Culture

Humans have cultivated plants outside their native ranges for thousands of years. But as the world became increasingly interconnected over the past five hundred years, the scale of cultivation of non-native plants for economic value - for example as food, ornamentation or for medicinal purposes - has intensified. For the first time, a team of researchers led by University of Konstanz ecologist Mark van Kleunen has carried out scientific analyses to assess how economic use of non-native plants relates to their naturalization success (i.e. their establishment in the wild) around the world.

Cultivation a major driver of the introduction of alien plants

The international team of biologists from the University of Konstanz, Taizhou University and Fudan University (both in China), the University of Vienna, the Czech Academy of Sciences, Durham University and Georg August University of Göttingen analysed a global dataset on 11,685 economic plant species (World Economic Plants database) in combination with a global dataset on 12,013 naturalized plant species (Global Naturalized Alien Flora database).

The results, which were published in Nature Communications this week, suggest that cultivation for economic use is the major pathway for the introduction of naturalized alien plants in regions across the globe.

Economic plants are more likely to naturalize

"As an ecologist, I'm mainly interested in what determines the success of a plant species, particularly alien plant species", says Mark van Kleunen, lead author on the study. "Many contemporary studies look into their spread, trying to understand why these aliens are able to establish themselves in areas well beyond their native ranges. What these studies tend not to take into account is how and why they were introduced in the first place".

The results of the study confirm that there is a direct link between cultivation for economic purposes and naturalization: Plants with an economic use were 18 times more likely to naturalize than species without any known economic use, and plants with multiple economic uses were the most likely to naturalize. More than 50 percent of the plant species used as ornamental garden plants or for the production of animal food, which are among the most widely cultivated plants, have become naturalized somewhere in the world.

Plants from Northern Hemisphere among the most successful

Previous studies have shown that Northern Hemisphere continents are the most prolific when it comes to donating naturalized species, especially Europe. "Our research suggests that this is because more plants from the Northern Hemisphere have been cultivated for economic use elsewhere, and not because they are in some way superior or have an innate ability to naturalize outside their native environments", says Dr Trevor Fristoe, another University of Konstanz author on the study. Economic plants of Asian origin, however, were shown to have the greatest naturalization success.

Cultivation bias drives phylogenetic patterns in naturalization

The study further shows that phylogenetic patterns in the naturalized flora are partly due to which plants we cultivate. Naturalized species have been shown to be far more frequent in some families of the world's global seed plant flora than in others. While these patterns have been attributed to shared traits among closely related species that promote naturalization success, the new insights generated by van Kleunen et al. raise the possibility that these patterns are caused by a phylogenetic bias in the species selected and cultivated for their economic value.

Facts:

- Pioneering global study led by University of Konstanz ecologist Mark van Kleunen on the naturalization of plants shows that the economic use of plants plays a crucial role in driving global plant naturalization patterns.

- Analyses of a global dataset on 11,685 economic plant species in combination with a global dataset on 12,013 naturalized plant species show that plants with an economic use were 18 times more likely to naturalize than species without any known economic use.

- Original publication: Mark van Kleunen, Xinyi Xu, Qiang Yang, Noëlie Maurel, Zhijie Zhang, Wayne Dawson, Franz Essl, Holger Kreft, Jan Pergl, Petr Pyšek, Patrick Weigelt, Dietmar Moser, Bernd Lenzner and Trevor S. Fristoe, Economic use of plants is key to their naturalization success, Nature Communications, 24 June 2020. URL: https://doi.org/10.1038/s41467-020-16982-3

- Plants with multiple economic uses were the most likely to naturalize, while economic plants of Asian origin showed the greatest naturalization success.

- The phylogenetic distribution of naturalized plants is caused in part by a phylogenetic bias among plants selected for economic use.

In the current issue of Communications Biology, Professor Jindrich Cinatl from the Institute for Medical Virology at Goethe University and Professor Martin Michaelis from the School of Biosciences at the University of Kent report on their investigations with nelarabine on different cell lines. "Nelarabine is the precursor of the drug, a prodrug, that does not become effective until it is combined with three phosphate groups in the leukaemia cell," explains Professor Cinatl. "In studies of various ALL cell lines and leukaemia cells from ALL patients, we have been able to demonstrate that the enzyme SAMHD1 splits the phosphate groups off so that the medicine loses its effect." Because B-ALL cells contain more SAMHD1 than T-ALL cells, nelarabine is less effective with B-ALL.

These results could improve the treatment of ALL in the future. In rare cases, B-ALL cells contain very little SAMHD1 so that treatment with nelarabine would be possible. On the contrary, there are also rare cases of T-ALL exhibiting a lot of SAMHD1. In such cases, the otherwise effective nelarabine would not be the right medication. Professor Michaelis observes: "SAMHD1 is thus a biomarker that allows us to better adapt treatment with nelarabine to the individual situation of ALL patients."

Tamara Rothenburger, whose doctoral dissertation was funded by the association "Hilfe für krebskranke Kinder Frankfurt e.V", is satisfied when she looks back at her research. "I hope that many children with leukaemia will benefit from the results." The research was also supported by the Frankfurt Stiftung für krebskranke Kinder. Additional members of the research group are Ludwig-Maximilians-Universität Munich, and University College London.

Cambridge UK, 24 June 2020: A research programme pioneering the use of whole genome sequencing in the NHS has diagnosed hundreds of patients and discovered new genetic causes of disease. Whole genome sequencing is the technology used by the 100,000 Genomes Project, a service set up by the government which aims to introduce routine genetic diagnostic testing in the NHS.

The present study, led by researchers at the National Institute for Health Research BioResource together with Genomics England, demonstrates that sequencing the whole genomes of large numbers of individuals in a standardised way can improve the diagnosis and treatment of patients with rare diseases.

The researchers studied the genomes of groups of patients with similar symptoms, affecting different tissues, such as the brain, eyes, blood or the immune system. They identified a genetic diagnosis for 60% of individuals in one group of patients with early loss of vision.

The programme, the results of which were published today in two articles in the journal Nature, offered whole-genome sequencing as a diagnostic test to patients with rare diseases across an integrated health system, a world first in clinical genomics. The integration of genetic research with NHS diagnostic systems increases the likelihood that a patient will receive a diagnosis and the chance that a diagnosis will be provided within weeks rather than months.

"Around 40,000 children are born each year with a rare inherited disease in the UK alone. Sadly, it takes more than two years, on average, for them to be diagnosed," says Willem Ouwehand, Professor of Experimental Haematology at the University of Cambridge, the National Institute for Health Research BioResource and NHS Blood and Transplant Principal Investigator. "We felt it was vital to shorten this odyssey for patients and parents."

"This research shows that quicker and better genetic diagnosis will be possible for more NHS patients."

In the study, funded principally by the National Institute for Health Research, the entire genomes of almost 10,000 NHS patients with rare diseases were sequenced and searched for genetic causes of their conditions. Previously unobserved genetic differences causing known rare diseases were identified, in addition to genetic differences causing completely new genetic diseases.

The team identified more than 172 million genetic differences in the genomes of the patients, many of which were previously unknown. Most of these genetic differences have no effect on human health, so the researchers used new statistical methods and powerful supercomputers to search for the differences which cause disease - a few hundred 'needles in the haystack'.

In one study from the programme, published as a standalone article in Nature, researchers examined 886 patients with primary immunodeficiency - a condition that affects the ability of the immune system to fight infections by microbes - and identified four novel associated genes.

"Providing the best treatment and the most appropriate care for patients with inherited immune disorders depends absolutely on a conclusive molecular diagnosis," says Professor Adrian Thrasher of the UCL Great Ormond Street Institute of Child Health (ICH) in London. "Our study demonstrates the value of whole-genome sequencing in this context and provides a suite of new diagnostic tools, some of which have already led to improved patient care."

Using a new analysis method developed specifically for the project, the team identified 95 genes in which rare genetic differences are statistically very likely to be the cause of rare diseases. Genetic differences in at least 79 of these genes have been shown definitively to cause disease.

The team searched for rare genetic differences in almost all of the 3.2 billion DNA letters that make up the genome of each patient. This contrasts with current clinical genomics tests, which usually examine a small fraction of the letters, where genetic differences are thought most likely to cause disease. By searching the entire genome researchers were able to explore the 'switches and dimmers' of the genome - the regulatory elements in DNA that control the activity of the thousands of genes.

The team showed that rare differences in these switches and dimmers, rather than disrupting the gene itself, affect whether or not the gene can be switched on at the correct intensity. Identifying genetic changes in regulatory elements that cause rare disease is not possible with the clinical genomics tests currently used by health services worldwide. It is only possible if the whole of the genetic code is analysed for each patient.

"We have shown that sequencing the whole genomes of patients with rare diseases routinely within a health system provides a more rapid and sensitive diagnostic service to patients than the previous fragmentary approach, and, simultaneously, it enhances genetics research for the future benefit of patients still waiting for a diagnosis," says Dr Ernest Turro from the University of Cambridge and the NIHR BioResource.

"Thanks to the contributions of hundreds of physicians and researchers across the UK and abroad, we were able to study patients in sufficient numbers to identify the causes of even very rare diseases."

Although individual rare diseases affect a very small proportion of the population, there exist thousands of rare diseases and, together, they affect more than three million people in the UK. To tackle this challenge, the NIHR BioResource created a network of 57 NHS hospitals which focus on the care of patients with rare diseases. Nearly 1000 doctors and nurses working at these hospitals made the project possible by asking their patients and, in some cases, the parents of affected children to join the NIHR BioResource.

"In setting up the NIHR BioResource Project, we were taking uncharted steps in a determined effort to improve diagnosis and treatment for patients in the NHS and further afield" says Dr Louise Wood, Director of Science, Research and Evidence at the Department of Health and Social Care and who together with the Chief Medical Officer Professor Chris Whitty has the overall responsibility for the National Institute for Health Research.

"The NIHR-funded researchers on this scientific report were part of those earliest discussions as we sought to ensure we could deliver the science and transform it into clinical practice across the NHS. This research has demonstrated that patients, their families and the health service can all benefit from placing genomic sequencing at the forefront of clinical care in appropriate settings.

"The pioneering work undertaken by the NHS in partnership with Genomics England and academic researchers across the UK has laid the foundation for applying the same genome test to patients with COVID-19, with the hope of finding clues why some patients experience such a severe form of this new disease."

Based on the emerging data from the present NIHR BioResource study and other studies by Genomics England, the UK government announced in October 2018 that the NHS will offer whole-genome sequencing analysis for all seriously ill children with a suspected genetic disorder, including those with cancer. The sequencing of whole genomes will expand to one million genomes per year by 2024.

Whole-genome sequencing will be phased in nationally for the diagnosis of rare diseases as the 'standard of care', ensuring equivalent care across the country.

The benefits include a hastened diagnosis for patients, reduced costs for health services, improved understanding of the reasons they suffer from disease for patients and their carers and improved provision of treatment.

Chemists have found a way to turn alcohol into amino acids, the building blocks of life.

In a study published Monday in the journal Nature Chemistry, researchers explained the transformation, which involves selectively identifying and replacing molecular bonds with unprecedented precision. The finding may make it easier to create some medications by expanding the types of new amino acids that can be made to more quickly build those medicines.

"One of the coolest applications of this research is that we found a new way to make unnatural amino acids - sometimes used in medicines to target diseases while avoiding natural metabolism," said David Nagib, a professor of chemistry at The Ohio State University and senior author of the paper. "And we may be able to use these unnatural amino acids to build new complex molecules that target various diseases."

Amino acids, which make up our proteins, are also sometimes used as building blocks in medicines, but creating new, artificial ones with correct three-dimensional geometry in a laboratory for pharmaceutical purposes can be an expensive and lengthy process.

Alcohol, though, is plentiful and cheap.

To transform alcohol into amino acids, researchers played with alcohol at the atomic level. An alcohol molecule is made of three different elements - hydrogen, carbon and oxygen. The researchers found a way to break the bonds between specific carbon and hydrogen atoms to introduce a nitrogen atom, the other most common element found in nature and medicines - a type of laboratory wizardry called "selective C-H functionalization."

"Carbon-hydrogen is the most ubiquitous bond - think of a field of grass in a park. Each piece of grass is a carbon-hydrogen bond, and the challenge of C-H functionalization is how do you pick the exact blade of grass you want to turn into a rose and ignore all the rest?" Nagib said. "How do you be selective about which bond you're transforming?"

Being able to choose the right bond is important. When chemists build new medications, they use molecules carefully assembled in a specific way, to target only a disease and not other biologically important machinery. Think of the molecules in humans, bacteria or viruses as individual locks, and medicines as a key: A good medicine, or key, fits only in the right lock.

"In alcohol, there are pairs of equal carbon-hydrogen bonds, but those bonds are not equal in their spatial arrangement on the molecule," Nagib said. "And now we can grab one of them over the others to make amines with various three-dimensional shapes, which will allow construction of new chemical structures to make drugs that may serve as a better key."

The glass structure of a material is often believed to mimic its corresponding liquid. Polyamorphism between ices has been used as a guide to elucidate the properties of liquid water. But how many forms of amorphous ices are there? Do we understand how metastable high-pressure crystalline ice evolves towards the thermally stable low-density form? An international research team led by Chuanlong Lin and Wenge Yang from HPSTAR and John S. Tse from the University of Saskatchewan has revealed a multiple-step transformation mechanism using state-of-the-art time-resolved in situ synchrotron x-ray diffraction. A temperature/time-dependent kinetic pathway with three distinctive transitions was identified in the structural evolution from metastable crystalline ice (ice VII or ice VIII) to the thermodynamically stable ice I. These intermediate processes compete against each other. The end result is a juxtaposition of these processes. The work is published in PNAS.

Water plays a vital role in the origin of life on Earth. In the liquid phase, it exhibits many unusual properties. In the solid phase, ordinary ice also displays diverse phase transitions at high pressure. Many theoretical and experimental studies have been devoted to understanding the underlying inter-conversion mechanisms. So far, most experiments have been ex situ measurements on recovered samples and lack detailed information on the structural evolution accompanying the transformation. Previous studies have been hindered by technical difficulties in monitoring the rapid structural change over a broad pressure and temperature range.

In 2017, Lin and his colleagues overcame the experimental challenge. A series of studies was conducted to investigate ice transitions by combining in situ time-resolved x-ray diffraction, and remote pressure control with different ramp rates within a low-temperature cryostat. This capability allowed the suppression of thermally-driven crystalline-crystalline transitions [PNAS 115, 2010-2015(2018)]. Important insights into the complexity of the poly-amorphous transformations were obtained, such as the kinetically-controlled two-step amorphization in ice Ih [Phys. Rev. Lett. 119, 135701(2017)] and the successful venture into the no man's land [Phys. Rev. Lett. 121, 225703(2018)].

Now, they try to answer what exactly is the nature of the amorphous-amorphous phase transformation processes? Using the newly developed techniques, they explored the "mirror" process, i.e., reverse transformation from a meta-stable high-density crystalline ice (i.e, ice VII or ice VIII) to the ambient stable ice I. They identified the temperature/time-dependent kinetic pathways and characterized the interplay/competition between the high density amorphous (HDA)-low density amorphous (LDA) transition and recrystallization. Contrary to previously reported ice VII (or ice VIII) -- LDA -- ice I transformation sequences, time-resolved measurements show a three-step process: initial transformation of ice VII to HDA, followed by a HDA -- LDA transition, and then crystallization of LDA into ice I. Both the amorphization of ice VII and the HDA to LDA transition show distinctive thermal activation mechanisms. Significantly, both processes exhibit the Arrhenius behavior with a temperature-dependent duration time (τ) and a 'transition' temperature at around 110-115 K.

Large-scale molecular-dynamics calculations also support their experimental findings. Furthermore, it shows the HDA to LDA transformation is continuous with a large density difference and involves substantial displacements of water in the nano-scale. This study presents a new perspective on the metastability and complexities in shaping ice-transition kinetic pathways.

A new study in JNCI: Journal of the National Cancer Institute finds that breast cancer screening using digital mammography technology is not associated with improved health outcomes when compared to older film detection technology.

In 2000, the US FDA approved digital mammography technology. Studies suggested the new technology was potentially more specific in its findings. Proponents of the technology believed it would reduce the number of callbacks for positive findings, find more disease, and lead to fewer cancers diagnosed in between screenings (interval cancers).

Researchers conducted a systematic review and searched seven databases for publications that compared film to digital mammography within the same population of asymptomatic women. Researchers looked for evidence of improved health outcomes in the newer digital technology, by analyzing detection rates, recall rates (patients contacted for further testing), and cancers diagnosed in between scheduled screenings.

The meta-analysis included 24 studies with 16,583,743 screening examinations (10,968,843 film and 5,614,900 digital). The difference in cancer detection rate showed an increase of 0.51 per 1,000 screens, and a recall rate increase of 6.95 per 1,000 screens after the transition from film to digital mammography.

The researchers found that the small increase in cancer detection following the switch to new digital mammography did not translate into a reduction in cancers diagnosed in between scheduled screenings

The researchers conclude that while digital mammography is beneficial for medical facilities due to easier storage and handling of images, these results suggest the transition from film to digital mammography has not resulted in health benefits for screened women.

"While the transition from film to digital may have been beneficial for technological reasons and for efficiencies in service screening, our research shows the increase in cancer detection was largely attributable to more detection of DCIS (ductal carcinoma in situ), with little difference in invasive cancer detection," said study's lead author, Rachel Farber. "At a time when new mammography and other imaging technologies are proposed for adoption in population screening, it is critical to carefully consider and evaluate the effect this could have on health outcomes."

Many people can recall shocking news images of Japan sustaining earthquake damage. Between 1996 and September of 2018, there were 155 earthquakes in Japan that resulted in human injuries. In 20 of these earthquakes, people have gone missing or were killed. During the Hyogo-ken Nanbu earthquake in 1995, 6,434 people were killed and 3 have gone missing. In 99 of the 155 earthquakes, damage to houses, school buildings, windows, water and sewage pipes, and landslides were recorded. Tsunami's occurred as a result of an earthquake in 18 of the 155 earthquakes.

Natural disasters cause damage to human life and also great disruption to economic activities. One of the economic activities that are effected by natural disasters are supply chains. Increasingly complex supply chains have caused risks in supply chain disruptions to also become complex, highly entangled and harder to access. Past disasters demonstrate the importance of forecasting economic damage from supply chain disruptions more accurately to structure risk-management schemes and minimize loss.

A study led by Senior Assistant Professor Michiyuki Yagi of Shinshu University used input-output analysis (IOA) to quantify economic damage associated with natural disasters; in particular, earthquakes. IOA is effective in evaluating economic impact at the regional/sectoral level. The researchers focused on the exogenous (flow) damage to focus on the monthly or quarterly levels of production statistics. They chose the Leontief price model to access the study, building on Ji Young Park (2007) that considered the supply constraint in the Ghosh price model to introduce the price elasticity of demand. This study modified Park (2007) to use the Leontief price model instead of the Ghosh price model and use the loss of social surplus as damage instead of the change in production.

The loss of social surplus was used instead of the change in production because production or sales is less informative as a damage index than profit (margin) because it can be any amount without considering profit. Production (sales) also does not identify how much damage is passed on to each supplier (upstream sector) and buyer (downstream sector).

The researchers found that previous studies' estimates of indirect damage estimation were similar to that of this study. The largest earthquakes in Japan tend to require 0.2 to 0.3 months of economic assistance for initial production immediately after the disaster within a damaged prefecture and more than 0.5 months or 50% of initial production in total until the first temporal recovery, which is the eighth month at most.

The earthquake known as the Great East Japan Earthquake required twice as much (fast) economic assistance in Fukushima, Iwate, Miyagi, Ibaraki, and Chiba prefectures. This had cumulatively, 25 month-production damage until the temporal recovery at the 37th month (to the five prefectures).

New Rochelle, NY, June 24, 2020--Bacteriophage can reduce bacterial growth in the lungs, limiting fluid build-up. This could decrease the mortality of patients affected by COVID-19, according to the peer-reviewed journal PHAGE: Therapy, Applications, and Research. Click here to read the article.

"The bacterial growth rate could potentially be reduced by the aerosol application of natural bacteriophages. These prey on the main species of bacteria known to cause respiratory failure," says Marcin Wojewodzic, PhD, University of Birmingham (U.K.).

Decreasing bacterial growth would also give the body more time to produce protective antibodies against the disease-causing coronavirus.

"Used correctly, phages have an advantage here of being able to very specifically target the bacteria that cause secondary infections," said Martha Clokie, PhD, Editor-in-Chief of PHAGE and Professor of Microbiology, University of Leicester (U.K.). "They would remove the problematic bacterium but leave an otherwise fragile microbiome intact."

Levitation has long been a staple of magic tricks and movies. But in the lab, it's no trick. Scientists can levitate droplets of liquid, though mixing them and observing the reactions has been challenging. The pay-off, however, could be big as it would allow researchers to conduct contact-free experiments without containers or handling that might affect the outcome. Now, a team reporting in ACS' Analytical Chemistry has developed a method to do just that. 

Scientists have made devices to levitate small objects, but most methods require the object to have certain physical properties, such as electric charge or magnetism. In contrast, acoustic levitation, which uses sound waves to suspend an object in a gas, doesn't rely on such properties. Yet existing devices for acoustic levitation and mixing of single particles or droplets are complex, and it is difficult to obtain measurements from them as a chemical reaction is happening. Stephen Brotton and Ralf Kaiser wanted to develop a versatile technique for the contactless control of two chemically distinct droplets, with a set of probes to follow the reaction as the droplets merge.

The team made an acoustic levitator and suspended two droplets in it, one above the other. Then, they made the upper droplet oscillate by varying the amplitude of the sound wave. The oscillating upper droplet merged with the lower droplet, and the resulting chemical reaction was monitored with infrared, Raman and ultraviolet-visible spectroscopies. The researchers tested the technique by combining different droplets. In one experiment, for example, they merged an ionic liquid with nitric acid, causing a tiny explosion. The new levitation method could help scientists study many different types of chemical reactions in areas such as material sciences, medicinal chemistry and planetary science, the researchers say.

Bristol innovation challenges regular touchscreens with new spray-on technique

A team at Bristol has challenged the idea that touchscreens are limited to 2D and rectangular shapes by developing an interactive display that can be sprayed in any shape.

Inspired by the way an artist creates graffiti on a wall and using a novel combination of sprayable electronics and 3D printing, the technique, called ProtoSpray, allows the creation of displays on surfaces that go beyond the usual rectangular and 2D shapes.

"We have liberated displays from their 2D rectangular casings by developing a process so people can build interactive objects of any shape. The process is very accessible: it allows end-users to create objects with conductive plastic and electroluminescent paint even if they don't have expertise in these materials," said Ollie Hanton, PhD student and lead author of the research.

Mr Hanton's paper on the innovation was presented and received an honourable mention at the ACM Conference on Human Factors in Computing Systems (CHI) - generally considered the most prestigious academic conference in the field of human-computer interaction.

The aim of the EPSRC-funded research was to broaden the scope of how people can interact with digital technologies.

The ProtoSpray process, developed in collaboration with the MIT media lab, opens up potential for makers, hobbyists and researchers to develop interactive objects of different (arbitrary) shapes.

"3D printers have enabled personal fabrication of objects but our work takes this even further to where we print not only plastic but also other materials that are essential for creating displays. Using 3D printing of plastics and spraying of materials that light up when electricity is applied, we can support makers to produce objects of all shapes that can display information and detect touch.

"Our vision is to make screen/display a fundamental expressive medium in the same way people currently use ink, paint, or clay," said Mr Hanton.

Dr Anne Roudaut, Associate Professor in Human-Computer Interaction at the University of Bristol, who supervised the research, said the next step would be to create a machine that can both 3D print and spray automatically onto the 3D printed objects.

A summer internship in Bilbao, Spain, has led to a paper in the journal Physical Review Letters for Jack Mayo, a Master's student at the University of Groningen, the Netherlands. He has helped to create a universal model that can predict the number distribution of topological defects in non-equilibrium systems. The results can be applied to quantum computing and to studies into the origin of structure in the early Universe.

Mayo, student of the Top Master Programme in Nanoscience at the Zernike Institute for Advanced Materials at the University of Groningen, spent his 2019 summer holidays on the Basque coast immersed in theoretical physics. The project in which he participated took place in the research group led by Professor Adolfo del Campo at the Donostia International Physics Center (DIPC), and was aimed at solving a problem in quantum computing - but it has much wider implications, from nanoscale magnets to the cosmos. In all these systems, the onset of order (for example, order induced by cooling) is almost always accompanied by the development of defects. 'Take a system in which particles have a magnetic moment that can flip between up and down,' Mayo explains. 'If you increase their attractive interaction, they will start to align with each other.'

Ice crystals

This alignment will begin at certain uncorrelated points in a medium and then grow - like ice crystals in water. The alignment of each domain (up or down in the example of the magnetic moments) is a matter of chance. 'Local alignments will grow outwards and at a certain stage, domains will begin to meet and interact,' says Mayo. For example, if an up-domain meets a down-domain, the result will be a domain wall at their interface - a symmetry-breaking defect in the ordered structure, leaving behind an artifact of the material in its higher-symmetry phase.

This annealing of a medium is described by the Kibble-Zurek mechanism, originally designed to explain how a phase transition resulted in ordered structures in the early Universe. It was subsequently discovered that it could be used to describe the transition of liquid helium from a fluid to a superfluid phase. 'The mechanism is universal and is also used in quantum computing based on quantum annealing,' explains Mayo. This technology is already on the market and is capable of solving complex puzzles such as the travelling salesman problem. However, a problem with this type of work is that defects that occur during the annealing process will distort the results.

Phase transitions

The number of defects that show up in quantum annealing depends on the time taken to pass the phase transition. 'If you have millions of years to slowly change the interactions between units, you do not get defects, but that is not very practical,' Mayo remarks. The trick is in designing finite-time - and therefore more practical - schedules to obtain an acceptable number of defects with high probability. The research project in which he participated was aimed at creating a model that could estimate the number of defects and guide the optimum design of these systems.

Statistical model

To do this, the physicists used theoretical tools to describe phase transitions and numerical simulations to estimate the defect distribution during cooling. As each domain can have one of two values (up or down in the example of the magnetic moments), they could estimate the chances of two opposite domains meeting and creating a defect. This led to a statistical model based on binomial distribution, which could be used to predict how a system should be cooled to create the smallest number of defects. The model was verified against independent numerical simulations and appeared to work well. This new model was described in a paper that was published on 17 June in Physical Review Letters and was accompanied by a 'Viewpoint' published in Physics, a comment on the results by the independent physicist Professor Smitha Vishveshwara from the University of Illinois at Urbana-Champaign.

A new study of childhood epilepsy has identified the world's first environmental risk factor for the disease - maternal smoking in pregnancy, and discovered a new genetic association with the condition, pointing to potential new treatments for the disease.

The research was led by an international team of clinicians and scientists including Professor Matt Brown, Professor of Medicine at King's College London and Director of the National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas'.

The study focussed on one of the most common forms of childhood epilepsy, Benign Childhood Epilepsy with Centrotemporal Spikes (BECTS). Around 1% of children globally suffer with epilepsy with around 15% of those affected by BECTS. Driven by tendency for BECTS to run in families, previous research efforts focussed on identifying potential rare genetic mutations associated with the disease, but offered no robust evidence for the genetic association for the condition.

Unlike previous studies, the study team used genome wide complex trait analysis to examine and explain the most common type of genetic variations in people with BECTS.

This enabled the team to demonstrate that BECTS does indeed have a significant common genetic component, for the first time demonstrating that the reason that BECTS runs in families is because of genetic variants carried by patients. The study identified an association with a gene called CHRNA5 being involved in BECTS risk.

It is commonly known that genetic variations within the CHRNA5 and related genes are associated with nicotine dependence and smoking associated lung disease. This along with suggestive evidence that smoking increases the risk of epilepsy overall led the team to perform analysis between risk factors and disease using summary-level data from independent genome-wide association studies from the UK Biobank. The analysis demonstrated that maternal smoking during pregnancy quadrupled the risk of BECTS. This is the first ever environmental risk factor identified for the disease.

Commenting on the findings Professor Matt Brown from King's College London said: "The new evidence in our study showing that common genetic variants play an important role in BECTS susceptibility opens up immense research possibilities to better understand how epilepsy is caused.

Maternal smoking in pregnancy being identified as the first ever environmental risk factor described in the development of BECTS offers a very clear message to clinicians and mothers about what can and should be done to limit the risk of children developing this common form of epilepsy."

He added: "With the association of the CHRNA5 gene which encodes a cholinergic receptor expressed in the brain involved in BECTS risk, our research also suggests that a class of drugs called 'anticholinergics' may be effective in the treatment of BECTS, however, further research into this is needed."

Invasive fire ants common in the Gulf Coast and Texas likely are limiting a tick-acquired meat allergy in these areas, scientists report.
The ants are moving northward and could reduce the prevalence of the red meat allergy in some Southern states. However, fire ant bites are also a cause of severe allergic reactions.
The new UVA research maps the extent of the red meat allergy in the United States.
The findings further implicate the lone star tick as the cause of the meat allergy and hint that the tick may be increasing in some Northern states.

Invasive fire ants with a nasty bite are limiting the spread of a dangerous meat allergy, new research suggests. But it’s not all good news, as the ants themselves can also cause severe allergic reactions.

School of Medicine researchers and their collaborators made the discovery while seeking to understand the scope of the “alpha-gal” meat allergy in the United States. Spread by the bite of the lone star tick, the allergy causes people to develop potentially severe allergic reactions to mammalian meat, including beef and pork.

The allergy is commonly seen throughout the Southeast, the Mid-Atlantic and the Midwest, but rarely in the Gulf Coast and Texas. That is likely caused by the steady expansion of fire ants accidentally imported from South America in the 1930s, the researchers conclude.

But the ants are no heroes, as their bites can be very painful and cause severe allergic reactions. In some cases, the bites can cause life-threatening anaphylaxis. That’s in addition to the dangers the ants pose to animals and crops. And the strong-jawed insects are marching relentlessly northward.

“We did not set out to study fire ants, but when the number of alpha-gal cases in the Gulf Coast was consistently lower than we expected, the fire ant emerged as an interesting explanation,” said UVA researcher Behnam Keshavarz, PhD, a co-first author of a new scientific paper outlining the discovery.

Mapping the Meat Allergy

The meat allergy was first identified more than a decade ago by UVA’s Thomas Platts-Mills, MD, PhD, an internationally renowned allergist. Since then, he and his colleagues have shed light on how and why the tick’s bite causes people to develop allergic reactions to a particular sugar, alpha-gal, present in meat and other mammalian products. The symptoms can include itchy rashes, nausea and difficulty breathing. Severe reactions can progress to anaphylaxis if untreated.

Until now, there has been little examination of the geographic scope of the allergy in the United States. The UVA researchers set out to change that. They surveyed allergists across the country to map out cases of the meat allergy. They also tested blood samples from two different geographic areas where it was particularly prevalent. The latter was important to show that the allergy is “immunologically similar” across the country.

The researchers found the meat allergy was common in significant portions of at least 14 states. Eleven states had at least one allergist report more than 100 case in their practice: Alabama, Arkansas, Georgia, Kentucky, Maryland, Missouri, New York, North Carolina, Oklahoma, Tennessee and Virginia.

In contrast, six of 10 allergy practices in Eastern Texas – the domain of the invasive fire ant – reported no cases of the meat allergy at all.

Weirdness in Minnesota

Oddly, there were an unexpectedly high number of cases in an area of Minnesota where the lone star tick is not thought common. Three separate providers in the northern portion of the state reported at least five cases of the meat allergy, with one reporting more than 40.

That, the UVA researchers note, may suggest there are more lone star ticks in the area than thought – or perhaps that another tick or even other parasite is spreading the meat allergy. Other species of ticks are known to cause the allergy outside North America.

“The best evidence is that lone stars are the dominant cause of the alpha-gal meat allergy in North America,” said co-first author Jeffrey Wilson, MD, PhD. “That said, we wouldn’t be surprised if other ticks, chiggers or even other kinds of parasitic organisms can occasionally contribute to allergic sensitization to alpha-gal.”

Fire Ants Marching

After collecting reports of the meat allergy from 44 states the researchers were surprised to see few cases in the Gulf Coast or Texas. This was unexpected because the lone star tick is usually reported on CDC maps in the area. After considering potential explanations, the researchers again surveyed many of the same allergists about allergic reactions caused by the fire ant. They overlaid their results, and the results showed a striking, inverse relationship: Areas with the most fire ant cases had the lowest presence of the meat allergy.

That suggests that the fire ants are either preying on or somehow competing with the ticks, limiting the spread of the meat allergy, the researchers say. They also identified an increasing number of allergy cases caused by the fire ants. This likely will continue as the fire ants spread north, they report.

The spread should help control the number of meat allergy cases in the Southeast and Mid-Atlantic, they predict. But it also likely will lead to an increase in allergic reactions caused by the fire ant.

“These are two arthropod-related allergic diseases that are connected with each other,” Platts-Mills concludes. “The situation is unique because we think we can predict how both will change over time.”

Read a patient’s experiences with the meat allergy.

Meat Allergy Findings

The researchers have published their findings in the Journal of Allergy and Clinical Immunology. The research team consisted of Wilson, Keshavarz, Maya Retterer, Lisa J. Workman, Alexander J. Schuyler, Emily C. McGowan, Charles Lane, Alaaddin Kandeel, Jane Purser, Eva Ronmark, Joseph LaRussa, Scott P. Commins, Tina Merritt and Platts-Mills. Platts-Mills and Merritt have a patent on a test for the meat allergy, while Wilson has received funding from Thermo Fisher/Phadia. A full list of disclosures is included in the paper.

The research was supported by the National Institutes of Health, grant R37 AI-20565.

To keep up with the latest medical research news from UVA, subscribe to the Making of Medicine blog.

Journal

Journal of Allergy and Clinical Immunology

DOI

10.1016/j.jaci.2020.05.034

As technology shrinks, the need to characterize the properties of very small materials?measured in nanometers (1 nanometer = 1 billionth of a meter)?has become increasingly important. Nanomaterials that measure from 1 and 20 nanometers show promise for use in next-generation electronic devices, solar cells, laser technology, and chemical and biosensors, to name a few. For scale, the width of a human hair is 75,000 nanometers.

To understand the surface potential of nanomaterials, the most commonly used nanoscience tool is the Kelvin Probe Force Microscopy (KPFM), which is an atomic force microscopy (AFM) based technique that measures work function and surface potential. Unfortunately, KPFM has its limitations due to its use of AC voltage to charge the AFM probe.

"Every KPFM technique operates on the same measurement paradigm: AC voltage is used to completely charge an AFM probe, thus producing a detectable electrostatic force for image acquisition," explains Xiaoji Xu, assistant professor in Lehigh University's Department of Chemistry. "Overloading the probe with charges forces a limit on the spatial resolution, since the charges are not limited to the apex of the AFM probe. Instead, excess charges occupy the entire cantilever and contribute to the signal."

Now, Xu and his graduate student Devon S. Jakob have introduced an entirely new measurement paradigm based on the alignment on Fermi levels. While traditional KPFM methods produce images with a spatial resolution of 30 to 100 nanometers, the new Xu Research Group method, called Pulsed Force Kelvin Probe Force Microscopy (PF-KPFM), allows for less than 10 nanometer measurements of work function and surface potential in a single-pass AFM scan. Their findings have been published in an article in ACS Nano: "Pulsed Force Kelvin Probe Force Microscopy." (Authors: Xiaoji Xu and graduate students Devon S. Jakob and Haomin Wang)

"In Pulsed Force Kelvin Probe Force Microscopy, we removed the need for the AC voltage by implementing a custom circuit of a field effect transistor between the tip and the sample which acts as a binary switch," says Xu. "When the switch is on, the circuit acts as a simple wire, allowing charges to pass between tip and sample. A small amount of charges spontaneously migrates between tip and sample based on the relative difference in their intrinsic Fermi levels. When the switch is off, the circuit does not allow for charges to pass, and acts as a capacitor to re-absorb the charges from the tip and sample region."

The PF-KPFM also exclusively operates in the pulsed force mode, according to Xu. By using the pulsed force mode, he says, PF-KPFM measurements can be accurately obtained at very small tip-sample distances, where the electrical force is large, allowing for small sample heterogeneities to be revealed.

"The next logical step was to combine PF-KPFM with Peak Force Infrared (PFIR) microscopy, an infrared imaging technique invented in our lab, since both techniques use the pulsed force mode," says Xu. "The resulting technique, named PFIR-KPFM, provides topographical, mechanical, chemical, and electrical information at

So, in addition to achieving significant improvements in measuring electrical potential in nanomaterials in a single-pass AFM scan, PF-KPFM can be combined with (PFIR) microscopy for high-throughput correlative measurements, according to the researchers. This follow-up study is described in an article, "Peak Force Infrared ? Kelvin Probe Force Microscopy," forthcoming in Angewandte Chemie International Edition. (Authors: Xiaoji Xu, Devon S. Jakob and Haomin Wang from Lehigh University; Yong Yan, San Diego State University; Guanghong Zeng, Danmarks Nationale Metrologiinstitut, A/S, DENMARK; and Daniel E. Otzen, Aarhus Universitet, iNANO, Denmark.

"Pulsed force KPFM is the first KPFM technique to truly implement the pulsed force mode of AFM for nanoscale surface potential characterization, and the first KPFM technique to be combined with simultaneous infrared detection in the same scan," says Xu.

The importance of accurately measuring the nanoelectrical properties of materials is far-reaching in both academia and industry, according to the researchers. Due to the increasingly smaller size of semiconductor devices, PF-KPFM may be especially helpful for technology companies, as the high spatial resolution of PF-KPFM reveals features that are too small for other KPFM techniques. Similarly, they say, PFIR-KPFM will be beneficial in revealing the correlations between chemical heterogeneity, structure, and electrical properties of lab-made solar cell components.

"Ultimately," says Xu, "we hope that our invention will open the door for characterization of new materials, and help pave the way for more efficient energy-related devices."

Xu's research group develops new methods and instruments for chemical measurement and imaging at the nanoscale with

Xu was named a 2020 Sloan Research Fellow. This prestigious award, funded by the Alfred P. Sloan Foundation, places Xu among "the most promising scientific researchers working today." Additionally, was named a Beckman Young Investigator, earning a prestigious grant awarded by the Arnold and Mabel Beckman Foundation for "the most promising young faculty members in the early stages of their academic careers in the chemical and life sciences."

PULLMAN, Wash. - As the SARS-CoV-2 puts new focus on zoonotic pathogens, a Washington State University researcher has developed a method to use environmental DNA (eDNA) to detect disease in the vast international trade of aquatic animals.

The problem with monitoring the pet trade is one of magnitude. In the Unites States alone, more than 225 million live animals are imported every year, the majority destined for the aquatic or pet industries. Creating a "clean trade" by detecting infections in these populations requires huge sample sizes, a labor-intensive and costly process.

In a paper published in Scientific Reports on June 24, Associate Professor of Disease Ecology Jesse Brunner outlines two potential ways to test captive animals for pathogen DNA: batching test samples from individuals and sampling eDNA from the water in the animals' tanks. The eDNA method proved to be much more efficient, Brunner said.

"The best way to prevent the emergence of these pathogens, and the diseases that come from them, is to keep them from getting here in the first place," said Brunner. "It's an important goal but a really hard one because of the scale of the problem. With the eDNA method you are theoretically sampling an entire population at once, so you are more likely to detect whatever is there, and you can do that much more efficiently than with traditional approaches."

Environmental DNA is already used to look for the presence of invasive species in places like the Great Lakes. Brunner saw that it might also be useful to sample water from the tanks of captive species being transported in the pet trade since infected animals will shed pathogens into their water.

As an example, Brunner used Bsal (Batrachochochytrium salamandrivorans) a chytrid fungus which threatens salamander populations. Bsal is a cousin of the devastating Bd (Batrachocytrium dendrobatidis) that was responsible for the decline of more than 500 amphibian species around the world, including 90 that likely went extinct.

Now Bsal has jumped into wild salamander populations in Europe from imported pets from Southeastern Asia. While it has not yet been found in North America, the threat of Bsal prompted the U.S. Fish and Wildlife Service to enact a ban in 2016 on the import of 201 species of salamanders into the United States, which is home to tremendous salamander diversity.

Brunner's paper outlines the statistical formulas needed to conduct surveillance of imported salamanders for Bsal using eDNA. It shows the volume of samples needed to be taken and tested to produce a good degree of confidence in a negative or positive result. If proven out, the method could reduce the amount of sampling and work required to effectively monitor for the pathogen. This paper provides the framework for the method, and Brunner and colleagues are currently testing it with real samples.

As part of a Bsal Task Force, Brunner and his colleagues are in conversation with the pet industry which is naturally interested in creating a clean trade for salamanders, but finding better solutions to test for pathogens in salamanders also has broader implications.

"The problem that we're having with amphibians is also the same problem that we're having with all sorts of wildlife and with human disease," said Brunner. "I think if we can solve this problem, we'll be in much better shape to solve others."