Culture

Scientists at Harvard University, collaborating with researchers at Bio-Rad Laboratories, have developed a new platform for rapid single-cell sequencing. The approach combines microfluidics and novel software to scale up single-cell ATAC-seq, which identifies parts of the genome that are open and accessible to regulatory proteins.

Published in Nature Biotechnology, the innovation signals a major acceleration in single-cell genomics research.

What is single-cell sequencing?

We all start out as a single cell, but quickly turn into trillions. The genome in that first cell is copied into all the rest - so how do we end up with so many different cell types? For many years, scientists have been trying to figure out how genes are turned on and off in different cells at different times in their development, so that cells can carry out specific functions.

Single-cell sequencing has transformed this area of research, allowing scientists to study genes in individual cells, rather than large pieces of tissue. When studying cells in bulk, the collection might appear uniform but actually contains many different cell types. Because of this, results represent an average. They point researchers in a promising direction but do not give precise insights.

By allowing researchers to examine just one cell at a time, single-cell sequencing is redefining anatomy. It sifts through cells that appear similar on the surface, highlighting new cell types and vastly improving the ability to find individual genes that drive healthy functions or disease processes in the body.

ATAC-seq

In this study, researchers focused on a type of sequencing called ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing). Each human cell contains two meters of DNA, tightly packed into the microscopic nucleus. ATAC-seq identifies which parts of the DNA are unwound and accessible to proteins.

"It's a bit like opening up a multidimensional suitcase to get at the clothes," said Fabiana Duarte, co-lead author of the study and a postdoctoral fellow in Jason Buenrostro's lab at Harvard. "If a part of the genome is accessible, an enzyme can make a cut and tag it. Then we find the sequences of all the tagged DNA."

Genes are controlled by many different proteins. Transcription factors, for example, bind to a piece of DNA and bring over the machinery that reads it. There are countless transcription factors, and each one recognizes and binds to a very specific DNA sequence. That sequence is called a motif, and because it is so specific it can be flagged in ATAC-seq data.

Since Buenrostro and colleagues first developed ATAC-seq in 2013, the field has moved rapidly. The technology is used ubiquitously in the genomics community, for example in the Human Cell Atlas project, to understand and map genome function. But the complex process has been time consuming and inefficient, with only a fraction of cells yielding reliable results.

Scaling up

The new approach developed in this study makes ATAC-seq much more efficient. Where previous approaches made it possible to profile 100 cells per reaction, the new method profiles 50,000.

"We've scaled it up so we can profile many cells in a human tissue in a straightforward way. The method is simple, so you can run the experiment in a day, start to finish. That will allow researchers to achieve much more in a far shorter time," said Buenrostro, assistant professor in Harvard's Department of Stem Cell and Regenerative Biology.

One of the biggest challenges in single-cell sequencing is isolating the cells to be studied. The new method resolves this problem using microfluidics and droplets.

"We worked with the Bio-Rad team on the method," Duarte said. "One channel of the device delivers a cell, and another adds a bead - and each bead has a bar-coded tag. Where they meet, there's oil - so you get droplets. Each droplet has a cell and a bead. You can add a lot of cells into the device to get data on individually labelled cells."

But the devil is in the details, as any computational biologist will tell you.

"Ideally you'd have one bead in each droplet. But in practice, to make sure that each cell is tagged, droplets can end up having more than one bead," said Caleb Lareau, co-lead author and graduate student in Buenrostro's lab. "Our new software identifies those cases and merges them, so you can identify single cells that might at first have looked like many."

"Because of experimental and computational innovations, we can now get profiles for 95% of the cells that are put into the machine. That's up from around 20 to 30% - like night and day," Lareau said.

Accelerating research

"This droplet approach will be available to biomedical researchers in all fields as an off-the-shelf technology, and I'm really proud that we helped it get to this stage," said Buenrostro, who is also a faculty member of the Harvard Stem Cell Institute. "In this study, we also developed a method within the method: barcoding added another layer of tagging that allowed us to increase the number of cells we could assay tenfold or more. It changes the questions you can ask, and how quickly you can find answers - I think we're going to see research moving much more rapidly now."

Nestled between the Pacific Ocean and the Andes mountains, Peru's coastal region relies on surface water from the Andes for drinking water, industry, and animal and crop farming.

The region, which includes Peru's capital city Lima, is often overwhelmed with rain in the wet season - but by the time the dry season comes, water is scarce.

These factors, together with Lima's rapidly growing population, mean the city struggles to supply water to its 12 million residents during the dry months of May to October.

Now, Imperial researchers and their colleagues at the Regional Initiative for Hydrological Monitoring of Andean Ecosystems in South America, have outlined how reviving ancient water systems could help save wet season water for the dry season, where it is desperately needed.

To do so, they studied a water system in Huamantanga, Peru - one of the last of its kind.

Coastal Peru's continuously stressed systems struggle to cope with increasing demand and are fragile - a landslide, for example, could easily cut off Lima's water supply.

Senior author Dr Wouter Buytaert, of Imperial's Department of Civil and Environmental Engineering, said: "The people of Lima live with one of the world's most unstable water situations. There's too much water in the wet seasons, and too little in the dry ones.

"The indigenous peoples of Peru knew how to get around this, so we're looking to them for answers."

Ancient Peruvian civilisations in 600 AD created systems within mountains to divert excess rainwater from source streams onto mountain slopes and through rocks.

The water would take some months to trickle through the system and resurface downstream - just in time for the dry season.

To study this, the researchers looked at one such system in Huamantanga. They used dye tracers and hydrological monitoring to study the system from the wet to dry seasons of 2014-2015 and 2015-2016. Social scientists involved also worked with Huamantanga's local people to understand the practice and help map the landscape.

They found the water took between two weeks and eight months to re-emerge, with an average time of 45 days. From these time scales, they calculated that, if governments upscale the systems to cater to today's population size, they could reroute and delay 35 per cent of wet season water, equivalent to 99 million cubic metres per year of water through Lima's natural terrain.

This could increase the water available in the dry season by up to 33 per cent in the early months, and an average of 7.5 per cent for the remaining months. The method could essentially extend the wet season, providing more drinking water and longer crop-growing periods for local farmers.

The study, published in Nature Sustainability, is the first to examine the pre-Inca system in this much detail to find answers to modern problems. The authors say their research shows how indigenous systems could complement modern engineering solutions for water security in coastal Peru.

Lead author Dr Boris Ochoa-Tocachi, also from Imperial's Department of Civil and Environmental Engineering, said: "With the advent of modern science, you'd be forgiven for wondering how ancient methods could apply to modern day problems. However, it turns out that we have lots to learn from our ancestors' creative problem-solving skills."

Dr Buytaert said: "Like many tropical cities, Lima's population is growing fast - too fast for water reserves to keep up during dry seasons.

"Upscaling existing pre-Inca systems could help relieve Peru's wet months of water and quench its dry ones."

The seasonal variability typical of coastal Peru is worsened by human impacts - particularly by melting glaciers caused by global warming. Humans also contribute to soil erosion, which renders soil too weak to support dams big enough to hold all the water.

Climate change also makes wet seasons wetter, and dry seasons drier - making the need for effective water storage in Peru even more urgent.

In addition, the uncertainty of our climate's future makes it difficult to design and build systems that are intended to last for decades into the future.

The authors say combining pre-Inca systems with classic structures, such as smaller dams, could spread the workload across methods and increase adaptability in an unpredictable climate.

Dr Buytaert explained: "Because we can't rely fully on one method, we must be open-minded and creative - but our study shows we have lots to learn from the way Peru's indigenous population intelligently managed their landscape 1,400 years ago."

The researchers looked only at one system, so the results of similar work will likely differ throughout Peru's coastal areas. However, they say their work presents a strong argument for using nature-based solutions to improve water security, which currently tops water agendas both locally and globally.

They continue to study the area to learn more about how indigenous knowledge, practices, and systems can help supply water to large urban populations in water-unstable, dry environments. In doing so, they hope to improve coastal Peru's water security and resilience to a changing and unpredictable climate.

Dr Ochoa-Tocachi concluded: "This is a fascinating example of ingenuity within local communities and shows the enormous potential of indigenous knowledge to complement modern science.

"Beyond this fascinating example of ingenious problem-solving, our research shows the enormous potential for indigenous knowledge and rural science to complement modern science".

Human screams convey a level of individual identity that may help explain their evolutionary origins, finds a study by scientists at Emory University.

PeerJ published the research, showing that listeners can correctly identify whether pairs of screams were produced by the same person or two different people -- a critical prerequisite to individual recognition.

"Our findings add to our understanding of how screams are evolutionarily important," says Harold Gouzoules, senior author of the paper and an Emory professor of psychology. "The ability to identify who is screaming is likely an adaptive mechanism. The idea is that you wouldn't respond equally to just anyone's scream. You would likely respond more urgently to a scream from your child, or from someone else important to you."

Jonathan Engelberg is first author of the paper and Jay Schwartz is a co-author. They are both Emory PhD candidates in Gouzoules' Bioacoustics Lab.

The ability to recognize individuals by distinctive cues or signals is essential to the organization of social behavior, the authors note, and humans are adept at making identity-related judgements based on speech -- even when the speech is heavily altered. Less is known, however, about identity cues in nonlinguistic vocalizations, such as screams.

Gouzoules first began researching monkey screams in 1980, before becoming one of the few scientists studying human screams about 10 years ago.

"The origin of screams was likely to startle a predator and make it jump, perhaps allowing the prey a small chance to escape," Gouzoules says. "That's very different from calling out for help."

He theorizes that as some species became more social, including monkeys and other primates, screams became a way to recruit help from relatives and friends when someone got into trouble. Previous research by Gouzoules and others suggests that non-human primates are able to identify whether a scream is coming from an individual that is important to them. Some researchers, however, have disputed the evidence, arguing that the chaotic and inconsistent nature of screams does not make them likely conduits for individual recognition.

Gouzoules wanted to test whether humans could determine if two fairly similar screams were made by the same person or a different person. His Bioacoustics Lab has amassed an impressive library of high-intensity, visceral sounds -- from TV and movie performances to the screams of non-actors reacting to actual events on YouTube videos.

For the PeerJ paper, the lab ran experiments that included 104 participants. The participants listened to audio files of pairs of screams on a computer, without any visual cues for context. Each pair was presented two seconds apart and participants were asked to determine if the screams came from the same person or a different person.

In some trials, the two screams came from two different callers, but were matched by age, gender and the context of the scream. In other trials, the screams came from the same caller but were two different screams matched for context. And in a third trial, the stimulus pairs consisted of a scream and a slightly modified version of itself, to make it longer or shorter than the original.

For all three of the experiments, most of the participants were able to correctly judge most of the time whether the screams were from the same person or not.

"Our results provide empirical evidence that screams carry enough information for listeners to discriminate between different callers," Gouzoules says. "Although screams may not be acoustically ideal for signaling a caller's identity, natural selection appears to have adequately shaped them so they are good enough to do the job."

The PeerJ paper is part of an extensive program of research into screams by Gouzoules. In previous work, his lab has found that listeners cannot distinguish acted screams from naturally occurring screams.

In upcoming papers, he is zeroing in on how people determine whether they are hearing a scream or some other vocalization and how they perceive the emotional context of a scream -- judging whether it's due to happiness, anger, fear or pain.

Since 2018, the immunosuppressant drug fingolimod has also been approved for children and adolescents aged 10 years and older whose relapsing remitting multiple sclerosis (RRMS) is highly active or severe and rapidly evolving. In an early benefit assessment conducted in the beginning of 2019, the German Institute for Quality and Efficiency in Health Care (IQWiG) had investigated whether the drug has an added benefit for these patients. No added benefit was proven for three of four patient groups; a hint of a non-quantifiable added benefit was found for the fourth group.

Added benefit in health-related quality of life

In the course of the hearing at the Federal Joint Committee (G-BA), the manufacturer of the drug subsequently submitted data from the study on which its dossier was based. The G-BA therefore commissioned IQWiG to analyse these data in an addendum. Now it was also possible to analyse the data on the outcome "health-related quality of life" for young patients with highly active RRMS who need to switch their basic therapy: Whereas children and adolescents in the comparator arm reported a worsening in their quality of life at the end of the study, there was clear improvement in the fingolimod arm. This resulted in a hint of an added benefit.

No relevant differences in cognitive function

The original dossier additionally lacked detailed results on cognitive function testing in the subjects. The study used five tests, which together covered all core areas of cognitive functioning. However, only two of them were used in all study centres: In the Symbol Digit Modality Test, subjects were asked to use a simple code table to match digits to specific symbols; in the test on so-called visual-motor integration, children traced simple shapes such as crosses or circles. Hence, not all core domains of cognition are covered anymore and the results are therefore not informative. Regardless of this, there were no relevant differences between the study arms anyhow.

"The addendum has not changed the overall conclusion on added benefit", says Stefan Lange, Deputy Director of IQWiG. "But we are pleased that we have been able to see informative data on health-related quality of life here. This is an extremely important treatment effect particularly for patients so young."

G-BA decides on the extent of added benefit

The dossier assessment is part of the early benefit assessment according to the Act on the Reform of the Market for Medicinal Products (AMNOG) supervised by the G-BA. After publication of the manufacturer's dossier and the IQWiG dossier assessment, the manufacturer submitted additional information in the commenting procedure. The G-BA subsequently commissioned IQWiG to assess the data subsequently submitted. IQWiG now presents this assessment in the form of an addendum. The G-BA makes a final decision on the extent of added benefit.

CHICAGO--June 24, 2019--A recent online survey of more than 2,000 U.S. adults, conducted by The Harris Poll on behalf of the American Osteopathic Association, revealed that more than two in five American adults (45%) say something has caused them to doubt vaccine safety.

The spread of negative attitudes towards vaccines is a phenomenon deeply rooted in human psychology and amplified by social media, according to perinatal psychiatrist Rachel Shmuts, DO.

"From an evolutionary perspective, humans are primed to pay attention to threats or negative information," she says. "So it makes sense that people hold onto fears that vaccines are harmful, especially when they believe their children are in danger."

She believes it is possible that, since vaccines have been so effective in eradicating disease, people may have more fear of possible vaccine side effects than the actual diseases vaccines prevent.

"For some, it really might be that vaccines are viewed as the more salient threat," says Dr. Shmuts.

Although 55% of Americans don't doubt vaccine safety, 45% noted at least one source that caused doubts about the safety of vaccination. The top three doubt-causing sources were online articles (16%), past secrets/wrongdoing by the pharmaceutical industry (16%) and information from medical experts (12%).

No more room for doubt

The survey also asked Americans to choose a statement that best represented their feelings about vaccine safety and efficacy. While the vast majority (82%) chose in favor of vaccines, 8% selected responses expressing serious doubt. An additional 9% said they were unsure.

Physicians say those small margins can cause significant damage to public health if the doubts result in more unvaccinated people.

"Some diseases, like measles, require as much as 95% of the population to be vaccinated in order to achieve herd immunity," says osteopathic family physician Paul Ehrmann, DO. "Our practice considers itself a steward of public health, so we do not take new patients who refuse to vaccinate."

Dr. Ehrmann explains that herd immunity is essential to maintain, because some people cannot be vaccinated due to medical conditions including allergies, illness, or a weakened immune system. Keeping the rest of the population vaccinated protects those who are vulnerable.

"People know that a lot of practices won't accept patients who don't vaccinate, so when they find one that will, they spread the word to their community that it's a safe place. Whether intentional or not, those doctors are often seen as endorsing anti-vaxxer beliefs," Dr. Ehrmann said.

Winning patients back

While social media has helped spread misinformation about vaccines, it has not been effective for countering those claims, even with scientific research, according to Dr. Shmuts.

She explains that confirmation bias--the tendency to trust new information that bolsters existing beliefs and discredit information that challenges those beliefs--makes it difficult to convince someone vaccines are safe, effective and necessary once they believe they are not.

"The number of people who believe vaccines are dangerous and refuse to get them is still relatively small. However, online support groups seem to solidify their beliefs, making them less susceptible to influence from their neighbors and real-world communities," says Dr. Shmuts.

Dr. Ehrmann agrees, adding that arguing or being judgmental with patients only pushes them further into communities that share their beliefs. Instead, he thinks policy changes are likely the most effective means to change behaviors, if not hearts and minds.

His home state of Michigan discontinued public education for vaccines in the mid-2000s and allows for medical, religious and philosophical exemptions for vaccination, making the state accommodating to anti-vaxxers. As recent as 2015, Michigan ranked 44th in the country for the number of vaccinated children 19 months to 35 months.

However, in 2017 the state, with other partners, launched a public information campaign that has significantly improved vaccination rates across demographics.

"Beliefs are hard to change especially when they're based in fear," says Dr. Ehrmann. "But, being responsible for our patients' health and the public's health, we can't afford to give in to those fears. We must insist on evidence-based medicine."

For over 20 years, a team of researchers at Lund University has worked on developing a drug against preeclampsia - a serious disorder which annually affects around 9 million pregnant women worldwide and is one of the main causes of death in both mothers and unborn babies.

Now the researchers have published a study in the journal Scientific Reports that opens up opportunities for further research towards a drug they hope will save the lives of many pregnant women in the future.

The study was conducted in a transgenic mouse model of preeclampsia, the results are important since they confirm previous studies by the research team showing that alpha-1-microglobulin has potential therapeutic effects in preeclampsia. Trials on patients have recently been launched.

"The treatment, based on the human body's own scavenger protein A1M (alpha-1-microglobulin) which is present in all vertebrates, has a good effect on the disease symptoms such as high blood pressure and protein leakage from the kidneys into the urine. We also observed an improvement in organ function in the kidneys and the placenta. We saw no indication of side effects. In the study now published using the preeclampsia mouse model, which best reflects the various stages of the disease during pregnancy, the mice develop serious preeclampsia in early pregnancy", says Stefan Hansson, professor of obstetrics and gynaecology at Lund University and senior consultant physician at Skåne University Hospital in Lund, who is the principal investigator behind the study together with colleagues including senior researcher Lena Erlandsson.

"This feels like a milestone in our research, as patient studies, known as Phase 1 clinical trials, began in the spring to establish the properties of A1M in order to develop a drug."

Together with his colleague, Bo Åkerström, professor of infection medicine, Stefan Hansson started the studies on A1M several years ago and observed that A1M stopped the leakage of protein in the kidneys. They also saw that the placenta was repaired and that the destroyed structures in the cells' smallest components were restored.

"In preeclampsia, the cells of the placenta looked approximately as though all the trees had been blown over in a storm, and after treatment with A1M they stood up again. When I saw that for the first time, I became a scientific believer", explains Stefan Hansson.

The date for a potential drug to see the light of day is still uncertain.

"Research takes time and costs a lot of money. Bo Åkerström has spent his entire professional life on understanding and describing the properties of the A1M protein and, in the last ten years, we have been studying it in the laboratory as a drug candidate. The results from the clinical trials will be crucial", concludes Stefan Hansson.

Surgery prompted by automobile accidents, combat wounds, cancer treatment and other conditions can lead to bone infections that are difficult to treat and can delay healing until they are resolved. Now, researchers have a developed a double-duty hydrogel that both attacks the bacteria and encourages bone regrowth with a single application containing two active components.

The injectable hydrogel, which is a network of cross-linked polymer chains, contains the enzyme lysostaphin and the bone-regenerating protein BMP-2. In a new study using a small animal model, researchers at the Georgia Institute of Technology showed significant reduction in an infection caused by Staphylococcus aureus - a common infection in orthopedic surgery - along with regeneration within large bone defects.

"Treatment for bone infections now often requires two surgeries to both eliminate the infection and heal the injured bone," said Andrés J. García, executive director of the Parker H. Petit Institute for Bioengineering & Bioscience at the Georgia Institute of Technology. "Our idea was to develop a bifunctional material that does both things in a single step. That would be better for the patient, cost less and reduce hospitalization time. We have shown that we can engineer the hydrogel to control the delivery and release of both the antimicrobial enzyme and the regenerative protein."

The hydrogel-based therapy could be used to treat established bone infections, and as a prophylactic during surgery to prevent infection. The study, funded by the National Institutes of Health, was reported May 17 in the journal Science Advances.

Bone infections today are often treated with systemic antibiotics and surgery to clean the injury. If the infection occurs with implants, they often must be removed. Once the infection is gone, additional surgery may be required to implant proteins that stimulate bone regrowth and restore the implant. And the dead bacteria can prompt a harmful inflammatory reaction.

García and his collaborators - including first author Christopher Johnson - chose lysostaphin, an enzyme that kills the bacteria by cleaving cell walls without generating inflammation. The enzyme keeps working within the hydrogel after it polymerizes.

"With this strategy, we can get rid of the bacteria in such a way that the body re-establishes a normal inflammatory environment that allows the bone to heal," García said. "Use of lysostaphin has been limited by poor stability inside the body, but in the gel, it can maintain stability for at least two weeks. That allows for controlled release over a longer period of time, which is sufficient for what we are trying to do."

Beyond treating infections, the new technique might be used to prevent infection during surgery. For instance, if a screw was being inserted to repair an injury, the hydrogel might be applied to the screw threads. The soft gel would not affect the repair.

The next step in the research would be to repeat the study in large animals, after which clinical trials could be considered if the material proves promising.

"The mechanisms used to fight off infection depends on the species," Garcia noted. "That's why it's so important to repeat the studies in a large animal after testing in mice or rats. Showing efficacy in a large animal model would be a key step toward human trials."

The hydrogel material has been used in the human body before, and is designed to quickly leave the treatment site. "The hydrogel breaks down into small building blocks that are excreted in the urine," Garcia said. "After several weeks, there is no synthetic material left in the body and it is replaced by normal healing tissue."

In a study using brain tissue from deceased human donors, Johns Hopkins Medicine researchers say they found new evidence that schizophrenia can be marked by the buildup of abnormal proteins similar to those found in the brains of people with such neurodegenerative disorders as Alzheimer's or Huntington's diseases.

Schizophrenia -- the specific cause of which remains generally unknown, but is believed to be a combination of genes and environment -- is a disabling mental disorder marked by jumbled thinking, feeling and behavior, as well as delusions or hallucinations. Striking an estimated 200,000 people in the United States each year, its symptoms may be eased with anti-psychotic medications, but the drugs don't work for everyone. Rather than rely on categorizing by symptoms, researchers have long sought to better classify types of schizophrenia -- such as those in which abnormal proteins appear to accumulate -- as a potential way to improve and tailor therapies as precision medicine. The researchers aren't sure how common this variation of the disorder is, although they did find it in about half of the brain samples analyzed.

The new findings were published online May 6 in the American Journal of Psychiatry.

"The brain only has so many ways to handle abnormal proteins," says Frederick Nucifora Jr., Ph.D., D.O., M.H.S., the leader of the study and an assistant professor of psychiatry and behavioral sciences at the Johns Hopkins University School of Medicine. "With schizophrenia, the end process is mental and behavioral, and doesn't cause the pronounced physical neural cell death we see with neurodegenerative diseases, but there are clearly some overall biological similarities."

Based on their experience with schizophrenia and neurodegenerative disorders, Nucifora and his team wanted to determine if the features of schizophrenia brains that are also seen in the brains of patients with Alzheimer's disease or other illnesses. In these neurodegenerative disorders, certain abnormal proteins are churned out but don't assemble into properly functioning molecules, instead ending up misfolded, clumping up and leading to disease.

Using brain tissue samples from the Harvard Brain Tissue Resource Center and brain banks at the University of Pittsburgh and the University of Texas Southwestern, the researchers studied 42 samples from brains of people with schizophrenia and a comparison set of samples from 41 brains from healthy controls. About three-quarters of the brains came from men, and 80% were from white people. The donor tissues were from people with an average age of about 49.

The team broke open the cells from the brain tissue samples and analyzed their contents by looking at how much of the cells contents could be dissolved in a specific detergent. The more dissolved contents, the more "normal" or healthy the cell's contents. Less dissolved cell contents indicate that the cell contains a high volume of abnormal, misfolded proteins, as found in other brain diseases. The researchers found that 20 of the brains from people with schizophrenia had a greater proportion of proteins that couldn't be dissolved in detergent, compared to the amount found in the healthy samples. These same 20 samples also showed elevated levels of a small protein ubiquitin that is a marker for protein aggregation in neurodegenerative disorders. Elevated levels of ubiquitin weren't seen in the healthy brain tissue samples.

The researchers wanted to show that the anti-psychotic medications the patients were taking before they died didn't cause the accumulation of abnormal proteins. To clarify whether the disease or the treatment caused the buildup, the team examined the proteins in the brains of rats treated with the antipsychotic drugs haloperidol or risperidone for 4.5 months compared to control rats treated with plain water. They found that treatment with the anti-psychotic medications didn't cause an accumulation of undissolvable proteins or extra ubiquitin tags, suggesting that the disease and not the medication caused abnormal proteins to build up in some of the brains with schizophrenia.

Next, the researchers used mass spectroscopy to determine the identity of these undissolvable proteins. They found that many of these abnormal proteins were involved in nervous system development, specifically in generating new neurons and the connections that neurons use to communicate with one another.

Nucifora says this main finding of the abnormal proteins involved in these processes is consistent with theories of schizophrenia that trace its origins to brain development and to problems with neural communication.

"Researchers have been so focused on the genetics of schizophrenia that they've not paid as much attention to what is going on at the protein level and especially the possibility of protein aggregation," says Nucifora. "This may be a whole new way to look at the disorder and develop more effective therapies."

Nucifora says Johns Hopkins researchers have pioneered a way to use samples of neurons taken from the nose in living patients as stand-ins for brain biopsies in their studies of schizophrenia and other brain disorders. They hope to now use this technique to study changes in these abnormal proteins over time in people with schizophrenia. They also want to see whether the substantial variety in the disorder's symptoms is linked to particular levels of excess abnormal proteins, and how this leads to the disease. The researchers are investigating if other psychiatric illnesses have similar irregularities too.

A large-scale study from The University of Toledo of young African Americans who have attempted or died by suicide suggests there is a greater need for mental health services in urban school districts, and that we need to do a better job in convincing parents and caregivers to safely secure firearms and ammunition in the home.
Taking those measures, Dr. James Price said, could save lives.

Price, UToledo professor emeritus of health education and public health at UToledo, recently authored the largest study to date that examines suicidal behaviors of African American adolescents between the ages of 13 and 19.

The study, which was published in the Journal of Community Health, found the rate of suicide deaths among young black males increased by 60 percent from 2001 through 2017. Researchers documented a 182 percent increase in the rate of suicide deaths of young black females during that same time period.

Georgia had the highest rate in the nation, at 5.8 per 100,000 people, between 2015 and 2017. Following that was Texas, Florida, North Carolina and Ohio.

"There are far more African American adolescents attempting suicide than has been recognized in the past, and their attempts are starting to be much more lethal," Price said.

Currently, suicide is the second leading cause of death after homicide for African Americans between the ages of 13 and 19, and the rate continues to climb. Equally troubling is that the methods black youth are using in suicide attempts are among the most lethal.

Price and a co-researcher at Ball State University found 52 percent of the 560 males aged 13 to 19 who died by suicide from 2015 to 2017 used firearms -- a method for which the fatality rate approaches 90 percent. Another 34 percent used strangulation or suffocation, which has a fatality rate of about 60 percent.

Among the 204 females who died by suicide over that time period, 56 percent used strangulation or suffocation and 21 percent used firearms.

"When we look at research with these adolescents, we find that they report their attempt to suicide is a cry for help. Two-thirds of the kids didn't really want to die, but they're using the most lethal form of attempting suicide," Price said. "If you can have those lethal forms of suicide inaccessible to them, then that period of crisis and not seeing the irreversibility of this impulsive decision will pass. And with adequate mental health services available to young people, you may actually reduce the chance they'll do that act again."

Previous surveys have found that among inner-city elementary school students whose parents own a handgun, three-quarters knew where the gun was kept.

Keeping firearms locked away, unloaded and separate from ammunition unequivocally would reduce unintentional firearm injuries and impulsive suicide attempts, Price said.

The research also suggests a far greater need for mental health services in African American communities. Public health researchers have repeatedly documented that black youth are less likely than the youth population as a whole to receive adequate mental health treatment, setting the stage for situations that contribute to self-harm.

"What needs to be done early on is to make sure that young people have adequate access to mental health-care services, and mental health-care services have always taken a backseat to other forms of health care," Price said. "If you look at where young people in urban areas, especially adolescents, are getting mental health care, it's in the schools."

Previous studies have found increasing mental health access in urban public schools could reduce suicide attempts by as much as 15 percent, Price said.

"While that doesn't solve all the problems, it's a good first step toward reducing the problem toward severe self-violence," he said.

Bottom Line: Food insecurity is when you worry that your food will run out before you have enough money to buy more. This study used nationally representative data to examine the association between food insecurity and migraine in young U.S. adults because the economic and education transition of young adulthood may increase risk for food insecurity. The study included almost 14,800 young people (ages 24 to 32). Overall, 11% of young adults were food insecure, and migraine was more common among young adults who were food insecure. Food insecurity may lead to some migraine triggers, including missed meals, stress, depression and poor sleep. And, migraine may contribute to food insecurity by leading to poor attendance and productivity at work, resulting in lost employment. Researchers suggest clinicians screen for food insecurity among people with migraine.

Authors: James M. Nagata, M.D., M.Sc., of the University of California, San Francisco, and coauthors

(doi:10.1001/jamaneurol.2019.1663)

Editor's Note: The article includes funding/support disclosures. Please see the article for additional information, including other authors, author contributions and affiliations, financial disclosures, funding and support, etc.

HANOVER, N.H. – June 24, 2019 –Using smartphones, fitness bracelets and a custom app, researchers have created a mobile-sensing system that judges employee performance.

The system works by monitoring the physical, emotional and behavioral well-being of workers to classify high and low performers.

The new mobile-sensing system opens the way for consumer technology to help employees optimize their performance while also allowing companies to assess how individuals are doing in their jobs. The approach can be both a complement and alternative to traditional performance tools like interviews and self-evaluations.

“This is a radically new approach to evaluating workplace performance using passive sensing data from phones and wearables,” said Andrew Campbell, a professor of computer science at Dartmouth. “Mobile sensing and machine learning might be the key to unlocking the best from every employee.”

In the new system, a smartphone tracks physical activity, location, phone usage and ambient light. A wearable fitness tracker monitors heart functions, sleep, stress, and body measurements like weight and calorie consumption. Location beacons placed in the home and office provide information on time at work and breaks from the desk.

The technology builds on earlier work by Campbell who developed StudentLife, an app that monitors student behavior and predicts academic performance. The sensing system integrates the off-the-shelf tech devices using a newly-designed phone app known as PhoneAgent that is based on StudentLife.

The information is processed by cloud-based machine learning algorithms trained to classify workers by performance level.

“This is the beginning step toward boosting performance through passive sensing and machine learning. The approach opens the way to new forms of feedback to workers to provide week-by-week or quarter-by-quarter guidance on how they are approaching their work,” said Campbell.

To test the system, the team assessed performance of supervisors and non-supervisors in different industries—including high-tech and management consulting—based on a series of self-reported behaviors provided by workers in the study group. Performance was then classified by factors such as the amount of time spent at the workplace, quality of sleep, physical activity and phone activity.

The study shows that higher performers tend to have lower rates of phone usage, experience longer deep sleep periods and are more physically active and mobile. When considering roles, high-performing supervisors are mobile, but visit a smaller number of distinctive places during working hours. High-performing non-supervisors spend more time at work during weekends.

With the ability to provide feedback to both the employee and employer, the mobile-sensing system is meant to unlock the behaviors that drive performance. The passive monitoring technique also offers benefits over traditional review techniques that require manual effort and are seen as burdensome, potentially biased and unreliable.

“Passive sensors, which are the heart of the mobile sensing system used in this research, promise to replace the surveys that have long been the primary source of data to identify key correlates of high and low performers,” said Pino Audia a professor of management and organizations at the Tuck School of Business at Dartmouth.

According to the research team, this is the first time that mobile sensing has been used to classify high and low performance in workers across different industries. In total, the technology was tested on 750 workers across the U.S. for an overall period of one year.

The system was found to distinguish between high performers and low performers with an accuracy of 80 percent.

“The passive monitoring system is meant to be empowering. This approach could certainly benefit companies, but can also be helpful to individual employees who are looking to boost their performance,” said Campbell.

The new technology can produce “a more objective measure of performance offering a better understanding of the workplace environment and the workforce both inside and outside of work,” according to a paper describing the study to be published in the Proceedings of the ACM on Interactive, Mobile Wearable and Ubiquitous Technology.

In the study, continuous monitoring using the consumer technology was combined with traditional questionnaires to categorize performance. The technology is not yet available in app stores, but could be coming to nearby cubicles over the next few years.

The research, supported by the Intelligence Advanced Research Projects Activity (IARPA) within the U.S. Office of the Director of National Intelligence, will be presented at the UbiComp Conference in London in September, 2019.

Researchers at the following institutions all contributed to this study: Dartmouth College; University of Notre Dame; Georgia Institute of Technology; University of Washington; University of Colorado Boulder; University of California, Irvine; The Ohio State University; University of Texas at Austin; Carnegie Mellon University.

Researchers at the Paul Scherrer Institute PSI in Villigen, Switzerland, have for the first time elucidated the structure of important enzymes in human cells that alter essential building blocks of the cellular cytoskeleton. This reveals the missing part of a cycle that regulates the build-up or breakdown of supporting elements of the cell. The enzymes investigated work as molecular scissors and can be involved in the development of various diseases, for example, cancer and diseases of the nervous system. Their structural elucidation provides approaches for the development of specific inhibitors and perhaps new therapies. The researchers gained detailed insights into the structure of the enzymes with the help of the Swiss Light Source SLS. They have now published their results in the journal Nature Structural & Molecular Biology.

They give human cells their shape, play a decisive role in cell division, and help to transport substances through the cell: the so-called microtubule filaments. The tasks they perform are of such central importance for life that they are found in the cells of all plants, animals, and humans. Microtubules can become up to several micrometer long, which is roughly the thickness of an average human hair.

The tubular structure of microtubules consists of a regular arrangement of two building blocks, the so-called tubulins (α-tubulin and β-tubulin). In a healthy cell, new microtubules are constantly formed from these building blocks - and are destroyed again. This process is regulated by numerous mechanisms, one of which is the so-called tubulin-tyrosine cycle. The amino acid tyrosine is either attached to the α-tubulin or cut off from it.

The enzymes that attach tyrosine to α-tubulin have been known for a long time. Without these enzymes nerve cells cannot connect properly in the brain. The enzymes that remove tyrosine from α-tubulin, the so-called vasohibins, have not been identified until 2017.

Studying molecular scissors at work

Cutting off the amino acid tyrosine from α-tubulin usually stabilises microtubules. Without tyrosine microtubules can remain intact for several hours, whereas the ones with tyrosine are usually broken down after a few minutes.

Researchers at the Paul Scherrer Institute PSI in Villigen have now succeeded for the first time in elucidating the exact structure of two vasohibins and studying how these enzymes remove the amino acid tyrosine from α-tubulin.

For this purpose, the vasohibins form a groove in their molecular structure that fits perfectly to the tyrosine-bearing end of α-tubulin. In order for this active centre to fit exactly to its target structure, the enzyme also needs an activator, the so-called "small vasohibin binding protein". This protein was previously only known as a stabiliser of vasohibins, but not as a stimulator of an enzymatic reaction. Precise structural analyses of the enzymatically active centre also show how inhibitors should look in order to inhibit vasohibins.

Another surprising result that the researchers achieved with their work: If the activity of the vasohibins is suppressed, disturbances occur in the development of nerve cells and their connections that are similar to those seen in the absence of their counterpart, the enzyme that attaches the amino acid tyrosine to α-tubulin. "A delicate balance between microtubules with and without tyrosine is the key for the normal formation of neurons", said Michel Steinmetz, head of the Laboratory for Biomolecular Research at PSI. "Our results clarify the structural basis of tubulin-detyrosination and clarify the relevance of this process for neuron development."

A possible route to new therapies

Since microtubules are involved in numerous other vital processes in the body in addition to the correct development of neuronal tissues, research on their formation and structure opens up new opportunities for medicine. For example, microtubules play an important role in the growth of tumours and the maintenance of healthy neurons. "With our structural elucidation of vasohibins in complex with inhibitors, we might now be able to develop novel types of drugs against diseases associated with unusual tubulin tyrosination, such as some cancers or possibly brain disorders", said Steinmetz.

With the structural elucidation of the vasohibins, it was possible for the first time to describe the complete tubulin-tyrosine cycle in detail. "This gives us completely new possibilities to intervene in this cycle with therapeutics and to develop new active substances for it", says Sung Ryul Choi, a biochemist at PSI and one of the first authors of the study.

To elucidate the structure of the vasohibins, the researchers used the Swiss Light Source SLS. "We were able to complete our structural work in about five months", said Choi. "This was only possible because here at PSI we have all the necessary expertise and infrastructure in one place."

INDIANAPOLIS - In a commentary published in JAMA Internal Medicine, three Regenstrief Institute research scientists write that while they and other researchers have identified a strong and consistent link between anticholinergic drugs and cognitive impairment from observational studies, randomized clinical trials represent the only rigorous method to definitively establish a causal relationship between these frequently used drugs and various dementias.

Drugs with anticholinergic properties are frequently prescribed for anxiety, depression, and certain types of pain or purchased over the counter for conditions including allergies or sleep problems.

The JAMA Internal Medicine commentary by Regenstrief Institute research scientists Noll Campbell, PharmD, M.S., a geriatric pharmacy researcher; Richard Holden, PhD, a human factors engineer and social-cognitive psychologist; and Malaz Boustani, M.D., MPH, a geriatrician and implementation scientist, call for randomized deprescribing trials to address anticholinergic drug use as a potentially modifiable and reversible risk factor for dementia, a growing public health issue.

That call was recently answered by a $3.3 million award from the National Institute on Aging to Dr. Campbell and colleagues to study whether there is a cause and effect relationship between this drug class and cognitive impairment.

If a causal link between anticholinergic medications and dementia is confirmed, changing from an anticholinergic to another drug would be less difficult than many other interventions known to modify dementia risk such as increasing physical activity, controlling diabetes, or decreasing blood pressure.

The three research scientists say that the next and definitive step to determine whether anticholinergic drugs cause dementia is to conduct long-term randomized deprescribing trials - decreasing or eliminating use of these very common medications - as they will be doing later this year, to see if cholinergic neurotransmission in the areas of the brain related to cognitive performance can be improved, ultimately reducing the risk of developing dementia or delaying onset.

Anticholinergics effect the brain by blocking acetylcholine, a nervous system neurotransmitter. These drugs are used by as many as half of older adults and it is not unusual for an older individual to be taking two or more anticholinergic medications regularly.

"Though we learn about potential risk factors through observational studies, the best way to define a causal relationship between anticholinergics and dementia requires a prospective, randomized trial," said commentary lead author and Regenstrief Institute research scientist Dr. Campbell, also a faculty member of Purdue University's College of Pharmacy. "In conducting such a trial, we can also learn about the risks and benefits of deprescribing medications, including the impact on symptom control, withdrawal or other adverse events, quality of life, and healthcare utilization."

Other areas for exploration noted in the commentary include whether a critical window of opportunity exists to capture the cognitive benefit of deprescribing anticholinergics, for example, whether deprescribing must be performed while these neurotransmitters are sufficiently healthy to benefit and show signs of improvement in cognition.

"Clinicians, health policy makers and patients need to understand the benefits and harms of deprescribing anticholinergics," Dr. Campbell added. "The bottom line is that we need as much high-quality evidence to understand risks and benefits of deprescribing a medication as we have to prescribe it. At the same time, we need to be exploring alternative medications which are known not to harm the aging brain and that patients can afford."

The commentary authors conclude that the ideal targets to reduce anticholinergic burden will be those anticholinergic medications that meet three criteria: (1) high risk of harm, (2) commonly used and (3) existence of an alternative drug to manage the patient's medical condition, if necessary.

Patients with type 1 diabetes have to regularly inject themselves with insulin, a hormone that helps their cells absorb glucose from the bloodstream. Another hormone called glucagon, which has the opposite effect, is given to diabetic patients to revive them if they become unconscious due to severe hypoglycemia.

The form of glucagon given to patients is powdered and has to be dissolved in liquid immediately before being injected, because if stored as a liquid, the protein tends to form clumps, also called amyloid fibrils. A new study from MIT reveals the structure of these glucagon fibrils and suggests possible strategies for altering the amino acid sequence so that the protein is less likely to become clumped.

"Insulin in solution is stable for many weeks, and the goal is to achieve the same solution stability with glucagon," says Mei Hong, an MIT professor of chemistry and one of the senior authors of the study. "Peptide fibrillization is a problem that the pharmaceutical industry has been working for many years to solve."

Using nuclear magnetic resonance (NMR) spectroscopy, the researchers found that the structure of glucagon fibrils is unlike any other amyloid fibrils whose structures are known.

Yongchao Su, an associate principal scientist at Merck and Co., is also a senior author of the study, which appears in Nature Structural and Molecular Biology. MIT graduate student Martin Gelenter is the lead author of the paper.

Fibril formation

Amyloid fibrils form when proteins fold into a shape that allows them to clump together. These proteins are often associated with disease. For example, the amyloid beta protein forms plaques associated with Alzheimer's disease, and alpha synuclein forms Lewy bodies in the neurons of Parkinson's disease patients.

Hong has previously studied the structures of other amyloid peptides, including one that binds to metals such as zinc. After giving a talk on her research at Merck, she teamed up with scientists there to figure out the structure of the fibrillized form of glucagon.

Inside the human body, glucagon exists as an "alpha helix" that binds tightly with a receptor found on liver cells, setting off a cascade of reactions that releases glucose into the bloodstream. However, when glucagon is dissolved in a solution at high concentrations, it begins transforming into a fibril within hours, which is why it has to be stored as a powder and mixed with liquid just before injecting it.

The MIT team used NMR, a technique that analyzes the magnetic properties of atomic nuclei to reveal the structures of the molecules containing those nuclei, to determine the structure of the glucagon fibrils. They found that the glucagon fibril consists of many layers of flat sheets known as beta sheets stacked on top of one another. Each sheet is made up of rows of identical peptides. However, the researchers discovered that, unlike any other amyloid fibril whose structure is known, the peptides run antiparallel to each other. That is, each strand runs in the opposite direction from the two on either side of it.

"All thermodynamically stable amyloid fibrils known so far are parallel packed beta sheets," Hong says. "A stable antiparallel beta strand amyloid structure has never been seen before."

In addition, the researchers found that the glucagon beta strand has no disordered segments. Each of the tens of thousands of peptide strands that make up the fibril is held tight in the antiparallel beta sheet conformation. This allows each peptide to form a 10-nanometer-long beta strand.

"This is an extremely stable strand, and is the longest beta strand known so far among any proteins," Hong says.

Stable structure

One major reason that glucagon fibrils are so stable is that side chains extending from the amino acids making up the glucagon peptides interact strongly with side chains of the peptides above and below them, creating very secure attachment points, also called steric zippers, that help to maintain the overall structure.

While all previously studied amyloid fibrils have a fixed set of residues that form the steric zippers, in glucagon fibrils, even-numbered residues from one strand and odd-numbered residues from the neighboring strand alternately form the steric zipper interface between two beta sheet layers. This conformational duality is another novel feature of the glucagon fibril structure.

"We can see from this structure why the fibril is so stable, and why it's so hard to prevent it from forming," Hong says. "To block it, you really have to change the identity of the amino acid residues. I'm now working with a colleague here to come up with ways to modify the sequence and break those stabilizing interactions, so that the peptide won't self-assemble to form this fibril."

Such alternative peptide sequences could remain shelf-stable for a longer period of time in solution, eliminating the need to mix glucagon with liquid before using it.

Boston, MA -- Every three minutes, a food-related allergic reaction sends someone to the emergency room in the U.S. Currently, the only way to prevent a reaction is for people with food allergies to completely avoid the food to which they are allergic. Researchers are actively seeking new treatments to prevent or reverse food allergies in patients. Recent insights about the microbiome -- the complex ecosystem of microorganisms that live in the gut and other body sites -- have suggested that an altered gut microbiome may play a pivotal role in the development of food allergies. A new study, led by investigators from Brigham and Women's Hospital and Boston Children's Hospital, identifies the species of bacteria in the human infant gut that protect against food allergies, finding changes associated with the development of food allergies and an altered immune response. In preclinical studies in a mouse model of food allergy, the team found that giving an enriched oral formulation of five or six species of bacteria found in the human gut protected against food allergies and reversed established disease by reinforcing tolerance of food allergens. The team's results are published in Nature Medicine.

"This represents a sea change in our approach to therapeutics for food allergies," said co-senior author Lynn Bry, MD, PhD, director of the Massachusetts Host-Microbiome Center at the Brigham. "We've identified the microbes that are associated with protection and ones that are associated with food allergies in patients. If we administer defined consortia representing the protective microbes as a therapeutic, not only can we prevent food allergies from happening, but we can reverse existing food allergies in preclinical models. With these microbes, we are resetting the immune system."

The research team conducted studies in both humans and preclinical models to understand the key bacterial species involved in food allergies. The team repeatedly collected fecal samples every four to six months from 56 infants who developed food allergies, finding many differences when comparing their microbiota to 98 infants who did not develop food allergies. Fecal microbiota samples from infants with or without food allergies were transplanted into mice who were sensitized to eggs. Mice who received microbiota from healthy controls were more protected against egg allergy than those who received microbiota from the infants with food allergies.

Using computational approaches, researchers analyzed differences in the microbes of children with food allergies compared to those without in order to identify microbes associated with protection or food allergies in patients. The team tested to see if orally administering protective microbes to mice could prevent the development of food allergies. They developed two consortia of bacteria that were protective. Two separate consortia of five or six species of bacteria derived from the human gut that belong to species within the Clostridiales or the Bacteroidetes could suppress food allergies in the mouse model, fully protecting the mice and keeping them resistant to egg allergy. Giving other species of bacteria did not provide protection.

"It's very complicated to look at all of the microbes in the gut and make sense of what they may be doing in food allergy, but by using computational approaches, we were able to narrow in on a specific group of microbes that are associated with a protective effect," said co-first author Georg Gerber, MD, PhD, MPH, co-director of the Massachusetts Host-Microbiome Center and chief of the Division of Computational Pathology in the Department of Pathology at the Brigham. "Being able to drill down from hundreds of microbial species to just five or six or so has implications for therapeutics and, from a basic science perspective, means that we can start to figure out how these specific bacteria are conferring protection."

To understand how the bacteria species might be influencing food allergy susceptibility, the team also looked at immunological changes, both in the human infants and in mice. They found that the Clostridiales and Bacteroidetes consortia targeted two important immunological pathways and stimulated specific regulatory T cells, a class of cells that modulate the immune system, changing their profile to promote tolerant responses instead of allergic responses. These effects were found both in the pre-clinical models and also found to occur in human infants.

The new approach represents a marked contrast to oral immunotherapy, a strategy that aims to increase the threshold for triggering an allergic reaction by giving an individual small but increasing amounts of a food allergen. Unlike this approach, the bacteriotherapy changes the immune system's wiring in an allergen-independent fashion, with potential to broadly treat food allergies rather than desensitizing an individual to a specific allergen.

"When you can get down to a mechanistic understanding of what microbes, microbial products, and targets on the patient side are involved, not only are you doing great science, but it also opens up the opportunity for finding a better therapeutic and a better diagnostic approach to disease. With food allergies, this has given us a credible therapeutic that we can now take forward for patient care," said Bry.

Bry and Gerber, along with senior author Talal Chatila, MD, of Boston Children's Hospital, are founders and have equity in ConsortiaTX, a company that is developing a live human biotherapeutic product (CTX-944). (Co-senior author Rima Rachid, MD, of Boston Children's Hospital, also has equity in the company.) ConsortiaTX is preparing for a Phase 1b trial in pediatric food allergy, followed by expansion into additional allergic diseases. ConsortiaTX has obtained an exclusive global license to the intellectual property related to the microbial discoveries published in the Nature Medicine paper.