Culture

Whether white blood cells can be found in the brain has been controversial, and what they might be doing used to be complete mystery. In a seminal study published in Cell, an international team of scientists led by Prof. Adrian Liston (VIB-KU Leuven, Belgium & Babraham Institute, UK) describe a population of specialized brain-resident immune cells discovered in the mouse and human brain, and show that the presence of white blood cells is essential for normal brain development in mice.

Like a highly fortified headquarters, our brain enjoys special protection from what is circulating in the rest of our body through the blood-brain barrier. This highly selective border makes sure that passage from the blood to the brain is tightly regulated.

The blood-brain barrier also separates the brain from our body's immune system, which is why it has its own resident immune cells, called microglia, which trigger inflammation and tissue repair. Microglia arrive in the brain during embryonic development, and later on, the population becomes self-renewing.

Yet, white blood cells--which are part of our immune system--have been found to play a role in different brain diseases, including multiple sclerosis, Alzheimer's and Parkinson's disease or stroke. Whether or not white blood cells can be found in healthy brains as well, and what they might be doing there, has been subject of intense debate. An interdisciplinary team of scientists led by Prof. Adrian Liston (VIB-KU Leuven, Babraham Institute) set out to find the answers.

White blood cells in the brain

"A misconception about white blood cells comes from their name," explains Dr. Oliver Burton (Babraham Institute). "These 'immune cells' are not just present in the blood. They are constantly circulating around our body and enter all of our organs, including--as it turns out--the brain. We are only just starting to discover what white blood cells do when they leave the blood. This research indicates that they act as a go-between, transferring information from the rest of the body to the brain environment"

The team quantified and characterized a small but distinct population of brain-resident T helper cells present in mouse and human brain tissue. T cells are a specific type of white blood cells specialized for scanning cell surfaces for evidence of infection and triggering an appropriate immune response. New technologies allowed the researchers to study the cells in great detail, including the processes by which circulating T cells entered the brain and began to develop the features of brain-resident T cells.

Dr. Carlos Roca (Babraham Institute): "Science is becoming increasingly multidisciplinary. Here, we didn't just bring in expertise from immunology, neuroscience and microbiology, but also from computer science and applied mathematics. New approaches for data analysis allow us to reach a much deeper level of understanding of the biology of the white blood cells we found in the brain."

An evolutionary role

When T helper cells are absent from the brain, the scientists found that the resident immune cells - microglia - in the mouse brain remained suspended between a fetal and adult developmental state. Observationally, mice lacking brain T cells showed multiple changes in their behavior. The analysis points to an important role for brain-resident T cells in brain development. If T cells participate in normal brain development in mice, could the same be true in humans?

"In mice, the wave of entry of immune cells at birth triggers a switch in brain development," says Liston. "Humans have a much longer gestation than mice though, and we don't know about the timing of immune cell entry into the brain. Does this occur before birth? Is it delayed until after birth? Did a change in timing of entry contribute to the evolution of enhanced cognitive capacity in humans?"

The findings open up a whole new range of questions about how the brain and our immune system interact. "It has been really exciting to work on this project. We are learning so much about how our immune system can alter our brain, and how our brain modifies our immune system. The two are far more interconnected than we previously thought," says Dr. Emanuela Pasciuto (VIB-KU Leuven).

The study also brings in a connection with the gut microbiome, says Liston: "There are now multiple links between the bacteria in our gut and different neurological conditions, but without any convincing explanations for what connects them. We show that white blood cells are modified by gut bacteria, and then take that information with them into the brain. This could be the route by which our gut microbiome influences the brain."

Taken together, the results contribute towards the increasing recognition of the role of immune cells in the brain and shed new light on its involvement in a range of neurological diseases.

In human reproduction, the genes of the mother and father are combined and mixed in countless variations. Their offspring can differ significantly from one another. However, bacteria multiply by simple cell division, so that the two daughter cells carry the same genetic material as the mother cell. A research team led by Dr. Simon Heilbronner from the Interfaculty Institute for Microbiology and Infection Medicine at the University of Tübingen and the German Center for Infection Research has recently discovered how infectious bacteria can produce genetic variants among sibling cells. Certain sections of the genetic material are doubled or multiplied. This gives the bacteria new capabilities that make it possible for them to influence the immune system of the host in their favour. The results of this study, published in the journal Nature Communications, provide important information on how pathogens develop and adapt in their battle against the human immune system.

If bacteria multiply by simple division, clones are created. The cells all have the same genetic composition and the same properties. "However, the bacteria must remain flexible, because their envi-ronmental conditions are constantly changing. This is particularly true of pathogens that are strug-gling with the human immune system and need to deal with any antibiotics that may be administered if they are to survive," says Dr. Heilbronner. His team has shown how the bacterial pathogen Staphy-lococcus aureus causes inflammation, and how variants develop if gene exchange with other bacterial communities is not possible.

Accordion genes expand the possibilities

"We found that in Staphylococcus aureus, some parts of the genetic material may be available in the form of several exact copies. The number of such copies varies greatly between closely related bacteria," according to Dr. Heilbronner. Genetic mechanisms during cell division result in duplicates being able to multiply in the genetic material of the bacteria. "They can expand and shorten again, like an accordion. This results in a variety of daughter cells with different properties in the course of a few generations." Expanded genetic material leads to stronger protein production by the bacterial cell. "For example, if these proteins transport antibiotics out of the cell or influence the immune system, the bacteria may improve their chances of survival," according to the researcher.

The Tübingen researchers have now shown that such genetic processes occur frequently in Staphylococcus aureus. "Administration of antibiotics can strengthen them. The pathogens now have better ways to respond to human immune cells." The team believes that these processes are important in the evolution of pathogens that are successful and therefore dangerous for humans. The team's findings will be used in the development of new forms of treatment by the Tübingen Cluster of Excellence "Controlling Microbes to Fight Infections".

Our planet's climate system is complex. Different components, like atmosphere, ocean, sea and land ice influence each other and cause natural climate variations on a range of timescales from months to decades. Particularly for the long timescales, the ocean plays an essential role. In a new study published today, a research team led by GEOMAR Helmholtz Centre for Ocean Research Kiel investigates the possibility of utilizing the wind field to predict the North Atlantic surface temperature variations several years into the future. Such variations of the sea surface temperature also have the potential to influence the climate in Europe.

'Predictions of climate variations are possible for certain regions on Earth', says Dr. Annika Reintges, scientist at GEOMAR and lead author of the study, that is now published in Geophysical Research Letters. One example is the, every couple of years, recurring El Niño phenomenon in the tropical Pacific, that can be predicted a few months ahead. 'Our study focuses on longer timescales, in a region where natural variability on decadal timescales is much larger than in the tropics', Reintges continues.

Are such predictions possible? What are the requirements and which kind of information can be provided by such predictions? These questions were addressed by a research team of GEOMAR and of the Leibniz Institute for Baltic Research Warnemünde. 'Indeed, long-term predictions are possible. This is enabled by the slow, over several years, varying oceanic processes', explains Dr. Reintges. The difficulty is that ocean observations--that are necessary to start the model computation--must be as accurate as possible. 'However, ocean observations, in particular below the surface, are limited in quantity and quality' says Reintges.

'For the predictions in our study, we did not use any ocean observations. Instead, we create oceanic start values, by prescribing only observed variations in the wind at the sea surface. After some time, this brings the ocean of the model into a state that is sufficiently realistic to start successful predictions for even more than 7 years into the future', explains the author of the study.

The research team suggests the following mechanism to explain this fact: The winds cause a change in the ocean circulation. By this, a certain region in the North Atlantic accumulates an anomalous amount of heat. This heat is then transported towards Northeast over a time of several years. This finally results in a warming of the sea surface in the eastern North Atlantic, in response to the winds many years before.

'Previous studies have shown that the sea surface temperature of the North Atlantic can influence the European climate. Therefore, such predictions of the North Atlantic surface temperature, covering several years are of great importance also for decision makers in politics, economy, society, and also for the public', Reintges concludes.

The brains of people living with Alzheimer's are riddled with plaques: protein aggregates consisting mainly of amyloid beta. Despite decades of research, the real contribution of these plaques to the disease process is still not clear. A research team led by Bart De Strooper and Mark Fiers at the VIB-KU Leuven Center for Brain & Disease Research in Leuven, Belgium used pioneering technologies to study in detail what happens in brain cells in the direct vicinity of plaques. Their findings, published in the prestigious journal Cell, show how different cell types in the brain work together to mount a complex response to amyloid plaques which is likely protective at first, but later on damaging to the brain.

The role of amyloid plaques in Alzheimer's disease has puzzled scientists ever since Alois Alzheimer first described them in the brain of a woman with young onset dementia. Now, over a century later, we have learned a lot about the molecular processes that lead to neurodegeneration and subsequent memory loss, but the relationship between the plaques and the disease process in the brain is still ambiguous.

"Amyloid plaques might act as a trigger or as a driver of disease, and the accumulation of amyloid beta in the brain likely initiates a complex multicellular neurodegenerative process," says professor Bart De Strooper (VIB-KU Leuven). His team set out to map the molecular changes that take place in cells near amyloid plaques.

"We used the latest technologies to analyze genome-wide transcriptomic changes induced by amyloid plaques in hundreds of small tissue domains," explains Mark Fiers, co-lead on the study. "In this way, we could generate a large data set of transcriptional changes that occur in response to increasing amyloid pathology, both in mouse and human brains."

Two co-expression networks

"We focused on the transcriptomic changes in the immediate neighborhood of the amyloid plaques, with a 50 micrometer perimeter," explains Wei-Ting Chen, a postdoc in De Strooper's team. In a well-studied genetic mouse model showing amyloid pathology, the scientists identified two novel gene co-expression networks that appeared highly sensitive to amyloid beta deposition.

Chen: "With increasing amyloid beta deposition, a multicellular co-expressed gene response was established encompassing no less than 57 plaque-induced genes." These genes were mainly expressed in astroglia and microglia, two types of supportive brain cells, and were not co-expressed in the absence of amyloid plaques.

"We also found interesting alterations in a second network, expressed mainly by another type of cells, namely oligodendrocytes," adds Ashley Lu, PhD student in the team. "This gene network was activated under mild amyloid stress but depleted in microenvironments with high amyloid accumulation."

"Many of the genes in both networks show similar alterations in human brain samples, strengthening our observations," adds Fiers.

Targeting plaques

"Our data demonstrate that amyloid plaques are not innocent bystanders of the disease, as has been sometimes suggested, but in fact induce a strong and coordinated response of all surrounding cell types," says De Strooper.

"Further work is needed to understand whether, and when, removal of amyloid plaques--for instance by antibody therapy currently in development to treat amyloid plaques--is sufficient to reverse these ongoing cellular processes."

Whether antibody binding to amyloid plaques could also modulate these glial responses remains to be determined. "It would in any case complicate the interpretation of the outcome of clinical trials as these cellular effects might be different between different antibodies," adds De Strooper.

More than 600,000 people worldwide have fallen victim to the lung disease COVID-19 so far, which is caused by the SARS coronavirus-2 (SARS-CoV-2). In order to obtain an effective therapy for COVID-19 as quickly as possible, drugs that are being used to treat other diseases are currently being repurposed for COVID-19 treatment. The Infection Biology Unit of the German Primate Center (DPZ) - Leibniz Institute for Primate Research in Göttingen, together with colleagues at the Charité in Berlin, was able to show that the malaria drug chloroquine, which has been demonstrated to inhibit the SARS-CoV-2 infection of African green monkey kidney cells, is not able to prevent infection of human lung cells with the novel coronavirus. Chloroquine is therefore unlikely to prevent the spread of the virus in the lung and should not be used for the treatment of COVID-19 (Nature).

It is known that SARS-CoV-2 is able to use two different routes to enter cells. First, after attaching to the cells, the virus can fuse directly with the plasma membrane and introduce its genetic material into the host cell. Second, it can enter the interior of the cells upon uptake via transport structures, called endosomes. In both cases, the attachment of the virus to the cells and subsequent entry is mediated by the viral spike protein. For this purpose, the spike protein must be activated either by the enzyme cathepsin L (in endosomes) or by the enzyme TMPRSS2 (on the cell surface). Depending on the cell type, both enzymes or only one of them can be available for activation.

Chloroquine is a drug that is used to treat malaria. Since chloroquine inhibits the infection of monkey kidney cells with SARS-CoV-2, chloroquine has been tested in clinical trials as a possible candidate for the treatment of COVID-19. However, how chloroquine inhibits the infection of monkey kidney cells was not clear. The current study shows that chloroquine inhibits viral entry into these cells, most likely by blocking cathepsin L activity. This raised the question whether chloroquine also inhibits the infection of lung cells that are known to produce TMPRSS2 but only a small amount of cathepsin L.

The study shows that chloroquine does not prevent SARS-CoV-2 entry into human lung cells and subsequent spread of the virus in these cells. "In this study, we show that the antiviral activity of chloroquine is cell type-specific and that chloroquine does not block the infection of lung cells. This means that in future tests of potential COVID-19 drugs, care should be taken that relevant cell lines are used for the investigations in order not to waste unnecessary time and resources in our search for effective COVID-19 therapeutics," says Stefan Pöhlmann, head of the Infection Biology Unit at DPZ, adding: "COVID-19 is primarily caused by the infection of lung cells, for this reason these cells should be given priority in efficacy tests."

University of Virginia School of Medicine scientists are harnessing the mind-bending potential of quantum computers to help us understand genetic diseases - even before quantum computers are a thing.

UVA's Stefan Bekiranov, PhD, and colleagues have developed an algorithm to allow researchers to study genetic diseases using quantum computers, once there are much more powerful quantum computers to run it. The algorithm, a complex set of operating instructions, will help advance quantum computing algorithm development and could advance the field of genetic research one day.

Quantum computers are still in their infancy. But when they come into their own, possibly within a decade, they may offer computing power on a scale unimaginable using traditional computers.

"We developed and implemented a genetic sample classification algorithm that is fundamental to the field of machine learning on a quantum computer in a very natural way using the inherent strengths of quantum computers," Bekiranov said. "This is certainly the first published quantum computer study funded by the National Institute of Mental Health and may be the first study using a so-called universal quantum computer funded by the National Institutes of Health."

Quantum Computing Basics

Traditional computer programs are built on 1s and 0s, either-or. But quantum computers take advantage of a freaky fundamental of quantum physics: Something can be and not be at the same time. Rather than 1 or 0, the answer, from a quantum computer's perspective, is both, simultaneously. That allows the computer to consider vastly more possibilities, all at once.

The challenge is that the technology is, to put it lightly, technically demanding. Many quantum computers have to be kept at near absolute zero, the equivalent of more than 450 degrees below zero on the Fahrenheit scale. Even then, the movement of molecules surrounding the quantum computing elements can mess up the calculations, so algorithms not only have to contain instructions for what to do, but for how to compensate when errors creep in.

"Our goal was to develop a quantum classifier that we could implement on an actual IBM quantum computer. But the major quantum machine learning papers in the field were highly theoretical and required hardware that didn't exist. We finally found papers from Dr. Maria Schuld, who is a pioneer in developing implementable, near-term, quantum machine learning algorithms. Our classifier builds on those developed by Dr. Schuld," Bekiranov said. "Once we started testing the classifier on the IBM system, we quickly discovered its current limitations and could only implement a vastly oversimplified, or 'toy,' problem successfully, for now."

Classifying Genomic Data

The new algorithm essentially classifies genomic data. It can determine if a test sample comes from a disease or control sample exponentially faster than a conventional computer. For example, if they used all four building blocks of DNA (A, G, C or T) for the classification, a conventional computer would execute 3 billion operations to classify the sample. The new quantum algorithm would need only 32.

That will help scientists sort through the vast amount of data required for genetic research. But it's also proof-of-concept of the usefulness of the technology for such research.

Bekiranov and collaborator Kunal Kathuria, PhD, were able to create the algorithm because they were trained in quantum physics, a field that even scientists often find opaque. Such algorithms are more likely to emerge from physics or computer science departments than medical schools. (Both Bekiranov and Kathuria conducted the study in the School of Medicine's Department of Biochemistry and Molecular Genetics. Kathuria is currently at the Lieber Institute for Brain Development.)

Because of the researchers' particular set of skills, officials at the National Institutes of Health's National Institute of Mental Health supported them in taking on the challenging project. Bekiranov and Kathuria hope what they have developed will be a great benefit to quantum computing and, eventually, human health.

"Relatively small-scale quantum computers that can solve toy problems are in existence now," Bekiranov said. "The challenges of developing a powerful universal quantum computer are immense. Along with steady progress, it will take multiple scientific breakthroughs. But time and again, experimental and theoretical physicists, working together, have risen to these challenges. If and when they develop a powerful universal quantum computer, I believe it will revolutionize computation and be regarded as one of greatest scientific and engineering achievements of humankind."

One in every 500 babies is born with a condition called ureteropelvic junction obstruction (UPJO), an obstruction of the ureter that prevents urine from flowing from one or both of the kidneys into the bladder. Usually diagnosed prenatally, UPJO can cause urinary tract infections and poor growth for infants; it can also result in chronic kidney disease and an increased risk for cardiovascular disease in later life.

A group of researchers at UConn Health, the University of Connecticut, Children's Hospital and Medical Center of Omaha, and Kravis Children's Hospital at the Mount Sinai Health System have developed a panel of five biomarker proteins for the diagnosis and monitoring of UPJO in infants and toddlers. They describe this non-invasive, cost-effective method of detecting and monitoring UPJO in a recent issue of the Journal of Pediatric Urology, and are hopeful this technology could be a breakthrough for those suffering from UPJO.

"Normally, the kidneys filter blood and remove waste in the form of urine that drains from the kidneys through the ureters to the bladder," explains Linda Shapiro, co-author of the study and UConn Health professor of cell biology and director of the Center for Vascular Biology. "For patients with UPJO, the infant is born with a block in the ureter that causes a backup of urine in the kidney resulting in distension, stretching, and damage to the kidney."

UPJO is a model system for other congenital anomalies of the urinary tract, the most common cause of renal failure in children.

Most of the time, kidney enlargement, or hydronephrosis, due to UPJO is detectable in the womb by ultrasound. Sometimes UPJO will resolve itself naturally, while other children require surgery. Urologists engage in a "watchful waiting" approach to determine if a child must undergo surgery. Unfortunately, during this period children may suffer irreversible damage to their developing kidneys. This biomarker panel could potentially be used to determine the severity of the damage resulting from obstruction and whether surgery is necessary.

Many molecules have been identified as biomarkers, but there is yet to be a "gold standard" for this condition, emphasizing an immediate need to develop noninvasive biomarkers to detect the severity of damage wrought by UPJO.

This study assessed urine samples from 22 males under two years old who were on their way to surgery with severe obstruction and samples from a group of 22 control patients who did not have UPJO. The researchers chose males for this pilot study as males are significantly more likely to have UPJO than females.

The researchers began by identifying 171 proteins detectable in the patients with UPJO but undetected in a majority of the controls. Of those 171, only 50 were present in more than half of the UPJO samples. These 50 were ranked using a diagnostic odds analysis to determine the top 10 that may be the most useful biomarkers for this condition. Five of those 10 proteins were found to be present at significantly higher concentrations in patients with UPJO than the control samples, thus creating the panel.

"If it works out well, we'd love to see it transition to the clinic," says Shapiro. "This work can potentially help patients, rather than being just another line in a textbook."

This invention, for which the researchers have filed a patent application, could potentially replace current diagnostic approaches which include expensive, invasive techniques.

This process is non-invasive and painless for the infants. Rather than the current standard of care that entails injecting babies with radiotracers or putting them through other painful procedures, this panel allows practitioners to simply test urine released directly from the bladder.

By using a panel of five biomarkers, the researchers took a probability approach. If a sample had only one or two of the markers, this did not necessarily indicate UPJO damage, but if the sample contained four or five of the markers, the probability they had UPJO was much higher.

Other current methods use a cutoff approach looking at if a patient has a certain concentration of a biomarker. But this approach is inconsistent across patient groups and it can be difficult to determine what a meaningful cutoff point is.

"Some control patients have one or two of these markers but not as many as the obstructed patients," author Charan Kumar Devarakonda, a postdoctoral fellow at UConn Health, says. "We're not testing for only one protein but rather a panel of proteins."

Tel Aviv University researchers have found that the short time period around tumor removal surgery (the weeks before and after surgery) is critical for the prevention of metastases development, which develop when the body is under stress.

According to the researchers, patients require immunotherapeutic treatment as well as treatment to reduce inflammation and physical and psychological stress. The research was conducted by Prof. Shamgar Ben-Eliyahu of TAU's School of Psychological Sciences and Sagol School of Neuroscience and Prof. Oded Zmora from Assaf Harofe Medical Center.

The research was published in the journal Cancer on June 13.

Immunotherapeutic treatment is a medical treatment that activates the immune system. One such treatment is the injection of substances with similar receptors to those of viruses and bacteria into the patient's body. The immune system recognizes them as a threat and activates itself, thus preventing a metastatic disease.

Prof. Ben-Eliyahu explains that surgery for the removal of the primary tumor is a mainstay in cancer treatment. But the risk of developing metastases after surgery is estimated at 10% among breast cancer patients, at 20%-40% among colorectal cancer patients, and at 80% among pancreatic cancer patients.

According to Prof. Ben-Eliyahu, when the body is under physiological or psychological stress such as a surgery, groups of hormones called prostaglandin and catecholamine are produced in large quantities. These hormones suppress the immune system cells' activity and indirectly increase the development of metastases. Additionally, these hormones help tumor cells left after the surgery to develop into life-threatening metastases. Exposure to those hormones causes tumor tissues to become more aggressive and metastatic.

"Medical and immunotherapeutic intervention to reduce psychological and physiological stress and activate the immune system in the critical period before and after the surgery can prevent development of metastases, which will be discovered months or years later," Prof. Ben-Eliyahu says.

Prof. Ben-Eliyahu adds that anti-metastatic treatment today skips the critical period around the surgery, leaving the medical staff to face the consequences of treating progressive and resistant metastatic processes, which are much harder to stop. Prof. Ben-Eliyahu's research contradicts the assumption, widespread in the medical community, that immunotherapeutic treatment for cancer patients in the month before and after the surgery is not recommended.

KAIST researchers used atomic force microscopy to quantitatively evaluate how acidic and sugary drinks affect human tooth enamel at the nanoscale level. This novel approach is useful for measuring mechanical and morphological changes that occur over time during enamel erosion induced by beverages.

Enamel is the hard-white substance that forms the outer part of a tooth. It is the hardest substance in the human body, even stronger than bone. Its resilient surface is 96 percent mineral, the highest percentage of any body tissue, making it durable and damage-resistant. The enamel acts as a barrier to protect the soft inner layers of the tooth, but can become susceptible to degradation by acids and sugars.

Enamel erosion occurs when the tooth enamel is overexposed to excessive consumption of acidic and sugary food and drinks. The loss of enamel, if left untreated, can lead to various tooth conditions including stains, fractures, sensitivity, and translucence. Once tooth enamel is damaged, it cannot be brought back. Therefore, thorough studies on how enamel erosion starts and develops, especially at the initial stages, are of high scientific and clinical relevance for dental health maintenance.

A research team led by Professor Seungbum Hong from the Department of Materials Science and Engineering at KAIST reported a new method of applying atomic force microscopy (AFM) techniques to study the nanoscale characterization of this early stage of enamel erosion. This study was introduced in the Journal of the Mechanical Behavior of Biomedical Materials (JMBBM) on June 29.

AFM is a very-high-resolution type of scanning probe microscopy (SPM), with demonstrated resolution on the order of fractions of a nanometer (nm) that is equal to one billionth of a meter. AFM generates images by scanning a small cantilever over the surface of a sample, and this can precisely measure the structure and mechanical properties of the sample, such as surface roughness and elastic modulus.

The co-lead authors of the study, Dr. Panpan Li and Dr. Chungik Oh, chose three commercially available popular beverages, Coca-Cola®, Sprite®, and Minute Maid® orange juice, and immersed tooth enamel in these drinks over time to analyze their impacts on human teeth and monitor the etching process on tooth enamel.

Five healthy human molars were obtained from volunteers between age 20 and 35 who visited the KAIST Clinic. After extraction, the teeth were preserved in distilled water before the experiment. The drinks were purchased and opened right before the immersion experiment, and the team utilized AFM to measure the surface topography and elastic modulus map.

The researchers observed that the surface roughness of the tooth enamel increased significantly as the immersion time increased, while the elastic modulus of the enamel surface decreased drastically. It was demonstrated that the enamel surface roughened five times more when it was immersed in beverages for 10 minutes, and that the elastic modulus of tooth enamel was five times lower after five minutes in the drinks.

Additionally, the research team found preferential etching in scratched tooth enamel. Brushing your teeth too hard and toothpastes with polishing particles that are advertised to remove dental biofilms can cause scratches on the enamel surface, which can be preferential sites for etching, the study revealed.

Professor Hong said, "Our study shows that AFM is a suitable technique to characterize variations in the morphology and mechanical properties of dental erosion quantitatively at the nanoscale level."

This work was supported by the National Research Foundation (NRF), the Ministry of Science and ICT (MSIT), and the KUSTAR-KAIST Institute of Korea.

A dentist at the KAIST Clinic, Dr. Suebean Cho, Dr. Sangmin Shin from the Smile Well Dental, and Professor Kack-Kyun Kim at the Seoul National University School of Dentistry also collaborated in this project.

The endoplasmic reticulum (ER) is an important part of eukaryotic cells (the type of cells that make up every living thing other than bacteria or viruses, including humans). They are a mass of tubes connected to the nucleus of the cell; the production of both proteins and lipids occur in the networks of the ER. For this organelle to properly function, cells routinely degrade portions of the ER so that it can be renewed. This process is called ER autophagy, or ER-phagy, where a structure called an "isolation membrane" expands and closes up to form an "autophagosome." The closure isolates various cellular materials including the ER within the autophagosome, which then transports the waste away for degradation.

While this process can be random, scientists have uncovered "autophagy receptors" that bind specifically to certain targets and interact with a group of proteins called Atg8, located on the isolation membrane. This interaction allows cells to target specific parts for degradation. In yeast, an organism commonly used for biological research, scientists have identified the protein Atg40 as an ER-phagy receptor, and also found that parts of its structure share similarities to a group of proteins called DP1/Yop1 (reticulon-like proteins), which "curves" the ER membranes into shape and maintains their tubular structures.

"Our previous work reveals that Atg40 is important for ER-phagy, but we actually know very little about how the process works," explained Dr. Hitoshi Nakatogawa of the Tokyo Tech, who led a team of scientists in research that investigated the mechanisms of Atg40 involvement in ER-phagy. "Because degradation of ER is so important for proper cellular function, gaining a better understanding of ER-phagy will improve basic biological knowledge."

Their experiments with yeast, the findings of which are published in Nature Communications, showed that Atg40 is important for "curving and folding" the ER membrane, and therefore has a similar function to DP1/Yop1, explaining their structural similarities. Atg40 is also necessary for ER-phagy, specifically being involved in breaking up the ER membrane so that it can be imbibed by autophagosomes. Researchers demonstrated that during this folding and fragmentation of the ER, Atg40 forms a protein assembly (cluster of proteins) by interacting with Atg8 located specifically at points of contact between the ER and the isolation membrane (as shown in Figure 1). In other words, Atg40 does not randomly or always remodel ER structure; it does so only for the ER parts that will be degraded.

Regarding the significance of these results, Dr. Nakatogawa commented: "What I find particular exciting is the insight we gained on a crucial part of how cells work, how they deal with waste or get rid of abnormal cell parts. Our work doesn't just have implications for ER-phagy though, it can also potentially tell us something about how other organelles, like the nucleus or mitochondria, are degraded."

Besides just being valuable basic research, these findings also have significant practical applications. Knowing the mechanisms of organelle degradation might help the development of drugs that target this process if it breaks down. This presents potential attractive solutions for diseases involving the malfunction of ER such as sensory neuropathy.

The aberrant buildup of misfolded proteins is a hallmark of a host of disorders, including neurodegenerative diseases such as Alzheimer's and Parkinson's. Aggregates of these toxic proteins wreak havoc on the function of cells, tissues, and organs, and despite intensive research over many decades, there are still no effective means to remove or to prevent their accumulation in humans.

One promising strategy to achieve this may someday come from an unexpected source--a common class of drugs used to treat erectile dysfunction.

In a recent study, scientists at Harvard Medical School have identified a new mechanism for activating the cell's protein quality-control system and improving its ability to dispose of misfolded proteins, including ones known to cause neurodegenerative diseases.

Reporting in the Proceedings of the National Academy of Sciences in June, the researchers describe how PDE5 inhibitors--which include the erectile dysfunction drugs sildenafil and tadalafil--lower the accumulation of mutant proteins and reduce cell death and anatomical defects in zebrafish models of neurodegeneration.

"Our study indicates a new approach to combat the basic cause of many neurodegenerative diseases as well as certain rare cardiac and muscle diseases, which are due to the buildup of misfolded intracellular proteins," said senior study author Alfred Goldberg, professor of cell biology in the Blavatnik Institute at HMS.

This approach is attractive because it utilizes a previously unknown mechanism that cells naturally have to remodel their protein composition through increased degradation, Goldberg added. "Hopefully, these findings will lead to novel therapies in the coming years," he said.

The results are an early step toward potentially addressing the failure of protein quality control and the accumulation of toxic proteins that underlies many neurodegenerative disorders, the authors said, but they caution that further, in-depth studies are needed.

"By turning on the cell's garbage disposal system, this widely prescribed class of drug could have a beneficial effect against disorders involving misfolded proteins," said study first author Jordan VerPlank, research fellow in cell biology in the Blavatnik Institute at HMS. "We now have a new point of entry to explore ways to treat or slow the progression of these diseases."

Enhancing destruction

In their study, Goldberg, VerPlank and colleagues sought to enhance the activity of the proteasome, one of the primary molecular machines that cells use to destroy proteins, especially ones that are misfolded, unnecessary or damaged.

They were intrigued by evidence in existing scientific literature suggesting that a drug that inhibits the enzyme PDE5--widely used to treat erectile dysfunction and pulmonary hypertension--can increase the degradation of a mutant protein that causes a rare inherited cardiac disease, a type of cardiomyopathy. PDE5 inhibitors function by raising levels of cGMP, a molecule that acts as an intracellular messenger.

To investigate if these drugs affect the proteasome, the research team selected several compounds that boost cGMP levels--sildenafil and tadalafil, PDE5 inhibitors that block the breaking down of cGMP--and two soluble guanylate cyclase activators, which directly increase cGMP production.

The proteasome degrades proteins that are marked for destruction through the attachment of the small molecule ubiquitin. The team found that raising cGMP both enhanced the addition of ubiquitin to proteins, which increased the marking of proteins for degradation, and enhanced the proteasome's ability to destroy them.

Applied to isolated human cells, these drugs not only rapidly raised proteasome activity, they greatly enhanced degradation of short-lived and long-lived proteins, the latter of which form the bulk of proteins within cells. Notably, this increased degradation occurred only though the proteasome and not through the other degradative system commonly used by cells known as autophagy.

Next, the team investigated whether this drug-enhanced proteasome activity could be effective against the abnormal buildup of misfolded proteins, particularly given that proteasome function is impaired in many neurodegenerative diseases.

To do so, they used zebrafish larvae, developed by collaborators at the University of Cambridge in the U.K., which have genetic mutations in proteins that in humans cause the neurodegenerative conditions Huntington's disease and tauopathies--a group of disorders caused by the abnormal accumulation of tau protein, including Alzheimer's disease and frontotemporal dementia.

Zebrafish larvae treated with cGMP-boosting drugs exhibited greater proteasome activity, with no apparent harmful effects.

Notably, treating larvae with these drugs increased the degradation of the mutant tau and huntingtin proteins, reducing the overall levels of these aberrant proteins within neurons. In addition, the team observed reductions in neuronal cell death and in the severity of an abnormal spine curvature caused by mutated tau protein.

Smarter than we thought

The authors caution that these findings do not suggest that PDE5 inhibitors are an immediate treatment for neurodegenerative diseases in humans.

"These results are very promising," Goldberg said. "But it will be necessary to determine the best and safest way to pharmacologically raise cGMP levels in the brain and to determine at what stage of the disease this approach may be of benefit."

They are now further probing the underlying mechanisms triggered by these drugs, with a focus on uncovering how cGMP-boosting drugs enhance proteasome activity and potential applications to other neurodegenerative diseases.

Increasing cGMP activates a signaling protein called protein kinase G, which their analysis revealed subsequently adds phosphate, a small chemical modification, to a specific region of the proteasome. Precisely how this regulates the proteasome, however, remains unknown.

"At the cell and molecular level, we have uncovered new ways that cells have to regulate their protein composition," Goldberg said. "But it is quite unclear how putting a small phosphate group on the very large proteasome particle can accelerate its function and alter cell protein composition. So, there's a lot to be explored."

In previous studies, the Goldberg lab has shown that raising the intracellular levels of another signaling molecule, cAMP, also enhances the activity of the proteasome. Their work had shown that cAMP, via protein kinase A, causes attachment of a phosphate group to a region of the proteasome that, in this new study, was not modified by cGMP and protein kinase G.

The researchers are now studying how these different modifications added by two distinct signaling systems enhance the proteasome's abilities and the degradation of different categories of proteins.

"For a long time, we thought that the proteasome mindlessly destroyed proteins that are tagged with ubiquitin," VerPlank said. "Our work is beginning to uncover that the proteasome is a lot smarter than we thought it was--and is making decisions through mechanisms that we still don't fully understand."

Stone tools move back the arrival of humans in America thousands of years

Findings of stone tools move back the first immigration of humans to America at least 15,000 years. This is revealed in a new international study from the University of Copenhagen, where researchers have analysed ancient material from a Mexican mountain cave.

The first humans arrived in America at least 30,000 years ago, approximately 15,000 before science was hitherto able to render it probable. This is the conclusion in new study published in the scientific journal, Nature.

The team behind the article consists of archaeologists and DNA experts from the University of Copenhagen and universities in Mexico, the UK, the US and Brazil, among others.

"The article in Nature is a scientific hand grenade. The fact that it moves back the time of early immigration to America significantly is guaranteed to ignite a heated debate," says Eske Willerslev, Professor and Head of Lundbeck Foundation Centre for GeoGenetics, Globe Institute at the University of Copenhagen.

Eske Willerslev and his two colleagues, Associate Professor Mikkel Winther Pedersen and Assistant Professor Martin Sikora, made up the Danish contribution to the international team of researchers.

The three scientists from UCPH have conducted the DNA analyses of ancient remains from animal and plant material found during the excavations of the Chiquihuite Cave in Northern Mexico.

1,900 stone tools

As far back as 30,000 years ago, humans had already developed techniques for producing tools. In the Mexican cave, researchers found 1,900 stone tools.

The unique feature of the Chiquihuite Cave is the "floor", which consists of six layers of detritus and dust - all in all, a ten-foot column of ancient remains - which is so compressed and stable that by using various advanced measuring methods, it has been possible to date the layers one by one, from top to bottom.

Each layer has contained deposits of stone tools such as knives, scrapers and arrowheads, which the researchers have also been able to date.

"The cave finds are extremely interesting. These archaeological finds are so far the oldest in America. And the excavated stone tools are of a type unique to America," Professor at Universidad Autónoma de Zacatecas, Mexico, Ciprian F. Ardelean, states.

Ice Cap Across North America

Until now, science has assumed that the earliest immigration to America took place approx. 15,000 years ago. At the time, a narrow opening in the ice along the northern Pacific coastline was created, which made it possible to walk from Siberia onto the American continent.

At the time, there were no other access routes to the continent, because North America was covered by a thick ice cap, which only later - approx. 13,000 years ago - melted enough to enable passage.

30,000 years ago, when the first stone tools were left in the Chiquihuite Cave, the massive ice cap had not yet covered all of North America, which means that it would have been possible to walk from Siberia and down through the American continent, Eske Willerslev explains.

"And that's how we must understand the presence of these humans in Mexico at this particular time - unfortunately though, we have no idea who they were. Because although we searched very thoroughly for human DNA in the samples we gathered during the ten days we spent at the Chiquihuite Cave, there were no human traces to be found. However, we may still be able to find some in the hundreds of earth samples we gathered, because we've not yet had time to analyse all of them."

According to Mikkel Winther Pedersen who was in charge of the DNA analyses, their finds contain DNA samples from numerous plants as well as animals. He elaborates:

"For example, we found DNA from an American black bear, a wide range of rodents, several types of bats as well as sparrow and falcon. These are all animals we would expect to find in Mexico at the time. Simultaneously, we were able to ascertain

CORVALLIS, Ore. - The discovery of the first active methane seep in Antarctica is providing scientists new understanding of the methane cycle and the role methane found in this region may play in warming the planet.

A methane seep is a location where methane gas escapes from an underground reservoir and into the ocean. Methane seeps have been found throughout the world's oceans, but the one discovered in the Ross Sea was the first active seep found in Antarctica, said Andrew Thurber, a marine ecologist at Oregon State University.

"Methane is the second-most effective gas at warming our atmosphere and the Antarctic has vast reservoirs that are likely to open up as ice sheets retreat due to climate change," Thurber said. "This is a significant discovery that can help fill a large hole in our understanding of the methane cycle."

The researchers' findings were published today in the journal Proceedings of the Royal Society B. Co-authors are Sarah Seabrook and Rory Welsh, who were graduate students at OSU during the expeditions. The research was supported by the National Science Foundation.

Methane is a greenhouse gas that is 25 times more powerful than carbon dioxide at warming the planet. Most methane in the ocean water and sediment is kept out of the atmosphere by microbes that consume it.

Thurber and his colleagues discovered that the microbes around the Antarctic seep are fundamentally different that those found elsewhere in the world's oceans. This helps researchers better understand methane cycles and the factors that determine whether methane will reach the atmosphere and contribute to further warming, Thurber said.

The Ross Sea seep was discovered in an area that scientists have studied for more than 60 years, but the seep was not active until 2011, said Thurber, an assistant professor in Oregon State's College of Earth, Ocean, and Atmospheric Sciences and the College of Science's Department of Microbiology.

An expansive microbial mat, about 70 meters long by a meter across, formed on the sea floor about 10 meters below the frozen ocean surface. These mats, which are produced by bacteria that exist in a symbiotic relationship with methane consumers, are a telltale indication of the presence of a seep, said Thurber.

"The microbial mat is the road sign that there's a methane seep here," Thurber said. "We don't know what caused these seeps to turn on. We needed some dumb luck to find an active one, and we got it."

Thurber happened to be in Antarctica in 2012 when another researcher told him about a "microbial waterfall" and thought it was something he should look at. Thurber was able to confirm the seep's presence, collect samples and analyze the seep and its environment. When he returned to the site in 2016 to conduct further study, he also discovered a second seep nearby.

Antarctica is believed to contain as much as 25 percent of Earth's marine methane. Having an active seep to study gives researchers new understanding of the methane cycle and how that process might differ in Antarctica compared to other places on the planet, Thurber said.

For example, researchers have found that the most common type of microbe that consumes methane took five years to show up at the seep site and even then those microbes were not consuming all of the methane, Thurber said. That means some methane is being released and is likely working its way into the atmosphere.

Studying the site over a five-year time span allowed researchers to see how microbes respond to the formation of a seep, said Seabrook, who earned her doctorate at OSU and is now a post-doctoral scholar at the National Institute of Water and Atmospheric Research in Wellington, New Zealand.

"What was really interesting and exciting was that the microbial community did not develop as we would have predicted based on other methane seeps we have studied around the globe," she said.

Researchers had assumed that microbes should respond really quickly to changes in the environment, but that wasn't reflected in what OSU's team saw in Antarctica, Thurber said.

"To add to the mystery of the Antarctic seeps, the microbes we found were the ones we least expected to see at this location," he said. There may be a succession pattern for microbes, with certain groups arriving first and those that are most effective at eating methane arriving later.

"We've never had the opportunity to study a seep as its forming or one in Antarctica, because of this discovery we can now uncover whether seeps just function differently in Antarctica or whether it may take years for the microbial communities to become adapted," Thurber said.

"Animals in Antarctica are very different than elsewhere in the world as the continent has been separated from the rest of the globe for more than 30 million years - a long time for evolution to act," he said. "That has resulted in a remarkable diversity of fauna that we only find there. That may also contribute to the differences in microbes there."

It is important to understand how methane seeps behave in this environment so researchers can begin factoring those differences into climate change models, Thurber said. He hopes to return to the site to monitor its evolution and conduct further research.

Adoptive cell transfer immunotherapy is one of the most promising new treatments for people with hard-to-treat cancers. However, the process is complex and needs fine-tuning in order to develop more treatment strategies that will work for more people.

In a new study looking at adoptive cell transfer products bearing a transgenic T-cell receptor (TCR), researchers at the UCLA Jonsson Comprehensive Cancer Center have identified a discordant phenomenon in which a subset of patients displayed profoundly decreased expression of the transgenic TCR over time, despite the transgenic TCR being present at the DNA level. This gave rise to the observation that structural changes to the DNA via DNA methylation make it inaccessible for transcription and translation, which is an influential step in the flow of genetic information from DNA to RNA. This can be one clue into why some patients stop responding to this type of immunotherapy.

"The issue is this phenomenon happens over time," said lead author Theodore Scott Nowicki, MD, PhD, clinical instructor of pediatrics and hematology/oncology at the David Geffen School of Medicine at UCLA. "We're hoping this can help inform the design of future generations of these types of therapies and pinpoint different vectors that might be more or less vulnerable to this phenomenon."

JOURNAL

The study was published online in Cancer Discovery, a journal of the American Association for Cancer Research.

BACKGROUND

Adoptive cell transfer immunotherapy works by taking a patient's own T cells, which are one of the components of the immune system, and genetically modifying them in the laboratory to target tumor-specific antigens on the surface of the tumor. The new army of tumor-specific T cells are then reinfused back into the patient to help attack the cancer.

A key component of adoptive cell transfer therapy requires genetically modifying T cells to target cancer cells. This is often done with viral transduction agents with either lentivirus- or retrovirus-based products to express either a cancer antigen-specific TCR or chimeric antigen receptor (CAR).

In order to develop more efficient cell therapies, Nowicki and colleagues are studying the genetic mutations of T cells to understand the structural changes to DNA over time. This could reveal why adoptive cell transfer therapy is more likely to work in some patients versus others and help inform the future design of next-generations of the therapy.

METHOD

The team analyzed 16 clinical transgenic adoptive cell therapy samples collected before and during treatment from patients with melanoma and sarcoma. This allowed the team to look at the expression of the transgenic TCR at the DNA and protein level. It gave them insight into what proportion of the cells displayed impaired expression of the transgenic TCR. They were then able to assess the degree of DNA methylation present in the retroviral vector's promoter region over time, and correlate this degree of DNA methylation with repression of the transgenic TCR.

IMPACT

The study can help researchers in the design of future generations of cellular immunotherapies to help treat people with advanced cancers.

The ability of the human brain to process and store information is determined to a large extent by the connectivity between nerve cells. Chemical synapses are very important in this context as they constitute the interface for the transmission of information between individual nerve cells. Abnormalities in the formation of synapses cause many neurological disorders such as autism. Neurobiologists at Johannes Gutenberg University Mainz (JGU) have found new evidence that specific calcium channel subunits play a crucial role in the development of excitatory and inhibitory synapses.

α2δ subunits have different effects on the formation of new synapses

Autism spectrum disorder is a condition involving impaired development that begins with birth and is usually manifested when the individual in question exhibits difficulties in social interaction and communication. It is postulated that the main underlying cause is disruption of synapse-mediated interaction between nerve cells.

The results of several studies indicate that so-called α2δ subunits of calcium channels are involved in the formation and fine-tuning of excitatory and inhibitory nerve cells, but little has been known to date about when and how specifically the four forms of α2δ subunits are involved. It is this aspect that the research team led by Professor Martin Heine of the Institute of Developmental Biology and Neurobiology at Mainz University has now addressed. What is particularly interesting is their research finding that the two dominant α2δ subunits in the hippocampus, α2δ1 and α2δ3, have different effects on synaptogenesis in neuronal networks.

In order to investigate the underlying mechanism, the researchers prepared isolated networks of hippocampal neurons. The results show that during the early phase of the development of neural networks, subunit α2δ3 promotes the release of an inhibitory neurotransmitter, triggers the formation of inhibitory synapses, and boosts the growth of axons from inhibitory neurons. "The α2δ3 subunit is obviously an important factor with regard to the early development of neural networks," explained Heine. At later development phases and in more mature neuronal networks, it is subunit α2δ1 that fosters excitatory stimulus transmission and synaptogenesis.

Connectivity relies on concerted cooperation between α2δ1 and α2δ3

In their article in The Journal of Neuroscience, the researchers proposed "that formation of connectivity in neuronal networks is associated with a concerted interplay of α2δ1 and α2δ3 subunits of calcium channels". Dr. Artur Bikbaev, one of the lead authors from JGU, further concluded that the calcium channel subunits are molecules that are relevant to the development of the brain. New data has confirmed the assumption that there is a link between an aberration in the genes that code for subunits α2δ1 and α2δ3 and autistic spectrum disorders. An imbalance in the ratio of excitatory to inhibitory neurons is also thought to be the cause of the epileptic seizures which very frequently accompany autism spectrum disorder.

In addition to the team at JGU, researchers at the Leibniz Institute for Neurobiology, the University of Münster, and the Medical University of Innsbruck were also involved in the project.