhoon on Thursday. Kammuri will be well west of the Marianas." The storm is at its closest to Guam now.

Kammuri is forecast to move west-northwest, later northwest and strengthen into a typhoon.

NASA launched JPSS-1 in Nov. 2017. JPSS-1 reached polar orbit on Saturday, November 18, and it officially became known as NOAA-20. JPSS-1 joined the NOAA/NASA Suomi NPP satellite in the same polar orbit, and will also provide scientists with observations of atmospheric temperature and moisture, clouds, sea-surface temperature, ocean color, sea ice cover, volcanic ash, and fire detection.

Typhoons and hurricanes are the most powerful weather event on Earth. NASA's expertise in space and scientific exploration contributes to essential services provided to the American people by other federal agencies, such as hurricane weather forecasting.

For updated forecasts. visit: https://www.weather.gov/gum/Cyclones

Credit: 
NASA/Goddard Space Flight Center

A record-setting transistor

image: Professor Yuping Zeng (right) and graduate student Peng Cui have worked on designs for transistors that could enable cheaper, faster wireless communications.

Image: 
Photo by Kathy F. Atkinson

Many of the technologies we rely on, from smartphones to wearable devices and more, utilize fast wireless communications. What might we accomplish if those devices transmitted information even faster?

That's what Yuping Zeng, assistant professor of electrical and computer engineering at the University of Delaware, aims to discover. She and a team of researchers recently created a high-electron mobility transistor, a device that amplifies and controls electrical current, using gallium nitride (GaN) with indium aluminum-nitride as the barrier on a silicon substrate. They described their results in the journal Applied Physics Express.

Among devices of its type, Zeng's transistor has record-setting properties, including record low gate leakage current (a measure of current loss), a record high on/off current ratio (the magnitude of the difference of current transmitted between the on state and off state) and a record high current gain cutoff frequency (an indication of how much data can be transmitted with a wide range of frequencies).

This transistor could be useful for higher bandwidth wireless communication systems. For a given current, it can handle more voltage and would require less battery life than other devices of its type.

"We are making this high-speed transistor because we want to expand the bandwidth of wireless communications, and this will give us more information for a certain limited time," said Zeng. "It can also be used for space applications because the gallium nitride transistor we used is radiation robust, and it is also wide bandgap material, so it can tolerate a lot of power."

This transistor represents innovation in both material design and device application design. The transistors are made on a low-cost silicon substrate, "and this process can also be compatible with silicon Complementary metal-oxide-semiconductor (CMOS) technology, which is the conventional technology used for semiconductors," said Zeng.

The transistor described in the recent paper was just the first of many to come.

"We are trying to continue to break our own record, both for the low power application as well as for the high-speed application," said Zeng. The team also plans to use their transistors to make power amplifiers that could be particularly useful for wireless communications as well as other internet-of-things.

Zeng's group is also working on titanium oxide transistors which are transparent and could be used for backplane displays, competing with the technology for currently commercially used indium-gallium-zinc oxide (InGaZnO) transistors.

Dennis Prather, Engineering Alumni Professor of Electrical and Computer Engineering, was a co-author on the Applied Physics Express paper.

"With the era of 5G upon us, it's very exciting to see Professor Zeng's record setting transistors as a leading contribution to this field," he said. "Her research is world renowned and the ECE Department is very lucky to have her on its faculty. To this end, 5G is ushering in a wave of new technologies in nearly every aspect of mobile communications and wireless networks, to have UD's ECE department at the leading edge, with Professor Zeng's outstanding research, is truly a wonderful thing."

Credit: 
University of Delaware

High levels of screen use associated with symptoms of anxiety in adolescence

A new study, by researchers Drs. Boers, Afzali and Conrod who are affiliated with CHU Sainte-Justine Research Center and the Department of Psychiatry at the University of Montreal, reveals that social media use, television viewing and computer use, but not video gaming, are linked to an increase in anxiety symptoms among adolescents.

The study, published in academic outlet the Canadian Journal of Psychiatry, shows that a higher than average frequency of social media use, television viewing and computer use over four years predicts more severe symptoms of anxiety over that same time frame. Over and above a potential common vulnerability to both sets of behaviours, the study demonstrates that if a teen experienced an increase in their social media use, television viewing and computer use in a given year which surpassed their overall average level of use, then his or her anxiety symptoms also increased in that same year. Furthermore, when adolescents decreased their social media use, television viewing, and computer use, their symptoms of anxiety became less severe. Thus, no lasting effects were found.

These are interesting findings considering another recent publication by the same authors, reporting associations of social media use and television viewing on symptoms of depression, but not computer use. Thus, it appears that computer use is uniquely associated to increases in anxiety, potentially in relation to using the computer for homework activities, but this needs further research, explains the study's lead author, Elroy Boers, post-doctoral researcher at UdeM's Department of Psychiatry.

This study could have important implications for how youth and families choose to regulate digital screen time in order to prevent and reduce symptoms of anxiety. The study findings indicate social media use, television viewing, and computer use are predictors of anxiety in adolescence. While our results are based on observational research design, the nature of statistical approach that we used to test possible causal effects robustly controlled for any potential common underlying vulnerability to high levels of screen time and anxiety. Nevertheless, more research is needed, including research that includes experimental designs, to confirm that it is exposure to social media, television, and computer use that is causing elevated rates of anxiety in young people," said Dr. Patricia Conrod, senior author and Professor of Psychiatry at the University of Montreal, and CHU Ste Justine.

Screen time and anxiety

Dr Conrod's team followed almost four thousand Canadian teenagers from age 12 to 16 who were part of the Co-Venture Trial. Each year of high school, teens were asked to self-report time spent in front of digital screens and specified amount of time spent engaging in four different types of screen time activities (social media, television, video gaming and computer use).

Moreover, the teenagers completed self-reported questionnaires on various anxiety symptoms at ages 12 to 16. Then, after data collection, state-of-the-art statistical analyses were performed to assess the between-person, with-person, and lagged-within person associations between screen time and anxiety in adolescence. These analyses augment standard analyses by modelling the year-to-year changes of both sets of problems, thus, taking into account possible common vulnerability and possible natural developmental changes in each set of behaviours or symptoms.

"These findings suggest that one way to help teens manage anxiety could be to help them limit the amount of time they spend in front screens", said Conrod. Conrod and her colleagues hope that this study helps guide the design of new intervention strategies for at-risk youth, before anxiety symptoms become clinically significant.

Credit: 
University of Montreal

New technology makes internet memes accessible for people with visual impairments

People with visual impairments use social media like everyone else, often with the help of screen reader software. But that technology falls short when it encounters memes, which don't include alternate text, or alt text, to describe what's depicted in the image.

To counter this, researchers at Carnegie Mellon University have developed a method to automatically identify memes and apply prewritten templates to add descriptive alt text, making them intelligible via existing assistive technologies.

Memes are images that are copied and then overlaid with slight variations of text. They are often humorous and convey a shared experience, but "if you're blind, you miss that part of the conversation," said Cole Gleason, a Ph.D. student in CMU's Human-Computer Interaction Institute (HCII.)

"Memes may not seem like the most important problem, but a vital part of accessibility is not choosing for people what deserves their attention," said Jeff Bigham, associate professor in the HCII. "Many people use memes, and so they should be made accessible."

Memes largely live within social media platforms that have barriers to adding alt text. Twitter, for example, allows people to add alt text to their images, but that feature isn't always easy to find. Of 9 million tweets the CMU researchers examined, one million included images and, of those, just 0.1 percent included alt text.

Gleason said basic computer vision techniques make it possible to describe the images underlying each meme, whether it be a celebrity, a crying baby, a cartoon character or a scene such as a bus upended in a sinkhole. Optical character recognition techniques are used to decipher the overlaid text, which can change with each iteration of the meme. For each meme type, it's only necessary to make one template describing the image, and the overlaid text can be added for each iteration of that meme.

But writing out what the meme is intended to convey proved difficult.

"It depended on the meme if the humor translated. Some of the visuals are more nuanced," Gleason said. "And sometimes it's explicit and you can just describe it." For example, the complete alt text for the so-called "success kid" meme states "Toddler clenching fist in front of smug face. Overlaid text on top: Was a bad boy all year. Overlaid text on bottom: Still got awesome presents from Santa."

The team also created a platform to translate memes into sound rather than text. Users search through a sound library and drag and drop elements into a template. This system was made to translate existing memes and convey the sentiment through music and sound effects.

"One of the reasons we tried the audio memes was because we thought alt text would kill the joke, but people still preferred the text because they're so used to it," Gleason said.

Deploying the technology will be a challenge. Even if it was integrated into a meme generator website, that alt text wouldn't be automatically copied when the image was shared on social media.

"We'd have to convince Twitter to add a new feature," Gleason said. It could be something added to a personal smartphone, but he noted that would put the burden on the user. CMU researchers are currently working on related projects, including a browser extension for Twitter that attempts to add alt text for every image and could include a meme system. Another project seeks to integrate alt text into the metadata of images that would stay with the image wherever it was posted.

This work was presented earlier this year at the ACCESS conference in Pittsburgh. Other researchers involved in the research include HCII postdoctoral fellow Amy Pavel, CMU undergraduate Xingyu Liu, HCII assistant professor Patrick Carrington, and Lydia Chilton of Columbia University.

Credit: 
Carnegie Mellon University

Big trucks, little emissions

One way of increasing sustainability is to reduce carbon fuel emissions within transportation. In 2017 greenhouse gas emissions (GHG) from this sector surpassed all others in the U.S., accounting for nearly 30% of total GHG emissions, according to the United States Environmental Protection Agency.

One strategy researchers are exploring for lowering emissions is to produce renewable fuels, like renewable jet fuel, with biofuel production already in place, such as ethanol — a fuel that is low cost, cleaner burning and widely available. But for this strategy to work, ethanol has to first be converted to a hydrocarbon fuel, a step that could add to overall costs.

A pioneering study released today reveals Vertimass’ new integrated, cost-efficient way of converting ethanol for fuel blends that can reduce greenhouse gas emissions between 40 and 96 percent. The discovery marks a major advance in the development of drop-in, or interchangeable, biofuels and can promote research to advance their use in aviation, shipping, long-haul truck and other forms of heavy-duty transportation.

The multidisciplinary team behind the discovery represents a wide range of academic and industry institutions and includes researchers from the U.S. Department of Energy’s (DOE) Argonne National Laboratory, as well as DOE’s National Renewable Energy Laboratory and Oak Ridge National Laboratory.

The researchers behind the study developed their new approach for converting ethanol using the latest advances in catalysis and process development. Unlike traditional methods which require three steps, new advances let researchers create a conversion process that combined all three steps, a measure that could lower the cost of conversion and environmental footprint.

To understand the full-scale impacts of their one-step conversion process, called Consolidated Alcohol Dehydration and Oligomerization, or CADO, researchers evaluated the environmental impacts of their system via a process called life-cycle analysis. Researchers also evaluated the technical and economic impacts of their approach.

To tackle this process, the team turned to the research group at Argonne that works on the Greenhouse Gases, Regulated Emissions, and Energy use in Transportation (GREET) model, a powerful analytical tool that simulates energy use and environmental outputs of various vehicle and fuel systems. Used by nearly 40,000 people worldwide, the GREET platform can analyze multiple vehicle and/or fuel systems, from when raw materials are mined or extracted to when they are disposed or emitted, to calculate the energy use and emission levels throughout.

“GREET is one of the only tools out there that can provide a complete picture of the energy and environmental impacts of an entire vehicle and fuel system,” said Michael Wang, the leader of the GREET team at Argonne, and one of the co-authors of the study.

Argonne researchers used GREET to calculate the life cycle GHG emissions produced by hydrocarbon fuels made from different raw materials and conversion methods. Some of the raw materials — also known as feedstocks — analyzed were corn and sugarcane, which are first generation feedstocks, as well as sugarcane straw and corn stover, which are non-food biomass, or the second generation feedstocks.

“Variations in the feedstock used to make ethanol and pathways used to convert it, yield different levels of GHG emissions,” said Argonne energy systems analyst Pahola Thathiana Benavides, another co-author.

Wang and Benavides’ analysis showed that hydrocarbon blends made using the CADO conversion process reduced greenhouse gas emissions anywhere from between 40% up to 96% depending on the feedstock and the conversion pathway. GHG emissions fell by 40% with corn grain, 70% with sugarcane juice and 70-96% with cellulosic biomass such as sugarcane straw and corn stover.

“In order to move towards more sustainable development, we will need fuels that can generate fewer emissions and that are economically feasible,” Benavides said. “This work is an exciting indicator that building such a future is possible.”

Credit: 
DOE/Argonne National Laboratory

How to measure inequality as 'experienced difference'

image: Figure 1. Experienced differences (left panel) and the edges used in the conventional measure (right panel). If nodes A, B, and C in Figure 1 have wealth 10, 4, and 3, for example, the Gini coefficient using the network representation in the left panel is 0.412. Using the network representation on the right, however, the Gini is estimated at 0.274

Image: 
Samuel Bowles and Wendy Carlin

A new way of measuring wealth inequality better accounts for the way we experience it. In a paper published in Economics Letters, economists Samuel Bowles of the Santa Fe Institute and Wendy Carlin of University College London and the Santa Fe Institute propose a novel twist on the widely used Gini coefficient--a workhorse statistical measure for gauging the gap between haves and have-nots.

In a perfectly egalitarian society, where all individuals are equally wealthy, the Gini co-efficient should be 0. Conversely, a society where a single individual holds all of the wealth should have a Gini coefficient equal to 1. Using the Gini coefficient, countries can be ranked from least to most unequal.

But individuals' wealth or income isn't the whole picture when it comes to inequality. According to Bowles and Carlin, the standard algorithm for calculating Gini coefficients produces odd results for example when a single individual owns all of the wealth the Gini coefficient is less than 1 which is the value it should attain under maximum inequality. Correcting that error, they show, requires a network-based fix that accounts for the relationships between individuals in the society.

"Some of the dimensions along which inequality is measured are best conceived as individual attributes, of which you simply have more or less, like height," explained Bowles. "But other dimensions - like wealth - are best conceived of as differences between people in their relationships with others."

The lefthand network in the image represents Bowles' and Carlin's approach, where the arrows connecting the nodes represent experienced social interactions. By their measure, it is the differences in wealth on these edges, not the wealth of each individual node, which is the basis of experienced inequality. In their paper, Bowles and Carlin also that show the correct Gini coefficient is calculated from the three differences associated with the three edges in the figure, and the average wealth. For example, say individual A has a wealth of 10, B has a wealth of 4, and C has a wealth of 3. Then the correctly measured Gini coefficient based on the differences along the three edges in the figure on the left is 0.41.

The standard algorithm illustrated on the righthand diagram in the image counts the difference between, say, person A and B twice (the two single-headed arrows); but an error in the algorithm arises because it also counts the "difference" between an individual's wealth and her own wealth (the curved arrows), which is always zero. As a result, the standard algorithm understates the degree of inequality, yielding a Gini coefficient of 0.27 for the same data as above.

The error becomes noticeable only when working with small populations, as archaeologists and biologists often do. In Carlin's case, a group of students in her econ 101 class tipped her off to the error when they applied a standard online algorithm for calculating Gini coefficients to a problem set.* The algorithm they had found online from Wolfram returned different answers for examples with small numbers of individuals from those found by applying the definition representing the network diagram on the left.

Bowles and Carlin also use differences in the network structure to look at the experience of inequality. If the three individuals in the complete network (on the left) were instead rearranged into a line, with the richer person in the center, as might represent a landlord with two isolated sharecroppers, then with no change in the wealth of the three individuals, the inequality experienced along the edges connecting the three would rise from 0.41 to 0.57.

They illustrate their method using social network data to estimate experienced inequality in a community of farmers in Nicaragua.

"Fixing the small numbers bias is not the main contribution of our paper," says Carlin. "It is that we have provided a way of understanding inequality consistent with our intuitions about how we experience economic disparities, that is by pairwise comparison of one's own wealth or income with that of others."

Credit: 
Santa Fe Institute

Drag can lift birds to new heights, Stanford researchers find

image: Sensors and high-speed cameras measure the forces of parrotlet Gary as he takes off and lands between two perches.

Image: 
Diana Chin

Future aerial design may owe a nod of thanks to five parrotlets flapping around in an instrumented flight chamber at Stanford University. They revealed that counter to conventional understanding of how animals and planes fly, the birds can utilize drag to support their body weight during takeoff and employ lift as a brake in their landings.

"The things you learn in class are not always true," said David Lentink, assistant professor of mechanical engineering. New findings can alter the understanding of familiar concepts. In this case, he said, "We must revise our idea of the function of drag."

Conventional wisdom tells us that drag is a force that slows an object down and lift is a force that counters gravity, lifting a bird or airplane into flight. But measurements taken by graduate student Diana Chin, published Nov. 25 in Nature Communications, show that birds actually draw on drag to support up to half their body weight during takeoff, and that lift helps them brake during landing.

Measuring forces of flight

To measure the horizontal and vertical forces instantaneously, Chin built a setup with sensor panels on the floor, ceiling, front and back of the birds' flight paths. Each panel contained three sensors, as did the two perches for bird liftoff and landing, summing a grand total of 18 sensors to measure the minuscule forces generated by a 30-gram bird.

Windows built into the panels allowed Chin to film wing movements with five high-speed cameras shooting at 1,000 frames per second. By combining the measured motion from the images as well as the force measurements from the sensors, Chin and Lentink could for the first time determine the magnitude of lift and drag at takeoff and landing.

"Something like this has never existed before," said Lentink. "The measuring technology itself is an engineering achievement." As such, it took Chin several iterations to successfully design and fabricate the structure. The next challenge was getting the lab's parrotlets - Gaga, Gary, Oreo, Aurora and Boy - to voluntarily fly inside it.

For the birds

Fortunately for Chin, parrotlets are very trainable birds and will happily fly the 80 centimeters from perch to perch for a millet seed. From these flights, Lentink and his team found that by tilting their wings at an incline during takeoff, the birds can orient their lift forward for acceleration and their drag upward to support up to half of their body weight.

"Takeoff is the most important thing, but you hope for a safe landing too," Lentink said. The repurposing of drag during takeoff actually maximizes the birds' generated forces, while reorienting lift can help them slow down without the power costs of braking before making the controlled collision they call a landing.

"Many other flapping animals probably make similar use of lift and drag during takeoff and landing," said Chin. Juvenile birds, seabirds who also swim underwater and more primitive bird species that have difficulty generating the necessary aerodynamic force with their wings would find this tactic especially useful.

Birds' ancient ancestors, called protobirds, also had wings that primarily generated drag. With the knowledge that drag could actually help support bodyweight in takeoff, Chin and Lentink both acknowledge that there may be some species that have previously been classified as flightless that could have used drag to become airborne.

After 150 million years of bird evolution, "if modern birds still make use of it, that tells you a lot," said Lentink. "That doesn't mean its efficient, but it's effective."

Revising the textbooks

Should we be rebuilding all airborne technologies to reflect this discovery? Not quite. While Lentink would leave the design of a Boeing 747 alone, he does suggest revisiting both the way the evolution of bird flight and aerodynamics are taught.

"I think a lot of drawings in flight textbooks can be misleading, especially when it comes to animal flight," Chin said. Drag could have played a significant role in the evolution of animal flight. For precursors to birds, using drag to support their body weight could have helped them ramp up their ability until their wings were able.

"None of the aerospace literature came up with using drag to support weight," said Lentink as he pulled both biology and aerodynamics textbooks off the shelves, pointing to diagrams of birds in flight with their associated forces drawn in. "That standard drawing has to be revised."

Even if conventional airplanes won't be drastically changing, Lentink does see potential applications in the design of aerial robots. Just as with birds, utilizing drag to get airborne may not be the most efficient method, but it could help get them off the ground.

Credit: 
Stanford University