Tag: Tokyo University of Science

Medusavirus, a giant virus, is more closely related to eukaryotic cells than other giant viruses are. In an exciting new study, scientists from Japan have used electron microscopy and time-course analysis to discover four different types of medusavirus particles within and outside infected amoeba cells, representing four different stages of virus maturation. Their results indicate that the medusavirus has a unique maturation process, providing new insights into the structural and behavioral diversity of giant viruses.

Giant viruses represent a unique group of viruses that are similar in size to small bacteria. Medusavirus—a special type of giant virus—was first isolated from a hot spring in Japan. Interestingly, genetic studies showed that medusavirus was more closely related to mature organisms called eukaryotes than to other giant viruses, suggesting that it may hold the key to understanding eukaryotic evolution. Although the details of medusavirus morphology and maturation in infected cells have so far remained elusive, the researchers behind its initial discovery now have some answers.

In a recent study published in Journal of Virology, a team of Japanese scientists led by Prof. Kazuyoshi Murata from the National Institutes of Natural Sciences and Prof. Masaharu Takemura from Tokyo University of Science has revealed, for the first time, a unique four-stage maturation process that the medusavirus undergoes within host cells. Prof. Takemura comments, “From an evolutionary perspective, the medusavirus is extremely interesting, as its replication process and genome are different from those of other viruses. Interestingly, medusavirus also has a unique particle structure. In this study, we wanted to make additional inroads towards elucidating the biology of this virus by characterizing its morphology and maturation process.”

To do this, the researchers used two techniques that allow the high-resolution visualization of viral infection—conventional transmission electron microscopy (C-TEM) and cryo-electron microscopy (cryo-EM). Using these techniques, they observed the detailed particle morphology of medusavirus in infected amoeba cells.

Their first and rather surprising discovery was the presence of four types of medusavirus particles both within and outside the infected host cells. Based on their features, these particles were named pseudo-DNA-empty (p-Empty, i.e., filled with spongy material but no DNA), DNA-empty (Empty, i.e., no spongy material or DNA), semi-DNA-full (s-Full, i.e., half-filled with DNA), and DNA-full (Full, i.e., completely filled with DNA) particles.

Subsequently, they performed time-course analysis, in which the gene expression was measured at several time points during maturation, and discovered that the four types of particles represented four consecutive stages of viral maturation. They found that unlike in other viruses, the viral capsid or shell of medusavirus was produced independently in the host cell’s cytoplasm, while the viral DNA was produced in the nucleus. Further, only empty capsids present near the host nucleus could incorporate viral DNA and become s-Full or DNA-full particles. These findings suggested that the medusavirus had a unique maturation process.

To observe the detailed structure of the four types of medusavirus particles, the team used the cryo-EM technique. They found that all the different particle types had a comparable outer structure, with the presence of three different spikes. The configuration of the capsid shell was also consistent with the structure of the membrane layer within the capsid. However, while s-Full and Full particles showed a complete internal membrane, p-Empty and Empty particles had “open membrane structures,” meaning the membrane had a gap at one end.

“Viruses are smart and can replicate and mature in various ways. Our findings reveal the unique way in which the medusavirus matures. The open membranes we observed in p-Empty and Empty particles were particularly interesting. We believe that the membrane gaps indicate an incompleteness and represent a state in which viral particles have not yet matured. The gaps are likely used to exchange DNA and proteins required for medusavirus maturation and disappear as the virus reaches its final stage,” explains Prof. Takemura.

These new insights not only demonstrate a novel mechanism of particle formation and maturation in medusavirus but also shed light on the great structural and behavioral diversity of giant viruses. They represent a “giant” leap in our knowledge of virus biology and call for further research into giant viruses, which could help answer numerous questions about evolution and infection.

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Reference

Title of original paper: Particle morphology of medusavirus inside and outside the cells reveals a new maturation process of giant viruses

Journal: Journal of Virology

DOI: https://doi.org/10.1128/jvi.01853-21

The fungus-derived compound neoechinulin B demonstrates promising antiviral activity. To realize its potential as an antiviral agent, however, a viable method for preparing more potent derivatives synthetically is necessary. In a recent breakthrough, scientists from Japan designed a simple route for synthesizing neoechinulin B and its derivatives under mild laboratory conditions. Neoechinulin B and six derivatives exhibited excellent antiviral activities against Hepatitis C virus and SARS-CoV-2, the virus responsible for the COVID-19 pandemic.

The solutions to many of humanity’s problems can be found within nature. For instance, who could have guessed that an antibiotic as powerful as penicillin would be found in a common mold, or that the drug aspirin would be derived from the bark of the willow tree?

Research into natural products has become a crucial part of drug discovery. Natural products have exhibited promising specificity and efficacy when used against a variety of pathogens, including viruses. For instance, an organic compound called neoechinulin B, isolated from the fungus Eurotium rubrum, has demonstrated antiviral activity against hepatitis C virus (HCV). However, the isolation of such compounds from natural sources can get quite tedious and expensive. Yet, the attempts to synthetically synthesize it seem to be very scarce.

Thus, a group of scientists from across Japan rose to the occasion and embarked on a mission: To discover a simple route for synthesizing neoechinulin B under laboratory conditions. The team included Prof. Kouji Kuramochi and Dr. Koichi Watashi from Tokyo University of Science, along with Dr. Hirofumi Ohashi, Dr. Shusuke Tomoshige, Dr. Kenji Ohgane, and Dr. Shinji Kamisuki from the National Institute of Infectious Diseases, Tohoku University, Ochanomizu University, and Azabu University, respectively. Their findings were recently published in the Journal of Natural Products.

Commenting on their strategy, Prof. Kuramochi, the lead author of the study, says: “We designed a streamlined two-step synthesis strategy to obtain diketopiperazine scaffold of neoechinulin B. The process involved the base-induced coupling of available piperazine-2,5-dione derivative was aldehydes. The coupled products were then treated with a commercial reagent called tetra-n-butylammonium fluoride (TBAF) which gave us neoechinulin B and its 16 other derivatives.”

To ascertain the efficacy of their products, the team tested the antiviral activity of neoechinulin B and its derivatives against different positive-strand RNA viruses, such as HCV and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). They found that some derivatives showed anti-HCV activity with minimal cell toxicity, while others showed anti-SARS-CoV-2. Moreover, six derivatives exhibited both strong anti-HCV and SARS-CoV-2.

Further studies by the research team uncovered that neoechinulin B and one derivative can reduced the transcriptional activity of liver X receptors (LXRs). This subsequently disrupts the formation of double-membrane vesicles (DMV), which are the sites where viral RNA replication occur. This process results in reduced viral replication in the infected cells.

Along with the 17 active compounds, the scientists also produced three other compounds which, while structurally related to the others, possessed none of the antiviral properties. Further investigation into their molecular structure revealed that inactive compounds were missing the exomethylene moiety which is the key to the antiviral activities of neoechinulin B and its 16 derivatives against HCV and SARS-CoV-2.

The team believes that the insights from this research could be used as a framework for the development of new broad-spectrum antiviral drugs. The study also solidifies the fact that natural products can act as promising lead compounds for the development of antiviral drugs. “The skeleton of neoechinulin B is simple, but only one chemical synthesis method has been reported in the past. Our research presented a simple and viable method for obtaining promising antiviral compounds bringing us one step closer to its practical application,” concludes Prof. Kuramochi.

 

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Reference

Authors: Kota Nishiuchi1, Hirofumi Ohashi1,2,3, Kazane Nishioka1,2, Masako Yamasaki1,2, Masateru Furuta1, Takumi Mashiko1, Shusuke Tomoshige1,4, Kenji Ohgane1,5, Shinji Kamisuki6, Koichi Watashi1,2,3, and Kouji Kuramochi1

Title of original paper: Synthesis and Antiviral Activities of Neoechinulin B and Its Derivatives

Journal: Journal of Natural Products

DOI: https://doi.org/10.1021/acs.jnatprod.1c01120

Affiliations:

1Department of Applied Biological Science, Tokyo University of Science, Japan.

2Department of Virology II, National Institute of Infectious

Diseases, Japan.

3Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Japan.

4Graduate School of Life Sciences, Tohoku University, Japan.

5Department of Chemistry, Ochanomizu University, Japan.

6School of Veterinary Medicine and Center for Human and Animal Symbiosis Science, Azabu University, Japan.

Energy management of commercial buildings is essential from a monetary and environmental perspective. However, unreliable power predictions make estimation of energy consumption in buildings difficult.

While new technologies improve accuracy, they are costly and time-consuming. Addressing this issue, researchers from Japan propose a method for accurately estimating energy consumption of unmonitored facilities using the readings for monitored facilities, outperforming the conventional technique and opening doors to better energy conservation.

Reducing energy consumption in commercial buildings, such as offices, is an important step towards lowering greenhouse gas emissions and achieving carbon-neutral goals. This requires determining the individual energy use of all the operational electrical equipment in the building. However, for large commercial spaces where it is impractical and expensive to install power measurement devices for every electrical facility, this can be difficult task. Instead, using a technology called “disaggregation,” the aggregated power readings of the entire building are broken down to estimate the power consumption of individual electrical facilities.

In most buildings, only the most demanding electrical facilities — such as air conditioners— are typically monitored. Other electrical facilities, such as lighting and electrical appliances, are usually left unmonitored and their operational statuses are estimated assuming a single periodic usage pattern. However, this is a largely oversimplified approach as most buildings have different usage patterns for workdays and holidays. This, in turn, reduces the disaggregation accuracy, and while it can be improved, it involves lengthy procedures and increases management cost.

Now, in a study by researchers from Tokyo University of Science, Japan, and Mitsubishi Electric Corporation, Japan, a disaggregation strategy for providing accurate power estimations with a limited number of monitoring points has been proposed. “The method can accurately estimate and specify the energy consumption of each monitored and unmonitored facility by using the status of the monitored facilities,” say the authors of the study. This paper was made available online on 01 November 2021 and was published in Volume 255 of the journal Energy and Buildings on 15 January 2022.

How exactly does the strategy accomplish this? The authors explain, “The consumption of the unmonitored facilities is estimated using the linear regression residuals of the monitored facilities and clustered with a daily routine. Next, linear basis function models with different diurnal periods are assigned to each cluster to estimate the daily variation in energy consumption of the unmonitored facilities.”

Put simply, the method involves making initial estimations of the unmonitored power consumption based on the total power consumption of the building and the monitored facilities. Based on the estimated power of the unmonitored facilities, these values are clustered. The purpose of the clusters is to reflect possible energy usage scenarios such as weekdays, holidays, and weekends. For each cluster, the daily variations in power consumption are then taken into account and used to estimate the energy consumption patterns for the electrical facilities.

The method was used to disaggregate the power consumption of an eight-story office building consisting of 94 monitored air-conditioners and unmonitored facilities including lightning, office automation equipment, and outlets. The power consumption of the unmonitored facilities was spread between three clusters. Compared to the conventional method that uses a consistent daily routine, the proposed method could apply different daily routines to match the power consumption scenarios of the three clusters. This, in turn, provided more accurate estimations for workdays and holidays than the conventional method.

Notably, the method only requires energy logs collected from the building, allowing accurate power consumption estimations to be made quickly. “The technology will enable commercial building energy-managers to make low-cost as well as highly accurate energy-saving proposals. This could become an indispensable technology for a carbon-neutral society in 2050,” the team adds.

The authors are now working to factor in seasonal trends into their estimations to make them even more accurate and reflect real-world usage. We certainly hope their efforts to build a greener society come to fruition soon.

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Reference

Title of original paper: Power disaggregation in commercial buildings considering unmonitored facilities and multiple routines

Journal: Energy and Buildings

DOI: https://doi.org/10.1016/j.enbuild.2021.111606

SOT-RAM, a promising type of next-generation magnetic memory, could pave the way to ultra-low-power electronics. However, scientists from Tokyo University of Science have identified a source of disturbance during the read operation in SOT-RAMs that compromises their reliability.

Fortunately, they also found a method to greatly reduce this disturbance by slightly modifying the SOT-RAM structure. Their findings will help make this type of memory faster and more reliable, helping its commercialization for sustainable IoT applications.

With the advent of the Internet of Things (IoT) era, many researchers are focused on making most of the technologies involved more sustainable. To reach this target of ‘green IoT,’ some of the building blocks of conventional electronics will have to be improved or radically changed to make them not only faster, but also more energy efficient. In line with this reasoning, many scientists worldwide are currently trying to develop and commercialize a new type of random-access memory (RAM) that will enable ultra-low-power electronics: magnetic RAMs.

Each memory cell in a magnetic RAM stores either a ‘1’ or a ‘0’ depending on whether the magnetic orientation of two magnetic layers are equal or opposite to each other. Various types of magnetic RAM exist, and they mainly differ in how they modify the magnetic orientation of the magnetic layers when writing to a memory cell. In particular, spin injection torque RAM, or STT-RAM, is one type of magnetic memory that is already being commercialized. However, to achieve even lower write currents and higher reliability, a new type of magnetic memory called spin orbit torque RAM (SOT-RAM), is being actively researched.

In SOT-RAM, by leveraging spin-orbit interactions, the write current can be immensely reduced, which lowers power consumption. Moreover, since the memory readout and write current paths are different, researchers initially thought that the potential disturbances on the stored values would also be small when either reading or writing. Unfortunately, this turned out not to be the case.

In 2017, in a study led by Professor Takayuki Kawahara of Tokyo University of Science, Japan, researchers reported that SOT-RAMs face an additional source of disturbance when reading a stored value. In conventional SOT-RAMs, the readout current actually shares part of the path of the write current. When reading a value, the readout operation generates unbalanced spin currents due to the Spin Hall effect. This can unintentionally flip the stored bit if the effect is large enough, making reading in SOT-RAMs less reliable.

To address this problem, Prof. Kawahara and colleagues conducted another study, which was recently published in IEEE Transactions on Magnetics. The team came up with a new reading method for SOT-RAMs that can nullify this new source of readout disturbance. In short, their idea is to alter the original SOT-RAM structure to create a bi-directional read path. When reading a value, the read current flows out of the magnetic layers in two opposite directions simultaneously. In turn, the disturbances produced by the spin currents generated on each side end up cancelling each other out. An explainer video on the same topic can be watched here: https://youtu.be/Gbz4rDOs4yQ.

In addition to cementing the theory behind this new source of readout disturbance, the researchers conducted a series of simulations to verify the effectiveness of their proposed method. They tested three different types of ferromagnetic materials for the magnetic layers and various device shapes. The results were very favorable, as Prof. Kawahara remarks: “We confirmed that the proposed method reduces the readout disturbance by at least 10 times for all material parameters and device geometries compared with the conventional read path in SOT-RAM.”

To top things off, the research team checked the performance of their method in the type of realistic array structure that would be used in an actual SOT-RAM. This test is important because the read paths in an array structure would not be perfectly balanced depending on each memory cell’s position. The results show that a sufficient readout disturbance reduction is possible even when connecting about 1,000 memory cells together. The team is now working towards improving their method to reach a higher number of integrated cells.

This study could pave the way toward a new era in low-power electronics, from personal computers and portable devices to large-scale servers. Satisfied with what they have achieved, Prof. Kawahara remarks: “We expect next-generation SOT-RAMs to employ write currents an order of magnitude lower than current STT-RAMs, resulting in significant power savings. The results of our work will help solve one of the inherent problems of SOT-RAMs, which will be essential for their commercialization.” Make sure to stay tuned for the next advances in magnetic memories, and let’s hope a green IoT world is not too far away!

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Reference

Title of original paper: Examination of Magnetization Switching Behavior by Bi-directional Read of Spin-orbit-torque MRAM

Journal: IEEE Transactions on Magnetics

DOI: https://doi.org/10.1109/TMAG.2022.3154025

Sugar chains confer functionality to many organic molecules in glycosides. Enzymes like glycosyltransferases catalyze the synthesis of these chains in various biological systems.

However, the commercial production of carbohydrate chains involving enzymes that are associated with β-1,2-glucan, a polysaccharide, poses technical challenges. Now researchers from Tokyo University of Science and Niigata University have been able to structurally and functionally identify a novel enzyme that catalyzes the easy formation of glycosidic bonds in β-1,2-glucooligosaccharide glycosides.

Carbohydrate chains play physiologically relevant roles. For instance, many biologically important proteins and lipids inside our body have carbohydrate chains attached to them. These “sugar” chains, in fact, even play key roles in altering the functions of organic molecules like aromatic compounds to which they are commonly attached. It is a known fact that these carbohydrate structures can alter the functions of compounds bound to them. The biological synthesis of these chains occurs via biochemical reactions that are catalyzed by enzymes such as glycosyltransferases. However, the commercial production of carbohydrate chains poses several technical challenges.

A group of collaborating researchers from the Tokyo University of Science and Niigata University have now been able to determine the structure and activity of a novel enzyme exhibiting glycosyltransferase activity. The results of this study were made available online on January 19, 2022 and published in Volume 298, Issue 3 of the Journal of Biological Chemistry.

Dr. Masahiro Nakajima, Associate Professor at Tokyo University of Science and senior author of the study explains, “The structures and functions of enzymes that synthesize and degrade carbohydrate chains have become extensively diversified through molecular evolution. To date, various kinds of enzymes related to carbohydrates have been found and added to the Carbohydrate-Active enZYmes or CAZy database. This database classifies these enzymes, called CAZymes, into families mainly based on their amino acid sequences and is now expanding. However, obtaining carbohydrates is often difficult because of their rarity or inhomogeneity in nature, which limits the exploration of novel enzymes.”

The polysaccharide β-1,2-glucan is a homopolymer comprising β-1,2-linked glucose units. This carbohydrate cannot be easily obtained in commercially viable quantities from natural resources using any of the known experimental techniques. Although β-1,2-glucans are involved in bacterial infection, hypo-osmotic adaptation, and iron storage, their precise mechanism of action remains elusive; largely limited by their non-availability. This non-availability stems from the paucity of research on the enzymes that are associated with β-1,2-glucan metabolism.

The enzyme endo-β-1,2-glucanase is involved in the metabolism of β-1,2-glucan. Using advanced structure determination and biochemical characterization techniques, including mutagenesis and estimation of reactions rates, the research team has identified the biochemical function of a novel β-1,2-glucan-associated enzyme.

Dr. Nakajima muses, “We have discovered an enzyme that performs a novel chemical reaction. Our newly discovered mechanism of action has paved the way for the synthesis of sugar chains that were incredibly difficult to synthesize. Although several glycans are involved in biologically important roles, there are many whose functions cannot be fully understood owing to low reaction yields. We believe that this discovery has expanded the possibilities for the successful development and use of sugar chains.”

The IALB_1185 protein (IaSGT), encoded in the gene cluster that codes for endo-β-1,2-glucanase homologs, is listed as a “glycoside hydrolase” family 35 (GH35) protein. However, contrary to expectations, the team noticed that IaSGT is in fact a “glycosyltransferase” acting on the β-1,2-glucosidic bonds. This was a novel catalytic activity demonstrated by the protein. Whereas glycoside hydrolases catalyze the breakage or hydrolysis of glycosidic bonds, a chemical reaction that involves water, glycosyltransferases do the exact opposite—they catalyze the formation of these bonds. Based on these findings, the team proposes “β-1,2-glucooligosaccharide:D-glucoside β-D-glucosyltransferase” as a systematic name and “β-1,2-glucosyltransferase” as an accepted name for IALB_1185.

Dr. Hiroyuki Nakai, Associate Professor at Niigata University and lead collaborator of the study, comments, “Glycosyltransfer reactions are useful for oligosaccharide synthesis, but glycosyltransferases in glycoside hydrolase families share their reaction mechanisms with glycoside hydrolases. Therefore, we need a complete comprehension of their reaction mechanism to control conversion between transferases and hydrolases freely. Our findings are important biochemical data for understanding the diversity of CAZymes and a fundamental structural basis for further investigation of the profound enigma of the reaction mechanisms of CAZymes.”

The research community surely hopes that the newly discovered and functionally characterized enzyme will accelerate the synthesis of carbohydrate chains that play key roles in various biological processes. Sweet news, indeed!

Reference

Title of original paper: Characterization and structural analyses of a novel glycosyltransferase acting on the β-1,2-glucosidic linkages

Journal: Journal of Biological Chemistry

DOI: https://doi.org/10.1016/j.jbc.2022.101606

In a discovery important for agriculture and food safety, scientists report the genetic regulation of a model plant’s immune response

The mechanism of plant defense mediated by the non-expressor of pathogenesis-related (NPR) genes in monocots (plants having a single embryonic leaf) is not well-documented. Now, scientists from Tokyo University of Science have discovered how the NPR family of genes regulate immune responses in the model monocot Brachypodium distachyon. These findings provide a blueprint for plants’ defense systems and might contribute to more research towards resilient crop species, boosting pesticide-free cereal crop cultivation.

Plants can be largely divided into dicotyledonous and monocotyledonous ones. These groups, apart from differing in their embryonic structure, have numerous other distinguishing factors. Which is why, it’s quite possible that their immune responses to certain threats would be different as well.

Immune responses in plants? Leaves you confused?

Well, though their immune systems are structured and function much differently than ours, plants, like humans, do respond to external threat. These immune responses have been studied extensively in dicot models, but lesser so in monocots.

The non-expressor of pathogenesis-related (NPR) family of genes are known to control defensive signaling during a pathogen attack. In Arabidopsis thaliana, a dicot, NPR1 (AtNPR1) serves as a binding site for salicylic acid (SA) and interacts with the TGA group of transcription factors (TFs)–which are responsible for turning genes ‘on’ or ‘off’ as needed. This activates defense genes, such as pathogenesis-related protein 1 (PR-1), which ultimately control the plant’s immunological response.

Does this happen in monocots as well? A research team, led by Prof. Gen-ichiro Arimura from Tokyo University of Science in Japan decided to find out.

They knew that some monocots, like rice and wheat, display a similar NPR1-mediated immune response on facing a pathogen attack. However, the team believed that other monocots may respond differently, and also wanted to investigate other NPRs, such as AtNPR3/AtNPR4, which might have the opposite effect of NPR1. Hence, Prof. Arimura and his colleagues chose to investigate NPR function and immune response in the model monocot Brachypodium distachyon, often known as the southern duckweed.

Their study, which was published in The Plant Journal, explains how NPR genes in B. distachyon regulate TGA-promoted transcription of defense-responsive genes.

The researchers first identified and cloned sequences of monocot B. distachyon’s NPR genes–BdNPR1, 2, and 3–which were similar to the NPR sequences of other dicot species, including Arabidopsis. On methyl salicylate treatment, the expression of BdNPR2 rose significantly, but not BdNPR1/BdNPR3, indicating its positive role in plant defense response. The researchers also confirmed that one of the BdNPRs (BdNPR2) activated BdTGA-1 in B. distachyon (just like other plants), by observing gene expression and molecular interactions in B. distachyon protoplasts.

These experiments revealed that BdTGA1 and BdNPR2 interacted with each other to upregulate PR-1 expression, thereby cementing the role of NPR2 in B. distachyon’s immune response.

Was this response mediated by SA? Another pertinent question, which the team answered by creating a created a mutant NPR2 gene. Prof. Arimura points out: “Certain amino acid residues–especially those of arginine (Arg)–are responsible for SA binding in Arabidopsis NPRs. So, our mutant NPR2 was missing a specific arginine residue–Arg468.”
This mutant was less effective than the normal wild-type NPR2 at increasing PR-1 expression, implying that Arg468 was critical for SA binding on NPR2, which, in turn, upregulated PR-1.

Interestingly, their experimental assays also found that BdNPR1 suppressed this upregulation, suggesting its role as an immune inhibitor in B. distachyon.

Prof. Arimura sums it all up for us. “When the plant is in a healthy state, BdNPR1 may stop BdNPR2 from activating BdTGA1, keeping the PR1 gene turned off. But when the plant is attacked by a pathogen, SA levels rise and stimulate BdNRP2 expression, which then cascades, and ‘turns on’ the PR1 gene.”

Surprised by how functionally unique BdNRP2 is, Prof. Arimura explains that the “sequence similarities between NPR2 from B. distachyon and other plants does not affect their functions which are distinctively different for every plant species.”

But how does this genetic research translate into real-life applications?
Many important crops, such as wheat and rice, are monocots. These plants, which are susceptible to microbial pathogens and pests, are treated with pesticides to avoid damage. The pesticides then cause environmental degradation. “This vicious cycle can be broken by understanding monocots’ defense systems, and addressing their susceptibility in a more sustainable way, with pesticide-free cultivation,” says Prof. Arimura, who hopes this research will be used to further plant biotechnology. It puts us one step closer to resolving the global environment and food security issues, allowing us to work towards a more sustainable society. Indeed, a ‘green solution for a green problem’!

Reference

Title of original paper: Immune gene activation by NPR and TGA transcriptional regulators in the model monocot Brachypodium distachyon

Journal: The Plant Journal

DOI: https://doi.org/10.1111/tpj.15681

Lignin, a chief component of cell walls in plants, is naturally degraded in the soil. Identifying new microorganisms involved in this degradation can help develop novel lignin breakdown processes in industrial settings.

Now, researchers from Tokyo University of Science have isolated 8 microorganisms that degrade the lignin model compound 2-phenoxyacetophenone (2-PAP). They found that one of these microbes uses a new, unidentified enzyme to cleave the ether-bonds in 2-PAP, resulting in the formation of phenol and benzoate.

Like all known life forms, plants have a body made of organic matter, including cell walls made of various components including lignin, a heterogenous polymer. Lignin is the second-most abundant organic substance on earth with great potential in the production of industrial chemicals, such as aromatic compounds.

Chemically, lignin is made up of multiple subunits linked by ‘ether’ and ‘carbon-carbon’ bonds, all of which need to be broken down for lignin decay. It is well known that microorganisms cleave ether bonds effectively through the production of extracellular enzymes, which aid in lignin degradation. Two microbes that perform this degradation were identified: white-rot fungi through the production of peroxidases and laccases and Sphingomonad bacteria with the help of intracellular enzymes.

These discoveries sparked curiosity among a team of researchers including Dr. Toshiki Furuya and Ms. Saki Oya from Tokyo University of Science, and Dr. Hiroshi Habe from National Institute of Advanced Industrial Science and Technology in Tokyo, on whether there are additional, unknown microorganisms that degrade lignin through different enzymes.

Identifying these microorganisms and finding out how they degrade lignin could enhance the overall understanding of the carbon cycle and facilitate the biotechnological applications of these microorganisms for lignin commercialization. The team also realized that none of the previous studies have focused on how microorganisms transform or degrade 2-PAP.

To find an answer to these questions, Dr. Furuya and his team conducted a study, published in Scientific Reports to screen microorganisms that utilize new ether-bond cleaving enzymes, to transform 2-PAP. The team initially used a direct screening method to isolate microorganisms from soil based on their ether-bond cleaving activity, by growing them on a medium containing humic acid, a soil-derived organic compound, as a carbon source. Next, they incubated the isolated microorganisms with 2-PAP to check specifically for 2-PAP ether bond-cleaving activity. The bond cleaving activity was confirmed depending on the presence of phenol, which is generally produced as a result of ether-bond cleavage.

This led to the isolation of not one, but eight 2-PAP–transforming microorganisms! These included 7 bacteria from the genus Acinetobacter, Cupriavidus, Nocardioides, and Streptomyces, and 1 fungus from the genus Penicillium. “To our knowledge, these are the first microorganisms demonstrated to cleave the ether bond of 2-PAP”, Dr. Furuya emphasized, when asked about these discoveries.

Among the isolated microorganisms, the team examined a gram-negative bacterium, Acinetobacter sp. TUS-SO1 in detail and discovered that it selectively and oxidatively cleaves ether bonds in 2-PAP, to produce phenol and benzoate. This was especially surprising, because β-etherase, a well-studied enzyme known to perform this cleaving, gives phenol and acetophenone. This implies that this bacterial strain cleaves the ether-bond of 2-PAP using an unidentified enzyme!

When asked about the implications of these findings, Dr. Furuya says, “These newly identified microorganisms might play important roles in the degradation of lignin-based compounds in nature. By clarifying the properties of these microorganisms, we can apply them to lignin-based compounds for the generation of aromatic compounds, as an alternative to petroleum. Moreover, they can be utilized for lignin valorization, especially for the conversion of low-molecular-weight compounds that have chemical structures similar to 2-PAP”.

How is the technique for the identification of lignin-degrading microorganisms useful in the long-run? Well, according to the authors, this established search technology can be widely applied to search for microorganisms that exhibit cleavage activity against other ether compounds, such as environmental pollutants.

These discoveries are indeed exciting and can lead to the developments not just in industries that use lignin, but also in mitigating the effects of environmental pollutants!

DOI: 10.1038/s41598-022-06816-1

Scientists have developed a simple strategy to enhance the structural properties of coordination nanosheets by mixing two metal ion solutions together, using a powerful organic ligand.

Coordination nanosheets are emerging 2D materials with a wide range of applications. However, highly crystalline nanosheets are difficult to synthesize through solution-based approaches. In a recent study, scientists found a simple strategy to improve the structural order and performance of nanosheet films by using two different metal ions instead of one. Their findings highlight a solution for the development of high-quality coordination nanosheets with superior crystallinity and conductivity.

Coordination nanosheets are a new and emerging class of two-dimensional materials, rapidly gaining importance in the field of nanomaterials. They consist of metal ions and organic ligand molecules, linked to each other to form one framework, via coordination bonds. These nanosheets act as building blocks, which can be mixed and matched to produce a large variety of planar structures, with potential applications in electronic devices, batteries, and catalytic systems.

In 2013, benzenehexathiolato (BHT) was discovered as a powerful organic ligand in coordination nanosheets. It was observed that upon changing the element used in the metal centers, it is possible to create BHT-based nanosheets with vastly different structural properties.

However, the synthesis of BHT-based coordination nanosheets via solution-based processes has proven challenging, which is rather unfortunate due to the economic viability and scalability of such approaches. The resultant nanosheets lack crystallinity, indicating the formation of small crystalline domains with poor orientation control. These structural shortcomings hinder the nanosheet’s performance and limit scientists from studying the nanosheet’s structure-property relationships.

Now, a team of researchers led by Professor Hiroshi Nishihara of Tokyo University of Science (TUS) Japan, has investigated whether BHT-based coordination nanosheets developed by the introduction of two metal ions could overcome the aforementioned challenges, in a new study, published in Advanced Materials, funded by Japan Science and Technology Agency, Japan Society for the Promotion of Science and the White Rock Foundation. To do so, the team, which also included Dr. Ryojun Toyoda and Dr. Naoya Fukui from TUS, and Professor Henning Sirringhaus from the University of Cambridge, and Professor Sono Sasaki from Kyoto Institute of Technology, prepared heterometallic nanosheet films at a liquid-liquid interface, by changing the mixing ratio of two metal ions – copper (Cu) and nickel (Ni), in an aqueous solution. Simply put, they poured an aqueous solution containing these two metal ions onto an organic solution containing a BHT precursor.

To their surprise, they found that a new structural phase had formed at the interface between the two phases, with intermediate ratios of nickel and copper. Moreover, they found that this NiCu2BHT film possessed much higher crystallinity than pure copper and nickel films!

Dr. Nishihara and team were especially excited with these findings, because such an approach normally yields nanosheets with poor crystallinity.

“Our results indicate that the nanosheets grow in a specific direction and with a fixed composition, NiCu2BHT, at the liquid–liquid interface when the two metal ions are mixed at an appropriate ratio,” explains Prof. Nishihara. “It is extraordinary that such simple mixing of different metal ions resulted in a unique structure with 2D periodicity and enhanced crystallinity, even in relatively thick films,” he adds.

With an increase in crystallinity, notable improvements were also observed in the performance of these heterometallic nanosheets. Electrical conductivity measurements together with the analysis of film morphology via electron microscopy techniques revealed that these films have lower activation energies and higher conductivities than copper films. In fact, researchers observed conductivities of up to 1300 S/cm with a dependency on temperature similar to that of good metal conductors. These observations are remarkable since such values are among the highest to be observed for 2D coordination nanosheets!

Finally, the team analyzed the underlying mechanisms that led to this improvement in crystalline order and suggested that NiCu2BHT films may naturally arrange themselves into a bilayer structure that releases the structural strain of the material.

“It is reasonable to assume that a bilayer structure is a more favorable structural phase for heterometallic BHT-based coordination nanosheets, rather than the distorted structures of the corresponding homometallic films. Overall, our findings open a powerful new pathway to improve the crystallinity and tuning of the functional properties of highly conducting coordination nanosheets for a wide range of device applications.” says Dr. Nishihara, while discussing his findings.

Let us hope this newfound approach helps researchers reap the many benefits of coordination nanosheets!

Titles of original paper: Heterometallic Benzenehexathiolato Coordination Nanosheets: Periodic Structure Improves Crystallinity and Electrical Conductivity

Journal: Advanced Materials

DOI: https://doi.org/10.1002/adma.202106204

Nanomaterials have revolutionized the world of cancer therapy, and plant-derived nanoparticles have the added advantage of being cost-effective and easy to mass produce.

Researchers from Tokyo University of Science have recently developed novel corn-derived bionanoparticles for targeting cancer cells directly, via an immune mechanism. The results are encouraging, and the technique has demonstrated efficacy in treating tumor-bearing laboratory mice. Moreover, no serious adverse effects have been reported in mice so far.

Nanoparticles, or particles whose size varies between 1 and 100 nanometers, have shown tremendous potential in many areas of science and technology, including therapeutics. However, conventional, synthetic nanoparticles are complicated and expensive to produce. Extracellular vesicles (EVs), which have emerged as an alternative option to synthetic nanoparticles, show challenges for mass production.

Another recently emerging option is that of plant-derived nanoparticles (NPs), which can be easily produced in high levels at relatively lower costs. Like EVs, these nanoparticle-based systems also contain bioactive molecules, including polyphenols (which are known antioxidants) and microRNA, and they can deliver drugs to target organs in our bodies.

Leveraging this knowledge, researchers from the Tokyo University of Science (TUS) recently developed bionanoparticles with anticancer activity, using corn (maize) as the raw material.

Prof. Makiya Nishikawa of Tokyo University of Science, Japan, who led the research team in this endeavor, elucidates, “By controlling the physicochemical properties of nanoparticles, we can control their pharmacokinetics in the body; so, we wanted to explore the nanoparticulation of edible plants. Maize, or corn, is produced in large quantities worldwide in its native form as well as in its genetically modified forms. That is why we selected it for our study.” The results of this study were published online on 24 November 2021 in Scientific Reports.

The team created a homogeneous mixture of super sweet corn in water, then centrifuged this corn juice at a high speed, subsequently filtering it through a syringe filter with a pore size of 0.45 μm. The filtered samples were then ultracentrifuged to obtain NPs derived from corn. The corn-derived NPs (cNPs) were approximately 80 nm in diameter. Quite interestingly, these cNPs also carried a tiny net negative charge of −17 mV.

The research team then set up experiments to see whether these cNPs were being taken up by various types of cells. In a series of promising results, the cNPs were taken up by multiple types of cells, including the clinically relevant colon26 tumor cells (cancer cells derived from mice), RAW264.7 macrophage-like cells, and normal NIH3T3 cells. RAW264.7 cells are commonly used as in vitro screens for immunomodulators—drugs that primarily target various cancer pathways.

The results were astounding: of the three types of cells, cNPs only significantly inhibited the growth of colon26 cells, indicating their selectivity for carcinogenic cell lines. Moreover, cNPs were able to successfully induce the release of tumor necrosis factor-α (TNF-α) from RAW264.7 cells. It is a well-documented fact that TNFα is primarily secreted by macrophages, natural killer cells, and lymphocytes—three key ingredients of our highly evolved immune system and which help mount an anticancer response.

“The strong TNFα response was encouraging and indicated the role of cNPs in treating various types of cancer,” explains Dr. Daisuke Sasaki, first author of the study and an instructor and researcher at TUS.

The research team then conducted a reporter assay with the enzyme “luciferase” (derived from fireflies), which is a sensitive reporter for studying various biological responses. This luciferase-based assay revealed that the potent combination of cNPs and RAW264.7 cells significantly suppressed the proliferation of colon26 cells.

Finally, the research team studied the effect of cNPs on laboratory mice bearing subcutaneous tumors. Once again, the results were astonishing: injecting cNPs into colon26 tumors on a daily basis significantly suppressed tumor growth, without causing serious side effects, or weight loss.

“By optimizing nanoparticle properties and by combining them with anticancer drugs, we hope to devise safe and efficacious drugs for various cancers,” observes an optimistic Prof. Nishikawa.

Summarizing these impactful findings, Dr. Kosuke Kusamori, co-author and assistant professor at TUS says, “These cNPs exhibit excellent anti-tumor properties, are easy to develop, and are economically viable. Moreover, they do not exhibit any serious adverse effects, at least in mice so far!”

Indeed, this could be the anti-cancer therapy of tomorrow; TUS has made a truly a-maize-ing discovery!

DOI: https://doi.org/10.1038/s41598-021-02241-y