I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data.

High-dimensional multi-omics microbiome data play an important role in elucidating microbial community interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data.

Solanoeclepin C, a root-secreted molecule converted by rhizosphere microbes to hatching factors for potato cyst nematodes.

Eclepins are root-secreted compounds that induce the hatching of cyst nematodes. Solanoeclepin A (SEA) and B (SEB) have been isolated as potent hatching factors for potato cyst nematodes (PCNs). SEB is biosynthesized in roots, released into the rhizosphere, and converted into SEA by soil microorganisms.

Metabolome Profiling and Predictive Modeling of Dark Green Leaf Trait in Bunching Onion Varieties.

The dark green coloration of bunching onion leaf blades is a key determinant of market value, nutritional quality, and visual appeal. This trait is regulated by a complex network of pigment interactions, which not only determine coloration but also serve as critical indicators of plant growth dynamics and stress responses. This study aimed to elucidate the mechanisms regulating the dark green trait and develop a predictive model for accurately assessing pigment composition.

Loss-of-functional mutation in ANGUSTIFOLIA3 causes leucine hypersensitivity and hypoxia response during Arabidopsis thaliana seedling growth.

Introduction: The ANGUSTIFOLIA3 (AN3) gene encodes a transcriptional co-activator for cell proliferation in Arabidopsis thaliana leaves. We previously showed that Physcomitrium patens AN3 orthologs promote gametophore shoot formation through arginine metabolism.

Objectives: We analyzed the role of AN3 in Arabidopsis thaliana to understand how seedling growth is regulated by metabolic and physiological modulations.

Distribution, biosynthesis, and synthetic biology of phenylethanoid glycosides in the order Lamiales.

Phenylethanoid glycosides (PhGs), with a C-C glucoside unit as the basic skeleton, are specialized (secondary) metabolites found in several medicinal plants. As PhGs exhibit various pharmacological activities, they are expected to be used as lead compounds in drug discovery. However, mass-production systems have not yet been established even for acteoside, a typical PhG that is widely distributed in nature (more than 150 species).

Multi-omics signatures of diverse plant callus cultures.

Callus cultures are fundamental for plant propagation, genetic transformation, and emerging biotechnological applications that use cellular factories to produce high-value metabolites like plant-based drugs. These applications exploit the diverse metabolic capabilities of various plant species. However, optimizing culture conditions for specific applications necessitates a deep understanding of the transcriptome, metabolome, and phytohormone profiles of different species.

Taurine promotes glucagon-like peptide-1 secretion in enteroendocrine L cells.

Taurine, an amino-sulfonic acid mainly sourced from food, suppresses blood glucose by stimulating insulin secretion from pancreatic β-cells. However, its relationship with glucagon-like peptide-1 (GLP-1) secretion from enteroendocrine L cells is unclear. This study aimed to determine the role of taurine in GLP-1 secretion from L cells.

Multiomics-based assessment of the impact of airflow on diverse plant callus cultures.

Plant cell culture has multiple applications in biotechnology and horticulture, from plant propagation to the production of high-value biomolecules. However, the interplay between cellular diversity and ambient conditions influences the metabolism of cultured tissues; understanding these factors in detail will inform efforts to optimize culture conditions. This study presents multiomics datasets from callus cultures of tobacco (Nicotiana tabacum), rice (Oryza sativa), and two bamboo species (Phyllostachys nigra and P.

Metabolite Profiling and Association Analysis of Leaf Tipburn in Heat-Tolerant Bunching Onion Varieties.

The bunching onion is an important leafy vegetable, prized for its distinctive flavor and color. It is consumed year-round in Japan, where a stable supply is essential. However, in recent years, the challenges posed by climate change and global warming have resulted in adverse effects on bunching onions, including stunted growth, discoloration, and the development of leaf tipburn, threatening both crop quality and yield.

Unelongated Stems are an Active Nitrogen-Fixing Site in Rice Stems Supported by Both Sugar and Methane Under Low Nitrogen Conditions.

Enhancing nitrogen (N) fixation in rice plants can reduce N fertilizer application and contribute to sustainable rice production, particularly under low-N conditions. However, detailed microbial and metabolic characterization of N fixation in rice stems, unlike in the well-studied roots, has not been investigated. Therefore, the aim of this study was to determine the active N-fixing sites, their diazotroph communities, and the usability of possible carbon sources in stems compared with roots.

Omics-based identification of the broader effects of 2-hydroxyisoflavanone synthase gene editing on a gene regulatory network beyond isoflavonoid loss in soybean hairy roots.

Soybean (Glycine max) is a leguminous crop cultivated worldwide that accumulates high levels of isoflavones. Although previous research has often focused on increasing the soybean isoflavone content because of the estrogen-like activity of dietary soy in humans, the rapidly increasing demand for soybean as a plant-based meat substitute has raised concerns about excessive isoflavone intake. Therefore, the production of isoflavone-free soybean has been anticipated.

Intestinal butyric acid-mediated disruption of gut hormone secretion and lipid metabolism in vasopressin receptor-deficient mice.

Objectives: Arginine vasopressin (AVP), known as an antidiuretic hormone, is also crucial in metabolic homeostasis. Although AVP receptor-deficient mice exhibit various abnormalities in glucose and lipid metabolism, the mechanism underlying these symptoms remains unclear. This study aimed to explore the involvement of the gut hormones including glucagon-like peptide-1 (GLP-1) and microbiota as essential mediators.

Genomic view of heavy-ion-induced deletions associated with distribution of essential genes in .

Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is a promising tool to induce large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm). Heavy-ion beams with different LET values induce different types and sizes of mutations.

Integration of cell differentiation and initiation of monoterpenoid indole alkaloid metabolism in seed germination of Catharanthus roseus.

In Catharanthus roseus, monoterpenoid indole alkaloids (MIAs) are produced through the cooperation of four cell types, with final products accumulating in specialized cells known as idioblasts and laticifers. To explore the relationship between cellular differentiation and cell type-specific MIA metabolism, we analyzed the expression of MIA biosynthesis in germinating seeds. Embryos from immature and mature seeds were observed via stereomicroscopy, fluorescence microscopy, and electron microscopy.

Plant metabolomics.

Plants are a treasure trove of metabolic compounds. The chemical diversity of plant cells has developed and been maintained through evolution and metabolic regulation, and plays a crucial role in plant physiology, development, and adaption to changing environmental situations. Metabolomics, when combined with genomics and proteomics, has opened up unprecedented opportunities to address the biological importance of metabolic diversity.

N-Acetylornithine deacetylase functions as a Cys-Gly dipeptidase in the cytosolic glutathione degradation pathway in Arabidopsis thaliana.

Glutathione (GSH) is required for various physiological processes in plants, including redox regulation and detoxification of harmful compounds. GSH also functions as a repository for assimilated sulfur and is actively catabolized in plants. In Arabidopsis, GSH is mainly degraded initially by cytosolic enzymes, γ-glutamyl cyclotransferase, and γ-glutamyl peptidase, which release cysteinylglycine (Cys-Gly).

The phosphorylated pathway of serine biosynthesis affects sperm, embryo, and sporophyte development, and metabolism in Marchantia polymorpha.

Serine metabolism is involved in various biological processes. Here we investigate primary functions of the phosphorylated pathway of serine biosynthesis in a non-vascular plant Marchantia polymorpha by analyzing knockout mutants of MpPGDH encoding 3-phosphoglycerate dehydrogenase in this pathway. Growth phenotypes indicate that serine from the phosphorylated pathway in the dark is crucial for thallus growth.

A simple method for creating transgenic pea hairy roots using a Japanese pea cultivar and a Japanese strain.

Pea () is an agriculturally important leguminous crop cultivated worldwide. It is also the plant from which phytoalexin was isolated for the first time. Several studies have investigated gene functions using pea hairy root culture systems.

Distinct lactate metabolism between hepatocytes and myotubes revealed by live cell imaging with genetically encoded indicators.

The process of glycolysis breaks down glycogen stored in muscles, producing lactate through pyruvate to generate energy. Excess lactate is then released into the bloodstream. When lactate reaches the liver, it is converted to glucose, which muscles utilize as a substrate to generate ATP.

Mitochondrial ATP concentration decreases immediately after glucose administration to glucose-deprived hepatocytes.

Hepatocytes can switch their metabolic processes in response to nutrient availability. However, the dynamics of metabolites (such as lactate, pyruvate, and ATP) in hepatocytes during the metabolic switch remain unknown. In this study, we visualized metabolite dynamics in primary cultured hepatocytes during recovery from glucose-deprivation.

Identification of a gene set that maintains tumorigenicity of the hepatocellular carcinoma cell line Li-7.

The identification and development of therapeutic targets in cancer stem cells that lead to tumor development, recurrence, metastasis, and drug resistance is an important goal in cancer research. The hepatocellular carcinoma cell line Li-7 contains functionally different types of cells. Cells with tumor-forming activity are enriched in cancer stem cell-like CD13CD166 cells and this cell population gradually decreases during culture in conventional culture medium (RPMI1640 containing 10% fetal bovine serum).

The Roles of Functional Amino Acids in Plant Growth and Development.

Plants incorporate acquired carbon and nitrogen into amino acid metabolism, whereby the building blocks of proteins and the precursors of various metabolites are produced. This fundamental demand requires tight amino acid metabolism to sustain physiological homeostasis. There is increasing evidence that amino acid metabolism undergoes plastic alteration to orchestrate specific growth and developmental events.

A metabolome genome-wide association study implicates histidine -pi-methyltransferase as a key enzyme in -methylhistidine biosynthesis in .

A genome-wide association study (GWAS), which uses information on single nucleotide polymorphisms (SNPs) from many accessions, has become a powerful approach to gene identification. A metabolome GWAS (mGWAS), which relies on phenotypic information based on metabolite accumulation, can identify genes that contribute to primary and secondary metabolite contents. In this study, we carried out a mGWAS using seed metabolomic data from accessions obtained by liquid chromatography-mass spectrometry to identify SNPs highly associated with the contents of metabolites such as glucosinolates.