Earth

Orchids are more than just decorative - they are also economically important in horticulture, in the pharmaceutical industry and even in the food industry. For example, vanilla orchids are grown commercially for their seed pods, and the economy on the northeast of Madagascar centers around the vanilla trade. But many of the approximately 29,000 orchid species face immediate threats by land conversion and illegal harvesting, resulting in an urgent need to identify the most endangered species and protect them from extinction. The global Red List of the International Union for the Conservation of Nature (IUCN) is the most widely used scheme to evaluate species' risk of extinction. The assessments are based on rigorous criteria and the best available scientific information, making them resource-intensive and, therefore, only available for a fraction of the species worldwide. To date, only about 1,400 of all orchid species have IUCN Red List assessments.

An international team led by researchers from the German Centre for Integrative Biodiversity Research (iDiv), Leipzig University (UL), Martin Luther University Halle-Wittenberg (MLU) and the Helmholtz Centre for Environmental Research (UFZ) addressed this issue with the help of an automated assessment approach including the use of machine learning algorithms - also known as deep learning. The integration of machine learning into automated conservation assessments may bring them to a whole new level. "Deep neural networks are widely used in other fields such as image recognition, but they can also help with conservation assessments," said Dr Alexander Zizka from iDiv and UL. "With our method, we can incorporate additional aspects such as climate, geographic region or traits related to the respective species - and we can do this very fast."

"Ideally, all orchid species would have IUCN Red List assessments - this way, the ones most urgently in need of conservation efforts most urgently are identified, which is the critical first step in conservation," said Dr Pati Vitt of Northwestern University in Evanston (USA). Vitt, an expert in the field of orchids, came on sabbatical to iDiv in 2018 and worked with scientists with expertise in automated assessments. Bringing together their different skills and expertise, the researchers assessed the risk of extinction for almost 14,000 orchid species - the first large-scale assessment of the conservation status of orchids.

The researchers found that out of the 14,000 orchid species more than 4,300 are possibly threatened with extinction. They were also able to identify the places where conservation efforts are most urgently needed: Madagascar, East Africa, south-east Asia, and several oceanic islands are priority areas for orchid conservation. The automated assessments identified threatened species with an accuracy of 84.3%.

The researchers also examined the cases in which the automated assessments classified species differently than the IUCN Red List. "This provides information on how we can best refine the automated assessments in the future to increase their accuracy even more," said Prof Tiffany Knight from iDiv, MLU and UFZ. "For orchids, we would need to incorporate information on species trade and local land use."

The automated approach the researchers applied for the orchid family may be a model for other species. In particular, the approach could be valuable for the species-rich, but poorly studied, tropical regions. Here, even preliminary assessments will be useful for informing conservation. "A particular strength of our approach is that it can be trained for other taxonomic groups or regions," said Zizka. "By doing so, it could speed up the conservation assessment of all species on Earth."

Introducing high doses of gluten from four months of age into infants' diets could prevent them from developing coeliac disease, a study has found.

These results from the Enquiring About Tolerance (EAT) Study, published today in JAMA Pediatrics, by researchers from King's College London, Guy's and St Thomas' NHS Foundation Trust, St George's, University of London, and Benaroya Research Institute, Seattle, suggest the early introduction of high-dose gluten may be an effective prevention strategy for the disease, though researchers say further studies are needed before being applied in practice.

Coeliac disease is an autoimmune disease whereby eating gluten causes the body's immune system to attack its own tissues. There are currently no strategies to prevent coeliac disease and treatment involves long-term exclusion of gluten from the diet. Even very small amounts of gluten in the diet of those with coeliac disease can cause damage to the lining of the gut, prevent proper absorption of food and result in symptoms including bloating, vomiting, diarrhoea, constipation, and tiredness.

Previous studies exploring early introduction of gluten in infants have varied in the amount of gluten consumed and the timing of the introduction. The EAT study investigated the effects of gluten alongside breastfeeding, from the age of four months. The results were compared to children who avoided allergenic foods and consumed only breast milk until age six months as per UK government guidelines.

Infants in the intervention arm of the EAT study were given 4g of wheat protein a week from four months of age. This was in the form of two wheat-based cereal biscuits such as Weetabix, representing an age-appropriate portion of wheat.

1004 children were tested for antitransglutanimase antibodies, an indicator of coeliac disease, at three years of age. Those with raised antibody levels were referred for further testing by a specialist.

The results showed that among children who delayed gluten introduction until after six months of age, the prevalence of coeliac disease at three years of age was higher than expected - 1.4% of this group of 516 children. In contrast, among the 488 children who introduced gluten from four months of age, there were no cases of coeliac disease.

Lead author Professor Gideon Lack, Professor of Paediatric Allergy at King's College London and head of the children's allergy service at Evelina London Children's Hospital said: "This is the first study that provides evidence that early introduction of significant amounts of wheat into a baby's diet before six months of age may prevent the development of coeliac disease. This strategy may also have implications for other autoimmune diseases such as Type 1 diabetes."

Author Dr Kirsty Logan, Researcher in Paediatric Allergy at King's College London said: "Early introduction of gluten and its role in the prevention of coeliac disease should be explored further, using the results of the EAT Study as the basis for larger clinical trials to definitively answer this question."

A molecule that can mimic the function of zaxinone, a natural growth-promoting plant metabolite, has been designed and fabricated by an international team led by KAUST and the University of Tokyo. Their successful mimic may have wide-reaching applications in plant biology and agriculture.

"We identified zaxinone in a previous study and found that it both stimulates the growth of rice plants and appears to reduce infestation by the root parasite Striga (witchweed)," says Jian You Wang, Ph.D. student under the supervision of Salim Al-Babili. "It is tempting to jump in and say we can harvest zaxinone from plants, study its activity and use it to boost crop yields, but it is not that simple."

Living organisms produce growth regulating metabolites, such as zaxinone, at very low concentrations, and the molecules themselves are often short-lived and unstable. The team realized that to make full use of their discovery, they would need to design a synthetic molecule that can mimic zaxinone's function, rather than using the metabolite itself.

"We first identified the parts of zaxinone that are crucial for its activity and the other parts that can be replaced or modified," says Wang. "These results helped our team to design a series of easy-to-synthesize zaxinone mimics called MiZax."

The team trialed MiZax by adding them to soil and measuring their ability to improve root growth and limit Striga infestation in rice plants. Two of the mimics, MiZax3 and MiZax5, proved particularly effective, with MiZax3 performing even better than zaxinone itself.

"We were excited to see the excellent activity and stability of MiZax3, even when it was used at very low concentrations," says Wang. "It is important to note that we still do not know precisely how zaxinone itself works. MiZax3 will help us investigate the mechanisms behind zaxinone's activity and how it changes plant hormone patterns and metabolism."

"We will also perform controlled field and safety tests to evaluate MiZax activity on cereals and horticultural crops in greenhouse and research farms in the Kingdom," says Al-Babili. "MiZax will help us improve our understanding of the development, growth and biotic interactions of cereals, particularly rice."

Methane is a powerful greenhouse gas that plays a central role in the global carbon cycle. At the same time, it is an important energy source for us humans. About half of its annual production is made by microorganisms known as methanogens that decompose organic material such as dead plants. This normally takes place in a habitat without oxygen as this gas is lethal to methanogens. But even in actually oxygen-free habitats, oxygen molecules occasionally appear. To render these intruders harmless, methanogens possess a special enzyme that is able to convert oxygen into water.

"Enzymes are vital components of the metabolism of all living organisms and the goal of our laboratory is to understand how these nanomachines are working at the molecular level," says Tristan Wagner from the Max Planck Institute for Marine Microbiology and first author of the study, published in the scientific journal Chemical Communication in September 2020. For the study, Wagner cultivated anaerobic microorganism called Methanothermococcus thermolithotrophicus, which originated from the sediment of the Gulf of Naples. He purified the enzyme F420-oxidase, a flavodiiron protein, and crystallized it, a common method to study the functioning of enzymes.

"It was already known that F420-oxidase can convert oxygen into water," says Wagner. "But we succeeded to decrypt the mechanism". The study is a cooperation of scientists from the Max Planck Institute for Marine Microbiology, the Max Planck Institute for Terrestrial Microbiology, the Paul Scherrer Institute, the Interdisciplinary Research Institute of Grenoble and the European Synchrotron Radiation Facility.

Oxygen is locked in

The mechanism, the researchers revealed, has an important requirement: Oxygen is very reactive, so it is crucial that the reaction is controlled correctly by the enzyme and no solvents are floating around. Otherwise the oxygen could accidentally be transformed in superoxide and kill the anaerobe. The trick of the enzyme F420-oxidase is to use a gas channel and a gating system. The oxygen molecule is first funneled in the specific channel to an appropriate anhydrous catalytic cavity containing iron. Then iron transforms the oxygen in water that will be released by a gating mechanism. For that the cavity begins to move and opens a small "door". Thanks to the movement, the newly generated water is transported outside. The empty cavity closes again and is available for the next oxygen molecule.

To gain insights into this mechanism the scientists used X-ray crystallography. They first obtained the crystal structure without oxygen, where they could see the anhydrous catalytic cavity isolated from the solvent. Then, they gassed the enzyme crystals with the inert gas krypton, which, unlike oxygen, can be made visible by X-rays. Afterwards they irradiated the enzyme crystals and were able to detect krypton atoms showing the gas channel leading to the catalytic cavity. The flavodiiron protein and its channel is conserved not only in methanogens, but also in other microorganisms like clostridia (who live mainly in soil or in the digestive tract), in the sulfur bacteria Desulfovibrio gigas or even in the intestinal parasite Giardia intestinalis.

The faster the better

"This reaction is really fast," says Sylvain Engilberge from the Paul Scherrer Institute and first author of the study next to Tristan Wagner. "This velocity is also the high importance of our investigation". Similar enzymes like laccase are much slower. "For future application of bio-inspired electrochemical processes, we need to learn more from the chemical reaction, structure and function of different groups of oxygen-reducing enzymes," says Engilberge. It would also pave the way of protein engineering to convert a high-rate O2-detoxifier into an electron sink for industrial processes.

"Our next step would be to understand the diversity of flavodiiron protein," says Tristan Wagner. Some homologues are not targeting oxygen but the poisonous nitric oxide, their enzymes can discriminate between both gases with high specificity. But what is the selective filter? The gas channel? The environment of the catalytic cavity? "More studies have to be carried out to understand how the protein discriminates oxygen and nitric oxide," adds Wagner. With such knowledge, it would be for instance possible to predict from genomic information if a flavodiiron protein would be an oxygen or a nitric oxide scavenger.

Cell plasticity is a property by which a cell can take on different and reversible identities. Cell plasticity is also essential for embryo development and for the correct function of the immune system. This property is also crucial in cancer as many cancer cells use it to gain resistance to chemotherapy and invade and colonise distant parts of the body.

Headed by the ICREA researcher Manuel Serrano, scientists at the Cellular Plasticity and Disease Laboratory at the Institute for Research in Biomedicine (IRB Barcelona) have discovered a way to regulate this plasticity by "blocking" plastic cells in one of their possible states.

"The identity of each cell type is defined by a particular gene expression program. What makes plastic cells special is that, in addition to their identity genes, they can express at low levels genes belonging to other cell identities. This sort of "background noise" is what allows them to change identity at a given time, and what was once "background noise" becomes the dominant genetic program," explains Serrano.

Regulating gene expression to modulate plasticity

Until now, the methods used to block cell plasticity were based on inhibiting some of the external stimuli that cells receive. But these approaches are usually incompatible with cell multiplication and can end up damaging the cells themselves.

The new method developed by Serrano's lab, which is supported by "la Caixa" Foundation, focuses on the profound mechanism that regulates gene expression, it does not affect cell viability, and it is completely reversible. The key to this new approach is the inhibition of the protein CDK8.

"We have observed that CDK8 inhibition strengthens the expression of genes that determine cell identity, and this occures at the expense of switching off the "background noise" of alternative identities. So the cells are fixed in a specific identity and they lose their plasticity," says Cian J Lynch, first author of the study and postdoctoral fellow in the same laboratory.

Important implications in biomedicine

Having the capacity to regulate cell plasticity can have many advantages in a biomedical research context as it allows researchers to study all the processes in which plasticity is a key element, such as cancer and embryo development. The present study has focused on embryonic stem cells. The great plasticity of this type of cells makes them highly attractive for cell therapy applications. However, this very same plasticity poses a real challenge when it comes to culturing these cells in the lab.

"Because of the intrinsic plasticity of embryonic stem cells, cultures produced in the lab are highly heterogeneous, and previous methods available to reduce plasticity were very harmful to the cells. This was a practical problem with no apparent solution," says Raquel Bernad, co-author of the study who has just completed her PhD. The researchers have demonstrated that it is possible to culture embryonic stem cells in the presence of a CDK8 inhibitor, thus making the culture less plastic, more homogeneous and without damaging the cells. Something that had not been achieved until now. Simply removing the CDK8 inhibitor restores plasticity to the cells.

Furthermore, scientists from other laboratories have observed that this new method may have implications in autoimmune diseases in which the plasticity of T cells make them adopt an overly active state, leading to an exacerbated immune response.

With respect to implications for oncology, "Cell plasticity is known to be a key factor underlying resistance to chemotherapy. By blocking cell plasticity, we hope to improve reactions to chemotherapy by achieving more homogeneous and lasting responses," adds Serrano.

The results obtained are very encouraging and the researchers hope to be able to make headway in a multifunctional cell therapy system to treat inflammatory bowel disease. In fact, they have already commenced studies on ulcerative colitis in animal models.

"Perhaps the best known side is the use of stem cells in regenerative therapies," said Rosa Hernández, professor of the Faculty of Pharmacy and researcher at CIBER-BBN, "since we have all heard for example about the use of chondrocytes in cartilage regeneration or cardiomyocytes to repair a heart following myocardial infarction. However, our research group is working on evaluating the therapeutic action of stem cells by means of their paracrine effects, in other words, mediated by a set of growth factors and cytokines released by the cells."

In a whole host of disorders with an inflammatory component, such as ulcerative colitis or Crohn's disease, a possible beneficial effect following delivery of stem cells has been seen. On the basis of this, this group of researchers, led by Dr Rosa Herná¡ndez and Dr Manoli Igartua, embarked on a highly ambitious project three years ago to try and develop systems designed to address the problems arising in clinical trials conducted with these stem cells. In fact, even though the potential of stem cells to treat these inflammatory disorders became clear in these trials, problems, such as the rapid elimination of cells from the body, the possible development of tumours or their reduced capability in releasing therapeutic substances were also detected, so new technological solutions had to be sought.

This group of UPV/EHU researchers, whose leading members are Ainhoa Gonzalez-Pujana and Dr Edorta Santos-Vizcaíno, successfully designed and tested a multifunctional system recently in collaboration with Harvard University in Cambridge (USA), specifically with the group led by Dr David J. Mooney. "Besides stem cells, the system incorporates other elements, such as biomaterials and microparticles that release interferon. That way, the activation of the cells can be prolonged so that they constantly release key cytokines and growth factors to treat these disorders; in addition, the persistence of the cells in the body and the biosafety of the therapy can be improved," said Dr Herná¡ndez.

The afterlife of plant matter plays a significant role in ecosystems, as a key processor and provider of key nutrients. The rate of decomposition for leaf litter, among other plant matter, heavily influences the health of animals and plants, and this rate is expected to significantly increase as Earth continues to warm. There is another factor that could hold impact these ecosystems even more than climate change: biodiversity.

An international team of researchers published a meta-analysis of 176 studies investigating the effect of diverse leaf litter decay on ecosystems around the world on Sept. 11 in Nature Communications.

"Biodiversity loss can alter ecosystem functioning; however, it remains unclear how it alters decomposition--a critical component of biogeochemical cycles in the biosphere," said paper author Akira S. Mori, associate professor in the Graduate School of Environment and Information Sciences at Yokohama National University. "We provide a global-scale meta-analysis to quantify how changes in the diversity of organic matter derived from plants, called litter, affect rates of decomposition."

They found that diversifying plant litter from single to mixed species increases the decomposition rate by 34.7%. It is projected that, in response to climate warming over the next 50 years, decomposition rates will increase by 13.6 to 26.4%.

"We found that the after-life effects of diversity to foster decomposition were significant, and of substantial magnitude, in different biomes including forests, grasslands and wetlands," Mori said. "Biodiversity changes cannot be solely viewed as a response to human influences, such as climate change, but it could also be, although less recognized, a non-negligible driver of future changes in biogeochemical cycles and climate feedbacks on Earth."

The roles of biodiversity have been largely ignored in the context of climate change mitigation and adaptation, according to Mori. In an effort to understand how biodiversity loss can alter ecosystem functioning, the researchers synthesized a comprehensive data set from 7,958 leaf litter comparisons across 2,453 different treatments reported in 176 studies.

"Our dataset and analysis are comprehensive by covering the broad range of climatic regions and extensive in considering many possible comparisons for decomposition rate between mixed and mono-species litter in different biomes," Mori said, noting the importance of understanding how the magnitude of these diversity effects compare to other decomposition regulators, such as climate. " After accounting for many confounding factors, we found that, across all studies, increasing plant diversity significantly increased the rate of decomposition."

It was previously assumed that the effects of plant diversity on decomposition were not as strong as the effects on biomass production, but the researchers found that to be false.

"We emphasize that incorporating the underexplored roles of biodiversity into the assessment of future changes in the biogeochemical cycles and climate feedbacks is critical in this era of global environmental changes," Mori said. "We aim to put biodiversity at the heart of nature-based approaches to solve many socio-environmental issues, including climate change."

According to Mori, further studies are needed to fully understand the roles of diverse plant communities for supporting naturally functioning ecosystems, but that this meta-analysis begins to bridge the gap in knowledge.

"The present study can inform the models needed to incorporate the unexplored roles of biotic interactions in determining carbon and nutrient flow through decomposer subsystems, which could be critical for improving future projections on climate feedbacks," Mori said.

The location of a country on the earth says a lot about its climate, its neighboring countries, and the resources that might be found there. The location therefore determines what kind of country you would expect to find at that point.

The same seems to apply to the brain. Every network is located at a certain place, which determines its function and neighbors but also the kind of function that occurs there. However, the rules that describe the relationships different brain regions have to each-other were not well understood until now. Scientists at the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig, Germany, and the Forschungszentrum Juelich, together with an international team of collaborators, have deciphered two axes along which the human brain is organized. It was found that these axes are mainly determined by genetic factors.

One axis stretches from the posterior (back) to the frontal part of the cortex. This reflects a functional hierarchy from basic capabilities such as vision and movement to abstract, highly complex skills such as cognition, memory, and social skills. A second axis leads from the dorsal (upper) to the ventral (lower) part of the cortex. Whereas the ventral system has been associated with functions assigning meaning and motivation, the dorsal system may relate to space, time, and movement.

"Interestingly, this vertical arrangement aligns with the long-held hypothesis of dual origin", says Sofie Valk, research group leader at the MPI CBS and Forschungszentrum Juelich and first author of the study, published in Science Advances. According to this hypothesis, the cerebral cortex developed from two different origins, the amygdala and olfactory cortex on the one hand and the hippocampus on the other hand. From these origins two different lines of cortical development arose, reflecting waves from less to more differentiated areas starting at each origin. Such distinctions between ventral and dorsal areas have been found in various mammals, such as non-human primates, cats, and rats. The scientists around Valk, however, have now provided evidence for it for the entire human cortex, and shown this may be a second important organizational principle next to the posterior-frontal axis.

This two-axis-organization, in turn, is largely determined by the genetic relation between brain regions. This means that the association between the structure of two brain regions is driven by shared genetic effects. Moreover, similar axes have been found in the brains of macaque monkeys, indicating these axes are conserved through primate evolution. "At the same time, even if genes and evolution shape the organization of brain structure, we must not forget the environment also plays a crucial role in shaping our brains and minds", Valk says. "Though we focused specifically on these genetic effects in the current study, other work of our team has shown that behavioral training can also alter brain structure." Further studies are planned to understand how these two factors that shape brain structure interact.

To understand the major axes of brain organization is like having a compass, and can help to better navigate in the brain. "We may better understand the evolution and function of specific regions and better evaluate the impact of brain disorders", Valk adds. For example, previous work of the authors has shown that organizational axes differ between individuals with autism spectrum disorder and healthy controls.

The scientists have investigated the organization of brain structure using a multi-level approach. First, they used monozygotic and dizygotic twins, as well as unrelated persons, to model how much of the brain's organization is genetically determined. They measured how the thickness of the cortex correlated across a group of individuals, which provided information on the structural and developmental relationship between different brain regions. If, for example, certain relationships were stronger in monozygotic twins than in other siblings, this would presumably be due to genetic factors. Using the genetic information of the relationships between different brain regions, they computed the major axes along which genetically similar brain structures are organized. They also compared the brain organization in humans with that in macaque monkeys. Finding similar axes in these animals, they concluded that this organization is conserved across primate evolution.

WASHINGTON, Sept. 28, 2020 -- Maybe you've seen a beautiful, color-changing tea on social media. Chances are, it's butterfly pea flower tea. This week, we're investigating what allows it to shift from one vibrant color to the next, and Sam and George play around to see how many different colors they can get: https://youtu.be/ORl6EKQI1ws.

Regrowing forests are absorbing just a small proportion of the carbon dioxide released from widespread deforestation in the Amazon, according to new evidence.

Secondary forests - areas of new forest growing on land that has previously been deforested - form a key part of policies aiming to tackle net carbon emissions and mitigate climate change.

In 2017 there were nearly 130,000 square kilometres of secondary forest in the Brazilian Amazon - roughly equivalent to the size of England.

Despite their scale and importance for climate targets, our understanding of their contribution to the tropical carbon balance is incomplete. It was not clear to what extent carbon emissions from deforestation have been offset by secondary forest growth, or how this has varied over time.

A new study by an international team of researchers from the UK and Brazil, published by Global Change Biology, used open source MapBiomas data to map the age, extent and carbon stock of secondary forests across the Brazilian Amazon between 1986 and 2017.

After calculating how much carbon had been lost through deforestation, the scientists discovered that, in more than 30 years, the regrowth of secondary forests in the Brazilian Amazon has offset less than 10 per cent of emissions from the loss of old-growth forests.

Charlotte Smith, a PhD researcher at Lancaster University and lead author of the study, said: "Secondary forests have an incredible potential to store large quantities of carbon. However, it takes a long time for them to build this carbon stock, so without a drastic decline in the rate of deforestation their environmental benefits will continue to be undermined."

Despite a fifth of deforested land now being covered in secondary forest, the researchers found that most secondary forests are relatively young - more than 85 per cent are younger than 20 years old and almost half (42 per cent) are less than five years old.

This is because secondary forests are also subject to deforestation. Areas of land have been repeatedly deforested - thus limiting secondary forests' effectiveness as a carbon store. "Of all the secondary forest mapped over the 32-year period, 60 per cent had been deforested again by 2017," said Charlotte.

The researchers then looked at other factors known to affect secondary forest growth and carbon up-take, such as climate, landscape and proximity to old-growth forests, which can act as a source of seeds.

They found that the majority of secondary forests are situated far from primary forests, in the drier parts of the Amazon. These factors suggest they will be relatively poor for taking-up carbon.

The findings highlight that halting deforestation, particularly of old-growth forest, is essential and that secondary forest growth alone is not sufficient to control carbon emissions in the Amazon.

Co-author, Professor Jos Barlow, said: "Although secondary forests could be an important part of the solution to climate change, it is also important not to overstate their relevance. Deforestation rates in the Brazilian Amazon surpassed 10,000km2 last year, and will almost certainly surpass that in 2020."

The researchers hope that these results will help inform policies and management proposals that can mitigate climate change more effectively. "We show that preventing further deforestation remains the most urgent priority to mitigate climate change," said Charlotte.

COLUMBIA, Mo. -- When Saathvik Kannan's father, a faculty member at the University of Missouri, saw his friend, Kamlendra Singh, a research professor at MU, on television being interviewed for his research identifying possible treatments for COVID-19, he called Singh to congratulate him on his work. After learning that his friend's son, Saathvik, had experience with and a passion for computer programming, Singh invited the 8th grader, who was a student at West Middle School in Columbia, Missouri, at the time, to collaborate with researchers at MU to identify mutations in the virus causing COVID-19.

Kannan teamed up with Singh and Austin Spratt, an MU undergraduate student studying mathematics, and together they analyzed protein sequences for COVID-19 samples from all over the world. They identified 3 specific mutations, D614G, P323L and C241U, that were co-existing in every single case of COVID-19 in the United States, which could suggest why the virus seems to be so infectious in the United States. Their newest unpublished research indicates that resurgent COVID-19 viruses in European countries also have all three of the identified mutations in nearly all European cases. The findings define the dynamics of COVID-19 evolution, and they can be useful for developers of COVID-19 treatments or vaccines to help them consider which mutations in the virus are necessary to target.

"By painting a more complete picture of what mutations are occurring in the virus, we can provide specific information to assist those developing treatments and vaccines for the disease," said Singh, the project supervisor, professor in the MU College of Veterinary Medicine, Bond Life Sciences Center investigator, and assistant director of the Molecular Interactions Core. "Our overall objective is to better understand what is causing the virus to be spreading so rapidly and efficiently, and our research has shown there may be multiple mutations involved that need to be considered when developing antiviral drugs or vaccines."

Singh mentored Kannan and Spratt by allowing these students to use their computer programming skills to advance scientific research aimed at addressing the challenges of the COVID-19 pandemic. By identifying patterns in the various sequences of COVID-19 virus samples from all over the world, the students were able to paint a clearer picture of co-evolving mutations occurring inside the virus that is causing it to spread.

"The antiviral drugs that are currently being made to treat COVID-19 are developed based off the current model for the virus," said Spratt. "But as these mutations are co-evolving and causing the virus' structure to change, the model becomes less accurate and so the current antiviral drugs may become less effective on the mutated versions of the virus. Therefore, by getting a clearer picture of how the virus' structure is evolving, we can create better models of the virus so better antiviral drugs and vaccines can be developed."

Now a freshman at Hickman High School, Kannan is proud of the team's work and grateful for the opportunity to be involved in such impactful research.

"I have always had a passion for computer science and data analytics," Kannan said. "It also feels good to provide my community with information that might help the situation in the future."

One of the biggest challenges to the development of medical treatments for cancer is the fact that there is no single kind of cancer. Cancers derive from many kinds of cells and tissues, and each have their own characteristics, behaviors, and susceptibilities to anti-cancer drugs. A treatment that works on colon cancer might have little to no effect on lung cancer, for example.

So, to create effective treatments for a cancer, scientists seek insight into what make its cells tick. In a new paper appearing in Nature Communications, Caltech researchers show that a framework they developed, using a specialized type of microscopy, allows them to probe the metabolic processes inside cancer cells.

The work was conducted by researchers from the laboratory of Lu Wei, assistant professor of chemistry, as well as from the Institute for Systems Biology in Seattle and UCLA. It utilizes a technique called Raman spectroscopy in conjunction with its advanced version, stimulated Raman scattering (SRS) microscopy. Raman spectroscopy takes advantage of the natural vibrations that occur in the bonds between the atoms that make up a molecule. In this method, a molecule is bombarded with laser light. As the laser light's photons bounce off the molecule, they gain or lose energy as a result of their interaction with the vibrations in the molecule's bonds. Because each kind of bond in a molecule affects photons in a unique and predictable way, the structure of the molecule can be deduced by how the photons "look" after they bounce off of it. By mapping the distribution of targeted chemical bonds, SRS microscopy then provides imagery of these molecular structures.

Using those combined techniques, Wei and her fellow researchers examined the metabolites present in five cell lines of melanoma commonly used in research. The melanoma cells were chosen, according to Wei, because they have a wide spectrum of metabolic characteristics that can be studied.

By studying the cells' metabolites, the researchers can begin to deduce how their metabolisms work, and how they could be targeted by drugs. This is similar to how a saboteur might gather information about the machinery in a factory in order to plan where they can cause the most damage.

"The question we are interested in is why all the cancer cells we look at have very different behaviors," Wei says. "Because some cells have higher reliance on some metabolic pathways, they are more susceptible to disruption of those pathways."

Wei says the team uncovered a few new metabolic susceptibilities in cancer cells, including fatty acid synthesis and mono-unsaturation, but adds that right now, the primary purpose of the research is to do fundamental science.

"We've introduced a framework of pushing Raman spectroscopy into systems biology," she says. "And we're using sub-cellular information we've gathered with it to guide our study into pharmacometabolomics--the study of how metabolism affects drugs."

James R. Heath of the Institute for Systems Biology in Seattle and co-author on the paper says this new technology allows researchers to obtain a more detailed look inside cancer cells than ever before.

"The chemical imaging methods developed in Lu's lab allowed us to identify druggable metabolic susceptibilities in some very aggressive cancer models. These metabolic weaknesses would be missed by any other analytical approach," Heath says.

Two groups of tiny, delicate marine organisms, sea butterflies and sea angels, were found to be surprisingly resilient--having survived dramatic global climate change and Earth's most recent mass extinction event 66 million years ago, according to research published this week in the Proceedings of the National Academy of Sciences led by Katja Peijnenburg from Naturalis Biodiversity Center in the Netherlands.

Sea butterflies and sea angels are pteropods, abundant, floating snails that spend their entire lives in the open ocean. A remarkable example of adaptation to life in the open ocean, these mesmerizing animals can have thin shells and a snail foot transformed into two wing-like structures that enable them to "fly" through the water.

Sea butterflies have been a focus for global change research because they make their shells of aragonite, a form of calcium carbonate that is 50 percent more soluble than calcite, which other important open ocean organisms use to construct their shells. As their shells are susceptible to dissolving in more acidified ocean water, pteropods have been called "canaries in the coal mine," or sentinel species that signal the impact of ocean acidification.

With some pteropods having thin shells and others having only partial or absent shells, such as the sea angels, their fossil record is patchy. Abundant pteropod fossils are only known from 56 million years ago onward and mostly represent the fully-shelled sea butterflies. These observations led to the notion that evolutionarily, pteropods are a relatively recent group of gastropods.

An international team of researchers sampled 21 pteropod species across two ocean transects as part of the Atlantic Meridional Transect programme and collected information on 2,654 genes. Analyzing these data and key pteropod fossils, the scientists determined that the two major groups of pteropods, sea butterflies and sea angels, evolved in the early Cretaceous, about 139 million years ago.

"Hence, both groups are much older than previously thought and must have survived previous episodes of widespread ocean acidification, such as at the end of the Cretaceous, 66 million years ago, and the Paleocene-Eocene Thermal Maximum, 56 million years ago," said Peijnenburg.

Knowing whether major groups of pteropods have been exposed to periods of high carbon dioxide is important as researchers attempt to predict how various marine species may respond to current and future global change.

"Although these results suggest that open ocean, shelled organisms have been more resilient to past ocean acidification than currently thought, it is unlikely that pteropods have experienced global change of the current magnitude and speed during their entire evolutionary history," said Erica Goetze, co-author and University of Hawai'i at Mānoa oceanographer.

It is still an open question whether marine organisms, particularly those that calcify, have the evolutionary resilience to adapt fast enough to an increasingly acidified ocean.

"Current rates of carbon release are at least an order of magnitude higher than we have seen for the past 66 million years," said Peijnenburg. Hence, she stressed the disclaimer "past performance is no guarantee of future results."

A routine test used to monitor patients' breathing may be unreliable and putting them at risk, a study suggests.

Incorrect results can mean clinical staff fail to spot how unwell a patient with respiratory problems is becoming, researchers say.

This widely used method, which counts breaths over a 30-second period, fails to take account of people's irregular breathing patterns, the team says.

The practice - key to assessing risk in many Covid-19 cases - could be improved by increasing the time of measurement to two minutes, the study concluded.

A team from the University of Edinburgh focused on what is referred to as the respiratory rate, which is the measurement of the number of breaths a person takes in one minute.

The rate is measured in all patients who arrive to hospital feeling unwell, as part of what is known as a warning score chart.

Most clinical staff believe that counting breaths taken over a 30-second period will give a reasonable measure of the respiratory rate, the researchers say.

As breathing is not always regular, however, there can be a variation in the respiratory rate when measuring it over a short time period.

The team analysed recordings of breathing in 25 hospital patients to determine how wide this variation can be. Each recording was made for between 30 minutes and an hour in patients with illnesses that included respiratory, cardiac, neurological and urinary conditions.

Researchers sampled the recordings at random, many times, in the same way the way clinical staff might measure the breathing rate.

It was found that there was a large variation in the respiration rate for each patient - more than half of the measurements differed by more than three breaths per minute.

This change may sound small but, in 40 per cent of cases, the incorrect rate would have meant the warning score chart was wrong.

The study is published in ERJ Open Research.

Dr Gordon Drummond, Honorary Clinical Senior Lecturer, from University of Edinburgh, said: "The lack of accuracy in measurement of respiration rate could have an impact on a patient's treatment. We think accuracy would be improved by increasing the time of measurement to two minutes and using specialist equipment to measure respiratory rate."

A new 3D-printing method will make it easier to manufacture and control the shape of soft robots, artificial muscles and wearable devices. Researchers at UC San Diego show that by controlling the printing temperature of liquid crystal elastomer, or LCE, they can control the material's degree of stiffness and ability to contract--also known as degree of actuation. What's more, they are able to change the stiffness of different areas in the same material by exposing it to heat.

As a proof of concept, the researchers 3D-printed in a single print, with a single ink, structures whose stiffness and actuation varies by orders of magnitude, from zero to 30 percent. For example, one area of the LCE structure can contract like muscles; and another can be flexible, like tendons. The breakthrough was possible because the team studied LCE closely to better understand its material properties.

The team, led by Shengqiang Cai, a professor in the Department of Mechanical and Aerospace Engineering at the UC San Diego Jacobs School of Engineering, details their work in the Sept. 25 issue of Science Advances.

Researchers were inspired to create this material with different degrees of actuation by examples in biology and nature. In addition to the combination of muscle and tendon, researchers took cues from the beak of the squid, which is extremely stiff at the tip but much softer and malleable where it is connected to the mouth of the squid.

"3D-printing is a great tool to make so many different things--and it's even better now that we can print structures that can contract and stiffen as desired under a certain stimuli, in this case, heat," said Zijun Wang, the paper's first author and a Ph.D. student in Cai's research group.

Understanding material properties

To understand how to tune the material properties of LCE, researchers first studied the material very closely. They determined that printed LCE filament is made of a shell and a core. While the shell cools off quickly after printing, becoming stiffer, the core cools more slowly, remaining more malleable.

As a result, researchers were able to determine how to vary several parameters in the printing process, especially temperature, to tune the mechanical properties of LCE. In a nutshell, the higher the printing temperature, the more flexible and malleable the material. While the preparation of the LCE ink takes a few days, the actual 3D print can be done in just 1 to 2 hours, depending on the geometry of the structure being printed.

"Based on the relationship between the properties of LCE filament and printing parameters, it's easy to construct structures with graded material properties," said Cai.

Varying temperature to 3D-printing structures

For example, researchers printed an LCE disk at 40 degrees C (104 F) and heated it up to 90 degrees C (194 F) in hot water. The disk deformed into a conical shape. But an LCE disk composed of areas that are printed at different temperatures (40, then 80 then 120 degrees Celsius, for example), deformed in a completely different shape when heated up.

Researchers also 3D-printed structures made of two layers of LCE with different properties and showed that this gave the material even more degrees of freedom to actuate. Researchers also printed lattice structures with the material, which could be used in medical applications.

Finally, as a proof of concept, the team 3D printed an LCE tube that they had tuned during 3D printing and showed that it could adhere to a rigid glass plate much longer when actuated at high temperatures, about 94 C (201 F), than a regular LCE tube with homogenous properties. This could lead to the manufacture of better robotic feet and grippers.

The actuation of the material could be activated not just in hot water but also by infusing LCE with heat-sensitive particles or particles that absorb light and convert it to heat--anything from black ink powder to graphene. Another mechanism would be to 3D print the structures with electric wires that generate heat embedded in LCE.

Next steps include finding a way to tune the material's properties more precisely and efficiently. Researchers also are working on modifying the ink so the printed structures can be self-repairable, reprogrammable, and recyclable.