Culture

Inside your mouth right now, there is a group of bacteria whose closest relatives can also be found in the belly of a moose, in dogs, cats, and dolphins, and in groundwater deep under the Earth's surface. In a stunning discovery, scientists have found that these organisms have adapted to these incredibly diverse environments--without radically changing their genomes.

The organisms are members of the TM7, or Sacchraribacteria, phylum. These are ultra-small, parasitic bacteria with small genomes that belong to a larger group called the Candidate Phyla Radiation (CPR). These CPR bacteria are mysterious "dark matter" that represent more than 25 percent of all bacterial diversity, yet we know very little about them since the vast majority remain uncultivated.

In research first published as a pre-print in 2018, and now formally in the journal Cell Reports, scientists describe their findings that Saccharibacteria within a mammalian host are more diverse than ever anticipated. The researchers also discovered that certain members of the bacteria are found in the oral cavity of humans, the guts of other mammals, and in groundwater. While these environments are all very different, the bacteria's tiny genomes remain minimally changed between humans and groundwater. This indicates that humans acquired the bacteria more recently, on an evolutionary timescale.

"It's the only bacteria we know that has hardly changed when they adapted to humans," said Dr. Jeffrey Scott McLean, a microbiologist and Associate Professor of Periodontics at the University of Washington School of Dentistry, and lead author of the paper.

The TM7 bacteria were a complete mystery to scientists until Dr. Xuesong He, Associate Member of Staff at the Forsyth Institute and co-author of the paper, first isolated the bacterium TM7x, a member of CPR, in 2014. Since then, researchers have learned that CPR includes a huge number of different bacteria, all with tiny genomes. These bacteria need a host to survive and are unique in that they can't make their own amino acids and nucleotides, which are essential building blocks for life.

"I see this as a huge discovery," said Wenyuan Shi, CEO and Chief Scientific Officer at the Forsyth Institute and co-author on the paper. "This creature survives in both humans and groundwater, which indicates there are similarities that allow these bacteria to adapt to humans."

Previous research by Dr. Batbileg Bor, Assistant Member of Staff at the Forsyth Institute and co-author of the paper, showed that TM7 can easily jump from one bacterial host to another. This could explain how they ended up in mammals, since mammals drink groundwater.

"The most likely reason we see a large diversity of these bacteria in humans, yet one group of bacteria remains nearly identical to those in groundwater, is that some groups were acquired in ancient mammal relatives and they expanded over time across mammals, whereas this one highly similar group more recently jumped directly into humans," McLean said.

TM7 and other ultra-small, parasitic bacteria within CPR may play important roles in health and disease that we have yet to discover. Since they act as parasites--living with and killing other bacteria--TM7 could change the overall microbiome by modulating the abundance of bacteria, McLean said. Scientists are just scratching the surface of understanding how much our microbiome impacts our overall health.

Another major contribution of this research has been developing a systematic way to name these newly discovered bacteria, setting the foundation for classifying other isolated strains in the future.

The fact that humans acquired TM7 recently is a discovery that has broader implications for understanding our co-evolutionary pathways with the microbes that live on and within us.

"There are only a couple hundred genes that are different in these ultra-small bacteria between what lives deep in the subsurface environment and those that have become common bacteria in our mouths," McLean said. "That is a remarkable feat for bacteria missing so many genes."

Researchers at the University of Bath have been working with GB skeleton athletes to develop a new type of motion capture technology that can accurately track the performance of the athlete during push start phase of performance.

Skeleton is a winter sport where athletes rapidly accelerate on ice whilst pushing a sled before launching forwards on to it and navigating the corners of the track at speeds of up to 90 mph. Improvements of fractions of a second made at the start can make all the difference at the finish line. Therefore, it is useful for both athletes and their coaching team to be able to monitor the performance of athletes during this start phase and how they respond to training.

Standard methods of optical motion capture, using multiple reflective markers on the athlete and the sled to measure their movement in 3D space, are time consuming to set up and can interfere with the athlete's natural performance.

To overcome this, researchers at CAMERA, the University of Bath's motion research centre, have developed a non-invasive markerless system using computer vision and deep learning methods to measure velocity and estimate poses by identifying body landmarks from regular image data.

The method was used at the University's push-track training facility, a concrete slope with straight metal rails, which allows athletes to train off-season using a wheeled practice sled.

The researchers used a set-up of nine cameras along both sides of the push-track for the markerless system, and compared measurements with those obtained using the conventional 15 camera marker-based camera system.

They tested the system on 12 athletes for 33 push trials and found that there was very good agreement in the data from both systems (measured sled and athlete velocities were within 0.015 and 0.029 m/s, respectively), validating the use of the markerless method as a non-invasive and accurate alternative to the traditional marker-based system.

Dr Laurie Needham, a post-doctoral researcher within CAMERA, said: "Our latest computer vision system allows us to break out of the laboratory and take biomechanics into the wild. The non-invasive nature of this approach not only means that we can capture push start information without interfering with the athlete's training session, but we can do so in way that conforms with the current need for social distancing."

Dr Steffi Colyer, from the University's Department of Health, said: "Conventional (marker-based) technologies, which we use every day in our laboratory research, are not feasible in many elite sports training and competition environments and so the future of sports biomechanics lies in finding accurate and unobtrusive markerless solutions. Our system can provide information about British skeleton athletes' start performances that was previously inaccessible to them and their coaches."

"We'd like to thank the British Bobsleigh and Skeleton Association for their time and support for this project. We hope that our system can be used by athletes in the future to monitor and improve their performance on the track."

Danny Holdcroft, Head of Performance Innovation and Applied Research at the British Bobsleigh and Skeleton Association, said "Our continuing relationship with University of Bath is something that we hold in high regards and value greatly as we see to support our athlete aspirations of winning Olympic Gold Medals in 2022 and 2026. The CAMERA project is an exciting piece of our larger jigsaw and will undoubtedly help us further explore beyond our current performance boundaries."

Biomedical engineers at Duke University have engineered a method for simultaneously detecting the presence of multiple specific microRNAs in RNA extracted from tissue samples without the need for labeling or target amplification. The technique could be used to identify early biomarkers of cancer and other diseases without the need for the elaborate, time-consuming, expensive processes and special laboratory equipment required by current technologies.

The results appeared online on May 4 in the journal Analyst.

"The general research focus in my lab has been on the early detection of diseases in people before they even know they're sick," said Tuan Vo-Dinh, director of the Fitzpatrick Institute for Photonics and the R. Eugene and Susie E. Goodson Distinguished Professor of Biomedical Engineering at Duke. "And to do that, you need to be able to go upstream, at the genomic level, to look at biomarkers like microRNA."

MicroRNAs are short RNA molecules that bind to messenger RNA and stop them from delivering their instructions to the body's protein-producing machines. This could effectively silence certain sections of DNA or regulate gene expression, thus altering the behaviors of certain biological functions. More than 2000 microRNAs have been discovered in humans that affect development, differentiation, growth and metabolism.

As researchers have discovered and learned more about these tiny genetic packages, many microRNAs have been linked to the misregulation of biological functions, resulting in diseases ranging from brain tumors to Alzheimer's. These discoveries have led to an increasing interest in using microRNAs as disease biomarkers and therapeutic targets. Due to the very small amounts of miRNAs present in bodily samples, traditional methods of studying them require genetic-amplification processes such as quantitative reverse transcription PCR (qRT-PCR) and RNA sequencing.

While these technologies perform admirably in well-equipped laboratories and research studies that can take months or years, they aren't as well-suited for fast diagnostic results at the clinic or out in the field. To try to bridge this gap in applicability, Vo-Dinh and his colleagues are turning to silver-plated gold nanostars.

"Gold nanostars have multiple spikes that can act as lighting rods for enhancing electromagnetic waves, which is a unique feature of the particle's shape," said Vo-Dinh, who also holds a faculty appointment in Duke chemistry. "Our tiny nanosensors, called 'inverse molecular sentinels,' take advantage of this ability to create clear signals of the presence of multiple microRNAs."

While the name is a mouthful, the basic idea of the nanosensor design is to get a label molecule to move very close to the star's spikes when a specific stretch of target RNA is recognized and captured. When a laser is then shined on the triggered sensor, the lightning rod effect of the nanostar tips causes the label molecule to shine extremely brightly, signaling the capture of the target RNA.

The researchers set this trigger by tethering a label molecule to one of the nanostar's points with a stretch of DNA. Although it's built to curl in on itself in a loop, the DNA is held open by an RNA "spacer" that is tailored to bind with the target microRNA being tested for. When that microRNA comes by, it sticks to and removes the spacer, allowing the DNA to curl in on itself in a loop and bring the label molecule in close contact with the nanostar.

Under laser excitation, that label emits a light called a Raman signal, which is generally very weak. But the shape of the nanostars--and a coupling effect of separate reactions caused by the gold nanostars and silver coating--amplifies Raman signals several million-folds, making them easier to detect.

"The Raman signals of label molecules exhibit sharp peaks with very specific colors like spectral fingerprints that make them easily distinguished from one another when detected," said Vo-Dinh. "Thus we can actually design different sensors for different microRNAs on nanostars, each with label molecules exhibiting their own specific spectral fingerprints. And because the signal is so strong, we can detect each one of these fingerprints independently of each other."

In this clinical study, Vo-Dinh and this team collaborated with Katherine Garman, associate professor of medicine, and colleagues at the Duke Cancer Institute to use the new nanosensor platform to demonstrate that they can detect miR-21, a specific microRNA associated with very early stages of esophageal cancer, just as well as other more elaborate state-of-the-art methods. In this case, the use of miR-21 alone is enough to distinguish healthy tissue samples from cancerous samples. For other diseases, however, it might be necessary to detect several other microRNAs to get a reliable diagnosis, which is exactly why the researchers are so excited by the general applicability of their inverse molecular sentinel nanobiosensors.

"Usually three or four genetic biomarkers might be sufficient to get a good diagnosis, and these types of biomarkers can unmistakably identify each disease," said Vo-Dinh. "That's why we're encouraged by just how strong of a signal our nanostars create without the need of time-consuming target amplification. Our method could provide a diagnostic alternative to histopathology and PCR, thus simplifying the testing process for cancer diagnostics."

For more than three years, Vo-Dinh has worked with his colleagues and Duke's Office of Licensing and Ventures to patent his nanostar-based biosensors. With that patent recently awarded, the researchers are excited to begin testing the limits of their technology's abilities and exploring technology transfer possibilities with the private sector.

"Following these encouraging results, we are now very excited to apply this technology to detect colon cancer directly from blood samples in a new NIH-funded project," said Vo-Dinh. "It's very challenging to detect early biomarkers of cancer directly in the blood before a tumor even forms, but we have high hopes."

Seated around the dinner table, faculty affiliated with Stanford ChEM-H - one of Stanford University's interdisciplinary institutes - spoke one-by-one, pitching ideas for collaborative research. Inspired by a recent medical conundrum, Gilbert Chu, a professor of medicine (oncology) and of biochemistry at Stanford Medicine, put out the call for a chemist who could help him create a sensor that could quickly, easily and accurately measure ammonia levels in blood. Just down the table Matthew Kanan, associate professor of chemistry, registered an impressive coincidence: his graduate student, Thomas Veltman, was working on a sensor for measuring ammonia in any liquid.

In the August issue of ACS Sensors, Chu, Kanan, Veltman and colleagues Natalia Gomez-Ospina and Chun Tsai have published the product of their collaboration: a handheld, portable ammonia detector that - like glucometers used to measure blood sugar - assesses ammonia levels from a finger or earlobe prick.

Ammonia is a natural product of digestion that is usually processed into urea by the liver and passed out of the body in urine. Too much ammonia in the blood can cause mental and physical dysfunction and is a concern for people with liver disease or genetic conditions that hinder ammonia metabolism. The new device could be especially beneficial for newborns with these metabolic diseases. In this population, brain damage can occur within hours of elevated ammonia levels and, for treatment, some families must drive long distances to obtain adequate testing.

"I've spoken with families who have children with this condition about having this kind of device and it makes them emotional because, for them, the consequences of not getting ammonia checked accurately and quickly are so severe," said Natalia Gomez-Ospina, assistant professor of pediatrics and co-author of the paper. "For these families, it could be life-changing."

The sensor has been tested on blood samples from patients prone to elevated ammonia levels, and a portable version of the device has been tested on blood samples dosed with ammonia. Results were accurate in both cases. Now, the researchers are making final adjustments to the design and manufacturing of the device, in hopes of readying it for a study that would be eligible for evaluation by the U.S. Food and Drug Administration (FDA).

A medical mystery

The patient that inspired Chu's collaboration proposal was brought into the hospital by her husband after weeks of worsening health. She was delirious and unable to walk. No one knew what was wrong until a standard blood plasma test revealed she had very elevated ammonia levels.

"The only thing that I could think of was: Could it have been my fault?" said Chu, who is co-senior author of the paper with Kanan. "I looked at her chemotherapy, which she had been taking. It was an oral form of fluorouracil, one of the oldest chemotherapy drugs. This was not a known side effect, but the timeline matched her symptoms."

Following this lead, Chu discovered that, unbeknownst to her, the patient had an anatomical anomaly as well as gene mutations that reduced her body's ability to metabolize ammonia. The chemotherapy drug she took blocked the body's machinery for using ammonia to make RNA. The block in turn caused the patient to become symptomatic.

Once understood, this was an easy issue to address with known treatments. But, along the way, Chu learned that the test for measuring ammonia levels was shockingly arduous - blood had to be drawn from a vein, quickly transported on ice to an analysis lab, centrifuged to separate plasma, and then processed by a biochemical assay. Even if everything goes perfectly, results take at least two hours, but problems arise frequently. In the course of treating his patient, the blood samples Chu took were rejected twice.

"I talked to the lab about their protocols and realized that, if I'm having this problem, there have to be many community hospitals that have even bigger struggles with these tests," said Chu.

One patient in the researchers' clinical study was a newborn with an ammonia metabolism disorder who had blood drawn 132 times in 31 days, an amount equal to over half the average newborn's total blood volume.

"The burden on the patients in our study was a powerful motivator. Some were having several tests a day for many days and every single one is a separate venous draw," said Kanan. "It's a lot of blood and pain, and if something goes wrong with the test, it's worthless."

Big, small problems

In contrast, the current device requires about one drop of blood - less than 1 percent of the blood for the standard test - and thus can be obtained with a small finger or earlobe stick. The device itself is about the size of a television remote and, as with a glucometer, the blood drops are dabbed onto a test strip that is inserted into one end. It reports the ammonia level in less than a minute.

While the sensor inside the device is very similar to existing ammonia sensors - used to detect toxic ammonia gas in industrial settings - the test strips are made from scratch. Blood applied to a small hole at one end of the strip zips through a microscopic channel and sinks into a paper-lined well at the opposite end, which is coated with an inexpensive chemical that liberates the ammonia from the sample. Inside the device, this well sits directly under the ammonia sensor.

In building and testing this prototype, Veltman designed and constructed the strips by hand. He made many step-wise improvements, optimizing the design so the strips can be mass-produced simply and inexpensively. For example, two of the greatest challenges in producing the strips were the tiny sample volume and ammonia's natural stickiness.

"The more we reduced the volume of blood, the more problems crept in," said Veltman, who is lead author of the paper. "When you have only a small amount of ammonia, surface chemistry issues become really important. If it isn't just right on every strip, you won't get an accurate reading because the ammonia sticks where it shouldn't."

The researchers have formed a company around their invention with the ultimate goal of attaining FDA clearance for the technology.

"From day one, the objective was a device that would be used by patients and their families to improve health outcomes," said Kanan. "Through all the challenges, having that goal has really held the collaborative effort together."

The rod-like spike proteins on the surface of SARS CoV-2 are the tip of the spear of the COVID-19 pandemic. The spikes bind to human cells via the ACE2 receptor and then dramatically change shape, jack-knifing to fuse the cell membrane with the coronavirus's outer membrane and opening the door to coronavirus infection. A study led by Boston Children's Hospital for the first time freeze-frames the spike protein in its "before" and "after" shapes.

The study, published July 21 in Science, also captured some surprise features of the spike protein, which is also the main protein targeted by our antibodies and the protein used in most vaccines now in human testing. The investigators, led by Bing Chen, PhD, believe the unexpected features may help SARS-CoV-2 hide from the immune system and survive longer in the environment. They may also have implications for vaccine and therapeutic development.

Using the technique of cryogenic electron microscopy, Chen and colleagues in Boston Children's Division of Molecular Medicine established the structure of the spike protein, both before and after fusion of the virus and cell membranes. In the "after," post-fusion state, the protein assumes a rigid hairpin shape folded in on itself, they showed.

Intriguingly, they also found that the spike protein sometimes goes from its original "before" shape into the "after" form prematurely, without the virus binding to the ACE2 receptor.

"We propose that there are two routes for the conformational changes," says Chen. "One is ACE2 dependent, and allows the virus to enter a host cell. The second is ACE2 independent."

A coronavirus defense mechanism?

As a result of the spontaneous shape change, coronavirus particles often bear both forms of the spike protein, with the rigid "after" form protruding slightly more from the virus surface. Chen suggests that being able to assume this alternate shape even without binding to a cell may help keep SARS-CoV-2 viable in the environment, preventing it from breaking down when it lands on a surface for example. That could explain why the virus appears to remain viable on various surfaces for hours to days.

"Most viruses don't survive long outside the host," Chen says. "We think the rigid structure of these post-fusion spikes protects the virus."

Evading immune detection

The researchers speculate that having some spikes assume the post-fusion form prematurely may also protect SARS-CoV-2 from our immune system, inducing antibodies that are non-neutralizing and ineffective in containing the virus. In effect, the post-fusion spikes may act as decoys that distract the immune system.

The team was also surprised to find that the post-fusion spikes, similar to the pre-fusion spikes, have glycans, or sugar molecules, at evenly spaced locations on their surface. Glycans are another feature that helps the virus avoid immune detection.

Chen believes his team's findings have implications for vaccine development. He notes that current vaccine formulations that use the spike protein to stimulate the immune system may have varying mixes of the pre- and post-fusion forms, and that this may limit their protective efficacy.

"We need to think about how to stabilize the spike protein," he says. "If the protein is not stable, you may be able to induce antibodies, but they will be less effective in terms of blocking the virus. There may be batch-to-batch variation."

Building on experience with HIV

Chen's many years of research on HIV have helped give his team a leg up on studying SARS-CoV-2. Both viruses are what's known as envelope viruses, and need to fuse their membranes with those of the cells they're seeking to enter. Both use the same jack-knifing shape change, and both have spike proteins on their surface that are decorated with sugars. Finally, HIV vaccine development is plagued by the challenge of developing neutralizing antibodies -- it, too, distracts the immune system into creating multiple antibodies that do not shut down the virus.

"I think SARS-CoV-2 is probably an easier target than HIV, but we will have to see," says Chen. "If this first round of vaccines does not work well in Phase 3 trials, this new understanding of the spike structure may help us design stronger vaccines."

Scientists report two new cryo-EM structures representing the pre- and postfusion conformations of the full-length SARS-CoV-2 spike (S) protein, an essential viral component responsible for host cell entry and the spread of infection. These reconstructions - derived from a full-length, fully wild-type form of the S protein - demonstrate critical differences from previous cryo-EM studies that used engineered, stabilized versions of the S protein. Based on their findings, the authors caution that current vaccine strategies informed by structures of the engineered S protein could be relying on limited and even misleading information about the protein's natural state. They say it's possible that vaccine strategies that employ full-length sequences of the S protein or whole inactivated SARS-CoV-2 (such as PiCoVacc), could spontaneously form the S protein's postfusion structure, found here to possess several features that could distract the patient's immune system. Therefore, these vaccine strategies may require further evaluation, the authors say. Using cryo-EM on full-length SARS-CoV-2 samples in their natural state, Yongfei Cai and colleagues imaged the pre-fusion S protein configuration, a semi-stable state when the protein is poised to fuse with host cell membranes, and the post-fusion conformational configuration, a stable, rigid state achieved when the S protein has gone through a conformational change that would promote viral fusion with a host cell membrane. They found their prefusion structure differed from previously described prefusion conformations in several ways, including the presence of previously unobserved disulfide bonds. The protein's spontaneous transition from the prefusion state to the postfusion state occurred independently of whether the spike had interacted with host cell membranes, the researchers also found. The postfusion structure was strategically "decorated" by N-linked glycans, forming spikes that might play protective roles against host immune responses, such as by inducing nonneutralizing antibody responses or shielding more vulnerable regions of the S protein. In future work, the researchers hope to image a higher-resolution structure of an intact S protein, and also aim to reconstruct regions where host cell membrane fusion occurs.

Airborne and potentially deadly, the virus that causes COVID-19 can only be studied safely under high-level biosafety conditions. Scientists handling the infectious virus must wear full-body biohazard suits with pressurized respirators, and work inside laboratories with multiple containment levels and specialized ventilation systems. While necessary to protect laboratory workers, these safety precautions slow down efforts to find drugs and vaccines for COVID-19 since many scientists lack access to the required biosafety facilities.

To help remedy that, researchers at Washington University School of Medicine in St. Louis have developed a hybrid virus that will enable more scientists to enter the fight against the pandemic. The researchers genetically modified a mild virus by swapping one of its genes for one from SARS-CoV-2, the virus that causes COVID-19. The resulting hybrid virus infects cells and is recognized by antibodies just like SARS-CoV-2, but can be handled under ordinary laboratory safety conditions.

The study is available online in Cell Host & Microbe.

"I've never had this many requests for a scientific material in such a short period of time," said co-senior author Sean Whelan, PhD, the Marvin A. Brennecke Distinguished Professor and head of the Department of Molecular Microbiology. "We've distributed the virus to researchers in Argentina, Brazil, Mexico, Canada and, of course, all over the U.S. We have requests pending from the U.K. and Germany. Even before we published, people heard that we were working on this and started requesting the material."

To create a model of SARS-CoV-2 that would be safer to handle, Whelan and colleagues - including co-senior author Michael S. Diamond, MD, PhD, the Herbert S. Gasser Professor of Medicine, and co-first authors Brett Case, PhD, a postdoctoral researcher in Diamond's laboratory, and Paul W. Rothlauf, a graduate student in Whelan's laboratory - started with vesicular stomatitis virus (VSV). This virus is a workhorse of virology labs because it is fairly innocuous and easy to manipulate genetically. Primarily a virus of cattle, horses and pigs, VSV occasionally infects people, causing a mild flu-like illness that lasts three to five days.

Viruses have proteins on their surfaces that they use to latch onto and infect cells. The researchers removed VSV's surface-protein gene and replaced it with the one from SARS-CoV-2, known as spike. The switch created a new virus that targets cells like SARS-CoV-2 but lacks the other genes needed to cause severe disease. They dubbed the hybrid virus VSV-SARS-CoV-2.

Using serum from COVID-19 survivors and purified antibodies, the researchers showed that the hybrid virus was recognized by antibodies very much like a real SARS-CoV-2 virus that came from a COVID-19 patient. Antibodies or sera that prevented the hybrid virus from infecting cells also blocked the real SARS-CoV-2 virus from doing so; antibodies or sera that failed to stop the hybrid virus also failed to deter the real SARS-CoV-2. In addition, a decoy molecule was equally effective at misdirecting both viruses and preventing them from infecting cells.

"Humans certainly develop antibodies against other SARS-CoV-2 proteins, but it's the antibodies against spike that seem to be most important for protection," Whelan said. "So as long as a virus has the spike protein, it looks to the human immune system like SARS-CoV-2, for all intents and purposes."

The hybrid virus could help scientists evaluate a range of antibody-based preventives and treatments for COVID-19. The virus could be used to assess whether an experimental vaccine elicits neutralizing antibodies, to measure whether a COVID-19 survivor carries enough neutralizing antibodies to donate plasma to COVID-19 patients, or to identify antibodies with the potential to be developed into antiviral drugs.

"One of the problems in evaluating neutralizing antibodies is that a lot of these tests require a BSL-3 facility, and most clinical labs and companies don't have BSL-3 facilities," said Diamond, who is also a professor of molecular microbiology, and of pathology and immunology. "With this surrogate virus, you can take serum, plasma or antibodies and do high-throughput analyses at BSL-2 levels, which every lab has, without a risk of getting infected. And we know that it correlates almost perfectly with the data we get from bona fide infectious SARS-CoV-2."

Since the hybrid virus looks like SARS-CoV-2 to the immune system but does not cause severe disease, it is a potential vaccine candidate, Diamond added. He, Whelan and colleagues are conducting animal studies to evaluate the possibility.

Irvine, CA - July 21, 2020 - Patients with Alzheimer's disease frequently suffer from spatial memory loss, such as no recognition of where they are, and forgetting where they put their belongings. They often show a wandering symptom, which is also a feature of spatial memory impairment. Until now, the brain network mechanism that causes spatial memory impairment had been unclear.

Published today in Neuron, the study titled, "Disrupted place cell remapping and impaired grid cells in a knockin model of Alzheimer's disease," reveals how the normal brain network function of hippocampus cells which works to discriminate a distinct spatial environment in a process called "remapping," was disrupted in Alzheimer's disease. The study, done Alzheimer's disease model mice, found that this disruption of hippocampus is most likely caused by the activity impairment of the entorhinal cortex, a brain region that supplies information to the hippocampus.

"We recorded the brain cell activity in the hippocampus, which is the memory center of the brain, responsible for spatial memory, among other things," said Kei Igarashi, PhD, an assistant professor in the Department of Anatomy & Neurobiology at the University of California, Irvine School of Medicine. "Our findings could lead to the development of a method to reactivate brain activity of the entorhinal cortex, which may help establish new treatments for preventing the progression of spatial memory impairment in Alzheimer's disease patients."

Igarashi has been studying brain network mechanisms for Alzheimer's disease since he started his lab in 2016. "Our memory comes from activities of the brain network. To find out the cure for memory impairment in Alzheimer's disease, we need to understand how the network function is impaired," he said.

Igarashi is 2019 New Vision Research and BrightFocus Foundation award recipient. The first author on this study, Heechul Jun, is a MD/PhD student in the UCI Medical Scientist Training Program.

According to the Alzheimer's Association, there are an estimated 5.8 million Americans living with Alzheimer's disease. By 2050, that number is expected to increase to 13.8 million people. Spatial memory impairment, such as wandering behavior, is one of the most troublesome symptoms in Alzheimer's disease, and it occurs in more than 60 percent of Alzheimer's patients. Despite recent molecular and cellular findings in Alzheimer's research, it is still largely unclear how deterioration of brain circuit function causes spatial memory loss.

COLUMBUS, Ohio - Despite the political tensions between the United States and China, scientists in the two countries are working together more than ever to study the COVID-19 virus, a new study suggests.

Researchers analyzed the scientific papers that researchers around the world produced on coronaviruses before and after the arrival of COVID-19. They found that the United States and China were world leaders in the topic area before COVID-19 and they remain so now.

"The collaborations between U.S. and Chinese scientists have intensified to the exclusion of most other countries, except the U.K." said Caroline Wagner, co-author of the study and associate professor in the John Glenn College of Public Affairs at The Ohio State University.

"There may be friction between the U.S. and China on the political level, but at the scientific level we see something different - a lot of collaboration."

The study was published today (July 21, 2020) in PLOS ONE.

Wagner and her colleagues analyzed a database of scientific articles on coronavirus-related research between Jan. 1, 2018, and Jan. 1, 2020. They compared that with a similar database of research from Jan. 1 to April 23, 2020.

They examined the country where the authors of each study were based to see if there were differences in the pre- and post-COVID-19 periods.

One key finding was how quickly China ramped up its coronavirus research after COVID-19 was first identified in Wuhan, China, late in 2019, Wagner said.

"Chinese researchers produced more scientific articles on coronavirus in the first four months of 2020 - more than 1,600 articles - than in the previous 24 months combined," she said.

Chinese papers on coronavirus tended to be published in higher-impact journals after the crisis than before - one indication of better-quality research.

The study also found that China has become the world leader in funding coronavirus research since COVID-19 was discovered.

Before COVID-19, the U.S. National Institutes of Health was the leading funder of coronavirus-related research.

But since then, Chinese governmental agencies are more likely than the NIH to be acknowledged as the funding source in published studies.

Even before COVID-19, China and the United States were at the center of the global network of coronavirus research, although scientists from many countries also participated, findings showed.

But research on coronaviruses today is driven by smaller teams with researchers from fewer countries. Scientists from China, the United States and the U.K. dominate international teams.

"The network has shifted. With the urgency of the crisis, it makes sense that researchers are looking for smaller teams that can speed up the research process," Wagner said.

In separate research published in December, Wagner and colleagues found that a growing number of Chinese scientists working in the United States were returning to their homeland. That has probably influenced coronavirus research, according to Wagner.

"Now, many of those Chinese scientists who went back home may be working with their former colleagues in the United States on coronavirus studies, among many other topics," she said.

While the close connections between U.S. and Chinese scientists may be good for speeding up research, it comes with a cost.

"There is a vulnerability for scientists in other countries who are no longer part of these research networks," she said. "It is good to have researchers from all over the world working on a crisis like this."

Below please find a summary and link(s) of new coronavirus-related content published today in Annals of Internal Medicine. The summary below is not intended to substitute for the full article as a source of information. A collection of coronavirus-related content is free to the public at http://go.annals.org/coronavirus.

More than 1 in 5 U.S. homes lack sufficient space and plumbing facilities to comply with recommendations to limit household spread of COVID-19

Minority and poor families disproportionately affected

The World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) advise those who are infected with or have been exposed to COVID-19 to isolate or quarantine at home in a separate bedroom and bathroom if possible. Researchers from Case Western Reserve University and the City University of New York at Hunter College used data from the American Housing Survey to determine the feasibility of separate rooms for isolation and quarantine for housing units in the United States. They found that more than 1 in 5 U.S. homes, housing about one quarter of all Americans, lack sufficient space and plumbing facilities to comply with WHO and CDC recommendations. This proportion is particularly high among homes occupied by minority and poor individuals and among apartments.

The authors suggest that policymakers consider offering (but not requiring) persons needing isolation or quarantine the option of staying at no cost in underutilized hotels, under medical supervision, with free meal delivery and internet and telephone access. Similar strategies have been used successfully by several Asian countries and might decrease COVID-19 transmission, particularly in minority communities. Read the full text: https://www.acpjournals.org/doi/10.7326/M20-4331.

Media contacts: A PDF for this article is not yet available. Please click the link to read full text. The lead author, Ashwini R. Sehgal, MD, can be reached at sehgal@case.edu.

CORVALLIS, Ore. - The global population of the critically endangered Chinese crested tern has more than doubled thanks to a historic, decade-long collaboration among Oregon State University researchers and scientists and conservationists in China, Taiwan and Japan.

The project included OSU's Dan Roby and Don Lyons and was led by Chen Shuihua of the Zhejiang Museum of Natural History. When it began, fewer than 50 of the seabirds remained.

"The species is still far from being safe from extinction, but the population is now well over 100 adults and the future is much brighter than 10 years ago," said Roby, professor emeritus in the Department of Fisheries and Wildlife in the College of Agricultural Sciences.

Findings were published in Biological Conservation.

First described in 1863, the Chinese crested tern has been a largely mysterious species and is arguably the world's most threatened seabird.

After 21 specimens were collected in 1937 along the coast of Shandong Province, China, it wasn't until 2000 that any other sightings were confirmed: four adults and four chicks within a large colony of greater crested terns in the Matsu Islands, Taiwan.

The discovery was big news in the ornithology world, which had generally considered the Chinese crested tern to be extinct. In the years since, breeding has been confirmed in five locations: three along the Chinese coast, plus an uninhabited island off the southwestern coast of South Korea and the Penghu Islands of Taiwan.

The Chinese crested tern is among the nearly one-third of seabird species threatened with extinction because of entanglement with fishing gear, reduction in food supplies, environmental contaminants, overharvest, and predation and other disturbances by invasive species.

"Most seabirds select nesting habitat largely by social cues, whose absence may delay recovery even when there is suitable habitat," Roby said. "Since the 1970s, new techniques have been developed and implemented to enhance seabird restoration efforts. These techniques are social attraction and chick translocation and have been used in at least 171 different seabird restoration projects conducted in 16 locations in an attempt to restore 64 seabird species."

Social attraction was the strategy for the Chinese crested tern project, the first major conservation effort for seabirds in the People's Republic of China.

"Terns feed their young and provide other parental care for extended periods post-fledging, suggesting that chick translocations would likely not result in fledged young that would survive to recruit into the breeding population," Roby said.

Social attraction involves decoys, recorded bird vocalizations, mirrors, scent and artificial burrows that work in concert to lure adult seabirds to restoration sites with the goal of establishing breeding colonies.

"The most serious immediate threat to the survival of the species was the illegal harvest of eggs by fishermen," Roby said. "Beyond just taking the eggs, the disturbance associated with fishermen landing on breeding islands to collect eggs or shellfish apparently caused breeding terns to abandon their nesting sites."

The scientists believed that if Chinese crested terns could be attracted to a site with suitable nesting habitat that was continuously monitored and secured against egg harvest and other human disturbances, the species could have a chance to recover from the brink of extinction.

In 2013, a tern restoration project was launched on Tiedun Dao, an uninhabited, densely vegetated, 2.58-hectare island in the Jiushan Islands, home to a former breeding colony of Chinese crested terns that was abandoned in 2007 in the wake of illegal egg harvesting.

"It's near the original breeding island of Jiangjunmao but was not known to have been previously occupied by breeding seabirds," Roby said. "To improve the chances for Chinese crested tern success, we used social attraction techniques to try to establish a new breeding colony of greater crested terns because since their rediscovery, Chinese crested terns had only been found nesting in large colonies of greater crested terns."

In 2015, Yaqueshan, a 1-hectare island in the Wuzhishan Archipelago, was chosen as a second restoration site, where social attraction would be deployed in an attempt to stabilize the breeding colony there.

Three years later, the researchers attracted a total of 77 breeding adult Chinese crested terns to the Tiedun Dao and Yaqueshan colonies - 88.5% of the known number of breeding adults in the global population for that year.

Also in 2018, 25 Chinese crested tern chicks fledged from the Tiedun Dao and Yaqueshan colonies, or 96% of the known number of Chinese crested tern fledglings produced that year.

"Consequently, we now know for the first time in history that the global population of Chinese crested terns exceeds 100," Roby said. "The population increase from under 50 to more than 100 is a cautiously hopeful sign that this species can be brought back from the very edge of extinction. The success of this international project is a testimony to what can be accomplished when scientists from China, the U.S. and Taiwan work together toward a common conservation goal."

For the first time, scientists at the Morgridge Institute for Research have generated near atomic resolution images of a major viral protein complex responsible for replicating the RNA genome of a member of the positive-strand RNA viruses, the large class of viruses that includes coronaviruses and many other pathogens.

The results should aid development of new types of antivirals and provide mechanistic insights into the virus life cycle.

"The rapidly advancing ability to visualize such crucial structures is game changing," says Paul Ahlquist, director of the John W. and Jeanne M. Rowe Center for Virology Research at the Morgridge Institute and professor of oncology and molecular virology at the University of Wisconsin-Madison. Other authors of the study included Nuruddin Unchwaniwala, Hong Zhan, Janice Pennington, Mark Horswill and Johan den Boon.

Using an advanced technique called cryoelectron microscope (cryo-EM) tomography, Ahlquist and his team built upon their previous work, which first revealed the existence of this crown-like viral RNA replication complex.

The new research, published July 20 in the Proceedings of the National Academy of Sciences (PNAS), shows the replication crown complex at a dramatically improved resolution of approximately 8.5 angstroms, which corresponds to the spacing of a few atoms.

"Cryo-EM has recently gone through a quantum leap in its capabilities," Ahlquist says. "In this study our research group combined multiple advances to greatly improve sample preparation, image acquisition and image processing, and to map the position of specific protein domains in the complex."

The positive-strand RNA viruses addressed in this work are the largest of six genetic classes of viruses and include many important pathogens such as the Zika, dengue and chikungunya viruses, as well as coronaviruses like SARS-CoV-2, cause of the current COVID-19 pandemic.

In each positive-strand RNA virus, most of the viral genes are devoted to a single process: replicating the viral RNA genome.

"Given this massive investment of resources, viral RNA genome replication is arguably one of the most important processes in infection, and It is already a major target for virus control," Ahlquist says.

Within an infected cell, viral RNA replication occurs at modified cellular membranes, often in association with spherules, virus-induced vesicles approximately 50-100 nanometers in size. Ahlquist and his team previously showed that in each such genome replication complex, a copy of the viral RNA genome or chromosome is protected inside the spherule vesicle to function as a replication template. The replication complex repeatedly copies this archival viral RNA chromosome to produce new progeny genomes that are released through a membranous neck on the vesicle into the cytoplasm, where they are incorporated as the payload of new infectious virions.

This prior work further showed that the key viral protein that induces the replication vesicles and copies the viral RNA resides in a striking ring or crown structure that sits atop the cytoplasmic side of the spherule neck that connects with the cytoplasm.

The new higher resolution cryo-EM images and complementary results show that the crown is composed of twelve copies of the key viral RNA replication protein arranged like staves in a barrel. Additionally, the images revealed zipper-like interactions that act like hoops on a barrel to join adjacent segments together to form the ring-like crown. These zippering interactions correspond well with multimerizing interactions that the Ahlquist group has previously mapped in this protein.

The viral RNA replication protein that forms the crown is an extremely large, multi-domain, multi-functional protein, nearly 1000 amino acids in size. This protein contains RNA polymerase and RNA capping domains-- two enzymatic domains that are conserved across numerous positive-strand RNA viruses for synthesizing new viral genome copies--plus other domains for multimerizing, binding membranes and other functions.

How these domains are physically organized in the crown structure is one of the most important issues for understanding how the replication complex functions, and was one of several strong motivations for defining the high-resolution crown structure.

Using an approach that combined a genetically engineered, site-specific tag with labeling by nanoscale gold particles visible in cryo-EM, the researchers found that the C-terminal polymerase end of the viral RNA replication protein is positioned at the apex of the crown, leaving the N-terminal capping domain at the bottom of the structure to interact with the membrane.

This apical position of the polymerase has important mechanistic implications for early steps in the replication process that recruit the starting viral RNA template into the complex and form the replication vesicle, as well as for later steps in which the template is copied to make new progeny genomes to be packaged into infectious virus particles. These results provide a strong foundation for further experiments to define the replication complex structure and function at even higher levels.

"We hope to continue to improve the RNA replication complex crown structure to provide additional important refinements in future," Ahlquist says. "We also hope to address growing indications from our work that conformational changes in these proteins are critical to their multiple functions."

"Such advances will reveal in increasing detail how these complexes assemble and operate, and thus how they might be best attacked," he adds. "These insights should provide the basis for novel, stronger antiviral mechanisms."

DURHAM, N.C. -- A chance mutation that led to spinal defects in a zebrafish has opened a little window into our own fishy past.

Rising fifth-year Duke graduate student Brianna Peskin, who started the project during her first-year rotation in Michel Bagnat's cell biology lab and "kinda kept coming back to it," was merely trying to figure out why this one mutation led to developmental issues in a zebrafish's spine.

What she found is that embryos of the mutant fish have a single-letter change in their DNA that alters the way they build the bones and other structures that make up their spine, leaving them with a shorter body and a tortured looking spine that contains clefts dividing their vertebrae in half.

The mutant fish are named spondo, short for spondylos which is Greek for spine, and also a reference to dispondyly, a condition where each vertebra has two bony arches not one.

But that's not the end of the story.

When Bagnat's research colleague Matthew Harris of Harvard Medical School showed some pictures of the mutant fish spine to a colleague in fish paleontology, Gloria Arratia at the University of Kansas, she immediately spotted that the mutants look a lot like fossil specimens of ancestral fish whose style of spine has gone out of fashion in most living fishes.

"And then they both got really excited because they were noticing these similarities between ancestral fossil specimens and our mutant," Peskin said.

The tiny mutation showed that both recipes for spine development are still to be found in the fish genome.

In the bony fish, known as teleosts, building the spine relies on a tube-like structure running the length of the developing embryo called the notochord. The notochord sets up the patterns that lead to articulated bones and cartilage in the developing spine by sending chemical signals that attract different molecules and cell types to different regions - bone parts here, cartilage parts there.

Human embryos start with a notochord too, but it doesn't pattern the bony vertebrae the way it does in teleosts; it ends up building the cartilage pucks between the bones, the intervertebral discs.

The gene that is mutated in spondo fish is unique to teleosts and the mutant fish's notochord doesn't set up the patterning the way it does in other fish. Rather, its patterning reverts to an ancestral form. So, this tiny difference in DNA may be where land animals like us parted company with our fish ancestors a very, very, very long time ago.

While the zebrafish (Danio rerio) has become a laboratory workhorse for all sorts of interesting studies, its usefulness as a model of human spine development has been in doubt because they grow their backbones differently.

But not anymore. The research team's new paper, which appears July 20 in Current Biology, shows that the difference between the way teleosts and land animals grow their spines comes down to signaling from the notochord, which was revealed by this single-letter change in the DNA.

And that, in turn, gives them the insight to study human spinal defects with these fast-growing, translucent fish, because the spondo mutants are sensitive to factors known to cause congenital scoliosis in human children, a curvature of the spine.

"This work not only gave us a glimpse into spine evolution, but also made us understand how the spine is put together in mammals," said Bagnat, who is an associate professor of Cell Biology in the Duke School of Medicine. "Moving forward, we'll be able to use mutations like spondo to unravel the complex genetics of scoliosis and other spine defects that are rooted in the biology of the notochord and have been intractable until now."

"Overall, what this study means is that notochord signals are key to establishing the spine. These signals have changed over evolutionary time and account for differences that exist in spine patterning strategies across vertebrates," Peskin said. "So we are all fish after all."

Argonne researchers quantify how to reduce emissions by farms changing their practices and adopting novel technologies.

Currently, the agriculture sector contributes significantly to the greenhouse gas (GHG) emissions in the United States, accounting for nine percent of the nation’s overall GHG emissions.  The practices that grain farmers use to produce their crops — managing fertility, tillage practice and crop rotations — influence the overall carbon footprint of U.S. agriculture.  By using sustainable practices, farmers could substantially reduce their carbon footprint and become a vital partner to the biofuel industry in its efforts to produce the lowest carbon fuels possible.

“This work is unique since we provide a complete quantification of carbon intensity (CI) for the cradle-to-farm-gate activities by conducting scenario-based analysis for selected farming practices that uses regionalized life cycle inventory data and a spatially explicit soil organic carbon modeling tool.” — Xinyu Liu, postdoctoral appointee

A recent study by researchers in the Energy Systems division at the U.S. Department of Energy’s (DOE’s) Argonne National Laboratory quantified how much farms might reduce emissions by changing their practices and adopting novel technologies. Xinyu Liu, a postdoctoral appointee, wrote about the pivotal research in Environmental Research Letters, published on July 20. She collaborated with Hoyoung Kwon, principal environmental scientist, and Michael Wang, manager of systems assessments, all of Argonne; and Daniel Northrup, a former contractor to DOE’s Advanced Research Projects Agency-Energy (ARPA-E), now with Benson Hill, a crop improvement company in St. Louis.

“This work is unique since we have quantified how the carbon intensity (CI) of corn feedstock would change with a wide range of farming practices and different farming regions. Besides the GHG emissions from manufacturing and applying farming inputs, we have also considered the impacts from soil organic carbon,” said Liu.

The research focused on the corn belt of Illinois, Indiana, Iowa, Minnesota, Nebraska, Ohio, Michigan, South Dakota and Wisconsin and showed how different farming practices affect feedstock CI. Sustainable farming professionals could implement lower CI practices, such as adopting conservation tillage, reducing nitrogen fertilizer use, and implementing cover crops, to reduce their carbon footprint, which could improve farm efficiency and help the environment. 

The Argonne team’s research has historically focused on the CI of biofuels, which is determined via the life-cycle analysis technique to account for the energy/material uses and emissions as feedstock is produced and converted to fuel. The technique is used by California Air Resources Board’s Low Carbon Fuel Standard (LCFS) program to calculate biofuel CI. Farms that reduce biofuel CI can generate LCFS credit, which has monetary value for biofuel producers and potentially for farmers supplying the lower carbon feedstocks. Biofuel producers can improve their overall CI score by rewarding feedstocks with lower CI, thereby further reducing the total CI of biofuels.

Currently, LCFS allows applications from individual biofuel conversion facilities, which resulted in significant investment and innovation in production processes to reduce CI. However, the board scores the CI for feedstocks based on a national average, regardless of the significant field-level variations in CI based on production practice. The Argonne work determines the source of the variation and suggests that a change in farming practice would lead to major emission reductions if implemented broadly.

“We conducted scenario-based CI analysis of corn ethanol, coupled with regionalized inventory data, for various farming practices to manage corn fields and identified key parameters affecting cradle-to-farm-gate GHG emissions,” said Liu. “The results demonstrate large spatial variations in CI for corn, and eventually for ethanol, due to farm input uses and land management practices.”

In addition to responding to electrical and chemical stimuli, many of the body's neural cells can also respond to mechanical effects, such as pressure or vibration. But these responses have been more difficult for researchers to study, because there has been no easily controllable method for inducing such mechanical stimulation of the cells. Now, researchers at MIT and elsewhere have found a new method for doing just that.

The finding might offer a step toward new kinds of therapeutic treatments, similar to electrically based neurostimulation that has been used to treat Parkinson's disease and other conditions. Unlike those systems, which require an external wire connection, the new system would be completely contact-free after an initial injection of particles, and could be reactivated at will through an externally applied magnetic field.

The finding is reported in the journal ACS Nano, in a paper by former MIT postdoc Danijela Gregurec, Alexander Senko PhD '19, Associate Professor Polina Anikeeva, and nine others at MIT, at Boston's Brigham and Women's Hospital, and in Spain.

The new method opens a new pathway for the stimulation of nerve cells within the body, which has so far almost entirely relied on either chemical pathways, through the use of pharmaceuticals, or on electrical pathways, which require invasive wires to deliver voltage into the body. This mechanical stimulation, which activates entirely different signaling pathways within the neurons themselves, could provide a significant area of study, the researchers say.

"An interesting thing about the nervous system is that neurons can actually detect forces," Senko says. "That's how your sense of touch works, and also your sense of hearing and balance." The team targeted a particular group of neurons within a structure known as the dorsal root ganglion, which forms an interface between the central and peripheral nervous systems, because these cells are particularly sensitive to mechanical forces.

The applications of the technique could be similar to those being developed in the field of bioelectronic medicines, Senko says, but those require electrodes that are typically much bigger and stiffer than the neurons being stimulated, limiting their precision and sometimes damaging cells.

The key to the new process was developing minuscule discs with an unusual magnetic property, which can cause them to start fluttering when subjected to a certain kind of varying magnetic field. Though the particles themselves are only 100 or so nanometers across, roughly a hundredth of the size of the neurons they are trying to stimulate, they can be made and injected in great quantities, so that collectively their effect is strong enough to activate the cell's pressure receptors. "We made nanoparticles that actually produce forces that cells can detect and respond to," Senko says.

Anikeeva says that conventional magnetic nanoparticles would have required impractically large magnetic fields to be activated, so finding materials that could provide sufficient force with just moderate magnetic activation was "a very hard problem." The solution proved to be a new kind of magnetic nanodiscs.

These discs, which are hundreds of nanometers in diameter, contain a vortex configuration of atomic spins when there are no external magnetic fields applied. This makes the particles behave as if they were not magnetic at all, making them exceptionally stable in solutions. When these discs are subjected to a very weak varying magnetic field of a few millitesla, with a low frequency of just several hertz, they switch to a state where the internal spins are all aligned in the disc plane. This allows these nanodiscs to act as levers -- wiggling up and down with the direction of the field.

Anikeeva, who is an associate professor in the departments of Materials Science and Engineering and Brain and Cognitive Sciences, says this work combines several disciplines, including new chemistry that led to development of these nanodiscs, along with electromagnetic effects and work on the biology of neurostimulation.

The team first considered using particles of a magnetic metal alloy that could provide the necessary forces, but these were not biocompatible materials, and they were prohibitively expensive. The researchers found a way to use particles made from hematite, a benign iron oxide, which can form the required disc shapes. The hematite was then converted into magnetite, which has the magnetic properties they needed and is known to be benign in the body. This chemical transformation from hematite to magnetite dramatically turns a blood-red tube of particles to jet black.

"We had to confirm that these particles indeed supported this really unusual spin state, this vortex," Gregurec says. They first tried out the newly developed nanoparticles and proved, using holographic imaging systems provided by colleagues in Spain, that the particles really did react as expected, providing the necessary forces to elicit responses from neurons. The results came in late December and "everyone thought that was a Christmas present," Anikeeva recalls, "when we got our first holograms, and we could really see that what we have theoretically predicted and chemically suspected actually was physically true."

The work is still in its infancy, she says. "This is a very first demonstration that it is possible to use these particles to transduce large forces to membranes of neurons in order to stimulate them."

She adds "that opens an entire field of possibilities. ... This means that anywhere in the nervous system where cells are sensitive to mechanical forces, and that's essentially any organ, we can now modulate the function of that organ." That brings science a step closer, she says, to the goal of bioelectronic medicine that can provide stimulation at the level of individual organs or parts of the body, without the need for drugs or electrodes.