Tokyo University of Agriculture

A 6-year-old, spayed female Boston Terrier presented with elevated ALT. The dog underwent abdominal ultrasound and computed tomography, which resulted in a suspected gallbladder neuroendocrine tumor. Complete tumor resection was achieved by cholecystectomy with hepatic parenchymal resection despite tumor invasion into the gallbladder. The diagnosis of neuroendocrine tumor was confirmed by histopathology. This case suggests the surgical technique described could be an effective treatment option for canine gallbladder neuroendocrine tumors.

Drought limits water availability and negatively impacts rice growth. One of the strategies to overcome drought stress is the genetic improvement of root traits by marker-assisted selection (MAS). Using the MAS strategy, pyramiding quantitative trait loci (QTLs) efficiently stacks multiple QTLs. To elucidate the effects of pyramiding root QTLs on shoot production under drought, we used near-isogenic lines (NILs) and pyramided lines (PYLs), introducing single or multiple QTLs derived from Kinandang Patong (upland rice) into IR64 (lowland rice). We selected one QTL from each root morphological trait: root growth angle (DRO1), root thickness (Sta1), root length (qRL6.1), and root volume (qFSR4). We evaluated the effects of pyramiding root QTLs on root system architecture (RSA). In the basket method and 3D imaging by X-ray computed tomography, all NIL and PYLs with DRO1 showed robustly steeper root growth angle. In a hydroponic culture assay, root length QTL qRL6.1 increased maximum root length. In a lysimeter experiment, root volume QTL qFSR4 increased root volume per stem. Next, we examined the NILs and PYLs for shoot biomass production under drought conditions in lysimeter and field experiments. Two lines (DRO1-NIL and Sta1+DRO1-PYL) had a higher shoot biomass production under drought than IR64. DRO1-NIL exhibited deeper RSAs and increased water uptake compared to IR64. Sta1+DRO1-PYL was not as deep as DRO1-NIL but had a higher normalized difference vegetation index, lower canopy temperature, and higher shoot biomass in the field experiment. In summary, DRO1 plays a critical role in RSA, and pyramiding Sta1 with DRO1 increases shoot biomass during drought. This suggests the pyramiding of root QTLs could improve RSA and enhance biomass production under drought stress.

Purpose This study aimed to determine the effects of yoga on the recovery of the cardiac autonomic nervous system and immunosuppression after intense exercise. Methods Seven healthy adult men were enrolled in two trials: rest for 30 min in a seated position (CON) and yoga for 30 min (YOG) after a treadmill running for 60 min at 75% O 2max in a randomized crossover design. Natural killer (NK) cell activity, salivary secretory immunoglobulin A (SIgA), cortisol, testosterone, and indicators related to heart rate variability, mood states, and muscle soreness were measured before exercise (Pre), immediately (P0) and 60 min (P1) after rest or yoga, and the following morning (P2). Results NK cell activity was significantly decreased in the CON trial ( P < 0.05) but not in the YOG trial. The decrease in NK cell activity from Pre at P0, P1, and P2 in the CON trial was significantly larger than that in the YOG trial ( P < 0.05). Testosterone secretion rate tended to be higher after yoga than at rest ( P = 0.052). The square root of the mean squared difference of successive normal-to-normal intervals (RMSSD) at P0 in the YOG trial was significantly higher than that in the CON trial ( P < 0.05). Changes in NK cell activity correlated with changes in RMSSD ( r = 0.445, P < 0.05). Conclusion This study showed that yoga can alleviate the decline of NK cell activity after intense exercise by enhancing parasympathetic nerve activity, thus suggesting that yoga may be an effective recovery method for athlete conditioning.

Soil carbon (C) credits provide monetary incentives to farmers who are motivated to improve soil organic carbon (SOC) stock through agricultural practices such as no‐tillage system, cover cropping, and complex crop rotation as a mitigation and adaptation strategy for climate change. Several major challenges associated with measuring SOC stock for C credit protocol include a high cost and variability. Thus, this study was aimed at characterizing the variability of bulk density (BD), SOC concentration, and stock at an on‐farm operation site under small and aggregated farms to suggest feasible soil sampling methods for SOC stock. In addition, 80% of the farmland is managed by smallholders who work on less than 1–10 ha and provide up to a large proportion of the food supply in Asia and sub‐Saharan Africa. Therefore, evaluating SOC stock, including variability under small and aggregated farms, is critically important. The objective of this study was to characterize the variability of soil parameters, such as BD, SOC concentration, and SOC stock, at an on‐farm operation site to suggest feasible soil sampling methods for assessing the SOC stock. The results show that the SOC stock variability (coefficient of variance; ranged from 6.9% to 21.2%) strongly affected BD and SOC concentration. The number of required samples could be minimized with acceptable uncertainty levels, and it was estimated that six samples are needed to achieve an error of 20% (110 ± 22 Mg ha⁻¹).

Pterostilbene, a polyphenolic compound and an analog of resveratrol, exerts various biological activities and has higher bioavailability and metabolic stability than resveratrol. However, the effectiveness of pterostilbene intake in humans, particularly its effect on blood microRNA (miRNA) expression levels, has not been evaluated. Accordingly, this pilot study aimed to investigate the effects of pterostilbene on blood biochemistry and blood miRNA expression levels and the safety of continuous intake at doses of 10 or 100 mg/d over 12 wk. A double-blind, placebo-controlled parallel-arm comparison trial was conducted with 30 healthy men. In the analysis of blood miRNA expression levels, miR-34a and miR-193b showed very high increases at week 4 and after week 4 of intake, respectively, suggesting that the responders might be present among participants in the pterostilbene intake group. No adverse events were reported during the trial in any participant, and no abnormalities were observed upon examination by the responsible physician. Thus, pterostilbene intake would regulate blood miRNA expression levels, and the results can be utilized in human studies investigating miRNA expression levels with functional food ingredients.

The giant Pacific octopus (Enteroctopus dofleini) is the world’s largest octopus and the most abundant species in coastal waters of the North Pacific. Despite the commercial importance of this species in Japan, studies of its genetic population structure have been limited to the Gulf of Alaska. This study was conducted to clarify the genetic diversity and population structure of the giant Pacific octopus (Enteroctopus dofleini) in Japan and evaluate genetic differences in this species between the northwest Pacific (NWP) and northeast Pacific (NEP) based on analyses of the mitochondrial cytochrome c oxidase subunit I (CO1) and cytochrome b (Cytb) genes. A total of 263 specimens were collected in Japan (NWP) during June 2020–August 2022, and the CO1 and Cytb genes were successfully sequenced and analyzed in 230 and 229 specimens, respectively. Diversity indices were also calculated for the NEP using previously published sequence data, and genetic variance was compared between the NEP and NWP. In Japan, ten CO1 haplotypes and nine Cytb haplotypes were detected, and genetic variation among sites was not significant. Comparisons of genetic diversity between the NWP and NEP were inconclusive, but clear genetic differentiation was found between the two regions. The genetic population structure of E. dofleini has likely been shaped by dispersal during the planktonic paralarval stage and plausibly by changes in climate that occurred during the Last Glacial Maximum.

Key message We performed GWAS for starch properties and eating, cooking and appearance quality characteristics traits in rice and then used PLS regression to show importance of different loci for different food applications. Abstract We performed a genome-wide association study for appearance, eating and cooking quality traits in grain of japonica rice cultivars and identified candidate genes for adhesiveness of cooked rice grains, amylopectin composition and β-glucanase activity in rice endosperm among a total of 525 quantitative trait nucleotide (QTN) loci. The study used 1,054,635 single-nucleotide polymorphisms (SNPs) based on genome sequence data of 150 rice cultivars and 89 grain appearance, eating and cooking quality traits. These included grain shape, protein content, amylose content, amylopectin chain length, starch viscosity properties, starch degradation enzyme activities, and physicochemical characteristics of cooked rice grains analyzed in three years. Cluster regions of genetic loci on rice chromosomes 1, 4, 5, 6, 8, 9, 10 and 11 were detected, with several regions co-located with starch biosynthesis and degradation genes. Partial least squares (PLS) regression analysis revealed that the QTN genotypes were unevenly distributed in subpopulations of rice cultivars classified by their primary application. We could therefore select and accumulate these QTNs to improve grain quality in further breeding programs by developing novel rice cultivars with appropriate phenotypes for each food usage: as high eating quality cooked rice, staple food rice, sushi rice, sake brewing rice, and high-yielding rice cultivars.

In dimorphic yeasts, hyphal growth is primarily associated with infection and mycosis progression, with Trichosporon asahii causing deep-seated mycosis and summer-type hypersensitivity pneumonitis. Magnesium accelerates hyphal growth in T. asahii , leading to multi-septation, vacuolar expansion, and decreased lipid droplet size. However, the commonality of these phenotypes has not been studied in Trichosporonales yeasts. Therefore, to explore whether similar magnesium-induced phenotypes occur across Trichosporonales yeasts, we examined hyphal growth, multi-septation, vacuolar extension, and lipid droplet size and number in 30 species. Cell length increased with magnesium treatment in 13 yeasts: 5 Trichosporon ( T. asahii , Trichosporon aquatile , Trichosporon asteroides , Trichosporon coremiiforme , and Trichosporon ovoides ), three Apiotrichum ( Apiotrichum brassicae , Apiotrichum montevideense , and Apiotrichum veenhuisii ), three Cutaneotrichosporon ( Cutaneotrichosporon cavernicola , Cutaneotrichosporon cutaneum , and Cutaneotrichosporon dermatis ), Pascua guehoae , and Takashimella koratensis. C. dermatis also underwent pseudo-hyphal growth. Multi-septation increased in seven dimorphic yeasts, including five Trichosporon spp., Trichosporon faecale , and C. dermatis . The vacuolar area was significantly extended in T. asahii , T. aquatile , T. ovoides , and C. dermatis . Lipid droplet size increased only in Trichosporon inkin ; however, it decreased in T. asahii , T. coremiiforme , and T. faecale . Additionally, lipid droplet number was preferentially altered in Apiotrichum and Cutaneotrichosporon . These results suggested that magnesium-induced multi-septation and vacuolar area expansion phenotypically distinguish Trichosporon hyphae from Apiotrichum and Cutaneotrichosporon hyphae and distinguish C. dermatis pseudo-hyphae from Cutaneotrichosporon spp. Moreover, differences in lipid droplet size can discriminate species within Trichosporon . Our results suggest that phenotypic alteration via magnesium treatment can contribute to the characterization of Trichosporonales yeasts. These findings provide insights into fungal pathogenesis and may support new treatment strategies. IMPORTANCE Magnesium sulfate considerably affects hyphal growth and cellular organization in Trichosporon asahii . To examine the commonality of this phenotype in Trichosporonales, we treated 30 Trichosporonales yeasts with magnesium sulfate and observed genus-level phenotypic alterations. Using cell length measurement, lipid droplet staining, septum staining, and vacuole staining, considerable hyphal diversity was observed among Trichosporonales. Notably, differences in the multi-septation phenotype and vacuolar size distinguished Trichosporon hyphae from Apiotrichum and Cutaneotrichosporon hyphae and distinguished Cutaneotrichosporon dermatis from other Cutaneotrichosporon spp. Moreover, differences in lipid droplet phenotype divided Trichosporon hyphae into two groups. Our study revealed the relationship between hyphal morphology and phylogenetic systematics in Trichosporonales.

This study presents a novel method of fermentation promotion using a peristaltic pump for large-scale fermentation. This pump physically crushes, mixes, and diffuses fermentation substrates to mimic fermentation in the human gut. The proposed device effectively mixes fermentation substrates according to their properties and promotes fermentation. Preliminary studies were conducted on fermentation experiments using this device with fibrous and porous substrates.

In processing pumpkin (buttercup squash), a seasonal vegetable, our objective was to develop a local pumpkin ice cream without a “best before date” as a regional specialty from the Okhotsk region of Hokkaido. However, the high starch content of pumpkin can pose challenges, such as increased torque on mixing equipment during freezing, which results in ice cream with a hard texture. Since sweet potato, another vegetable, is rich in β-amylase activity, we developed an ice cream with improved overrun by converting pumpkin starch to maltose during the pasteurization process. Then, using an ice cream mix containing pumpkin and sweet potato juice, we successfully reduced the increase in viscosity during freezing. Compared to commercial pumpkin ice cream, our product exhibited a richer pumpkin taste, smoother texture, and an improved melt-in-the-mouth feel.

The diary offers a detailed account of his voyage to Vladivostok via the Suez Canal accompanied by two whale-catchers, Nikolai and Georgy. Subsequently, he constructed a whaling station in Gaydamak, near Vladivostok, which is now part of Nakhodka City. The whaling station, which employs personnel from Japan, China, Korea, and several other countries, constitutes the focal point for whaling operations spanning the Russian Far East and the Korean Peninsula. The diary records the number and species of whales captured by the company. From the description of the diary, Walby was employed by a Japanese whaling company to supervise the construction of a whale-catcher in Osaka and to participate in whaling operations as a gunner in the Sea of Japan, from the Tsushima Strait to the Korean Peninsula, and off Kagoshima Prefecture in southern Kyushu. The diary indicates that he visited a hot spring in Unzen and the ancient capital Nara from Osaka, during the period of unemployment, prior to his contract with a Japanese whaling company. A review of the diary entries and articles in fishing journals of the same period revealed that Walby started working as a gunner in 1899 for a Japanese whaling company, a year later than the descriptions of Akashi (1910) and Tønnessen (1967). Nevertheless, Walby was the first gunner of a modern Japanese whaling company to be recorded and the first to hunt a whale with a whaling cannon. The value of Walby’s diary lies in its detailed internal record of whaling companies, which makes it an invaluable source of information on the earliest days of modern whaling, from the Russian Far East to the Korean coast, and to Japan at the end of the 19th century.

To survive in harsh natural environments, translation and mRNA metabolism must be tightly and coordinately controlled, as saving biological costs increases fitness. However, the roles of protein chaperones in this control system are unclear. This study proposes the novel aspect of the link between translation and mRNA metabolism, that is, the co-translational DnaJK chaperone activity is involved in changes in mRNA metabolism by RNase P. We found that the expression of proBA, which encodes proline biosynthetic enzymes, is regulated by ylxR(rnpM) through the proBA promoter. YlxR(RnpM), which is associated with RNase P, was also involved in the posttranscriptional regulation of proBA. To clarify this posttranscriptional regulation, we screened transposon (Tn)-inserted mutants for cells with low proB::lacZ expression and identified the DnaJK chaperone as a regulator of proB. To explore the possibility that the complex of YlxR(RnpM) and RNase P might work with DnaJK, we performed an epistatic analysis using the lacZ fusions, which revealed that the regulation of proB by DnaJK/YlxR(RnpM)/RNase P, that is, co-translational chaperone activity, controlled mRNA metabolism. RNA sequencing analysis of cells deficient in the RNA component of RNase P (rnpB) revealed that 261 genes were upregulated in the rnpB::Tn strain. Among them, we identified yoyD/yodF, besA, and epeXE, which were also under the control of DnaJK/YlxR(RnpM)/RNase P regulatory cascade. Finally, we performed yeast two-hybrid analysis using DnaK as bait and identified two genes, spoIVCA and nupG, whose expression was post-transcriptionally regulated by DnaJK but independent of YlxR(RnpM). These results suggest a broader role for posttranscriptional gene regulation by DnaJK. IMPORTANCE Bacillus subtilis lacking the DnaJK chaperone has not been reported to exhibit a distinct phenotype. However, our study revealed proline-dependent growth in a minimal medium in the dnaJ::Tn strain. Inhibition of spoIVCA expression in this strain was identified as a probable cause of the sporulation deficiency in previous and current studies using a single cell-level analysis. We also observed posttranscriptional regulation of proBA by the DnaJK and YlxR(RnpM)/RNase P complex. LacZ analyses of proB::lacZ in different backgrounds suggested that the above regulation ultimately functions in mRNA metabolism. In DnaJK-deficient cells, the nascent peptide may be misfolded, and if DnaJK chaperone activity is lost, such a signal may be transferred to RNase P. Therefore, proBA mRNA may be degraded in an RNase P-dependent manner if the misfolding of the polypeptide translated from this mRNA is detected. This system is useful for reducing the biological costs of futile mRNA elongation.

Background: Myxol, a monocyclic carotenoid with β- and ψ-end groups, has been identified in only a limited number of bacteria, such as flavobacteria and cyanobacteria. Despite its biological significance, the biosynthetic pathway of myxol is not well understood, and studies on its physiological functions and biological activities are limited because of its rarity. Methods: BLAST homology searches for carotenoid biosynthesis genes in the genome of Nonlabens were performed. The carotenogenesis-related genes in the genome of the marine flavobacteria Nonlabens spongiae were individually cloned and functionally characterized using a heterologous Escherichia coli expression system. Carotenoids from N. spongiae were identified using an LC-MS analysis. Results: We identified a gene cluster involved in carotenoid biosynthesis in the genome of N. spongiae. This cluster includes genes encoding phytoene synthase (CrtB), phytoene desaturase (CrtI), lycopene cyclase (CrtY), carotenoid 1,2-hydratase (CruF), carotenoid 3,4-desaturase (ψ-end group) (CrtD), carotenoid 2-hydroxylase (ψ-end group) (CrtA-OH), and carotene hydro-xylase (CrtZ). Based on the characteristics of these enzymes, the primary products were predicted to be myxol and/or zeaxanthin. A spectroscopic analysis confirmed that myxol was the primary carotenoid. Furthermore, a plasmid containing a reconstructed gene cluster and geranylgeranyl pyrophosphate synthase (CrtE) located outside the cluster was introduced into E. coli. This system predominantly accumulated myxol, indicating that the reconstructed gene cluster enabled efficient myxol production in E. coli. Conclusions: This study highlighted the potential biotechnological applications of the carotenoid biosynthesis gene clusters for myxol production.

Japan adopted German medicine during the Meiji era and ousted traditional Chinese medicine [1]. The study of physiology and biochemistry, such as energy metabolism, protein amino acid metabolism, and digestion, greatly advanced at the end of the nineteenth century. Tadasu Saeki, who studied at Yale University, proposed the concept of “nutrition science” based on his experiences upon returning to Japan, and in 1920, he established the National Institute of Nutrition. The term Nutrition originates from the Greek word meaning “to nourish,” sharing the same root as the word nurse. Saeki’s nutrition science made significant contributions to improving the nutrition of the Japanese people, but it was not recognized as a discipline and was taught in home economics departments as a subject for women. Even now, there is no nutrition science in medical education, and the training of dietitians is based in home economics departments. On the other hand, Japan has had the concept of dietary health since the Heian period. The “Yojokun” written by Ekiken Kaibara during the Edo period became a long-read classic. In the Meiji era, Sagyen Ishizuka, who became the army’s pharmaceutical supervisor, advocated brown rice vegetarianism and the concept of “Shindo-Fuji,” and formed the Shoku-Yo-Kai. This trend was passed on to Kenzo Futaki and Joichi Sakurazawa and is active as the Japan Comprehensive Medical Association and Macrobiotics. Brown rice vegetarianism became a national movement before the war. With the longevity of the population in the 2000s, the limitations of Western medicine have become apparent. Home medical care has become important in the medical system, and individualized medicine and integrated medicine that emphasize dietary habits to maintain high patient QOL are increasing within the Anti-Aging Medical Society [2].

Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic phototrophic purple sulfur bacterium isolated from a hypersaline lake in the Libyan Desert whose total salinity exceeded 35% at pH 10.7. Here we present a cryo-EM structure of the native LH1–LH2 co-complex from strain BN9622 at 2.22 Å resolution. Surprisingly, the LH1–LH2 co-complex consists of a double-ring cylindrical structure with the larger LH1 ring encircling a smaller LH2 ring. The Hlr. halophila LH1 contains 18 αβ-subunits and additional bacteriochlorophyll a (BChl a) molecules that absorb maximally at 797 nm. The LH2 ring is composed of 9 αβ-subunits, and the BChl a molecules in the co-complex form extensive intra- and inter-complex networks to allow near 100% efficiency of energy transfer to its surrounding LH1. The additional LH1-B797 BChls a are located in such a manner that they facilitate exciton transfer from monomeric BChls in LH2 to the dimeric BChls in LH1. The structural features of the strain BN9622 LH1–LH2 co-complex may have evolved to allow a minimal LH2 complex to maximize excitation transfer to the core complex and effectively harvest light in the physiologically demanding ecological niche of this purple bacterium.

Purpose Dimethyl sulfoxide (DMSO) alters DNA methylation in vitrified-warmed embryos and potentially affects subsequent development. This study aimed to examine possible countermeasures against DMSO-induced demethylation. Methods In vitro-produced bovine embryos (8-cell stage) were vitrified using a combination of DMSO and ethylene glycol (EG) or propylene glycol (PG) + EG. After warming, the lipid content and expression levels of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), DNMTs, and TETs were examined. In addition, RNA-sequencing was performed on blastocysts derived from the vitrified embryos. Furthermore, the effect of supplementation with a vitrification medium containing DMSO and N-acetyl-l-cysteine (NAC, 5 mM) on the levels of 5mC in embryos was examined. Results Vitrification decreased the levels of 5mC and increased the levels of 5hmC in 8-cell stage embryos. Low levels of 5mC persisted until the blastocyst stage in the DMSO group but increased in the PG group. The expression level of TET3A was higher in the DMSO group than in the fresh group, but not in the PG group. Both cryoprotectants reduced the lipid levels in post-warmed 8-cell stage embryos. The addition of NAC ameliorated DMSO-induced demethylation at both the 8-cell and blastocyst stages. RNA-seq analysis revealed that PG-specific pathways included ribosomes and mitochondria and that both DMSO and PG affected cGMP-PGK, MAPK, Wnt, and insulin secretion–related signaling. The K-medoids method predicted that DMSO affected cell adhesion molecules and that MAPK signaling was affected the most. Conclusions PG and NAC may antagonize DMSO-induced demethylation; however, PG exerts adverse effects on embryos.

Fruit consumption is highly recommended due to its health benefits. Passiflora species are a good source of vitamins and antioxidant compounds such as carotenoids that are associated with a reduction in cellular oxidative processes, as well as against cardiovascular diseases and cancer development. As a result, purple passion fruit (P. edulis) and yellow passion fruit (P. edulis f. flavicarpa) are economically important crops that are cultivated based on the demand for their flavor and nutraceutical properties. The objective of this study was to determine the components of carotenoids and sugars in the pulp juice of passion fruit. Two Ecuadorian yellow passion fruit strains (‘INIAP 2009’ and ‘POR1’), one Ecuadorian purple passion fruit variety (‘Gulupa’) and two Asian hybrid cultivars (P. edulis × P. edulis f. flavicarpa; ‘Summer Queen’ and ‘Ruby Star’) were used for this research. The results showed that ‘POR1’ had high acidity and contained all carotenoids, but had the lowest amount of vitamin C, whereas ‘INIAP 2009’ had high contents of organic acids, vitamin C and β-cryptoxanthin. ‘Gulupa’ had the lowest acidity, α-carotene and citric acid content, but the highest amount of glucose, fructose, malic acid and vitamin C; this variety also showed high values of β-carotene and β-cryptoxanthin. On the other hand, ‘Summer Queen’ had high sucrose, malic acid, α and β-carotene and good amount of vitamin C, while ‘Ruby Star’ had high amounts of α-carotene, β-cryptoxanthin and citric acid, but low vitamin C content. These results can be used for further breeding programs focused on improving passion fruit quality.

Introduction This cross-sectional study aimed to characterize the viable vaginal microbiota and identify host factors influencing this microbiota by employing a combination of relative and quantitative analyses. Methods Twenty-four vaginal fluid samples were collected from healthy adult Japanese women for analysis. Vaginal fluid pH was measured using a portable pH meter. DNA was extracted from the vaginal fluid, and the 16S ribosomal RNA gene sequences in the V3-V4 regions were analyzed to identify bacterial species. Additionally, the vaginal fluid was cultured on four types of selective agar plates. The predominant species in the growing colonies were identified using colony polymerase chain reaction, and the colonies were counted. Results The vaginal microbiota was classified into four categories based on the characterization of the dominant bacterial population: Lactobacillus crispatus, Lactobacillus iners, Lactobacillus gasseri, and a diversity group. The predominant bacterial species were consistent across methods; however, the levels of the viable population varied significantly. Body mass index had a significant influence on the total number of viable bacteria and vaginal pH, while age only affected vaginal pH. Conclusions Our findings indicate that the vaginal microbiome of healthy Japanese women is not only highly diverse but also affected by host factors such as BMI and age.