Ishikawa Prefectural University

Torularhodin is the monocyclic C40 carotenoid with the β-ring and a terminal carboxyl group at the acyclic part, with long conjugated double bonds, only synthesized in fungi called red (oleaginous) yeasts, e.g., the genera Rhodotorula and Sporobolomyces. This unique red pigment with strong antioxidant properties is promising for use in food additives, nutritional supplements, and cosmetics. We aimed to produce torularhodin in Escherichia coli through the identification of the biosynthesis genes needed for its heterologous production, while no genes oxidizing torulene to torularhodin had been reported. The Rhodotorula toruloides crtI (CAR1) and crtYB (CAR2) genes, which were chemically synthesized, proved to lead to the complete conversion of phytoene into torulene when they were introduced into an E. coli cell that carried the Pantoea ananatis crtE and Haematococcus pluvialis IDI genes. We found that the Planococcus maritimus genes coding for C30 carotenoid terminal oxidase (crtP/crtNb/cruO) and aldehyde dehydrogenase (aldH/crtNc), through their introduction into the E. coli transformant synthesizing torulene, mediated the efficient oxidations of torulene to torularhodin, and resulted in the production of torularhodin as the dominant carotenoid. This is the first report of torularhodin production in a heterologous host. We also identified the aldH/crtNc gene in R. toruloides.

Antibiotics are the primary treatment for bacterial urinary tract infections (UTIs). However, overuse of antibiotics promotes the emergence of antibiotic-resistant bacteria; therefore, it is desirable to develop drugs that specifically inhibit virulence without promoting the emergence of antibiotic resistance. Proteus mirabilis causes UTI and uniquely uses putrescine for cell-cell communication during urinary tract invasion. Inhibition of putrescine-mediated cell-cell communication in P. mirabilis impairs its invasion of urothelial cells. Therefore, proteins responsible for putrescine-mediated cell-cell communication are a potential target for treating P. mirabilis UTIs. However, the putrescine exporter of P. mirabilis has yet to be identified. Here, we identified two putrescine exporters of P. mirabilis, PstSCAB and SapBCDF. Furthermore, P. mirabilis ΔpstSCAB and ΔsapBCDF strains showed a lack of swarming activity. This study indicates PstSCAB and SapBCDF as potential targets for treating UTIs caused by P. mirabilis.

Epidemiological studies in humans have suggested that tomato consumption and the compositional ratios of Prevotella, Megamonas, and Streptococcus in the intestinal microbiota are related to intestinal permeability. In this study, we investigated the causal relationship using Caenorhabditis (C.) elegans. We cultured Escherichia coli OP50 (the standard C. elegans food), Prevotella (P.) copri JCM 13464T, Megamonas funiformis JCM 14723T, and Streptococcus salivarius JCM 5707T in either normal medium or medium containing 1% (v/v) tomato juice (TJ medium), fed these bacteria to C. elegans for three days, and evaluated intestinal permeability using the Smurf assay. The proportion of Smurf individuals was significantly lower in C. elegans fed P. copri cultured in TJ medium than in those fed the same bacteria cultured in normal medium, while other strains showed no such medium-dependent differences. Interestingly, heat-killed P. copri grown in normal medium also reduced the proportion of Smurf individuals. Furthermore, P. copri grown in TJ medium exhibited a lower survival rate after seeding on nematode growth medium, an effect not observed in other strains. Liquid chromatography-tandem mass spectrometry analysis revealed that P. copri cultured in TJ medium accumulated L-(-)-3-phenyllactic acid (L-(-)-3-PLA), a compound known for its antibacterial properties through oxidative stress and its protective effects on the intestinal barrier. In contrast, the levels of known antioxidants such as 2,3,4,9-tetrahydro-1H-β-carboline-3-carboxylic acid and Cyclo(phenylalanyl-prolyl) were decreased. Culturing P. copri in normal medium supplemented with L-(-)-3-PLA alone did not reduce survival, suggesting that both L-(-)-3-PLA accumulation and the depletion of antioxidants contribute to reduced viability. Additionally, L-(-)-3-PLA directly suppressed intestinal permeability in C. elegans. In conclusion, the results of this study suggest that TJ may inhibit increased intestinal permeability through both rendering P. copri vulnerable and the direct effects of L-(-)-3-PLA. Further studies are needed to determine the relevance of these findings to humans.

Iron (Fe) is essential for all living organisms, including plants. Plants upregulate the expression of several genes involved in Fe uptake and translocation in response to Fe deficiency. Hemerythrin motif-containing RING and zinc (Zn)-finger proteins (HRZs) are potential intracellular Fe sensors in plants. Rice (Oryza sativa) OsHRZs are ubiquitin ligases containing hemerythrin domains, a CHY Zn-finger, a CTCHY Zn-finger, a RING Zn-finger, and a rubredoxin-type fold, with each capable of binding Fe or Zn. In this study, we explored whether the OsHRZs sense Fe status by modulating their function depending on metal binding to these domains. The OsHRZ1 protein overexpressed in rice was rapidly degraded in roots, primarily because of the instability of the C-terminal domains. An N-terminal OsHRZ1 sequence with two hemerythrin domains was stably overexpressed in rice and exhibited an enhanced Fe-deficiency response in a dominant-negative manner. CRISPR/Cas9-based rice lines harboring mutations at the C-terminal RING Zn-finger domain or rubredoxin-type fold of OsHRZ1 or OsHRZ2 exhibited Fe-deficiency tolerance and Fe accumulation in grains, indicating the important function of these domains in planta. OsHRZ1 and OsHRZ2 proteins were degraded in vitro through the proteasome pathway, which was dependent on the OsHRZ1 RING Zn-finger domain. Degradation was enhanced under Fe-deficient conditions or with excess Zn bound to the OsHRZ1 protein. The self-ubiquitinating activity of OsHRZ1 and OsHRZ2 was enhanced by excess Zn binding. The results suggest that the stability and function of OsHRZs are affected by Fe nutritional conditions through Zn or Fe binding to multiple domains in the OsHRZ proteins.

Research surveys in disaster-affected areas always conflict between providing important information and recommendations regarding the actual status of damage, recovery, and reconstruction and, contrastingly, the need for more careful ethical considerations. It has been reported that the 2004 Aceh Tsunami and the 2011 Great East Japan Earthquake and Tsunami, certain research activities caused difficulties for afflicted people and affected areas. The above can be divided into two main categories: the problem of the capacity, burden, and exhaustion of the research subjects and the ethical issue related to the methods, content, and approach of individual studies. However, the former analysis of solutions remains almost completely unaddressed in disaster science. Thus, this study considered how academia should behave, collaborate, and coordinate through the case of Japan in 2024. As a result, while Japan has a comprehensive federation of researchers and academic societies, coordinating the research activities has been challenging. This difficulty stems from the federation’s lack of authority to control academic societies and researchers, lack of consensus building regarding the “fallacy of composition” in disaster science, and the involvement of numerous stakeholders. The plethora of research opportunities and the various grants have been identified as risk factors contributing to project fragmentation and research duplication. It was suggested that questions could improve the composition of grant reviews to prevent research duplication and the depletion of subject areas. Furthermore, it is crucial to pre-determine which university or institution would take the lead when a disaster occurs in each region.

石川県が新たに開発した「石川酒68号（百万石乃白）」の精米歩合別の試料を調製し，澱粉，胚乳貯蔵蛋白質及び遊離アミノ酸について分析するとともに，「山田錦」，「五百万石」，及び「石川門（石川酒52号）」についても同様の分析をした．各品種の玄米について比較してみると，「石川酒68号」と「山田錦」のToは「石川門」及び「五百万石」と比較して5°C低かった．また，各精米歩合の試料においても「石川酒68号」と「山田錦」のToは「石川門」と「五百万石」のToに比べ3–4°C低かった．各品種の玄米の粗蛋白質含量は6.2–7.0 g/100 gであったが，精米が進むにつれて減少し，50%精米した「石川酒68号」と「山田錦」は3.1 g/100 gであり，「石川門」及び「五百万石」は3.3 g/100 g及び3.4 g/100 gであった．各精米歩合別に品種間の胚乳貯蔵蛋白質の構成比を比較したが，いずれの品種も37–39 kDaグルテリン及び26 kDaグロブリンと22–23 kDaグルテリン（塩基性）が他の胚乳貯蔵蛋白質と比較して多く含まれていた．「石川酒68号」の玄米における遊離アミノ酸含量は他の品種の玄米と比較してAsp, Asn, Glu, Arg, Lys, His,及びTyrの含量が有意に低かった．

Arabidopsis is a widely used model plant to study physiology and development. Live imaging is an important technique to visualize and quantify processes in plant growth and cell division, where accurate cell tracking is essential. The commonly used software TrackMate adopts a tracking-by-detection approach, applying Laplacian of Gaussian (LoG) for blob detection and a Linear Assignment Problem (LAP) tracker for tracking. However, its performance declines when cells are densely arranged. To overcome this limitation, we propose an accurate tracking method based on a Genetic Algorithm (GA) that incorporates knowledge of Arabidopsis root cellular patterns and spatial relationships among volumes. Our method follows a coarse-to-fine strategy: first performing relatively simple line-level tracking of nuclei, then refining associations based on the linear arrangement of cell files and their spatial relationships. We evaluated the method on long-term live imaging datasets of Arabidopsis root tips, and with minor manual correction, it achieved accurate nuclear tracking. To the best of our knowledge, this represents the first successful attempt to address a long-standing problem in time-lapse microscopy of the root meristem by providing an accurate tracking method for Arabidopsis root nuclei.