Culture

New test to study language development in youth with Down syndrome

Expressive language sampling (ELS) is a useful tool for measuring communication development in youth with Down syndrome, a new multi-site study has found.

The study, co-led by Angela Thurman and Leonard Abbeduto from the UC Davis MIND Institute and the Department of Psychiatry and Behavioral Sciences, focused on language as an outcome measure to detect meaningful changes in communication skills of individuals with Down syndrome. It successfully tested and validated ELS as a reliable set of procedures for collecting, measuring and analyzing the spoken language of participants interacting in a naturalistic setting.

Down syndrome and language delays

Down syndrome is the leading genetic cause of intellectual disability. Approximately one in every 700 babies in the United States is born with Down syndrome. Individuals with Down syndrome frequently have speech and language delays that might severely affect their independence and successful community inclusion.

"Interventions leading to improvements in language would have great impacts on the quality of life of individuals with Down syndrome," said Abbeduto, director of the UC Davis MIND Institute, professor of psychiatry and behavioral sciences and senior author of the study. "To develop and evaluate such interventions, we need a validated measurement tool and ELS provides that."

The ELS procedure

During the ELS procedure, researchers collect samples of participants' speech during two types of natural interactions: conversation and narration.

In conversation, trained examiners engage participants on a variety of topics in a sequenced and standardized manner. They start the conversation with a subject the participants find interesting then introduce a topic from predetermined age-appropriate lists. In their interactions, they follow a script to minimize their participation and maximize the participants' contribution. On average, the conversation lasts around 12 minutes.

In narration, the participants independently construct and tell the story in a wordless picture book. This process usually takes 10 to 15 minutes.

The researchers analyze the collected conversation and narration samples. In a previous ELS application involving participants with fragile X syndrome, the researchers derived five language outcome measures: talkativeness, lexical diversity (vocabulary), syntax, dysfluency (utterance planning) and unintelligibility (speech articulation).

Validity and reliability of the ELS measures in Down syndrome studies

For this study, four university testing sites recruited 107 participants with Down syndrome (55 males, 52 females). Participants were between the ages of 6 and 23 (mean age of 15.13 years) and with IQ levels under 70 (mean IQ of 48.73).

The participants came for a first visit to complete the ELS procedures and to take assessment tests of their IQ, autism symptom severity and other measures. Four weeks later, they revisited for a retest of the ELS procedures. This retest was to assess practice effects over repeated administrations and to check the reliability of ELS measures.

The study found that the ELS measures were generally valid and reliable across ages and IQ levels. It showed that the vocabulary, syntax and speech intelligibility variables demonstrated strong validity as outcome measures. Also, the ELS procedures were feasible for the majority of participants who successfully completed the tasks. Youth who were under 12, had phrase-level speech or less, and had a 4-year-old developmental level or lower found it more difficult to complete.

"Spoken language is the primary way we interact with the people around us, making language a frequent target of treatment. However, we have not had tools sensitive and accurate enough to confidently measure change in language treatment studies," said Thurman, associate professor of psychiatry and first author on the study. "The data from this study provide a critical first step indicating these procedures can be used to effectively measure language for people with Down syndrome."

The study, published April 8 in Journal of Neurodevelopmental Disorders, is available online. The researchers provided online manuals to help other investigators with the administration, training and assessment of fidelity of ELS procedures.

Credit: 
University of California - Davis Health

An atmosphere of intrafamily trust tends to prevent problematic internet use

Cyberbullying already accounts for one in four cases of bullying and, according to the latest UNICEF report issued on the occasion of 'Safer Internet Day', it affects at least two students per class in Spanish schools.

In this regard, the Laboratory of Studies on Coexistence and Violence Prevention at the University of Cordoba, under the direction of professors Rosario Ortega-Ruiz and Eva M. Romera, has just published a study examining family communication and its impact on cyber-gossip and the excessive use of social media-two of the main factors with the greatest influence on cyber-bullying. Their results point in the same direction: an atmosphere of trust in the family is an antidote to this type of behaviour, reducing the risk of schoolchildren engaging inproblematic use of the Internet and excessive involvement in cyber-gossip.

The study, completed by professors Eva Romera, Rosario Ortega-Ruiz and young researchers Antonio Camacho and Daniel Falla, stresses the impact of what in the scientific literature is called "filial disclosure", a term referring to the relationship of trust between children, adolescents and young people and their parents.

"Dialogue between parents and their children, when it allows them to speak spontaneously, revealing their own ideas, feelings and interests, has very positive effects. An affectionate, warm and convivial intra-family climate encourages children to express themselves naturally and reveal their emotions, worries, ideasand problems. A parental bond of this nature provides security and favours an ability to face many of the challenges that cyber behaviour entails", the researchers stress.

They are not referring to a control mechanism exercised by parents, and far less a "heavy-handed" disciplinary approach, but rather cultivating a climate of trust and security. "According to our results," says Prof. Eva Romera, "the communicational mechanism of filial disclosure tends to shield schoolchildren from the risks that lead them to become involved in phenomena like cyberbullying, excessive use of the Internet and cyber-gossip, fostered by social situations that can be problematic and, in some cases, precipitate the emergence of other cyber behaviour problems."

The study, which was carried out with a large sample of Andalusian primary school students from urban, rural, public and state-subsidized schools, was published in Comunicar, the Spanish journal with the greatest international impact in the field, and its results also reveal that the age factor is very important.

In this regard, early adolescence (ages 12-13) is a critical evolutionary period. On the one hand, schoolchildren are at greater risk, and on the other, it is a period in which there is the most pronouncedcorrelation between the variables studied. "Parents should always pay attention to the quality of their communication with their sons and daughters, but in these years they should know that there is a lot at stake, in order to steer them away from cyberbullying and to prevent, through their dialogue and trust, specific episodes of cyberbullying and problematic use of the Internet from seriously affecting them", stresses Professor Eva Romera.

The study, whose results could inform the designs of virtual harassment prevention programs, underscores the importance of family climates and that, rather than excessive control, communication, trust and dialogue are often the keys to effective child-raising.

Credit: 
University of Córdoba

Light shed on the coordination of neural stem cell activation

image: Left: Neural stem cells covering both cerebral hemispheres of an adult zebrafish.
Center: Magnification enabling identification of stem cells that are quiescent (green only), activated (green and magenta), and in the process of differentiation (magenta only).
Right: Neurons generated by these stem cells during adulthood.

Image: 
© Nicolas Dray, Laure Mancini and Laure Bally-Cuif, Institut Pasteur

In all adult vertebrates, neural stem cells can be recruited to produce new neurons in the brain. However, little is known about these so-called "activation" processes.

Scientists at the Institut Pasteur, CNRS, and Tel Aviv University working in collaboration with the École Polytechnique and INRAE have successfully performed 3D visualization and spatial and temporal distribution analysis of neural stem cell activation in the adult brain of a zebrafish vertebrate model.

Their findings demonstrate for the first time that activation events for these cells are coordinated in time and space. In particular, these results may help improve our understanding of regulation processes triggered during brain tumor formation. These findings are published in the April 5, 2021 issue of the journal Cell Stem Cell.

Stem cells, which are found in many adult organs in vertebrates including humans, are capable of proliferating and differentiating to generate new functional cells. For instance, stem cells in the brain (neural stem cells) produce new neurons in adulthood. Most of the time, neural stem cells are in a dormant state known as "quiescence". In order to produce neurons, they must therefore first activate and then divide. This activation stage is crucial: it is a prerequisite for stem cell recruitment and is also critical to their survival (cells that activate excessively become exhausted quickly) and to the position and type of neurons formed.

Within their niche, neural stem cells activate and return to a dormant state in random order and asynchronously, suggesting that these events may be coordinated at cell population level. Scientists in the Zebrafish Neurogenetics Unit at the Institut Pasteur chose zebrafish to test this hypothesis, since zebrafish adult brains contain large quantities of neural stem cells, otherwise similar to mammalian stem cells. Through intravital (non-invasive) two-photon imaging of adult fish, they were able to film stem cells in their niche for several weeks and study the activation pattern of each cell in relation to neighboring cells in real time. Spatial statistical analysis and modeling performed both in real time and in long-term computational simulations demonstrated the existence of inhibitory interactions generated by activated cells, delaying the activation of other adjacent stem cells by several days. By administering a pharmacological molecule in vivo, the scientists also identified the molecular pathway involved, which is known as the Notch signaling pathway. Finally, they demonstrated that these interactions enabled steady neuronal production in time and space.

"This is the first real-time and long-term imaging of an entire neural stem cell population in the brain of an adult vertebrate. These findings demonstrate for the first time that neural stem cell activation events in the vertebrate brain are coordinated in time and space within the niche," commented Laure Bally-Cuif, CNRS scientist, lead author of the study, and Head of the Zebrafish Neurogenetics Unit1 at the Institut Pasteur. Unexpectedly, this study has also demonstrated that the stem cells themselves are involved in this coordination. Therefore, this research has prompted the emergence of a new concept whereby stem cell populations self-organize as a dynamic system enabling spatiotemporal coordination of the behavior of each individual cell.

Such regulation may occur in tumor masses containing cancerous stem cells, in which stem cells in various states of quiescence or activation have been observed. It is also likely that such regulation takes place in the stem cell populations of other adult organs where stem cells are found in compact niches, such as epithelia.

Link a to a video showing stem cells covering one of the cerebral hemispheres of an adult fish. The stem cells were monitored for 23 days to analyze their positions, activation events, and differentiation. The fish were anesthetized and filmed using a two-photon microscope every 3 days. The dots show the center of each cell and the arrows show dividing stem cells : https://www.youtube.com/watch?v=bPZsMz5tsGM

Credit: 
Institut Pasteur

A new agent for the brain diseases: mRNA

image: Brain-derived neurotrophic factor (BDNF) serves as a potential candidate neuroprotective agent, but there are almost no successful clinical trials due to high hurdle in brain access and short half-life. Fukushima et al. show intraventriclarly administered BDNF mRNA using polyplex nanomicelle exerted a prominent effect to prevent neuronal death with the unique mechanism of action. BDNF mRNA was extensively introduced into the astrocytes to generate a higher level BDNF protein in ischemic lesion.

Image: 
Department of Biofunction Research,TMDU

Researchers from Tokyo Medical and Dental University (TMDU) demonstrate an mRNA delivery system that effectively produces BDNF protein in rat brain to protect neurons from ischemia

Tokyo - A lack of oxygen to brain tissue--known as ischemia--leads to the death of neurons, which results in stroke. Despite considerable research, there are currently no treatments that successfully prevent neuronal death. Now, Tokyo Medical and Dental University (TMDU) researchers have reported a way of delivering mRNA to produce a therapeutic protein that protects neurons. Their findings, demonstrated in rats, are published in Biomaterials.

Brain-derived neurotrophic factor (BDNF) is a protein that enhances the survival and function of neurons. However, the BDNF molecule is too large to cross the brain's protective barrier and is rapidly removed from the central nervous system, making it difficult for BDNF to make its mark as a treatment.

The researchers therefore devised a way of producing BDNF where it is needed most.

They designed a delivery system containing BDNF messenger RNA (mRNA), which is the information molecule needed to make BDNF. When the mRNA gets inside a cell, it can be used as a blueprint to make the protein.

Their system--known as an mRNA nanomicelle--is a tiny ball-like parcel of mRNA surrounded by polymer strands. The polymer protects the mRNA from molecules that might break it down and helps to disguise it from the immune system.

"As well as protecting the mRNA by providing containment, the polymer allows the release of the cargo to be controlled," study first author Yuta Fukushima explains. "By selecting polymers with particular properties, we can ensure the mRNA is released when and where it is needed."

The effectiveness of the mRNA therapy was tested on rats that had experienced brain ischemia. The nanomicelles were found to increase the survival of hippocampal neurons. In particular, the nanomicelles showed better effects when administered 2 days after the ischemia than when given immediately. This indicates that the nanomicelles extend the opportunity for providing effective treatment.

In addition, long-term therapeutic benefits were observed 20 days after ischemia when the mRNA nanomicelle was administered on both days 2 and 5. Treated rats showed better spatial memory than untreated rats in a maze experiment.

"We are very encouraged by the performance of our system," says study corresponding author Keiji Itaka. "Our experiments not only demonstrated that the mRNA nanomicelle could prevent neuron death, but also that the potential treatment window could be extended. We expect these findings to have a significant impact on the development of practical clinical treatments."

Credit: 
Tokyo Medical and Dental University

Curtin research finds introduced honeybee may pose threat to native bees

A Curtin University study has found the introduced European honeybee could lead to native bee population decline or extinction when colonies compete for the same nectar and pollen sources in urban gardens and areas of bush.

Published in the 'Biological Journal of the Linnean Society', the research found competition between the native bees and the introduced European honeybee could be particularly intense in residential gardens dominated by non-native flowers, and occurred when the bees shared the same flower preferences.

Under these conditions, it would appear that European honeybees, being very abundant, and effective foragers, with the ability to exploit a wide range of flowers, can outcompete native bees for nectar and pollen resources.

Lead author, Forrest Foundation Scholar Miss Kit Prendergast, from Curtin's School of Molecular and Life Sciences said the research was conducted over two years in urban gardens and areas of native vegetation on the Swan Coastal Plain at Perth, Western Australia and revealed a complex relationship between native and introduced bees.

"Not all native bee species were impacted, but when native bees preferred many of the same flower species as honeybees or were of larger body size, meaning they needed more food, this was when honeybees had a negative impact on native bees," Miss Prendergast said.

"This occurs due to resource competition, where honeybees were more successful at exploiting food resources from flowers, leaving not enough nectar and pollen to support native bee populations.

Unlike native bees, honeybees occur in colonies of tens of thousands of individuals, and are better at telling other colony members where flower patches are. This communication is done by using a combination of movement and vibrations known as the "waggle dance" and using scent.

"Competition from honeybees was particularly fierce in residential gardens where there are lower proportions of the native wildflowers that our native bees have co-evolved to forage on," Miss Prendergast said.

"This impact of competition with a super-abundant, domesticated and feral introduced bee, when combined with pressures from habitat loss as a result of increasing urbanisation and agriculture, especially livestock agriculture, places some native bee species at risk of becoming endangered or even extinct."

Miss Prendergast said planting more flowering plants, particularly those preferred by vulnerable species of native bees, could help prevent them from declining in number. Controlling the density of honeybees would also be critical in reducing the pressure on vulnerable native bees.

"Native bees are an integral and important part of any ecosystem, including in the Southwest Australian biodiversity hotspot in which our research was conducted," Miss Prendergast said.

"European honeybees have been introduced around the world and pose an added threat to many native bee species already at risk of declining numbers or even extinction due to increasing urbanisation."

Credit: 
Curtin University

Lockdown for genome parasites

video: Arabidopsis chromatin remodeller DDM1 (Decreased DNA Methylation I) silences transposons by binding and depositing the histone variant H2A.W, locking the Transposable Elements in tightly packed chromatin.

Image: 
Copyright: FloorFour/GMI

Researchers at GMI - Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences - uncover an ingenious mechanism by which Arabidopsis safeguards the integrity of its genome. The paper is published in the journal Nature Cell Biology.

Is it possible for one single gene product to silence undesirable genetic elements? Can such a strong effect be seen in the regulation of Transposable Elements (TEs), or genome parasites? If yes, how does this gene product singlehandedly keep transposons in check? New research from Frédéric Berger's group at GMI provides answers to these questions and dissects a mechanism of gene silencing that has long remained shrouded in mystery.

Genome parasites

Although jumping transposons promote genomic variation at an evolutionary scale, their effects on an individual organism are massively deleterious. If left unregulated, they could give rise to genome instability and various diseases. In the model plant Arabidopsis, loss of function of one single gene product identified 30 years ago, Decreased DNA Methylation I (DDM1), was shown to result in vast and uncontrollable transposition events. DDM1 is a chromatin remodeler that helps keep DNA tightly packed to silence TEs, but the underlying mechanism how DDM1 silences TE was still unknown.

Trapped before they jump!

The team around GMI group leader Frédéric Berger, with co-first authors Akihisa Osakabe and Bhagyshree Jamge, describe the molecular mechanism of action of DDM1. They show that DDM1 targets TEs by binding H2A.W, a variant of the histone H2A, one of the building blocks that coat DNA to form the condensed and tightly packed heterochromatin. The team demonstrates that the deposition of H2A.W by DDM1 on DNA regions rich with TEs is not only necessary, but also sufficient to remodel the chromatin and silence the TEs. Importantly, the team shows that this mechanism dominates by far other known TE silencing mechanisms in Arabidopsis and that the effect of DDM1 is specific for jumping genes with intact transposing potential, i.e., potentially mobile TEs. "Transposons integrate the genome and thus share chromatin with the host. They can be viewed as enemies hiding in houses. What makes these houses distinct from those hosting protein coding genes? - The material used to build these houses is different: it enshrines transposons such that they can't go out and multiply," says Frédéric Berger. The silencing mechanism described does not affect fragments of jumping genes that have lost their ability to transpose independently, neither does it affect protein coding genes. Frédéric Berger does not hesitate to describe the mechanism with some humor: "Basically, the strategy is: enshrine your enemy in building blocks made of special material and send him to hell!".

Sent to hell packaged by DHL

The association with hell comes from "Hells", the name of the human ortholog of Arabidopsis DDM1. The researchers propose a new class of chromatin remodelers, grouping DDM1 and Hells together with their mouse ortholog Lsh, that they term "DHL". The DHL chromatin remodelers show conserved binding sites for the histone variants. In addition, all three remodelers have been associated with genomic instability and disease in their respective organisms, in case mutations lead to their loss of function.

DHL remodelers control transposons dynamics

DDM1 is the key factor in "camouflaging" TEs away from the transcriptional machinery by utilizing special "building blocks" that prevent their recognition. Asked about the broader impact of this novel mechanism, Frédéric Berger states: "DDM1 orthologs in mammals deposit the H2A.W ortholog variant macroH2A, which has been implicated in various human syndromes and cancers. Better insight into the mechanism of action of this class of histone binding proteins will advance our understanding of genome dynamics with impacts on medicine and evolution".

Engineering silencing mechanisms in yeast

Frédéric Berger, who has received funding from the "1000 Ideen" grant for high-risk research from the Austrian Science Fund (FWF), is already investigating emergent properties of these histone variants and chromatin remodelers and engineering novel silencing pathways in yeast based on the Arabidopsis H2A.W and DDM1.

Credit: 
Gregor Mendel Institute of Molecular Plant Biology

Novel PF74-like small molecules targeting the HIV-1 capsid protein

image: HIV-1 capsid protein (CA)-targeting PF74 suffers from prohibitively low metabolic stability. Structural modifications have yet to produce analogs with balanced potency and metabolic stability. Replacing the inter-domain interacting indole ring with less electron-rich isosteres allowed the identification of compound 20 with drastically improved metabolic stability while largely maintaining antiviral potency.

Image: 
Acta Pharmaceutica Sinica B

Novel PF74-like small molecules targeting the HIV-1 capsid protein: Balance of potency and metabolic stability
https://doi.org/10.1016/j.apsb.2020.07.016

Of all known small molecules targeting human immunodeficiency virus (HIV) capsid protein (CA), PF74 represents by far the best characterized chemotype, due to its ability to confer antiviral phenotypes in both early and late phases of viral replication. However, the prohibitively low metabolic stability renders PF74 a poor antiviral lead. The authors report on their medicinal chemistry efforts toward identifying novel and metabolically stable small molecules targeting the PF74 binding site. Specifically, they replaced the inter-domain-interacting, electron-rich indole ring of PF74 with less electron-rich isosteres, including imidazolidine-2,4-dione, pyrimidine-2,4-dione, and benzamide, and identified four potent antiviral compounds (10, 19, 20 and 26) with markedly improved metabolic stability. Compared to PF74, analog 20 exhibited similar submicromolar potency, and much longer (51-fold) half-life in human liver microsomes (HLMs). Molecular docking corroborated that 20 binds to the PF74 binding site, and revealed distinct binding interactions conferred by the benzamide moiety. Collectively, the authors data support compound 20 as a promising antiviral lead.

Credit: 
Compuscript Ltd

Archaeologists uncover earliest evidence of domesticated dogs in Arabian Peninsula

image: This burial site in a badlands area of AlUla in north-west Saudi Arabia is currently rare for Neolithic-Chalcolithic Arabia in being built above-ground and meant to be visually prominent.

Image: 
Royal Commission of Al-Ula

A team of archaeologists in north-west the Kingdom of Saudi Arabia has uncovered the earliest evidence of dog domestication by the region's ancient inhabitants.

The discovery came from one of the projects in the large-scale archaeological surveys and excavations of the region commissioned by the Royal Commission for AlUla (RCU).

The researchers found the dog's bones in a burial site that is one of the earliest monumental tombs identified in the Arabian Peninsula, roughly contemporary with such tombs already dated further north in the Levant.

Evidence shows the earliest use of the tomb was circa 4300 BCE and received burials for at least 600 years during the Neolithic-Chalcolithic era - an indication that the inhabitants may have had a shared memory of people, places and the connection between them.

"What we are finding will revolutionize how we view periods like the Neolithic in the Middle East. To have that kind of memory, that people may have known for hundreds of years where their kin were buried - that's unheard of in this period in this region," said Melissa Kennedy, assistant director of the Aerial Archaeology in the Kingdom of Saudi Arabia (AAKSAU) - AlUla project.

"AlUla is at a point where we're going to begin to realize how important it was to the development of mankind across the Middle East," said the AAKSAU director, Hugh Thomas.

This is the earliest evidence of a domesticated dog in the Arabian Peninsula by a margin of circa 1,000 years.

The findings are published in the Journal of Field Archaeology.

The project team, with Saudi and international members, focused its efforts on two above-ground burial sites dating to the 5th and 4th millennia BCE and located 130 kilometers apart, one in volcanic uplands and the other in arid badlands. The sites were above ground, which is unique for that period of Arabian history, and were positioned for maximum visibility.

The research team detected the sites by using satellite imagery and then by aerial photography from a helicopter. Ground fieldwork began in late 2018.

It was in the volcanic uplands site that 26 fragments of a single dog's bones were found, alongside with bones from 11 humans - six adults, an adolescent and four children.

The dog's bones showed signs of arthritis, which suggests the animal lived with the humans into its middle or old age.

After assembling the bones, the team then had to determine that they were from a dog and not from a similar animal such as a desert wolf.

The team's zoo archaeologist, Laura Strolin, was able to show it was indeed a dog by analyzing one bone in particular, from the animal's left front leg. The breadth of this bone was 21.0 mm, which is in the range of other ancient Middle Eastern dogs. In comparison, the wolves of that time and place had a breadth of 24.7 to 26 mm for the same bone.

The dog's bones were dated to between circa 4200 and 4000 BCE.

Rock art found in the region indicates that the Neolithic inhabitants used dogs when hunting ibex, and other animals.

The fieldwork uncovered other noteworthy artefacts, including a leaf-shaped mother-of-pearl pendant at the volcanic uplands site and a carnelian bead found at the arid badlands site.

The researchers expect more findings in future as a result of the massive survey from the air and on the ground, and multiple targeted excavations in the AlUla region undertaken by the AAKSAU and other teams, which are operating under the auspices of the Royal Commission for AlUla (RCU). The AAKSAU team is led by researchers from the University of Western Australia in Perth, Australia.

The researchers note that AlUla is a largely unexplored area located in a part of the world that has a fertile archaeological heritage of recognized global value.

"This article from RCU's work at AlUla establishes benchmarks. There is much more to come as we reveal the depth and breadth of the area's archaeological heritage," said Rebecca Foote, Director of Archaeology and Cultural Heritage Research for RCU.

Credit: 
Taylor & Francis Group

Living fossils: Microbe discovered in evolutionary stasis for millions of years

image: Equipment for subsurface sampling of microbes stands in Death Valley, California. New research led by Bigelow Laboratory for Ocean Sciences has revealed that a group of microbes, Candidatus Desulforudis audaxviator, have been at an evolutionary standstill for millions of years.

Image: 
Photo by Duane Moser, Desert Research Institute.

It's like something out of science fiction. Research led by Bigelow Laboratory for Ocean Sciences has revealed that a group of microbes, which feed off chemical reactions triggered by radioactivity, have been at an evolutionary standstill for millions of years. The discovery could have significant implications for biotechnology applications and scientific understanding of microbial evolution.

"This discovery shows that we must be careful when making assumptions about the speed of evolution and how we interpret the tree of life," said Eric Becraft, the lead author on the paper. "It is possible that some organisms go into an evolutionary full-sprint, while others slow to a crawl, challenging the establishment of reliable molecular timelines."

Becraft, now an assistant professor of biology at the University of Northern Alabama, completed the research as part of his postdoctoral work at Bigelow Laboratory and recently published it in the Nature publishing group's ISME Journal.

The microbe, Candidatus Desulforudis audaxviator, was first discovered in 2008 by a team of scientists, led by Tullis Onstott, a co-author on the new study. Found in a South African gold mine almost two miles beneath the Earth's surface, the microbes acquire the energy they need from chemical reactions caused by the natural radioactive decay in minerals. They inhabit water-filled cavities inside rocks in a completely independent ecosystem, free from reliance on sunlight or any other organisms.

Because of their unique biology and isolation, the authors of the new study wanted to understand how the microbes evolved. They searched other environmental samples from deep underground and discovered Candidatus Desulforudis audaxviator in Siberia and California, as well as in several additional mines in South Africa. Since each environment was chemically different, these discoveries gave the researchers a unique opportunity to look for differences that have emerged between the populations over their millions of years of evolution.

"We wanted to use that information to understand how they evolved and what kind of environmental conditions lead to what kind of genetic adaptations," said Bigelow Laboratory Senior Research Scientist Ramunas Stepanauskas, the corresponding author on the paper and Becraft's postdoctoral advisor. "We thought of the microbes as though they were inhabitants of isolated islands, like the finches that Darwin studied in the Galapagos."

Using advanced tools that allow scientists to read the genetic blueprints of individual cells, the researchers examined the genomes of 126 microbes obtained from three continents. Surprisingly, they all turned out to be almost identical.

"It was shocking," Stepanauskas said. "They had the same makeup, and so we started scratching our heads."

Scientists found no evidence that the microbes can travel long distances, survive on the surface, or live long in the presence of oxygen. So, once researchers determined that there was no possibility the samples were cross-contaminated during research, plausible explanations dwindled.

"The best explanation we have at the moment is that these microbes did not change much since their physical locations separated during the breakup of supercontinent Pangaea, about 175 million years ago," Stepanauskas said. "They appear to be living fossils from those days. That sounds quite crazy and goes against the contemporary understanding of microbial evolution."

What this means for the pace of microbial evolution, which often happens at a much more accelerated rate, is surprising. Many well-studied bacteria, such as E. coli, have been found to evolve in only a few years in response to environmental changes, such as exposure to antibiotics.

Stepanauskas and his colleagues hypothesize the standstill evolution they discovered is due to the microbe's powerful protections against mutation, which have essentially locked their genetic code. If the researchers are correct, this would be a rare feature with potentially valuable benefits.

Microbial enzymes that create copies of DNA molecules, called DNA polymerases, are widely used in biotechnology. Enzymes with high fidelity, or the ability to recreate themselves with little differences between the copy and the original, are especially valuable.

"There's a high demand for DNA polymerases that don't make many mistakes," Stepanauskas said. "Such enzymes may be useful for DNA sequencing, diagnostic tests, and gene therapy."

Beyond potential applications, the results of this study could have far-reaching implications and change the way scientists think about microbial genetics and the pace of their evolution.

"These findings are a powerful reminder that the various microbial branches we observe on the tree of life may differ vastly in the time since their last common ancestor," Becraft said. "Understanding this is critical to understanding the history of life on Earth."

Credit: 
Bigelow Laboratory for Ocean Sciences

More than 5,000 tons of extraterrestrial dust fall to Earth each year

image: Electron micrograph of a Concordia micrometeorite extracted from Antarctic snow at Dome C

Image: 
© Cécile Engrand/Jean Duprat

Every year, our planet encounters dust from comets and asteroids. These interplanetary dust particles pass through our atmosphere and give rise to shooting stars. Some of them reach the ground in the form of micrometeorites. An international program conducted for nearly 20 years by scientists from the CNRS, the Université Paris-Saclay and the National museum of natural history with the support of the French polar institute, has determined that 5,200 tons per year of these micrometeorites reach the ground. The study will be available in the journal Earth & Planetary Science Letters from April 15.

Micrometeorites have always fallen on our planet. These interplanetary dust particles from comets or asteroids are particles of a few tenths to hundredths of a millimetre that have passed through the atmosphere and reached the Earth's surface.

To collect and analyse these micrometeorites, six expeditions led by CNRS researcher Jean Duprat have taken place over the last two decades near the Franco-Italian Concordia station (Dome C), which is located 1,100 kilometres off the coast of Adélie Land, in the heart of Antarctica. Dome C is an ideal collection spot due to the low accumulation rate of snow and the near absence of terrestrial dust.

These expeditions have collected enough extraterrestrial particles (ranging from 30 to 200 micrometres in size), to measure their annual flux, which corresponds to the mass accreted on Earth per square metre per year.

If these results are applied to the whole planet, the total annual flux of micrometeorites represents 5,200 tons per year. This is the main source of extraterrestrial matter on our planet, far ahead of larger objects such as meteorites, for which the flux is less than ten tons per year.

A comparison of the flux of micrometeorites with theoretical predictions confirms that most micrometeorites probably come from comets (80%) and the rest from asteroids.

This is valuable information to better understand the role played by these interplanetary dust particles in supplying water and carbonaceous molecules on the young Earth.

Credit: 
CNRS

How to tame a restless genome

image: This is a structure of the Asterix/Gtsf1 protein. Asterix/Gtsf1 helps immobilize so-called "jumping genes" in germ cells, a type of cell important for sexual reproduction. CSHL Professor & HHMI Investigator Leemor Joshua-Tor and a research investigator in her lab, Jonathan Ipsaro, used two different biophysical techniques, cryo-EM and NMR, to develop their model. In this NMR structure, the purple helix binds to a tRNA, a special class of RNA, which is speculated to escort it to a jumping gene. The blue surface of the protein is positively charged, which helps it bind to negatively charged RNA molecules. The red area on the right is negatively charged.

Image: 
Ipsaro/Joshua-Tor lab, CSHL/2021

Short pieces of DNA--jumping genes--can bounce from one place to another in our genomes. When too many DNA fragments move around, cancer, infertility, and other problems can arise. Cold Spring Harbor Laboratory (CSHL) Professor & HHMI Investigator Leemor Joshua-Tor and a research investigator in her lab, Jonathan Ipsaro, study how cells safeguard the genome's integrity and immobilize these restless bits of DNA. They found that one of the jumping genes' most needed resources may also be their greatest vulnerability.

The mammalian genome is full of genetic elements that have the potential to move from place to place. One type is an LTR retrotransposon (LTR). In normal cells, these elements don't move much. But if something happens to allow them to move, say during sexual reproduction or in cancerous cells Joshua-Tor says:

"Sometimes they jump into very important spots, either genes themselves or in areas of the genome that is important for regulating genes."

In this study, Joshua-Tor and Ipsaro examined a mouse protein called Asterix/Gtsf1 that immobilizes LTRs. To understand how this protein locks down LTRs, Ipsaro used several techniques, including cryo-EM, to take a closer look at the protein structure. Joshua-Tor says:

"Structure just informs us in many ways, like how things work. If you can see something, you have a way better idea of how it works."

Ipsaro found Asterix/Gtsf1 binds directly to a particular class of RNA called transfer RNA (tRNA). tRNAs normally are part of the cell's protein manufacturing machinery. LTRs have borrowed that part of the protein-making machinery to replicate their genetic material. Asterix/Gtsf1 overrides what the LTRs are trying to do by freezing the otherwise mobile element in place, shutting down their ability to move. Ipsaro says:

"It's trying to copy and paste itself all over the genome. A part of it evolutionarily has depended on tRNA binding in order to replicate."

Instead of freezing the entire genome, scientists think Asterix/Gtf1 is using tRNAs to suppress small specific regions, like LTRs. Researchers are trying to figure out how cells protect themselves against these and other types of mobile genetic elements. They hope that someday they might tame an overly restless genome, preventing new mutations in the germline and in tumors.

Credit: 
Cold Spring Harbor Laboratory

How people decide when they have so many choices

video: This animation shows what one study participant looked at before choosing from among 16 snacks. The current gaze position is indicated by a white box, while the choice is indicated by a red box. For better visibility, gaze durations have been increased by a factor of two.

Image: 
Ian Krajbich

COLUMBUS, Ohio - It's one thing to decide among two or three snacks available at a friend's house. But what do people do when they're faced with a vending machine offering 36 different options?

A new study using eye-tracking technology suggests that the amount of time people spend looking at individual items may actually help them decide. Findings showed that people tended to choose snacks they spent more time looking at, sometimes even over snacks that they rated more highly.

"We could do pretty well predicting what people would choose based just on their ratings of the snacks available to them. But we could do an even better job by accounting for how much they looked at each item," said Ian Krajbich, co-author of the study and associate professor of psychology and economics at The Ohio State University.

But the amount of time people spend looking at individual items isn't the whole story of how people decide when they have many alternatives, Krajbich said.

"It's a little more complicated than that," he said.

Krajbich conducted the study with lead author Armin Thomas of Technische Universität Berlin and Felix Molter of Freie Universität Berlin. The research was published this week in the journal eLife.

The study involved 49 people who said they were fans of snack foods and who agreed to fast for at least four hours before the study - to make sure the task was relevant to them.

On a computer screen, the participants were shown sets of 9, 16, 25 or 36 different snack foods and asked to choose which snack they would like to eat the most at the end of the experiment.

They did this multiple times over the course of the experiment. An eye tracker recorded exactly where they looked while making these choices.

After the experiments, participants rated how much they liked all 80 snacks that were part of the study.

The results showed that people didn't look carefully at all the items before making a choice, or even just look at each item until they found one of their favorites. Instead, they looked around in a way that at first glance looked random, but depended on the physical location of the items as well as how much they were liked.

"There is this peripheral screening process where people learn to avoid even looking directly at the snacks they don't really like," Krajbich said.

"This is not something that we see in studies where participants only have two alternatives. It only occurs when they have lots of options."

One of the leading theories among researchers is that when people are presented with many choices, they scan until they find something that is "good enough" - in this case a snack they will enjoy, regardless of whether it is their favorite.

But that's not what happened, Krajbich said. If this "satisficing" model were true, people would quit looking as soon as they found a snack that was good enough. But results showed that participants chose the last snack they looked at only about 45% of the time.

Instead, what seemed to happen most often is that people would look through the items, often going back and forth between them, until one item stood out from the others - often the snack they looked at the most.

"People made a choice when they concluded the best option was sufficiently better than the next-best option," he said.

Where the snacks appeared in the display - left or right, top or bottom - didn't play much of a role in people's decision-making. Participants often started searching in the top left of the display and then looked left to right, top to bottom - but only to a limited extent.

"Pretty quickly their attention gets drawn to their higher-value options. That influences their search process and their gaze starts to jump around less predictably," he said.

Credit: 
Ohio State University

Team cracks eggs for science

image: A brown-headed cowbird snuck three eggs into a prothonotary warbler's nest.

Image: 
Photo by Jeffrey P. Hoover

CHAMPAIGN, Ill. -- Avian brood parasites lay their eggs in the nests of other bird species, forcing the hosts to do the hard work of raising the unrelated young. A team of scientists wanted to simulate the task of piercing an egg - a tactic that only a minority of host birds use to help grasp and eject the foreign eggs. Their study offers insight into some of the physical challenges the discriminating host birds face.

The new findings appear in the Journal of Experimental Biology.

Take cowbirds, for example. Their eggs look nothing like the host birds' eggs, "yet most of their hosts do not reject the parasite eggs," said study co-author Mark Hauber, a professor of evolution, ecology and behavior at the U. of I. and a brood parasitism expert. "One explanation is that the cowbird eggshell is too thick and strong for a small host's beak to pierce."

To determine whether the difficulty of piercing a brood parasite's egg played a role in whether the host bird tried to eject it, Daniel Clark, an undergraduate student working in Hauber's laboratory, teamed up with another professor in the same department, Philip Anderson, an expert in the biomechanics of piercing, slashing and stabbing. Anderson has previously studied the characteristics that contribute to the cutting and crushing ability of teeth and the piercing power of viper fangs and cactus spines.

The team used chicken eggs in the experiments because collecting and destroying wild bird eggs would be ethically problematic and difficult to standardize. The researchers wanted to determine which elements influenced an egg's ability to withstand being pierced.

"The factors we specifically looked at in the paper were the presence of a nest, the sharpness of the bird's beak and the speed at which it struck the egg," Clark said.

The team measured the energy required to pierce the eggs under different conditions: with and without a nest supporting the egg, with a piercing object approaching the eggs at high or low speeds, and with dull or sharp objects. The researchers used the sharp end of a nail to simulate a sharp beak, and the nail head as a proxy for a dull beak. The experiments involved either a fast-swinging pendulum-mounted nail or a materials-testing device that slowly pushed the nail into the egg.

The researchers said they were surprised to find that the dull end of the nail did a better job of piercing the egg than the sharp end, particularly when striking the egg at a higher speed.

"My lab has done a lot of research on puncture and cutting mechanics, but we've always been looking at soft materials such as skin or muscle," Anderson said. "An eggshell is brittle - more like ceramic than skin. If you're trying to break something brittle, like glass, it makes more sense to use a hammer than a knife, so this result is not as surprising at it seemed at first."

The experiments also revealed that nests absorb some of the energy of the nail strike, particularly when the nail moves at slower speeds.

"In the slow-moving experiment, the nest mattered a lot, but the sharpness or dullness of the nail mattered less," Clark said. "In the fast-moving experiment, the nest mattered less but the sharpness of the nail ended up mattering a lot."

The team also discovered that the act of repeatedly striking eggs dulled even the sharp end of a steel nail.

"This shows that biological surfaces are a lot more tough and durable than we think," Clark said.

If pecking at a foreign egg rapidly in the bottom of a nest damages its beak, the host bird might reduce its ability to preen, weave its own nest or feed itself and its young. These findings offer clues to the factors that influence how - and whether - a host bird responds to the arrival of a foreign egg in its nest, the researchers said.

"Our experiments help us to understand the long-standing conundrum of why most hosts of the cowbird and its conspicuous egg have not evolved to eject the parasitic egg from the nest," Hauber said.

Credit: 
University of Illinois at Urbana-Champaign, News Bureau

Dogs act jealously even when they don't see their rival

Past surveys have shown that more than 80% of dog owners report observing jealous behaviors from their dogs--vocalizations, agitated behavior, pulling on a leash--when they give attention to other dogs. New research published in the journal Psychological Science supports these observations and finds that dogs also exhibit jealous behaviors when they merely imagine that their owner is interacting with a potential rival, in this case, a highly realistic artificial dog.

"Research has supported what many dog owners firmly believe--dogs exhibit jealous behavior when their human companion interacts with a potential rival," said Amalia Bastos with the University of Auckland and lead author on the paper. "We wanted to study this behavior more fully to determine if dogs could, like humans, mentally represent a situation that evoked jealousy."

Dogs appear to be one of the few species that might display jealous behaviors in ways similar to a human child showing jealousy when their mother gives affection to another child. In humans, jealousy is closely linked with self-awareness, which is one reason animal-cognition researchers are so interested in studying jealousy and other secondary emotions in animals.

To test how and when dogs display jealous behavior, the researchers presented 18 dogs with situations where they could imagine a social interaction between their human companion and either a realistic fake dog or a fleece cylinder. The fake dog served as a potential rival for attention while the cylinder served as a control.

In the experiment, the dogs observed the fake-dog rival positioned next to their owner. A barrier was then placed between the dog and the potential rival obscuring them from view. Despite blocking the line of sight, the dogs forcefully attempted to reach their owners when they appeared to stroke the rival fake dog behind the barrier. In a repeat experiment using a fleece cylinder rather than a fake dog, the dogs pulled on the lead with far less force.

Through their study, Bastos and her colleagues found that dogs showed three human-like signatures of jealous behavior. Jealous behavior emerged only when their owner interacted with a perceived social rival and not an inanimate object; occurred as a consequence of that interaction and not due to a potential rival's mere presence; and emerged even for an out-of-sight interaction between their owner and a social rival.

"These results support claims that dogs display jealous behavior. They also provide the first evidence that dogs can mentally represent jealousy-inducing social interactions," said Bastos. "Previous studies confounded jealous behavior with play, interest, or aggression, because they never tested the dogs' reactions to the owner and the social rival being present in the same room but not interacting."

"There is still plenty of work to do to establish the extent of the similarities between the minds of humans and other animals, especially in terms of understanding the nature of nonhuman animals' emotional experiences," said Bastos. "It is too early to say whether dogs experience jealousy as we do, but it is now clear that they react to jealousy-inducing situations, even if these occur out-of-sight."

Credit: 
Association for Psychological Science

Corals carefully organize proteins to form rock-hard skeletons

image: Stylophora pistillata, a common stony coral in the Indo-Pacific.

Image: 
Kevin Wyman/Rutgers University

Charles Darwin, the British naturalist who championed the theory of evolution, noted that corals form far-reaching structures, largely made of limestone, that surround tropical islands. He didn't know how they performed this feat.

Now, Rutgers scientists have shown that coral structures consist of a biomineral containing a highly organized organic mix of proteins that resembles what is in our bones. Their study, published in the Journal of the Royal Society Interface, shows for the first time that several proteins are organized spatially - a process that's critical to forming a rock-hard coral skeleton.

"Our research revealed an intricate network of skeletal proteins that interact spatially, which likely applies to all stony corals," said Manjula P. Mummadisetti, who led the research while she was a postdoctoral associate in the Rutgers Environmental Biophysics and Molecular Ecology Laboratory led by senior author Paul G. Falkowski. She is now a senior scientist at AVMBioMed in Pottstown, Pennsylvania. "It's important to understand the mechanisms of coral biomineralization and how these invaluable animals persist during the era of anthropogenic climate change."

"Our findings suggest that corals will withstand climate change caused by human activities, based on the precision, robustness and resilience of their impressive process for forming rock-hard skeletons," said Falkowski, a Distinguished Professor in the School of Arts and Sciences and School of Environmental and Biological Sciences at Rutgers University-New Brunswick.

Coral reefs protect shorelines threatened by erosion and storms, and provide fish habitat, nursery and spawning grounds. Indeed, coral reefs provide food for about a half-billion people, who also depend on them to make a living. However, warming ocean waters from climate change put corals at risk from deadly bleaching and disease. More acidic ocean waters, sea-level rise, unsustainable fishing, vessels that damage reefs, invasive species, marine debris and tropical cyclones pose additional threats, according to the National Oceanic and Atmospheric Administration.

Rutgers scientists studied the spatial interactions of the proteins embedded within the skeleton of Stylophora pistillata, a common stony coral in the Indo-Pacific. Stony corals have evolved over more than 400 million years, forming enormous reefs in shallow subtropical and tropical seas. They've been called the "rainforests of the sea."

Predicting the survival of corals based on how they adapted to global climate change over millions of years requires understanding, among other things, how they build reefs by secreting calcium carbonate. That process is called biomineralization.

The scientists showed that several proteins work together to create optimal conditions for biomineralization. These proteins are not located randomly but are well-organized spatially, which the scientists detailed for the first time. The scientists revealed the spatial patterns as new mineral is formed between the living tissue of the animal and its base or an older skeleton.

Credit: 
Rutgers University