Culture

BOSTON -- Gaurav Gaiha, MD, DPhil, a member of the Ragon Institute of MGH, MIT and Harvard, studies HIV, one of the fastest-mutating viruses known to humankind. But HIV's ability to mutate isn't unique among RNA viruses -- most viruses develop mutations, or changes in their genetic code, over time. If a virus is disease-causing, the right mutation can allow the virus to escape the immune response by changing the viral pieces the immune system uses to recognize the virus as a threat, pieces scientists call epitopes.

To combat HIV's high rate of mutation, Gaiha and Elizabeth Rossin, MD, PhD, a Retina Fellow at Massachusetts Eye and Ear, a member of Mass General Brigham, developed an approach known as structure-based network analysis. With this, they can identify viral pieces that are constrained, or restricted, from mutation. Changes in mutationally constrained epitopes are rare, as they can cause the virus to lose its ability to infect and replicate, essentially rendering it unable to propagate itself.

When the pandemic began, Gaiha immediately recognized an opportunity to apply the principles of HIV structure-based network analysis to SARS-CoV-2, the virus that causes COVID-19. He and his team reasoned that the virus would likely mutate, potentially in ways that would allow it to escape both natural and vaccine-induced immunity. Using this approach, the team identified mutationally constrained SARS-CoV-2 epitopes that can be recognized by immune cells known as T cells. These epitopes could then be used in a vaccine to train T cells, providing protective immunity. Recently published in Cell, this work highlights the possibility of a T cell vaccine which could offer broad protection against new and emerging variants of SARS-CoV-2 and other SARS-like coronaviruses.

From the earliest stages of the COVID-19 pandemic, the team knew it was imperative to prepare against potential future mutations. Other labs already had published the protein structures (blueprints) of roughly 40% of the SARS-CoV-2 virus, and studies indicated that patients with a robust T cell response, specifically a CD8+ T cell response, were more likely to survive COVID-19 infection.

Gaiha's team knew these insights could be combined with their unique approach: the network analysis platform to identify mutationally constrained epitopes and an assay they had just developed, a report on which is currently in press at Cell Reports, to identify epitopes that were successfully targeted by CD8+ T cells in HIV-infected individuals. Applying these advances to the SARS-CoV-2 virus, they identified 311 highly networked epitopes in SARS-CoV-2 likely to be both mutationally constrained and recognized by CD8+ T cells.

"These highly networked viral epitopes are connected to many other viral parts, which likely provides a form of stability to the virus," says Anusha Nathan, a medical student in the Harvard-MIT Health Sciences and Technology program and co-first author of the study. "Therefore, the virus is unlikely to tolerate any structural changes in these highly networked areas, making them resistant to mutations."

You can think of a virus's structure like the design of a house, explains Nathan. The stability of a house depends on a few vital elements, like support beams and a foundation, which connect to and support the rest of the house's structure. It is therefore possible to change the shape or size of features like doors and windows without endangering the house itself. Changes to structural elements, like support beams, however, are far riskier. In biological terms, these support beams would be mutationally constrained -- any significant changes to size or shape would risk the structural integrity of the house and could easily lead to its collapse.

Highly networked epitopes in a virus function as support beams, connecting to many other parts of the virus. Mutations in such epitopes can risk the virus's ability to infect, replicate, and ultimately survive. These highly networked epitopes, therefore, are often identical, or nearly identical, across different viral variants and even across closely related viruses in the same family, making them an ideal vaccine target.

The team studied the identified 311 epitopes to find which were both present in large amounts and likely to be recognized by the vast majority of human immune systems. They ended up with 53 epitopes, each of which represents a potential target for a broadly protective T cell vaccine. Since patients who have recovered from COVID-19 infection have a T cell response, the team was able to verify their work by seeing if their epitopes were the same as ones that had provoked a T cell response in patients who had recovered from COVID-19. Half of the recovered COVID-19 patients studied had T cell responses to highly networked epitopes identified by the research team. This confirmed that the epitopes identified were capable of inducing an immune reaction, making them promising candidates for use in vaccines.

"A T cell vaccine that effectively targets these highly networked epitopes," says Rossin, who is also a co-first author of the study, "would potentially be able to provide long-lasting protection against multiple variants of SARS-CoV-2, including future variants."

By this time, it was February 2021, more than a year into the pandemic, and new variants of concern were showing up across the globe. If the team's predictions about SARS-CoV-2 were correct, these variants of concerns should have had little to no mutations in the highly networked epitopes they had identified.

The team obtained sequences from the newly circulating B.1.1.7 Alpha, B.1.351 Beta, P1 Gamma, and B.1.617.2 Delta SARS-CoV-2 variants of concern. They compared these sequences with the original SARS-CoV-2 genome, cross-checking the genetic changes against their highly networked epitopes. Remarkably, of all the mutations they identified, only three mutations were found to affect highly networked epitopes sequences, and none of the changes affected the ability of these epitopes to interact with the immune system.

"Initially, it was all prediction," says Gaiha, an investigator in the MGH Division of Gastroenterology and senior author of the study. "But when we compared our network scores with sequences from the variants of concern and the composite of circulating variants, it was like nature was confirming our predictions."

In the same time period, mRNA vaccines were being deployed and immune responses to those vaccines were being studied. While the vaccines induce a strong and effective antibody response, Gaiha's group determined they had a much smaller T cell response against highly networked epitopes compared to patients who had recovered from COVID-19 infections.

While the current vaccines provide strong protection against COVID-19, Gaiha explains, it's unclear if they will continue to provide equally strong protection as more and more variants of concern begin to circulate. This study, however, shows that it may be possible to develop a broadly protective T cell vaccine that can protect against the variants of concern, such as the Delta variant, and potentially even extend protection to future SARS-CoV-2 variants and similar coronaviruses that may emerge.

What The Study Did: Researchers estimated the frequency and magnitude of surprise bills for deliveries and newborn hospitalizations, which are the leading reasons for hospitalization in the United States, to illustrate the  potential benefits of federal legislation that will protect families from most surprise bills. Potential surprise bills were defined as claims from out-of-network clinicians and ancillary service providers, such as an ambulance.

Authors: Kao-Ping Chua, M.D., Ph.D., of the University of Michigan Medical School in Ann Arbor, is the corresponding author.

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

(doi:10.1001/jamahealthforum.2021.1460)

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

PHILADELPHIA-- While more women are entering the field of academic medicine than ever before, they are less likely to be recognized as experts and leaders; they are less likely to receive prestigious awards, be promoted to full professorships, hold leadership roles, or author original research or commentaries in major journals. What's more, articles published by women in high-impact medical journals also have fewer citations than those written by men, especially when women are primary and senior authors, according to new research from the Perelman School of Medicine and the Leonard Davis Institute of Health Economics at the University of Pennsylvania, published today in JAMA Open Network.

Researchers found that of the 5,554 articles published in 5 leading academic medical journals between 2015 and 2018, 35.6 percent had a female primary author, and 25.8 percent had a female senior author. During this period, the articles with women as primary author were referenced in other academic articles a median of 36 times, compared 54 citations of articles with male primary authors. The trend extended to articles with female senior authors, which were cited a median of 37 times, while articles by male counterparts received a median of 51 citations. Original articles with women as both primary and senior authors were cited the fewest times, with a median of 33 citations, whereas articles authored by men as both primary and senior author were cited the most, a median of 59 times.

"The number of times a peer-reviewed articles cited by other researchers is commonly used as a metric for academic recognition, influence, as well as in professional evaluations and promotions," says lead author Paula Chatterjee, MD, MPH, an assistant professor of General Internal Medicine at Penn Medicine. "Female academics already face a number of barriers to career advancement, and the disparity in citations only broadens the gap between them and their male peers."

Authors also note that some of the journals included in the study focus on the field of internal medicine, which typically has a higher proportion of women represented than other clinical specialties. As a result, the findings may actually underestimate differences in scholarly article citations between male and female authors.

"Gender disparities in citations are just one way in which inequities in academic medicine should be examined. Our findings highlight that disparities stem in part from inequities in recognition and amplification of research. This imbalance will not be solved through hiring and mentoring more women alone," said senior author, Rachel Werner, MD, PhD, Executive Director of the Leonard Davis Institute for Health Economics. "We must also work to ensure that women already in academic medicine are equally valued and promoted for their contributions and their successes. From the journals publishing this work, to academic institutions promoting articles once published, everyone should be invested in bridging this gender divide."

The human brain is a wonderfully enigmatic organ, helping to juggle multiple tasks efficiently to help us get through a long day! This feature, called executive function, seats primates like us at the pinnacle of evolution. The prospect of losing the spectacular flow of neural information in our brains because of an accident or disease is, thus, unnerving. In the event of such an unfortunate occurrence, to restore the brain to its previous working condition with full functionality--to reboot it, so to speak--would need a better understanding of the specific neural pathways involved in our daily activities that rely on working memory and decision-making--two important executive functions.

To achieve this objective, a group of researchers from National Institutes for Quantum and Radiological Science and Technology (QST), Japan, were hard at work at devising a technique they call "imaging-guided chemogenetic synaptic silencing" to decipher the specific neural pathways involved in high-order executive functions. In a pioneering study published in Science Advances, the researchers now report successfully delineating specific neural pathways involved in working memory and decision-making using this technique.

The group, led by eminent researcher Dr. Takafumi Minamimoto from the Department of Functional Brain Imaging, QST, focused on studying the dorsolateral part of the prefrontal cortex (dlPFC) in the monkey brain, to apply their novel technique, and further identify the neural pathways of interest. It is interesting to note this choice, not only because it is the brain region partially responsible for controlling executive functions, but also since this specialized region is only present in primates.

Importantly, the role of dlPFC is supported by brain regions like the dorsal caudate (dCD) and lateral mediodorsal thalamus (MDl) too. This intricate association is further explained by Dr. Kei Oyama, who is the first author of the study, as follows, "The primate prefrontal cortex (PFC), especially its dorsolateral part (dlPFC), is well known to serve as the center of higher-order executive functions; it is uniquely developed in primates and underlies their distinctive cognitive abilities. These functions, however, do not solely rely on dlPFC neurons but also on their cooperative interactions with subcortical structures, including the dorsal caudate (dCD) nucleus and lateral mediodorsal thalamus (MDl)."

Next, the researchers wanted to understand the who-does-what for working memory and decision-making. Given that the dlPFC, MDI, and dCD neurons are connected, they selectively silenced specific neuronal synapses to disrupt the flow of information, and achieve just dlPFC-dCD and dlPFC-MDl projections, either unilaterally (involving just one side of the brain), or bilaterally (involving both sides). To achieve this, they made the dlPFC neurons express designer receptors exclusively activated by designer drugs (DREADDs). Further, the monkeys involved in the study were analyzed for behavioral changes, to understand the effect of chemogenetic silencing.

Interestingly, the researchers observed that silencing the bilateral dlPFC-MDl projections in the monkeys, but not their dlPFC-dCD projections, caused problems in the working memory related to their surroundings. On the contrary, silencing their unilateral dlPFC-dCD projections, but not their unilateral dlPFC-MDl projections, altered their preference in decision-making. These results reveal that the two higher-brain functions, working memory and decision-making, which are essential for our daily lives, are controlled by different neural pathways linking specific brain areas.

Overall, this study lays the foundation for further explorations of the intricacies of the complex primate brain. In this regard, Dr. Oyama explains the potential clinical and research applications of these findings, "Many psychiatric disorders, including depression, are thought to be associated with disturbances in the transmission of neural information through neural circuits between specific brain regions. Our findings are expected to deepen our understanding of mental disorders and lead to the discovery of treatments and remedies. The successful development of a novel technique in our study will serve as a key technology for the next-generation of researchers to investigate primate brain functions, which will contribute to broad areas in life by dramatically deepening our understanding of the mechanism of higher-brain functions."

The world will indeed wait with bated breath for future mysteries to unravel as explorations take researchers deeper into the labyrinthine maze that is the mind.

Guadalupe fur seals (Arctocephalus townsendi) have established a large resting colony in the Gulf of California--bringing the total number of sites where this endangered species now occurs to just four. This new haul-out was discovered on El Farallón de San Ignacio Island, along the mainland coast of Mexico, according to researchers from Mexico and the University of British Columbia.

Guadalupe fur seals were hunted for their furs and declared extinct in the late 1800's. However, 14 individuals were discovered on Guadalupe Island in 1950--and the population has grown since then. While still designated as vulnerable to extinction, according to IUCN, the population is believed to total 41,000 individuals and is growing at an annual rate of 10-11 per cent per year.

While the only breeding site for this species continues to be on Guadalupe Island, a large resting colony or 'haul-out' was established in the late 1990s on the nearby San Benito Islands in the Pacific Ocean, off the coast of Baja California.

Now, a second, well-populated haul-out colony has also begun forming, this time off the Mexican coast in the Gulf of California.

"We observed a single adult male Guadalupe fur seal ashore at El Farallón de San Ignacio Island in 2008, and later spotted several juvenile fur seals in 2014 and 2016. This led us to increase our observation efforts in 2019, with wonderful results," said Claudia Hernández-Camacho, corresponding author, and professor in the Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional. "During our visits to El Farallón in 2020, we counted 492 individuals in January, and 771 in November. Most of the animals we have seen have been juveniles, and all have appeared to be in good body condition."

"We at first thought that the animal sighted in 2008 was an anomaly," said Andrew Trites, professor in the Marine Mammal Research Unit, based in UBC's Institute for the Oceans and Fisheries, and co-author of the research findings. "El Farallón is a small, hot and arid island, and not a place where anyone would have expected to find fur seals. However, the past six years of observation have shown that the young Guadalupe fur seals clearly like it. The question is why?"

Trites and Hernández-Camacho suspect this new haul-out is centered in a new seasonal feeding area used by young Guadalupe fur seals. Guadalupe fur seals are known to feed mainly on opalescent squid, Humboldt squid and purpleback squid.

In addition to the new colony discovered at El Farallón de San Ignacio Island, a smaller haul-out also in the southern Gulf of California has also been growing since 2019 on nearby Las Animas Islet.

Both of these haul-outs in the Gulf of California are in protected areas, known as Áreas de Protección de Flora y Fauna Islas del Golfo de California. However the needs of Guadalupe fur seals are not addressed by those protected areas because the seals were previously considered only as occasional visitors.

With the confirmed establishment of the El Farallón colony, it is important that Mexico develop a conservation policy that addresses the importance of the southern Gulf of California as a feeding ground for vulnerable Guadalupe fur seals.

Overall, Guadalupe fur seals are slowly increasing in the southern Gulf of California--and are known to range as far as the coastlines of Washington and British Columbia. However, they only occur in just four places in Mexico.

"Guadalupe fur seals have only one breeding colony, so the new haul-outs in the southern Gulf of California provide some good news. However, the new sites will need regular monitoring to document their growth and possible changes in body conditions, age and sex-composition, and breeding potential", said Trites.

"This species escaped extinction once and remains vulnerable."

Fukuoka, Japan--Medical researchers led by Kyushu University have revealed a possible underlying genetic pathway behind the neurological dysfunction of Rett syndrome. The team found that deficiencies in key genes involved in the pathology triggers neural stem cells to generate less neurons by producing more astrocytes--the brain's maintenance cells.

The researchers hope that the molecular pathology they identified, as reported in the journal Cell Reports, can lead to potential therapeutic targets for Rett syndrome in the future.

Rett syndrome is a progressive neurodevelopmental disorder characterized by impairments in cognition and coordination--with varying severity--and occurs in roughly one in every 10,000 to 15,000 female births. However, it is difficult to initially identify because children appear to develop normally in the first 6-18 months.

"Rett syndrome is caused by mutations in a single gene called methyl-CpG binding protein 2, or MeCP2. The gene was identified over two decades ago and much has been uncovered since, but exactly how the mutations cause the pathology remains elusive," explains first author Hideyuki Nakashima of Kyushu University's Faculty of Medical Sciences

In their past research, the team had identified that MeCP2 acts as a regulator for the processing of specific microRNAs to control the functions of neurons. So, they went back to investigate if that pathway was also involved in the differentiation of neural stem cells.

Compared to messenger RNA, the final template transcribed from DNA that is used by a cell to synthesize proteins, microRNAs--or miRNAs--are much smaller and act to regulate messenger RNA to make sure the cell is making the correct amount of the desired protein.

"Through our investigation, we found several microRNAs associated with MeCP2, but only one affected the differentiation of neural stem cells: a microRNA called miR-199a," says Nakashima. "In fact, when either MeCP2 or miR-199a are disrupted, we found that it increased the production of cells called astrocytes."

Astrocytes are like the support cells of your brain. While neurons fire off the electrical signals, astrocytes are there to help maintain everything else. During development, astrocytes and neurons are generated from the same type of stem cells, known as neural stem cells, where their production is carefully controlled. However, dysfunction in MeCP2 or miR-199a causes these stem cells to produce more astrocytes than neurons.

"Further analysis showed that miR-199a targets the protein Smad1, a transcription factor critical for proper cellular development. Smad1 functions downstream of a pathway called BMP signaling, which is known to inhibit the production of neurons and facilitate the generation of astrocytes," states Nakashima.

To investigate the process further, the team established a brain organoid culture--a 3D culture of neural stem cells that can mimic aspects of brain development--from iPS cells derived from patients with Rett syndrome. When they inhibited BMP, short for bone morphogenetic protein, the team was able to reduce abnormal neural stem cell differentiation.

"Our findings have given us valuable insight into the role of MeCP2, miR-199a, and BMP signaling in the pathology of Rett syndrome," concludes Kinichi Nakashima, who headed the team. "Further investigation is needed, but we hope this can lead to clinical treatments for Rett syndrome symptoms."

Japanese astronomers have developed a new artificial intelligence (AI) technique to remove noise in astronomical data due to random variations in galaxy shapes. After extensive training and testing on large mock data created by supercomputer simulations, they then applied this new tool to actual data from Japan's Subaru Telescope and found that the mass distribution derived from using this method is consistent with the currently accepted models of the Universe. This is a powerful new tool for analyzing big data from current and planned astronomy surveys.

Wide area survey data can be used to study the large-scale structure of the Universe through measurements of gravitational lensing patterns. In gravitational lensing, the gravity of a foreground object, like a cluster of galaxies, can distort the image of a background object, such as a more distant galaxy. Some examples of gravitational lensing are obvious, such as the "Eye of Horus". The large-scale structure, consisting mostly of mysterious "dark" matter, can distort the shapes of distant galaxies as well, but the expected lensing effect is subtle. Averaging over many galaxies in an area is required to create a map of foreground dark matter distributions.

But this technique of looking at many galaxy images runs into a problem; some galaxies are just innately a little funny looking. It is difficult to distinguish between a galaxy image distorted by gravitational lensing and a galaxy that is actually distorted. This is referred to as shape noise and is one of the limiting factors in research studying the large-scale structure of the Universe.

To compensate for shape noise, a team of Japanese astronomers first used ATERUI II, the world's most powerful supercomputer dedicated to astronomy, to generate 25,000 mock galaxy catalogs based on real data from the Subaru Telescope. They then added realist noise to these perfectly known artificial data sets, and trained an AI to statistically recover the lensing dark matter from the mock data.

After training, the AI was able to recover previously unobservable fine details, helping to improve our understanding of the cosmic dark matter. Then using this AI on real data covering 21 square degrees of the sky, the team found a distribution of foreground mass consistent with the standard cosmological model.

"This research shows the benefits of combining different types of research: observations, simulations, and AI data analysis." comments Masato Shirasaki, the leader of the team, "In this era of big data, we need to step across traditional boundaries between specialties and use all available tools to understand the data. If we can do this, it will open new fields in astronomy and other sciences."

Microorganisms produce natural products, for example, as disease-causing virulence factors or as defense substances against predators and competitors. A team led by Dr. Robin Teufel and first author Ying Duan from the Institute of Biology II at the Faculty of Biology of the University of Freiburg, together with researchers from the University of Bonn, have now discovered a novel enzyme that is crucial for the production of so-called bacterial tropone natural products. The researchers presented their results in the current issue of the Journal of the American Chemical Society.

Previously unknown enzyme type

Bacteria found in terrestrial and marine environments produce tropone natural products, among other things, when they interact symbiotically with plants, algae or lower animals, for example as presumed protective substances against microbial pathogens in corals and sponges. The Freiburg researchers now investigated how the symbiotic bacteria produce these bioactive agents. Teufel and his team discovered a completely new type of enzyme that is essential for the production of these bacterial tropones.

Key intermediate in tropone biosynthesis

The scientists found that this enzyme activates oxygen in a previously unknown way and incorporates it into a chemical precursor compound. In the process, the basic structure of the tropone is generated. Using chemical and biochemical methods, the researchers were able to investigate the functions of this enzyme in more detail and thereby elucidate novel intermediates in tropone biosynthesis. "We succeeded in taking a crucial step toward better understanding the biological production of these significant compounds," Teufel explains. "These findings can serve as a basis for better combating certain pathogens in the future or for obtaining novel tropone compounds using biotechnological methods."

"We have studied which temperatures are preferable and which are harmful in humans, cattle, pigs, poultry, and agricultural crops and found that they are surprisingly similar," says Senthold Asseng, Professor of Digital Agriculture at TUM. According to the study, preferable temperatures range from 17 to 24 degrees Celsius.

When does it become too hot for humans?

At high humidity, mild heat strain for humans begins at about 23 degrees Celsius and at low humidity at 27 degrees Celsius. "If people are exposed to temperatures above 32 degrees Celsius at extremely high humidity or above 45 degrees Celsius at extremely low humidity for a lengthy period of time, it can be fatal," says Prof. Asseng. "During extreme heat events with temperatures far above 40 degrees Celsius, such as those currently being observed on the U.S North West Coast and in Canada, people require technical support, for example in the form of air-conditioned spaces."

To mitigate increasing heat strain, Prof. Asseng cites a variety of strategies, including increasing natural shade from trees or structural shading. Cities and buildings can be made more temperature-passive, for example, by using roof and wall insulation or by using lighter, reflective roof and wall colors to reduce heat strain.

How do high temperatures affect livestock?

In cattle and pigs, heat strain occurs at 24 degrees Celsius with high humidity and at 29 degrees Celsius with low humidity. The milk yield from cows can decrease by 10 to 20 percent when exposed to heat stress, and the fattening performance in pigs is also reduced. The comfortable temperature range for poultry is 15 to 20 degrees. Chickens experience mild heat strain at 30 degrees Celsius. At 37 degrees Celsius and above, they experience severe heat stress and their egg laying rate declines.

Heat stress overall leads to reduced growth in cattle and dairy cows, pigs, chickens and other livestock, which means both lower yields and reproductive performance. "There are examples of evolutionary adaptations to warm weather in terrestrial mammals. Transylvanian naked chickens are more heat tolerant than other varieties of chickens because of a complex genetic mutation that suppresses feather growth. They are naturally air-conditioned because they lack feathers on their necks," says Prof. Asseng.

How do crops react to high temperature?

"In crops, the optimal temperature zone and temperature thresholds seem to be more diverse due to differences between species and varieties," explains Prof. Asseng.

Cold-temperate crops such as wheat, for example, do better at cooler temperatures, while warm-temperature crops such as corn are sensitive to frost but can tolerate warmer temperatures. Strategies to reduce heat stress in crop production include changes in planting dates to avoid heat stress later in the season, irrigation (if feasible), switching to more heat-resistant crops, and breeding to increase heat tolerance.

How is climate change affecting life on Earth?

"By the end of the century, 45 to 70 percent of the global land area could be affected by climate conditions in which humans cannot survive without technological support, such as air conditioning. Currently, it's 12 percent," says Prof. Asseng. This means that in the future, 44 to 75 percent of the human population will be chronically stressed by heat. A similar increase in heat stress is expected for livestock, poultry, agricultural crops and other living organisms.

"Genetic adaptation to a changing climate often takes many generations. The time available is too short for many higher forms of life. If current climate trends persist, many living things could be severely affected or even disappear completely from Earth due to temperature change," concludes Prof. Asseng.

Plastics are a growing problem for natural ecosystems around the globe, and in particular for our marine and freshwater environments. Rivers are the leading source of plastic pollution, as it has been estimated that they deliver several million metric tons of plastic annually to our oceans from poor land-based waste management. The problem is that the estimates made for plastics flowing from the rivers are tens to hundreds of times higher than the quantity of plastics floating on the ocean's surface. So where is all of this river-derived plastic actually going - is there a missing plastic 'sink' somewhere in the ocean? Are the estimates correct?

In a paper published today in Science, Dr. Lisa Weiss and her colleagues from the Centre of Education and Research on Mediterranean Environments (CEFREM), a joint research laboratory between the University of Perpignan (UPVD) and the French National Centre for Scientific Research (CNRS), and a team of researchers from a number of research institutions in France and the University of Barcelona in Spain demonstrate that current river flux assessments are overestimated by two to three orders of magnitude from previous estimates. This would explain why a large volume of microplastics seems to disappear into a mysterious ocean 'plastic sink'.

However, these findings do not suggest that plastics are less of a problem than previously thought. In fact, through their analyses, researchers actually found that plastics remain at the ocean's surface much longer than previously estimated - further exacerbating the effects of plastic pollution on natural systems.

The mysterious ocean plastic sink

Rivers are the main source of plastic discharge into the oceans. According to current assessments, the floating stock of microplastics on the ocean's surface - from tens to hundreds of metric tons - is just a small fraction of the millions of metric tons that are discharged by rivers each year. This unequal balance has led to the 'plastic sink' hypothesis whereby the amount of microplastics in the 'plastic sink' plus the plastics at the surface would equal those presumably discharged by rivers into the sea.

According to the study's lead author Dr. Lisa Weiss from the CEFREM laboratory at the University of Perpignan, 'The in situ data that we now have for microplastics in rivers, compared to early empirical modelling studies, allowed us to assemble a robust database which we were then able to analyse to obtain a more reliable estimate for the quantity of microplastics being discharged from rivers into the sea. This process revealed several significant methodological errors in previous flux estimates. When we then corrected these mistakes we found that the global river flux estimates are two to three orders of magnitude less than previously thought. Further, we found that the average residence time for microplastics at the surface of the oceans may actually be a few years as opposed to only several days, as previously estimated."

According to the study's lead author Dr. Lisa Weiss from the CEFREM laboratory at the University of Perpignan, 'The in situ data that we now have for microplastics in rivers, compared to early empirical modelling studies, allowed us to assemble a robust database which we were then able to analyse to obtain a more reliable estimate for the quantity of microplastics being discharged from rivers into the sea. This process revealed several significant methodological errors in previous flux estimates. When we then corrected these mistakes we found that the global river flux estimates are two to three orders of magnitude less than previously thought. Further, we found that the average residence time for microplastics at the surface of the oceans may actually be a few years as opposed to only several days, as previously estimated."

"We can now confirm that the search for the missing 'plastic sink' is over, as the missing plastics have been found through the correction of the river flux estimate", states Professor Miquel Canals, head of the Consolidated Research Group on Marine Geosciences at the University of Barcelona and one of the co-authors of the study.

The new study identifies the main methodological mistakes which led to inaccurate assessments of the fluxes and overall mass of microplastics discharged by rivers into the sea at a global scale. In particular, mistakes were made because of a systematic overestimation of the average microplastic particle weight in river samples; from the integration of incompatible data that were obtained through different sampling techniques; and from assessments based on the relation between microplastic fluxes and the MPW index (mismanaged plastic waste).

A fight without borders to preserve our planet's oceans

Marine waste does not care about borders and has reached the most remote corners of our oceans and seas. According to Dr. Wolfgang Ludwig, the Director of the CEFREM laboratory and co-author of the study, "the only way we are going to have a chance at winning the fight against microplastic pollution will be to target the sources where microplastic waste is generated. We need to take action at the human level. We need to change our consumption habits, better manage our waste and we need to do this at a global scale."

"Our study shows that marine microplastic pollution not only comes from developing countries - with little to no waste management - as one might think, but also comes from countries with well-established waste management systems. If we were to stop the discharge of microplastics from rivers to the sea today, the amount of floating particles and their harmful effects on marine ecosystems would persist for at least another several years", states Dr Ludwig.

Next steps...

The impacts of plastics on the marine environment is an emerging field of scientific research that has generated a large number of scientific publications over the last few years. Still, we have only just begun to understand how plastics cycle in the oceans. There are many plastic size classes, oceanic compartments and land-to-sea transfer processes for which further research is urgently needed to properly evaluate the stock sizes and exchange fluxes between compartments. Going forward, we will need the best available science if we are to have a chance at winning the battle against plastic pollution. To do this, the scientific community must work together to overcome inertia from the past, correct mistakes and work with common protocols and guidelines in order to provide the best possible decision-making advice needed to protect our oceans and seas.

Originally discovered as a bacterial mode of defense against invading viruses, the remarkable ability of CRISPR-Cas9 to modify specific locations of DNA has made it a researcher favorite among gene editing tools. The ongoing effort to explore further possibilities of the CRISPR-Cas9 system is ushering in newer developments to this tool. In one of the latest refinements of the technique, as illustrated in a study published in BioDesign Research, scientists from Stanford University, USA have developed a CRISPR-Cas9 system that induces highly effective silencing of target genes.

The versatility of CRISPR-Cas9 based gene editing is largely achieved by modifying the Cas9 protein itself. In this approach, the endonuclease property of the Cas9 protein is removed, yielding a deactivated Cas9, or dCas9. Many effector proteins, including a wide variety of gene expression-altering enzymes, are then fused with dCas9 for targeted binding to specific sites on the DNA. When fused with an activating or repressing transcription factor, the dCas9 complex upregulates or downregulates the target gene, respectively. However, the gene-altering ability of such complexes is transient, as the effects persist only while the effector domains of the regulatory proteins remain physically bound or actively targeted to the region of interest.

For practical purposes, such as suppressing the effect of a disease-causing mutation, a longer-lasting effect of silencing is desirable. Dr. Lei S. Qi from Stanford University, the corresponding author of the study, and colleagues explain this concept further: "The Cas9 endonuclease, that stops the expression of a target gene, is analogous to a brake which stops the car by breaking its engine. In a modified dCas9-repressor fusion system, that contains a transcriptional repressor, the car remains stopped as long as one holds down the brake pedal actively. However, we aimed to develop a silencing system that, like a parking gear, prevents wheel movement until you switch the car out of it".

To achieve this goal, the researchers adopted an approach based on the epigenetic regulation of the eukaryotic genome where gene expression is altered stably and reversibly by the direct modification of genomic regions. Epigenetic silencing involves methylation of both histone proteins and DNA. In the present study, Dr. Qi and his colleagues fused dCas9 protein with a transcription repressor domain KRAB (Krüppel-associated box) and DNA methylating domains of DNMT3L and DNMT3A- two potent epigenetic modifiers. They named the construct dCas9-KAL and tested its silencing capacity in a cell-based reporter system. When stably integrated into human cells expressing fluorescent protein EGFP, the dCas9-KAL construct, designed to localize at the promoter of EGFP, repressed fluorescence for weeks.

The success in developing a robust and long-term epigenetic repressor has multifold implications. Successful silencing of critical or disease-inducing genetic elements can provide better treatment options for cancer and other genetic ailments. Additionally, the unique construct-synthetic reporter system developed in this study will help the scientists in assessing the activity of various domains or their combinations fused to dCas9. As Dr. Muneaki Nakamura from Stanford University, the lead author of the study, explains: "Since its adoption, CRISPR-Cas9 has revolutionized the face of genetic modification. Our system, as a powerful addition to the CRISPR toolbox, will facilitate further research in the field. It can be used to better engineer cells with desired behaviors, which could find use in the development of custom cell types with wide-ranging research and therapeutic applications,". reflects Dr. Qi.

The team's findings certainly make a noteworthy addition to the molecular Swiss knife that is the CRISPR-Cas9 system!

NDIANAPOLIS--Indiana University School of Medicine researchers are developing a new, noninvasive brain stimulation technique to treat neurological disorders, including pain, traumatic brain injury (TBI), epilepsy, Parkinson's disease, Alzheimer's disease and more.

"Given the increasing use of brain stimulation in human brain study and treatment of neurological diseases, this research can make a big impact on physicians and their patients," said Xiaoming Jin, PhD, associate professor of anatomy, cell biology and physiology.

When someone experiences a brain injury, nerve injury, or neurodegeneration, such as in epilepsy and TBI, there is damage to the brain which can lead to loss and damage of nerve or neurons and development of hyperexcitability that underlies some neurological disorders such as neuropathic pain and epilepsy.

"The conventional treatment is mainly to try to directly inhibit such hyperexcitability," Jin said, "but we found the initial damage of the brain or nerve system was caused by a loss of brain tissue, which causes the nervous system to compensate for loss of function by working harder, so we need to stimulate activity instead of inhibit it."

The technique, described in a newly published paper in Neurotherapeutics, uses a new type of magnetoelectric nanoparticles that can be delivered to a specific part of the brain using a magnetic field. After, a magnetic wave can be emitted to stimulate neural activity in that particular part of the brain. The method is noninvasive, good for stimulating deep brain function and is more efficient than traditional methods of brain stimulation, without the need for genetic manipulation.

"This is the only new type of nanoparticle that allows us to effectively stimulate the brain without doing any invasive procedures," Jin said. "We can inject the nanoparticle as a solution into the vein and then bring it to any part of the body. When you apply a magnet on the head, you can localize and deliver the nanoparticle to the targeted brain region."

The team has been working on the technique for five years in collaboration with the University of Miami and hopes to begin studying the method in humans in the next couple of years. The study has received funding from the Defense Advanced Research Projects Agency (DARPA) of the United States Department of Defense, National Science Foundation, as well as the Indiana Clinical and Translational Sciences Institute (CTSI), which helped provide funding for a medical neuroscience graduate student, Tyler Nguyen, to participate in the research. Read the full published paper in Neurotherapeutics.

Ibaraki, Japan - The flavor of a tomato is an interaction between its taste and aroma. Now, researchers from Japan and the United States have revealed that the pigments that determine the colors of tomatoes also affect their flavor.

In a study published this month, researchers from University of Tsukuba developed a new method to rapidly measure the pigment profiles of tomatoes and used the technique to explore how pigments affect the taste and aroma of different tomato varieties.

The color of tomatoes is produced by combinations of different types of pigments, including carotenoids and chlorophylls. These pigments can also affect the accumulation of flavor-related compounds such as sugars, which affect the taste of tomatoes, and volatile organic compounds (VOCs), which determine the aroma. As tomato fruits ripen from green to red, the amounts of pigments and flavor-related compounds change but until now the relationship between color and flavor has been unclear.

"Pigments like carotenoids have no taste," says lead author Professor Miyako Kusano, "but they are precursors for compounds called apocarotenoid-VOCs (AC-VOCs) which produce the fruity/floral smell of tomatoes and increase the perception of sweetness--characteristics that appeal to consumers."

Traditional methods for identifying and measuring pigments can be slow, so the researchers developed a simple method to rapidly analyze large numbers of samples. Using the new technique, the team measured the amounts of carotenoids and chlorophylls in 157 different varieties of tomato and then analyzed the flavors of each variety to find the links between pigments and flavor.

The results showed that tomato varieties with an abundance of chlorophyll also had a high sugar content, contributing to a sweet taste. They also found that the carotenoid profiles of the fruit reflected the appearance of the fruit, as well as AC-VOC levels.

"The pigment profile of one of the orange-colored varieties called "Dixie Golden Giant" was particularly interesting," explains Professor Kusano. "It had very high levels of AC-VOCs, but the carotenoid content wasn't that high. We discovered that the pigment prolycopene was abundant in this variety, which explained the high AC-VOC levels."

The carotenoid content of fruit is influenced by growing conditions, like temperature and amount of light. By looking at the pigment profiles and AC-VOC content of fruits in different environments, it may be possible to find ways of improving AC-VOC production, which is good for both consumers and producers.

Given its speed, the new method developed by the team is a powerful tool for analyzing pigment concentrations in large numbers of samples and could also be used for other fruits and vegetables.

Elephants and their forebears were pushed into wipeout by waves of extreme global environmental change, rather than overhunting by early humans, according to new research.

The study, published today in Nature Ecology & Evolution, challenges claims that early human hunters slaughtered prehistoric elephants, mammoths and mastodonts to extinction over millennia. Instead, its findings indicate the extinction of the last mammoths and mastodonts at the end of the last Ice Age marked the end of progressive climate-driven global decline among elephants over millions of years.

Although elephants today are restricted to just three endangered species in the African and Asian tropics, these are survivors of a once far more diverse and widespread group of giant herbivores, known as the proboscideans, which also include the now completely extinct mastodonts, stegodonts and deinotheres. Only 700,000 years ago, England was home to three types of elephants: two giant species of mammoths and the equally prodigious straight-tusked elephant.

An international group of palaeontologists from the universities of Alcalá, Bristol, and Helsinki, piloted the most detailed analysis to date on the rise and fall of elephants and their predecessors, which examined how 185 different species adapted, spanning 60 million years of evolution that began in North Africa. To probe into this rich evolutionary history, the team surveyed museum fossil collections across the globe, from London's Natural History Museum to Moscow's Paleontological Institute. By investigating traits such as body size, skull shape and the chewing surface of their teeth, the team discovered that all proboscideans fell within one of eight sets of adaptive strategies.

"Remarkably for 30 million years, the entire first half of proboscidean evolution, only two of the eight groups evolved," said Dr Zhang Hanwen, study coauthor and Honorary Research Associate at the University of Bristol's School of Earth Sciences.

"Most proboscideans over this time were nondescript herbivores ranging from the size of a pug to that of a boar. A few species got as big as a hippo, yet these lineages were evolutionary dead-ends. They all bore little resemblance to elephants."

The course of proboscidean evolution changed dramatically some 20 million years ago, as the Afro-Arabian plate collided into the Eurasian continent. Arabia provided crucial migration corridor for the diversifying mastodont-grade species to explore new habitats in Eurasia, and then into North America via the Bering Land Bridge.

"The immediate impact of proboscidean dispersals beyond Africa was quantified for the very first time in our study," said lead author Dr Juan Cantalapiedra, Senior Research Fellow at the University of Alcalá in Spain.

"Those archaic North African species were slow-evolving with little diversification, yet we calculated that once out of Africa proboscideans evolved 25 times faster, giving rise to a myriad of disparate forms, whose specialisations permitted niche partition between several proboscidean species in the same habitats. One case in point being the massive, flattened lower tusks of the 'shovel-tuskers'. Such coexistence of giant herbivores was unlike anything in today's ecosystems."

Dr Zhang added: "The aim of the game in this boom period of proboscidean evolution was 'adapt or die'. Habitat perturbations were relentless, pertained to the ever-changing global climate, continuously promoting new adaptive solutions while proboscideans that didn't keep up were literally, left for dead. The once greatly diverse and widespread mastodonts were eventually reduced to less than a handful of species in the Americas, including the familiar Ice Age American mastodon."

By 3 million years ago the elephants and stegodonts of Africa and eastern Asia seemingly emerged victorious in this unremitting evolutionary ratchet. However, environmental disruption connected to the coming Ice Ages hit them hard, with surviving species forced to adapt to the new, more austere habitats. The most extreme example was the woolly mammoth, with thick, shaggy hair and big tusks for retrieving vegetation covered under thick snow.

The team's analyses identified final proboscidean extinction peaks starting at around 2.4 million years ago, 160,000 and 75,000 years ago for Africa, Eurasia and the Americas, respectively.

"It is important to note that these ages do not demarcate the precise timing of extinctions, but rather indicate the points in time at which proboscideans on the respective continents became subject to higher extinction risk," said Dr Cantalapiedra.

Unexpectedly, the results do not correlate with the expansion of early humans and their enhanced capabilities to hunt down megaherbivores.

"We didn't foresee this result. It appears as if the broad global pattern of proboscidean extinctions in recent geological history could be reproduced without accounting for impacts of early human diasporas. Conservatively, our data refutes some recent claims regarding the role of archaic humans in wiping out prehistoric elephants, ever since big game hunting became a crucial part of our ancestors' subsistence strategy around 1.5 million years ago," said Dr Zhang.

"Although this isn't to say we conclusively disproved any human involvement. In our scenario, modern humans settled on each landmass after proboscidean extinction risk had already escalated. An ingenious, highly adaptable social predator like our species could be the perfect black swan occurrence to deliver the coup de grâce."

Understanding how viral infection occurs can provide important clues for researchers to develop strategies to prevent viral transmission and develop effective therapeutic agents and vaccines. SARS-CoV-2, the causative agent of COVID-19, enters the host cells through interaction between the virus's spike protein and the extracellular receptor binding domain of ACE2. The viral entry into the cells is completed by various proteases, which allow the viral and cell membranes to fuse together. While it is known that the upper respiratory tract becomes compromised in the early infection, the exact types of the cells that the virus infects at the earliest stage have not yet been identified.

Led by Director KOH Gou Young, scientists from the Center for Vascular Research within the Institute for Basic Science, South Korea, have recently uncovered the processes involved in the earliest stages of COVID-19 infection. The group accomplished this by combining immunofluorescence staining (IFS) and single-cell RNA-sequencing (scRNA-seq) of the molecules that are involved in the viral entry process. Through this, Koh and his colleagues identified the exact target of the coronavirus at the cellular level by comparing the results of the subjects infected with COVID-19 with those of healthy controls.

The researchers first looked for the presence of ACE2, TMPRSS2, and FURIN, which are the predominant SARS-CoV-2 entry-related molecules, on the surfaces of various types of cells in the nasal epithelium. It was found that these proteins were present in high quantities on ciliated cells. Moreover, the apical (upper) sides of these cells showed higher levels of these molecules in comparison to the basal (bottom) side. The levels of these proteins were highest in fully differentiated multiciliated cells. On the other hand, viral entry proteins were not found in the undifferentiated epithelial cells or secretory cells such as the goblet cells.

Next, the researchers further studied these nasal epithelial cells using scRNA-seq and visualized the cells into different clusters using UMAP. Samples were collected from 4 patients on the first day of their COVID-19 diagnosis, which were compared against 2 samples from healthy donors. It was found that the fraction of multicilial cells was greatly reduced in the samples from infected patients, while there was an increase in the secretory cells and differentiating cells. This hinted that multicilial cells were the first to be attacked and killed off by the virus, which are then replaced by the latter types of cells.

The study also measured the level of SARS-CoV-2 mRNA transcripts within the various types of cells. Among all the epithelial cells in COVID-19 infected patients, 38% of the cells were labeled as SARS-CoV-2hi cells. Up to 75% of the detected genes in these cells were of viral origin, compared to less than 1% for other clusters of cells. This means that these cells serve as the main factories for the mass production of SARS-CoV-2 viruses. While it was not possible to directly identify these cells through RNA seq due to the fact that they primarily produce viral mRNA, the researchers employed pseudo-time-trajectory analysis to predict their differentiation paths. The differentiation trajectory showed that SARS-CoV-2hi cells likely originated from ciliated cells. Further IFS analysis on the infected patients' samples conclusively determined that up to 85% of SARS-CoV-2 factories were in fact multiciliated cells.

This study was able to determine that multiciliated cells in the nasal epithelium are the first cells that are targeted in the early COVID-19 infection. This implies that targeting these cells using specific treatments, such as through nasal sprays, can be an ideal strategy to curb COVID-19 infection in the early stages.