Tech

Yeast mating -- more than meets the eye

image: "When yeast cells kiss": two haploid yeast cells of different mating types approach each other for mating.

Image: 
Max Planck Institute for Terrestrial Microbiology/Sourjik

Researchers from the Max-Planck Institute for Terrestrial Microbiology have discovered a surprising asymmetry in the mating behavior of unicellular yeast that emerges solely from molecular differences in pheromone signaling. Their results, published in the current issue of "Science Advances", might shed new light on the evolutionary origins of sexual dimorphism in higher eukaryotes.

Resemblant of higher organisms, yeast gametes communicate during the mating process by secreting and sensing sexual pheromones. However, in contrast to higher eukaryotes, budding yeast is isogamous: seen through a microscope, gametes of both mating types ("sexes"), MATa and MATα, look exactly the same. Since anisogamy -- difference in size between male and female gametes --was considered to be the starting point of sexual selection that drives the evolution of differences in sexual behavior, mating types of S. cerevisiae were assumed to be not only morphologically but also behaviorally symmetric.

Now a research team led by Victor Sourjik from the Max-Planck Institute for Terrestrial Microbiology and his former postdoctoral fellow Alvaro Banderas, now at the Institut Curie in Paris, has discovered a hidden behavioral asymmetry that emerges solely from molecular differences in pheromone signaling between the two mating types, which might have wide-reaching implications for understanding evolution of sexual dimorphism in higher organisms.

Yeast mating involves a- and α-pheromones that trigger the interactions between the two different types, MATa and MATα. Although the pheromones and their respective receptors are chemically different, the remainder of the pheromone response pathway (one of the best-studied models for eukaryotic signal transduction) is the same for both mating types. It was therefore thought that in yeast, as well as in other isogamous eukaryotic microorganisms, molecular differences between the a- and α-pheromones and their receptors are only required in order to ensure self-incompatibility between the two mating types but have no further functional consequences.

"As a matter of fact, our original intention was to confirm that the behavior of both mating types is similar. Yet, to our surprise, we found it to be strikingly different", says Alexander Anders, first author of the manuscript.

Remarkably, the observed differences, with MATa cells exhibiting exploratory search behavior and MATα cells showing short-range gradient sensing and polarization towards the proximal mate, resemble well-established asymmetries between gametes in anisogamous organisms. "It turns out that behavioral asymmetry of the gametes is not necessarily a consequence of anisogamy, but could actually have preceded it - this challenges the previous assumptions on evolution by sexual selection as the sole generative mechanism of differences in mating behavior between sexes", says Alvaro Banderas, the co-corresponding author of the manuscript.

Importantly, mathematical modeling and computer simulations suggest that such asymmetric behavior might provide selective fitness advantage by enhancing efficiency of mating over a wide range of environments. "Behavioral asymmetry could maximize frequency of mating encounters under different conditions, meaning that it might be an evolutionary selected emergent property", says Remy Colin, who performed mathematical modeling.

What do these findings tell us about the origins of sexual behavior? "Although further theoretical analysis is clearly required to test our hypothesis", emphasizes Victor Sourjik, "our work on mating of a model unicellular eukaryote provides a new perspective on what might have been the starting point for the evolution of the amazing diversity of sexual dimorphisms observed today".

Credit: 
Max-Planck-Gesellschaft

MD Anderson research highlights for June 16, 2021

HOUSTON — The University of Texas MD Anderson Cancer Center's Research Highlights provides a glimpse into recently published studies in basic, translational and clinical cancer research from MD Anderson experts. Current advances include a new combination therapy for acute myeloid leukemia (AML), a greater understanding of persistent conditions after AML remission, the discovery of a universal biomarker for exosomes, the identification of a tumor suppressor gene in hepatocellular carcinoma (HCC) and characterization of a new target to treat Clostridioides difficile (C. difficile) infections.

Utilizing combination therapy for AML

While a majority of patients with acute myeloid leukemia (AML) respond favorably to initial therapy, many will experience a subsequent relapse. Once relapse occurs, outcomes are poor and novel therapeutic options are needed. A study led by Courtney DiNardo, M.D., and Hagop Kantarjian, M.D., found that an intensive treatment regimen of fludarabine, cytarabine, granulocyte colony-stimulating factor and idarubicin (FLAG-IDA) combined with the B-cell lymphoma-2 inhibitor venetoclax is effective in both relapsed/refractory and newly diagnosed patients with AML. In the study group, anticipated and manageable side effects included chemotherapy-induced cytopenias and neutropenic infections. The combination therapy produced deep remissions and helped bridge patients to successful stem cell transplants. Learn more in the Journal of Clinical Oncology.

Examining clinical outcomes of AML post-remission clonal hematopoiesis

Clonal hematopoiesis (CH) is a condition that develops when a hematopoietic stem cell, which is a stem cell that typically develops into various types of blood cells, instead makes cells that all have the same genetic mutation. CH can lead to acute myeloid leukemia (AML), and it can persist after patients are in remission. A study led by Tomoyuki Tanaka, M.D., Ph.D, Kiyomi Morita, M.D., Ph.D., and Koichi Takahashi, M.D., Ph.D., examined 164 cases of AML and found that post-remission CH occurred in around half of the patients but had little impact on their risk of relapse, their non-relapse mortality or their risk of cardiovascular disease. The findings suggest that while CH after remission from AML is resistant to treatment, it generally does not negatively affect clinical outcomes. Learn more in Blood.

Discovery of a universal biomarker for exosomes

Exosomes are virus-sized, membrane-bound particles released by all cells that are thought to carry information important for cell-cell communication. Exosomes are produced at high levels by cancer cells and contain DNA, RNA and proteins that could be useful for cancer screening, diagnostics and treatment response monitoring. A new study led by Fernanda G. Kugeratski, Ph.D., and Raghu Kalluri, M.D., Ph.D., found that exosomes contain a core proteome of approximately 1,200 proteins common to exosomes from all cells. The researchers also discovered that syntenin-1 is the most abundant protein across all exosomes, making it a potential universal marker of exosomes. Such a protein marker makes it easier to isolate and study exosomes to clarify their function and to develop approaches for using exosomes in the clinic. Learn more in Nature Cell Biology.

Immune activating tumor suppressor for treating HCC

Hepatocellular carcinoma (HCC) is the leading cause of cancer deaths worldwide, and more research is required to fully understand the biology of this disease for developing effective treatment. A research team led by Shulin Li, Ph.D., discovered WSX1 acts as an 'immune' tumor suppressor gene in HCC, effectively downregulating neoplastic PD-L1 expression in abnormal hepatocytes or HCC cells to boost immune surveillance. The suppression of PD-L1 in HCCs by WSX1 occurs through de-stabilization of a novel subtype of AKT protein. This result uncovered a novel target for cancer immunotherapies to treat HCC. Learn more in Nature Communications.

Characterizing a new target for treating C. difficile infections

Clostridioides difficile (C. difficile) is one of the leading causes of hospital-acquired infections in the U.S., and more effective therapeutic interventions are needed. The recently discovered CamA enzyme, which appears to be specific to C. difficile, catalyzes DNA methylation and is essential for spore formation and biofilm production, making it an attractive therapeutic target. A research team led by Jujun Zhou, Ph.D.; John R. Horton, Ph.D.; Xing Zhang, Ph.D.; and Xiaodong Cheng, Ph.D., performed in-depth enzymatic and structural analysis of CamA to learn how it interacts with DNA to perform its role. Their crystal structure of CamA bound to DNA provide the roadmap necessary for developing drugs to block the protein's activity. Learn more in Nature Communications.

Credit: 
University of Texas M. D. Anderson Cancer Center

UChicago scientists identify properties that allow proteins to strengthen under pressure

image: In a simulated actin network, actin filaments are randomly oriented before pressure application (left) but align after pressure application (right), altering the network's material properties.

Image: 
Scheff et al

A new rubber band stretches, but then snaps back into its original shape and size. Stretched again, it does the same. But what if the rubber band was made of a material that remembered how it had been stretched? Just as our bones strengthen in response to impact, medical implants or prosthetics composed of such a material could adjust to environmental pressures such as those encountered in strenuous exercise.

A research team at the University of Chicago is now exploring the properties of a material found in cells which allows cells to remember and respond to environmental pressure. In a paper published on May 14, 2021 in Soft Matter, they teased out secrets for how it works--and how it could someday form the basis for making useful materials.

Protein strands, called actin filaments, act as bones within a cell, and a separate family of proteins called cross-linkers hold these bones together into a cellular skeleton. The study found that an optimal concentration of cross-linkers, which bind and unbind to permit the actin to rearrange under pressure, allow this skeletal scaffolding to remember and respond to past experience. This material memory is called hysteresis.

"Our findings show that the properties of actin networks can be changed by how filaments are aligned," said Danielle Scheff, a graduate student in the Department of Physics who conducted the research in the lab of Margaret Gardel, Horace B. Horton Professor of Physics and Molecular Engineering, the James Franck Institute, and the Institute of Biophysical Dynamics. "The material adapts to stress by becoming stronger."

To understand how the composition of this cellular scaffolding determines its hysteresis, Scheff mixed up a buffer containing actin, isolated from rabbit muscle, and cross-linkers, isolated from bacteria. She then applied pressure to the solution, using an instrument called a rheometer. If stretched in one direction, the cross-linkers allowed the actin filaments to rearrange, strengthening against subsequent pressure in the same direction.

To see how hysteresis depended on the solution's consistency, she mixed different concentrations of cross-linkers into the buffer.

Surprisingly, these experiments indicated that hysteresis was most pronounced at an optimal cross-linker concentration; solutions exhibited increased hysteresis as she added more cross-linkers, but past this optimal point, the effect again became less pronounced.

"I remember being in lab the first time I plotted that relationship and thinking something must be wrong, running down to the rheometer to do more experiments to double-check," Scheff said.

To better understand the structural changes, Steven Redford, a graduate student in Biophysical Sciences in the labs of Gardel and Aaron Dinner, Professor of Chemistry, the James Franck Institute, and the Institute for Biophysical Dynamics, created a computational simulation of the protein mixture Scheff produced in the lab. In this computational rendition, Redford wielded a more systematic control over variables than possible in the lab. By varying the stability of bonds between actin and its cross-linkers, Redford showed that unbinding allows actin filaments to rearrange under pressure, aligning with the applied strain, while binding stabilizes the new alignment, providing the tissue a 'memory' of this pressure. Together, these simulations demonstrated that impermanent connections between the proteins enable hysteresis.

"People think of cells as very complicated, with a lot of chemical feedback. But this is a stripped-down system where you can really understand what is possible," said Gardel.

The team expects these findings, established in a material isolated from biological systems, to generalize to other materials. For example, using impermanent cross-linkers to bind polymer filaments could allow them to rearrange as actin filaments do, and thus produce synthetic materials capable of hysteresis.

"If you understand how natural materials adapt, you can carry it over to synthetic materials," said Dinner.

Credit: 
University of Chicago

Study: Complexity holds steady as writing systems evolve

video: How do writing systems change over time -- and what forces drive that evolution?

Santa Fe Institute Fellow Helena Miton and Olivier Morin at the Max Planck Institute for the Science of Human History recently used computer-aided methods to test the conclusions of previous research into the complexity of scripts and characters.

Prior work suggests two pressures that may push writing to get simpler over time: 1) More complex characters require more effort to distinguish from each other (making them more difficult to copy without error); and 2) Figures with more strokes require more movement to create. In short, simple letters are not only easier to read, but easier to make -- up to some lower bound at which characters are too simple to tell apart. Also, cultural transmission research shows that in lab experiments, complex drawings simplify as they are copied. Conufusingly, previous studies found both a universal average of three strokes per character AND an increase in complexity as the inventory of scripts grow.

In their new paper in the journal Cognition, Miton and Morin offer several hypotheses to test with their analysis:

1 - Scripts with more characters will have more complex symbols.
2 - Most variance in character complexity between scripts is caused by the script (rather than the type of script).
3 - Parentless, newly-invented (or idiosyncratic) scripts are more complex than ancient scripts.
4 - Parent scripts have more complex characters than their offspring.
5 - Contrary to earlier psychology experiments that suggest the lefthand side of characters is always simpler, the authors suspect that characters are more complex on the side that comes first when read and written (i.e., on the right if the language is read right to left).

Their data set they analyzed comprises nearly 48,000 characters from 133 scripts. Miton and Morin measured two kinds of complexity: perimetric complexity, the ratio of a given character's "coastline" to its area, or how twisty it is; and algorithmic complexity, or how much code is required to store a compressed image file of each character.

The variables they tracked included script sources, size, family, type, direction, and whether or not they were "idiosyncratic" (made up from scratch by known persons less than 200 years ago). The authors predicted idiosyncractic scripts would be less subject to evolutionary pressures and historical constraints. But are they? Likewise, branching events in written language would seem to provide the perfect occasion to "improve" a script by simplifying it. But do they?

Here are their findings:

The more characters in a script, the more complex the characters. BUT removing scripts of over 200 characters, mostly East Asian scripts that use logograms instead of letters, voids this result. It turns out that the TYPE of script -- the linguistic units encoded by its characters -- matters more than the script itself.
Characters from idiosyncratic scripts are generally no more complex than characters from any other. (But this might be because they quickly simplify, and the study used "late data points.")
There is no tendency for scripts to be simpler than their ancestors, suggesting a minimal viable complexity for written language.
The first half of a character as it is read or written -- left-first or right-first -- is in fact more complex.

Through the lens of cultural evolution, their results support a growing body of work on the ways in which letter shapes fit subtle cognitive and perceptual biases with roots in the visual and motor constraints on reading and writing. Or, in the words of Albert Einstein, "Everything should be made as simple as possible, but no simpler."

Image: 
Michael Garfield/Santa Fe Institute

A new paper in the journal Cognition examines the visual complexity of written language and how that complexity has evolved.

Using computational techniques to analyze more than 47,000 different characters from 133 living and extinct scripts, co-authors Helena Miton of the Santa Fe Institute and Oliver Morin of the Max Planck Institute for the Science of Human History, addressed several questions around why and how the characters of different writing systems vary in how complex they appear.

"When we started this project, we wanted to test whether you find a general simplification of characters over time," Miton says. "Do scripts simplify their characters as they spend more time exposed to evolutionary pressures from the humans who are learning them and using them?"

We interact with most types of writing through our visual system, so the characters and scripts that make up the hundreds of writing systems humans have used through history are limited to, and optimized for, the way our brains process visual information. Part of that optimization, write the authors, is the graphic complexity of the characters in a script.

Morin illustrates this in a Twitter thread, offering an image of two characters, one apparently more complex, with more detail and contours, than the other. He writes, "Why care about this? Because your brain does. Simpler letters are easier and faster to process." He goes on, "Any small improvements in processing speed can accumulate into big-time gains for readers. Letters are under pressure to simplify, but also have to carry information."

A highly cited study from 2005 suggests that writing systems tend to settle on a common solution to these pressures: using about three strokes per character. In this new paper, Miton and Morin push back against that finding, and others, by studying a larger and broader set of scripts and incorporating new methods that account for cultural evolution and lineages in writing.

Miton and Morin used two measures of graphic complexity to compare characters and scripts from the massive dataset drawn from geographic locations around the world. The first measure, "perimetric" complexity, is a ratio of inked surface to its perimeter. The other measure, "algorithmic," is the number of bytes needed to store a compressed image of a character.

Among their results, they found that large scripts -- those with more than 200 characters -- had, on average, more complex characters than scripts with a smaller number of characters. Relatedly, the study suggests that the main driver of characters' complexity was which linguistic units (e.g., phoneme, syllable, entire word, etc.) the characters encode.  

They were surprised to find little evidence for evolutionary change in complexity: scripts that were invented in the past 200 years used characters of similar complexity to those that have been around for longer.  In forthcoming work led by Piers Kelly, Miton and Morin investigate whether written characters follow an optimization process that happens more quickly than was captured in the current study's dataset.

Credit: 
Santa Fe Institute

Are zoos inadvertently complicit in wildlife trade? The case of a rare Borneo lizard

image: Earless monitor lizard

Image: 
Chien C. Lee, Wild Borneo.

Should zoos display legally protected species that have been smuggled out of their range countries? A new study suggests that a pause and rethink may be needed, as it reports that accredited zoos have acquired a rare and legally protected reptile, the earless monitor lizard endemic to Borneo, without any evidence that the animals were legally exported.

The earless monitor lizard occurs only on the island of Borneo and has been described as a "miniature Godzilla" and "the Holy Grail of Herpetology." Discovered by western scientists almost 150 years ago, for most of this period the species was known largely from pickled specimens in natural history collections, and wasn't recorded from the wild for decades. In the 1970s, the three countries that make up Borneo - Indonesia, Malaysia and Brunei - added it to their protected species lists. This means that the species can neither be legally traded within these countries, nor legally exported out of them.

Despite legal protection and lack of export permissions, reptile enthusiasts and unscrupulous traders have long been smuggling small numbers of earless monitor lizards out of Indonesia and Malaysia, eventually bringing them to Europe. This greatly accelerated in 2012, when the species' rediscovery was announced in a scientific journal. In 2016, all 183 countries that are signatory to the Convention on international trade in endangered species agreed to regulate global trade in earless monitor lizards in order to limit the negative effects of smuggling on wild populations. Agreed export numbers were set at zero.

Enforcing the laws has proven to be challenging, however, and to date only two smuggling attempts have been thwarted. In both cases, German smugglers were apprehended at Indonesian airports while attempting to move respectively eight and seventeen earless monitor lizards out of the country.

The first zoo that proudly announced it had obtained earless monitor lizards was Japan's iZoo in 2013. This zoo is not accredited, and the ways in which the animals were obtained remain questionable. In Europe, the first zoos to openly display earless monitor lizards were located in Hungary, Austria and the Czech Republic. The animals were obtained from what zoos referred to as "private individuals" or "dedicated hobby breeders", and, in one instance, from iZoo. Just like in Japan, how these animals ended up in Europe is questionable, but perhaps not illegal - and it is evident that no export permits were ever issued.

In recent years, more and more zoos in Europe, and since the beginning of this year also in the United States, have started displaying earless monitor lizards. Some cases were part of zoo exchanges, others were obtained from private individuals, and a handful were placed in zoos by authorities after they were seized, but it is clear that many were at one point illegally exported out of Indonesia, Malaysia or Brunei, or were illegally imported into non-range countries.
The acquisition of these protected lizards by zoos is neither in line with the intentions of national laws of their countries of origin, nor with international wildlife trade regulations. Moreover, it is diametrically opposed to the commitments the international zoo community has made to address illegal wildlife trade.

"To me, the current situation concerning the purchasing and proudly displaying of earless monitor lizards by accredited zoos can be compared with a road safety organisation posting online videos of its CEO doing wheelies on a motorbike and then adding that it was done on a private road where neither wearing a helmet nor having a driver's licence is required," said Vincent Nijman of the Oxford Wildlife Trade Research Group, author of the study that was published in the open-access journal Nature Conservation. "Both may be legal in a technical sense, but the optics are not good."

"Modern, scientifically managed zoos are increasingly organising themselves with set ethical values and binding standards which go beyond national legislation on conservation and sustainability, but, unfortunately, this still only counts for a small proportion of zoos worldwide," said Dr Chris R. Shepherd, Executive Director of Monitor Research Conservation Society. "Zoos that continue to obtain animals that have been illegally acquired, directly or indirectly, are often fuelling the illegal wildlife trade, supporting organised crime networks and possibly contributing to the decline in some species."

Seven years ago, the price for a single earless monitor lizard was in the order of EUR 8,000 to 10,000 , so any zoo or hobbyist wanting to have one or more pairs had to make a serious financial commitment. These high prices put a restriction on the number of people that wanted to acquire them and could afford them. It probably also gave potential buyers a tacit reminder that the trade was illicit. In recent years, however, prices have come down, to less than EUR 1,000. Now that earless monitor lizards are more affordable, and with accredited zoos giving a sense of legitimacy, Nijman is concerned that it might become more and more acceptable to keep these rare animals as pets.

"When I grew up in the 1970s, it was still perfectly acceptable for what we now see as accredited zoos to regularly buy rare and globally threatened birds, mammals and reptiles from commercial animal traders. Few questions were asked about the legitimacy of this animal trade. This has dramatically changed for the better, and now many of the animals we see in zoos today have been bred in captivity, either in the zoo itself, or in partner zoos", Nijman said. He added that in many ways zoos are a force for good in the global challenge to preserve species and conserve habitats. "It is imperative that these efforts are genuinely adopted by all in the zoo community, and, when there is doubt about the legitimacy of animals in trade, that a cautionary approach is adopted."

Credit: 
Pensoft Publishers

Over-the-counter fungicide can disrupt hormones

Steroid (sex) hormones play a central role in sexual development: They help determine how boys become boys and girls become girls. If these hormones are disrupted during fetal life, it can lead to a string of reproductive disorders at birth and later in life, including malformed genitals and decreased fertility.

Many environmental chemicals are known to disrupt the hormone system and are often referred to as endocrine disrupting chemicals. Azole fungicides constitute one group that can act as endocrine disruptors. Azoles are used to combat yeast infestations in seed and food crops, but are also used in medications for humans.

Most azoles used in medicines are tightly regulated and their use is well controlled. However, some are sold over-the-counter, for instance clotrimazole, which is used to treat various fungal infections, including vaginal thrush.

Significantly altered sex hormones

In a recent study, researchers from the National Food Institute have shown that clotrimazole can significantly alter sex hormones in pregnant rats and their developing fetuses.

These effects were observed at the same exposure concentrations as those observed in pregnant women, who use clotrimazole to treat thrush. The study also found that the chemical is rapidly eliminated from the rat body, just as in humans. Nevertheless, clotrimazole affects the endocrine system during a sensitive time of development, causing concern that human exposure can give rise to similar effects.

Another study in humans had already raised concern about the potential for clotrimazole to disrupt male sexual development. This new study confirms that clotrimazole can disrupt hormones in the rat fetuses, which can have consequences for sexual development.

The researchers are concerned that indiscriminate use of the medication during pregnancy could potentially have negative effects on sexual development of the fetus - particularly if the mother-to-be is also exposed to other endocrine disrupting chemicals at the same time, such as paracetamol and other substances such as phthalates and bisphenols from plastics.

Need for more research

It is not necessarily exposure to clotrimazole alone that is a problem, but rather the combined exposure to endocrine disruptors that women may be exposed to during pregnancy. Further research could help to determine this, which is why the National Food Institute's researchers are calling for more knowledge about this issue.

Read more

The study is described in further detail in an article in the journal Toxicology and Applied Pharmacology: Human-relevant concentrations of the antifungal drug clotrimazole disrupt maternal and fetal steroid hormone profiles in rats. The study was carried out under the Danish Centre on Endocrine Disrupters (CeHoS).

Credit: 
Technical University of Denmark

Alternate-day intermittent fasting leads to less fat loss than traditional daily energy restriction

An alternate-day intermittent fasting schedule offered less fat-reducing benefits than a matched "traditional" diet that restricts daily energy intake, according to a new, 3-week randomized trial involving 36 participants. The study, which is one of the first to tease apart the effects of fasting and daily energy restriction in lean individuals, indicates that alternate-day fasting may offer no fasting-specific health or metabolic benefits over a standard daily diet. However, the authors caution that longer studies with larger groups are needed. Intermittent fasting, which involves cycling through voluntary fasting and non-fasting periods, has become one of the most popular approaches to losing weight. There are many different intermittent fasting schedules, ranging from fasting for part of each day to the popular 5:2 diet (eating 5 days a week and fasting 2 days) to alternate-day fasting (eating one day, fasting the next). Many participants report that fasting schedules are relatively easy to adopt and stick by, and theories suggest that fasting can trigger beneficial changes in metabolism that encourage weight loss. However, few studies have examined the fasting-specific effects of intermittent fasting or compared its effects to diets that simply reduce daily net calories. Iain Templeman and colleagues recruited 36 lean participants and split them into 3 groups of 12, who followed different diets for 3 weeks. The first group followed a restricted, alternate-day fasting diet (eating 150% of their habitual daily energy intake only every other day), the second group followed an energy-matched non-fasting diet with 75% daily energy intake, and the last group followed an alternate-day fasting diet with no restriction in energy intake (200% daily energy intake every other day). After 3 weeks, the second group showed the greatest losses of both weight and fat, with an average fat loss of 1.57 kg. Meanwhile, the first group of alternate-day fasters lost weight but lost fat less effectively (an average of .74 kg), and the last group showed no significant drops in either weight or fat. Further studies showed there were no key differences in cardiometabolic health, metabolic molecules, or gene expression in fat cells between the 3 groups. Templeman et al. noted that the alternate-day fasters tended to be less active than before starting the diet, hinting at one factor that may have impacted fat loss. The authors speculate that individuals considering alternate-day fasting should make sure to include opportunities for physical activity to maintain their energy expenditure.

Credit: 
American Association for the Advancement of Science (AAAS)

Subterranean investigations

We've seen robots take to the air, dive beneath the waves and perform all sorts of maneuvers on land. Now, researchers at UC Santa Barbara and Georgia Institute of Technology are exploring a new frontier: the ground beneath our feet. Taking their cues from plants and animals that have evolved to navigate subterranean spaces, they've developed a fast, controllable soft robot that can burrow through sand. The technology not only enables new applications for fast, precise and minimally invasive movement underground, but also lays mechanical foundations for new types of robots.

"The biggest challenges with moving through the ground are simply the forces involved," said Nicholas Naclerio, a graduate student researcher in the lab of UC Santa Barbara mechanical engineering professor Elliot Hawkes and lead author of a paper on the cover of the journal Science Robotics. Whereas air and water offer little resistance to objects moving through them, he explained, the subterranean world is another story.

"If you're trying to move through the ground, you have to push the soil, sand or other medium out of the way," Naclerio said.

Fortunately, the natural world provides numerous examples of underground navigation in the form of plants and fungi that build underground networks and animals that have mastered the ability to tunnel directly through granular media. Gaining a mechanical understanding of how plants and animals have mastered subterranean navigation opens up many possibilities for science and technology, according to Daniel Goldman, Dunn Family Professor of Physics at Georgia Tech.

"Discovery of principles by which diverse organisms successfully swim and dig within granular media can lead to development of new kinds of mechanisms and robots that can take advantage of such principles," he said. "And reciprocally, development of a robot with such capabilities can inspire new animal studies as well as point to new phenomena in the physics of granular substrates."

The researchers had a good head start with a vine-like soft robot designed in the Hawkes Lab that mimics plants and the way they navigate by growing from their tips, while the rest of the body remains stationary. In the subterranean setting, tip extension, according to the researchers, keeps resisting forces low and localized only to the growing end; if the whole body moved as it grew, friction over the entire surface would increase as more of the robot entered the sand until the robot could no longer move.

Burrowing animals, meanwhile, serve as inspiration for an additional strategy called granular fluidization, which suspends the particles in a fluid-like state and allows the animal to overcome the high level of resistance presented by sand or loose soil. The southern sand octopus, for instance, expels a jet of water into the ground, and uses its arms to pull itself into the temporarily loosened sand. That ability made its way onto the researchers' robot in the form of a tip-based flow device that shoots air into the region just ahead of the growing end, enabling it to move into that area.

"The biggest challenge we found and what took the longest to solve was when we switched to horizontal burrowing, our robots would always surface," Naclerio said. Whereas gases or liquids evenly flow over and under a traveling symmetric object, he explained, in fluidized sand, the distribution of forces is not as balanced, and creates a significant lift force for the horizontally travelling robot. "It's much easier to push the sand up and out of the way than it is to compact it down."

To understand the robot's behavior and the largely unexplored physics of air-aided intrusions, the team took drag and lift measurements as a result of different angles of airflow into from the tip of a solid rod shoved horizontally into sand.

"Frictional force response in granular materials greatly differs from that of Newtonian fluids, as intruding into sand can compact and stress large swaths of terrain in the direction of motion due to high friction," said Andras Karsai, a graduate student researcher in Goldman's lab. "To mitigate this, a low-density fluid that lifts and pushes grains away from an intruder will often reduce the net frictional stress it has to overcome."

Unlike with gas or liquid, where a downward fluid jet would create lift for the travelling object, in sand the downward air flow reduced the lift forces and excavated the sand below the robot's growing tip. This, combined with inspiration from the sandfish lizard, whose wedge-shaped head favors downward movement, allowed the researchers to modulate the resisting forces and keep the robot moving horizontally without rising out of the sand.

A small, exploratory, soft robot such as this has a variety of applications where shallow burrowing through dry granular media is needed, such as soil sampling, underground installation of utilities and erosion control. Tip extension enables changes in direction, while also allowing the body of the robot to modulate how firmly anchored it is in the medium -- control that could become useful for exploration in low gravity environments. In fact, the team is working on a project with NASA to develop burrowing for the moon or even more distant bodies, like Enceladus, a moon of Jupiter.

"We believe burrowing has the potential to open new avenues and enable new capabilities for extraterrestrial robotics," Hawkes said.

Credit: 
University of California - Santa Barbara

Semiconductor technology mitigates fire risk in electric vehicle batteries

image: Top-view SEM images and photographs (inset) of plain-Li, and Li@p-PCL electrodes after cycling tests with Li|Li symmetrical cells at 1.0 mA cm-2 and 1.0 mAh cm-2

Image: 
Korea Institute of Science and Technology(KIST)

Despite rapid development of electric vehicles (EVs), the safety of the lithium-ion (Li-ion) batteries remains a concern as they are as a fire and explosion risk. Among the various approaches to tackle this issue, Korean researchers have used semiconductor technology to improve the safety of Li-ion batteries. A research team from the Korea Institute of Science and Technology (KIST) led by Dr. Joong Kee Lee of the Center for Energy Storage Research has succeeded in inhibiting the growth of dendrites, crystals with multiple branches that cause EV battery fires by forming protective semiconducting passivation layers on the surface of Li electrodes.

When Li-ion batteries are charged, Li ions are transported to the anode (the negative electrode) and are deposited on the surface as Li metal; at this point, tree-like dendrites are formed. These Li dendrites are responsible for the uncontrollable volumetric fluctuations and leads to reactions between the solid electrode and the liquid electrolyte, which causes a fire. Unsurprisingly, this severely degrades battery performance.

To prevent dendrite formation, the research team exposed fullerene (C60), a highly electronic conductive semiconductor material, to plasma, resulting in the formation of semiconducting passivation carbonaceous layers between the Li electrode and the electrolyte. The semiconducting passivation carbonaceous layers allow Li-ions to pass through while blocking electrons due to generation of Schottky barrier, and by preventing electrons and ions from interacting on the electrode surface and inside, they stops the formation of Li crystals and the consequent growth of dendrites.

*fullerene : a particular physical form of carbon in which 60 carbon atoms are connected by single and double bonds in a pentagonal shape to form a soccer ball-like shape

The stability of the electrodes with the semiconducting passivation carbonaceous layers was tested using Li/Li symmetric cells in extreme electrochemical environments where typical Li electrodes remain stable for up to 20 charge/discharge cycles. The newly developed electrodes showed significantly enhanced stability, with Li dendrite growth suppressed for up to 1,200 cycles. Moreover, using a lithium cobalt oxide (LiCoO2) cathode in addition to the developed electrode, approximately 81% of the initial battery capacity was maintained after 500 cycles, representing an improvement of approximately 60% over conventional Li electrodes.

Lead researcher Dr. Joong Kee Lee said, "The effective suppression of dendrite growth on Li electrodes is instrumental for improving battery safety. The technology for developing highly safe Li-metal electrodes proposed in this study provides a blueprint for the development of next-generation batteries that do not pose a fire risk." As Dr. Lee explains, his team's next goal is improving the commercial viability of this technology, "We aim to make the fabrication of the semiconducting passivation carbonaceous layers more cost-effective by substituting fullerene with less expensive materials."

Credit: 
National Research Council of Science & Technology

Nematic transition and nanoscale suppression of superconductivity in an iron chalcogenide

image: Examining an iron chalcogenide high-temperature superconductor, Boston College physicist Ilija Zeljkovic and an international team of researchers report in Nature Physics that just before the material fully enters the nematic state, electronic nematicity first appears in nanoscale patches on its surface, represented in this image by the dark markings.

Image: 
Ilija Zeljkovic/Boston College

Chestnut Hill, Mass. (6/16/2021) - In unconventional superconductors, electrons often exhibit a tendency towards spatial ordering within their atomic structure.

In high-temperature superconductors, this comes in the form of the electronic structure exhibiting a pronounced difference in the lattice-bound directions along which atoms are ordered.

Within these materials, this electronic activity in turn breaks the rotational symmetry of the crystal, a phase known as electronic nematicity. Researchers have sought to better understand this novel electronic state, which co-exists with superconductivity.

Boston College Associate Professor of Physics Ilija Zeljkovic and an international team of researchers set out to better understand the atomic-scale signature of electronic nematic transition in Fe(Te,Se) -- a class of materials known as iron chalcogenide superconductors -- in a particularly formulated composition of the material where electronic nematicity may spatially change most rapidly or fluctuate over time.

A focus of researchers trying to understand superconducting properties, iron chalcogenides are defined by their composition from varying percentages of sulfur, selenium, and tellerium. For their experiments, the team created compound samples containing between 35 to 50 percent selenium, ultimately finding that a 45-percent selenium construct revealed electronic nematicity that is spatially inhomogeneous, or failing to occur equally at each point in the material.

Using low-temperature spectroscopic-imaging scanning tunneling microscopy (STM), the team found that at the transition point -- just before the material enters the nematic state -- electronic nematicity first appears in localized nanoscale regions, Zeljkovic and colleagues reported in the online edition of the journal Nature Physics.

In addition, the team discovered that in the same 45-percent selenium composition tiny amounts of "strain" -- a stretching of the material along one direction -- of just a fraction of a percent can lead to the appearance of local nematicity, which in turn suppresses superconductivity. This was not the case for Fe(Te,Se) samples constructed at a lower Se composition of 35 percent, which show negligible effects on superconductivity from the same amounts of strain.

The team found that in certain compositions of Fe(Te,Se) the nematic fluctuations can be "pinned" by structural disorder, which hinders superconductivity in particular regions of the material, said Zeljkovic, joined on the project by his Boston College colleagues Professor of Physics Ziqiang Wang and graduate students He Zhao and Hong Li, as well as researchers from other institutions in the U.S. and China.

"It was surprising that nematic regions appear to be not superconducting at all, despite the fact that the superconducting transition temperature should be the highest at the 45-percent composition," said Zeljkovic. "This could be indicative of nematic 'fluctuations', thought to enhance superconductivity near the nematic transition, becoming static and thus reducing superconducting properties locally."

Zeljkovic said the results indicate that a hidden quantum critical point -- a sought-after benchmark at the transition between different states in matter at zero degrees Kelvin -- may exist in Fe(Te,Se). He said further research into the material would be required to determine if that is the case.

Credit: 
Boston College

Fuel flow, heat fluctuations drive dangerous oscillations in rocket engines

image: Combustion chamber during combustion oscillations in a model rocket engine.

Image: 
Hiroshi Gotoda

WASHINGTON, June 8, 2021 -- Combustion engines can develop high frequency oscillations, leading to structural damage to the engines and unsafe operating conditions. A detailed understanding of the physical mechanism that causes these oscillations is required but has been lacking until now.

In Physics of Fluids, by AIP Publishing, research from the Tokyo University of Science and the Japan Aerospace Exploration Agency clarifies the feedback processes that give rise to these oscillations in rocket engines.

The investigators studied simulated combustion events in a computational model of a rocket combustor. Their analysis involved sophisticated techniques, including symbolic dynamics and the use of complex networks to understand the transition into oscillatory behavior.

The symbolic dynamics techniques allowed the scientists to determine similarities in behavior between two variables that characterize the combustion event. They found a relationship between fluctuations in the flow velocity of the fuel injector and fluctuations in the heat release rate of the combustor.

A rocket engine uses injectors to deliver a fuel, typically hydrogen gas, H2, and an oxidizer, oxygen gas, O2, to a combustion chamber where ignition and subsequent combustion of the fuel occurs.

"Periodic contact of the unburnt H2/O2 mixture with high-temperature products of the H2 [and] air flame gives rise to significant fluctuations in the ignition location," said author Hiroshi Gotoda.

Fluctuations in the ignition location produce fluctuations in the heat release rate, which affects pressure fluctuations in the combustor.

"We found that the heat release fluctuations and pressure fluctuations synchronize to each other," said Gotoda.

The product of the pressure and the heat release rate fluctuations in the combustor is an important physical quantity for understanding the origin of combustion oscillations. Regions where this product is greater than zero correspond to acoustic power sources that drive the oscillations.

The investigators discovered power sources in the shear layer near the injector rim. These power sources would suddenly collapse and reemerge upstream in a periodic fashion, leading to oscillations in combustion.

"The repetition of the formation and collapse of thermoacoustic source clusters in the hydrodynamic shear layer region between the inner oxidizer and outer fuel jets plays an important role in driving combustion oscillations," said Gotoda.

The investigators believe their analysis method will lead to a better understanding of the dangerous oscillations that sometimes arise in rocket engines and other combustors.

Credit: 
American Institute of Physics

Scientists discover unreported plant body part

image: Cantils, so named for their cantilever function of supporting the flower-bearing stalk, are newly reported plant structures that develop in wild-type Arabidopsis as a consequence of delayed flowering under short-day lengths. The image shows a FLOWERING LOCUS T mutant strain (ft-10) flowering under a long-day length. One long and two short cantils are visible.

Image: 
Timothy Gookin

For many, the Thale cress (Arabidopsis thaliana) is little more than a roadside weed, but this plant has a long history with scientists trying to understand how plants grow and develop. Arabidopsis was first scientifically described as early as the 16th century and the first genetic mutant was identified in the 1800s. Since the 1940s, Arabidopsis has increased in popularity within the scientific community, which continues to use it as a model system to explore plant genetics, development and physiology to this day.

One might expect that after decades of scientific scrutiny the structure of Arabidopsis had been fully documented, but a new study from scientists from The Pennsylvania State University, USA, has revealed that this humble plant still has some surprises. The researchers describe a previously unreported structure called the 'cantil', which connects to the stem at one end and hangs in the air to hold up the flower-bearing stalk, similar to the function of a cantilever in structural engineering.

"I first observed the cantils in 2008," said Dr Timothy Gookin, a postdoctoral researcher working in the group of Professor Sarah Assmann. "I initially didn't trust any of the results; I thought it must be an artefact of genetic contamination, perhaps combined with environmental contamination of the water, soil, fertilizer or even the building air supply."

How have cantils eluded scientists for so long? First, cantils are rare; they only develop under certain conditions that cause the plant to delay flowering, such as short day lengths, and cantils only form at the precise point at which the plant begins to flower. In addition, as Dr Gookin discovered, some popular Arabidopsis strains have genetic mutations that make them incapable of producing cantils at all.

Nonetheless, Dr Gookin set about the gargantuan task of proving that cantils are a naturally occurring structure and not an artefact of mutation or contamination - an effort that took more than a decade. "It took over 12 years of experimentation to really get a grasp on what we were seeing and to understand how cantils were regulated. This study required the growth of 3,782 plants to full maturity and the manual inspection of over 20,000 flower-bearing stalks in 34 unique plant lines," explained Dr Gookin. "I finally deemed the cantils a natural phenomenon after identifying them in wild-type (non-mutant) plants from different sources, which were growing in independent locations and diverse conditions."

During his extensive research, Dr Gookin identified a number of mutant plants in which cantils appear more frequently, revealing some of the genetic factors that control cantil development. The discovery of cantils is not only a lesson in the virtues of perseverance, but their development also provides important clues for understanding the conditional growth of plant structures in response to their environment. "One speculative interpretation is that the cantil represents a highly repressed ancestral linkage between different types of flowering plant architectures; the multiple layers of genetic and environmental factors that regulate cantil development are certainly quite striking," said Dr Gookin.

Credit: 
The Company of Biologists

USC Stem Cell scientists make big progress in building mini-kidneys

image: Novel kidney organoid recapitulating the patterned distribution of principal cells (red) and intercalated cells (green) of an adult kidney's collecting duct system.

Image: 
Zipeng Zeng/Li Lab

A team of scientists at the Keck School of Medicine of USC has created what could be a key building block for assembling a synthetic kidney. In a new study in Nature Communications, Zhongwei Li and his colleagues describe how they can generate rudimentary kidney structures, known as organoids, that resemble the collecting duct system that helps maintain the body's fluid and pH balance by concentrating and transporting urine.

"Our progress in creating new types of kidney organoids provides powerful tools for not only understanding development and disease, but also finding new treatments and regenerative approaches for patients," said Li, the study's corresponding author and an assistant professor of medicine, and of stem cell biology and regenerative medicine.

Creating the building blocks

The first authors of the study, PhD student Zipeng Zeng and postdoc Biao Huang, and the team started with a population of what are known as ureteric bud progenitor cells, or UPCs, that play an important role in early kidney development. Using first mouse and then human UPCs, the scientists were able to develop cocktails of molecules that encourage the cells to form organoids resembling uretic buds--the branching tubes that eventually give rise to the collecting duct system. The scientists also succeeded in finding a different cocktail to induce human stem cells to develop into ureteric bud organoids.

An additional molecular cocktail pushed ureteric bud organoids--grown from either mouse UPCs or human stem cells--to reliably develop into even more mature and complex collecting duct organoids.

The human and mouse ureteric bud organoids can also be genetically engineered to harbor mutations that cause disease in patients, providing better models for understanding kidney problems, as well as for screening potential therapeutic drugs. As one example, the scientists knocked out a gene to create an organoid model of congenital anomalies of the kidney and urinary tract, known as CAKUT.

In addition to serving as models of disease, ureteric bud organoids could also prove to be an essential ingredient in the recipe for a synthetic kidney. To explore this possibility, the scientists combined mouse ureteric bud organoids with a second population of mouse cells: the progenitor cells that form nephrons, which are the filtering units of the kidney. After inserting the tip of a lab-grown ureteric bud into a clump of NPCs, the team observed the growth of an extensive network of branching tubes reminiscent of a collecting duct system, fused with rudimentary nephrons.

"Our engineered mouse kidney established a connection between nephron and collecting duct--an essential milestone towards building a functional organ in the future," said Li.

Credit: 
Keck School of Medicine of USC

Association of sweetened beverage tax with purchases of beverages, high-sugar foods

What The Study Did: Researchers examined whether a sweetened beverage tax in Philadelphia was associated with sustained changes in beverage prices and purchases of sweetened beverages and high-sugar foods two years after implementation of the tax.

Authors: Christina A. Roberto, Ph.D., of the University of Pennsylvania Perelman School of Medicine in Philadelphia, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamanetworkopen.2021.13527)

Editor's Note: The article includes conflicts of interest and funding/support disclosures. Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support.

Credit: 
JAMA Network

Young adults' alcohol use increases when casually dating

image: Jennifer Duckworth

Image: 
Washington State University

When young adults are more interested in socializing and casually dating, they tend to drink more alcohol, according to a new paper led by a Washington State University professor.

On the other hand, scientists found that when young adults are in serious relationships, are not interested in dating or place less importance on friendship, their alcohol use was significantly lower.

Published June 15 in the journal Substance Use & Misuse, the study included more than 700 people in the Seattle area aged 18-25 who filled out surveys every month for two years. The study used a community sample that was not limited to college students.

"Young adults shift so much in terms of social relationships that having this monthly data really allowed us to hone in on nuances and see these changes in alcohol use depending on social situations," said Jennifer Duckworth, the lead author on the paper. "The idea is to understand whether young adults may be viewing alcohol as a way to facilitate relationships. They may think of alcohol as a way to make hanging out easier or more fun."

Being able to look at young adult behavior over a longer period allowed the research team to see how alcohol use was related to socializing and relationships.

"If a college student has mid-terms, they may have less interest in spending time with friends," said Duckworth, an assistant professor in WSU's Department of Human Development. "But if it's spring break, they may place more importance on those friendships. And when friendships become more important, we found alcohol use tends to be higher."

For relationships, Duckworth and her co-authors separated single young adults into two groups: casually dating and not interesting in dating. That distinction showed a significant difference in alcohol use. Since the survey tracked people every month, they could study changes as participants moved in and out of different relationship statuses.

"For instance, one month, someone may not be interested in dating and their alcohol use tended to be lower," Duckworth said. "Then, if they start dating, alcohol use tended to be higher."

Previous research has shown that young adults in relationships tend to drink less than single people, but those studies didn't separate the term single into two separate groups based on whether or not the young adults were interested in dating.

Young adults have more high-risk alcohol use than any other age group, she said. The overall goal of this research is to understand the context for greater alcohol use by young adults.

"Understanding what's going on in their lives across time is very useful if we want to mitigate high-risk use of alcohol," Duckworth said. "We can focus on interventions that help educate young adults on what is motivating their behaviors. We're bridging alcohol use with development research in a meaningful way that can really help people."

Credit: 
Washington State University