Kazusa DNA Research Institute

Rice endosperm protein hydrolysate B (REPH-B) is produced by enzymatic degradation of rice endosperm protein. REPH-B contains the following peptides: QAFEPIRSV, pEAFEPIRSV, and TNPWHSPRQGSF. A previous study reported that REPH-B has the ability to induce plasma acylated ghrelin secretion and increase food intake in animal models. In this study, we investigated the effect of REPH-B on appetite in healthy adults aged over 40 y who had a relatively low visual analogue scale (VAS) score for hunger. Forty-six healthy subjects who were aware that their appetite had decreased were enrolled. Subjects were randomly allocated to one of two groups. The influence of REPH-B on appetite was evaluated by VAS under two conditions: repeated intake over 2 wk (Study 1) and single intake (Study 2). Though a single intake of REPH-B had no influence on any of the parameters evaluated, repeated intake of REPH-B significantly improved the VAS score for hunger. In conclusion, repeated intake of REPH-B might increase hunger in healthy adults who suffer from a lack of appetite. This study was registered with UMIN Clinical Trials Registry as UMIN000049108.

The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be "hidden" by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.

Abstract Aging leads to cognitive decline with considerable individual variability, yet the biological mechanisms remain unclear. Here we performed ultrastructural and proteomic analyses of the medial prefrontal cortex (mPFC) alongside behavioral assessments of attentional set shifting in mice across age groups. Although reduced synaptic density did not consistently lead to cognitive decline, proteomic analyses of synaptosomes and whole tissue revealed that the molecular signatures associated with individual variability in cognitive decline were distinct from those associated with chronological aging, and that synaptic mitochondria and their proteins were more abundant in aged mice with greater cognitive decline. Moreover, treatment with the mitochondria-targeted antioxidant MitoQ reduced the abundance of synaptic mitochondrial proteins, including pro-apoptotic proteins, and mitigated age-related cognitive decline. These findings demonstrate that synaptic mitochondrial oxidative stress in the mPFC, distinct from chronological age-related processes, contributes to individual variability in age-related cognitive decline and offers a potential target for prevention and intervention.

Type I interferonopathy is characterized by aberrant upregulation of type I interferon signaling. The mRNA interferon signature is a useful marker for activation of the interferon pathway and for diagnosis of type I interferonopathy; however, early diagnosis is challenging. This study sought to identify the proteomic interferon signature in dried blood spot (DBS) samples. The aim was to evaluate the usefulness of the interferon signature for neonatal screening and to gain insight into presymptomatic state of neonates with inborn errors of immunity (IEIs). DBS samples from healthy newborns/adults, patients with type I interferonopathy or other IEIs as well as from neonates with viral infections, including some samples obtained during the presymptomatic neonatal period, were examined by nontargeted proteome analyses. Expression of interferon-stimulated genes (ISGs) was evaluated and a DBS-interferon signature was defined. Differential expression/pathway analysis was also performed. The ISG products IFIT5, ISG15, and OAS2 were detected. Expression of IFIT5 and ISG15 was upregulated significantly in individuals with type I interferonopathy. We defined the sum of the z scores for these as the DBS-interferon signature, and found that patients with IEIs other than type I interferonopathy, such as chronic granulomatous disease (CGD), also showed significant elevation. Additionally, neonatal samples of type I interferonopathy and CGD patients showed high interferon signatures. Pathway analysis of neonatal CGD samples revealed upregulation of systemic lupus erythematosus-like pathways. Upregulation of the interferon pathway exists already at birth-not only in neonates with type I interferonopathy but also in other IEIs, including CGD.

Shikonin, a 1,4-naphthoquinone derivative produced by several Boraginaceae species, exhibits unique pharmacological properties and is used as a natural dye. The regulatory factors of shikonin production have been demonstrated using a cell culture system of Lithospermum erythrorhizon. Among these factors, copper is known to be the strongest enhancer of shikonin production. Although shikonin biosynthesis has been studied for over 40 years, the steps of naphthalene ring formation are still unknown, as is the reason for the effect of copper. In this study, we explored candidate genes associated with shikonin production using a PCR-select subtraction experiment. Polyphenol oxidase (PPO), a dicopper-dependent oxidoreductase, was highlighted because it showed synchronous expression with shikonin production. Transcriptome analysis of hairy roots and cultured cells of this plant revealed that, of the five PPO genes expressed in L. erythrorhizon, only PPO1 showed a strong correlation with shikonin production. Next, we generated genome-edited hairy roots of LePPO1 using CRISPR/Cas9-mediated mutagenesis to analyze its impact on shikonin derivative and other specialized metabolite production. The results showed that shikonin content was markedly reduced in all LePPO1-ge lines. Interestingly, the content of deoxyshikonofuran, a hydroquinone derivative and shunt product that branches after GHQ-3′′-OH in the shikonin biosynthetic pathway, remained unaffected in the LePPO1-ge lines. These findings suggest that LePPO1 participates in naphthalene ring formation and explain why a copper ion is crucial for shikonin biosynthesis.

The nutritional environment in early life, referred to as the nutrition history, exerts far-reaching health effects beyond the developmental stage. Here, with Drosophila melanogaster as a model, we fed larvae on diets consisting of a variety of yeast mutants and explored the resulting histories that impacted adult lifespan. A larval diet comprised of yeast nat3 KO shortened the lifespan of male adults; and remarkably, this diet diminished the function of histone acetyltransferase Gcn5 in larvae. Concordantly, perturbation of Gcn5-mediated gene regulation in the larval whole body or neurons significantly contributed to the earlier death of adults. The nat3 KO diet is much more abundant in long-chain fatty acids and branched-chain amino acids (BCAAs) than the control yeast diet. Supplementing the control diet with a combination of oleic acid, valine, and acetic acid recapitulated the effects of the nat3 KO diet on the larval transcriptome and the lifespan of males. Our findings strongly suggest a causal link between a fatty acids- and BCAA-rich diet in developmental stages and lifespan reduction via the adverse effect on the Gcn5 function.

Key messageHerein, a method has been proposed for selecting optimal cross pairs based on the genetic potential of progeny in interpopulation crosses, considering different genetic effects among populations.In the breeding programs for self-pollinating plants, genetic improvements in multiple traits can be challenging when relying solely on a single biparental population, and interpopulation crosses are employed to integrate favorable alleles from multiple biparental populations to overcome this limitation. In this context, it is crucial to consider distinct genetic effects in different populations. In this study, we used a selection method based on the usefulness criterion (UC) to identify cross pairs suitable for interpopulation crosses. We expanded this approach to enhance breeding programs by accounting for varying genetic backgrounds within the genomic selection framework. Using the medicinal plant perilla as the study material, we performed simulations to compare the efficacy of selection based on the estimated genotypic values with that of selection based on UC. Our findings demonstrate that the proposed method is effective in facilitating the simultaneous improvement of multiple traits, particularly by considerably increasing the genetic gains among the top-performing individuals in the population. Furthermore, we provide guidelines for implementing interpopulation crosses, including recommendations for the optimal generation for crossing and an appropriate reference generation for calculating UC. The results obtained in this study offer valuable insights for small-scale breeding programs aimed at simultaneously enhancing multiple traits through interpopulation crosses and can be applied to a wide range of crops, including neglected and underutilized species.

CD4+ helper T (Th) cell subsets play an essential role in the regulation of adaptive immunity. Th9, Th17, and regulatory T (Treg) cells require transforming growth factor-beta (TGF-β) for their differentiation; however, their respective functions are highly distinct. Recent studies have highlighted the critical role of cellular metabolism in initiating clonal expansion and facilitating the effector differentiation of Th cells. Upon antigen exposure, naïve CD4+ T cells undergo metabolic reprogramming to fulfill their bioenergetic and biosynthetic demands. This process involves a shift from fatty acid oxidation to glycolysis, which ensures a sufficient energy supply for activation and proliferation. Lipid metabolism plays a pivotal role in modulating the differentiation and function of Th17, Treg, and Th9 cells. This review explores the influence of metabolic pathways on key transcription factors, including retinoic-acid-related orphan receptor gamma t (RORγt) and SMADs, and emphasizes their regulatory roles in Th cell differentiation. Furthermore, it discusses emerging therapeutic strategies aimed at targeting cellular metabolism to address autoimmune and inflammatory diseases associated with these T-cell subsets.

Primary adrenal insufficiency (PAI) is a rare, life-threatening condition, and at times is associated with differences of sexual differentiation (DSD). Cytochrome P450 enzymes, which are essential for steroidogenesis in adrenals and gonads, have heme in their active center. CPOX encodes an enzyme coproporphyrinogen oxidase (CPOX) that is involved in the synthesis of heme. This study aims to report the identification of biallelic inactivating CPOX variants in 3 unrelated patients with PAI and their clinical characteristics. We report 3 patients with childhood-onset PAI, including 2 with 46,XY DSD. All 3 had adrenal hypoplasia. Additionally, they commonly had severe neonatal jaundice; 2 developed skin blisters in the areas exposed to phototherapy and 2 showed severe neonatal anemia requiring transfusions. Exome sequencing was performed to explore the genetic basis of the patients. The pathogenicity of the identified variants was confirmed with targeted mRNA and proteomic analyses of the patient-derived peripheral blood cells. We identified biallelic rare CPOX variants in each patient, including c.2T > G, p.Arg426*, c.1277G > A, and p.Tyr429Cysfs33*. The 3 patients commonly had the start codon-altering c.2T > G variant. Analysis of the mRNA and proteome of peripheral blood cells from 1 patient (c.2T > G and p.Arg426*) showed that CPOX mRNA expression was comparable to controls; however, CPOX protein expression was significantly decreased to 1%. We provided genetic evidence linking CPOX deficiency and PAI with 46,XY DSD, suggesting that the heme synthesis pathway plays an important role in human steroidogenesis.