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Bilingual children are strong, creative storytellers, study shows

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Bilingual children use as many words as monolingual children when telling a story, and demonstrate high levels of cognitive flexibility, according to new research by University of Alberta scientists.

“We found that the number of words that bilingual children use in their stories is highly correlated with their cognitive flexibility — the ability to switch between thinking about different concepts,” said Elena Nicoladis, lead author and professor in the Department of Psychology in the Faculty of Science. “This suggests that bilinguals are adept at using the medium of storytelling.”

Vocabulary is a strong predictor of school achievement, and so is storytelling. “These results suggest that parents of bilingual children do not need to be concerned about long-term school achievement, said Nicoladis. “In a storytelling context, bilingual kids are able to use this flexibility to convey stories in creative ways.”

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The research examined a group of French-English bilingual children who have been taught two languages since birth, rather than learning a second language later in life. Results show that bilingual children used just as many words to tell a story in English as monolingual children. Participants also used just as many words in French as they did in English when telling a story.

Previous research has shown that bilingual children score lower than monolingual children on traditional vocabulary tests, meaning this results are changing our understanding of multiple languages and cognition in children.

“The past research is not surprising,” added Nicoladis. “Learning a word is related to how much time you spend in each language. For bilingual children, time is split between languages. So, unsurprisingly, they tend to have lower vocabularies in each of their languages. However, this research shows that as a function of storytelling, bilingual children are equally strong as monolingual children.”

This research used a new, highly sensitive measure for examining cognitive flexibility, examining a participant’s ability to switch between games with different rules, while maintaining accuracy and reaction time. This study builds on previous research examining vocabulary in bilingual children who have learned English as a second language.

Fossils of the future to mostly consist of humans, domestic animals

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As the number and technology of humans has grown, their impact on the natural world now equals or exceeds those of natural processes, according to scientists.

Many researchers formally name this period of human-dominance of natural systems as the Anthropocene era, but there is a heated debate over whether this naming should take place and when the period began.

Fossils of the future to mostly consist of humans, domestic animals
Fossils of the future to mostly consist of humans, domestic animals

In a co-authored paper published online in the journal Anthropocene, University of Illinois at Chicago paleontologist Roy Plotnick argues that the fossil record of mammals will provide a clear signal of the Anthropocene.

He and Karen Koy of Missouri Western State University report that the number of humans and their animals greatly exceeds that of wild animals.

As an example, in the state of Michigan alone, humans and their animals compose about 96% of the total mass of animals. There are as many chickens as people in the state, and the same should be true in many places in the United States and the world, they say.

“The chance of a wild animal becoming part of the fossil record has become very small,” said Plotnick, UIC professor of earth and environmental sciences and the paper’s lead author. “Instead, the future mammal record will be mostly cows, pigs, sheep, goats, dogs, cats, etc., and people themselves.”

While humans bury most of their dead in cemeteries and have for centuries, their activities have markedly changed how and where animals are buried.

These impacts include alterations in the distribution and properties of natural sites of preservation, associated with shifts in land use and climate change; the production of novel sites for preservation, such as landfills and cemeteries; and changes in the breakdown of animal and human carcasses.

Additionally, the use of large agricultural equipment and increased domestic animal density due to intensive animal farming likely increases the rate of and changes the kind of damage to bones, according to the paleontologists.

“Fossil mammals occur in caves, ancient lakebeds and river channels, and are usually only teeth and isolated bones,” he said. “Animals that die on farms or in mass deaths due to disease often end up as complete corpses in trenches or landfills, far from water.”

Consequently, the fossils from the world today will be unique in the Earth’s history and unmistakable to paleontologists 100,000 years from now, according to the researchers.

“In the far future, the fossil record of today will have a huge number of complete hominid skeletons, all lined up in rows,” Plot nick said.

Unprecedented and worrying rise in sea levels

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A new study led by Simon Fraser University’s Dean of Science, Prof. Paul Kench, has discovered new evidence of sea-level variability in the central Indian Ocean.

The study, which provides new details about sea levels in the past, concludes that sea levels in the central Indian Ocean have risen by close to a meter in the last two centuries.

Prof. Kench says, “We know that certain types of fossil corals act as important recorders of past sea levels. By measuring the ages and the depths of these fossil corals, we are identifying that there have been periods several hundred years ago that the sea level has been much lower than we thought in parts of the Indian Ocean.”

He says understanding where sea levels have been historically, and what happens as they rise, will provide greater insights into how coral reefs systems and islands may be able to respond to the changes in sea levels in the future.

Unprecedented and worrying rise in sea levels
Unprecedented and worrying rise in sea levels

Underscoring the serious threat posed to coastal cities and communities in the region, the ongoing study, which began in 2017, further suggests that if such acceleration continues over the next century, sea levels in the Indian Ocean will have risen to their highest level ever in recorded history.

3D atlas of bone marrow — in single cell resolution

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Stem cells located in the bone marrow generate and control the production of blood and immune cells. Researchers from EMBL, DKFZ and HI-STEM have now developed new methods to reveal the three-dimensional organization of the bone marrow at the single cell level. Using this approach the teams have identified previously unknown cell types that create specific local environments required for blood generation from stem cells. The study, published in Nature Cell Biology, reveals an unexpected complexity of the bone marrow and its microdomains at an unprecedented resolution and provides a novel scientific basis to study blood diseases such as leukemias.

3D atlas of bone marrow -- in single cell resolution
3D atlas of bone marrow — in single cell resolution

In the published study researchers from European Molecular Biology Laboratory (EMBL), the German Cancer Research Center (DKFZ) and the Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH) present new methods permitting the characterisation of complex organs. The team focused their research on the murine bone marrow, as it harbours blood stem cells that are responsible for life-long blood production. Because of the ability to influence stem cells and to sustain blood production, there is a growing interest in exploiting the bone marrow environment, also called niche, as a target for novel leukemia treatments. “So far, very little was known about how different cells are organised within the bone marrow and how they interact to maintain blood stem cells,” explains Chiara Baccin, post-doc in the Steinmetz Group at EMBL. “Our approach unveils the cellular composition, the three-dimensional organisation and the intercellular communication in the bone marrow, a tissue that has thus far been difficult to study using conventional methods,” further explains Jude Al-Sabah, PhD student in the Haas Group at HI-STEM and DKFZ.

In order to understand which cells can be found in the bone marrow, where they are localised and how they might impact on stem cells, the researchers combined single-cell and spatial transcriptomics with novel computational methods. By analysing the RNA content of individual bone marrow cells, the team identified 32 different cell types, including extremely rare and previously unknown cell types. “We believe that these rare ‘niche cells’ establish unique environments in the bone marrow that are required for stem cell function and production of new blood and immune cells,” explains Simon Haas, group leader at the DKFZ and HI-STEM, and one of the initiators of the study.

Using novel computational methods, the researchers were not only able to determine the organisation of the different cell types in the bone marrow in 3D, but could also predict their cellular interactions and communication. “It’s the first evidence that spatial interactions in a tissue can be deduced computationally on the basis of genomic data,” explains Lars Velten, staff scientist in the Steinmetz Group.

“Our dataset is publicly accessible to any laboratory in the world and it could be instrumental in refining in vivo studies,” says Lars Steinmetz, group leader and director of the Life Science Alliance at EMBL Heidelberg. The data, which is now already used by different teams all over the world, is accessible via a user-friendly web app.

The developed methods can in principle be used to analyse the 3D organisation of any organ at the single cell level. “Our approach is widely applicable and could also be used to study the complex pathology of human diseases such as anemia or leukemia” highlights Andreas Trumpp, managing director of HI-STEM and division head at DKFZ.

Teams of microbes are at work in our bodies. Here’s how to figure out what they’re doing

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In the last decade, scientists have made tremendous progress in understanding that groups of bacteria and viruses that naturally coexist throughout the human body play an important role in some vital functions like digestion, metabolism and even fighting off diseases. But understanding just how they do it remains a question.

Researchers from Drexel University are hoping to help answer that question through a clever combination of high-throughput genetic sequencing and natural language processing computer algorithms. Their research, which was recently published in the journal PLOS ONE, reports a new method of analyzing the codes found in RNA that can delineate human microbial communities and reveal how they operate.

Teams of microbes are at work in our bodies. Here's how to figure out what they're doing
Teams of microbes are at work in our bodies. Here’s how to figure out what they’re doing

Much of the research on the human microbial environment — or microbiome — has focused on identifying all of the different microbe species. And the nascent development of treatments for microbiota-linked maladies operates under the idea that imbalances or deviations in the microbiome are the source of health problems, such as indigestion or Crohn’s disease.

But to properly correct these imbalances it’s important for scientists to have a broader understanding of microbial communities as they exist — both in the afflicted areas and throughout the entire body.

“We are really just beginning to scrape the surface of understanding the health effects of microbiota,” said Gail Rosen, PhD, an associate professor in Drexel’s College of Engineering, who was an author of the paper. “In many ways scientists have jumped into this work without having a full picture of what these microbial communities look like, how prevalent they are and how their internal configuration affects their immediate environment within the human body.”

Rosen heads Drexel’s Center for Biological Discovery from Big Data, a group of researchers that has been applying algorithms and machine learning to help decipher massive amounts of genetic sequencing information that has become available in the last handful of years. Their work and similar efforts around the world have moved microbiology and genetics research from the wet lab to the data center — creating a computational approach to studying organism interactions and evolution, called metagenomics.

In this type of research, a scan of a genetic material sample — DNA or RNA — can be interpreted to reveal the organisms that are likely present. The method presented by Rosen’s group takes that one step farther by analyzing the genetic code to spot recurring patterns, an indication that certain groups of organisms — microbes in this case — are found together so frequently that it’s not a coincidence.

“We call this method ‘themetagenomics,’ because we are looking for recurring themes in microbiomes that are indicators of co-occurring groups of microbes,” Rosen said. “There are thousands of species of microbes living in the body, so if you think about all the permutations of groupings that could exist you can imagine what a daunting task it is to determine which of them are living in community with each other. Our method puts a pattern-spotting algorithm to work on the task, which saves a tremendous amount of time and eliminates some guesswork.”

Current methods for studying microbiota, gut bacteria for example, take a sample from an area of the body and then look at the genetic material that’s present. This process inherently lacks important context, according to the authors.

“It’s impossible to really understand what microbe communities are doing if we don’t first understand the extent of the community and how frequently and where else they might be occurring in the body,” said Steve Woloszynek, PhD, and MD trainee in Drexel’s College of Medicine and co-author of the paper. “In other words, it’s hard to develop treatments to promote natural microbial coexistence if their ‘natural state’ is not yet known.”

Obtaining a full map of microbial communities, using themetagenomics, allows researchers to observe how they change over time — both in healthy people and those suffering from diseases. And observing the difference between the two provides clues to the function of the community, as well as illuminating the configuration of microbe species that enables it.

“Most metagenomics methods just tell you which microbes are abundant — therefore likely important — but they don’t really tell you much about how each species is supporting other community members,” Rosen said. “With our method you get a picture of the configuration of the community — for example, it may have E. coli and B. fragilis as the most abundant microbes and in pretty equal numbers — which may indicate that they’re cross-feeding. Another community may have B. fragilis as the most abundant microbe, with many other microbes in equal, but lower, numbers — which could indicate that they are feeding off whatever B. fragilis is making, without any cooperation.”

One of the ultimate goals of analyzing human microbiota is to use the presence of certain microbe communities as indicators to identify diseases like Crohn’s or even specific types of cancer. To test their new method, the Drexel researchers put it up against similar topic modeling procedures that diagnose Crohn’s and mouth cancer by measuring the relative abundance of certain genetic sequences.

The themetagenomics method proved to be just as accurate predicting the diseases, but it does it much faster than the other topic modeling methods — minutes versus days — and it also teases out how each microbe species in the indicator community may contribute to the severity of the disease. With this level of granularity, researchers will be able to home in on particular genetic groupings when developing targeted treatments.

The group has made its themetagenomics analysis tools publicly available in hopes of speeding progress toward cures and treatments for these maladies.

“It’s very early right now, but the more that we understand about how the microbiome functions — even just knowing that groups may be acting together — then we can look into the metabolic pathways of these groups and intervene or control them, thus paving the way for drug development and therapy research,” Rosen said.

Computing with molecules: A big step in molecular spintronics

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Spintronics or spin electronics in contrast to conventional electronics uses the spin of electrons for sensing, information storage, transport, and processing. Potential advantages are nonvolatility, increased data processing speed, decreased electric power consumption, and higher integration densities compared to conventional semiconductor devices. Molecular spintronics aims for the ultimate step towards miniaturization of spintronics by striving to actively control the spin states of individual molecules. Chemists and physicists at Kiel University joined forces with colleagues from France, and Switzerland to design, deposit and operate single molecular spin switches on surfaces. The newly developed molecules feature stable spin states and do not lose their functionality upon adsorption on surfaces. They present their results in the current issue of the   journal Nature Nanotechnology.

Mitochondria are the 'canary in the coal mine' for cellular stress
Mitochondria are the ‘canary in the coal mine’ for cellular stress

The spin states of the new compounds are stable for at least several days. “This is achieved by a design trick that resembles the fundamental electronic circuits in computers, the so-called flip-flops. Bistability or switching between 0 and 1 is realized by looping the output signal back to the input,” says experimental physicist Dr. Manuel Gruber from Kiel University. The new molecules have three properties that are coupled with each other in such a feedback loop: their shape (planar or flat), the proximity of two subunits, called coordination (yes or no), and the spin state (high-spin or low-spin). Thus, the molecules are locked either in one or the other state. Upon sublimation and deposition on a silver surface, the switches self-assemble into highly ordered arrays. Each molecule in such an array can be separately addressed with a scanning tunneling microscope and switched between the states by applying a positive or negative voltage.

“Our new spin switch realizes in just one molecule what takes several components like transistors and resistors in conventional electronics. That’s a big step towards further miniaturisation,” Dr. Manuel Gruber und organic chemist Prof. Dr. Rainer Herges explain. The next step will be to increase the complexity of the compounds to implement more sophisticated operations.

Molecules are the smallest constructions that can be designed and built with atomic precision and predictable properties. Their response to electrical or optical stimuli and their custom-designed chemical and physical functionality make them unique candidates to develop new classes of devices such as controllable surface catalysts or optical devices.

Mitochondria are the ‘canary in the coal mine’ for cellular stress

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Mitochondria, tiny structures present in most cells, are known for their energy-generating machinery. Now, Salk researchers have discovered a new function of mitochondria: they set off molecular alarms when cells are exposed to stress or chemicals that can damage DNA, such as chemotherapy. The results, published online in Nature Metabolism on December 9, 2019, could lead to new cancer treatments that prevent tumors from becoming resistant to chemotherapy.

“Mitochondria are acting as a first line of defense in sensing DNA stress. The mitochondria tell the rest of the cell, ‘Hey, I’m under attack, you better protect yourself,'” says Gerald Shadel, a professor in Salk’s Molecular and Cell Biology Laboratory and the Audrey Geisel Chair in Biomedical Science.

Most of the DNA that a cell needs to function is found inside the cell’s nucleus, packaged in chromosomes and inherited from both parents. But mitochondria each contain their own small circles of DNA (called mitochondrial DNA or mtDNA), passed only from a mother to her offspring. And most cells contain hundreds — or even thousands — of mitochondria.

Mitochondria are the 'canary in the coal mine' for cellular stress
Mitochondria are the ‘canary in the coal mine’ for cellular stress

Shadel’s lab group previously showed that cells respond to improperly packaged mtDNA similarly to how they would react to an invading virus — by releasing it from mitochondria and launching an immune response that beefs up the cell’s defenses.

In the new study, Shadel and his colleagues set out to look in more detail at what molecular pathways are activated by the release of damaged mtDNA into the cell’s interior. They homed in on a subset of genes known as interferon-stimulated genes, or ISGs, that are typically activated by the presence of viruses. But in this case, the team realized, the genes were a particular subset of ISGs turned on by viruses. And this same subset of ISGs is often found to be activated in cancer cells that have developed resistance to chemotherapy with DNA-damaging agents like doxyrubicin.

To destroy cancer, doxyrubicin targets the nuclear DNA. But the new study found that the drug also causes the damage and release of mtDNA, which in turn activates ISGs. This subset of ISGs, the group discovered, helps protect nuclear DNA from damage — and, thus, causes increased resistance to the chemotherapy drug. When Shadel and his colleagues induced mitochondrial stress in melanoma cancer cells, the cells became more resistant to doxyrubicin when grown in culture dishes and even in mice, as higher levels of the ISGs were protecting the cell’s DNA.

“Perhaps the fact that mitochondrial DNA is present in so many copies in each cell, and has fewer of its own DNA repair pathways, makes it a very effective sensor of DNA stress,” says Shadel.

Most of the time, he points out, it’s probably a good thing that the mtDNA is more prone to damage — it acts like a canary in a coal mine to protect healthy cells. But in cancer cells, it means that doxyrubicin — by damaging mtDNA first and setting off molecular alarm bells — can be less effective at damaging the nuclear DNA of cancer cells.

“It says to me that if you can prevent damage to mitochondrial DNA or its release during cancer treatment, you might prevent this form of chemotherapy resistance,” Shadel says.

His group is planning future studies on exactly how mtDNA is damaged and released and which DNA repair pathways are activated by the ISGs in the cell’s nucleus to ward off damage.