Faculty of Agriculture | Okayama University / 2021-06-24 /agr/research_highlights.php?id=20 Source: Okayama University (JAPAN), Public Relations Division For immediate release: 23 June 2021 Okayama University research: Meeting high demand: Increasing the efficiency of antiviral drug production in bacteria. (Okayama, 23 June) In a study published in the journal Bioscience, Biotechnology, and Biochemistry, researchers from Okayama University induce mutations in a bacterial strain to increase the production of an antiviral chemical it secretes. The COVID-19 pandemic has shed light on the need for antiviral drugs which are effective in suppressing viruses. Sinefungin is one such antibiotic produced by the bacteria Streptomyces incarnatus NRRL8089 (S. incarnatus) and has shown efficacy against multiple viruses including the SARS coronavirus. However, to understand its full potential in clinical studies large quantities of the compound are required. Now, Professor TAMURA Takashi and his Okayama University research team have found a way to increase to triple the production efficiency of sinefungin by inducing multiple mutations in S. incarnatus. For more information, please refer to the following URL. http://www.okayama-u.ac.jp/eng/research_highlights/index_id137.html 2021-06-23 /agr/research_highlights.php?id=18 Release Subtitle: Scientists explore geographical variation in the biological clock of a new model organism, the Japanese red flour beetle Release Summary Text: Biological clocks are ubiquitous in living organisms and govern their behavioral pattern, from sleep-wake cycle to reproduction. Although they are well-understood, how they differ based on geographic location is unclear. In a new study, scientists from Japan report variations in the biological clocks of red flour beetles across the country, offering new insights into how they work. Full text of release: One of the most intriguing features in all living beings is the “biological clock”, an internal time-keeping mechanism that governs our behavioral pattern (such as the sleep-wake cycle). In fact, the biological clock dictates the developmental timing of various processes, such as when flowers bloom and insects reproduce. Biologists refer to these activities collectively as “circadian rhythms,” owing to the rhythmic pattern in which they occur. Since their discovery, circadian rhythms have been studied extensively, and today we know a great deal about how they work. But, it is still not understood why, in some species, these rhythmic traits can vary based on geographical location (also called “cline”). While studies focusing on the relationship between the strength of “amplitude” of the rhythm (time variation in the level of a particular measure, such as activity level) and latitude (variation between north and south) have been conducted in fruit flies, the findings are contradictory. In a new study published in PLoS One, scientists in Japan, led by Prof. Takahisa Miyatake from Okayama University, decided to explore the problem using a new biological model: the red flour beetle, a common insect found throughout Japan. He explains, “Organisms living in northern and southern countries should have different rhythm traits and it would be interesting to know why these differences exist. We came up with the idea that such geographical variation in traits could be easily studied in the red flour beetle, which can be collected in a wide range of latitudes from all over the country.” Accordingly, the scientists collected more than 35 places of the red flour beetles from 37 rice mills in different parts of Japan and nurtured them under laboratory conditions emulating their natural environment. After an initial nurturing period of 20 days, they assessed the circadian rhythm of individual beetles (more than 1500 samples) by monitoring their locomotor activity (movement) for 10 days. The findings showed that the rhythm strength decreased with increasing latitude such that beetles from the northern parts showed weaker circadian rhythms than their southern counterparts. However, changing longitudes (east to west) showed no significant difference. Interestingly enough, despite the large sample size, they did not observe any variation in the rhythm period with latitude or longitude, which contradicted the findings of previous studies. The scientists ascribed the weaker rhythmic amplitude at higher altitudes to its more extreme and harsh environments, which possibly had more influence on the beetle’s behavior than its biological clock. As for the unchanging rhythm period with location, they speculated that the flow of genetic material from one beetle population to another was likely more than hypothesized, thus washing out their genetic differences and leading to uniform rhythm periods. Prof. Miyatake is excited by these findings and their possible implications. He concludes, “Many insects are expanding their distribution areas to the north due to global warming, and the nature of their circadian rhythms may change accordingly. We may be able to open up a new research field to see if the nature of variation in the biological clock of insects is also applicable to humans!” Does this mean our bodies might be working in a certain way depending on our location? We don’t entirely know yet, but hopefully, future studies will reveal a lot more. Release URL: https://www.eurekalert.org/pub_releases/2021-02/ou-hld021821.php[New window] Reference: Title of original paper: Amplitude of circadian rhythms becomes weaken in the north, but there is no cline in the period of rhythm in a beetle Journal: PLoS One DOI: http://dx.doi.org/10.1371/journal.pone.0245115 Contact Person: MIYATAKE Takahisa Dr. Takahisa Miyatake is a Professor at the Graduate School of Environmental and Life Science at Okayama University, Japan. His research areas include evolutionary ecology, insect behavior, applied entomology, and ethology. As a senior researcher and professor, he has more than 200 publications to his credit with over 4,000 citations. He also received the Hidaka Prize from Japan Ethological Society in 2016. 2021-02-18 /agr/research_highlights.php?id=16 Release Subtitle: Scientists use a deep learning approach to look at internal diseases in persimmon fruits, but with a different perspective Release Summary Text: Scientists from Japan have used a ‘feature visualization’ based explanatory deep learning approach to diagnose symptoms of “hetasuki” disorder in persimmon fruit, that have long eluded even professionals. In their latest paper, based on the relevant features detected by the artificial intelligence, they recommend uneven coloring patterns as a possible indication of disorder. These findings showcase a novel use for deep neural networks in plant physiology. Full text of release: While originally modeled on the human brain, deep neural networks (DNNs) today can surpass our capabilities in many activities; a DNN model named ResNet50, for instance, has been shown to classify images better than a human eye. Consequently, DNNs have been deployed for activities that would otherwise require a trained human eyesight, such as identifying symptoms of diseases in plants or telling moss species apart. But what about identifying disorders that present no apparent symptoms (such as an internal damage)? Till now, DNNs have found little use in such cases. A possible reason might be that until recently, DNNs have largely been a “black box” that only makes predictions but doesn’t tell you how they are made. This meant having no information on what regions of the image contributed to the prediction; one couldn’t tell if DNNs would provide any insight that couldn’t be discerned by a trained professional. Fortunately, various feature visualization methods are now available that can significantly alleviate the “black box” situation, telling us if DNNs can see things a “professional eye” cannot. In a new study published in Plant & Cell Physiology, scientists from Japan decided to employ DNNs for diagnosing an internal disorder in persimmon fruits called “hetasuki” ( Japanese for “calyx-end cracking”) signified by appearance of cracks around the calyx (leafy part on top of the fruit). “Hetasuki has been well classified into five grades; the higher degrees not only visually spoil the fruit quality, but often become a trigger of quick softening. However, no clear outer symptoms or biomarkers have yet been identified. Moreover, only very few experts with decades of experience in persimmon cultivation can identify hetasuki from its external appearance. We, therefore, wanted to examine the utility of DNN for diagnosis of internal reactions in fruit,” explains Associate Professor Takashi Akagi from Okayama University, who led the study. The scientists collected a total of 3,173 colored images of the fruit apex and fed them into pre-trained DNNs for a binary (positive or negative) classification between different pairs of cracking levels. They chose five different DNN models for the classification and compared their performance against one another. To visualize the relevant image regions for the diagnosis, they applied feature visualization methods on the relatively simpler VGG16 model and compared their outcomes. The team found that all the five DNN models performed well in classifying the fruits for the level pairs considered except for the pair 0-3 vs. 4, which they attributed to a severe imbalance of samples (level 0-3 occupied >98% of the samples). Among the models, InceptionResNetV2 showed the highest accuracy (>90%); however, due to its highly complicated layer structure, scientists chose VGG16 for feature visualization. Nevertheless, the relevant regions were often inconsistent among the applied methods. However, looking at the distribution of relevance values as a function of distance from the outer contour of fruit, the relevance regions were located either around the apex or close to the periphery of the fruit. Interestingly, while the relevance of periphery can be explained based on uneven coloring observed in cracked fruits, that of the apex has no such visual guide and is therefore a feature picked up only by an AI! With this finding, scientists are looking forward to more extensive applications of AI in the field of plant physiology. “Our study shows that DNN can act as an ‘artificial professional eye’ for fruit physiology diagnosis. In the future, maybe in just 10 years, when most of the old experts on persimmon fruit cultivation will be retired, this would help the situation greatly. Instead of a competition between humans and AI, I look forward to an ‘interaction’ between them that would help overcome seemingly impossible challenges,” concludes Dr. Akagi. Maybe having AI outperform humans isn’t such a bad thing when it can serve to push the limits of our abilities further! Reference: Title of original paper: Explainable Deep Learning Reproduces a ‘Professional Eye’ on the Diagnosis of Internal Disorders in Persimmon Fruit Journal: Plant & Cell Physiology DOI: 10.1093/pcp/pcaa111 Contact Person: AKAGI Takashi Dr Akagi is Associate Professor at the Graduate School of Environmental and Life Science at Okayama University, Japan. He conducts research on diverse control mechanisms for sex determination and expression in floral organs of horticultural crops, as well as on the shape and physiological disorders of fruits. He also strives to clarify the factors that contribute to the quality judgment and preference of fruits and vegetables assisted by deep learning (AI) technology. Dr. Akagi has 47 publications to his credit, with over 1000 citations. Contact: E-mail: takashia(a)okayama-u.ac.jp For inquiries, please contact us by replacing (a) with the @ mark. 2021-02-05 /agr/research_highlights.php?id=17 Release Subtitle: Scientists demonstrate in a species of beetle that males adopt different survival tactics depending on the size of their mandibles, which they use as weapons Release Summary Text: When males have to fight for reproductive rights, having larger weapons such as horns gives them an edge. However, this can also limit their mobility, making them more vulnerable to predators. In a recent study, scientists from Japan proved, for the first time, that males of a species adopt different anti-predator tactics—tonic immobility or escape—based on the size of their weapons, opening doors to a better understanding of the evolution of animal behaviors. Full text of release: Across many animal species there is great evolutionary pressure on males, who often engage in combat for the rights to copulation. This phenomenon, called sexual selection, often ends up favoring males with larger weapons, such as horns or pincers. Interestingly, scientists have noted that males endowed with smaller weapons adopt alternative reproductive tactics in some species. For example, instead of fighting other more powerful males, they may try to sneak around or disperse in search of a lonely female. Variability in sexual behavior according to a male’s weapon size has been widely studied. However, it’s worth noting that bigger is not always better. Though larger weapons usually help in fights for reproductive rights, they can also be a hinderance because they lower the animal’s overall mobility. This has been proven in males of a species of Japanese rhinoceros beetle, who fall prey to predators more easily when their horns, which they use as weapons, are bigger. Could it be that, just as males with smaller weapons adopt alternative sexual tactics, males with larger weapons adopt different anti-predator strategies? In a recent study published in Biology Letters, a team of scientists from Okayama University, Japan, proved that this is most likely the case. Led by Professor Takahisa Miyatake, they focused on a species of beetle called Gnathocerus cornutus, the males of which bear large mandibles as weapons for male-on-male combat. When threatened, G. cornutus exhibits two very distinct behaviors: escape or tonic immobility, also called death feigning. The team investigated whether differences in weapon size caused males to behave differently when faced by a predator. They obtained nearly two hundred male G. cornutus beetles from a laboratory and conducted two types of experiments. First, they pitted male beetles against one of their natural predators, a jumping spider. When attacked by the spider, most beetles froze in place, which seemed to cause the spider to quickly lose interest. On the other hand, the beetles that tried to struggle or run away were repeatedly attacked by the spider and killed. These initial experiments proved that tonic immobility is a useful anti-predator strategy. In the second series of experiments, the researchers measured the size of the mandibles of male beetles and then tried to get them to exhibit tonic immobility by gently touching their abdomen with a thin stick. Unlike previous behavioral studies, which exclusively focused on the duration of tonic immobility once triggered, the team also quantified the frequency of tonic immobility. Whereas no statistical relationship was found between weapon size and tonic immobility duration, a link was very apparent between weapon size and frequency; individuals with larger mandibles were generally more prone to exhibit tonic immobility when stimulated. Excited about the results, Dr. Kentarou Matsumura remarks: “For animals that fight with weapons, the costs of having larger weapons are well known. However, this is the first time we have scientifically determined that anti-predator tactics can vary among males according to their weapon size.” The results and the research strategy adopted by the team will help biologists unravel the mysteries of the evolution of behaviors, as Miyatake explains: “As the first study of predator-avoidance tactics in animals that have weapons for male-to-male fighting, we believe this is an opportunity to delve deeper on the relationship between the evolution of weapons and anti-predator behavior.” Miyatake also states that these new discoveries will spawn a new research topic in the evolution of survival tactics, which in turn will increase our overall scientific understanding of this challenging field in the future. What other fascinating evolutionary secrets could be hiding out there in the behaviors of different animals? Let us hope this study acts as a springboard for finding the answers! Release URL: https://www.eurekalert.org/pub_releases/2021-01/ou-smh012721.php[New window] Reference: Title of original paper: Anti-predator behaviour depends on male weapon size Journal: Biology Letters DOI: http://dx.​doi.​org/​10.​1098/​rsbl.​2020.​0601 Contact Person: Takahisa Miyatake and Kentarou Matsumura (Kagawa University) Contact: E-mail: miyatake(a)okayama-u.ac.jp (Miyatake), ag20110(a)s.okayama-u.ac.jp (Matsumura) For inquiries, please contact us by replacing (a) with the @ mark. 2021-01-28 /agr/research_highlights.php?id=15 Source: Okayama University (JAPAN), Public Relations Division For immediate release: 05 March 2020 Okayama University research: Green leafy vegetables contain a compound which can fight cancer cells (Okayama, 05 March) In a study recently published in Scientific Reports scientists at Okayama University describe how an ingredient of cruciferous vegetables prevents the growth of cancer cells. Cruciferous vegetables like broccoli, cauliflower, and cabbage are rich in a class of compounds called ‘isothiocyanates’. A key member of this class, benzyl isothiocyanate (BITC), effectively prevents the growth of tumors in laboratory rats and mice. However, the exact mechanism behind its ability to do so is still unknown. A research team spearheaded by Professor NAKAMURA Yoshimasa and Associate Professor MORIYA Hisao at Okayama University recently used yeast cells to explain how BITC can abate the development of cancer. Yeast cells make a convenient experimental model as they are easy to manipulate, and they share a significant amount of their genetic make-up with mammalian cells. Thus, discoveries made in yeast cells can often be translated to human cells. The team first treated yeast cells with different concentrations of BITC and found that higher concentrations of BITC suppressed the growth of the cells. An optimum concentration that could suppress the growth of yeast cells to an easily measurable extent was chosen. Next, a battery of genes within the cells was screened to find candidates that may be altered upon exposure to BITC. Twelve genes were found to be potentially involved. The researchers then artificially enhanced the levels of these twelve genes and observed that the yeast cells subsequently developed a resistance to BITC-induced death. To further understand how the effects of BITC might be associated with these genes, one such gene was analyzed in detail—the MTW1 gene. The MTW1 gene is responsible for producing a protein in yeast cells which is very similar in functionality as well as genetic sequence to Mis12, a protein found in human cells. Human colon cancer cells were then employed to see if BITC treatment affected the Mis12 protein. Indeed, an artificial reduction in Mis12 levels enhanced the cancer-killing effects of BITC whereas an increase in Mis12 levels protected the cells from death. What’s more, BITC directly reduced the amount of Mis12 by channeling it towards degradation. This degradation of Mis12 further sensitized the cells to apoptosis, a harsh process that leads to cellular death. The Mis12 protein was found to be the direct link between BITC and cancer cell death. “Our data indicated that the proteasome-dependent decrease in Mis12…enhances the BITC-induced apoptosis, which contributes to the suppression of cancer cell proliferation by BITC”, concludes the team. This study is the first to explain the anticancer properties of BITC in detail, using a novel screening system within yeast cells. This system can be used in the future for screening other anticancer drugs. Background BITC: Benzyl isothiocyanate (BITC) is an organic compound present naturally in several plants and vegetables. Experiments in rodent models have shown the ability of BITC to reduce ovarian, lung, and bladder tumors. Researchers have long been analyzing these properties of BITC in an attempt to understand how it fights cancer and the doses required for preventing tumor growth. Yeast cells: Yeast, a type of fungi, are single-celled organisms found abundantly in nature. In spite of their simple structure, yeast cells have complex biological processes ongoing within them, many of them similar to mammalian cells. Therefore, they are often used in experiments to understand cellular processes and the effects of chemicals or drugs better. Reference Naomi Abe-Kanoh, Narumi Kunisue, Takumi Myojin, Ayako Chino, Shintaro Munemasa, Yoshiyuki Murata, Ayano Satoh, Hisao Moriya & Yoshimasa Nakamura. Yeast screening system reveals the inhibitory mechanism of cancer cell proliferation by benzyl isothiocyanate through down-regulation of Mis12. Scientific Reports, 2019 Jun 20;9(1):8866. DOI : 10.1038/s41598-019-45248-2. Yeast screening system reveals the inhibitory mechanism of cancer cell proliferation by benzyl isothiocyanate through down-regulation of Mis12 | Scientific Reports[New window] Correspondence to Professor NAKAMURA Yoshimasa, Ph.D. Department of Food Biochemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan E-mail: yossan(a)okayama-u.ac.jp For inquiries, please contact us by replacing (a) with the @ mark. https://yossan24okayama.jimdofree.com/ 2020-03-05 /agr/research_highlights.php?id=14 Source: Okayama University (JAPAN), Public Relations and Information Strategy For immediate release: 18 March 2019 Okayama University research: Game changer: How do bacteria play Tag? (Okayama, 18 March) In a recent study published in Proteins and Proteomics researchers at Okayama University show how bacteria attach to organisms before infecting them. Bacteria have been long invading animals and plants. One of their most intricate but less understood mechanisms is their ability to adhere to other organisms. A research team led by Professor Takashi Tamura at Okayama University has unravelled the role of a molecule, DsbA, and how its chemical properties control this adhering function of bacteria. Professor Tamura have previously shown that before bacteria can adhere to other living objects certain structures on the bacteria’s surface must be stabilized to form a strong scaffold. Special proteins found within the bacteria are responsible for this stabilization. To understand this process better, Professor Takashi Tamura’s team used a virus that attacks bacteria only (bacteriophage). This virus binds to an appendage-like structure found on the bacterial surface. DsbA is the protein responsible for stabilizing this appendage to facilitate this attachment. To decipher how DsbA does its job, the team created several mutants of bacteria, each with a different form of the DsbA protein. The code responsible for conferring DsbA a chemical charge was different in each mutant. A bacteriophage called as M13 was then introduced into these bacteria, grown on a plate. Ideally, when M13 successfully attaches to and infects bacteria, “plaques” of viral colonies will be observed on the plate, in place of the bacterial colonies. These plaques were measured for all the different mutants. It was found that one particular mutant (DsbA [CDIC]) had 40 times more plaques than any other mutant or the unmutated bacteria. The charge on this mutant was much lower than the unmutated protein. However, another mutant, also with a low charge, did not have more plaques. This suggested that the mutated code of (DsbA [CDIC]) could be bringing about additional effects. Using structural mapping the team then found that DsbA [CDIC] had enlarged binding pockets, compared to the other variants. This could facilitate better binding of the scaffolding appendage. Insights into these mechanisms of their attachment can help build strategies to combat bacteria. Antibiotic resistance is also spread from one bacterium to another by close contact. Designing drugs that could inactivate the factors driving DsbA function seems like one such strategy. Background Proteins and structure: Proteins that bind to and modulate the activity of other proteins are known as enzymes. Special regions on these proteins called active sites are responsible for this function. The active site consists of a ‘binding site’, a pocket where the partner protein actually binds and a ‘catalytic site’ which gives the protein a chemical charge. This charge provides the energy for the protein to undergo a chemical reaction. In the case of DsbA, codes on the catalytic site were changed to create the mutants. Bacteriophage: Bacteriophage or “bacteria eaters” are viruses that attack and subsequently hijack bacteria. The first step in this process requires the bacteriophage to attach itself onto the bacterial surface. Typically, the bacteriophage does this by binding to F-pilus, an appendage-like structure found on the bacteria’s surface. Reference Shinya Sutoh, Yuko Uemura, Yuko Yamaguchi, Asako Kiyotou, Rena Sugihara, Makiko Nagayasu, Mihoko Kurokawa, Koreaki Ito, Naoki Tsunekawa, Michiko Nemoto, Kenji Inagaki, Takashi Tamura. Redox-tuning of oxidizing disulfide oxidoreductase generates a potent disulfide isomerase. Biochimica et Biophysica Acta - Proteins and Proteomics, 1867(2019), 194-201. DOI : doi.org/10.1016/j.bbapap.2018.12.005[New window] Okayama University Medical Research Updates （OU-MRU） 2019-03-19 /agr/research_highlights.php?id=13 Scientific Reports of the Faculty of Agriculture Vol.108 was published. For details, please see the following URL: http://ousar.lib.okayama-u.ac.jp/ja/journal/srfa Okayama University Repository for Academic Resources 2019-02-05 /agr/research_highlights.php?id=12 Scientific Reports of the Faculty of Agriculture Vol.107 was published. For details, please see the following URL: http://ousar.lib.okayama-u.ac.jp/ja/journal/srfa Okayama University Repository for Academic Resources 2018-02-01 /agr/research_highlights.php?id=9 Okuma, Munemasa, and Murata collaborated with Dr. Kwak (DGIST, Korea) and Dr. Pei (Duke, NC) to clarify that plant glutamate receptor homologs formed Ca2+ channels activated by L-methionine at physiological concentrations and regulate stomatal apertures and plant growth. The findings suggest that administration of methionine easily improves drought stress tolerance of plants. The administration of methionine is useful because methionine is a cheap amino acids, meaning it is economical and harmless. Cell Reports (2016) Dec 6; 17(10), 2553-2561, DOI: 10.1016/j.celrep.2016.11.015. Kong D#, Hu HC#, Okuma E#, Lee Y, Lee HS, Munemasa S, Cho D, Pedoeim L, Rodriguez B, Im W, Murara Y, Pei ZM, Kwak JM. (#: Co-first authors) 2017-01-13 /agr/research_highlights.php?id=10 Dr. Takahisa Miyatake was awarded Hidaka Prize from Japan Ethological Society　on 12nd November, 2016 2016-11-12