Integration of metabolomics and other omics: from microbes to microbiome.

Metabolomics is a cutting-edge omics technology that identifies metabolites in organisms and their environments and tracks their fluctuations. This field has been extensively utilized to elucidate previously unknown metabolic pathways and to identify the underlying causes of metabolic changes, given its direct association with phenotypic alterations. However, metabolomics inherently has limitations that can lead to false positives and false negatives.

PRMT1-mediated methylation regulates MLL2 stability and gene expression.

The interplay between multiple transcription factors precisely regulates eukaryotic transcription. Here, we report that the protein methyltransferases, MLL2/KMT2B and PRMT1, interact directly and act collectively to regulate gene expression. PRMT1 binds to the N-terminal region of MLL2, considered an intrinsically disordered region, and methylates multiple arginine residues within its RGG/RG motifs.

All Roads Lead to Rome: Pathways to Engineering Disease Resistance in Plants.

Unlike animals, plants are unable to move and lack specialized immune cells and circulating antibodies. As a result, they are always threatened by a large number of microbial pathogens and harmful pests that can significantly reduce crop yield worldwide. Therefore, the development of new strategies to control them is essential to mitigate the increasing risk of crops lost to plant diseases.

Molecular Characterization of Subdomain Specification of Cochlear Duct Based on Foxg1 and Gata3.

The inner ear is one of the sensory organs of vertebrates and is largely composed of the vestibule, which controls balance, and the cochlea, which is responsible for hearing. In particular, a problem in cochlear development can lead to hearing loss. Although numerous studies have been conducted on genes involved in the development of the cochlea, many areas still need to be discovered regarding factors that control the patterning of the early cochlear duct.

Design and evaluation of anaplastic lymphoma kinase degraders using a covalent fumarate handle.

Targeted protein degradation has emerged as a novel therapeutic paradigm in drug discovery. Despite the FDA approval of anaplastic lymphoma kinase (ALK) inhibitors, the pursuit of compounds with enhanced potency and prolonged efficacy remains crucial to mitigate inevitable adverse effects. In this context, we endeavored to develop ALK degraders utilizing FDA-approved ALK inhibitors-crizotinib, ceritinib, brigatinib, and alectinib-as ALK binders, along with 4-methoxyphenylfumarate as a covalent handle to bind to RNF126 E3 ligase.

Highly Stretchable 3D Microelectrode Array for Noninvasive Functional Evaluation of Cardiac Spheroids and Midbrain Organoids.

Organoids are 3D biological models that recapitulate the complex structures and functions of human organs. Despite the rapid growth in the generation of organoids, in vitro assay tools are still limited to 2D forms. Thus, a comprehensive and continuous functional evaluation of the electrogenic organoids remains a challenge.

Radiation-Resistant Bacteria Deinococcus radiodurans-Derived Extracellular Vesicles as Potential Radioprotectors.

The increasing use of radiation presents a risk of radiation exposure, making the development of radioprotectors necessary. In the previous study, it is investigated that Deinococcus radiodurans (R1-EVs) exert the antioxidative properties. However, the radioprotective activity of R1-EVs remains unclear.

Transcriptomic landscapes of STING-mediated DNA-sensing reveal cellular response heterogeneity.

Transfection of plasmid DNA (pDNA) encoding target genes is a routine tool in gene function studies and therapeutic applications. However, nucleic acid-sensing-mediated innate immune responses influence multiple intracellular signaling pathways. The stimulator of interferon genes (STING) is a crucial adapter protein for DNA sensors in mammalian cells.

Toxin production in bloom-forming, harmful alga Alexandrium pacificum (Group IV) is regulated by cyst formation-promoting bacteria Jannaschia cystaugens NBRC 100362.

Harmful algal blooms (HABs) caused by dinoflagellates like Alexandrium pacificum pose significant ecological and public health risks due to their production of paralytic shellfish toxins (PSTs). Bacterial populations, particularly Alexandrium cyst formation-promoting bacteria (Alex-CFPB), are known to significantly influence growth, encystment, toxin synthesis, the composition of toxic components, and bloom dynamics of these dinoflagellates. However, the role of Alex-CFPB in Alexandrium toxin synthesis and the mechanisms thereof are still unclear.

Comprehensive analysis of primary and secondary metabolites and antioxidant activities provides insights into metabolic profiling of different organs of Pimpinella brachycarpa Nakai.

Pimpinella brachycarpa Nakai is a perennial plant that has been widely used as a traditional medicine. However, the comprehensive analysis of primary and secondary metabolites and antioxidant activities in different organs (flowers, leaves, stems, and roots) has not been extensively studied. A comprehensive analysis using GC-qMS, GC-TOFMS, and HPLC metabolomic analyses identified 66 known metabolites in different organs of P.

Regulatory effects of extract and Diphlorethohydroxycarmalol on skin barrier function.

Ethnopharmacological Relevance: The pharmacological potential of marine organisms remains largely unexplored. commonly known as Pae, is extensively distributed over Asia. Its antioxidant, antibacterial, antiobesity, and anti-inflammatory properties are also being investigated.

Gonyaulax montresoriae sp. nov. (Dinophyceae) from the Adriatic Sea produces predominantly yessotoxin.

Yessotoxin is one of the shellfish toxins leading to mussel farm closures in the Adriatic Sea of Italy. Two putative Gonyaulax spinifera strains GSA0501 and GSA0602 are known as yessotoxins producers, but their identities have remained elusive since 2005. To address this gap, we established five Gonyaulax strains by incubating sediments from the Adriatic Sea and subsequently isolating single cells.

Intracellular gene transfer (IGT) events from the mitochondrial genome to the plastid genome of the subtribe ferulinae drude (Apiaceae) and their implications.

Background: Intracellular gene transfer (IGT) is a phenomenon in genome evolution that occurs between the nuclear and organellar genomes of plants or between the genomes of different organelles. The majority of the plastid genomes (plastomes) in angiosperms have a conserved structure, but some species exhibit unexpected structural variations.

Results: In this study, we focused on the Ferulinae, which includes Ferula, one of the largest genera in the Apiaceae family.

Curvature-Specific Coupling Electrode Design for a Stretchable Three-Dimensional Inorganic Piezoelectric Nanogenerator.

Structures such as 3D buckling have been widely used to impart stretchability to devices. However, these structures have limitations when applied to piezoelectric devices due to the uneven distribution of internal strain during deformation. When strains with opposite directions simultaneously affect piezoelectric materials, the electric output can decrease due to cancellation.

sp. nov., a new member of the phylum , from forest soil in a geothermal area.

Three Gram-stain-positive aerobic bacteria, characterized by branched mycelia with putative sporangia, were isolated from forest soil inside a decayed bamboo stem from a geothermal area in West Java, Indonesia. The strain S3.2.

Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.

V(D)J recombination secures the production of functional immunoglobulin (Ig) genes and antibody diversity during the early stages of B-cell development through long-distance interactions mediated by cis-regulatory elements and trans-acting factors. O-GlcNAcylation is a dynamic and reversible posttranslational modification of nuclear and cytoplasmic proteins that regulates various protein functions, including DNA-binding affinity and protein-protein interactions. However, the effects of O-GlcNAcylation on proteins involved in V(D)J recombination remain largely unknown.

The anticancer effect of metformin targets VDAC1 via ER-mitochondria interactions-mediated autophagy in HCC.

Metformin (MetF) is used worldwide as a first-line therapy for type 2 diabetes. Recently, interest in the pleiotropic effects of MetF, such as its anticancer and antiaging properties, has increased. However, the molecular target of MetF and the detailed mechanism underlying its ability to inhibit cell growth through autophagy induction remain incompletely understood.

EPRS1-mediated fibroblast activation and mitochondrial dysfunction promote kidney fibrosis.

Kidney fibrosis causes irreversible structural damage in chronic kidney disease and is characterized by aberrant extracellular matrix (ECM) accumulation. Although glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is a crucial enzyme involved in proline-rich protein synthesis, its role in kidney fibrosis remains unclear. The present study revealed that EPRS1 expression levels were increased in the fibrotic kidneys of patients and mice, especially in fibroblasts and proximal tubular epithelial cells, on the basis of single-cell analysis and immunostaining of fibrotic kidneys.

Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi.

Two Gram-stain-positive, facultatively anaerobic, non-hemolytic, coccoid-shaped bacterial strains, designated MS01 and MS02, were isolated from cabbage watery kimchi in the Republic of Korea. Cellular growth occurred at 5-25 ℃ (optimum, 20 ℃), pH 5-8 (optimum, pH 7) and in the presence of 0-5% (w/v) NaCl (optimum, 1%). Results of 16S rRNA gene-based phylogenetic analyses showed that strains MS01 and MS02 shared identical sequences, clustered within the Leuconostoc clade in phylogenetic trees, and were most closely related to Leuconostoc inhae IH003 and Leuconostoc gasicomitatum LMG 18811 with sequence similarities of 98.