Quasicrystal-clear: Material Reveals Unique Shifting Surface Structure under Microscope (Material Science)

Scientists reveal peculiar surface structure in materials resembling quasicrystals with interesting implications for its magnetic properties

Ever since their discovery, quasicrystals have garnered much attention due to their strange structure. Today, they remain far from being well-understood. In a new study, scientists reveal, for the first time, a unique shifting surface atomic structure in a material emulating quasicrystals, opening doors to the better understanding of magnetic and superconducting properties of quasicrystals, and potential applications in semiconductor film growth.

Between chemistry classes, gemstones, and electronics, the idea of crystals, substances with an ordered and periodic arrangement of atoms is quite common. But about 40 years ago, a strange particle was discovered by scientists that hasn’t become commonplace in our world yet: quasicrystals. These are structures with curious atomic arrangements, which, while superficially similar to crystals, lack periodicity despite being ordered. Because of their structures, quasicrystals exhibit symmetries forbidden to crystals and are endowed with interesting properties that crystals cannot show, such as high resistance to heat flow, current flow, and corrosion.

Since their discovery, quasicrystals have been researched extensively by materials scientists around the world. Due to their rarity, scientists have often resorted to studying models mimicking them, called approximants. Recently, in a class of gold-based approximants, called “Tsai-type approximants”, the presence of magnetic order was detected whose type can be controlled by the composition of the approximants-an exciting possibility for material scientists to explore.

In such approximants of increasing complexity, such as that composed of gold (Au), aluminum (Al), and terbium (Tb), the magnetic order was found to be antiferromagnetic, where each ion in the crystal acts as a small magnets with its poles opposite to those of its neighbors. In a new study published in Physical Review B, Prof. Ryuji Tamura from the Tokyo University of Science (TUS), Japan, along with his colleagues Sam Coates of TUS, and Hem Raj Sharma and Ronan McGrath of the University of Liverpool, explored the atomic structure of the antiferromagnetic surface this Tsai-type approximant. Prof. Tamura, who led the study, says: “Au-based Tsai approximants are under-researched compared to their silver (Ag)-based counterparts, particularly in the field of surface science. Understanding the structures of these Tsai-type materials will allow for in-depth interpretations of their specific properties, such as magnetic transitions, electronic features, and superconductivity.” Their study yielded unexpected results.

The building blocks of Tsai-type approximants are “Tsai-type clusters”, polyhedral shells whose number of sides depends on the variant of the approximant. In their study, Prof. Tamura’s team chose a 1/1 variant of the Au-Al-Tb approximant in which a tetrahedral unit was enclosed within a dodecahedron, icosahedron, icosidodecahedron, and rhombic triacontahedron. The Tb atoms occupied the vertices of the icosahedron while the Au/Al atoms occupied the vertices of the remaining shells.

The scientists looked into a specific surface of a single crystal of the 1/1 Au-Al-Tb using a scanning tunneling microscope (STM) and backed up their observations with density functional theory (DFT) calculations.

They found that the surface had a peculiar step-terrace-like structure with the terraces ending at planes containing Tb atoms and a step height that, interestingly, appeared to minimize the number of incomplete icosahedrons. Furthermore, they found that the terrace structure depended on the sign of the biasing voltage applied to the sample. While at positive bias, the Tb atoms showed a rhombohedral or hexagonal arrangement, negative bias revealed the Au/Al atoms to be arranged in a linear row-like structure, a kind of switching not observed in a Tsai-type material before. “As this is the first Tsai-type material to show such a scheme, we need to further investigate Au-based Tsai types to assess whether chemical composition has a role to play in surface structure,” comments Prof. Tamura. The observations were consistent with DFT calculations.

While quasicrystals have found several applications, ranging from surgical instruments, LEDs to non-stick frying pans, they are far from being well understood and the recent findings in quasicrystal-like structures serve to hint at the untapped exotic possibilities they harbor. “The unique structure of the Tsai-type surface suggests that quasicrystals could be used as a template for molecular adsorption in the creation of organic semiconducting thin films,” Prof. Tamura says. “Understanding of how the structure change corresponds to the magnetism can open doors to new applications,” he adds.

One thing’s for sure: the quasicrystal is a little clearer!

Featured image: The Tsai-type clusters one inside another of the Au-Al-Tb approximant the scientists chose (a), and the corresponding spin icosahedra (b). Photo courtesy: Ryuji Tamura of Tokyo University of Science

Reference: Sam Coates, Kazuki Nozawa, Masahiro Fukami, Kazuki Inagaki, Masahiko Shimoda, Ronan McGrath, Hem Raj Sharma, and Ryuji Tamura, “Atomic structure of the (111) surface of the antiferromagnetic 1/1 Au-Al-Tb approximant”, Phys. Rev. B 102, 235419 – Published 15 December 2020. https://journals.aps.org/prb/abstract/10.1103/PhysRevB.102.235419 https://doi.org/10.1103/PhysRevB.102.235419

Provided by Tokyo University of Science

Noninvasive Way For Identifying the Major Functions of Gastrointestinal Tract (Chemistry)

A healthy person has a general balance of good and bad bacteria. But that balance is thrown off when someone gets sick. So, to help boost their levels of good bacteria, many people take probiotic supplements — live bacteria inside of a pill. Various commercial probiotic supplements are available for consumer purchase, and while health experts generally agree about their overall safety, controversy surrounds their efficacy.

Inside the human body lives a large microscopic community called the microbiome, where trillions of bacteria engage in a constant “tug of war” to maintain optimal levels of good and bad bacteria. Most of this struggle takes place within the body’s gastrointestinal tract, as bacteria help with digesting food and support the immune system. Although health experts believe good “gut” health is key to a person’s health and well-being, scientists are still developing a detailed picture of what goes on inside a person’s gastrointestinal tract.

“Until now, we have not had any ways to noninvasively monitor activity in the intact gastrointestinal tract, given the unique chemical environment, variable distribution and highly dynamic nature of the gut microbiota,” said Elena Goun, an associate professor in the Department of Chemistry at the University of Missouri.

In a new study published in Science Advances, Goun and an international team of scientists have developed a noninvasive diagnostic imaging tool to measure the levels of a naturally occurring enzyme — bile salt hydrolase — inside the body’s entire gastrointestinal tract. Goun said their tool accomplishes three major functions:

  • Predicts the clinical status of inflammatory bowel disease, such as Crohn’s disease and ulcerative colitis.
  • Determines the efficacy of many commercially available probiotic supplements by testing for the level of bile salt hydrolase, which is responsible for all of the major health-promoting functions of probiotics.
  • Evaluates whether certain types of prebiotics — dietary fibers known to support digestive health — can increase bile salt hydrolase levels in a similar way that probiotic supplements do.

Goun, who specializes in the development of biomedical imaging tools to advance the knowledge and understanding of various processes underlying human diseases, believes their findings are exciting, especially with the discovery related to prebiotics, which can be naturally found in foods such as whole grains, nuts and seeds, and fruits and vegetables.

Elena Goun © University of Missouri

“Prebiotics are often used in combination with probiotics to enhance their functions in the body,” Goun said. “We show for the first time that certain types of prebiotics alone are capable of increasing bile salt-hydrolase activity of the gut microbiota, which among other health benefits has been shown to decrease inflammation, reduce blood cholesterol levels, and protect against colon cancer and urinary tract infections. In my opinion, this discovery is huge because the production and storage of prebiotics is less expensive than with probiotics.”

Previous reports have noted high bile salt-hydrolase activity of the gastrointestinal tract is reflective of better digestive health and a lack of inflammation in the body. Goun said their noninvasive method uses bioluminescence — a chemical reaction that produces light inside a living organism — to measure the level of bile salt-hydrolase activity throughout the entire gastrointestinal tract.

“Our imaging tool is a bioluminescent probe in the form of a capsule,” Goun said. “When someone swallows it, it’s exposed to the intact gut microbiota while traveling throughout the harsh environment of a person’s entire gastrointestinal tract. After it passes out of the body, we can analyze a person’s stool sample. We can take the results from that analysis and correlate it with the amount of bile salt-hydrolase activity within the human gastrointestinal tract.”

Goun believes this research could lead to better precision medicine treatments by providing a way for scientists to better understand how a person’s individual gut health is connected to various human pathologies, or the origin and nature of human diseases.

“This is the first example of the use of bioluminescent imaging probes in humans,” Goun said. “The gut microbiome plays a huge role in various health issues such as cancer, diabetes, obesity, Parkinson’s disease, depression and autism, and now, this new tool will help us better understand the relationship between the gut function and these diseases. In addition, it will allow us to develop more effective probiotics and prebiotics to improve gut health.”

Highlighting the promise of personalized health care and the impact of large-scale interdisciplinary collaboration, the University of Missouri System’s NextGen Precision Health initiative is bringing together innovators from across the system’s four research universities in pursuit of life-changing precision health advancements. It’s a collaborative effort to leverage the strengths of Mizzou and entire UM System toward a better future for Missouri’s health. An important part of the initiative is the construction of the new NextGen Precision Health building, which will expand collaboration between researchers, clinicians and industry leaders in a state-of-the-art research facility.

Noninvasive imaging and quantification of bile salt hydrolase activity: from bacteria to humans,” was published in Science Advances. This was a highly collaborative work, including institutions such as the Swiss Federal Institute of Technology in Lausanne, Switzerland; Nestlé Institute of Health Sciences in Lausanne, Switzerland; University of North Carolina at Chapel Hill; and Nationwide Children’s Hospital in Columbus, Ohio.

Featured image: An illustration of the non-invasive way for identifying the major functions of the gastrointestinal tract. Illustration is courtesy of Marina Resnyanskaya.

Provided by University of Missouri

Best of Both Worlds: A Hybrid Method For Tracking Laparoscopic Ultrasound Transducers (Medicine)

Combined hardware- and computer vision-based strategy will help improve laparoscopic ultrasound imaging

Laparoscopic surgery, a less invasive alternative to conventional open surgery, involves inserting thin tubes with a tiny camera and surgical instruments into the abdomen. To visualize specific surgical targets, ultrasound imaging is used in conjunction with the surgery. However, ultrasound images are viewed on a separate screen, requiring the surgeon to mentally combine the camera and ultrasound data.

Modern augmented reality (AR)-based methods have overcome this issue by embedding ultrasound images into the video taken by the laparoscopic camera. These AR methods precisely map the ultrasound data coordinates to the coordinates of the images seen through the camera. Although the process is mathematically straightforward, it can only be done if the pose (position and orientation) of the ultrasound probe (transducer) is known by the camera coordinate system. This has proven to be challenging, despite many strategies for tracking the laparoscopic transducer. Hardware-based tracking by attaching electromagnetic (EM) sensors to the probe is a feasible approach, but it is prone to errors due to calibration and hardware limitations. Camera vision (CV) systems can also be used to process the images acquired by the camera and determine the probe’s pose. However, because they rely entirely on camera data, such methods fail if the probe is defocused or if the camera’s view is occluded. Thus, such CV systems are not yet ready for clinical settings.

To this end, in a recent study published in the Journal of Medical Imaging, a team of scientists from the US have come up with a creative solution. Instead of relying entirely on either hardware- or CV-based tracking, they propose a hybrid approach that combines both methods. Michael Miga, Associate Editor of the journal, explains, “In the context of interventional imaging with laparoscopic ultrasound, tracking the flexible ultrasound probe for correlation with preoperative images is a challenging task. The team led by Dr. Shekhar has demonstrated an impressive tracking ability with the proposed hybrid approach; these types of capabilities will be needed to advance the field of image-guided surgery.”

To begin with, the team designed and 3D-printed a custom tracking mount to be placed on the tip of the transducer. This mount contained a sensor for EM-based tracking and several flat surfaces on which black-and-white markers can be attached for CV-based tracking. These markers, which resemble QR codes, are detected in the images recorded by the camera using an open-source AR algorithm called ArUco. Once two or more markers were detected in a frame, the scientists could immediately calculate the pose of the transducer.

Because CV-based tracking is more accurate than EM-based, the system defaults to using the former to track the transducer. And whenever markers are undetectable in a frame, the system adaptively switches to EM-based tracking. Moreover, to enhance their approach beyond the simple combination of both techniques, the scientists developed an algorithm that can perform corrections to the EM-based tracking results based on previous camera frames. This greatly reduces the errors associated with the EM sensor, especially those due to rotations of the laparoscopic probe.

The team demonstrated the effectiveness of their strategy through experiments on both a realistic tissue phantom and live animals. Excited about the results, Raj Shekhar, who led the study, concludes, “Our hybrid method is more reliable than using CV-based tracking alone and more accurate and practical than using EM-based tracking alone. It has the potential to significantly improve tracking performance for AR applications based on laparoscopic ultrasound.”

As this hybrid strategy undergoes further improvements, it can pave the way for laparoscopic surgery to be more effective and safer, leading to faster recoveries and better patient outcomes overall.

Read the original research article by Xinyang Liu, William Plishker, and Raj Shekhar: “Hybrid electromagnetic-ArUco tracking of laparoscopic ultrasound transducer in laparoscopic video,” J. of Medical Imaging 8(1), 015001 (2021), doi 10.1117/1.JMI.8.1.015001.

Featured image: Multimedia still images showing the results of the ArUco tracking (green), the corrected EM tracking using Algorithm 2 (yellow) and the original EM tracking (red), from Liu, Plishker, and Shekhar, doi 10.1117/1.JMI.8.1.015001

Provided by SPIE

A Single-Molecule Guide to Understanding Chemical Reactions Better (Chemistry)

Scientists at Tokyo Institute of Technology (Tokyo Tech) report measurement of electrical conductivity of single DNA molecules as a way of monitoring the formation of double-stranded DNA on a gold surface. In their latest paper, they investigate the time evolution of the reaction and report findings not observed previously, demonstrating the suitability of the single-molecule approach in elucidating reaction pathways and exploring novel chemical processes.

Scientists globally aim to control chemical reactions—an ambitious goal that requires identifying the steps taken by initial reactants to arrive at the final products as the reaction takes place. While this dream remains to be realized, techniques for probing chemical reactions have become sufficiently advanced to render it possible. In fact, chemical reactions can now be monitored based on the change of electronic properties of a single molecule! Thanks to the scanning tunneling microscope (STM), this is also simple to accomplish. Why not then utilize a single-molecule approach to uncover reaction pathways as well?

With this goal, scientists from Tokyo Institute of Technology, Japan decided to explore DNA “hybridization” (formation of a double-stranded DNA from two single-stranded DNA) by measuring the changes in single-molecule electrical conductivity using an STM. “Single-molecule investigations can often reveal new details on chemical and biological processes that cannot be identified in a bulk collection of molecules due to the averaging out of individual molecule behavior,” explains Prof Tomoaki Nishino, who was part of the study, recently published in Chemical Science.

The scientists attached a single-stranded DNA (ssDNA) to an STM tip made of gold and used a flat gold film to stick the complementary strand on it via a process known as “adsorption.” They then applied a bias voltage between the coated STM tip and the gold surface and brought the tip extremely near to the surface without touching it (Fig. 1). This, in turn, allowed a current to flow through the space in between due to a process known as “quantum tunneling”. Chemists monitored the time variation of this tunneling current as the DNA strands interacted with each other.

The team obtained current traces depicting plateau regions formed of steep inclines and subsequent declines in the tunneling current. Further, these plateaus did not form when either the gold surface was not modified with ssDNA or was modified with a non-complementary strand. Based on this, scientists attributed the plateaus to the formation of a double-stranded DNA (dsDNA) resulting from hybridization of ssDNA on the STM tip and the surface. Equivalently, they attributed the abrupt decrease in current to the breakdown or “dehybridization” of the dsDNA due to thermal agitation.

The team next investigated the kinetics (time evolution of reaction) of the dehybridization and hybridization processes using experimental results and molecular dynamics simulations. The former revealed a plateau conductance independent of DNA concentration, confirming that the current measurements reflected single-molecule conductance, while the latter suggested the formation of a partially hybridized DNA intermediate that could not be detected from conductance alone.

Interestingly, the hybridization efficiency was higher for high DNA concentration samples, contradicting the findings of a previous study made with bulk ssDNA solution. Chemists attributed this observation to the absence of bulk diffusion in their study.

“These new insights should contribute to improved performance for many DNA-based diagnoses,” observes Prof Nishino, excited about the findings, “In addition, our method can be extended to the investigation of intermolecular chemical reactions between a variety of single molecules, enabling a mechanistic understanding of chemical reactions as well as discovery of novel chemical reactivity from a single-molecule perspective.”

Featured image: The methodology they have described can be extended to the investigation of intermolecular chemical reactions between a variety of single molecules and can lead to mechanistic understanding of chemical reactions and exploration of novel reactivity from a single-molecule perspective. © Tokyo Tech

Reference: Takanori Harashima, Yusuke Hasegawa, Satoshi Kaneko, Yuki Jono, Shintaro Fujii, Manabu Kiguchi, and Tomoaki Nishino, “Elementary Processes of DNA Surface Hybridization Resolved by Single-molecule Kinetics: Implication for Macroscopic Device Performance”, Chemical Science, 2021. DOI :10.1039/D0SC04449K

Provided by Tokyo Institute of Technology

New Methods For Exploring the ‘Dark Matter’ of Biology (Biology)

New tools and methods have been described by WEHI researchers to study an unusual protein modification and gain fresh insights into its roles in human health and disease.

The study – about how certain sugars modify proteins – was published today in Nature Chemical Biology. Led by WEHI researcher Associate Professor Ethan Goddard-Borger, this work lays a foundation for better understanding diseases like muscular dystrophy and cancer.

At a glance

— WEHI researchers have developed new tools and methods to determine how ‘tryptophan C-mannosylation’, an unusual protein modification, impacts the stability and function of disease-relevant proteins.

— These tools have been used to map the prevalence of this protein modification in healthy tissue.

— This work lays the foundation for future studies into the role this protein modification plays in diseases as diverse as muscular dystrophy and cancer.

The ‘dark matter’ of biology

Glycosylation is the process by which proteins are modified with sugars. About 90 per cent of proteins on the surface of human cells – and half of the cells’ total proteins – are modified with sugars. These modifications can range from the addition of a single sugar, to long complex polymer chains. They’ve been described as the ‘dark matter’ of biology because their distribution, variability and biological functions are, for the most part, not well understood.

Associate Professor Goddard-Borger said his team, and the glycobiology field more generally, are making concerted efforts to build a better understanding of the roles that glycosylation plays in health and disease.

“There are a whole range of diseases that feature aberrant cellular glycosylation – a change in ‘normal’ glycosylation patterns,” he said.

“These changes may yield new therapeutic strategies, however a better understanding of what constitutes ‘normal’ glycosylation is required before we can further develop drugs targeting protein glycosylation.”

“It’s a scenario that is akin to the ‘dark matter’ of the universe: we know that all of this protein glycosylation exists in the body, but we don’t fully appreciate its composition and function.”

Shedding light on a sweet process

Glycosylation usually occurs on the nitrogen or oxygen atoms of a protein. However, it can also occur on carbon atoms through the process of ‘tryptophan C-mannosylation’. This latter protein modification is particularly poorly understood and so the WEHI team set out to develop tools and methods to shed light on this aspect of the biological ‘dark matter’.

“We’ve developed methods that will enable researchers to easily install this unusual modification on nearly any protein they want, allowing them to investigate its effect on protein stability and function,” Associate Professor Goddard-Borger said.

“In this work, we’ve shown that a common feature of tryptophan C-mannosylation is that it stabilises proteins. Diverse, unrelated proteins all appear to be more stable once modified. However, we’ve also demonstrated for the first time that some proteins’ functions can be modulated by tryptophan C-mannosylation’. There is clearly much left to learn about this process and now we have the means to perform these studies.”

Mapping the prevalence of tryptophan C-mannosylation

Associate Professor Goddard-Borger said the tools developed by his team also enable the abundance of this poorly understood protein modification to be determined in healthy and diseased tissues, which will fortify efforts by scientists around the world to map and understand protein glycosylation in health and disease.

“The methods we describe combine state-of-the-art mass spectrometry techniques with recombinant antibody tools generated at WEHI,” he said.

“We’ve reported some really unexpected results regarding the prevalence of this modification in healthy brain tissue. At present, we are extending this to map the modification across most tissues in the body to better understand the biology of this weird and wonderful form of protein glycosylation, as well as its role in cancer and muscular dystrophies.”

This research was funded by the Brian M Davis Charitable Foundation, the Australian National Health and Medical Research Council and the Victorian Government.

Featured image: Structural model of antibody with glycan bound © WEHI

Reference: John, A., Järvå, M.A., Shah, S. et al. Yeast- and antibody-based tools for studying tryptophan C-mannosylation. Nat Chem Biol (2021). https://www.nature.com/articles/s41589-020-00727-w https://doi.org/10.1038/s41589-020-00727-w

Provided by Walter and Eliza Hall Institute

Researchers From NUS Create ‘Whirling’ Nano-structures in Anti-ferromagnets (Physics)

Today’s digital world generates vast amounts of data every second. Hence, there is a need for memory chips that can store more data in less space, as well as the ability to read and write that data faster while using less energy.

Researchers from the National University of Singapore (NUS), working with collaborators from the University of Oxford, Diamond Light Source (the United Kingdom’s national synchrotron science facility) and University of Wisconsin Madison, have now developed an ultra-thin material with unique properties that could eventually achieve some of these goals. Their results were first published online in the journal Nature on 4 February 2021.

Storing data in anti-ferromagnets

In existing ferromagnet memory devices like hard drives, information is stored into specific patterns of atoms (called bits), within which all the little magnetic poles are oriented in the same direction. This arrangement makes them slow and susceptible to damage by stray magnetic fields. In contrast, a special class of materials called anti-ferromagnets, made up with magnetic poles on adjacent atoms aligned oppositely, are emerging to be important for future memory technology.

In particular, there is a lot of interest in creating special magnetic nano-patterns in anti-ferromagnets that are shaped as whirls or vortices. In essence, each pattern consists of many little magnetic poles winding around a central core region in a clockwise or anti-clockwise manner, very much like air circulating inside a tornado or whirlwind. When realised experimentally, combinations of these anti-ferromagnetic whirls would be quite useful, as they are very stable structures and can potentially be moved along magnetic ‘race tracks’ at whirlwind speeds of a few kilometres per second!

They could act as new types of information bits that not only store memory but also participate in computational operations. Hence, they would enable a new generation of chips that are significantly faster yet more energy-efficient than today’s devices.

Experimental discovery of whirls

To date, constructing and manipulating patterns in anti-ferromagnetic materials has been very challenging, as they appear almost non-magnetic from afar. “Standard approaches for control, such as using external fields, fail to work on these materials. Therefore, to realise these elusive anti-ferromagnetic whirls, we came up with a novel strategy that combined high-quality film synthesis from materials engineering, phase transitions from physics and topology from mathematics,” explained Dr Hariom Jani, who is the lead author of the paper and a Research Fellow from the NUS Department of Physics.

High-quality film of iron-oxide grown via pulsed laser deposition (left), is seen to host complex spin structures shown in RGB colours (right), including a family of anti-ferromagnetic whirls (indicated in circles). Credit: J. Chen and Neocera

To grow these materials, the researchers fired a laser at an extremely common and cheap material – iron-oxide, which is the main component of rust. By using ultra-short pulses of laser, they created a hot vapour of atomic particles that formed a thin film of iron-oxide on a surface.

Professor Thirumalai Venky Venkatesan, who led the NUS group and invented the pulsed laser deposition process for making the thin film, highlighted the versatility of the team’s approach. “The deposition process allows precise atom-level control during the growth, which is important for making high-quality materials. Our work points to a large class of anti-ferromagnetic material systems, containing phase transitions, in which one can study the formation and control of these whirls for eventual technological applications,” he said.

Explaining the underlying mechanism, Professor Paolo Radaelli, leader of the Oxford group, shared, “We drew inspiration from a celebrated idea in cosmological physics, from nearly 50 years ago, which proposed that a phase transition in the early universe, during the expansion after the Big Bang, may have resulted in the formation of cosmic whirls. Accordingly, we investigated an analogous magnetic process occurring in high-quality iron-oxide, which allowed us to create at will a large family of anti-ferromagnetic whirls.”

The team’s next step is to construct innovative circuits that can electrically control the whirls.

Featured image: A family of anti-ferromagnetic whirls in iron-oxide that are generated after performing a magnetic transition analogous to the Big Bang cooling. Credit: R. Shetty, K. Jani, H.Jani.

Reference: Jani, H., Lin, JC., Chen, J. et al. Antiferromagnetic half-skyrmions and bimerons at room temperature. Nature 590, 74–79 (2021). https://doi.org/10.1038/s41586-021-03219-6

Provided by NUS news

How Metal Atoms Can Arrange Themselves on an Insulator? (Physics)

Bielefeld researchers publish study in Nature Communications

In order to produce tiny electronic memories or sensors in future, it is essential to be able to arrange individual metal atoms on an insulating layer. Scientists at Bielefeld University’s Faculty of Chemistry have now demonstrated that this is possible at room temperature: molecules of the metal-containing compound molybdenum acetate form an ordered structure on the insulator calcite without jumping to other positions or rotating. Their findings have been presented in the Nature Communications journal. The work was done in cooperation with researchers from the universities of Kaiserslautern, Lincoln (UK) and Mainz.

‘Until now, it has been difficult to arrange metal atoms on an insulator surface. It’s easier on a metal surface, but that’s not of much benefit for use in electronic components,’ says Professor Dr Angelika Kühnle, who heads the Physical Chemistry I working group at the Faculty of Chemistry. ‘That’s what’s special about our study: we’ve found a way to arrange metal atoms on insulators in a lattice-like structure.’ Insulators are materials in which electrons cannot move freely and are therefore very poor conductors of electricity.

The scientists use atomic force microscopy for their study. Photo: Bielefeld University/M.-D. Müller

The difficulty is in robustly anchoring metal atoms even at room temperature – without them attracting each other, jumping to other positions or rotating. Until now, scientists have been able to arrange small molecules on insulators at very low temperatures, but at room temperature they were too mobile. Larger molecules solved the problem of mobility, but quickly formed clusters.

For their research, Kühnle and her working group used molybdenum acetate, a compound that contains two atoms each of the metal molybdenum. The fact that this compound shows interesting structural properties on a gold surface had previously been discovered by a research team from the Technical University of Kaiserslautern. ‘If molybdenum acetate is now applied to a calcite surface, the molecules form an ordered structure. This means that the molybdenum atoms are also arranged in an ordered array,’ says Dr Simon Aeschlimann, who conducted research in Kühnle’s group and is lead author of the published study. ‘By means of various experiments and simulations, we were able to show that the molybdenum acetate molecules neither jump nor rotate, nor do they form clusters. They are firmly anchored on the calcite surface.’

The scientists conducted the experiments with the aid of an atomic force microscope. ‘In atomic force microscopy, a tiny needle scans the surface of materials – like a record player, except that the needle does not touch the surface directly, but is deflected by atomic forces. This then creates an image of the surface structure,’ says Aeschlimann. The scientists examined, for example, where the molybdenum acetate molecules are located on the calcite surface and in which direction they align themselves.

The ordered structure is created because the molybdenum acetate molecules align themselves precisely with the charge distribution on the calcite surface. Calcite consists of calcium and carbonate building blocks that form a regular lattice structure. ‘Each molybdenum acetate molecule fits only in a very specific place on the calcite surface and at the same time does not interact with its neighbouring molybdenum acetate molecules. That means it is firmly anchored,’ says Kühnle. 

As a scientist engaged in pure research, Kühnle is interested in the question of how molecular structures form on surfaces or interfaces. But the results are also relevant for electronic applications: if, for example, magnetic metals can be arranged according to the same principle, this could be used in nanotechnology to produce data storage – i.e. memories that are only a few millionths of a millimetre in size. Other possible areas of application include optical or chemical sensors.

Featured image: In a new study, Professor Dr Angelika Kühnle investigates how metal atoms can be arranged on an insulator. © Photo: Bielefeld University/M.-D. Müller

Simon Aeschlimann, Sebastian V. Bauer, Maximilian Vogtland, Benjamin Stadtmüller, Martin Aeschlimann, Andrea Floris, Ralf Bechstein, Angelika Kühnle: Creating an Array of Metal-Complexing Molecules on an Insulator Surface at Room Temperature. Nature Communications, https://doi.org/10.1038/s41467-020-20189-x, published on 21 December 2020.

Provided by Universität Beilefeld

How Elephants Evolved to Become Big and Cancer-resistant? (Biology)

A study shows that elephants possess a large toolbox of genes for evading cancer, and suggests that evolution of tumor suppression capabilities contributed to the development of big bodies

All things being equal, large, long-lived animals should have the highest risk of cancer.

The calculation is simple: Tumors grow when genetic mutations cause individual cells to reproduce too quickly. A long life creates more opportunities for those cancerous mutations to arise. So, too, does a massive body: Big creatures — which have many more cells — should develop tumors more frequently.

Why, then, does cancer rarely afflict elephants, with their long lifespans and gargantuan bodies? They are some of the world’s largest land animals.

A new study delves into this sizeable mystery, showing that elephants possess extra copies of a wide variety of genes associated with tumor suppression.

But this phenomenon is not unique to elephants, scientists say: The research concluded that duplication of tumor suppressor genes is quite common among elephants’ living and extinct relatives, including in small ones like Cape golden moles (a burrowing animal) and elephant shrews (a long-nosed insectivore). The data suggest that tumor suppression capabilities preceded or coincided with the evolution of exceptionally big bodies, facilitating this development.

The study was published on Jan. 29 in the journal eLife by biologists Vincent Lynch at the University at Buffalo and Juan Manuel Vazquez at the University of California, Berkeley.

“One of the expectations is that as you get a really big body, your burden of cancer should increase because things with big bodies have more cells,” says Lynch, PhD, assistant professor in the Department of Biological Sciences in the UB College of Arts and Sciences. “The fact that this isn’t true across species — a long-standing paradox in evolutionary medicine and cancer biology — indicates that evolution found a way to reduce cancer risk.”

In the new study, “We explored how elephants and their living and extinct relatives evolved to be cancer-resistant,” Lynch says. “We have past research looking at TP53, a well-known tumor suppressor. This time, we said, ‘Let’s just look at whether the entire elephant genome includes more copies of tumor suppressors than what you’d expect.’ Is the trend general? Or is the trend specific to one gene? We found that it was general: Elephants have lots and lots and lots of extra copies of tumor suppressor genes, and they all contribute probably a little bit to cancer resistance.”

Elephants do have enhanced cancer protections, compared with relatives

Though many elephant relatives harbor extra copies of tumor suppressor genes, the scientists found that elephant genomes possess some unique duplications that may contribute to tumor suppression through genes involved in DNA repair; resistance to oxidative stress; and cellular growth, aging and death.

“By determining how big, long-lived species evolved better ways to suppress cancer we can learn something new about how evolution works and hopefully find ways to use that knowledge to inspire new cancer treatments,” says Vazquez, PhD, a postdoctoral researcher at UC Berkeley who completed much of the project while earning his PhD at the University of Chicago.

A related mystery: How did giant sloths and ancient mega-armadillos get so big?

Artist’s illustration of species within the taxonomic order Proboscidea, which includes elephants. Credit: Liam Elward

Elephants are a great case study for understanding the evolution of cancer protection because they belong to a group of mammals — the Afrotherians — that are mostly small-bodied.

The study searched for extra copies of tumor suppressor genes in the DNA of Asian, African savanna and African forest elephants, as well as in the genomes of a number of fellow Afrotherians, such as Cape golden moles, elephant shrews, rock hyraxes, manatees, extinct woolly mammoths, extinct mastodons and more. The team also studied certain species belonging to a group of mammals called Xenarthra that is closely related to Afrotherians, and found some extra copies of tumor suppressors in those animals’ genomes as well.

Given the findings, Lynch wonders whether the duplication of tumor suppressors may have aided the evolution of other ancient large bodies within these groups.

“If you pick a weird mammal, there’s a good chance that it will be in these groups, the Afrotherians and Xenarthrans: armadillos, aardvarks, sloths, anteaters, all of these weird mammals,” Lynch says. “We found that within these groups of organisms, the ones we studied all seem to have extra copies of tumor suppressor genes. That may be why in the last Ice Age, there were giant sloths and ancient mega-armadillos. There’s even an extinct species of manatee relative called the Steller’s sea cow that was elephant-big. Extra copies of tumor suppressors may have helped all of these animals get really, really big.”

Featured image: Artist’s illustration of species within the taxonomic order Proboscidea, which includes elephants. Credit: Liam Elward

Reference: Juan M Vazquez, Vincent J Lynch et al., “Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk”, eLife, 2021. DOI: 10.7554/eLife.65041

Provided by University at Buffalo

Fast-flying Bats Rely On Late-night Updrafts to Reach Great Heights (Biology)

Although scientists knew that some bats could reach heights of over 1,600 meters (or approximately one mile) above the ground during flight, they didn’t understand how they managed to do it without the benefit of thermals that aren’t typically available to them during their nighttime forays. Now, researchers reporting in the journal Current Biology on February 4th have uncovered the bats’ secret to high-flying.

It turns out that the European free-tailed bats they studied–powerful fliers that the researchers documented sometimes reaching speeds of up to 135 kilometers (84 miles) per hour in self-powered flight–do depend on orographic uplift that happens when air is pushed up over rising terrain to help them fly high, just as birds do during the day. But, because that’s harder to find during the cooler night, they have to rely on just the right sort of areas to reach those high altitudes.

“We show that wind and topography can predict areas of the landscape able to support high-altitude ascents, and that bats use these locations to reach high altitudes while reducing airspeeds,” explains Teague O’Mara (@teague_o), of Southeastern Louisiana University and the Max Planck Institute of Animal Behavior. “Bats then integrate wind conditions to guide high-altitude ascents, deftly exploiting vertical wind energy in the nocturnal landscape.”

This photo shows a dorsal view of a bat with a GPS tag on its back. © Teague O’Mara

To make these discoveries, O’Mara and colleagues fitted the free-tailed bats with high-resolution GPS loggers that recorded their location in three-dimensional space every 30 seconds, tracking them for up to three days during the approximately six-hour night. The data show that bats emerge just after sunset and fly constantly throughout the night before returning to roost.

They observed that the bats’ flight would typically follow the terrain they crossed, but that occasionally they would climb to extreme heights, reaching nearly a mile above ground level in less than 20 minutes. During these high-altitude ascents, the bats would climb faster, longer, and at a lower airspeed than during more moderate ascents to around 300 meters. Most bats descended quickly after reaching their peak elevation, resulting in a kind of rollercoaster flight path.

The researchers were surprised to discover just how predictable the bats’ high-flying ascents were across the landscape. The data show that bats are using the same types of places–although not necessarily always the exact same locations–where the wind sweeps up a slope to carry them to high altitudes.

This photo shows the region in northern Portugal where the researchers tracked the bats. © Teague O’Mara

“We were ready to see that these bats flew fast, so that wasn’t a surprise to us,” O’Mara said. “But the fast, uplifting wind-supported flights were something our team really wasn’t looking for or prepared for.”

The findings show that bats are solving the problems of flight in similar ways to birds–just at night, the researchers note.

“These free-tailed bats seem to find ways to minimize how much energy they have to spend to find food each night,” O’Mara said. “It’s a pretty incredible challenge for an animal that can only really perceive the 30 to 50 meters ahead of it in detail. It takes a lot of energy to fly up to 1,600 meters above the ground, and these bats have found a way to ride the wind currents up.”

Although the researchers already had a pretty good idea based on past work that the bats also could fly amazingly fast, they say this fast-flying ability remains “a bit of an unsolved problem.”

“Their small body sizes and large, flexible wings covered in a thin membrane were assumed to prevent these really fast speeds,” O’Mara said. “But it’s now clear that bats can fly incredibly fast when they choose. It’s up to us to figure out how they do that and if it can be applied to other scenarios,” such as engineering bio-inspired high-speed and low-energy flight.

This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy, the Fundação para a Ciência e a Tecnologia, Portugal, and the Energias de Portugal Biodiversity Chair.

Featured image: This photo shows a bat with a GPS tag on its back. © Teague O’Mara

Reference: O’Mara et al., “Bats use topography and nocturnal updrafts to fly high and fast”, Current Biology, 2021. https://www.cell.com/current-biology/fulltext/S0960-9822(20)31894-7

Provided by Cell press