SARS-CoV-2 seasonal behavior traced back to genetics and global change

Peer-Reviewed Publication

UNIVERSITY OF ILLINOIS COLLEGE OF AGRICULTURAL, CONSUMER AND ENVIRONMENTAL SCIENCES

 

IMAGE: GUSTAVO CAETANO-ANOLLÉS (PICTURED) AND HIS UNIVERSITY OF ILLINOIS RESEARCH TEAM PROVIDE NEW EVIDENCE OF SARS-COV-2 SEASONALITY IN TWO PAPERS, INCLUDING ONE CORRELATING SEASONAL VIRAL BEHAVIOR WITH METRICS OF ENVIRONMENTAL HEALTH AND ANOTHER ANALYZING 12 MILLION VIRAL GENOMES OVER TWO YEARS OF THE PANDEMIC. THE DISCOVERIES COULD GUIDE POLICY, PUBLIC HEALTH, AND PHARMACEUTICAL INTERVENTIONS. PHOTO CREDIT L. BRIAN STAUFFER, UNIVERSITY OF ILLINOIS. view more 

CREDIT: L. BRIAN STAUFFER, UNIVERSITY OF ILLINOIS.

URBANA, Ill. — As the northern hemisphere heads into summer, we may be in for a COVID-19 reprieve. Not because the pandemic is over; the Omicron subvariant ‘Arcturus’ is still creeping upward and causing new symptoms. But two new studies from the University of Illinois add evidence supporting a seasonal pattern in the behavior of the SARS-CoV-2 virus. 

The first study, published in Evolutionary Bioinformatics, correlates two years of pandemic data (COVID cases and deaths) with average annual temperature and latitude in 171 countries across the globe. The researchers also evaluated relationships between COVID and environmental health, including indicators of global change. 

“We found correlations were significant and maintained as the pandemic progressed, regardless of vaccines or the appearance of new viral variants. Results provide strong evidence that the virus is seasonal,” said study author Gustavo Caetano-Anollés, professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences (ACES) at U of I. Caetano-Anollés is also an affiliate of the Carl R. Woese Institute for Genomic Biology. “Remarkably, the seasonal effects we uncovered were not obscured by the wide range of elimination and mitigation policies applied throughout the world.”

Caetano-Anollés and co-author Nicolas Hernandez showed that correlations between COVID-19 metrics (new cases and deaths, total cases and deaths) and temperature and latitude strengthened during cooler months and at higher latitudes. 

“We found that countries with colder average temperatures were generally correlated with higher incidence and mortality rates across the pandemic. This pattern suggests that future seasonal changes could lead to more predictable trends in COVID-19 cases and deaths,” said Hernandez, an undergraduate researcher studying in the Department of Animal Sciences in the College of ACES.

The team also evaluated relationships between COVID-19 metrics and environmental health indicators using Yale’s Environmental Performance Index (EPI) and the State of Global Air report. These databases include scores relating to climate change, pollution emissions, household air pollution, and similar metrics for more than 150 countries globally. 

When the team analyzed patterns for March 2021, they found total COVID-19 cases and deaths were correlated with countries' overall proactiveness to reduce pollutant emissions, such as carbon dioxide, sulfur dioxide, and nitrogen oxides. The analysis also showed higher particulate matter levels and household use of solid fuels were strongly correlated with COVID-19 cases and deaths.

“To improve public health, responsible environmental policies must be established at the country level. These policies should aim to reduce the impact of biotic and environmental stressors,” Caetano-Anollés said. “Harming the environment harms public health as a whole.”

In a second paper, published in F1000Research, Caetano-Anollés teamed up with doctoral student Tre Tomaszewski in the School of Information Sciences at U of I to analyze sequences of more than 12 million SARS-CoV-2 genomes between the start of the pandemic and late July 2022. They watched in a time-series analysis as more than 180,000 mutations appeared, coalesced, persisted, and/or died away across three major variants of concern (VOCs), Alpha, Delta, and Omicron. 

The research team tracked the progression across climate zones, finding a marked difference in the uptake of certain groups of presumably advantageous mutations across regions. For example, several haplotypes–gene variations inherited together–weren’t as prominent in the tropics as they were in the northern temperate zone, especially early in the pandemic. 

“We found many haplotypes were decoupled by latitude, suggesting seasonal behavior of SARS-CoV-2 is genetically encoded,” Tomaszewski said. “Consequently, seasonal effects could be potentially manipulated through vaccine design.”

Both studies build on earlier work by Caetano-Anollés’ team showing strong latitude-dependent trends in viral evolution. They found latitude-linked patterns in a global analysis of viral genomes early in the pandemic and again in Australia, more recently. They also identified a molecular temperature sensor on the virus, limiting infectivity in hot, humid conditions. Along with the new analyses, the researchers say it all points to seasonality of SARS Co-V 2, regardless of the variant. 

“Worldwide correlations support COVID-19 seasonal behavior and impact of global change” is published in Evolutionary Bioinformatics [DOI: 10.1177/11769343231169377]. Authors include Nicolas Hernandez and Gustavo Caetano-Anollés. The research was supported by the College of ACES and the National Center for Supercomputing Applications at the University of Illinois. 

“Seasonal effects decouple SARS-CoV-2 haplotypes worldwide” is published in F1000Research [DOI: 10.12688/f1000research.131522.1]. Authors include Tre Tomaszewski, Muhammad Asif Ali, Kelsey Caetano-Anollés, and Gustavo Caetano-Anollés. The research was supported by the National Institute of Food and Agriculture [ILLU-802-909 and ILLU-483-625], the College of ACES and the National Center for Supercomputing Applications at the University of Illinois.

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JOURNAL

Evolutionary Bioinformatics

DOI

10.1177/11769343231169377 

Avian influenza: new aspects of an old threat

From seasonal phenomenon linked to migratory birds in some regions to a constant global risk: highly pathogenic avian influenza has become a threat to wild birds as well as mammals causing issues for the poultry sector and public health.

Peer-Reviewed Publication

EUROPEAN CENTRE FOR DISEASE PREVENTION AND CONTROL (ECDC)

In Europe, epidemics of highly pathogenic avian influenza (HPAI) used to be a seasonal phenomenon associated with migratory waterfowl that were returning to their overwintering sites in the autumn. Since 2020, however, this picture has changed. HPAI viruses, particularly of the influenza A(H5) subtype, have caused the worst epidemics in birds observed to date, with more than 14,000 reported outbreaks and culling of roughly 96 million farmed birds in Europe. [1]

In their editorial published in Eurosurveillance, Cornelia Adlhoch (European Centre for Disease Prevention and Control, ECDC) and Francesca Baldinelli (European Food Safety Authority, EFSA) look at the rapid HPAI development in recent years with a move away from seasonality which has been accompanied by a large geographical extension: from west to east along the migratory bird routes towards south-east Asia. Recently, A(H5N1) virus introductions from Europe to North America was observed in an east to west spread via Iceland and Greenland for the first time from Europe to North America, progressing rapidly across large areas of Canada and the United States (US). Respectively, a north (Europe and North America) to south (Africa and Central/South America) spread during autumn bird migration occurred to as far down as the southern tip of Chile. [2]

They note that risk for human health is currently limited but warn that introduction of avian influenza viruses into mammalian populations could increase the risk of reassortment of influenza viruses that could adapt to mammals and spread among them: “With the ongoing global presence of A(H5) HPAI viruses, further sporadic spill-over events to humans cannot be excluded.”

Avian influenza: from virus evolution and diversification
The authors summarise that the recent “rapid spread of A(H5N1) viruses to many previously unaffected areas globally and their successful persistence during the summer months was likely facilitated by the ongoing evolution and reassortment with local low pathogenic avian (LPAI) viruses, leading to their adaptation to newly or previously very rarely affected wild bird species such as barnacle geese or sea birds.”

With this rapid and extensive spread, HPAI viruses affect wild bird populations e.g. in South America, where influenza A(H5N1) led to the death of more than 40% of the pelican population in Chile and Peru. In addition, Adlhoch and Baldinelli refer to reports from across the globe about transmission of HPAI to mammals such as minks and sea lions. Such events also increase the risk of the virus spilling over to pet animals through contact with for example dead or sick wild birds or mammals such as foxes.

So far, human infections with A(H5N1) have been reported only in a few countries with no or just mild symptoms (United Kingdom, Spain and the United States), related to exposure to infected birds or culling activities but also severe disease or even death (Chile, China, Ecuador and Vietnam) after exposure to sick or dead backyard poultry or to contaminated environment.

The authors highlight that “although currently circulating avian influenza viruses retain a preference for avian-type receptors, different mutations associated with transmission to and pathogenicity in mammals have been observed. These mutations were detected sporadically in infected wild and domestic birds and more often emerged upon transmission events to mammals.”

To tackle the threat of avian influenza, they conclude “a One Health approach is needed through: rapid sharing of information about outbreaks, provision of sequence data and reference viruses, and close collaboration between the different sectors locally and globally. Communication campaigns may help to increase awareness in the population and recognise avian influenza viruses as a threat to animal and human health, in order to reduce the risk of contact with potentially infected animals.”

----Ends----

References/notes to editors:
[1] Avian influenza (AI) is a highly contagious viral disease that affects both domestic and wild birds. AI viruses have also been isolated, although less frequently, from mammalian species, including humans. This complex disease is caused by viruses divided into multiple subtypes (i.e. H5N1, H5N3, H5N8 etc.) whose genetic characteristics rapidly evolve. See: https://www.woah.org/en/disease/avian-influenza/

The most significant impacts of influenza viruses on humans are those arising from the influenza A strains. The natural reservoir of influenza A strains is a diverse pool of viruses among aquatic wild bird populations – the AI viruses. These viruses are of high pathogenicity (HPAI) and low pathogenicity (LPAI), according to their severity in the avian species they usually infect. See: https://www.ecdc.europa.eu/en/avian-influenza

[2] Adlhoch Cornelia, Baldinelli Francesca. Avian influenza, new aspects of an old threat. Euro Surveill. 2023;28(19):pii=2300227. Available from: https://doi.org/10.2807/1560-7917.ES.2023.28.19.2300227

[3] Avian influenza overview March – April 2023, EFSA Journal 2023;21(5):8039. Available from: https://www.efsa.europa.eu/en/efsajournal/pub/8039

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JOURNAL

Eurosurveillance

DOI

10.2807/1560-7917.ES.2023.28.19.2300227 

ARTICLE TITLE

Avian influenza, new aspects of an old threat

ARTICLE PUBLICATION DATE

11-May-2023

The brains of modern dog breeds are larger than those of ancient breeds

Domestication has reduced, modern-day demands have increased the brain size of dogs

Peer-Reviewed Publication

EÖTVÖS LORÁND UNIVERSITY (ELTE), FACULTY OF SCIENCE

 

IMAGE: MODERN DOG BREEDS THAT ARE GENETICALLY MORE DISTANT FROM WOLVES HAVE A RELATIVELY LARGER BRAIN SIZE COMPARED TO ANCIENT BREEDS THAT ARE THOUSANDS OF YEARS OLD, ACCORDING TO THE FINDINGS OF HUNGARIAN AND SWEDISH RESEARCHERS. view more 

CREDIT: PHOTO: BENCE JÁRDÁNY

Modern dog breeds that are genetically more distant from wolves have a relatively larger brain size compared to ancient breeds that are thousands of years old, according to the findings of Hungarian and Swedish researchers. The increase in brain size cannot be attributed to the roles or life history characteristics of the breeds, suggesting that it is likely influenced by urbanization and a more complex social environment.

Even today, the known four hundred dog breeds have developed relatively quickly and exhibit great diversity, making them a treasure trove for researchers interested in rapid changes within a species. Scientists have long been curious about the factors that affect brain size because the human brain is unusually large in comparison to body size. Comparing the various dog breeds can help answer some questions.

Is there a correlation between brain size and the specific tasks for which a breed was bred? Are there differences, for example, between lap dogs and hunting dogs? Or is it more influenced by life expectancy and the challenges of offspring rearing? What we know for certain is that

 thinking and cognitive processes require a lot of energy, and maintaining a larger brain is costly.

 László Zsolt Garamszegi, an evolutionary biologist at the Ecological Research Centre in Hungary, has been studying the evolution of brain size for a long time. "The brains of domesticated animals can be up to twenty percent smaller than those of their wild ancestors. The likely reason for this is that the lives of domesticated species are simpler compared to those of their wild counterparts. In the safe environment provided by humans, there is no need to fear predator attacks or hunt for food. Therefore, there is no need to sustain the energetically costly large brain, and the freed-up energy can be directed towards other purposes, such as producing more offspring, which is important for domesticated animals.”

Niclas Kolm, at  Stockholm University, focuses on brain evolution and the link between variation in brain morphology and behaviour. “Different dog breeds live in varying levels of social complexity and perform complex tasks, which likely require a larger brain capacity. Therefore, we hypothesize that the selective pressures on the brain can vary within the dog species, and we may find differences in brain size among breeds based on the tasks they perform or their genetic distance from wolves."

This is the first comprehensive study regarding the brain size of different dog breeds, and its preparation took several decades.

Tibor Csörgő, a senior research fellow at the Department of Anatomy, Cell and Developmental Biology at Eötvös Loránd University (ELTE), has been collecting skulls for decades. CT scans of the skulls were performed by Medicopus Nonprofit Ltd. in Kaposvár.

Based on the CT images, veterinarian Kálmán Czeibert reconstructed the brains and determined their exact volume. This invaluable collection was complemented by the Canine Brain and Tissue Bank, operated by ELTE for the past seven years, which enabled the verification of brain volumes calculated from skull images using actual brains. In the end, data was gathered from 865 individuals representing 159 dog breeds, with 48 specimens representing wolves.

According to the results published in the journal Evolution, wolves have an average brain volume of 131 cm3, associated with an average body weight of 31 kg. In the case of dogs in a similar weight category, the brain volume is only about three-quarters of that, approximately 100 cm3. This confirms that domestication has also led to a decrease in brain size in dogs. However, what surprised researchers is that the further a dog breed is genetically distant from wolves, the larger its relative brain size becomes. Contrary to expectations, the original role of the breeds, average litter size, and life expectancy are independent of brain size.

"The domestication of dogs began approximately twenty-five thousand years ago, but for ten thousand years, dogs and wolves did not differ in appearance. Many ancient breeds, such as sled dogs, still resemble wolves today. However, the transition to settlement, agriculture, pastoralism, and the accumulation of wealth offered various tasks for dogs, requiring guard dogs, herding dogs, hunting dogs, and even lap dogs. However, a significant portion of the distinct-looking breeds known today has only emerged since the industrial revolution, primarily in the last two centuries, as dog breeding has become a kind of hobby," says Enikő Kubinyi, a senior research fellow at the Department of Ethology at ELTE.

"The results show that the breeding of modern dog breeds has been accompanied by an increase in brain size compared to ancient breeds. We couldn't explain this based on the tasks or life history characteristics of the breeds, so we can only speculate about the reasons. Perhaps the more complex social environment, urbanization, and adaptation to more rules and expectations have caused this change, affecting all modern breeds."

These findings are supported by research indicating that ancient breeds known for their independence are less attentive to human cues and bark less, thus exhibiting differences in visual and acoustic communication compared to modern breeds.

Domestication has reduced, modern-day demands have increased the brain size of dogs

CREDIT

made by Kálmán Czeibert

Original publication: László Zsolt Garamszegi, Enikő Kubinyi, Kálmán Czeibert, Gergely Nagy, Tibor Csörgő, Niclas Kolm, Evolution of relative brain size in dogs – no effects of selection for breed function, litter size or longevity, Evolution, 2023, qpad063, https://doi.org/10.1093/evolut/qpad063

Funding: The study was supported by the Hungarian Academy of Sciences via a grant to the Hungarian Academy of Sciences (grant no. PH1404/21) and National Brain Programme 3.0 (NAP2022-I-3/2022), and by the National Research, Development and Innovation Office (grant no. 2019-2.1.11-TÉT-2020-00109) and Swedish Research Council (grant no. 2021-04476).

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JOURNAL

Evolution

DOI

10.1093/evolut/qpad063 

ARTICLE TITLE

Evolution of relative brain size in dogs—no effects of selection for breed function, litter size, or longevity

Resistant fungal species spreads

Peer-Reviewed Publication

UNIVERSITY OF WÜRZBURG

Among the yeasts from the Candida genus that cause infections in humans, the species Candida auris is still relatively new: this species was only described in 2009, and to date no evidence has been found before the 1990s. It is unclear what ecological niche C. auris colonizes and why human infections have increased since around the turn of the millennium.

Treatment of C. auris infections is greatly complicated by the pathogen's potential to develop resistance to all available antifungal classes. In addition, unlike other Candida species, C. auris can be efficiently transmitted from patient to patient via direct and indirect contact, leading to hospital outbreaks that are difficult to control.

Dramatic increase in the USA

Such outbreaks have now been observed worldwide, including in England, Spain and Italy. In April 2023, a dramatic increase in C. auris infections was shown for the U.S., along with further resistance development. A recent analysis by the European Centre for Disease Prevention and Control also shows a significant increase in case numbers for Europe.

As a result, the U.S. Centers for Disease Control classify C. auris as an "urgent threat" - the highest prioritization category within multidrug-resistant pathogens. In the 2023 list published by the World Health Organization for prioritizing fungi that cause human infections, C. auris is also grouped as one of only four pathogens in the highest priority level.

Increase in case numbers also in Germany

In Germany, there have only been isolated cases in which C. auris has been detected since 2015. However, an analysis now published in the Deutsches Ärzteblatt shows that the number of cases has also increased in Germany in recent years. Responsible for this study were Dr. Alexander Aldejohann from the Institute for Hygiene and Microbiology at the Julius-Maximilians-Universität Würzburg (JMU) and scientists from the National Reference Center for Invasive Fungal Infections (NRZMyk) and the Robert Koch Institute. Also involved was Professor Oliver Kurzai, Director of the Institute of Hygiene and Microbiology and Head of the NRZMyk.

The study is based on a comparison of C. auris data from the NRZMyk and the antibiotic resistance surveillance network of the Robert Koch Institute. A total of 43 C. auris cases were recorded in the two databases by the end of 2022. Colonization was detected in 19 cases and infection requiring therapy in 16 cases. In almost 42 percent of the cases, a stay abroad was documented shortly before the detection of infection.

Resistant to common drugs

80 percent of the fungal strains available at NRZMyk were highly resistant to fluconazole, a commonly used antifungal agent. In one case, there was resistance to echinocandin, a comparatively new class of substances for the treatment of fungal infections. The data analysis also recorded probable nosocomial transmissions in Germany for 2021 and 2022 - i.e. infections contracted by patients in connection with a medical procedure, for example in hospitals, care facilities or outpatient practices.

In summary, the authors conclude that the absolute number of C. auris infections in Germany remains low. However, the significant increase in the number of infections during the past two years and the detection of the first transmission events in Germany should, in their opinion, be interpreted as an alarm signal.

Comments on the publication

"Compared to other European countries such as Spain, Italy or Great Britain, the case numbers in our country are fortunately still low. We must do everything we can to keep it that way for as long as possible - our experience shows that any infection with Candida auris is difficult to treat and potentially life-threatening for patients. However, the good news at the moment is that no patient in a German hospital has to be afraid of becoming infected with Candida auris." (Dr. A. Aldejohann, Specialist in Microbiology, Virology and Infectious Disease Epidemiology, Institute of Hygiene and Microbiology, University of Würzburg)

"Our analyses show - fortunately still at a very low level - a significant increase in C. auris imports into Germany. At the same time, we were able to prove that the cases are currently not completely recorded in any database - we have to assume an unreported number. In view of the fact that we are also already finding the first transmission events in Germany, I have recommended to the Robert Koch Institute the introduction of a statutory laboratory reporting requirement for the detection of C. auris. In my view, this can be implemented with reasonable effort and, in addition to a precise recording of the epidemiology, would also make it possible to initiate infection protection measures at an early stage in the event of detection." (Prof. Dr. Oliver Kurzai, Chair of Medical Microbiology and Mycology, University of Würzburg and Head, NRZMyk)

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JOURNAL

Deutsches Ärzteblatt Online

DOI

10.3238/arztebl.m2023.0047 

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Cells

ARTICLE TITLE

Rise in Candida auris cases and first nosocomial transmissions in Germany

ARTICLE PUBLICATION DATE

11-May-2023

Meeting more UK Government dietary guidelines during childhood could improve future cardiometabolic health, new research suggests.

Peer-Reviewed Publication

UNIVERSITY OF BRISTOL

The study, led by researchers from University of Bristol, is based on data from the world-renowned longitudinal health study, Children of the 90s (officially known as the Avon Longitudinal Study of Parents and Children, ALSPAC). The findings have been recently published in the British Journal of Nutrition.

The researchers assessed how well school-age children in the study complied to key UK Government dietary recommendations and then analysed the relationship between meeting these dietary recommendations during childhood and future cardiometabolic health.

An Eatwell Guide score (C-EWG score) was calculated when the participants were 7, 10 and 13 years old, to assess how well their habitual diet aligned to nine dietary recommendations represented within the Eatwell Guide. Cardiometabolic health was evaluated when these same participants were 17 and 24 years old, by using a cardiometabolic (heart/diabetes) risk score, which took into account the participant’s blood levels of certain fats, their blood pressure, insulin resistance and body fat.

Dr Genevieve Buckland, lead author of the study, from Bristol Medical School, said: “In general, the majority of the children in the study didn’t meet the dietary guidelines for many key foods and nutrients, because their diets contained too much saturated fat, sugar and salt and not enough fruit and vegetables, fibre and fish, particularly oily fish.”

The study also found that almost a third of the children in the study only met one out of nine key Eatwell Guide dietary recommendations, while 12-15% didn’t meet any of them. Children who met fewer dietary recommendations were more likely to come from a lower-socio-economic position and have mothers who were overweight or obese.

“A key finding was that children with diets which were more in line with UK guidelines had better cardiometabolic health when they were young adults. For example, children who met three or more dietary recommendations at 7 years had a lower cardiometabolic risk score at 24 years compared to those who didn’t meet any dietary recommendations. This reduction was largely driven by lower levels of body fat, cholesterol, blood pressure and insulin resistance,” says Dr Buckland.

The research adds to the evidence on the health benefits of following UK Government dietary recommendations from childhood and highlights the importance of creating healthy dietary habits from young ages to maintain future cardiovascular health.

Dr Buckland explains that: “The large gap between what school-age children in this cohort were eating and what they should be eating, according to Government dietary guidelines, implies that a huge amount of work still needs to be done to help UK children adopt healthier eating habits. Public health initiatives and policies particularly need to target children and their parents from lower socio-economic positions, because poorer dietary habits amongst these groups of children could be contributing to social inequalities in cardiovascular health later in life.”

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JOURNAL

British Journal Of Nutrition

DOI

10.1017/S0007114523000685 

ARTICLE TITLE

Prospective association between adherence to UK dietary guidelines in school-age children and cardiometabolic risk markers in adolescence/early adulthood in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort

Researchers at Purdue discover superconductive images are actually 3D and disorder-driven fractals

Peer-Reviewed Publication

PURDUE UNIVERSITY

Meeting the world’s energy demands is reaching a critical point. Powering the technological age has caused issues globally. It is increasingly important to create superconductors that can operate at ambient pressure and temperature. This would go a long way toward solving the energy crisis. 

Advancements with superconductivity hinge on advances in quantum materials.  When electrons inside of quantum materials undergo a phase transition, the electrons can form intricate patterns, such as fractals. A fractal is a never-ending pattern. When zooming in on a fractal, the image looks the same. Commonly seen fractals can be a tree or frost on a windowpane in winter. Fractals can form in two dimensions, like the frost on a window, or in three-dimensional space like the limbs of a tree. 

Dr. Erica Carlson, a 150th Anniversary Professor of Physics and Astronomy at Purdue University, led a team that developed theoretical techniques for characterizing the fractal shapes that these electrons make, in order to uncover the underlying physics driving the patterns. 

Carlson, a theoretical physicist, has evaluated high resolution images of the locations of electrons in the superconductor Bi2-xPbzSr2-yLayCuO6+x (BSCO), and determined that these images are indeed fractal and discovered that they extend into the full three-dimensional space occupied by the material, like a tree filling space.

What was once thought of as random dispersions within the fractal images are purposeful and, shockingly, not due to an underlying quantum phase transition as expected, but due to a disorder-driven phase transition.

Carlson led a collaborative team of researchers across multiple institutions and published their findings, titled "Critical nematic correlations throughout the superconducting doping range in Bi2-xPbzSr2-yLayCuO6+x," in Nature Communications.

The team includes Purdue scientists and partner institutions. From Purdue, the team includes Carlson, Dr. Forrest Simmons, recent PhD student, and former PhD students Dr. Shuo Liu and Dr. Benjamin Phillabaum. The Purdue team completed their work within the Purdue Quantum Science and Engineering Institute (PQSEI). The team from partner institutions includes Dr. Jennifer Hoffman, Dr. Can-Li Song, Dr. Elizabeth Main of Harvard University, Dr. Karin Dahmen of the University of Urbana-Champaign, and Dr. Eric Hudson of Pennsylvania State University.

“The observation of fractal patterns of orientational (‘nematic’) domains – cleverly extracted by Carlson and collaborators from STM images of the surfaces of crystals of a cuprate high temperature superconductor – is interesting and aesthetically appealing on its own, but also of considerable fundamental importance in coming to grips with the essential physics of these materials,” says Dr. Steven Kivelson, the Prabhu Goel Family Professor at Stanford University and a theoretical physicist specializing in novel electronic states in quantum materials. “Some form of nematic order, typically thought to be an avatar of a more primitive charge-density-wave order, has been conjectured to play an important role in the theory of the cuprates, but the evidence in favor of this proposition has previously been ambiguous at best. Two important inferences follow from Carlson et al.’s analysis:  1) The fact that the nematic domains appear fractal implies that the correlation length – the distance over which the nematic order maintains coherence – is larger than the field of view of the experiment, which means that it is very large compared to other microscopic scales.  2)  The fact that patterns that characterize the order are the same as those obtained from studies of the three dimensional random-field Ising model – one of the paradigrmatic models of classical statistical mechanics – suggests that the extent of the nematic order is determined by extrinsic quantities and that intrinsically (i.e. in the absence of crystalline imperfections) it would exhibit still longer range correlations not just along the surface, but extending deep into the bulk of the crystal.”

High resolution images of these fractals are painstakingly taken in Hoffman’s lab at Harvard University and Hudson’s lab, now at Penn State, using scanning tunneling microscopes (STM) to measure electrons at the surface of the BSCO, a cuprate superconductor. The microscope scans atom by atom across the top surface of the BSCO, and what they found was stripe orientations that went in two different directions instead of the same direction. The result, seen above in red and blue, is a jagged image that forms interesting patterns of electronic stripe orientations.

“The electronic patterns are complex, with holes inside of holes, and edges that resemble ornate filigree,” explains Carlson. “Using techniques from fractal mathematics, we characterize these shapes using fractal numbers. In addition, we use statistics methods from phase transitions to characterize things like how many clusters are of a certain size, and how likely the sites are to be in the same cluster.” 

Once the Carlson group analyzed these patterns, they found a surprising result. These patterns do not form only on the surface like flat layer fractal behavior, but they fill space in three dimensions. Simulations for this discovery were carried out at Purdue University using Purdue’s supercomputers at Rosen Center for Advanced Computing. Samples at five different doping levels were measured by Harvard and Penn State, and the result was similar among all five samples.

The unique collaboration between Illinois (Dahmen) and Purdue (Carlson) brought cluster techniques from disordered statistical mechanics into the field of quantum materials like superconductors.  Carlson’s group adapted the technique to apply to quantum materials, extending the theory of second order phase transitions to electronic fractals in quantum materials.  

“This brings us one step closer to understanding how cuprate superconductors work,” explains Carlson. “Members of this family of superconductors are currently the highest temperature superconductors that happen at ambient pressure.  If we could get superconductors that work at ambient pressure and temperature, we could go a long way toward solving the energy crisis because the wires we currently use to run electronics are metals rather than superconductors. Unlike metals, superconductors carry current perfectly with no loss of energy. On the other hand, all the wires we use in outdoor power lines use metals, which lose energy the whole time they are carrying current. Superconductors are also of interest because they can be used to generate very high magnetic fields, and for magnetic levitation. They are currently used (with massive cooling devices!) in MRIs in hospitals and levitating trains.”

Next steps for the Carlson group are to apply the Carlson-Dahmen cluster techniques to other quantum materials.

“Using these cluster techniques, we have also identified electronic fractals in other quantum materials, including vanadium dioxide (VO2) and neodymium nickelates (NdNiO3). We suspect that this behavior might actually be quite ubiquitous in quantum materials,” says Carlson.

This type of discovery leads quantum scientists closer to solving the riddles of superconductivity.

“The general field of quantum materials aims to bring to the forefront the quantum properties of materials, to a place where we can control them and use them for technology,” Carlson explains. “Each time a new type of quantum material is discovered or created, we gain new capabilities, as dramatic as painters discovering a new color to paint with."

Funding for the work at Purdue University for this research includes the National Science Foundation, the Bilsland Dissertation Fellowship (for Dr. Liu), and Research Corporation for Science Advancement.

 

About the Department of Physics and Astronomy at Purdue University

Purdue Department of Physics and Astronomy has a rich and long history dating back to 1904. Our faculty and students are exploring nature at all length scales, from the subatomic to the macroscopic and everything in between. With an excellent and diverse community of faculty, postdocs, and students who are pushing new scientific frontiers, we offer a dynamic learning environment, an inclusive research community, and an engaging network of scholars.  

Physics and Astronomy is one of the seven departments within the Purdue University College of Science. World-class research is performed in astrophysics, atomic and molecular optics, accelerator mass spectrometry, biophysics, condensed matter physics, quantum information science, particle and nuclear physics. Our state-of-the-art facilities are in the Physics Building, but our researchers also engage in interdisciplinary work at Discovery Park District at Purdue, particularly the Birck Nanotechnology Center and the Bindley Bioscience Center.  We also participate in global research including at the Large Hadron Collider at CERN, Argonne National Laboratory, Brookhaven National Laboratory, Fermilab, the Stanford Linear Accelerator, the James Webb Space Telescope, and several observatories around the world. 

 

About the Purdue Quantum Science and Engineering Institute (PQSEI)

Located in Discovery Park District, PQSEI fosters the development of practical and impactful aspects of quantum science and focuses on discovering and studying new materials, devices, and basic physical quantum systems that will be suited for integration into tomorrow’s technology. It encourages interdisciplinary collaboration leading to the design and realization of quantum devices with enhanced functionality and performance close to the fundamental limit, aiming to ultimately bring them to a vast community of users. PQSEI faculty work on a broad range of topics in quantum science and engineering including quantum materials and devices, quantum photonics, atomic molecular and optical physics, quantum chemistry, quantum measurement and control, quantum simulation, and quantum information and computing. Finally, PQSEI works to train the next generation of quantum scientists and engineers in order to meet the growing quantum workforce demands.

About Purdue University

Purdue University is a top public research institution developing practical solutions to today’s toughest challenges. Ranked in each of the last five years as one of the 10 Most Innovative universities in the United States by U.S. News & World Report, Purdue delivers world-changing research and out-of-this-world discovery. Committed to hands-on and online, real-world learning, Purdue offers a transformative education to all. Committed to affordability and accessibility, Purdue has frozen tuition and most fees at 2012-13 levels, enabling more students than ever to graduate debt-free. See how Purdue never stops in the persistent pursuit of the next giant leap at https://stories.purdue.edu.

 

Written by Cheryl Pierce, Communications Specialist

Contributors: Erica Carlson, 150th Anniversary Professor of Physics and Astronomy at Purdue University and Steven Kivelson, the Prabhu Goel Family Professor at Stanford University

Citation: "Critical nematic correlations throughout the superconducting doping range in Bi2−zPbzSr2−yLayCuO6+x" 
by Can-Li Song, Elizabeth J. Main, Forrest Simmons, Shuo Liu, Benjamin Phillabaum, Karin A. Dahmen, Eric W. Hudson, Jennifer E. Hoffman & Erica W. Carlson, Nature Communications 14, 2622 (2023)

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JOURNAL

Nature Communications

DOI

10.1038/s41467-023-38249-3 

ARTICLE TITLE

Critical nematic correlations throughout the superconducting doping range in Bi2−zPbzSr2−yLayCuO6+x

‘Nature is messy': Pioneers in landscape transcriptomics study genes in the wild

Peer-Reviewed Publication

PENN STATE

 

IMAGE: IN THE COLLEGE OF AGRICULTURAL SCIENCES A NUMBER OF FACULTY, SUCH AS THE ENTOMOLOGISTS STUDYING BEES, ARE USING TRANSCRIPTOMICS IN THEIR RESEARCH ALREADY, AND THEY ARE DEEPLY INTERESTED IN THE CONSERVATION AND NATURAL RESOURCE MANAGEMENT APPLICATIONS. view more 

CREDIT: HEATHER HINES

UNIVERSITY PARK, Pa. — An interdisciplinary team in Penn State’s College of Agricultural Sciences — in an initiative aimed at better understanding the implications of climate change for animal and plant life and agricultural systems — is focusing on an emerging field of study called landscape transcriptomics.

In an invited technical review paper recently published in Molecular Ecology Resources, team leader Jason Keagy, assistant research professor of wildlife behavioral ecology, explained that landscape transcriptomics studies how patterns of gene expression in living organisms relate to changes in environment — including habitat, weather, climate and contaminants — as well as the subsequent effects on the function of plants and animals.

He explained that a transcriptome is the total of all the RNA molecules expressed from the genes of an organism, essentially a collection of all the gene readouts present in a cell. By looking at finer scale gene expression differences over larger scale environments, trends emerge that offer new insight into how life on Earth is adapting to change, he said.

We sat down with Keagy to learn more about the new, complex field.

Q: What is landscape transcriptomics?

Keagy: Transcriptomics is the study of all the RNA molecules in a given tissue at a certain point in time. Why do we care about RNA? DNA is basically a memory-storage device. For a gene to actually do anything, the letters of DNA must be rewritten as letters of RNA and then translated into a protein.

We can literally read the RNA letters to find out which genes are active and how active they are. We can then ask: How is the active part of the DNA code affected by an environmental stressor? That’s where the landscape part comes in. Typically, we would do experiments to answer this question. But some things just can’t be studied well in the lab. Nature is messy and understanding that messiness is important.

So, what if we instead grabbed samples from across the landscape and asked how some variable — temperature, altitude, shade — influenced gene expression, the transcriptome? That, in a nutshell, is landscape transcriptomics.

Q: What can researchers accomplish using landscape transcriptomics?

Keagy: In the paper we just published, we outline three major areas of research that we envision landscape transcriptomics will address: understanding molecular pathways involved in response to the environment, generating and testing hypotheses about the mechanisms and evolution of these responses to the environment, and applying this knowledge to species conservation and management.

The first two are important from the point of view of understanding how organisms respond to the environment, whereas the third is important from a more practical point of view.

Q: What are practical applications of this approach?

Keagy: We envision a number of ways landscape transcriptomics can be used for conservation and management. One way is in the development of biomarkers. For example, we could survey brook trout from various streams over a period of time to discover a set of genes that reliably tracks temperature stress. Using this information, we could identify populations that are at risk and target them for habitat or other mitigation.

We could also identify populations that are especially resilient to thermal stress and use those for reintroduction or assisted migration. Because gene expression flexibly responds to the environment and because we can often get tissue through non-lethal means — for example, by extracting a tiny piece of gill — it could allow us to much better track population stress.

Under a potential future scenario, a technician conducting an electro-fishing survey for the Pennsylvania Fish and Boat Commission could take a small piece of gill, put it in a provided vial to preserve it, and mail to Penn State. We would be able to tell the commission whether that fish was exhibiting signs of thermal stress or other stressors for which we had information.

Q: Why isn’t everyone already using this approach?

Keagy: Genomic sequencing is expensive, but it is getting cheaper. We point out in our paper that it is possible to get samples sequenced with certain technologies below $100 per sample. That price will likely continue to come down as there are new generation sequencers coming onto the market.

There are also challenges to the approach both from an experimental design and statistical analysis side. We discuss these in the paper and offer some suggestions, although point out that the field could benefit from more work in figuring out the best way to do analysis efficiently.

The team

The landscape transcriptomics initiative at Penn State — which includes Christina Grozinger, Publius Vergilius Maro Professor of Entomology; Heather Hines, associate professor of biology and entomology; and Tyler Wagner, assistant unit leader USGS Cooperative Fish and Wildlife Research Unit and adjunct professor of fisheries ecology — received a Strategic Networks and Initiatives Program Grant Level I from the College of Agricultural Sciences.

By supporting the team’s research efforts, the college is recognizing that Penn State is uniquely positioned to make advances in the emerging field, explained Blair Siegfried, associate dean of research for the college.

“Here in the College of Agricultural Sciences at Penn State, a number of faculty using transcriptomics in their research already are deeply interested in all the questions outlined in the just-published paper, including the conservation and natural resource management applications,” he said. “We are excited about this interdisciplinary, faculty-driven research initiative and the directions this team is opening up for future research.”

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JOURNAL

Molecular Ecology Resources

DOI

10.1111/1755-0998.13796 

METHOD OF RESEARCH

Literature review

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Landscape transcriptomics as a tool for addressing global change effects across diverse species