High-Fiber Diet Keeps Gut Microbes From Eating the Colon's Lining, Protecting Against Infection

It sounds like the plot of a 1950s science fiction movie: normal, helpful bacteria that begin to eat their host from within, because they don’t get what they want.

But new research shows that’s exactly what happens when microbes inside the digestive system don’t get the natural fiber that they rely on for food.

Starved, they begin to munch on the natural layer of mucus that lines the gut, eroding it to the point where dangerous invading bacteria can infect the colon wall.

In a new paper in Cell, an international team of researchers show the impact of fiber deprivation on the guts of specially raised mice. The mice were born and raised with no gut microbes of their own, then received a transplant of 14 bacteria that normally grow in the human gut. Scientists know the full genetic signature of each one, making it possible to track their activity over time.

The findings have implications for understanding not only the role of fiber in a normal diet, but also the potential of using fiber to counter the effects of digestive tract disorders.

“The lesson we’re learning from studying the interaction of fiber, gut microbes and the intestinal barrier system is that if you don’t feed them, they can eat you,” says Eric Martens, Ph.D., an associate professor of microbiology at the University of Michigan Medical School, who led the research along with his former postdoctoral fellow Mahesh Desai, Ph.D., now a principle investigator at the Luxembourg Institute of Health.

Using U-M’s special gnotobiotic, or germ-free, mouse facility, and advanced genetic techniques that allowed them to determine which bacteria were present and active under different conditions, they studied the impact of diets with different fiber content – and those with no fiber. They also infected some of the mice with a bacterial strain that does to mice what certain strains of Escherichia coli can do to humans – cause gut infections that lead to irritation, inflammation, diarrhea and more. 

The result: the mucus layer stayed thick, and the infection didn’t take full hold, in mice that received a diet that was about 15 percent fiber from minimally processed grains and plants. But when the researchers substituted a diet with no fiber in it, even for a few days, some of the microbes in their guts began to munch on the mucus.

They also tried a diet that was rich in prebiotic fiber – purified forms of soluble fiber similar to what some processed foods and supplements currently contain. This diet resulted in a similar erosion of the mucus layer as observed in the lack of fiber.

The researchers also saw that the mix of bacteria changed depending on what the mice were being fed, even day by day. Some species of bacteria in the transplanted microbiome were more common – meaning they had reproduced more – in low-fiber conditions, others in high-fiber conditions.

And the four bacteria strains that flourished most in low-fiber and no-fiber conditions were the only ones that make enzymes that are capable of breaking down the long molecules called glycoproteins that make up the mucus layer.

In addition to looking at the of bacteria based on genetic information, the researchers could see which fiber-digesting enzymes the bacteria were making. They detected more than 1,600 different enzymes capable of degrading carbohydrates – similar to the complexity in the normal human gut.

Just like the mix of bacteria, the mix of enzymes changed depending on what the mice were being fed, with even occasional fiber deprivation leading to more production of mucus-degrading enzymes.

Images of the mucus layer, and the “goblet” cells of the colon wall that produce the mucus constantly, showed the layer was thinner the less fiber the mice received. While mucus is constantly being produced and degraded in a normal gut, the change in bacteria activity under the lowest-fiber conditions meant that the pace of eating was faster than the pace of production – almost like an overzealous harvesting of trees outpacing the planting of new ones.

When the researchers infected the mice with Citrobacter rodentium – the E. coli-like bacteria – they observed that these dangerous bacteria flourished more in the guts of mice fed a fiber-free diet. Many of those mice began to show severea signs of illness and lost weight.

When the scientists looked at samples of their gut tissue, they saw not only a much thinner or even patchy mucus later – they also saw inflammation across a wide area. Mice that had received a fiber-rich diet before being infected also had some inflammation but across a much smaller area.

“To make it simple, the “holes” created by our microbiota while eroding the mucus serve as wide open doors for pathogenic micro-organisms to invade,” explains Desai, who is Group Leader at LIH’s Department of Infection and Immunity.

Martens notes that in addition to the gnotobiotic facility, the research was possible because of the microbe DNA and RNA sequencing capability built up through the Medical School’s Host Microbiome Initiative, as well as the computing capability to plow through all the sequence data.

“Having all the resources here was the key to making this work, and the fact that it was all across the street from our lab allowed us to pin it all together,” he says. He also notes the role of U-M colleagues led by Gabriel Nunez and Nobuhiko Kamada in providing the C. rodentium pathogen model, and of French collaborators from the Aix-Marseille Université in studying the enzymes in the mouse gut. 

Going forward, Martens and Desai intend to look at the impact of different prebiotic fiber mixes, and of diets with more intermitted natural fiber content over a longer period. They also want to look for biomarkers that could tell them about the status of the mucus layer in human guts – such as the abundance of mucus-digesting bacteria strains, and the effect of low fiber on chronic disease such as inflammatory bowel disease.

“While this work was in mice, the take-home message from this work for humans amplifies everything that doctors and nutritionists have been telling us for decades: Eat a lot of fiber from diverse natural sources,” says Martens. “Your diet directly influences your microbiota, and from there it may influence the status of your gut’s mucus layer and tendency toward disease. But it’s an open question of whether we can cure our cultural lack of fiber with something more purified and easy to ingest than a lot of broccoli.”

In addition to Martens, Desai, Nunez and Kamada and the French collaborators, the paper’s authors are U-M’s Anna Seekatz, Nicole Koropatkin, Nicholas Pudlo, Sho Kitamoto and Vincent Young, and colleagues from the Washington University School of Medicine and the Luxembourg Centre for Systems Biomedicine and the Luxembourg Institute of Health. The research was funded by the Luxembourg National Research Fund and Luxembourg Ministry of Higher Education and Research; the National Institutes of Health (GM099513) and the U-M Host Microbiome Initiative and Center for Gastrointestinal Research (DK034933).

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Laboratory

Helpful Forms of E. Coli May Protect Babies from Infections

Some of the first living things to greet a newborn baby do a lot more than coo or cuddle: They help the little one’s digestive system prepare for a lifetime of fighting off dangerous germs.

These things? Not parents, grandparents or siblings, but helpful bacteria.

New research suggests such bacteria may help the lining of the newborn gut prepare for the surge of other bacteria that will soon enter the body, and eventually make up the thriving and diverse population of microbes that lives within each of us.

In a new paper published in the journal eLife, a team from the University of Michigan Medical School reports its findings about the impact of a helpful strain of E. coli on the cells that line the gut.

The team concludes that nonpathogenic E. coli serves a crucial function of preparing the gut for the development of the microbiome to come, and the onslaught of pathogenic, or harmful, microbes.

The new results may help explain what past research has shown about the connection between the gut microbiome and the development of the newborn immune system. They may also lead to better understanding of what can protect or rescue premature newborns from the rare but devastating gut infection condition necrotizing enterocolitis, in which bacteria invade the gut wall and cause potentially fatal infection and inflammation.

Mini guts stand in for little guts

To do the research, the team studied a strain of E. coli related to ones commonly found in newborn babies’ stool. The researchers couldn’t do their research in actual newborns’ intestines, of course. Instead, they used stem cells to grow miniature versions of the gut lining, called human intestinal organoids.

Each HIO, as they’re called, is made up of thousands of cells that the scientists coax to grow, divide and organize into structures that resemble the actual gut. At each HIO’s center is a hollow area called a lumen, which mimics the hollow inner portion of the tube-like human intestine.

“We have previously shown that HIOs closely resemble the immature human intestine,” says lead author David Hill, Ph.D., a postdoctoral fellow in gastroenterology at Michigan Medicine, U-M’s academic medical center. “In this study, we wanted to discover the effects of colonization on the intestine with a nonharmful strain of E. coli, a type of bacteria that is commonly found in the guts of newborn babies.”

During growth, they kept these HIOs germ-free, just like the gut of a fetus in the womb. Then, they introduced the helpful E. coli into the hollow center of the organoids. They tracked what happened inside the cells whose surfaces face the center and in the spaces between the cells. They looked at how the cells were altering gene activity over time in response to the introduction of E. coli.

The results were clear. After the scientists introduced the E. coli, the cells facing the lumen began to mature, form tighter connections with one another and produce mucus to coat their surface.

Genes involved in cell-to-cell communication, and the physical structures cells use to link with their neighbors, activated. So did genes involved in making antimicrobial substances and mucus and transporting them to the cell surface, and in adaptation to low oxygen, which is caused by bacterial metabolism and is a hallmark of the mature adult intestine.

This activity led the HIOs to develop better resistance to inflammation-causing stimuli, which meant less damage to the cells lining the lumen.

“Our results show that colonization of the immature intestinal tract with E. coli results in intestinal tissue that is more robust to challenge by potentially damaging pathogens or inflammatory substances,” says senior author Jason Spence, Ph.D., an associate professor of internal medicine and of cell and developmental biology at U-M.

“We have developed a system that faithfully reproduces the physiology of the immature human intestine, and will now make it possible to study a range of host-microbe interactions in the intestine to understand their functional role in health and disease,” adds co-senior author Vincent Young, M.D., Ph.D.

Young is a professor of internal medicine who specializes in infectious diseases and is also a professor of microbiology and immunology at Michigan Medicine and a leader of U-M’s Host Microbiome Initiative.

What’s next

The research grew out of cooperation between the Spence lab, which focuses on HIOs, and the Young lab, which focuses on the gut microbiome. The work was made possible by funding from the National Institutes of Health, and by investments the Medical School has made in tools that help with organoid, microbiome and DNA sequencing research.

The team is now studying additional strains of nonharmful E. coli and other bacteria that take up long-term residence in the newborn gut, as well as pathogens.

“We hope to examine whether different bacteria produce different types of responses in the gut,” says Hill. “This type of work might help to explain why different types of gut bacteria seem to be associated with positive or negative health outcomes.”

The Spence team is preparing to launch a “core” service to provide HIOs for other researchers to study.

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Laboratory

New early signals to quantify the magnitude of strong earthquakes

After an earthquake, there is an instantaneous gravitational disturbance that could be recorded before the seismic waves that seismologists can detect. In a study published in Science on December 1, 2017, a team comprising researchers from CNRS, IPGP, the Université Paris Diderot and Caltech has managed to observe these weak signals related to gravity and to understand where they come from. Because they are sensitive to the magnitude of earthquakes, these signals may play an important role in the early identification of the occurrence of a major earthquake.

This work came out of the interaction between seismologists who wanted to better understand earthquakes and physicists who were developing fine gravity measurements with a view to detecting gravitational waves. Earthquakes brutally change the equilibrium of forces on Earth and emit seismic waves whose consequences can be devastating. But these same waves also disturb the Earth's field of gravity, which produces a different signal. This is particularly interesting with a view to fast quantification of tremors, because it moves at the speed of light, unlike tremor waves, which propagate at speeds between three and 10 km/s. So seismometers at a station located 1000 km from the epicenter may potentially detect this signal more than two minutes before the seismic waves arrive.

The work presented here follows on a 2016 (J.-P. Montagner et al., Nat. Commun. 7, 13349 (2016)) study that demonstrated this signal for the first time. First, the scientists observed these signals on the data from about 10 seismometers located between 500 and 3000 km from the epicenter of the 2011 Japanese earthquake (magnitude 9.1). From their observations, the researchers then demonstrated that these signals were due to two effects. The first is the gravity change that occurs at the location of the seismometer, which changes the equilibrium position of the instrument's mass. The second effect, which is indirect, is due to the gravity change everywhere on Earth, which disturbs the equilibrium of the forces and produces new seismic waves that will reach the seismometer.

Taking account of these two effects, the researchers have shown that this gravity-related signal is very sensitive to the earthquake's magnitude, which makes it a good candidate for rapidly quantifying the magnitude of strong earthquakes. The future challenge is to exploit this signal for magnitudes below about eight to 8.5, because below this threshold, the signal is too weak relative to the seismic noise emitted naturally by Earth, and dissociating it from this noise is complicated. So Researchers plan to test several technologies, including some inspired from instruments developed to detect gravitational waves.

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PHYS.ORG

Married people are much less likely to get dementia

An analysis of more than 800,000 people has concluded that people who remain single for life are 42 per cent more likely to get dementia than married couples.

The study also found that people who have been widowed are 20 per cent more likely to develop the condition, but that divorcees don’t have an elevated risk.

Previous research has suggested that married people may have healthier lifestyles, which may help explain the findings. Another hypothesis is that married people are more socially engaged, and that this may protect against developing the condition. The stress of bereavement might be behind the increased risk in those who have been widowed.

But marriage isn’t always good for the health. While men are more likely to survive a heart attack if they are married, single women recover better than those who are married.

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New Scientist

Threat of group extinction proves a powerful motivator

Charles Darwin was right: Groups enjoy an advantage whose members are "ready to aid one another and to sacrifice themselves for the common good," according to a new study by researchers at Rice University, Texas A&M University and the University of East Anglia.

Using variations of the public goods game, the researchers showed that when no other mechanism is present to reinforce group cooperation, the threat of group extinction is sufficiently powerful to motivate and increase cooperation within a group.

"The finding is stunning for what it says about group extinction," said Rice Professor Rick Wilson, one of the authors of the paper appeared this week in the journal PLOS ONE. "People respond to threats to their group. They're willing to forego opportunities to free ride on the efforts of their group members."

The article, "Group-Level Selection Increases Cooperation in the Public Goods Game," provides insight into the origins of group conflict and "supports the notion that competition between groups is part of what has cultivated human cooperation," the authors said.

"History seems to support the idea that a group working together can overcome another group and drive them to extinction," said Wilson, the Herbert S. Autrey Professor of Political Science, professor of statistics and of psychology at Rice. "But it had not been clear whether this was due to groups cooperating when in competition or to pressure of extinction through selection."

The researchers conducted a controlled laboratory experiment to determine whether competition or extinction drives increased cooperation within groups. The experiment was based on the public goods game in which participants in groups are each given a set amount of money. Each group member secretly chooses how much to put into the group account and how much to retain for their own account. The amount in the group account is multiplied by a set factor, and the payoff is equally divided among the members of the group; participants also keep the money they did not contribute to the group account.

In the researchers' experiment, 168 undergraduate students were randomly assigned to groups of four. No participant knew who their fellow group members were, and all interactions were conducted anonymously over a computer network.

The game consisted of two blocks of 10 periods. Each period every subject was given 50 monetary units and decided how much to keep in their private account and how much to put in the group account. The private account paid one to one. The contributions to the group account were doubled by the experimenters, and the total of the group account was divided equally among each member of the group.

"This basic experimental design has been used hundreds of times, and free riding is common," he said. "We wanted to know whether competition or extinction works to eliminate free riding in the way that Darwin suggests."

The researchers used four treatments in their experiment:

The first treatment replicated the standard public goods game. At the end of each period, subjects found out how much was contributed by others in their group to the group account. They were told nothing about the contributions of participants in the other groups.

Group competition was introduced in the second treatment. Subjects saw the same information as in the first treatment; however, they were told that at the end of the first 10 periods their group would be ranked in terms of total earnings against the other groups in the experiment.

In the third treatment, extinction was introduced. Subjects were told that at the end of 10 periods their earnings would be compared with all other subjects' earnings. One-third of the lowest earners would be removed from the experiment and not allowed to participate in the second block of 10 periods.

In the fourth treatment, extinction was applied to groups rather than individuals. Subjects were told that at the end of the first 10 periods their group's earnings would be compared with the other groups' earnings. Groups that fell in the bottom one-third of earners would be removed from the experiment and would not participate in the second block of 10 periods.

The researchers found that in treatments one through three, average contributions declined steadily over the first 10 periods. "Over time, people contribute less to the public good and favor their private investments," Wilson said.

"But when we introduce group extinction, we see a remarkably different result," he said. "At the outset, individuals contribute almost everything to the group account. The pressure of group extinction results in individuals cooperating within the group."

Researchers found that group extinction, the fourth treatment, led to greater contributions to the group account (92 percent of the endowment, on average) than any other treatment (35 percent in first treatment, 36 percent in third treatment, or individual extinction, and 42 percent in the second treatment, group comparison).

The authors noted that "group extinction leads to enhanced cooperation as long as the selection mechanism is present. Once it is removed, contributions remain higher for a time, but fall quickly toward ... zero contributions. The culture of cooperation engendered by the group extinction mechanism has only a brief longer-term carryover after the mechanism is removed."

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Science Daily

Language of women versus men: 'Wonderful' and 'thankful' versus 'battle' and 'enemy' Do women and men communicate differently?

In a computational analysis of the words used by more than 65,000 consenting Facebook users in some 10 million messages, it was discovered that women use language that is warmer and more agreeable than men. Additionally, algorithms of language use predicted one's gender on Facebook 90 percent of the time. The findings are published in PLOS ONE.

In the paper, titled "Women are Warmer but No Less Assertive Than Men: Gender and Language on Facebook," some of the most commonly cited topics, or automatically derived clusters of related words, used by women included words such as wonderful, happy, birthday, daughter, baby, excited, and thankful. Some of the words most commonly cited by men included freedom, liberty, win, lose, battle and enemy.

These language differences by gender on Facebook are being investigated by a team of researchers comprised of psychologists and computer scientists from Stony Brook University, the University of Pennsylvania and the University of Melbourne in Australia. Gender is a complex, multi-faceted and fluid concept. Their paper helps to illuminate some of that complexity through big data and computational analysis, and the findings suggest gender influences the way people express themselves on Facebook.

"Looking at language in social media offers a fresh perspective on understanding gender differences," said H. Andrew Schwartz, PhD, Assistant Professor of Computer Science in the College of Engineering and Applied Sciences at Stony Brook University and a co-author of the paper.

The analysis automatically identified differences in the types of words used by women and men. Women mentioned friends, family and social life more often, whereas men swore more, used angrier and argumentative language, and discussed objects more than people. On average, women used language that was characteristic of compassion and politeness while men were more hostile and impersonal.

Some findings, added Schwartz, illustrated nuances and differences in language by gender not previously revealed.

"We were able to explore the dimensions of warmness and assertiveness with a novel data-driven technique," explained Schwartz, citing one example. "While some previous work suggests men are generally more assertive, the language in Facebook did not reflect this, showing woman use slightly more assertive language than men."

In the analysis, the topics expressed via the Facebook language were rated for how affiliative (socially connected) and assertive they were. The authors built gender-linked language around an interpersonal circumplex. While most language appeared with both genders, other language use was clearly gender-linked.

Psychologist Dr. Margaret Kern, of the University of Melbourne and one of the study authors, noted that "in many ways, the topics most used by women versus men are not surprising -- they fit common gender stereotypes. The computational methods let us make visible what the human mind does to automatically categorize people and thanks that we encounter in our everyday life."

The study also demonstrates a method to test psychological theories at a large scale, with a way to visualize the results.

With such large-scale computational studies, generating thousands of statistical results, visualization is key.

"This is a good example of visualization helping us to see the bigger picture with complex data," said lead author Dr. Gregory Park, a psychologist from the University of Pennsylvania. "If we only look at individual topics in isolation, it's difficult to see patterns in the kind of topics that are used more by women or men. However, when we visualize them together, it's clear that many of the language differences break down along these interpersonal dimensions."

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Science Daily

Common painkillers are more dangerous than we think

Many patients are prescribed NSAIDs for the treatment of painful conditions, fever and inflammation. But the treatment also comes with side effects, including the risk of ulcers and increased blood pressure. A major new study now gathers all research in the area. This shows that arthritis medicine is particularly dangerous for heart patients, and also that older types of arthritis medicine, which have not previously been in focus, also appear to be dangerous for the heart.

"It's been well-known for a number of years that newer types of NSAIDs -- what are known as COX-2 inhibitors, increase the risk of heart attacks. For this reason, a number of these newer types of NSAIDs have been taken off the market again. We can now see that some of the older NSAID types, particularly Diclofenac, are also associated with an increased risk of heart attack and apparently to the same extent as several of the types that were taken off the market," says Morten Schmidt, MD and PhD from Aarhus University, who is in charge of the research project. He adds:

"This is worrying, because these older types of medicine are frequently used throughout the western world and in many countries available without prescription."

Each year, more than 15 per cent of the population in western countries are given a prescription for NSAIDs. This figure increases with age. Sixty per cent of the adult population in Denmark collects at least one prescription for an NSAID within a ten-year period. Heart patients are no exception and previous studies have shown that up to forty per cent of Danish patients with heart failure or previous heart attacks are prescribed NSAIDs.

The study, which was carried out in collaboration between 14 European universities and hospitals, including a number of leading European heart specialists, is today being published in the most prestigious European journal of heart medicine, European Heart Journal.

New guidelines

In the study, the researchers have gathered all research on the use of NSAIDs in patients with heart disease. The survey means that the European Society of Cardiology has now for the first time formulated a number of recommendations about what doctors should consider before prescribing painkillers to their patients.

"When doctors issue prescriptions for NSAIDs, they must in each individual case carry out a thorough assessment of the risk of heart complications and bleeding. NSAIDs should only be sold over the counter when it comes with an adequate warning about the associated cardiovascular risks. In general, NSAIDs are not be used in patients who have or are at high-risk of cardiovascular diseases," says another of the authors, Professor in cardiology Christian Torp-Pedersen, Aalborg University, Denmark.

Consumption should be reduced even more

For a number of years, Danish researchers have made significant contributions in the field. One result of this work has been a reduction in the use of Diclofenac in Denmark. However, according to Morten Schmidt, there is still room for improvement:

"Many European countries consume more of these drugs than Denmark. But we can still do better and it's often the case that paracetamol, physiotherapy, mild opioids or other types of NSAIDs with less risk for the heart would be better for the patients. Of course, the recommendations that have been introduced following our study and its review of the heart-related risks are a big step in the right direction in relation to patient safety," says Morten Schmidt.

FACTS about arthritis medicine (NSAID):

• NSAIDs is an abbreviation for Nonsteroidal Anti-Inflammatory Drugs and is used to treat a wide range of diseases, in particular disorders in the muscular and bone system, where the drug counteracts swelling, pain and limitations in movement associated with inflammation.
• NSAIDs are not antibiotics and therefore do not help to fight infections caused by bacteria.
• NSAIDs are in Denmark sold both in low doses (Ibuprofen 200 mg/tablet) without a prescription and in higher doses and other types with a prescription.
• Story Source:Science Daily

Eating polyunsaturated fats linked to slowing diabetes progress for some

Research led by a dietitian at King’s College London has found that replacing saturated fat in the diet with polyunsaturated fat, found in foods such as vegetable oils or nuts, is linked to slower progress of type 2 diabetes in people with prediabetes whose muscles do not take up glucose properly.

Prediabetes is a condition in which blood glucose levels are higher than normal but not high enough to be classified as type 2 diabetes. Previous evidence has shown that prediabetes can be split into two distinct conditions, one in which the liver produces too much glucose and one in which glucose is not taken up properly by the muscles.

The study, published in PLOS ONE, is the first to consider the differing effects of dietary fats on prediabetes as two separate conditions, although previous studies have shown that dietary fats have an effect on insulin sensitivity.

This study also considers the distinct paths of diabetes development compared with previous studies which have predominantly used ‘full blown’ diabetes as the measure of progression for the condition.

Currently, weight loss is regarded as the most effective way to prevent the progression of diabetes in patients with prediabetes but researchers examined whether a targeted dietary intervention could have additional impact for patients alongside a weight loss programme.

Scientists tested small groups of people across a wide spectrum of glucose levels including healthy (15) athletic (14), and obese (23) people, and people with prediabetes (10) or type 2 diabetes (11) using robust analysis of glucose levels and fatty acids in their blood. Participants’ diets were evaluated using a dietary questionnaire.

They found that, in the condition where glucose uptake into muscles is impaired, replacing saturated fats in the diet with polyunsaturated fats had a beneficial effect in slowing the development of diabetes. It is thought that this is because polyunsaturated fats promote uptake of glucose by the insulin receptors in the muscles.

In people whose livers were producing too much glucose, reducing saturated fat was found to be linked to slower progress of diabetes but replacing it with polyunsaturated fat was found to have no effect.

Lead author, Dr Nicola Guess, Division of Diabetes and Nutritional Sciences at King’s College London said: ‘This study is the first to explore whether we can target dietary advice taking into account the underlying differences in the two prediabetes states.

‘The findings suggest that increasing dietary intake of polyunsaturated fats may have a beneficial effect for patients with a certain type of prediabetes but also illuminates why certain dietary changes may have no effect on progression of type 2 diabetes in the other subtype.  We intend to build on this work with larger studies, and ultimately test this idea in a randomised trial’.

Limitations of the study included the small number of participants in each group and the overall small sample size of the study. The cross-sectional design of the study also means the authors cannot confirm causality, i.e. a cause-and-effect.
Source:
TECHNOLOGY.ORG

Man gets seizures from sudoku

Mental puzzles are supposed to be good for the brain, but for one young man they had a surprising side effect: seizures that made his left arm jerk and twitch. The seizures started shortly after the 25-year-old student was buried in an avalanche, where his brain was deprived of oxygen for 15 minutes. Several weeks later, the tremors came on when he tried to solve a sudoku puzzle, researchers report today in JAMA Neuroscience. Sudoku puzzles are 9-by-9 grids with numbers in some of the squares; to solve them, a person must fill in the other squares with the right pattern of numbers. According to neurologist Berend Feddersen from the University of Munich in Germany, who is first author on the paper, the man tried solving the puzzles by imagining them in 3D. The harder he focused, the more his arm moved. Based on MRI scans, the researchers attribute the seizures to damaged inhibitory fibers on the right side of the man’s central parietal cortex, a brain region near the crown of the head. The unusual case suggests that when inhibitory fibers are damaged, brain activity in one area can spill into neighboring areas—in this case, the part of the brain that that controlled arm movement, Feddersen says. Despite this damage, the solution was simple: The man stopped tackling sudoku puzzles, and has been seizure-free for 5 years. 

http://news.sciencemag.org

Super-dark chameleon material shifts colour to boost solar power

It is one of the blackest materials on Earth – but it can transform light into any colour you want. Simple to make, this chameleon material could one day boost solar power.

The world record for blackness is held by a material made from carbon nanotubes, which absorb 99.8 per cent of light when they are layered a millimetre thick.

But a nano-material consisting of tiny hammer-like shapes made of gold, shown above, has achieved almost as much blackness – and researchers have discovered that with a small addition it can also reflect any colour you choose.

Andrea Fratalocchi at King Abdullah University of Science and Technology in Saudi Arabia was inspired by beetles whose thin shells reflect all wavelengths of light, making them appear whiter than any artificial material.

Fratalocchi wondered if the effect could be reversed. He designed a theoretical system that involved a tiny concave shell, attached to an infinitely long tube designed to guide waves. If you could build such a structure, light would enter the shell and then travel along the tube, never to be seen again.

Then, using plasmonics – materials that bend light along different paths and could make invisibility cloaks a real possibility – Fratalocchi approximated this design with gold nanorods.

At just a hundredth of a millimetre thick, the material absorbed 98.43 per cent of light. This level of light absorption means it could be painted onto other surfaces to turn light into heat. Because gold is an excellent conductor, it would transfer heat more efficiently than carbon nanotubes, says Yuri Kivshar at the Australian National University in Canberra.

But when a simple dye is added to the material, its behaviour changes drastically: rather than absorbing the light energy and emitting it as heat, it emits it again as light, but at a single frequency. Everything in the visual and infrared spectrum is converted to the colour of the dye.

If a lot of sunlight were focused onto the material so that it exceeded a threshold energy, “you should be able to capture a large portion of the sun spectrum and transfer it on a single colour”, says Fratalocchi. This could improve the efficiency of photovoltaic cells, which work best with particular frequencies of light, he says. “We have ongoing research in this direction.”

https://www.newscientist.com

Hacking for peace: hi-tech solutions for the humanitarian field

“Hacking a rice bag” might seem like a lot of non-sense to you – but not the enthusiastic participants ofTHE Port Hackathon, who had been hacking for “peace and health” at CERN and Campus Biotech earlier this month.

Image courtesy of THE Port and Light My Photo team.

The event (already reported in more detail here) invited experts from a variety of disciplines to put their heads (and skills) together, and develop functioning tech-enabled tools ranging from a better airdrop bag for humanitarian cargo to explosion detector with forensic precision for conflict zones.

Humanitarian food air delivery could be more efficient

Delivering aid to crisis regions is not an easy task, especially where conflict and natural disasters leave large areas completely inaccessible by land. For this reason, humanitarian organizations, e.g. Red Cross, have recently come to use “airdrop bags” for delivering food and other goods by air.

Bags are dropped from as high as 125 metres so, quite naturally, have to be reliable and burst-free. The bags are therefore often folded up to 6 times, which makes their production a time-consuming, not to mention an environmentally unfriendly process.

After three days of “tailoring and dropping” at THE Port, the team “Cargo Cult” has come up with an innovative design for an airdrop bag, which is easier to put together, yet withstands impact and leaves cargo unharmed.

Rice airdrop bag test. Credit: THE Port and Cargo Cult.

Perhaps unsurprisingly, the best results were achieved with more elastic materials. The ultimate “winner” in the end was ROLAMIT®, which, according to the manufacturers, is flexible and has tear resistance, as well as puncture and chemical resistance properties. The team also proposed an inspired idea to sow the bags in an accordion-like fashion to allow easy expansion. Another inspired idea including taping, rather than sowing the bags together, which proved to be reliable and saved valuable production minutes.

While this may seem like small improvements in general, when 4 million bags like these are dropped per year, it is bound to make a big difference. Continuing experimentations and taking advantage of new high-tech materials that are increasingly becoming more affordable, could lead to even more economically and environmentally friendly solutions.

Empowering women in a crisis    

Going beyond the basic needs of crisis refugees, the team “Bridge it” took up the task to reduce the technology gender gap that is prevalent in the developing countries. Be it cultural or economic circumstances (or both), men often dominate technology in more disadvantaged places of the world; however, an ability to use something as mundane to us as a mobile phone would enable women to express their needs and feel more secure, especially so in already adverse settings.

Using a case of internally displaced person (IDP) camps in Iraq, the team developed an easy-to-use application for women, which could run on tablets and smartphones allocated to women-friendly zones in IDP camps. The interface, based on icons (already familiar in humanitarian context), text and audio, allows to send and receive information regardless of the user’s literacy.

Mock-up interface of “Bridge it” app for women in IDP camps. Credit: teambridgeit.com.

Women could use the app to submit specific requests for aid (e.g. food or diapers), anonymous complaints (e.g. reporting abuse) and receive important notifications from any NGO, which has access to the system. Gamified elements could extend the use of the technology to children as well.

The team has communicated with external advisors from the camps, to ensure the app is usable and acceptable in actual IDP settings. According to the members of “Bridge it”, this might be a small, but nevertheless significant step to bridging technology gender gap where it is most prevalent: “We won’t necessarily change the world, but if we can make even a small difference, then it is still a great start!”

One platform to collect and visualize humanitarian data real-time

Humanitarian aid faces many challenges – first and foremost, it is essential to know where and what help is needed. Unfortunately, collecting and analysing humanitarian data can be a challenge; often there is a wide variety of sources, a range of data formats, and the amount of information can simply be overwhelming to individual humanitarian workers.

Team “Datasaurus” have proposed a universal way for integrating various types of data for just this purpose. Uploaded data would be organized and analysed automatically, while a powerful visualization engine would allow to create detailed 3D maps of disaster areas. These could further be overlaid with other desired information – e.g. logs of human right violations, status and feedback of humanitarian actions taken etc.

Most importantly, such visualizations could be accessible real-time, which would help to allocate resources to regions that need them the most. Such “coordinated effort” would by all means exceed any isolated endeavours, and ensure that more people in crisis situations get at least their basic needs met, including access to food, water and safe shelter.

Forensic fingerprinting of explosions for 20$

Armed conflict did not go undetected at THE Port either – in fact, team Blastbusters.org have proposed a powerful solution for tracking explosions in warzones. According to the team, their constructed e3e Monitor (Explosion and Extreme Energy Event Monitor) could finally provide “data that bears witness”, as up until now, data on such extreme events have been limited to eye-witness reports or official statements, which can never tell the whole story.

A 7-component system would cost less than 20$ to produce, yet be able to detect precise acoustic signature of any explosion, and track pre- and post-explosion acoustics. As armed forces tend to use unique explosives and delivery mechanisms, such data could help to get “forensically close” to the source (and culprit) of the explosion. Extra power of the system would come from making the data publically available as soon as it comes in.

Acoustic signatures could be combined with other data as well, e.g. geolocated tweets and emotional mapping (Emo-mapping) of victims and witnesses. Such an approach would, for the first time, be able to generate precise empirical data around explosions, rather than relying on subjective reports.

e3e Monitor can be easily disguised and parachuted into any area, and, according to the team, “keeps its secrets safe”, as all data is encrypted. Since it is so cheap to produce, it could be easily scaled up to track extreme events throughout the world.

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The prototypes have been developed in consultation with representatives of the humanitarian field, and have realistic potential to become functional tools that help maintain peace and equity in the world – all that in 60 hours of brainstorming and hacking at THE Port.

Written by Eglė Marija Ramanauskaitė

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Team describes rapid, sensitive test for HIV mutations

Tests that can distinguish whether HIV-positive people are infected with a drug-resistant strain or a non-resistant strain allow patients to get the most effective treatment as quickly as possible. In the edition of the Journal of Molecular Diagnostics, a team of Brown University researchers describes a new method that works faster and more sensitively in lab testing than the current standard technologies.

A Brown team has developed a new method for analyzing the the RNA (green strands) of HIV for mutations (red dot) that convey drug resistance. The system does not require reverse transcription of RNA to DNA, as current technologies do, and works within one solution (purple droplet). Image credit: Lei Zhang/Brown University

The main advance enabling that improved performance is that the system operates directly on the virus’ more readily available RNA rather than requiring extra, potentially error-prone steps to examine DNA derived from RNA. In a single tube, the system can first combine two engineered probes (ligation) if a mutation is present and then make many copies of those combined probes (amplification) for detection.

“LRA (ligation on RNA amplification) uniquely optimizes two enzymatic reactions — RNA-based ligation, and quantitative PCR (polymerase chain reaction) amplification — into a single system,” said Anubhav Tripathi, professor of engineering at Brown and corresponding author on the paper. “Each HIV contains about 10,000 nucleotides, or building blocks, in its genetic material, and a drop of blood from a patient with resistant HIV can contain thousands to millions of copies of HIV. To find that one virus, out of thousands to millions, which is mutated at just a single nucleotide is like finding a needle in a haystack.”

The experiments reported in the paper show that the LRA test was sensitive enough to find a commonly sought K103N mutation in concentrations as low as one mutant per 10,000 strands of “normal” viral RNA. The LRA detection worked within two hours, while alternative technologies such as ASPCR or pyrosequencing, can take as long as eight.

LRA works by sending in many copies of a pair of short engineered probes of genetic material to complement the RNA in the HIV sample. Under optimized conditions, those pairs that perfectly match the target HIV RNA containing a mutation that causes drug resistance can rapidly become fused together, or ligated, by an enzyme. If there is a single nucleotide difference, the pair won’t fuse.

The fusing of the engineered genetic probes is designed to happen at room temperature. After a short period, the LRA system then heats the slightly alkaline solution, which shuts off the fusing reaction but turns on the amplification (copying) of fused pairs. That allows the LRA system to produce a strong signal of fused pairs, if there are any. All this happens in a single step, without any need to change solution.

Aiming for the clinic

The development of LRA is the product of a collaboration led by Tripathi and Dr. Rami Kantor, associate professor of medicine in the Warren Alpert Medical School. Kantor, who is also an HIV specialist at The Miriam Hospital and co-senior author of the paper, works in developing nations such as Kenya and India, monitoring HIV resistance. One day when Tripathi was at the Lifespan/Tufts/Brown Center for AIDS Research Retrovirology Core Laboratory to discuss his work, Kantor suggested a collaboration with the end goal of developing a cheap, quick and accurate HIV drug resistance mutation detection system for use in developing nations.

“We met soon thereafter and started working together on various developments and implementations of the ideas and on the integration of our worlds,” Kantor said.

The authors acknowledge in the paper that what they demonstrate, while successful in the lab, is clearly not ready for deployment in the field. The lab tests, for example, are shown to work on HIV RNA derived from plasmids, laboratory viral strains, not on samples from circulating viruses found in ailing patients. The RNA fragments were prepared in Kantor’s lab by Dr. Mia Coetzer, assistant professor of medicine and a co-author on the paper.

“The next steps are to continue the development of LRA and other methods on patient samples to detect additional mutations and address specific HIV challenges related to mutation detection, such as enormous genomic diversity,” Kantor said, “and work on incorporation of such methods onto a point-of-care device that would satisfy the infrastructure and low-cost needs of resource limited settings.”

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