3D epigenomics and 3D epigenopathies.

Mammalian genomes are intricately compacted to form sophisticated 3-dimensional structures within the tiny nucleus, so called 3D genome folding. Despite their shapes reminiscent of an entangled yarn, the rapid development of molecular and next-generation sequencing technologies (NGS) has revealed that mammalian genomes are highly organized in a hierarchical order that delicately affects transcription activities. An increasing amount of evidence suggests that 3D genome folding is implicated in diseases, giving us a clue on how to identify novel therapeutic approaches. In this review, we will study what 3D genome folding means in epigenetics, what types of 3D genome structures there are, how they are formed, and how the technologies have developed to explore them. We will also discuss the pathological implications of 3D genome folding. Finally, we will discuss how to leverage 3D genome folding and engineering for future studies.

Heat-Killed Lactilactobacillus sakei WB2305 and Lactiplantibacillus plantarum WB2324 Inhibited LPS-Induced Inflammation in Human Airway Epithelial Cells.

Asthma is characterized by inflammation of the airways, including the inflammatory and airway structural cells. Probiotics, which have diverse effects, even within the same species, are being studied to prevent and mitigate the severity of asthma. Lactilactobacillus sakei WB2305 and Lactiplantibacillus plantarum WB2324 were isolated from kimchi. These strains have acceptable probiotic properties and are safe. In addition, the anti-inflammatory potential of the heat-killed isolates against lipopolysaccharide (LPS)-induced inflammation in the human pulmonary epithelial cell line (A549) was investigated. The heat-killed Lact. sakei WB2305 and Lact. plantarum WB2324 reduced the chemokine and cytokines mRNA expression levels, as shown by the results of using real-time polymerase chain reaction. Western blotting results showed that the nuclear factor-kappa B (NF-κB) activation and mitogen-activated protein kinases (MAPK) signaling pathways were suppressed by treatment with the heat-killed strains. The production amounts of eotaxin, tumor necrosis factor-ɑ (TNF-α), and interleukin-6 (IL-6) were lower than those in LPS-only treated cells. Additionally, 2',7'-dichlorofluorescein diacetate (DCFH-DA) staining confirmed decreased reactive oxygen species (ROS) production in A549 cells. Therefore, the results of present study demonstrate the anti-inflammatory and anti-asthmatic activities of heat-killed Lact. sakei WB2305 and Lact. plantarum WB2324 in human airway epithelial cells.

Unraveling diffusion behavior in Cu-to-Cu direct bonding with metal passivation layers.

Cu/SiO2 hybrid bonding presents a promising avenue for achieving high-density interconnects by obviating the need for microbumps and underfills. Traditional copper bonding methods often demand temperatures exceeding 400 °C, prompting recent endeavors to mitigate bonding temperatures through investigations into metal passivation bonding. In this study, we scrutinized the diffusion behavior associated with various metal passivation layers (Platinum, Titanium, Tantalum, and Chromium) in the context of low-temperature direct copper bonding and delved into the essential bonding mechanisms. We observed a deviation from conventional metal-metal bonding factors, such as surface roughness and grain size, in the diffusion behavior. Remarkably, our analysis revealed a pronounced correlation between the crystallinity of the metal passivation layers and diffusion behavior, surpassing the influence of other experimental factors. Subsequent post-bonding examinations corroborated consistent diffusion behavior in Pt and Cr passivation samples with disparate crystallinities, reinforcing the significance of crystallinity in the bonding process. Our findings underscore crystallinity as a pivotal factor governing diffusion behavior, even under varied bonding conditions. These insights are instrumental in achieving exceptional bonding characteristics at lower temperatures in Cu/SiO2 hybrid bonding. Implications of this study extend to the prospect of advancing highly integrated systems through die-to-wafer bonding, marking a substantial stride toward future applications.

CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces.

The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer, anthelmintic, and immunosuppressive functions. Among microbes, the genus Streptomyces holds particular significance for secondary metabolite discovery. Each Streptomyces species typically encodes approximately 30 secondary metabolite biosynthetic gene clusters (smBGCs) within its genome, which are mostly uncharacterized in terms of their products and bioactivities. The development of next-generation sequencing has enabled the identification of a large number of potent smBGCs for novel secondary metabolites that are imbalanced in number compared with discovered secondary metabolites. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has revolutionized the translation of enormous genomic potential into the discovery of secondary metabolites as the most efficient genetic engineering tool for Streptomyces. In this review, the current status of CRISPR/Cas applications in Streptomyces is summarized, with particular focus on the identification of secondary metabolite biosynthesis gene clusters and their potential applications.This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production. ONE-SENTENCE SUMMARY: This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.

Atypical formations of gintonin lysophosphatidic acids as new materials and their beneficial effects on degenerative diseases.

Fresh ginseng is prone to spoilage due to its high moisture content. For long-term storage, most fresh ginsengs are dried to white ginseng (WG) or steamed for hours at high temperature/pressure and dried to form Korean Red ginseng (KRG). They are further processed for ginseng products when subjected to hot water extraction/concentration under pressure. These WG or KRG preparation processes affect ginsenoside compositions and also other ginseng components, probably during treatments like steaming and drying, to form diverse bioactive phospholipids. It is known that ginseng contains high amounts of gintonin lysophosphatidic acids (LPAs). LPAs are simple lipid-derived growth factors in animals and humans and act as exogenous ligands of six GTP-binding-protein coupled LPA receptor subtypes. LPAs play diverse roles ranging from brain development to hair growth in animals and humans. LPA-mediated signaling pathways involve various GTP-binding proteins to regulate downstream pathways like [Ca2+]i transient induction. Recent studies have shown that gintonin exhibits anti-Alzheimer's disease and anti-arthritis effects in vitro and in vivo mediated by gintonin LPAs, the active ingredients of gintonin, a ginseng-derived neurotrophin. However, little is known about how gintonin LPAs are formed in high amounts in ginseng compared to other herbs. This review introduces atypical or non-enzymatic pathways under the conversion of ginseng phospholipids into gintonin LPAs during steaming and extraction/concentration processes, which exert beneficial effects against degenerative diseases, including Alzheimer's disease and arthritis in animals and humans via LPA receptors.

A retrospective comparative study of maxillofacial injury patterns caused by electric scooters and bicycles.

BACKGROUND/AIM: The emergence of shared stand-up electric scooters has led to an increase in their usage and, subsequently, an increase in the incidence of maxillofacial trauma. This study aimed to investigate the trauma pattern associated with the use of stand-up electric scooters compared with that related to the use of bicycles, which was a popular mode of personal mobility before the emergence of stand-up electric scooters. MATERIALS AND METHODS: This study investigated the medical records of patients who visited Wonju Christian Hospital for maxillofacial trauma due to the use of stand-up electric scooter and bicycles between November 1, 2017 and October 31, 2022. Maxillofacial trauma was analyzed based on medical records, including those in the evaluation results of teeth, maxillofacial bones, and soft tissues. RESULTS: Crown fractures and tooth avulsions were observed more frequently with the use of stand-up electric scooters than with the use of bicycles. In contrast, crown-root fractures, tooth subluxation, and extrusive luxation were more commonly observed in bicycle riders. Additionally, the proportion of root fractures was similar between the two groups. However, no vertical root fractures were observed in patients who rode bicycles. The maxillofacial bone fracture rates between the two groups were similar, although the fracture patterns were different. CONCLUSION: The number of patients using stand-up electric scooters is increasing, and they are likely to have a worse prognosis compared with those using existing personal mobility devices.

Analysing the Effects of Sales Stand Installations on Evacuation Dynamics in Indoor Sports Blocks / Análisis de los efectos de las instalaciones de puestos de venta en la dinámica de evacuación en bloques deportivos cubiertos

Indoor sports clubs, gymnasiums, and sports blocks and complexes have the potential for causing significant casualties in the event of a fire. As a result, there is a significant amount of research being done on fire safety. The impact of sales stands on fire safety is a vital aspect that needs to be considered to ensure comprehensive safety measures. This study seeks to assess the effect of sales stands on the time it takes to evacuate indoor sports blocks in the event of a fire. A fire and evacuation simulation programme were utilised to analyse the characteristics of fire and evacuation. The findings indicated that the sales stand had an impact on the time it took for sports athletes and physical workers to complete the evacuation, particularly when the corridor width was wide. However, there was no significant effect observed when the hallway width was narrow. Instead, they expanded the congested area in the hallway, resulting in a longer resolution time. It is evident that sales stand in indoor sports blocks and sports centres or complexes could potentially jeopardise evacuation safety. This study can serve as a basis for implementing safety measures. It examines how obstacles in corridors, such as those found in schools and hotels, impact the evacuation behaviour of individuals. These findings are particularly relevant for indoor sports facilities, which share similar spatial characteristics.(AU)

Gintonin Alleviates HCl/Ethanol- and Indomethacin-Induced Gastric Ulcers in Mice.

Gintonin, newly extracted from ginseng, is a glycoprotein that acts as an exogenous lysophosphatidic acid (LPA) receptor ligand. This study aimed to demonstrate the in vivo preventive effects of gintonin on gastric damage. ICR mice were randomly assigned to five groups: a normal group (received saline, 0.1 mL/10 g, p.o.); a control group (administered 0.3 M HCl/ethanol, 0.1 mL/10 g, p.o.) or indomethacin (30 mg/kg, p.o.); gintonin at two different doses (50 mg/kg or 100 mg/kg, p.o.) with either 0.3 M HCl/ethanol or indomethacin; and a positive control (Ranitidine, 40 mg/kg, p.o.). After gastric ulcer induction, the gastric tissue was examined to calculate the ulcer index. The expression of gastric damage markers, such as tumor necrosis factor (TNF)-α, cyclooxygenase 2 (COX-2), and LPA2 and LPA5 receptors, were measured by Western blotting. Interleukin-6 (IL-6) and prostaglandin E2 (PGE2) levels were measured by enzyme-linked immunosorbent assay. The platelet endothelial cell adhesion molecule (PECAM-1), Evans blue, and occludin levels in gastric tissues were measured using immunofluorescence analysis. Both HCl/ethanol- and indomethacin-induced gastric ulcers showed increased TNF-α, IL-6, Evans blue permeation, and PECAM-1, and decreased COX-2, PGE2, occludin, and LPA5 receptor expression levels. However, oral administration of gintonin alleviated the gastric ulcer index induced by HCl/ethanol and indomethacin in a dose-dependent manner. Gintonin suppressed TNF-α and IL-6 expression, but increased COX-2 expression and PGE2 levels in mouse gastric tissues. Gintonin intake also increased LPA5 receptor expression in mouse gastric tissues. These results indicate that gintonin can play a role in gastric protection against gastric damage induced by HCl/ethanol or indomethacin.

Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.

Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.

Reassembled Vacuoles for Drug Delivery Carriers Using Yeast Vacuoles for Enhanced Antibacterial Activity.

In this study, we aimed to develop an efficient drug delivery system by reassembling vacuoles isolated from Saccharomyces cerevisiae. Initially, we assessed the impact of vacuolar enzymes on the efficacy of the loaded antibiotic polymyxin B (PMB), by conducting antibacterial activity tests using Shigella flexneri and Salmonella enteritidis. The results showed that vacuolar enzymes inhibited the effectiveness of PMB, highlighting the limitations of using natural vacuoles as drug carriers. To overcome this, we proposed a new drug delivery system called reassembled vacuoles (ReV). ReV particles were created by removing vacuolar enzymes and reassembling the vacuolar membrane through extrusion. ReV demonstrated improved structural stability, a more uniform size, and enhanced PMB release compared to natural vacuoles. Encapsulation efficiency tests revealed high loading efficiency for both normal vacuoles (NorV) and ReV, with over 80% efficiency at concentrations up to 600 µg/mL. The antibacterial activity of PMB-loaded ReV showed comparable results to PMB alone, indicating the potential of ReV as a drug delivery system. In conclusion, reassembled vacuoles offer a promising approach for drug delivery, addressing the limitations of natural vacuoles and providing opportunities for targeted and efficient drug release.

Increase CO2 recycling of Escherichia coli containing CBB genes by enhancing solubility of multiple expressed proteins from an operon through temperature reduction.

IMPORTANCE: In a previous study, we successfully engineered Escherichia coli capable of endogenous CO2 recycling through the heterologous expression of the Calvin-Benson Bassham genes. Establishing an efficient gene expression environment for recombinant strains is crucial, on par with the importance of metabolic engineering design. Therefore, the primary objective of this study was to further mitigate greenhouse gas emissions by investigating the effects of culture temperature on the formation of inclusion bodies (IB) and CO2 fixation activity in the engineered bacterial strain. The findings demonstrate that lowering the culture temperature effectively suppresses IB formation, enhances CO2 recycling, and concurrently increases the accumulation of organic acids. This temperature control approach, without adding or modifying compounds, is both convenient and efficient for enhancing CO2 recycling. As such, additional optimization of various environmental parameters holds promise for further enhancing the performance of recombinant strains efficiently.

The cover of an ear thermometer probe as a split-thickness skin graft mold in external auditory canal reconstruction.

Maintaining the patency of the external auditory canal (EAC) during reconstruction is important because of its physiological role in hearing and immunological protective functions. The curved shape of the EAC presents a challenge when performing a skin graft. One of the key points for a successful skin graft is to ensure compression on the wound bed, and many novel methods, including prefabricated ear molds, have been reported for this purpose. In this study, we present a case of a skin graft performed to reconstruct a skin defect following excision of actinic keratosis in the EAC, using the cover of an ear thermometer probe as a mold for the graft to match the curvature of the EAC. This is an economical and practical method for secure compression dressing of a skin graft in the EAC.

Yeast vacuolar enzymes as novel hatching inhibitors for aquatic organisms, Daphnia magna and Danio rerio eggs.

Concerns over the spread of non-native species in aquatic environments have led to the need for effective methods to prevent and control their spread while protecting native species. This study investigated the potential of yeast vacuolar enzymes as a natural hatching inhibitor for controlling aquatic organisms. Hatching experiments with Daphnia magna eggs demonstrated that exposure to yeast vacuole enzymes inhibited hatching in a concentration-dependent manner, suggesting their potential as an effective inhibitor of egg hatching in aquatic organisms. Interestingly, the protease used for comparative purposes did not inhibit hatching, but instead increased the mortality of hatched D. magna. Additionally, chorionic changes were observed in non-hatched D. magna eggs and zebrafish eggs exposed to yeast vacuole enzymes, suggesting that the enzyme can alter the chorion and interfere with hatching. These findings suggest that yeast vacuolar enzymes may be a promising and natural management tool for controlling the spread of harmful aquatic organisms, and further research is warranted to explore their potential for species-specific control.

Inhibition of tau phosphorylation and Aß accumulation by S. cerevisiae-derived vacuoles in LPS-induced SH-SY5Y cells.

Neurodegenerative diseases, such as Alzheimer's disease (AD), are characterized by the accumulation of intracellular tau and amyloid beta (Aß) proteins, which lead to neuroinflammation and neuronal apoptosis. In this study, we investigated the potential of a bioengineered vacuoles derived from Saccharomyces cerevisiae-derived vacuoles to treat neuroinflammation and protein accumulation in AD. The yeast-derived vacuole is a small organelle that achieves efficient degradation by utilizing a diverse array of hydrolytic enzymes. These hydrolytic enzymes break down and process proteins into smaller fragments. We found that vacuoles treatment significantly reduced LPS-primed cell apoptosis and diminished Aß42 secretion in vitro, potentially through the inhibition of the NF-kB p65 signaling pathway. Additionally, vacuole pre-treatment down-regulated NF-κB translocation and reduced phosphorylated tau levels in LPS-induced SH-SY5Y cells. Our results suggest that the vacuoles have potential as a therapeutic agent for neurodegenerative diseases. The vacuole's small size and diverse hydrolytic enzymes make it a promising drug delivery system for targeting intracellular proteins. Future studies may explore the use of vacuoles in animal models of AD to determine their therapeutic potential.

Gintonin-Induced Wound-Healing-Related Responses Involve Epidermal-Growth-Factor-like Effects in Keratinocytes.

Epidermal growth factor (EGF) receptor activation and related downstream signaling pathways are known to be one of the major mechanisms of the proliferation and migration of keratinocytes. The heparin-binding EGF-like growth factor (HB-EGF) binds to EGF receptors and stimulates keratinocyte proliferation and migration. Gintonin, a novel ginseng compound, is a lysophosphatidic acid (LPA) receptor ligand. Gintonin has skin-wound-healing effects. However, the underlying mechanisms for these gintonin actions remain unclear. In this study, we aimed to elucidate the involvement of EGFRs in gintonin-induced wound repair in HaCaT keratinocytes. In this study, a water-soluble tetrazolium salt-based assay, a modified Boyden chamber migration assay, and immunoblotting were performed. Gintonin increased EGF receptor activation in HaCaT cells. However, the gintonin-induced phosphorylation of the EGF receptor was markedly reduced via treatment with the LPA inhibitor Ki16425 or the EGF receptor inhibitor erlotinib. Gintonin-enhanced proliferation and migration were blocked by the EGF receptor inhibitors (erlotinib and AG1478). Additionally, gintonin stimulated the expression and release of HB-EGF in HaCaT cells. EGF receptor inhibitors blocked gintonin-enhanced HB-EGF expression. These results indicate that the wound-healing effects of gintonin are closely related to the collaboration between EGF receptor activation and HB-EGF release-mediated downstream signaling pathways.

Volunteer Plants' Occurrence and the Environmental Adaptability of Genetically Modified Fodder Corn upon Unintentional Release into the Environment.

The number of corn cultivars that have been improved using genetically modified technology continues to increase. However, concerns about the unintentional release of living-modified organisms (LMOs) into the environment still exist. Specifically, there are cases where LMO crops grown as fodder are released into the environment and form a volunteer plant community, which raises concerns about their safety. In this study, we analyzed the possibility of weediness and volunteer plants' occurrence when GMO fodder corn grains distributed in Korea are unintentionally released into the environment. Volunteer plants' occurrence was investigated by directly sowing grains in an untreated field. The results showed that the germination rate was extremely low, and even if a corn seed germinated, it could not grow into an adult plant and would die due to weed competition. In addition, the germination rate of edible and fodder grains was affected by temperature (it was high at 20 °C and 30 °C but low at 40 °C and extremely low at 10 °C), and it was higher in the former than in the latter. And the germination rate was higher in Daehakchal (edible corn grains) than in Gwangpyeongok (fodder corn grains). The environmental risk assessment data obtained in this study can be used for future evaluations of the weediness potential of crops and the development of volunteer plant suppression technology in response to unintentional GMO release.

Enhanced Operational Characteristics Attained by Applying HfO2 as Passivation in AlGaN/GaN High-Electron-Mobility Transistors: A Simulation Study.

This study investigates the operating characteristics of AlGaN/GaN high-electron-mobility transistors (HEMTs) by applying HfO2 as the passivation layer. Before analyzing HEMTs with various passivation structures, modeling parameters were derived from the measured data of fabricated HEMT with Si3N4 passivation to ensure the reliability of the simulation. Subsequently, we proposed new structures by dividing the single Si3N4 passivation into a bilayer (first and second) and applying HfO2 to the bilayer and first passivation layer only. Ultimately, we analyzed and compared the operational characteristics of the HEMTs considering the basic Si3N4, only HfO2, and HfO2/Si3N4 (hybrid) as passivation layers. The breakdown voltage of the AlGaN/GaN HEMT having only HfO2 passivation was improved by up to 19%, compared to the basic Si3N4 passivation structure, but the frequency characteristics deteriorated. In order to compensate for the degraded RF characteristics, we modified the second Si3N4 passivation thickness of the hybrid passivation structure from 150 nm to 450 nm. We confirmed that the hybrid passivation structure with 350-nm-thick second Si3N4 passivation not only improves the breakdown voltage by 15% but also secures RF performance. Consequently, Johnson's figure-of-merit, which is commonly used to judge RF performance, was improved by up to 5% compared to the basic Si3N4 passivation structure.

Preparation of Red Ginseng Marc-Derived Gintonin and Its Application as a Skin Nutrient.

Ginseng is one of the traditional herbal medicines for tonic. Gintonin is a new material derived from white/red ginseng and its lysophosphatidic acids (LPAs) play as a ligand for G protein-coupled LPA receptors. Korean red ginseng marc (KRGM) is a by-product after the KRG processes. We developed a low-cost/high-efficiency method for KRGM gintonin production. We further studied the KRGM gintonin-mediated anti-skin aging effects under UVB exposure using human dermal fibroblasts (HDFs). KRGM gintonin yield is about 8%. KRGM gintonin contains a high amount of LPA C18:2, lysophosphatidylcholine (LPC), and phosphatidylcholine (PC), which is similar to white ginseng gintonin. KRGM gintonin induced [Ca2+]i transient via LPA1/3 receptors and increased cell viability/proliferation under UVB exposure. The underlying mechanisms of these results are associated with the antioxidant action of KRGM gintonin. KRGM gintonin attenuated UVB-induced cell senescence by inhibiting cellular ß-galactosidase overexpression and facilitated wound healing. These results indicate that KRGM can be a novel bioresource of KRGM gintonin, which can be industrially utilized as new material for skin nutrition and/or skin healthcare.

Crystal structure of the engineered endolysin mtEC340M.

Endolysins produced by bacteriophages play essential roles in the release of phage progeny by degrading the peptidoglycan layers of the bacterial cell wall. Bacteriophage-encoded endolysins have emerged as a new class of antibacterial agents to combat surging antibiotic resistance. The crystal structure of mtEC340M, an engineered endolysin EC340 from the PBEC131 phage that infects Escherichia coli, was determined. The crystal structure of mtEC340M at 2.4 Šresolution consists of eight α-helices and two loops. The three active residues of mtEC340M were predicted by structural comparison with peptidoglycan-degrading lysozyme.

Probiotic Weissella cibaria displays antibacterial and anti-biofilm effect against cavity-causing Streptococcus mutans.

Streptococcus mutans is a significant contributor to dental caries and causes functional and aesthetic discomfort. Weissella cibaria strains were isolated from kimchi, and their functional properties were determined. In this study, the antibacterial and antibiofilm effects of four W. cibaria strains (D29, D30, D31, and B22) were evaluated against three S. mutans strains using culture fluid and cell-free supernatants. The results showed that W. cibaria reduced the exopolysaccharides production and auto-aggregation, increased co-aggregation, and downregulated virulence factors, leading to the inhibition of bacterial growth and biofilm formation. These findings were confirmed using scanning electron microscopy and confocal laser scanning microscopy. These results indicate that oral health can be potentially improved by W. cibaria.