Mucin-dependent transcriptional dynamics of Akkermansia muciniphila in co-culture with human colonic organoids.

Akkermansia muciniphila, a mucin-degrading gut bacterium, contributes to intestinal homeostasis and metabolic disorders, yet its transcriptional response to human colonic mucin remains unclear. Here, we used human colonic organoids derived from either a healthy tissue (wild-type) or ATOH1-knockout lines lacking goblet cell differentiation. Co-culturing wild-type or ATOH1-knockout organoids with A.

Polyamine distributions in invertebrates VI: Comparative cellular polyamine analysis of unicellular choanoflagellates and multicellular sponges, comb jellies, hydras, jellyfishes, sea anemones and soft corals.

The more than 35 described biogenic polyamines have important roles in physiological processes ranging from acid-base buffering to the scavenging of oxygen free radicals. As such they have key cellular- and organismal-level functions in environmental adaptation, cell growth, cell differentiation, fertilization, and biomineralization. To determine cellular polyamine distribution profiles in animals at the base of the phylogenetic tree, the acid-extracted polyamines from cultured cells of a unicellular choanoflagellate and whole bodies of five multicellular invertebrate groups (total 20 species) were quantitatively analyzed using high-performance liquid chromatography and high-performance gas chromatography.

Cell Sensing via a Peptide/Single-Strand DNA Probe-Modified Au Screen-Printed Electrode.

An electron-transfer/His-tag peptides-single-strand (ss) DNA probe is designed for the detection of cancer cells. Human myeloid leukemia cells (K562 cells) are commonly used as a model for target cancer cells. An electron-transfer peptide plays the role of a sensing moiety, and a His-tag moiety is introduced to purify the probe.

Spectroelectrochemical Fiber-Optic Sensor Based on Localized Surface Plasmon Resonance for Simultaneous Multiselective Electroactive Species Detection.

Herein, we report the development of a novel sensor combining electrochemistry, localized surface plasmon resonance (LSPR) in nanoparticles, and fiber-optic sensing for the first time. The sensor developed comprises an indium tin oxide (ITO)-coated multimodal optical fiber with gold nanoparticles immobilized on the ITO surface via electrostatic self-assembly. Two types of sensing methods are demonstrated: one based on shift in LSPR peak wavelength accompanying electrochemical oxidation-reduction of an analyte and the other based on potential scanning-based detection of refractive index change.

Selective Notch Frequency Technology for EMI Noise Reduction in DC-DC Converters: A Review.

This review presents our band-selective frequency technology of Electromagnetic Interference (EMI) noise spread spectrum in the DC-DC switching converter for communication devices. The DC-DC switching converter generates electromagnetic interference (EMI) noise. To comply with EMI regulations and reduce the need for bulky filters and shielding, noise spread spectrum technology is commonly employed.

Epigenetic disruption of adipogenic gene enhancers in dedifferentiated liposarcomas and its therapeutic value.

Liposarcoma (LPS) is the most common soft-tissue sarcoma in adults, and well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS) are the most frequent subtypes. These LPSs are considered to develop due to disturbances in the adipogenic differentiation of mesenchymal stem cells. However, the molecular mechanisms underlying the disturbances remain unclear.

Cancer-Type-Specific DNA Methylation Is a Source of Vulnerability in Liver Cancer Cells.

DNA methylation, a pivotal epigenetic mechanism, plays a critical role in various pathological conditions, including cancers. Notably, cancer-type-specific DNA methylation can be advantageous for survival only in specific environments while being disadvantageous in others. To investigate the role of cancer-type-specific methylation as a vulnerability in cancer cells, we bioinformatically profiled genome-wide DNA methylation in 1165 human cancer cell lines across 25 cancer types.

CRISPR-Cas9 genome editing of miso and soy source yeast Zygosaccharomyces sp.

Genome modification would be useful for developing breeding techniques for haploid Zygosaccharomyces rouxii and natural hybrid allodiploid Zygosaccharomyces sp. yeast strains used in miso and soy sauce production. In this study, genome editing using CRISPR-Cas9 was attempted in Zygosaccharomyces sp.

Unveiling the effects of metabolites on the material properties of natural rubber by the integration of metabolomics and material characteristics.

Natural rubber (NR) is an important material with excellent physical properties. Unlike synthetic rubber from petroleum, NR contains non-rubber components such as proteins, lipids, and metal ions. The non-rubber components are known to affect the properties of NR.

Insights Into the Genome Structure of Natural Hybrid Zygosaccharomyces sp. Yeasts Isolated From Miso.

There is currently much interest in the Zygosaccharomyces sp. used to produce fermented foods. Here we have used sequencing and PCR to explore differences in the genomic structures of various haploid and allodiploid Zygosaccharomyces sp.

Sensitivity improvement by Langmuir film formation on a spectroelectrochemical fiber-optic sensor surface.

This study introduces a method for enhancing spectroelectrochemical sensor sensitivity by incorporating optical fiber technology. The sensor comprises a gold mesh electrode coated on the surface of an exposed optical fiber core. Total reflection attenuation spectroscopy was employed to measure the optical properties of the fiber core surface.

Fluorescence molecular imaging-guided photodynamic therapy for early breast cancer in the prone position: Feasibility evaluation with Monte Carlo simulations.

Introduction: The successful diagnosis and treatment of early-stage breast cancer enhances the quality of life of patients. As a promising alternative to recently developed magnetic resonance imaging-guided radiotherapy, we proposed fluorescence molecular imaging-guided photodynamic therapy (FMI-guided PDT), which requires no expensive equipment. In the FMI simulations, ICG-C11 which has emission peaks at near-infrared wavelengths was used as the FMI agent.

Electromyography of Flight Muscles in Free-Flying Chestnut Tiger Butterfly, .

The chestnut tiger butterfly, , can undertake long-distance migrations. They flap their wings for power flight and hold the wings for gliding; such repertoires of wing movements may be the key to explaining their excellent flight abilities. Measuring flight muscle activity using the electromyogram (EMG) is the first step toward understanding the neuromuscular mechanism of active flight control.

The blue light signaling inhibitor 3-bromo-7-nitroindazole affects gene translation at the initial reception of blue light in young seedlings.

Initial light reception after germination is a dramatic life event when a seedling starts proper morphogenesis. Blue light contains a range of light wavelengths that plants can perceive. A previous report suggested that the chemical compound 3-bromo-7-nitroindazole (3B7N) inhibits blue light-mediated suppression of hypocotyl elongation by physically interacting with the blue light receptor Cryptochrome 1 (CRY1).

Effects of acetic acid fermentation product and its components on defense signaling in rice.

Acetic acid fermentation product made from isomalto-oligosaccharide as the main raw material is composed of isomalto-oligosaccharide and acetic acid. In this paper, we have shown that the fermentation product enhanced the expression of disease resistance genes in rice, and that its main functional component was acetic acid. It has been reported so far that acetic acid enhances the jasmonic acid signaling pathway, while the role of isomalto-oligosaccharide in plant defense signaling remains unclear.

A novel quadrant spatial assay reveals environmental preference in mouse spontaneous and parental behaviors.

Environmental factors have well-documented impacts on brain development and mental health. Therefore, it is crucial to employ a reliable assay system to assess the spatial preference of model animals. In this study, we introduced an unbiased quadrant chamber assay system and discovered that parental pup-gathering behavior takes place in a very efficient manner.

GeF-seq: A Simple Procedure for Base-Pair Resolution ChIP-seq.

Nucleotide sequences recognized and bound by DNA-binding proteins (DBPs) are critical to controlling and maintaining gene expression, replication, chromosome segregation, cell division, and nucleoid structure in bacterial cells. Therefore, determination of the binding sequences of DBPs is important not only to study DBP recognition mechanisms but also to understand the fundamentals of cell homeostasis. While ChIP-seq analysis appears to be an effective way to determine DBP binding sites on the genome, the resolution is sometimes not sufficient to identify the sites precisely.

GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.

GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations.

Inhibiting proBDNF to mature BDNF conversion leads to ASD-like phenotypes in vivo.

Autism Spectrum Disorders (ASD) comprise a range of early age-onset neurodevelopment disorders with genetic heterogeneity. Most ASD related genes are involved in synaptic function, which is regulated by mature brain-derived neurotrophic factor (mBDNF) and its precursor proBDNF in a diametrically opposite manner: proBDNF inhibits while mBDNF potentiates synapses. Here we generated a knock-in mouse line (BDNF) in which the conversion of proBDNF to mBDNF is attenuated.

Caspase-mediated processing of TRBP regulates apoptosis during viral infection.

RNA silencing is a post-transcriptional gene-silencing mechanism mediated by microRNAs (miRNAs). However, the regulatory mechanism of RNA silencing during viral infection is unclear. TAR RNA-binding protein (TRBP) is an enhancer of RNA silencing that induces miRNA maturation by interacting with the ribonuclease Dicer.

Never-Ending Learning for Explainable Brain Computing.

Exploring the nature of human intelligence and behavior is a longstanding pursuit in cognitive neuroscience, driven by the accumulation of knowledge, information, and data across various studies. However, achieving a unified and transparent interpretation of findings presents formidable challenges. In response, an explainable brain computing framework is proposed that employs the never-ending learning paradigm, integrating evidence combination and fusion computing within a Knowledge-Information-Data (KID) architecture.

Construction of Biosensing System for Glycated Albumin Using an Electron Transfer Peptide-Modified Protein Probe.

Glycated albumin (GA) is one of the proteins that replaces several sugar moieties and can be used as an indicator of diabetes mellitus. We developed a sensing system that uses GA in the early detection of diabetes mellitus. In this study, HYC acetylated (Ac-) at the N-terminals of the peptide was combined with wheat germ agglutinin (WGA) to recognize glucose moieties.