Brain

How do you study a group of organisms with over 300,000 species, dispersed across all seven continents, and with up to 50 times as much DNA content as the human genome?

This is the question posed to biologists studying the evolutionary history of flowering plants, called angiosperms, whose rapid diversification was so convoluted a problem that Darwin referred to it as the 'abominable mystery.'

This month, both the American Journal of Botany (AJB) and Applications in Plant Sciences (APPS) are devoting their July issues to what has recently become a turning point in the way scientists study the relationships among flowering plants. Dubbed Angiosperms353, the initiative combines new and innovative DNA sequencing techniques with genetic information from 1KP, a massive data resource with DNA from more than 1,000 species that took an international team over a decade to complete.

"Using these gene sequences as a common tool opens up new questions that could not have been looked at before," said Dr. Matthew Johnson, assistant professor and herbarium director at Texas Tech University and one of the original architects of Angiosperms353.

The Greater Phylogenetic Good

Until now, geneticists have had to choose between two options when designing a study: either obtain small amounts of DNA for a large number of organisms or the reverse.

After DNA sequencing was originally developed in the mid-1960s, scientists primarily went with the first option. They began stitching together the tree of life by comparing genetic sequences shared widely among species. Named after its founder, Sanger sequencing was used to assemble trees by examining just a small number of genes, somewhat like trying to understand a country by only visiting its capital.

With the advent of next-generation sequencing at the turn of the century, some researchers began specializing in the opposite approach, meticulously assembling a single organism's entire genetic code. The first test case, the Human Genome Project, was completed in 2003, spurring the new age of genomics.

Today, next-generation sequencing has largely replaced older methods in most labs. However, costs remain prohibitively high for many researchers. And while knowing the genetic code of an organism's entire genome comes in handy when trying to answer specific questions, such as how proteins and cells function at a molecular level, comparing genomes is an inefficient way of piecing together relationships.

To overcome these challenges, researchers have adopted a technique called target sequence capture, which leverages the advantages of next-generation sequencing while focusing in on defined sets of hundreds of genes. This method of retrieving DNA has boomed in popularity in the past few years, allowing scientists filling in the branches and leaves on the tree of life to probe both deeply and widely within and between species.

But target sequence capture still has one major drawback in that, unlike its Sanger counterpart, there hasn't yet been a widely standardized set of sequences with which to compare across multiple studies and to build upon their results. Every time a researcher wants to analyze evolutionary patterns in a group of organisms, they have to design new probes to extract genetic information.

"These increasingly popular genomic methods allow scientists to fish out hundreds of genes; however, the probes needed to do this are expensive and complex to design, and usually only work for a narrowly defined group," said Dr. William Baker, a Senior Research Leader at the Royal Botanic Gardens, Kew, and a lead guest editor for the AJB special issue.

This limitation has hampered the development of large studies on the evolutionary history of plants, but is an issue scientists identified early on and have worked diligently over the past decade to avoid. Starting in 2019 with the release of two combined probe sets -- Angiosperms353 for flowering plants and GoFlag for groups including ferns and mosses -- they're now starting to reap the rewards of their labor.

"Angiosperms353 targets a standardized set of genes, which means published data can be re-used and synthesized across studies for the 'greater phylogenetic good,'" Baker said.

The Splash Zone

Plant biologists haven't wasted any time in putting the Angiosperms353 probes to use. The 20 studies published in these special issues span the breadth of angiosperm diversity, encompassing over 500 genera and several times as many species. And because of the broad utility of the probes, each study also zooms in on a particular group at different magnifications.

Many of the genetic sequences the probes correspond to have been relatively stable throughout the 140-million-year history of flowering plants. These DNA strands accumulate mutations at a glacial pace and are thus useful in constructing the main branches of the angiosperm tree of life.

Other sequences mutate at a much faster clip, to the extent that no two are alike in any given species. And while most of the probes correspond to DNA actively used by cells to create proteins, they also adhere to small portions of DNA that flank either end of a protein-coding strand, regions emblematically referred to as 'the splash zone.'

These flanking regions don't actively code for proteins; in fact, scientists are still unsure exactly what they do. What they do know is this non-coding DNA mutates quickly, similar to the types of genes used for forensic testing in crime labs. In plants, they can be used to illuminate close relationships among closely related species or to reveal patterns of genetic diversity among individuals, filling in the small twigs and leaves on the tree of life and providing an important roadmap for conservation efforts.

Past, Present, and Future

Sequence capture also has an important advantage over previous techniques in that it can be reliably used to retrieve old DNA. This feature is extremely important in a field where some estimates suggest the majority of the 70,000 or so plant species yet to be discovered have already been collected and stored in herbaria. Some species, such as Miconia abscondita, were only discovered through genetic analysis of herbarium tissue after they'd gone extinct in the wild. And analyses of plant communities from ages past have been used in multiple cases to study how plants are responding to climate change.

The studies in these issues offer a glimpse into the future of plant phylogenetics, one in which researchers can obtain immense quantities of data in a fraction of the time it would have taken them just 20 years ago. For Baker, who will be publishing Angiosperms353 data for over 7,000 flowering plant genera later this year, that future looks bright. In concert with the Royal Botanic Gardens, Kew, he and several colleagues have been using the new probe set to construct the plant tree of life through the PAFTOL project. He's also helped launch a free repository called the Kew Tree of Life Explorer to store and distribute the growing amounts of genetic data from researchers around the world who are using the probes.

"The standardization of these targeted genes will pay dividends for decades to come, as we inch towards our collective goal of a complete tree of life for all species," Baker said.

The Covid-19 pandemic and the politicization of health-prevention measures such as vaccination and mask-wearing have highlighted the need for people to accept and trust science.

But trusting science isn't enough.

A new study finds that people who trust science are more likely to believe and disseminate false claims containing scientific references than people who do not trust science. Reminding people of the value of critical evaluation reduces belief in false claims, but reminding them of the value of trusting science does not.

"We conclude that trust in science, although desirable in many ways, makes people vulnerable to pseudoscience," the researchers write. "These findings have implications for science broadly and the application of psychological science to curbing misinformation during the COVID-19 pandemic."

"People are susceptible to being deceived by the trappings of science," said co-author Dolores Albarracín, the Alexandra Heyman Nash Penn Integrates Knowledge University Professor of the University of Pennsylvania. She said, for example, that Covid-19 vaccines have been the target of false claims that they contain pollutants or other dangerous ingredients. "It's deception but it's pretending to be scientific. So people who are taught to trust science and normally do trust science can be fooled as well."

Albarracín, a social psychologist and director of the Science of Science Communication Division of the Annenberg Public Policy Center of the University of Pennsylvania, said, "What we need are people who also can be critical of information. A critical mindset can make you less gullible and make you less likely to believe in conspiracy theories."

The study, conducted by Albarracín and colleagues when she was in her former position at the University of Illinois at Urbana-Champaign, was published recently in the Journal of Experimental Social Psychology.

The experiments: Misinformation about a virus and GMOs

For the study, researchers conducted four preregistered experiments with online participants. The researchers created two fictitious stories - one about a virus created as a bioweapon, mirroring claims about the novel coronavirus that causes Covid-19, and the other about an unsubstantiated conspiracy theory about the effects of genetically modified organisms or GMOs on tumors.

The invented stories contained references to either scientific concepts and scientists who claimed to have done research on the topic or descriptions from people identified as activists. Participants in each experiment, ranging from 382 to 605 people, were randomly assigned to read either the scientific or non-scientific versions of the stories.

Findings

What the researchers found was that among people who did not have trust in science, the presence of scientific content in a story did not have a significant effect. But people who did have higher levels of trust in science were more likely to believe the stories with scientific content and more likely to disseminate them.

In the fourth experiment, participants were prompted to have either a "trust in science" or a "critical evaluation" mindset. Those primed to have a critical mindset were less likely to believe the stories, whether or not the stories used seemingly scientific references. "The critical mindset makes you less gullible, regardless of the information type," Albarracín said.

"People need to understand how science operates and how science arrives at its conclusions," Albarracín added. "People can be taught what sources of information to trust and how to validate that information. It's not just a case of trusting science, but having the ability to be more critical and understand how to double-check what information is really about."

The lead author, postdoctoral researcher Thomas C. O'Brien of the University of Illinois at Urbana-Champaign, added, "Although trust in science has important societal benefits, it is not a panacea that will protect people against misinformation. Spreaders of misinformation commonly reference science. Science communication cannot simply urge people to trust anything that references science, and instead should encourage people to learn about scientific methods and ways to critically engage with issues that involve scientific content."

The researchers concluded: "Although cynicism of science could have disastrous impacts, our results suggest that advocacy for trusting science must go beyond scientific labels, to focus on specific issues, critical evaluation, and the presence of consensus among several scientists... Fostering trust in the 'healthy skepticism' inherent to the scientific process may also be a critical element of protecting against misinformation ... Empowering people with knowledge about the scientific validation process and the motivation to be critical and curious may give audiences the resources they need to dismiss fringe but dangerous pseudoscience."

Canada should anticipate a resurgence of a childhood respiratory virus as COVID-19 physical distancing measures are relaxed, authors warn in CMAJ (Canadian Medical Association Journal).

Cases of respiratory syncytial virus (RSV) have risen sharply in Australia and, more recently, the United States as COVID-19 case counts have waned and pandemic public health measures have been relaxed. Respiratory syncytial virus affects the lower respiratory tract and can cause serious illness and death. Before the COVID-19 pandemic, about 2.7 million children worldwide were infected with RSV each year, and it was the fourth most common cause of death in young children.

"The off-season resurgence in seasonal respiratory viruses now potentially poses a threat to vulnerable infants," writes Dr. Pascal Lavoie, BC Children's Hospital Research Institute and the University of British Columbia, Vancouver, BC, with coauthors.

During the COVID-19 pandemic, Canada, like other countries, has seen very few cases of RSV, with only 239 positive cases between August 29, 2020, and May 8, 2021, compared with 18,860 positive tests in a similar period the previous year (between August 25, 2019, and May 2, 2020). The virus seemed to disappear over the last year.

However, an increased number of cases of RSV in Canada this summer, as in other jurisdictions, could stretch health care resources in pediatric intensive care units (ICUs). Most pregnant women and very young infants did not develop immunity in the previous season, so children may develop more severe illness this year.

In anticipation of a potential resurgence of RSV, the authors suggest:

Continued emphasis on handwashing and basic hygiene measures and other protective measures such as breastfeeding when possible

Continued testing to confirm RSV when required

Planning by pediatric ICUs to manage increases in severe RSV cases

Administering preventive treatment to highest-risk infants in the summer if cases increase to the level of the normal fall season.

"Potential resurgence of respiratory syncytial virus in Canada" is published July 26, 2021.

Advanced technologies have been used to solve a long-standing mystery about why some people develop serious illness when they are infected with the malaria parasite, while others carry the infection asymptomatically.

An international team used mass cytometry - an in-depth way of characterising individual cells - and machine learning to discover 'immune signatures' associated with symptomatic or asymptomatic infections in people infected with the Plasmodium vivax parasite. This uncovered an unexpected role for immune T cells in protection against malaria, a finding that could help to improve the development of much-needed malaria vaccines.

The research, which was published in the journal JCI Insight was led by WEHI's Dr Lisa Ioannidis and Associate Professor Diana Hansen, in collaboration with Professor Ric Price from the Menzies School of Health Research, Darwin, and Dr Rintis Noviyanti from the Eijkman Institute for Molecular Biology, Indonesia.

At a glance

Advanced technologies have revealed 'immune signatures' that differentiate immune responses that drive symptomatic or asymptomatic Plasmodium vivax malaria infections.

The international collaboration revealed a previously unrecognised role for immune CD4 T cells in preventing serious disease and controlling asymptomatic infection of low parasite burden.

The findings could guide to the development of better vaccines against malaria, a disease that kills hundreds of thousands of people around the world each year.

Variable immune responses

Malaria is a parasitic disease impacting hundreds of millions of people each year. After infection, people develop immunity to the Plasmodium parasite that causes malaria - but this immunity only reduces the disease severity rather than preventing infection altogether. Despite the immense global impact of malaria, there are not yet vaccines in clinical use to prevent this disease.

The immune response to malaria is a 'double-edged sword', Associate Professor Hansen said. "While an immune response to the parasite can prevent severe disease, in some people it is an excessive immune response - driving severe inflammation - that exacerbates malaria, causing the most severe, and potentially fatal, symptoms," she said.

"Our research has investigated the longstanding question of how immune responses differ between people with symptomatic and asymptomatic malaria infections. We focussed on the Plasmodium vivax form of malaria, which is most common in the Asia-Pacific and Latin America. This species is a particular challenge to control as infected people can carry it for many months in the liver without symptoms."

Using the University of Melbourne's mass cytometry facility, the research team were able to undertake in-depth, multi-dimensional assessments of the immune cells in blood samples provided by people living in a vivax malaria-endemic region of Indonesia. Dr Ioannidis said the team compared many aspects of immunity in samples from people who were uninfected, asymptomatically infected, or symptomatically infected with P. vivax.

"In collaboration with a WEHI bioinformatics team led by Professor Gordon Smyth, we used machine learning to develop an 'immune signature' that distinguised between these three categories of samples. These signatures could be applied to new blood samples from people infected with malaria, to accurately predict the severity of their infection," Dr Ioannidis said.

Enhancing malaria control

Dr Ioannidis said the immune signatures revealed the key components of the immune response that drive immunity to malaria. "Antibodies produced by B cells were one important component, especially in people with high parasite loads and symptomatic disease, but we also discovered that certain types of CD4 T cells were critical to keep infections in check, preventing symptoms," she said.

"This is the first time CD4 T cells have been shown to be important for controlling asymptomatic P. vivax infections."

Associate Professor Hansen said the discovery could lead to better approaches to controlling - or even eliminating - malaria. "Malaria vaccine development has focussed almost entirely on measuring antibody responses as a marker of vaccine success. Our research has revealed the important role of CD4 T cells in controlling malaria infections - and we think these cells need much more consideration when designing malaria vaccines. Because vivax malaria can persist in asymptomatic people, it is critical that vaccines activate CD4 T cells to control these low-grade infections," Associate Professor Hansen said.

Due to the global efforts to meet sustainability standards, many countries are currently looking to replace concrete with wood in buildings. France, for example, will require that all new public buildings will be made from at least 50 percent wood or other sustainable materials starting in 2022.

Because wood is prone to degradation when exposed to sunlight and moisture, protective coatings can help bring wood into wider use. Researchers at Aalto University have used lignin, a natural polymer abundant in wood and other plant sources, to create a safe, low-cost and high-performing coating for use in construction.

'Our new coating has great potential to protect wood. It's more water repellent than a lot of commercial coatings because it retains the natural structure of wood and its micro-scaled roughness. Since it's hydrophobic, the coating is also quite resistant to stains, while lignin's inherent structure resists colour changes from sunlight. It also does an excellent job of retaining wood's breathability,' explains Alexander Henn, doctoral candidate at Aalto University, The School of Chemical Engineering.

Lignin is often regarded as a waste product of pulping and biorefinery processes. Each year, about 60-120 million tonnes of lignin is isolated worldwide, of which 98 percent is incinerated for energy recovery. Lignin has several beneficial properties; however, the poor solubility of most lignin types and the mediocre performance of lignin-based products have so far limited its commercial applications.

'Lignin as a coating material is actually very promising with its many benefits compared to the synthetic and bio-based coatings currently used. It has excellent anti-corrosion, anti-bacterial, anti-icing, and UV-shielding properties. Our future research will concentrate on developing characteristics like elasticity of the coating', says Monika Österberg, Head of the Department of Bioproducts and Biosystems at Aalto University.

Currently, widely used mechanically protective coatings for materials such as wood, concrete, metals, and composites are petroleum-based, which include substances that are harmful for the environment. Vegetable-oil coatings -- like those made from tall, linseed, coconut, soybean, and castor -- can be more sustainable alternatives but they often lack durability. As a result, these oils are often combined with synthetic materials to improve their performance.

More sustainable and non-toxic alternatives can help the coating industry meet new safety regulations. For example, the amount of volatile organic compounds (VOCs) has been regulated not only due to their impact on health but also on the ozone layer. Similarly, the European Union (EU) has placed restrictions on some chemicals used by the coating industry, such as bisphenol A and formaldehyde (used in epoxy and polyurethane coatings), and recently classified titanium dioxide -- one of the most widely used pigments in paints -- as a class II carcinogen.