Genome-Wide Identification and Biochemical Characterization of Alcohol Acyltransferases for Aroma Generation in Isolates from Fermented Food.

The importance of nonconventional yeasts has increasingly been highlighted, particularly for aroma formation in fermented foods. Here, we performed whole-genome sequencing of , which produces a variety of volatile flavor compounds, leading to the identification of the alcohol acyltransferase (AATase) family of genes. The genome of contains seven AATase genes, encoding alcohol--acetyltransferases (ATFs) and ethanol acetyltransferase 1 (EAT1) for acetate ester formation, along with ethanol hexanoyl transferase 1 (EHT1) for ethyl ester formation.

Positive Selection of Mitochondrial Gene in the Marine Bivalve (Bivalvia, Cardiidae).

The mitochondrial genome provides valuable data for phylogenetic analysis and evolutionary research. In this study, we sequenced, assembled, and annotated the mitochondrial genome of using the Illumina platform. The genome spanned 16,967 bp and included 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs.

Comparative genomic analysis of copepod humoral immunity genes with sex-biased expression in Labidocera rotunda.

Studies of innate immune system function in invertebrates have contributed significantly to our understanding of the mammalian innate immune system. However, in-depth research on innate immunity in marine invertebrates remains sparse. We generated the first de novo genome and transcriptome sequences of copepod Labidocera rotunda using Illumina paired-end data and conducted a comparative genome analysis including five crustaceans (four copepods and one branchiopod species).

Do red tide events promote an increase in zooplankton biodiversity?

Red tides occurring off the southern coast of Korea impact the marine ecosystem and aquaculture industries. Zooplankton are crucial in the food web, connecting primary producers to higher predators and interact diversely with red tide organisms. This study explores dynamics of the zooplankton community over seven years including three red tide and four non-red tide years in Tongyeong using metabarcoding.

Highly contiguous genome assembly and gene annotation of the short-finned eel (Anguilla bicolor pacifica).

In East Asia, anguillid eels are commercially important. However, unlike other species, they have not been successfully cultivated throughout their lifecycle. Facing population decline due to overharvesting and environmental pressures, the industry is turning to alternatives, such as Anguilla bicolor pacifica (short-finned eel).

The occurrence of positive selection on BicA transporter of Microcystis aeruginosa.

The rapid growth of cyanobacteria, particularly Microcystis aeruginosa, poses a significant threat to global water security. The proliferation of toxic Microcystis aeruginosa raises concerns due to its potential harm to human health and socioeconomic impacts. Dense blooms contribute to spatiotemporal inorganic carbon depletion, promoting interest in the roles of carbon-concentrating mechanisms (CCMs) for competitive carbon uptake.

Genomic analysis uncovers that cold-inducible RNA binding protein is associated with estrogen receptor in breast cancer.

Background: RNA-binding proteins (RBPs) perform various biological functions in humans and are associated with several diseases, including cancer. Therefore, RBPs have emerged as novel therapeutic targets. Although recent investigations have shown that RBPs have crucial functions in breast cancer (BC), detailed research is underway to determine the RBPs that are closely related to cancers.

The mA writer RBM15 drives the growth of triple-negative breast cancer cells through the stimulation of serine and glycine metabolism.

N-adenosine methylation (mA) is critical for controlling cancer cell growth and tumorigenesis. However, the function and detailed mechanism of how mA methyltransferases modulate mA levels on specific targets remain unknown. In the current study, we identified significantly elevated levels of RBM15, an mA writer, in basal-like breast cancer (BC) patients compared to nonbasal-like BC patients and linked this increase to worse clinical outcomes.

Transcriptome and functional analyses of phenotypic plasticity in sea grape Caulerpa okamurae.

Caulerpa is a marine green macroalga distinguished by a large single cell with multiple nuclei. It also exhibits remarkable morphological intraspecies variations, in response to diverse environmental types. However, the molecular mechanisms underlying this phenotypic plasticity remain poorly understood.

BRD2-specific inhibitor, BBC0403, inhibits the progression of osteoarthritis pathogenesis in osteoarthritis-induced C57BL/6 male mice.

Background And Purpose: The discovery of new bromo- and extra-terminal inhibitors presents new drugs to treat osteoarthritis (OA).

Experimental Approach: The new drug, BBC0403, was identified in the DNA-encoded library screening system by searching for compounds that target BRD (bromodomain-containing) proteins. The binding force with BRD proteins was evaluated using time-resolved fluorescence energy transfer (TR-FRET) and binding kinetics assays.

Dietary exposure of the water flea to microcystin-LR.

Harmful substances like the cyanotoxin microcystin-leucine-arginine (MC-LR) are commonly found in eutrophic freshwater environments, posing risks to aquatic organisms. The water flea, , is a well-established model organism for environmental toxicology research. Nevertheless, there is currently insufficient research on the genes that respond to MC-LR in .

Comparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity.

Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A.

AMPK-HIF-1α signaling enhances glucose-derived de novo serine biosynthesis to promote glioblastoma growth.

Background: Cancer cells undergo cellular adaptation through metabolic reprogramming to sustain survival and rapid growth under various stress conditions. However, how brain tumors modulate their metabolic flexibility in the naturally serine/glycine (S/G)-deficient brain microenvironment remain unknown.

Methods: We used a range of primary/stem-like and established glioblastoma (GBM) cell models in vitro and in vivo.

Integrated genomics and phenotype microarray analysis of Saccharomyces cerevisiae industrial strains for rice wine fermentation and recombinant protein production.

The industrial potential of Saccharomyces cerevisiae has extended beyond its traditional use in fermentation to various applications, including recombinant protein production. Herein, comparative genomics was performed with three industrial S. cerevisiae strains and revealed a heterozygous diploid genome for the 98-5 and KSD-YC strains (exploited for rice wine fermentation) and a haploid genome for strain Y2805 (used for recombinant protein production).

Novel molecule BBC0901 inhibits BRD4 and acts as a catabolic regulator in the pathogenesis of osteoarthritis.

Osteoarthritis (OA) is induced by matrix degradation and inflammation mediated by bromo-domain-containing protein 4 (BRD4)-dependent catabolic factors. BRD4 acts as both a transcriptional regulator and an epigenetic reader. BBC0901 was identified as an inhibitor of BRD4 using a DNA-encoded library screening system.

Blockade of Activin Receptor IIB Protects Arthritis Pathogenesis by Non-Amplification of Activin A-ACVR2B-NOX4 Axis Pathway.

Although activin receptor IIB (ACVR2B) is emerging as a novel pathogenic receptor, its ligand and assembled components (or assembly) are totally unknown in the context of osteoarthritis (OA) pathogenesis. The present results suggest that upregulation of ACVR2B and its assembly could affect osteoarthritic cartilage destruction. It is shown that the ACVR2B ligand, activin A, regulates catabolic factor expression through ACVR2B in OA development.

Galectin-4 increases the ability of M2 macrophages to enhance antiviral CD4+ T-cell responses.

Galectin-4 (Gal-4) is a β-galactoside-binding protein belonging to the galectin family. Although Gal-4 is known to be involved in several physiologic processes of the gastrointestinal tract, its immunomodulatory roles remain unclear. In this study, we investigated whether Gal-4 influences the function of M1 and M2 macrophages.

A practical comparison of the next-generation sequencing platform and assemblers using yeast genome.

Assembling fragmented whole-genomic information from the sequencing data is an inevitable process for further genome-wide research. However, it is intricate to select the appropriate assembly pipeline for unknown species because of the species-specific genomic properties. Therefore, our study focused on relatively more static proclivities of sequencing platforms and assembly algorithms than the fickle genome sequences.

Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products.

In this review, we describe the genomic and physiological features of the yeast species predominantly isolated from Nuruk, a starter for traditional Korean rice wines, and Jang, a traditional Korean fermented soy product. Nuruk and Jang have several prevalent yeast species, including Saccharomycopsis fibuligera, Hyphopichia burtonii, and Debaryomyces hansenii complex, which belong to the CUG clade showing high osmotic tolerance. Comparative genomics revealed that the interspecies hybridization within yeast species for generating heterozygous diploid genomes occurs frequently as an evolutional strategy in the fermentation environment of Nuruk and Jang.

A New (Aphroditiformia: Polynoidae) Scale Worm from the Onnuri Deep-sea Hydrothermal Vent Field, Northern Central Indian Ridge.

Deep-sea hydrothermal vents are dynamic environments with exotic fauna, including bathymodiolin mussels and scale worm annelids that are often in close association. In this study, we found a new species of (Aphroditiformia: Polynoidae) living in the recently discovered mussel in deep-sea hydrothermal vents and methane seeps at 2,014-2,023 m depth. Based on the morphology and full mitochondrial genome sequences of specimens of from the Onnuri vent field (OVF) on the northern Central Indian Ridge, we describe them as a new species: sp.

The complete mitochondrial genome of Mori, 1929 (Copepoda: Calanoida) from Jeju Island, Korea.

We sequenced the complete mitochondrial genome of the copepod (family Pontellidae) collected from Ihotaewoo Beach in Jeju, Korea. The mitochondrial genome was 16,564 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The concatenated phylogenetic tree of was reconstructed using the maximum-likelihood method based on the eight PCGs obtained from eight species of copepods including .

LCK-Mediated RIPK3 Activation Controls Double-Positive Thymocyte Proliferation and Restrains Thymic Lymphoma by Regulating the PP2A-ERK Axis.

Receptor-interacting protein kinase 3 (RIPK3) is the primary regulator of necroptotic cell death. RIPK3 expression is often silenced in various cancer cells, which suggests that it may have tumor suppressor properties. However, the exact mechanism by which RIPK3 negatively regulates cancer development and progression remains unclear.

The complete mitochondrial genome of the sand dollar (Verrill, 1867) (Echinoidea: Astriclypeidae) in the subtidal sand flat in Jeju Island off the south coast of Korea.

We sequenced the complete mitochondrial genome of sand dollar (Verrill 1867) (Echinoidea: Astriclypeidae) occurring in the subtidal sand flat in Jeju Island off the south coast of Korea. The mitochondrial genome was 15,744 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and 140 nucleotides representing the putative control region. We reconstructed the concatenated phylogenetic tree based on 13 PCGs of 18 echinoderms, including .