Culture

Menlo Park, Calif. -- Researchers from the Department of Energy's SLAC National Accelerator Laboratory have discovered a strange new feature of a protein that's thought to be important in the development of tuberculosis: The protein contains a "huge" interior pocket, the likes of which has never before been seen, that appears capable of passing a wide range of other molecules into the bacterial cell.

Cornelius Gati, a structural biologist at SLAC, discovered the pocket while investigating the role this "transporter protein" on the surface of tuberculosis bacteria plays in sucking up vitamin B12 from surrounding cells. As far as anyone knew, transporter proteins that import molecules into cells tend to be quite specialized, with nooks and crannies tailored to grab onto particular molecules and move them into cells. This one, Gati found, was a generalist that could in principle bring in small nutrients, larger molecules like vitamin B12 or even some antibiotics.

In theory, the new findings could lead to new ways to treat tuberculosis, but the for the moment Gati and colleagues are simply trying to get a better handle on what the protein can and cannot transport - as well as what purpose such an odd protein might serve.

"We've never seen anything like this before," Gati said. "It doesn't really make sense."

The research, which Gati performed in collaboration with researchers at the University of Groningen, Stockholm University, and the Moscow Institute of Physics and Technology, was published March 25 in the journal Nature.

A still-deadly disease

Although tuberculosis is largely a thing of the past in the United States, it remains a serious public health threat in other parts of the world. There were 10 million new cases in 2018, and 1.5 million people died from tuberculosis that year alone, according to the World Health Organization. Worldwide, it remains one of the top 10 leading causes of death, the leading cause of death from infectious disease and the leading cause of death for people with HIV.

Yet Mycobacterium tuberculosis, the bacterium that causes tuberculosis, remains relatively poorly understood, as does the process of turning a tuberculosis infection into active disease. In the United States, for example, around 13 million people are infected with the bacteria, but only about one in 10 will ever actually develop the disease, and no one is quite sure why.

One clue to understanding the disease concerns the tuberculosis bacterium's uptake of vitamin B12, a step that seems to be crucial for the bacteria's survival and for the shift from TB infection to disease. How the bacteria imports the vitamin, however, was a mystery. Researchers could find no transporter protein in the bacterium's outer membrane that was dedicated specifically to vitamin B12. The one Gati and team studied had been linked via genetic studies to B12 uptake, but it was known for shuttling an entirely different class of molecules, including the antimicrobial bleomycin. Still, Gati and team knew that the protein and its connection to B12 was essential. "Without this transporter, tuberculosis bacteria cannot survive," Gati said.

A cryogenic magnifying glass

To get a handle on the transporter protein's structure, Gati turned to cryo-electron microscopy. Known as cryo-EM for short, the technique involves freezing molecules in place so that they can be studied in more or less their natural state under an electron microscope. Although the technique was first developed in the 1970s, a series of advances in the last few decades have made it more and more practical to use the technique to study biological molecules.

Still, when Gati took images of the transporter protein and analyzed the data, he was not entirely prepared for what it was about to show him. Rather than uncovering a hidden nook tailored to vitamin B12, cryo-EM revealed a cavity within the transporter roughly 8 cubic nanometers in size - a tiny volume by our everyday standards, but absolutely enormous in the context of transporter proteins. The pocket could easily fit a number of water molecules, vitamin B12 and perhaps many other molecules.

That generalist nature is particularly exciting, said Laura Dassama, a chemist at Stanford University and Stanford ChEM-H. "We have seen transporters that move a variety of drugs and molecules out of a cell, with little specificity, but not importers. If this is really an importer that can recognize and import multiple unrelated molecules, that would be fantastic" and might suggest a way to move antibiotics into the tuberculosis cell.

The million dollar question

Although the most tantalizing possibility is that the transporter protein discovery could lead to new treatments for the disease, Gati said the team still doesn't know what exactly their molecule can and cannot transport. While they have a sense of what can fit inside the cavity, for example, they still do not know what can get in and out. So far, the team has only been able to observe the cavity in its closed state. To figure out what can actually get into the cavity and back out again, the team needs to catch the cavity with its doors open.

Even then, the team will not know what the molecule actually does transport in practice. Future structural studies and biochemical screens, Gati said, could help answer those questions, although they will not be easy: Tuberculosis bacteria tend to grow and reproduce very slowly, which in turn hampers the methods scientists would normally use to study transporter molecules.

But even if Gati and his colleagues figure out exactly what their molecule is doing, there remain deeper questions: Why did nature cook up this molecule and its enormous interior cavity, why are such molecules so rare, and what purpose do they serve? On one hand, a cavity like the one the team has discovered is an "Achilles heel," particularly if it can help transport tuberculosis-killing antibiotics. On the other hand, it remains possible there is some evolutionary advantage to the structure.

"That is the million-dollar question," Gati said.

A high-salt diet is not only bad for one's blood pressure, but also for the immune system. This is the conclusion of a current study under the leadership of the University Hospital Bonn. Mice fed a high-salt diet were found to suffer from much more severe bacterial infections. Human volunteers who consumed an additional six grams of salt per day also showed pronounced immune deficiencies. This amount corresponds to the salt content of two fast food meals. The results are published in the journal Science Translational Medicine.

Five grams a day, no more: This is the maximum amount of salt that adults should consume according to the recommendations of the World Health Organization (WHO). It corresponds approximately to one level teaspoon. In reality, however, many Germans exceed this limit considerably: Figures from the Robert Koch Institute suggest that on average men consume ten, women more than eight grams a day.

This means that we reach for the salt shaker much more than is good for us. After all, sodium chloride, which is its chemical name, raises blood pressure and thereby increases the risk of heart attack or stroke. But not only that: "We have now been able to prove for the first time that excessive salt intake also significantly weakens an important arm of the immune system," explains Prof. Dr. Christian Kurts from the Institute of Experimental Immunology at the University of Bonn.

This finding is unexpected, as some studies point in the opposite direction. For example, infections with certain skin parasites in laboratory animals heal significantly faster if these consume a high-salt diet: The macrophages, which are immune cells that attack, eat and digest parasites, are particularly active in the presence of salt. Several physicians concluded from this observation that sodium chloride has a generally immune-enhancing effect.

The skin serves as a salt reservoir

"Our results show that this generalization is not accurate," emphasizes Katarzyna Jobin, lead author of the study, who has since transferred to the University of Würzburg. There are two reasons for this: Firstly, the body keeps the salt concentration in the blood and in the various organs largely constant. Otherwise important biological processes would be impaired. The only major exception is the skin: It functions as a salt reservoir of the body. This is why the additional intake of sodium chloride works so well for some skin diseases.

However, other parts of the body are not exposed to the additional salt consumed with food. Instead, it is filtered out by the kidneys and excreted in the urine. And this is where the second mechanism comes into play: The kidneys have a sodium chloride sensor that activates the salt excretion function. As an undesirable side effect, however, this sensor also causes so-called glucocorticoids to accumulate in the body. And these in turn inhibit the function of granulocytes, the most common type of immune cell in the blood.

Granulocytes, like macrophages, are scavenger cells. However, they do not attack parasites, but mainly bacteria. If they do not do this to a sufficient degree, infections proceed much more severely. "We were able to show this in mice with a listeria infection," explains Dr. Jobin. "We had previously put some of them on a high-salt diet. In the spleen and liver of these animals we counted 100 to 1,000 times the number of disease-causing pathogens." Listeria are bacteria that are found for instance in contaminated food and can cause fever, vomiting and sepsis. Urinary tract infections also healed much more slowly in laboratory mice fed a high-salt diet.

Sodium chloride also appears to have a negative effect on the human immune system. "We examined volunteers who consumed six grams of salt in addition to their daily intake," says Prof. Kurts. "This is roughly the amount contained in two fast food meals, i.e. two burgers and two portions of French fries." After one week, the scientists took blood from their subjects and examined the granulocytes. The immune cells coped much worse with bacteria after the test subjects had started to eat a high-salt diet.

In human volunteers, the excessive salt intake also resulted in increased glucocorticoid levels. That this inhibits the immune system is not surprising: The best-known glucocorticoid cortisone is traditionally used to suppress inflammation. "Only through investigations in an entire organism were we able to uncover the complex control circuits that lead from salt intake to this immunodeficiency," stresses Kurts. "Our work therefore also illustrates the limitations of experiments purely with cell cultures."

Can robots be effective tools in combating the COVID-19 pandemic? A group of leaders in the field of robotics, including Henrik Christensen, director of UC San Diego's Contextual Robotics Institute, say yes, and outline a number of examples in an editorial in the March 25 issue of Science Robotics. They say robots can be used for clinical care such as telemedicine and decontamination; logistics such as delivery and handling of contaminated waste; and reconnaissance such as monitoring compliance with voluntary quarantines.

"Already, we have seen robots being deployed for disinfection, delivering medications and food, measuring vital signs, and assisting border controls," the researchers write.

Christensen, who is a professor in the Department of Computer Science and Engineering at UC San Diego, particularly highlighted the role that robots can play in disinfection, cleaning and telepresence.

Other co-authors include Marcia McNutt, president of the National Research Council and president of the National Academy of Sciences, as well as a number of other robotics experts from international and U.S. universities.

"For disease prevention, robot-controlled noncontact ultraviolet (UV) surface disinfection has already been used because COVID-19 spreads not only from person to person via close contact respiratory droplet transfer but also via contaminated surfaces," the researchers write.

"Opportunities lie in intelligent navigation and detection of high-risk, high-touch areas, combined with other preventative measures," the researchers add. "New generations of large, small, micro-, and swarm robots that are able to continuously work and clean (i.e., not only removing dust but also truly sanitizing/sterilizing all surfaces) could be developed."

In terms of telepresence, "the deployment of social robots can present unique opportunities for continued social interactions and adherence to treatment regimes without fear of spreading more disease," researchers write. "However, this is a challenging area of development because social interactions require building and maintaining complex models of people, including their knowledge, beliefs, emotions, as well as the context and environment of interaction."

"COVID-19 may become the tipping point of how future organizations operate," researchers add. "Rather than cancelling large international exhibitions and conferences, new forms of gathering--virtual rather than in-person attendance--may increase. Virtual attendees may become accustomed to remote engagement via a variety of local robotic avatars and controls."

"Overall, the impact of COVID-19 may drive sustained research in robotics to address risks of infectious diseases," researchers go on. "Without a sustainable approach to research and evaluation, history will repeat itself, and technology robots will not be ready ready to assist for the next incident."

PITTSBURGH--Robots could perform some of the "dull, dirty and dangerous" jobs associated with combating the COVID-19 pandemic, but that would require many new capabilities not currently being funded or developed, an editorial in the journal Science Robotics argues.

The editorial, published today and signed by leading academic researchers including Carnegie Mellon University's Howie Choset, said robots conceivably could perform such tasks as disinfecting surfaces, taking temperatures of people in public areas or at ports of entry, providing social support for quarantined patients, collecting nasal and throat samples for testing, and enabling people to virtually attend conferences and exhibitions.

In each case, the use of robots could reduce human exposure to pathogens -- which will become increasingly important as epidemics escalate.

"The experiences with the (2015) Ebola outbreak identified a broad spectrum of use cases, but funding for multidisciplinary research, in partnership with agencies and industry, to meet these use cases remains expensive, rare and directed to other applications," the researchers noted in the editorial.

"Without a sustainable approach to research, history will repeat itself, and robots will not be ready for the next incident," they added.

In addition to Choset, a professor in CMU's Robotics Institute and one of the founding editors of Science Robotics, the authors of the editorial include Marcia McNutt, president of the National Academy of Science; Robin Murphy of Texas A&M University; Henrik Christensen of the University of California, San Diego; and former CMU faculty member Steven Collins, now at Stanford University.

Choset stressed that the idea behind the editorial wasn't solely to prescribe how robots might be used in a pandemic.

"Rather, we hope to inspire others in the community to conceive of solutions to what is a very complicated problem," he explained.

Choset also emphasized that, like robots, artificial intelligence could help in responding to epidemics and pandemics. Researchers at Carnegie Mellon, for instance, are performing research to address humanitarian aid and disaster response. For that task, they envision a combination of AI and robotics technologies, such as drones. Human-robot interaction, automated monitoring of social media, edge computing and ad hoc computer networks are among the technologies they are developing.

CHAMPAIGN, Ill. -- Researchers have developed the first computational model of a human cell and simulated its behavior for 15 minutes - the longest time achieved for a biological system of this complexity. In a new study, simulations reveal the effects of spatial organization within cells on some of the genetic processes that control the regulation and development of human traits and some human diseases.

The study, which produced a new computational platform that is available to any researcher, is published in the journal PLOS Computational Biology.

"This is the first program that allows researchers to set up a virtual human cell and change chemical reactions and geometries to observe cellular processes in real time," said Zhaleh Ghaemi, a research scientist at the University of Illinois at Urbana-Champaign and lead author of the study.

Working off the notion the insides of cells are packed with various organelles and molecules, the group, led by U. of I. chemistry professor Zaida Luthey-Schulten, focuses on how the movement of individual molecules around the many obstacles affects the chemical reactions inside cells.

To test the new model, the team performed simulations of a process called RNA splicing, which is one of the most complex cellular processes and a hallmark of human cellular biology, the researchers said.

"RNA splicing changes the messenger RNA molecules that carry information needed from DNA to form proteins," Ghaemi said. "The process uses a complex cellular machine - called a spliceosome - that requires the trafficking of precursor and mature components around the highly compartmentalized parts of a cell. This makes RNA splicing ideal for studying how spatial arrangement affects the various chemical reactions that take place in cells."

The new simulations revealed a rationale for why precursors of the spliceosome move between the nucleus and cytoplasm compartments, the researchers said.

"Even though this movement seems somewhat inefficient and counterintuitive at first glance, our simulations indicate that they are essential to the proper RNA splicing, and therefore protein synthesis," said Martin Gruebele, a chemistry professor and study co-author. "When protein synthesis goes awry, it can lead to disease, including cancer,"

The researchers designed the computational platform to model a variety of cellular processes while being fully customizable by the researcher using it. "For example, we could use this model to observe what types of proteins will form if the RNA-splicing process were to remove only two parts of a DNA sequence instead of three," Luthey-Schulten said. "This could provide insights into how different proteins form and influence the development of cancer cells."

Although the most comprehensive human cell model to date, the computational model still has ample room for advancement and customization to study other cellular processes, the researchers said.

"This simulation allowed us to observe the RNA splicing for 15 minutes," Gruebele said. "Ultimately, we would like to be able to run the program for much longer and include all of the proteins that are required for gene replication, allowing us to observe cell division in real-time. The possibilities for our group - and others because the program is open access - are endless."

Nationwide survey data on more than 230,000 U.S. adolescents over the period 2005 to 2018 suggest that anxiety, depression, suicidal thoughts, and other "internalizing" problems account for an increasing share of the adolescent mental health burden, according to a study from researchers at Johns Hopkins Bloomberg School of Public Health and Columbia University.

The study, to be published online March 25 in JAMA Psychiatry, also found that the percentage of adolescent girls seeking mental health care each year rose significantly during the period, as did the use of outpatient mental health care services by adolescent girls.

"We aren't sure why this is occurring, but it is clear from this evidence and other epidemiological studies that anxiety, depression, and other internalizing problems are becoming more prevalent among adolescents relative to other types of mental health problems," says study lead author Ramin Mojtabai, MD, PhD, MPH, a professor in the Department of Mental Health at the Bloomberg School.

Much of what is known about rates of depression and other mental health problems among U.S. adolescents comes from the U.S. Substance Abuse and Mental Health Services Administration's National Survey of Drug Use and Health (NSDUH), an annual nationwide survey of tens of thousands of Americans age 12 and up. NSDUH data have shown, for example, that at the time of the 2017 survey, 20 percent of adolescent girls ages 12 to 17 reported having had at least one major depressive episode in the prior year, compared to 8.7 percent of adult women.

In the new study, Mojtabai and co-author Mark Olfson, MD, PhD, of Columbia University's Vagelos College of Physicians and Surgeons, examined long-term trends in NSDUH data on adolescents with an analysis of survey data from January 1, 2005 to December 31, 2018. The researchers grouped the 14 annual surveys into seven sets of two consecutive surveys, to address short-term variability in the data and make longer-term trends more evident.

During the 2005 to 2018 period, 203,070 adolescents had been interviewed, and of these 47,090 (19.7 percent) reported prior-year treatment or counseling for mental health problems. Mojtabai and Olfson found that the percentage of surveyed adolescents who reported treatment or counseling didn't change significantly from 2005-06 to 2017-18. However, the proportion of adolescent girls reporting treatment or counseling did rise significantly, from an average of 22.8 percent in the 2005-06 surveys to 25.4 percent in 2017-18, an 11.4 percent increase, while the proportion of boys reporting treatment or counseling declined from 17.8 percent to 16.4 percent, a decrease of 7.9 percent, over the same interval. Most of those changes occurred after 2011-12.

The mental health problems were categorized by researchers into several categories including internalizing problems (anxiety, depression, suicidal thinking, somatization disorders), externalizing problems (conduct and substance-use problems), relationship problems, and problems at school. Mojtabai and Olfson found that internalizing problems accounted for an increasing proportion of the total during the study window--from 48.3 percent in 2005-06 to 57.8 percent in 2017-18, a 19.7 percent increase. Among internalizing problems, suicidal thoughts or attempts increased most sharply, by 63.3 percent, from 15.0 percent to 24.5 percent of the total.

"These trends in the types of reported problems were seen across different care settings, from school counseling to inpatient mental health services," Mojtabai says.

There were also trends in the types of services reported by the survey respondents; in particular, the researchers found a 15.8 percent increase in reliance on outpatient mental health services--such as psychiatric and psychotherapy clinics--which 67.3 percent of respondents reported using in 2017-18 vs. 58.1 percent in 2005-06. There was a corresponding drop in the reported use of school counseling services, from 49.1 percent to 45.4 percent, a decrease of 7.5 percent. Changes in the use of inpatient mental health care and general medical services were slight.

The authors did not attempt to address these trends in this study, although they did note that other research suggests a link between internet social media use and texting, on the one hand, and increased rates of depression on the other. Increased use of psychiatic drugs for children, and decreased exposure to environmental lead compounds--which are known to cause neurological problems associated with aggressive behavior--are two other factors noted that might explain declines in externalizing problems.

Psychiatrists have long observed that mental health problems are more likely to manifest in girls and women as internalizing problems, and in boys and men as externalizing problems. The increased proportion of girls reporting mental health problems during 2005-18 is thus a potential factor underlying the observed increase in internalizing problems. However, Mojtabai and Olfson found that this trend remains in place even when adjusting for sex and other factors. "This trend cannot be completely explained by the larger proportion of girls seeking treatment in later years," he says.

He adds that policymakers, education system planners, and the medical profession should be aware of the observed trends in the uses of different mental health services, in particular the shift away from school counseling towards more use of outpatient mental health services.

A transport protein that is used by the human pathogen Mycobacterium tuberculosis to import vitamin B12 turns out to be very different from other transport proteins. It contains a huge water-filled cavity, in which hydrophilic substances are transported across the cell membrane. This discovery, which changes our understanding of bacterial physiology, was made by imaging the transport protein using cryo-electron microscopy. The results were published in the journal Nature on 26 March.

The tuberculosis bacterium has all the genes required to produce vitamin B12 but, for some reason, it still needs to import this vitamin for successful cell division. To do so, it uses a transport protein that is part of a large family of ATP-binding cassette (ABC) transporters. Interestingly, the vitamin B12 transporter is also implicated in the transport of antimicrobial peptides such as bleomycin. 'And it is very odd to have a single transporter for two very different types of molecules,' says Professor of Biochemistry Dirk Slotboom.

Cavity

Slotboom and his team, together with their colleague Albert Guskov, set out to elucidate the protein structure of the enigmatic transporter. 'This was a long process but we finally cracked it using cryo-electron microscopy,' says Slotboom. This was performed at the SLAC National Accelerator Laboratory, Menlo Park, CA, USA. The structure revealed a major surprise: a water-filled cavity that spans the entire cell membrane, measuring a massive 7,700 cubic Angstrom. 'That is as big as seven vitamin B12 molecules.'

This cavity appears to simply transport water together with any substances that might be in it. 'You could compare it with a sluice,' explains Slotboom. 'You let the water in and everything that is in it.' It does explain why the transporter can handle both antibiotic peptides and vitamin B12. Since it is non-selective, it must be an inefficient transport system. This does not matter for the uptake of vitamin B12 by Mycobacterium tuberculosis, as the cells only need to take up very few of these molecules during their reproductive cycle, which lasts around 24 hours.

Antibiotics

The non-selective transport system is totally different from known transporters. 'As such, it changes the way that we look at the physiology of bacteria. There are strong indications that other bacterial species have a similar system, which means that they pick up random molecules from their environment.' It also offers an interesting perspective on the treatment of tuberculosis: 'If we could stimulate the activity of this transporter, it might import antibiotics more efficiently, making it easier to kill these cells. We realize, though, that this may not be straightforward, as the bacterium uses effective strategies to keep antibiotics out.'

The next step is to find out how the transporter works. 'We expect that inside the cell, the sluice is emptied by binding and hydrolysing ATP. But we do not know how it opens on the outside, to let new molecules in.' The transport protein is a dimer and the two halves appear to protrude on the outside - where they may somehow open up to let fresh cargo in. 'Maybe we can find a way to loosen this cap and let more antibiotics in.'

Human cells

There is also a distinct possibility that a similar sluice-type transporter is present in human cells, says Slotboom. In our intestines, vitamin B12 is first bound to a peptide called intrinsic factor and then taken up by epithelial cells. 'It ends up in lysosomes, vesicles full of enzymes, where the intrinsic factor is degraded. Next, the vitamin B12 is released from the lysosome into the cells. I strongly suspect that this involves a similar non-specific transporter.'

What The Study Did: This observational study of 416 patients in Wuhan, China, with confirmed coronavirus disease 2019 (COVID-19) reports that cardiac injury is a common condition among hospitalized patients with COVID-19 and it is associated with higher risk of in-hospital mortality.

Authors: Bo Yang, M.D., Ph.D., and He Huang, M.D., Ph.D., of Renmin Hospital of Wuhan University in China, are the corresponding authors.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/ 

(doi:10.1001/jamacardio.2020.0950)

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

What The Study Did: Researchers examined changes over time in the kinds of mental health problems for which adolescents in the United States received care and where they got that care in this survey study with findings that should be interpreted within the context of several limitations including self-reported information.

Authors: Ramin Mojtabai, M.D., Ph.D., M.P.H., of the  Johns Hopkins Bloomberg School of Public Health in Baltimore, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(10.1001/jamapsychiatry.2020.0279)

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

CRISPR-Cas9 gene editing technology is best known for its potential role in correcting genetic diseases. But it can also be used as a tool to find genes that act as supporting players, making the disease better or worse. Such genes might make good targets for new treatments.

A new study led by Louis Kunkel, PhD, and research fellow Angela Lek, PhD at Boston Children's Hospital used CRISPR-Cas9 to better understand facioscapulohumeral muscular dystrophy (FSHD) and explore potential treatments. FSHD causes muscle weakness in the face, shoulder blades, and upper arms, and currently has no treatment other than supportive care.

In FSHD, the gene DUX4, normally active mainly during fetal development, is inappropriately "turned on." This causes toxic DUX4 protein to be produced in muscle cells when it shouldn't be, leading to cell death and muscle weakness.

Kunkel, Lek, and colleagues wondered if other genes could be targeted to prevent or compensate for this problem. They decided to use CRISPR-Cas9 to systematically mutate every gene in the genome. Their goal: to find genes that, when knocked out, enable human muscle cells to survive even when the DUX4 protein is being made.

"We essentially utilized the CRISPR screen technique as a shortcut to illuminate 'druggable' pathways for FSHD," says Lek, the paper's first author.

Preventing muscle cells from dying

The CRISPR-Cas9 screening process yielded about a half-dozen strong "hits." Among them were several genes that play a role in the cellular response to low-oxygen conditions, or hypoxia. That, it turns out, is the main driver of cell death caused by DUX4. When the team exposed muscle cells to compounds known to inhibit this hypoxia response, the cells stayed alive.

"Our results show that knockout of key genes involved in hypoxia signaling can desensitize cells to toxicity from DUX4, and prevent them from dying," says Kunkel.

Going a step further, the team created muscle cell lines from actual patients with FSHD. When treated with the same compounds, these cells showed fewer of the known biomarkers of the disease.

Finally, the researchers created two live zebrafish models of FSHD. When they exposed the fish to compounds that inhibit hypoxia signaling, the fish showed improvements in muscle structure and function and more swimming activity.

Moving forward

Kunkel and Lek have filed a patent application covering their discoveries. Lek, now at the Yale School of Medicine, is moving the drug experiments into mouse models of FSHD, while Kunkel plans further zebrafish studies at Boston Children's.

"The most encouraging finding about this study is that we discovered that there are FDA-approved drugs that can overcome DUX4's toxic effect," says Lek. "We now have a collection of drugs to test and figure out which is most suitable for long-term dosing in patients with FSHD."

Kunkel believes the process used in this study could be applied to many other diseases.

"Our approach could provide an accelerated path to understanding complex genetic diseases, discovering therapeutic targets, and testing potential treatments," he says.

New artifacts uncovered at the Waim archaeological site in the highlands of New Guinea - including a fragment of the earliest symbolic stone carving in Oceania - illustrate a shift in human behavior between 5050 and 4200 years ago in response to the widespread emergence of agriculture, ushering in a regional Neolithic Era similar to the Neolithic in Eurasia. The location and pattern of the artifacts at the site suggest a fixed domestic space and symbolic cultural practices, hinting that the region began to independently develop hallmarks of the Neolithic about 1000 years before Lapita farmers from Southeast Asia arrived in New Guinea. While scientists have known that wetland agriculture originated in the New Guinea highlands between 8000 and 4000 years ago, there has been little evidence for corresponding social changes like those that occurred in other parts of the world. To better understand what life was like in this region as agriculture spread, Ben Shaw et al. excavated and examined a trove of artifacts from the recently identified Waim archaeological site. "What is truly exciting is that this was the first time these artifacts have been found in the ground, which has now allowed us to determine their age with radiocarbon dating," Shaw said. The researchers analyzed a stone carving fragment depicting the brow ridge of a human or animal face, a complete stone carving of a human head with a bird perched on top (recovered by Waim residents), and two ground stone pestle fragments with traces of yam, fruit and nut starches on their surfaces. They also identified an obsidian core that provides the first evidence for long-distance, off-shore obsidian trade, as well as postholes where house posts may have once stood.

In this post-industrialization age, electricity has become the backbone of our society. However, using fossil fuels to generate it is not the best option because of their limited availability and harmful nature. In the last two decades, significant efforts have been made to develop techniques to foster sustainable energy. Against this backdrop, solid oxide fuel cells (SOFCs) have risen as a clean and highly efficient alternative that can generate electrical energy. However, a major drawback of SOFCs is their high operating temperatures, restricting their widespread usage.

Various previous studies have attempted to overcome this drawback by improving conductivity at high temperatures using fluorite type oxides like CeO2-δ. Normally, these fluorite oxides are available in porous form, and their mechanism of conductivity is believed to be dependent on the surface adsorption of water molecules, which is the process of adhesion of atoms or molecules to a surface.

A team of scientists from Tokyo University of Science, led by Dr Tohru Higuchi, took this research one step forward. In their new study published in Nanoscale Research Letters, the researchers explored the effect of "doping," which is the process of adding impurities to alter their conductivity, on these oxides, which are a very good candidate for SOFCs. Researchers "doped" the oxide with a metal called Samarium (Sm). Then, they deposited thin films of this doped oxide on a substrate of Aluminium oxide (Al2O3) in a specific direction known to enhance the conductivity. Dr Higuchi considers this an advantage, stating, "When considering practical devices, thin film forms are more suitable than porous or nanocrystalline forms."

Then, the research team characterized the crystalline quality and electronic structure of the novel film. They also compared the difference in conductivity between this novel film and thick ceramic oxides commonly used in the industry. Their findings revealed that the ceramic sample exhibited poor crystallinity and had poor proton conductivity compared to the thin film sample.

What's more, the "resistivity"--or the resistance to electrical flow--of the thin film was found to decrease with increasing humidity due to the "proton conduction" in fluorite type oxides, as explained by Grotthuss mechanism. A water molecule consists of two atoms of oxygen and one atom of hydrogen. The molecules of water have bonds between them, called "hydrogen bonds." The Grotthuss mechanism (or the "hop-turn" mechanism) allows the water molecules to be split into ions that increase the conductivity, and hence they move from one hydrogen bond to another. The novel film was found to exhibit surface protonic conduction in the low temperature region below 100°C.

This novel film, with its high conductivity at room temperatures, is sure to have several applications in the future. As far as SOFCs are concerned, Dr Higuchi concludes, "Our study on electrolyte membranes presents radical findings that can help lower the operating temperature of SOFCs, and may be an alternative system for making more practical devices using fluorite type oxides in SOFCs, and open up new avenues for nuclear and thermal power generation in the future."

Most people know about the painkiller paracetamol, commonly used against headaches and ingested orally.

However, in hospitals, paracetamol is administered intravenously. In this way, doctors and nurses can help critically ill patients who are unable to swallow one or more pills.

Furthermore, the substance acts much faster intravenously, and the method allows healthcare professionals to control the doses and the timing of their effect very precisely.

Nevertheless, the intravenous paracetamol has a serious side effect: namely, a temporary large drop in blood pressure.

'Previous studies suggest it is quite a sizable drop. We are, for example, talking about drops in the range of 25-30 mm Hg from a systolic pressure of 120, and we now believe that we know the mechanism underlying this dangerous side effect', says Assistant Professor Thomas Qvistgaard Jepps from the Department of Biomedical Sciences.

He adds that the drop in blood pressure is found in both common and critically ill patients. In the latter category, six out of ten have been reported to experience the side effect. One third of these to such an extent that it requires medical intervention.

This research is rather timely, given the unprecedented COVID-19 crisis and dramatic increase in critically ill patients that maybe receiving intravenous paracetamol in the hospitals to help with pain and fever management.

Different kinds of metabolism
Despite the statistics, intravenous paracetamol is considered to be a relatively stable drug that is used increasingly in the healthcare system, even though many doctors and nurses are aware of the potential side effects.

On this background, Thomas Qvistgaard Jepps and his team set out to find a cause for the steep drop in blood pressure. As the first in the world, they have now succeeded through studies in rats.

'Paracetamol bypasses the liver when administered intravenously, therefore it is metabolised differently to when you ingest it orally', says Thomas Qvistgaard Jepps, adding:

'It still gets metabolised, but it happens elsewhere in the body, where the subsequent chemicals can cause an effect that wouldn't normally happen, if the drug was taken orally'.

The Assistant Professor emphasises that most people should not be afraid to take painkillers as usual. As long as you still stay within the maximum recommended dose.

The solution to the pressure drop
More precisely, it appears that the residual products of the painkiller affect some of the potassium channels, which, among other things, regulate how your blood vessels contract and relax, thereby controlling your blood pressure.

By using drugs that block these potassium channels, specifically, the research team subsequently succeeded in reducing the side effect of the large drop in blood pressure in the test rats.

'Because we have identified the mechanism of how the side effect occurs, we believe we are able to offer a potential pharmaceutical design for a new kind of co-therapy: A type of paracetamol infused with another drug that prevents the drop in blood pressure', says Thomas Qvistgaard Jepps.

'However, blockers of the potassium channels we have investigated are not yet approved for human consumption and need to be developed and tested properly. We wouldn't want to replace one side effect with another'.

The next step of the research group is therefore to investigate how drugs that block the potassium channels may be adapted for humans. They are also investigating alternatives for blocking the potassium channels, for example, by affecting the enzymes involved in metabolising paracetamol outside the liver.

CAMBRIDGE, MA -- Researchers at MIT and the University of Colorado at Denver have proposed a stopgap measure that they believe could help Covid-19 patients who are in acute respiratory distress. By repurposing a drug that is now used to treat blood clots, they believe they could help people in cases where a ventilator is not helping, or if a ventilator is not available.

Three hospitals in Massachusetts and Colorado are developing plans to test this approach in severely ill Covid-19 patients. The drug, a protein called tissue plasminogen activator (tPA), is commonly given to heart attack and stroke victims. The approach is based on emerging data from China and Italy that Covid-19 patients have a profound disorder of blood clotting that is contributing to their respiratory failure.

"If this were to work, which I hope it will, it could potentially be scaled up very quickly, because every hospital already has it in their pharmacy," says Michael Yaffe, a David H. Koch Professor of Science at MIT. "We don't have to make a new drug, and we don't have to do the same kind of testing that you would have to do with a new agent. This is a drug that we already use. We're just trying to repurpose it."

Yaffe, who is also a member of MIT's Koch Institute for Integrative Cancer Research and an intensive care physician at Boston's Beth Israel Deaconess Medical Center/Harvard Medical School, is the senior author of a paper describing the new approach.

The paper, which appears in the Journal of Trauma and Acute Care Surgery, was co-authored by Christopher Barrett, a surgeon at Beth Israel Deaconess and a visiting scientist at MIT; Hunter Moore, Ernest Moore, Peter Moore, and Robert McIntyre of the University of Colorado at Denver; Daniel Talmor of Beth Israel Deaconess; and Frederick Moore of the University of Florida.

Breaking up clots

In one large-scale study of the Covid-19 outbreak in Wuhan, China, it was found that 5 percent of patients required intensive care and 2.3 percent required a ventilator. Many doctors and public health officials in the United States worry that there may not be enough ventilators for all Covid-19 patients who will need them. In China and Italy, a significant number of the patients who required a ventilator went on to die of respiratory failure, despite maximal support, indicating that there is a need for additional treatment approaches.

The treatment that the MIT and University of Colorado team now proposes is based on many years of research into what happens in the lungs during respiratory failure. In such patients, blood clots often form in the lungs. Very small clots called microthrombi can also form in the blood vessels of the lungs. These tiny clots prevent blood from reaching the airspaces of the lungs, where blood normally becomes oxygenated.

The researchers believe that tPA, which helps to dissolve blood clots, may help patients in acute respiratory distress. A natural protein found in our bodies, tPA converts plasminogen to an enzyme called plasmin, which breaks down clots. Larger amounts are often given to heart attack patients or stroke victims to dissolve the clot causing the heart attack or stroke.

Animal experiments, and one human trial, have shown potential benefits of this approach in treating respiratory distress. In the human trial, performed in 2001, 20 patients who were in respiratory failure following trauma or sepsis were given drugs that activate plasminogen (urokinase or streptokinase, but not tPA). All of the patients in the trial had respiratory distress so severe that they were not expected to survive, but 30 percent of them survived following treatment.

That is the only study using plasminogen activators to treat respiratory failure in humans to date, largely because improved ventilator strategies have been working well. This appears not to be the case for many patients with Covid-19, Yaffe says.

The idea to try this treatment in Covid-19 patients arose, in part, because the Colorado and MIT research team has spent the last several years studying the inflammation and abnormal bleeding that can occur in the lungs following traumatic injuries. It turns out that Covid-19 patients also suffer from inflammation-linked tissue damage, which has been seen in autopsy results from those patients and may contribute to clot formation.

"What we are hearing from our intensive care colleagues in Europe and in New York is that many of the critically ill patients with Covid-19 are hypercoagulable, meaning that they are clotting off their IVs, and having kidney and heart failure from blood clots, in addition to lung failure. There's plenty of basic science to support the idea that this concept should be beneficial," Yaffe says. "The tricky part, of course, is figuring out the right dose and route of administration. But the target we are going after is well-validated."

Potential benefits

The researchers will test tPA in patients under the FDA's "compassionate use" program, which allows experimental drugs to be used in cases where there are no other treatment options. If the drug appears to help in an initial set of patients, its use could be expanded further, Yaffe says.

"We learned that the clinical trial will be funded by BARDA [the Biomedical Advanced Research and Development Authority], and that Francis Collins, the NIH director, was briefed on the approach yesterday afternoon," he says. "Genentech, the manufacturer of tPA, has already donated the drug for the initial trial, and indicated that they will rapidly expand access if the initial patient response is encouraging."

Based on the latest data from their colleagues in Colorado, these groups plan to deliver the drug both intravenously and/or instill it directly into the airways. The intravenous route is currently used for stroke and heart attack patients. Their idea is to give one dose rapidly, over a two-hour period, followed by an equivalent dose given more slowly over 22 hours. Applied BioMath, a company spun out by former MIT researchers, is now working on computational models that may help to refine the dosing schedule.

"If it were to work, and we don't yet know if it will, it has a lot of potential for rapid expansion," Yaffe says. "The public health benefits are obvious. We might get people off ventilators quicker, and we could potentially prevent people from needing to go on a ventilator."

The hospitals planning to test this approach are Beth Israel Deaconess, the University of Colorado Anschultz Medical Campus, and Denver Health. The research that led to this proposal was funded by the National Institutes of Health and the Department of Defense Peer Reviewed Medical Research Program.

The study, conducted by Imperial College London on data from 2009 to 2018, looked at a third of a million passenger responses to Customer Satisfaction Surveys (CSSs) from 28 cities across four continents.

They found that on average, women are ten per cent more likely than men to feel unsafe on metro trains (trains that go underground) and six per cent more likely than men to feel unsafe on buses.

The largest difference between women and men's perceptions of safety was in Europe, where women were 12 per cent more likely to report feeling unsafe than men.

The smallest difference was in South America, where women were nine per cent more likely to report feeling unsafe than men.
The researchers say the findings highlight an important social issue that could be preventing some women from thriving both personally and professionally.

Lead author Laila Ait Bihi Ouali, of Imperial's Department of Civil and Environmental Engineering, said: "Feeling unsafe can lead to social, professional, economic, and health problems for those affected. In this case, women who feel unsafe on public transport might turn down shift work at certain times of day, or avoid social or work events that require travelling a certain route."

"Our study was conducted on data from before the coronavirus outbreak, but its message will be just as important when life resumes as normal."

The results are published today in Journal of the Royal Statistical Society: Series A.

Safety and satisfaction

Public transport operators send online CSSs every year to passengers that are designed to measure general feelings of satisfaction with their networks. The surveys ask passengers their level of agreement with various statements about availability, time, information, comfort, security, customer care, accessibility, environment, and overall satisfaction.

The response options are usually: agree strongly; agree; neither agree nor disagree; disagree; or disagree strongly.

To carry out the study, the researchers looked at 327,403 completed responses to CSSs from 2009 to 2018.

As well as measuring overall satisfaction scores, they focussed on responses to three questions [see notes to Eds] pertaining to feelings of 'security' and assigned numbers from one to five for each potential response (one for 'agree strongly; five for 'disagree strongly') to quantify the responses.

They then compared the scores between men and women, and looked at whether they differed alongside characteristics of the transport network like rates of violence on the network, numbers of cars per train, and busyness of vehicles and stations.

They found that around half of women surveyed felt safe on urban public transport (45 per cent felt safe in metro trains and stations; 55 per cent felt safe in buses), but that women were ten per cent more likely than men to report feeling unsafe in metro trains and stations, and six per cent more likely than men to feel unsafe in buses.

The study also showed that women were overall less satisfied than men with public transport services, but the gap between genders for satisfaction was far less than for safety (gap of three per cent gap for satisfaction on metros; 2.5 per cent gap for satisfaction on buses). The researchers say that this demonstrates that safety is an important part of overall passenger satisfaction.

Carriage characteristics

The team found that having more staff on metro trains doesn't seem to be correlated with feelings of safety, but that more staff at stations were correlated with increased feelings of safety, as were metro trains, metro stations, and buses with more passengers onboard.

Higher rates of violence on transport networks - particularly robberies - were linked to decreased feelings of safety, as were having more carriages per train, and carriages that were larger.

The researchers say that quantifying feelings of safety on public transport with operators' own data could help contribute towards creating tangible goals, which operators could use to improve people's feelings of safety.

Laila said: "Our research exposes a gap in passenger safety levels that's often overlooked. We hope that by putting a figure on feelings of safety, urban metro and bus companies can take measures to boost women's feelings of safety and reduce the gap between genders."

Study co-author Professor Dan Graham, also of Imperial's Department of Civil and Environmental Engineering, said: "Feeling unsafe on public transport can prevent people from living as they otherwise would at certain times or on certain routes. We hope our results will highlight the gender gap in feelings of safety and nudge transport companies to implement changes to help women feel safer using public transport."

Next, the researchers will look more closely at the links between transport characteristics and feelings of safety to try to decipher which characteristics companies might change to boost feelings of safety in passengers.
They will also look at how far the gap between men and women's perceptions of safety reflects the wider urban environment.