Background Long COVID, including symptoms such as asthma, allergies, musculoskeletal pain, diabetes, insomnia, headaches, chronic fatigue, and frailty persisting for at least 2 months following acute SARS-CoV-2 infection, is a global health concern with no established treatments. While some studies demonstrated efficacy using mesenchymal stem cells (MSCs), outcomes have been inconsistent. Methods In the present study, we evaluated a small, distinct subset of SSEA-3(+) MSCs, known as multilineage-differentiating stress-enduring (Muse) cells, in a preclinical model of SARS-CoV-2 infection. Here, in a Syrian hamster model of SARS-CoV-2 infection, Syrian hamsters were intranasally inoculated with SARS-CoV-2 on day 0, and then on day 2, the hamsters were intravenously administered Muse cells, non-Muse cells, or vehicle (saline). On day 8, the hamsters were sacrificed, and the lungs and olfactory bulb (OB) were removed from the body to perform the experiments including inflammatory response, apoptosis, fibrosis (lung only). At the same time, total RNA was extracted from the lung and OB for RNA-seq and IPA analysis. Results We demonstrated that intravenous treatment with human-bone marrow-derived Muse cells more effectively reduced inflammation, fibrosis, and apoptosis than non-Muse-MSCs while preserving oxygen saturation, body weight, lung and olfactory bulb structure, and alveolar air space. RNA sequencing identified 64 differentially expressed genes associated with Muse cell-mediated tissue protection, with distinct profiles in olfactory bulb and lung tissues. Although this study does not directly assess long COVID, the marked suppression of severe COVID-associated pathology suggests that Muse cell treatment holds promise as a potential therapeutic approach for long COVID. Conclusions Our findings demonstrated that Muse cells suppressed the expression of inflammatory, apoptosis, fibrosis mediators that may exacerbate severe COVID-19 pathology as ARDS. Some reports suggest that SARS-CoV-2 infection in the olfactory bulb provides a route for SARS-CoV-2 viral invasion of the brain, leading to neurologic symptoms of long COVID. Therefore, we propose that Muse cells could ameliorate both pulmonary and neurologic components of long COVID by suppressing key inflammatory and fibrotic pathways. Because Finally, these findings suggest that Muse cells may be a promising therapeutic approach for mitigating the symptoms of severe COVID-19 infection and preventing long COVID.

Acetic acid bacteria convert environmental sugars and alcohols into acetic acid and various sugars through oxidative fermentation, resulting in the accumulation of these compounds at high concentrations in the culture medium. One such product is the rare sugar 5-keto-d-fructose (5-KF). In Gluconobacter species, 5-KF is transported into the cell and reduced to fructose in a single step by 5-ketofructose reductase, allowing entry into glycolysis. However, it remains unclear whether eukaryotic microorganisms can metabolize 5-KF or which genes are involved in this process. In this study, we investigated the ability of various yeasts to utilize 5-KF and identified genes involved in its metabolism. The model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe were unable to grow on 5-KF, whereas the oleaginous yeast Lipomyces starkeyi efficiently metabolized this sugar. RNA-seq analysis of L. starkeyi grown on 5-KF revealed genes specifically upregulated in response to 5-KF. Based on gene annotation and expression profiles, a putative metabolic pathway was proposed. Gene knockout analyses showed that mutants deficient in specific steps of the pathway grew on downstream intermediates but failed to grow on upstream substrates, indicating loss of the corresponding enzymatic functions. These results suggest that L. starkeyi metabolizes 5-KF via a multistep pathway, 5-KF → l-sorbose → d-sorbitol → d-fructose. This study provides the first evidence of a 5-KF metabolic pathway in yeast, distinct from the single-step conversion to fructose observed in Gluconobacter species.

Abstract Domestication often modifies multiple traits in concert, but whether fruit quality and reproductive mode share a genetic basis in perennial crops has not been tested at multi-omics resolution. In fig ( Ficus carica ), one of the earliest domesticated fruit trees and a crop with archaeobotanical evidence of cultivation over 11,000 years ago, domestication yielded both distinctive flavour and parthenocarpy, fruit development without pollination. We integrated whole-genome resequencing, transcriptomics, volatile and metabolite profiling, and taste sensor data across a diverse accession panel, using Bayesian GWAS/TWAS and multi-omics factor analysis. Flavour emerges as an integrated sensory system led by aroma, which modulates taste through cross-modal interactions, with sugar–acid balance as a secondary axis; these quality traits map to numerous independent loci. Parthenocarpy instead traces to a single perfectly concordant chromosome 04 haplotype ( Eden ) centred on FcMYB101-like , carrying a selective-sweep signature and a derived allele fixed in cultivated figs but rare across the genus. Flavour and reproductive mode thus evolved along separate genomic trajectories, allowing each to be improved independently.

A novel slow-growing bacterium, designated strain ag2_l2_5AT, was isolated from pine forest soil at Kagamiyama, Hiroshima, Japan, by using a gel microdroplet cultivation approach. The strain was characterized as a Gram-negative, non-motile bacterium with a short rod-shaped morphology. The strain formed small, circular, smooth and umbonate colonies after prolonged incubation on agar plates. Cells accumulated intracellular polyphosphate and produced membrane vesicles during the exponential growth phase. The strain grew optimally at 20-30 °C and pH 6.0-7.5, utilizing various sugars, amino acids and organic acids as carbon sources. The genomic G+C content was 62.8%. The major fatty acids were iso-C15 : 0, C16 : 1 ω7c, iso-C16 : 0, iso-C17 : 0 and C16 : 0. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain ag2_l2_5AT belongs to the class Gemmatimonadetes within the phylum Gemmatimonadota. Its closest relatives were Gemmatimonas phototrophica AP64T (91.3% gene sequence similarity), Gemmatimonas aurantiaca T-27T and Pseudogemmatithrix spongiicola 318T. Based on polyphasic characterization, the strain ag2_l2_5AT represents a novel genus and species of the class Gemmatimonadetes, for which the name Leucogemmata humicola gen. nov., sp. nov. is proposed. The type strain is ag2_l2_5AT (=NBRC 117234T=DSM120521T).

Geobacillus kaustophilus GBlys is a lysogenic strain of the temperate phage phiOH2, which is 3,644,428 bp long, has a GC content of 52%, and contains 3,595 predicted protein-coding genes. Here, we report a resequenced GBlys genome obtained by deep sequencing with long and short reads.

Shiga toxin-producing Escherichia coli (STEC) causes hemorrhagic colitis, hemolytic uremic syndrome, and acute encephalopathies that may lead to sudden death or severe neurologic sequelae. Current treatments, including immunoglobulin G (IgG) immunoadsorption, plasma exchange, steroid pulse therapy, and the monoclonal antibody eculizumab, have limited effects against the severe neurologic sequelae. Multilineage-differentiating stress-enduring (Muse) cells are endogenous reparative non-tumorigenic stem cells that naturally reside in the body and are currently under clinical trials for regenerative medicine. When administered intravenously, Musecells accumulate to the damaged tissue, where they exert anti-inflammatory, anti-apoptotic, anti-fibrotic, and immunomodulatory effects, and replace damaged cells by differentiating into tissue-constituent cells. Here, severely immunocompromised non-obese diabetic/severe combined immunodeficiency (NOD-SCID) mice orally inoculated with 9 × 109 colony-forming units of STEC O111 and treated 48 h later with intravenous injection of 5 × 104 Muse cells exhibited 100% survival and no severe after-effects of infection. Suppression of granulocyte-colony-stimulating factor (G-CSF) by RNAi abolished the beneficial effects of Muse cells, leading to a 40% death and significant body weight loss, suggesting the involvement of G-CSF in the beneficial effects of Muse cells in STEC-infected mice. Thus, intravenous administration of Muse cells could be a candidate therapeutic approach for preventing fatal encephalopathy after STEC infection.

Intestinal bacteria play a crucial role in human health, for example, by maintaining immune and metabolic homeostasis and protecting against pathogens. Survival in the human intestine depends on the bacterium's ability to utilize complex carbohydrates. Some species are known to use host-derived glycans; for example, Bifidobacteria can utilize O-glycan of mucin. However, there are few studies on intestinal bacteria utilizing host-derived N-glycan. Here, we identified the mechanism underlying the breakdown and utilization of complex-type N-glycan by the human intestinal bacterium Barnesiella intestinihominis. A growth assay showed that B. intestinihominis can utilize complex-type N-glycan as a carbon source, while RNA-seq analysis identified enzymes and transporters involved in the mechanism of N-glycan breakdown. In particular, the expression of three genes encoding glycoside hydrolase 85 endo-β-N-acetylglucosaminidase (endo-BIN1, endo-BIN2, and endo-BIN3) rose markedly in bacterial cells cultured in complex-type N-glycoprotein medium. We also found that the susC and susD genes, encoding the SusC/SusD membrane complex, form a gene cluster with endo-BIN genes, suggesting that SusC/SusD is involved in transportation of the glycan into the cell. Other genes encoding exo-type glycoside hydrolase enzymes showed elevated expression in cells grown in complex-type N-glycoprotein medium, suggesting that these enzymes function in further degradation of glycan for metabolism by the bacterium. Collectively, these findings suggest the survival strategy of an intestinal bacterium that has a unique metabolic pathway to use host-derived complex-type N-glycan as a nutrient.

ABSTRACT The oleaginous yeast Lipomyces starkeyi is an attractive industrial yeast that can accumulate high amounts of intracellular lipids. Identification of genes involved in lipid accumulation contributes not only to elucidating the lipid accumulation mechanism but also to breeding industrially useful high lipid-producing strains. In this study, the suppressed lipid accumulation-related gene (SLA1) was identified as the causative gene of the sr22 mutant with decreased lipid productivity. Suppressed lipid accumulation-related gene mutation reduced gene expression in lipid biosynthesis and increased gene expression in β-oxidation. Our results suggest that SLA1 mutation may leads to decreased lipid productivity. Suppressed lipid accumulation-related gene deletion also exhibited decreased gene expression in β-oxidation and increased lipid accumulation, suggesting that SLA1 deletion is a useful tool to improve lipid accumulation in L. starkeyi for industrialization.

Despite its significance in breeding and agricultural practices, the genetic mechanisms that determine sex in the fig (Ficus carica) are not clearly understood, highlighting the need for comprehensive genomic and genetic research to clarify these complex processes. With the aim to accurately identifying the genetic loci involved in sex-related traits of the fig, two chromosome-scale genome sequences for 'Horaishi' (a female line) and 'Caprifig 6085 ' (a male line) were determined, and a genome-wide association study (GWAS) was subsequently conducted using single nucleotide polymorphisms (SNPs) obtained from whole genome sequencing across genetically diverse lines and a biparental mapping population derived from a cross between the two lines. As a result, two major GWAS signals were detected. Of these, only the SNPs on FcRAN1 were found to perfectly associate with the sex phenotype, which was suggested as a sex determinant in our previous study. On the other hand, the SNP pattern of FcAG did not perfectly match the sex phenotype, but FcAG was located near and showed another strong GWAS signal, and in contrast, the polymorphisms in the deletion of FcAG did not contradict the sex phenotype or the SNP pattern of FcRAN1. These results suggest that the candidate genes for the sex-linked traits in figs are narrowed down to both FcRAN1 and FcAG, indicating that they are not limited to one or the other. Furthermore, they suggest some potential scenarios, including the possibility that the sex-linked traits are controlled either complementarily or collaboratively by these two genes, which are in linkage disequilibrium. In addition, we confirmed that a non-recombining sex-linked region exists between these two gene loci. The genome information and the finding for sex-related traits would be helpful to understand sex determination mechanisms in Ficus plants as well as the fig breeding programs.

In this study, we investigated a deleterious mutation in the β-xylosidase gene, xylA (AkxylA), in Aspergillus luchuensis mut. kawachii IFO 4308 by constructing an AkxylA disruptant and complementation strains of AkxylA and xylA derived from A. luchuensis RIB2604 (AlxylA), which does not harbor the mutation in xylA. Only the AlxylA complementation strain exhibited significantly higher growth and substantial β-xylosidase activity in medium containing xylan, accompanied by an increase in XylA expression. This resulted in lower xylobiose and higher xylose concentrations in the mash of barley shochu. These findings suggest that the mutation in xylA affects xylose levels during the fermentation process. Because the mutation in xylA was identified not only in the genome of strain IFO 4308 but also the genomes of other industrial strains of A. luchuensis and A. luchuensis mut. kawachii, these findings enhance our understanding of the genetic factors that affect the fermentation characteristics.

Genome editing is a technology that can remarkably accelerate crop and animal breeding via artificial induction of desired traits with high accuracy. This study aimed to develop a chub mackerel variety with reduced aggression using an experimental system that enables efficient egg collection and genome editing. Sexual maturation and control of spawning season and time were technologically facilitated by controlling the photoperiod and water temperature of the rearing tank. In addition, appropriate low-temperature treatment conditions for delaying cleavage, shape of the glass capillary, and injection site were examined in detail in order to develop an efficient and robust microinjection system for the study. An arginine vasotocin receptor V1a2 ( V1a2 ) knockout (KO) strain of chub mackerel was developed in order to reduce the frequency of cannibalistic behavior at the fry stage. Video data analysis using bioimage informatics quantified the frequency of aggressive behavior, indicating a significant 46% reduction (P = 0.0229) in the frequency of cannibalistic behavior than in wild type. Furthermore, in the V1a2 KO strain, the frequency of collisions with the wall and oxygen consumption also decreased. Overall, the manageable and calm phenotype reported here can potentially contribute to the development of a stable and sustainable marine product.

Short-chain peptides derived from various protein sources have been shown to exhibit diverse bio-modulatory and health-promoting effects in animal experiments and human trials. We recently reported that the oral administration of the Tyr–Trp (YW) dipeptide to mice markedly enhances noradrenaline metabolism in the brain and ameliorates the working-memory deficits induced by the β-amyloid 25–35 peptide (Aβ25–35). In the current study, we performed multiple bioinformatics analyses of microarray data from Aβ25–35/YW-treated brains to determine the mechanism underlying the action of YW in the brain and to infer the molecular mechanisms and networks involved in the protective effect of YW in the brain. We found that YW not only reversed inflammation-related responses but also activated various molecular networks involving a transcriptional regulatory system, which is mediated by the CREB binding protein (CBP), EGR-family proteins, ELK1, and PPAR, and the calcium-signaling pathway, oxidative stress tolerance, and an enzyme involved in de novo l-serine synthesis in brains treated with Aβ25–35. This study revealed that YW has a neuroprotective effect against Aβ25–35 neuropathy, suggesting that YW is a new functional-food-material peptide.

The oleaginous yeast Lipomyces starkeyi has considerable potential in industrial application, since it can accumulate a large amount of triacylglycerol (TAG), which is produced from sugars under nitrogen limitation condition. However, the regulation of lipogenesis in L. starkeyi has not been investigated in depth. In this study, we compared the genome sequences of wild-type and mutants with increased TAG productivity, and identified a regulatory protein, LsSpt23p, which contributes to the regulation of TAG synthesis in L. starkeyi. L. starkeyi mutants overexpressing LsSPT23 had increased TAG productivity compared with the wild-type strain. Quantitative real-time PCR analysis showed that LsSpt23p upregulated the expression of GPD1, which encodes glycerol 3-phosphate dehydrogenase; the Kennedy pathway genes SCT1, SLC1, PAH1, DGA1, and DGA2; the citrate-mediated acyl-CoA synthesis pathway-related genes ACL1, ACL2, ACC1, FAS1, and FAS2; and OLE1, which encodes ∆9 fatty acid desaturase. Chromatin immunoprecipitation-quantitative PCR assays indicated that LsSpt23p acts as a direct regulator of SLC1 and PAH1, all the citrate-mediated acyl-CoA synthesis pathway–related genes, and OLE1. These results indicate that LsSpt23p regulates TAG synthesis. Phosphatidic acid is a common substrate of phosphatidic acid phosphohydrolase, which is used for TAG synthesis, and phosphatidate cytidylyltransferase 1 for phospholipid synthesis in the Kennedy pathway. LsSpt23p directly regulated PAH1 but did not affect the expression of CDS1, suggesting that the preferred route of carbon is the Pah1p-mediated TAG synthesis pathway under nitrogen limitation condition. The present study contributes to understanding the regulation of TAG synthesis, and will be valuable in future improvement of TAG productivity in oleaginous yeasts. LsSpt23p was identified as a positive regulator of TAG biosynthesis LsSPT23 overexpression enhanced TAG biosynthesis gene expression and TAG production LsSPT23 M1108T overexpression mutant showed fivefold higher TAG production than control

A putative methyltransferase, LaeA, controls citric acid production through epigenetic regulation of the citrate exporter gene, cexA, in the white koji fungus Aspergillus luchuensis mut. kawachii. In this study, we investigated the role of another epigenetic regulator, heterochromatin protein 1, HepA, in citric acid production. The ΔhepA strain exhibited reduced citric acid production in liquid culture, although to a lesser extent compared to the ΔlaeA strain. In addition, the ΔlaeA ΔhepA strain showed citric acid production similar to the ΔlaeA strain, indicating that HepA plays a role in citric acid production, albeit with a less-significant regulatory effect than LaeA. RNA-seq analysis revealed that the transcriptomic profiles of the ΔhepA and ΔlaeA strains were similar, and the expression level of cexA was reduced in both strains. These findings suggest that the genes regulated by HepA are similar to those regulated by LaeA in A. luchuensis mut. kawachii. However, the reductions in citric acid production and cexA expression observed in the disruptants were mitigated in rice koji, a solid-state culture. Thus, the mechanism by which citric acid production is regulated differs between liquid and solid cultivation. Further investigation is thus needed to understand the regulatory mechanism in koji.

Aspergillus luchuensis mut. kawachii is used primarily in the production of shochu, a traditional Japanese distilled alcoholic beverage. Here, we report the chromosome-level genome sequence of A. luchuensis mut. kawachii IFO 4308 (NBRC 4308) and a comparison of the sequence with that of A. luchuensis RIB2601. The genome of strain IFO 4308 was assembled into nine contigs consisting of eight chromosomes and one mitochondrial DNA segment. The nearly complete genome of strain IFO 4308 comprises 37,287,730 bp with a GC content of 48.85% and 12,664 predicted coding sequences and 267 tRNAs. Comparison of the IFO 4308 and RIB2601 genomes revealed a highly conserved structure; however, the IFO 4308 genome is larger than that of RIB2601, which is primarily attributed to chromosome 5. The genome sequence of IFO 4308 was deposited in DDBJ/ENA/GenBank under accession numbers AP024425–AP024433.

The epigenetic regulatory system significant influences the fate determination of cells during developmental processes. Prdm12 is a transcriptional regulator that modulates gene expression epigenetically. The Prdm12 gene has been shown to be expressed in neural tissues, specifically during development, but its detailed function is not fully understood. This study investigated the function of the Prdm12 gene in P19 mouse embryonic tumor cells as a model for neural differentiation. A decrease in the expression of neuron-specific genes and the alterations of dendrites and axons morphology was confirmed in Prdm12-knockout P19 cells. In addition, almost no astrocytes were generated in Prdm12-knockout P19 cells. Comprehensive gene expression analysis revealed that there was a reduction in the expression of the inhibitory neuron-specific genes Gad1/2 and Glyt2, but not the excitatory neuron-specific gene VGLUT2, in Prdm12-knockout P19 cells. Furthermore, the expression of inhibitory neuron-related factors, Ptf1a, Dbx1, and Gsx1/2, decreased in Prdm12-knockout P19 cells. Gene expression analysis also revealed that the Ptf1a, Hic1, and Foxa1 genes were candidate targets of Prdm12 during neurogenesis. These results suggest that Prdm12 regulates the differentiation of inhibitory neurons and astrocytes by controlling the expression of these genes during the neural differentiation of P19 cells.

Aspergillus puulaauensis strain MK2 was isolated from a dead hard tick ( Haemaphysalis longicornis ). Here, we determined the chromosome-level genome sequence of A. puulaauensis MK2.

Light stimulates carotenoid production in an oleaginous yeast Rhodosporidium toruloides NBRC 10032 by promoting carotenoid biosynthesis genes. These genes undergo two-step transcriptional activation. The potential light regulator, Cryptochrome DASH (CRY1), has been suggested to contribute to this mechanism. In this study, based on KU70 (a component of nonhomologous end joining (NHEJ)) disrupting background, CRY1 disruptant was constructed to clarify CRY1 function. From analysis of CRY1 disruptant, it was suggested that CRY1 has the activation role of the carotenogenic gene expression. To obtain further insights into the light response, mutants varying carotenoid production were generated. Through analysis of mutants, the existence of the control two-step gene activation was proposed. In addition, our data analysis showed the strong possibility that R. toruloides NBRC 10032 is a homo-diploid strain.

l-Serine (Ser) is synthesized de novo from 3-phosphoglycerate via the phosphorylated pathway committed by phosphoglycerate dehydrogenase (Phgdh). A previous study reported that feeding a protein-free diet increased the enzymatic activity of Phgdh in the liver and enhanced Ser synthesis in the rat liver. However, the nutritional and physiological functions of Ser synthesis in the liver remain unclear. To clarify the physiological significance of de novo Ser synthesis in the liver, we generated liver hepatocyte-specific Phgdh KO (LKO) mice using an albumin-Cre driver. The LKO mice exhibited a significant gain in body weight compared to Floxed controls at 23 weeks of age and impaired systemic glucose metabolism, which was accompanied by diminished insulin/IGF signaling. Although LKO mice had no apparent defects in steatosis, the molecular signatures of inflammation and stress responses were evident in the liver of LKO mice. Moreover, LKO mice were more vulnerable to protein starvation than the Floxed mice. These observations demonstrate that Phgdh-dependent de novo Ser synthesis in liver hepatocytes contributes to the maintenance of systemic glucose tolerance, suppression of inflammatory response, and resistance to protein starvation.

Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data ( http://marine-meta.healthscience.sci.waseda.ac.jp/omd/ ), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.