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News Article | May 5, 2017
Site: www.materialstoday.com

Stress sensors are important tools when it comes to evaluating the robustness of a material exposed to strong mechanical forces. In a paper in Advanced Materials, researchers at Okinawa Institute of Science and Technology Graduate University (OIST) in Japan report a new kind of sensor molecule that brightens when the material it is incorporated into comes under heavy mechanical stress. Such light-based sensing molecules, known as photoluminescent mechanophores, are not new, but current applications of them are single-use only. They typically involve a strong force – compressing, twisting or stretching for example – breaking a specific chemical bond between two atoms or irreversibly pulling apart two complexes in the sensing molecule. This changes the wavelength – and thus the color – of the light emitted by the mechanophore. Once these molecules have radically changed their structure in response to this force, however, it is extremely difficult for them to return to the initial situation. So while these mechanophores are useful for understanding the mechanical properties of an item or a material, they are not well suited for investigating repeated exposure to mechanical stress. To overcome this issue, Georgy Filonenko and Julia Khusnutdinova from OIST’s Coordination Chemistry and Catalysis Unit designed a photoluminescent mechanophore that retains its properties over time and under repeated incidences of mechanical stress. The researchers incorporated this stress-sensing molecule into polyurethane, which is widely used in everyday items such as mattresses and cushions, inflatable boats, car interiors, woodworking glue and even spandex. The scientists then stretched the resulting material with increasing force, triggering a correspondingly brighter glow under an ultraviolet light. This reaction happens within hundreds of milliseconds, resulting in an up to two-fold increase in luminescence intensity. When the mechanical stress stops, the polymer material and the mechanophore revert to their initial position, leading to a drop in intensity. This is critical as it allows for repeated applications of mechanical force. This new mechanophore is a photoluminescent compound from recently published work by Filonenko and Khusnutdinova. Despite its very simple structure, the molecule is extremely responsive to the physical environment, producing the rapid change in luminescence intensity. The researchers incorporated these molecules directly within the repeated patterns of the polymer material. Filonenko and Khusnutdinova found that the high mobility of the mechanophore molecules in the polymer was key to the sensor performance. When the mechanophores could move rapidly in the relaxed polymer sample, the luminescence intensity was low due to these molecular motions preventing the mechanophore from emitting light. Subjecting the material to mechanical force slowed down the polymer chain motions, allowing the mechanophore to emit light more efficiently. “Our material shows how a macroscopic force as basic as stretching a flexible strand of material can efficiently trigger microscopic changes all the way down to isolated molecules,” said Filonenko. This story is adapted from material from OIST, with editorial changes made by Materials Today. The views expressed in this article do not necessarily represent those of Elsevier. Link to original source.


News Article | February 15, 2017
Site: www.eurekalert.org

There are many different structures in our eyes that work in conjunction to allow us to see. These structures are strikingly similar between different species, from zebrafish to humans. The growth of ocular tissues must be tightly controlled in order to maintain the correct eye size and shape that allow us to see. This tight regulation has intrigued developmental biologists for decades. The lens of the eye focuses incoming light on the retina, which then converts the light into electrical signals allowing us to see. Two distinct cell types comprise the lens: epithelial cells, which cover the front, or anterior, portion of the lens, and fiber cells, which populate the back, or posterior, portion. It has been shown that epithelial cells proliferate in the anterior half of the lens and move towards the posterior half, differentiating, or transforming, into fiber cells when they reach the equator between the two halves. In order to elucidate the underlying mechanisms that drive this movement, the Developmental Neurobiology Unit at the Okinawa Institute of Science and Technology Graduate University (OIST), led by Prof. Ichiro Masai, employed time-lapse imaging techniques to observe real time lens development in zebrafish. Their results were recently published in Development. Dr. Toshiaki Mochizuki, along with OIST students Yi-Jyun Luo and Hsieh-Fu Tsai, developed a technique that allowed them to track the movement and development of lens epithelial cells in a live zebrafish embryo in real-time. The researchers used genetically engineered zebrafish that contain two different fluorescent proteins, mCherry-zGem and GFP-histones, that would fluoresce, or emit light to produce a color, at different points in the cell cycle. During the initial G1 phase of the cell cycle, only GFP is expressed, giving the cells a green appearance under a confocal microscope. As the cell then enters the S phase, during which DNA replication occurs, expression of the mCherry-zGem protein begins, changing the color from green to yellow. As the expression of the mCherry-zGem proteins increases in the subsequent G2 and M phases, the color shifts to red and deep red, respectively. Cells that do not enter the cell cycle, and stay in the quiescent G0 phase, never express the mCherry-zGem protein and thus remain green throughout the experiment. The color changes, or lack thereof, effectively allow the scientists to monitor the phases of the cell cycle of each epithelial cell. The OIST researchers then analyzed the time lapse images from the zebrafish lens to reveal that the epithelial cells segregate into dividing cells and non-dividing cells. Dividing cells enter the cell cycle and thus display a change in color, while non-dividing cells remain green throughout the duration of the experiment. The scientists saw that groups of non-dividing cells would move as a cluster in a spiral-like pattern following division of neighboring cells. This division would prompt the non-dividing cells to move towards the equator of the lens, towards differentiation into fiber cells. Additionally, the Developmental Neurobiology Unit discovered that the movement of cells in the lens also appeared to be regulated by two related proteins: E-cadherin, expressed in lens epithelial cells, and N-cadherin, expressed in lens fiber cells. These proteins exert opposite forces on neighboring cells, with E-cadherin exerting a trapping force and N-cadherin exerting a pulling force. Together, E-cadherin and N-cadherin also help regulate cell movement through the modulation of the lens epithelial cells' adhesion and tension. "I'm very proud that our group was able to develop a technique that allowed us to observe these cells in a living zebrafish over a long period of time", explained Masai, "This is the first time that the growth of individual lens epithelial cells has been tracked over such a long period of time. This research has allowed us to determine the factors responsible for the regulation of eye development. Without these factors, correct eye development would not be possible!"


News Article | November 8, 2016
Site: www.eurekalert.org

A little frustration can make life interesting. This is certainly the case in physics, where the presence of competing forces that cannot be satisfied at the same time - known as frustration - can lead to rare material properties. Just as water molecules become more ordered when they cool and freeze into ice crystals, the atoms of magnets become more ordered with decreasing temperature as the tiny magnetic fields or 'spins' of individual atoms start to point in the same direction. So-called 'spin liquids' are the exception to this rule, with spins continuing to fluctuate and point in different directions even at very low temperatures. They offer exciting possibilities for new discoveries in physics. Scientists from the Okinawa Institute of Science and Technology Graduate University (OIST) have modelled a particular spin liquid, showing that disorder can co-exist with order. Three major publications mark the milestones in this field of research. First, Dr. Ludovic Jaubert from OIST's Theory of Quantum Matter Unit worked alongside scientists at University College London and the Ecole Normale Supérieure of Lyon to propose a model for the co-existence of both magnetic order and disorder back in 2014. By simulating what would happen when neutrons are fired at frustrated magnets - so-named because of the strong competition of forces between the spins of individual atoms - Jaubert and colleagues were able to produce brightly-colored neutron-scattering maps. If the spins in the atoms of the material were lining up in an ordered fashion in the magnet you would expect to see spots on the maps known as 'Bragg peaks', whereas with spin liquids you would expect to see bow-tie shapes, called 'pinch points'. To their surprise, the scientists noticed both Bragg peaks and pinch points on their neutron-scattering maps, suggesting that the disordered properties of a spin liquid can simultaneously exist with ordered magnetism. "Spin liquids are paragons of magnetic disorder. It was very exciting to see the characteristic features of a spin liquid in a partially ordered magnet. It is really motivating to think of the fundamental opportunities this offers for our understanding of condensed matter," says Jaubert. The second milestone in this field of research occurred earlier this year, when a publication in Nature Physics showed that the theory of Dr. Jaubert and coworkers held up in experimental observation, using the magnetic material neodymium zirconate (Nd2Zr2O7). "The results of this experiment confirm the theory that Dr. Jaubert presented on the co-existence of magnetic order and disorder in 2014," says Dr. Owen Benton, a former Postdoctoral Scholar in the Theory of Quantum Matter Unit, led by Professor Nic Shannon. However, more work was necessary to link this new experiment to Jaubert's original idea. To uncover how neodymium zirconate could be both ordered and disordered at the same time, Benton set to work on the latest milestone of this research, theorizing an appropriate microscopic model for this magnetic material. Using his model, Benton showed that neodymium zirconate exists in both an ordered and fluctuating state, making it a very unusual kind of magnet. The work also shows that neodymium zirconate is on the edge of becoming a quantum spin liquid - a rare state of matter opening a back door into the quantum world. In a true quantum spin liquid, the spins of a material would not just fluctuate through many different directions as a function of time but would point in many different directions at the same time. "If you could show that there was such a thing as a quantum spin liquid it would be like an example of Schrodinger's cat on a large object," says Benton. Schrodinger's cat is a famous thought experiment in physics in which a cat in a sealed box with a radioactive source is both alive and dead at the same time. Just as the cat exists in multiple states, i.e. alive and dead, simultaneously, this research paves the way for finding real magnets that are in many states at once. "This study also demonstrates that we can get a very complete picture of the physics of neodymium zirconate using a model," says Benton. Further theoretical and experimental research of this and related materials could reveal even more unexpected and exciting phenomena.


News Article | February 21, 2017
Site: www.eurekalert.org

OIST researchers have successfully adapted a parent-training program for ADHD for use with families in Japan, where ADHD-specific behavioral interventions are limited. The results of the proof-of-concept of the new program, the "New Forest Parenting Programme-Japan", published in Japanese Psychological Research, show reductions in children's ADHD symptoms and improvements in parent-child relationships, suggesting that the parent-training program might prove to be an effective mainstream behavioral treatment for ADHD in Japan. International guidelines for the management of ADHD in children recommend approved medications and/or behavioral therapy. Compared with many western countries, Japan has fewer pharmacological and behavioral options. The availability of behavioral therapy is further limited by a shortage of trained specialists. Researchers at the Okinawa Institute of Science and Technology Graduate University (OIST) first recruited Japanese parents of children with ADHD for a pilot study using standard behavioral strategies to see if Japanese parents would be comfortable with the program content, assessment strategies and group delivery of the program. Though the researchers did not specify the gender of the parents, only mothers contacted the researchers to participate in the study and five mothers were recruited for the study. The mothers embraced the group setting, expressing the importance of interacting with other mothers who could understand the challenges of parenting a child with ADHD. However, they articulated a desire to have more information about the causes of ADHD as well as extra practice using behavioral strategies specifically targeting ADHD. In response, the OIST researchers adapted the New Forest Parenting Programme, with the support of the program originators, for use with Japanese parents. "It is important that children with ADHD are rewarded with positive praise after engaging in appropriate behaviors," says Dr. Shizuka Shimabukuro from OIST's Human Development Neurobiology Unit, who is the driving force behind adapting the NFPP for Japanese families. "In general, Japanese parents praise their children more sparingly than Western parents. Overcoming this cultural norm can be challenging for many mothers." Based on the feedback from the pilot study, researchers in OIST's Human Development Neurobiology Unit recruited mothers only for the proof-of-concept study. They modified the programme to replace four general parenting strategy sessions with six sessions that were specifically designed for parents of children with ADHD and also added five extra support sessions to the beginning of the training program to increase mothers' understanding of ADHD and increase their confidence in participating in the parenting program. The researchers then conducted a proof-of-concept study with the new extended program, known as the NFPP-Japan, with 17 Japanese mothers, to assess the effects of the program on child behavior, mothers' well-being and parenting skills. Mothers' reports before and after the program indicated significant reductions in children's ADHD symptoms, reductions in mothers' reactivity to their child's behavioral difficulties and reductions in the stress they experienced in their roles as parents. "Because the results of the study are based on self-reports from the mothers, we cannot rule out that the positive results we saw are due to changes in mothers' perceptions of, or attitudes toward, their child's behavior," says Professor Gail Tripp, head of OIST's Human Development Neurobiology Unit. "Nevertheless, improving the parent-child relationship is an important step in managing ADHD." Future studies of the NFPP-Japan will focus on using objective evaluations of child behavior and the parent child-relationship. A randomized control trial of the NFPP-Japan is currently underway. If the program proves successful, it might eventually become generally available in Japan as an effective treatment for managing symptoms of ADHD.


News Article | February 18, 2017
Site: phys.org

Top: Diacamma ant. Diacamma ants show no physical differences between the worker and reproductive castes, and each individual has the potential to reproduce up to early adulthood. Bottom: Representing the more typical condition, Wasmannia auropunctata queens are surrounded by much smaller worker ants. Differences between queens and workers are fixed in early larval development. Credit: Okinawa Institute of Science and Technology Social insects, such as ants, bees and wasps, display an organizational complexity, called eusociality, where individual members of a colony act more like parts of a whole rather than independent organisms. In their colonies, each individual performs specific tasks based on which caste they belong to: either the reproductive caste or the worker caste. In many species, the reproductive role is determined in early development – by the time they are adults, queens and workers have set roles, complete with distinct appearances and functions. Remarkably, although ants, bees and wasps all evolved eusociality separately, all of their societies display this caste distinction. This begs the question: in these different organisms, have the same, or similar, genes evolved to differentiate social castes? One way to answer this question is to look at exceptions to the general rule. In many ant species, queen ants are much larger than their worker counterparts. However, in some species, such as the native Okinawan Diacamma species, there are few differences in appearance between the worker caste and reproductive caste. These species are called "queenless ants" as a result, though a social hierarchy that includes both reproductive and worker castes exists within their colonies. The lack of physiological differences between the different castes makes Diacamma a particular intriguing ant to study. "Unlike most ant species, where the ability to reproduce is determined during early development, Diacamma display an unusual biology in that every ant has the potential to become part of the reproductive caste until early adulthood," explains Prof. Alexander Mikheyev, leader of the Ecology and Evolution Unit at the Okinawa Institute of Science and Technology Graduate University (OIST). When adult female Diacamma ants first emerge from their pupal case, they have a pair of wing-like structures called gemmae. Every female who retains her gemmae can reproduce, but horrifyingly, the reigning reproductive female, called a gamergate, attacks these young ants and mutilates the gemmae. This violent mutilation prohibits these females from developing ovaries, causing irreversible sterility. The sterile females then become part of the worker caste. However, if no gamergate is present, young females retain their gemmae and become part of the reproductive caste. The scientists wanted to determine how this mutilation affects the ants at the molecular level. To do this, the Ecology and Evolution Unit at OIST collaborated with researchers at the University of the Ryukyus and the University of Tokyo to collect Diacamma colonies from different locations on the island of Okinawa and study their gene expression patterns. In every organism, genes can be turned "on" or "off" depending on how they are regulated. Organisms with identical DNA can have different appearances, abilities, or functionalities based on which genes are turned "on", or expressed. "We wanted to compare gene expression between the mutilated and non-mutilated ants at the same stage in development to see which genes determined caste differentiation." Mikheyev describes, "from there, we could compare the gene expression patterns between different castes in Diacamma ants to those of other species to elucidate the evolutionary origins of eusociality." This research revealed that only a small number of genes differentiated the reproductive caste from the worker caste, primarily in genes related to nutrition. This hints that increased energy requirement of reproduction may be a factor in the evolution of eusociality. Some of these genes have also been found to affect caste determination in other species, such as bees, wasps and other ants, though typically during development. The Ecology and Evolution Unit at OIST plans to use the results, published in Molecular Ecology, from this study to further investigate the evolutionary origins of eusociality. "We are in the process of conducting a follow-up study, comparing developmental profiles of gene expression in ants and honey bees, to explore parallels in how castes repeatedly evolved" says Mikheyev. Explore further: Uncovering the evolution of queen-worker ant differences More information: Yasukazu Okada et al. Social dominance alters nutrition-related gene expression immediately: transcriptomic evidence from a monomorphic queenless ant, Molecular Ecology (2017). DOI: 10.1111/mec.13989


News Article | February 17, 2017
Site: www.eurekalert.org

Social insects, such as ants, bees and wasps, display an organizational complexity, called eusociality, where individual members of a colony act more like parts of a whole rather than independent organisms. In their colonies, each individual performs specific tasks based on which caste they belong to: either the reproductive caste or the worker caste. In many species, the reproductive role is determined in early development - by the time they are adults, queens and workers have set roles, complete with distinct appearances and functions. Remarkably, although ants, bees and wasps all evolved eusociality separately, all of their societies display this caste distinction. This begs the question: in these different organisms, have the same, or similar, genes evolved to differentiate social castes? One way to answer this question is to look at exceptions to the general rule. In many ant species, queen ants are much larger than their worker counterparts. However, in some species, such as the native Okinawan Diacamma species, there are few differences in appearance between the worker caste and reproductive caste. These species are called "queenless ants" as a result, though a social hierarchy that includes both reproductive and worker castes exists within their colonies. The lack of physiological differences between the different castes makes Diacamma a particular intriguing ant to study. "Unlike most ant species, where the ability to reproduce is determined during early development, Diacamma display an unusual biology in that every ant has the potential to become part of the reproductive caste until early adulthood," explains Prof. Alexander Mikheyev, leader of the Ecology and Evolution Unit at the Okinawa Institute of Science and Technology Graduate University (OIST). When adult female Diacamma ants first emerge from their pupal case, they have a pair of wing-like structures called gemmae. Every female who retains her gemmae can reproduce, but horrifyingly, the reigning reproductive female, called a gamergate, attacks these young ants and mutilates the gemmae. This violent mutilation prohibits these females from developing ovaries, causing irreversible sterility. The sterile females then become part of the worker caste. However, if no gamergate is present, young females retain their gemmae and become part of the reproductive caste. The scientists wanted to determine how this mutilation affects the ants at the molecular level. To do this, the Ecology and Evolution Unit at OIST collaborated with researchers at the University of the Ryukyus and the University of Tokyo to collect Diacamma colonies from different locations on the island of Okinawa and study their gene expression patterns. In every organism, genes can be turned "on" or "off" depending on how they are regulated. Organisms with identical DNA can have different appearances, abilities, or functionalities based on which genes are turned "on", or expressed. "We wanted to compare gene expression between the mutilated and non-mutilated ants at the same stage in development to see which genes determined caste differentiation." Mikheyev describes, "from there, we could compare the gene expression patterns between different castes in Diacamma ants to those of other species to elucidate the evolutionary origins of eusociality." This research revealed that only a small number of genes differentiated the reproductive caste from the worker caste, primarily in genes related to nutrition. This hints that increased energy requirement of reproduction may be a factor in the evolution of eusociality. Some of these genes have also been found to affect caste determination in other species, such as bees, wasps and other ants, though typically during development. The Ecology and Evolution Unit at OIST plans to use the results, published in Molecular Ecology, from this study to further investigate the evolutionary origins of eusociality. "We are in the process of conducting a follow-up study, comparing developmental profiles of gene expression in ants and honey bees, to explore parallels in how castes repeatedly evolved" says Mikheyev.


News Article | February 15, 2017
Site: phys.org

A diagram of the zebrafish eye. Left: photograph of the zebrafish eye under a microscope, with the anterior region situated at the top of the photograph and the posterior region at the bottom. Right: diagram of the zebrafish eye lens depicting where the lens epithelial and fiber cells are relative to the rest of the eye. Credit: Prof. Ichiro Masai There are many different structures in our eyes that work in conjunction to allow us to see. These structures are strikingly similar between different species, from zebrafish to humans. The growth of ocular tissues must be tightly controlled in order to maintain the correct eye size and shape that allow us to see. This tight regulation has intrigued developmental biologists for decades. The lens of the eye focuses incoming light on the retina, which then converts the light into electrical signals allowing us to see. Two distinct cell types comprise the lens: epithelial cells, which cover the front, or anterior, portion of the lens, and fiber cells, which populate the back, or posterior, portion. It has been shown that epithelial cells proliferate in the anterior half of the lens and move towards the posterior half, differentiating, or transforming, into fiber cells when they reach the equator between the two halves. In order to elucidate the underlying mechanisms that drive this movement, the Developmental Neurobiology Unit at the Okinawa Institute of Science and Technology Graduate University (OIST), led by Prof. Ichiro Masai, employed time-lapse imaging techniques to observe real time lens development in zebrafish. Their results were recently published in Development. Dr. Toshiaki Mochizuki, along with OIST students Yi-Jyun Luo and Hsieh-Fu Tsai, developed a technique that allowed them to track the movement and development of lens epithelial cells in a live zebrafish embryo in real-time. The researchers used genetically engineered zebrafish that contain two different fluorescent proteins, mCherry-zGem and GFP-histones, that would fluoresce, or emit light to produce a color, at different points in the cell cycle. During the initial G1 phase of the cell cycle, only GFP is expressed, giving the cells a green appearance under a confocal microscope. As the cell then enters the S phase, during which DNA replication occurs, expression of the mCherry-zGem protein begins, changing the color from green to yellow. As the expression of the mCherry-zGem proteins increases in the subsequent G2 and M phases, the color shifts to red and deep red, respectively. Cells that do not enter the cell cycle, and stay in the quiescent G0 phase, never express the mCherry-zGem protein and thus remain green throughout the experiment. The color changes, or lack thereof, effectively allow the scientists to monitor the phases of the cell cycle of each epithelial cell. The OIST researchers then analyzed the time lapse images from the zebrafish lens to reveal that the epithelial cells segregate into dividing cells and non-dividing cells. Dividing cells enter the cell cycle and thus display a change in color, while non-dividing cells remain green throughout the duration of the experiment. The scientists saw that groups of non-dividing cells would move as a cluster in a spiral-like pattern following division of neighboring cells. This division would prompt the non-dividing cells to move towards the equator of the lens, towards differentiation into fiber cells. Additionally, the Developmental Neurobiology Unit discovered that the movement of cells in the lens also appeared to be regulated by two related proteins: E-cadherin, expressed in lens epithelial cells, and N-cadherin, expressed in lens fiber cells. These proteins exert opposite forces on neighboring cells, with E-cadherin exerting a trapping force and N-cadherin exerting a pulling force. Together, E-cadherin and N-cadherin also help regulate cell movement through the modulation of the lens epithelial cells' adhesion and tension. "I'm very proud that our group was able to develop a technique that allowed us to observe these cells in a living zebrafish over a long period of time", explained Masai, "This is the first time that the growth of individual lens epithelial cells has been tracked over such a long period of time. This research has allowed us to determine the factors responsible for the regulation of eye development. Without these factors, correct eye development would not be possible!" Explore further: Shaping the way to see the world


News Article | February 27, 2017
Site: www.eurekalert.org

Chemical compounds that emit light are used in a variety of different materials, from glow-in-the-dark children's toys to LED lights to light-emitting sensors. As the demand for these compounds increases, finding new efficient methods for their production is essential. New research from the Coordination Chemistry and Catalysis Unit at the Okinawa Institute of Science and Technology Graduate University (OIST) describes a new strategy for producing photoluminescent (PL) compounds with increased capabilities. This research was recently published in the Journal of Materials Chemistry C. Production of PL compounds is typically centered around two main methods: the conventional metal-ligand system or an aggregation based system. The first method requires a complex ligand, or compound, that strongly binds to a metal ion in a way that would allow for the complex to emit light of certain wavelength. Unfortunately, this system is rigid and unable to be modified once the complex is produced. In contrast, the aggregation-based system is driven by weak interactions between different molecules or their parts. This allows for tunability by shifting the color of light emitted based on interactions of the PL compound with the local environment. However, aggregation is typically difficult to control and thus not feasible to use in systems requiring precision. Recent research from OIST scientists combines the best parts of both methods to produce PL molecules. "We wanted to create better photoluminescent compounds by combining the two previous concepts: the flexibility of the weak aggregation driven complexes and the controllability of the conventional metal-ligand system", explained Dr. Georgy Filonenko, postdoctoral researcher from the Coordination Chemistry and Catalysis Unit at OIST. Researchers, led by Prof. Julia Khusnutdinova, designed compounds whose photoluminescence depended on weak interactions between atoms within the single compound molecule itself. As a result, they obtained the tunability of the aggregation-based system confined to a single molecule, without the need for intermolecular aggregation. Akin to the conventional metal-ligand system, the molecules synthesized by Filonenko consist of a ligand and a copper ion which interact to produce photoluminescence. However, the ligand in the OIST-synthesized molecules is not rigid and has two cyclic-bonded atom structure, referred to as rings, stacked on top of one another that can interact just like in the aggregation system, but within a single molecule. Interestingly, researchers discovered that they could adjust the color emitted from these molecules based on the distance between these rings. "We found that we could change the color produced by the compound based on what other groups of atoms were bound to the ligand," illuminates Filonenko. "Larger groups would cause the rings to move closer together, shifting the color to the orange-yellow range, while smaller substituents would make the rings move apart, turning the emission color red. The ability to tune the wavelength of light emitted from these molecules provides a huge advantage over the traditional metal-ligand PL complexes". The tunability and controllability of these complexes makes them an attractive candidate for many applications. "We see a high potential for these compounds to be used as sensors due to their very high sensitivity to the surrounding environment," revealed Filonenko.


News Article | February 23, 2017
Site: www.eurekalert.org

New research supports a structure-based classification system for viruses which could help in the identification and treatment of emerging viruses. Professor Robert Sinclair at the Okinawa Institute of Science and Technology Graduate University (OIST) and Professor Dennis Bamford and Dr. Janne Ravantti from the University of Helsinki have found new evidence to support a classification system for viruses based on viral structure. The team developed a new highly-sensitive computational prototype tool, and used it to detect similarities in the genetic code of viruses with similar outer structures, that conventional tools have failed to detect, suggesting that they share a common ancestor. This is not what would have been expected if similarities in the structure of viruses were due to similar environmental pressures - a phenomenon known as convergence. The results, published in the Journal of Virology, suggest that viral structure could provide a means of categorizing viruses with their close relatives - a potentially superior approach to current classification systems. Application of this new structure-based classification system could make it easier to identify and treat newly emerging viruses that cannot easily be classified with existing classification systems. Viruses are notoriously difficult to classify due to their enormous diversity, high rates of change and tendency to exchange genetic material. They challenge the very concept of a clear distinction between the living and the dead, with many characteristics resembling those of living things, but lacking the ability to reproduce themselves, without the help of a host cell. As such, they do not fit neatly into the established biological classification system for cellular organisms. Existing classification systems are imperfect and often lead to very similar viruses being categorized as entirely different entities. These systems are also unable to account for the fact that viruses are constantly changing. If scientists could identify something that viruses are unable to change, it could provide a basis for a more meaningful approach to classification and enable the scientific community to tackle emerging viruses, such as HIV, SARS coronavirus and Zika virus, more easily. Previously observed similarities between the protein shell, or 'capsid', of viruses - that encloses and protects the genetic material - provide a basis for a classification system based on capsid structure, as previously proposed by Prof. Bamford. The few ways in which viruses package themselves are very similar, even between viruses that are likely to have had their common relative more than a billion years ago. Whether this conservation is due to convergence or common descent has been disputed. For a classification system based on virus capsid structure to be meaningful, the amino acids that provide the building blocks of the capsid proteins should be similar in related viruses. A seeming lack of sufficient amino acid sequence similarity picked up by conventional sequence analysis tools previously undermined capsid structure as a viable way to classify viruses. Using ideas from mathematics and computer science, Professor Sinclair from OIST's Mathematical Biology Unit worked with scientists at the University of Helsinki to reinvestigate whether the structure-based classification for viral capsids is in fact supported by previously undetected sequence similarity. "The conventional tools for detecting sequence similarity are very fast but they can miss things," says Professor Sinclair. "We used a more classical approach that takes longer but is much more sensitive." The team developed a computational prototype tool called the 'Helsinki Okinawa Sequence Similarity' or HOSS for short, to detect amino acid sequence similarity in viral coat proteins of icosahedral virus capsids - polyhedral capsids with 20 faces. The team also looked at nucleotide sequence similarity. "By randomly reshuffling the order of amino acids and nucleotides in pairs or triplets of viral sequences, we used statistics to find previously undetected similarities below 17% protein sequence identity, well below what conventional tools are capable of detecting," says Professor Dennis Bamford. The detection of extremely weak similarities in protein and coding sequences by HOSS suggests that viral capsid similarities are due to common descent, not convergence as previously suspected. This may reflect an aspect of viruses that is extremely difficult to change, and hence provide both a viable approach to classification and a potential therapeutic target. "Our work is the first to tie structural lineages to sequences so comprehensively," says Professor Sinclair. The team also demonstrated the power of their method by identifying a candidate capsid gene in the Pandoravirus salinus genome, something which no other team had been able to do. Now that the researchers have shown that there are similarities between viruses that were previously undetected, further work will focus on finding more efficient methods of data extraction, beyond the HOSS prototype. "We have also begun shifting our focus to RNA viruses, of which Zika virus and Ebola virus are examples. The genomes of RNA viruses tend to be more highly variable than DNA viruses, and are therefore even more challenging," says Professor Sinclair. "But with a refined method, it could well be possible."


News Article | February 27, 2017
Site: phys.org

Photoluminescent compounds synthesized by the Coordination Chemistry and Catalysis Unit glowing under a UV light. Credit: Okinawa Institute of Science and Technology Chemical compounds that emit light are used in a variety of different materials, from glow-in-the-dark children's toys to LED lights to light-emitting sensors. As the demand for these compounds increases, finding new efficient methods for their production is essential. New research from the Coordination Chemistry and Catalysis Unit at the Okinawa Institute of Science and Technology Graduate University (OIST) describes a new strategy for producing photoluminescent (PL) compounds with increased capabilities. This research was recently published in the Journal of Materials Chemistry C. Production of PL compounds is typically centered around two main methods: the conventional metal-ligand system or an aggregation based system. The first method requires a complex ligand, or compound, that strongly binds to a metal ion in a way that would allow for the complex to emit light of certain wavelength. Unfortunately, this system is rigid and unable to be modified once the complex is produced. In contrast, the aggregation-based system is driven by weak interactions between different molecules or their parts. This allows for tunability by shifting the color of light emitted based on interactions of the PL compound with the local environment. However, aggregation is typically difficult to control and thus not feasible to use in systems requiring precision. Recent research from OIST scientists combines the best parts of both methods to produce PL molecules. "We wanted to create better photoluminescent compounds by combining the two previous concepts: the flexibility of the weak aggregation driven complexes and the controllability of the conventional metal-ligand system", explained Dr. Georgy Filonenko, postdoctoral researcher from the Coordination Chemistry and Catalysis Unit at OIST. Researchers, led by Prof. Julia Khusnutdinova, designed compounds whose photoluminescence depended on weak interactions between atoms within the single compound molecule itself. As a result, they obtained the tunability of the aggregation-based system confined to a single molecule, without the need for intermolecular aggregation. Akin to the conventional metal-ligand system, the molecules synthesized by Filonenko consist of a ligand and a copper ion which interact to produce photoluminescence. However, the ligand in the OIST-synthesized molecules is not rigid and has two cyclic-bonded atom structure, referred to as rings, stacked on top of one another that can interact just like in the aggregation system, but within a single molecule. Interestingly, researchers discovered that they could adjust the color emitted from these molecules based on the distance between these rings. "We found that we could change the color produced by the compound based on what other groups of atoms were bound to the ligand," illuminates Filonenko. "Larger groups would cause the rings to move closer together, shifting the color to the orange-yellow range, while smaller substituents would make the rings move apart, turning the emission color red. The ability to tune the wavelength of light emitted from these molecules provides a huge advantage over the traditional metal-ligand PL complexes". The tunability and controllability of these complexes makes them an attractive candidate for many applications. "We see a high potential for these compounds to be used as sensors due to their very high sensitivity to the surrounding environment," revealed Filonenko. Prof. Julia Khusnutdinova (left) and Dr. Georgy Filonenko (right) of the Coordination Chemistry and Catalysis Unit at OIST. Credit: Okinawa Institute of Science and Technology More information: G. A. Filonenko et al. Intramolecular non-covalent interactions as a strategy towards controlled photoluminescence in copper() complexes, J. Mater. Chem. C (2017). DOI: 10.1039/C6TC04989C

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