Effect of gut microbiota-derived metabolites and extracellular vesicles on neurodegenerative disease in a gut-brain axis chip.

A new perspective suggests that a dynamic bidirectional communication system, often referred to as the microbiome-gut-brain axis, exists among the gut, its microbiome, and the central nervous system (CNS). This system may influence brain health and various brain-related diseases, especially in the realms of neurodevelopmental and neurodegenerative conditions. However, the exact mechanism is not yet understood. Metabolites or extracellular vesicles derived from microbes in the gut have the capacity to traverse the intestinal epithelial barrier or blood-brain barrier, gaining access to the systemic circulation. This phenomenon can initiate the physiological responses that directly or indirectly impact the CNS and its function. However, reliable and controllable tools are required to demonstrate the causal effects of gut microbial-derived substances on neurogenesis and neurodegenerative diseases. The integration of microfluidics enhances scientific research by providing advanced in vitro engineering models. In this study, we investigated the impact of microbe-derived metabolites and exosomes on neurodevelopment and neurodegenerative disorders using human induced pluripotent stem cells (iPSCs)-derived neurons in a gut-brain axis chip. While strain-specific, our findings indicate that both microbial-derived metabolites and exosomes exert the significant effects on neural growth, maturation, and synaptic plasticity. Therefore, our results suggest that metabolites and exosomes derived from microbes hold promise as potential candidates and strategies for addressing neurodevelopmental and neurodegenerative disorders.

Benefits of Music Intervention on Anxiety, Pain, and Physiologic Response in Adults Undergoing Surgery: A Systematic Review and Meta-analysis.

PURPOSE: Evidence on factors influencing the variations of music's effect on anxiety and pain in surgical patients is unclear. We aimed to elucidate the effects of music intervention on anxiety and pain throughstudy characteristics. METHODS: We conducted a search on the PubMed, CINAHL, Embase, Cochrane, and Web of Science databases from March 7 to April 21, 2022, for randomized controlled trials (RCTs) for the effect of music intervention on anxiety, pain, and physiological responses in surgical patients. We included studies published within the last 10 years. We assessed the risk of bias in the study using the Cochrane risk of bias tool for randomized trials and performed meta-analyses using a random-effects model for all outcomes. We used change-from-baseline scores as summary statistics and computed bias-corrected standardized mean differences (Hedges'g) for anxiety and pain outcomes and mean differences (MD) for blood pressure and heart rate. RESULTS: Of the 454 records retrieved, 30 RCTs involving 2280 participants were found to be eligible. Music intervention was found to be superior to standard care in reducing anxiety (Hedges' g = -1.48, 95% confidence interval: -1.97 to -0.98), pain (Hedges's g = -0.67, -1.11 to -0.23), systolic blood pressure (MD = -4.62, -7.38 to -1.86), and heart rate (MD = -3.37, -6.65 to -0.10) in surgical patients. The impact of music on anxiety and pain relief varied significantly depending on the duration of the intervention. The largest effect was observed in interventions lasting between 30 and 60 minutes, with a decrease in anxiety and pain. CONCLUSIONS: Music intervention is an effective way to reduce anxiety, pain, and physiological responses in surgical patients. Future reviews examining the influence of different types of surgery on the effects of music would add to the body of knowledge in this field. This study has been registered on the International Prospective Register of Systematic Reviews (PROSPERO) under the number CRD42022340203, with a registration date of July 4, 2022.

Characterization and activity-folding relationship of serine protease from Antarctic krill (Euphausia superba).

Euphausia superba (Antarctic krill) serine protease (ESP) was investigated to gain insights into the activity-structural relationship, folding behavior, and regulation of the catalytic function. We purified ESP from the krill muscle and characterized biochemical distinctions via enzyme kinetics. Studies of inhibition kinetics and unfolding in the presence of a serine residue modifier, such as phenylmethanesulfonyl fluoride, were conducted. Structural characterizations were measured by spectrofluorimetry, including 1-anilinonaphthalene-8-sulfonate dye labeling for hydrophobic residues. The computational simulations such as docking and molecular dynamics were finally conducted to detect key residues and folding behaviors in a nano-second range. The kinetic parameters of ESP were measured as KmBANH = 0.97 ± 0.15 mM and kcat/KmBANH = 4.59 s-1/mM. The time-interval kinetics measurements indicated that ESP inactivation was transformed from a monophase to a biphase process to form a thermodynamically stable state. Spectrofluorimetry measurements showed that serine is directly connected to the regional folding of ESP. Several osmolytes such as proline and glycine only partially protected the inactive form of ESP by serine modification. Computational molecular dynamics and docking simulations showed that three serine residues (Ser183, Ser188, and Ser207) and Cys184, Val206, and Gly209 are key residues of catalytic functions. Our study revealed the functional roles of serine residues as key residues of catalytic function at the active site and of the structural conformation as key folding factors, where ESP displays a flexible property of active site pocket compared to the overall structure.Communicated by Ramaswamy H. Sarma.

Transformation of Bacillus thuringiensis plasmid DNA by a new polyethylenimine polymeric nanoparticles method.

Although electroporation technique has been mostly used to transform Bacillus thuringiensis (Bt), this method is not readily applicable to strains other than the one for which it was optimized. Polyethylenimine (PEI) is a golden standard non-viral vector that interacts with plasmids to form compact polymeric nanoparticles (PNPs) via electrostatic interactions. This PNPs system is very attractive because they are easily prepared, able to carry large nucleic acid constructs, and show low toxicity. In this study, PEI/pBTdsSBV-VP1 PNPs were successfully prepared at various N/P ratios which is positively-chargeable polymer amine (N = nitrogen) groups to negatively-charged nucleic acid phosphate (P) groups, and the internalization of the complexes into Bt 4Q7 was confirmed by confocal laser scanning microscopy. The PEI-mediated transformation showed similar efficiency comparable to that of electroporation method, suggesting that the method of PNPs will be an effective alternative for transformation of Bt strains.

Mean platelet volume is the most valuable hematologic parameter in differentiating testicular torsion from epididymitis within the golden time.

Background: We aimed to assess the diagnostic value of hematologic parameters in the differential diagnosis of testicular torsion and epididymitis within and after the golden time. Methods: We retrospectively reviewed the records of 250 patients aged <25 years who were diagnosed with epididymitis (n=119) or testicular torsion (n=131). The characteristics and hematologic parameters of patients in the two groups were analyzed. Receiver operating characteristic (ROC) curves were used to assess the validity of hematologic parameters as differential diagnostic tools with respect to the golden time (defined as 6 h of symptom duration). Further, we evaluated the predictive factors associated with orchiectomy in patients with testicular torsion. Results: The mean patient age was 14.4 years. Among patients with testicular torsion, 91.40% (53 of 58) underwent detorsion and orchiopexy within the golden time, whereas only 27.40% (20 of 73) of the affected testes were preserved after the golden time. Within the golden time, mean platelet volume (MPV) seemed to be the most valuable hematologic parameter [area under the curve (AUC) 0.855, 95% confidence interval (CI): 0.778-0.932]. In a multivariate analysis, symptom duration (symptoms beyond the golden time) was associated with orchiectomy in patients with testicular torsion. Conclusions: MPV showed the greatest hematologic value in the early stage of testicular torsion and epididymitis, suggesting its potential use for the differential diagnosis of these two conditions within the golden time.

Role of oral pentosan polysulfate in Bacillus Calmette-Guérin therapy in patients with non-muscle-invasive bladder cancer.

PURPOSE: Intravesical Bacillus Calmette-Guérin (BCG) instillation, although an important treatment for non-muscle-invasive bladder cancer, exerts local and systemic adverse effects. Pentosan polysulfate (PPS) is a bladder mucosal protective drug that acts by replacing mucus in the glycosaminoglycan layer of the damaged urothelium. We hypothesized that co-administration of oral PPS with BCG instillation would relieve BCG-related adverse effects without affecting its efficacy. MATERIALS AND METHODS: A total of 217 patients receiving BCG instillation were enrolled. They were placed in two groups and analyzed retrospectively: group A (n=122) received BCG instillation only and group B (n=95) received 100 mg of PPS thrice daily during the BCG treatment. RESULTS: After BCG instillation, the rate of BCG-treatment discontinuation owing to adverse effects was 15.6% in group A and 6.3% in group B (p=0.034). The proportion of patients with bacteriuria after BCG was higher in group B; however, no statistical difference was observed (28.7% vs. 41.1%; p=0.057). The proportion of patients with pyuria was significantly higher in group B (81.1% vs. 91.6%; p=0.029). The proportion of patients using antibiotics was significantly higher in group A (73.8% vs. 43.2%; p=0.001). The recurrence rate within 1 year was 29 (23.8%) in group A vs. 19 (20.0%) in group B (p=0.507). Univariate and multivariate analyses showed that antibiotic use had a statistically significant effect on BCG discontinuation. CONCLUSIONS: Oral PPS effectively decreased the discontinuation rate and antibiotic use without affecting the BCG efficacy.

Single-cell transcriptome of the mouse retinal pigment epithelium in response to a low-dose of doxorubicin.

Cellular senescence of the retinal pigment epithelium (RPE) is thought to play an important role in vision-threatening retinal degenerative diseases, such as age-related macular degeneration (AMD). However, the single-cell RNA profiles of control RPE tissue and RPE tissue exhibiting cellular senescence are not well known. We have analyzed the single-cell transcriptomes of control mice and mice with low-dose doxorubicin (Dox)-induced RPE senescence (Dox-RPE). Our results have identified 4 main subpopulations in the control RPE that exhibit heterogeneous biological activities and play roles in ATP synthesis, cell mobility/differentiation, mRNA processing, and catalytic activity. In Dox-RPE mice, cellular senescence mainly occurs in the specific cluster, which has been characterized by catalytic activity in the control RPE. Furthermore, in the Dox-RPE mice, 6 genes that have not previously been associated with senescence also show altered expression in 4 clusters. Our results might serve as a useful reference for the study of control and senescent RPE.

Second-Generation JK-206 Targets the Oncogenic Signal Mediator RHOA in Gastric Cancer.

Ras homologous A (RHOA), a signal mediator and a GTPase, is known to be associated with the progression of gastric cancer (GC), which is the fourth most common cause of death in the world. Previously, we designed pharmacologically optimized inhibitors against RHOA, including JK-136 and JK-139. Based on this previous work, we performed lead optimization and designed novel RHOA inhibitors for greater anti-GC potency. Two of these compounds, JK-206 and JK-312, could successfully inhibit the viability and migration of GC cell lines. Furthermore, using transcriptomic analysis of GC cells treated with JK-206, we revealed that the inhibition of RHOA might be associated with the inhibition of the mitogenic pathway. Therefore, JK-206 treatment for RHOA inhibition may be a new therapeutic strategy for regulating GC proliferation and migration.

Isolation and molecular characterization of Bacillus thuringiensis subsp. kurstaki toxic to lepidopteran pests Spodoptera spp. and Plutella xylostella.

BACKGROUND: Bacillus thuringiensis (Bt) has been widely used as a biological control agent for lepidopteran pests. However, resistance to Bt is a major concern associated with Spodoptera spp. (Noctuidae) and Plutella xylostella (Plutellidae). For efficient control of Noctuidae and Plutellidae, novel Bt strains which have high toxicity and a broad host range are needed. RESULTS: To develop novel Bt strains as used for bio-insecticides, the Bt IMBL-B9 with high toxicity against Spodoptera exigua, Spodoptera frugiperda and P. xylostella was isolated and characterized. The Bt kurstaki IMBL-B9 strain produced bipyramidal and cuboidal crystals consisting of cry toxins with molecular weights of 130 and 65 kDa, respectively. This strain harbors eight crystal protein genes in total, including cry1Ea and one vegetative insecticidal protein gene. The median lethal concentration (LC50 ) values of IMBL-B9 against S. exigua and S. frugiperda were 21.8- and 19.3-fold lower than those of the Bt kusrstaki strain, and 5.6- and 4.9-fold lower than those of Bt aizawai strain, respectively. To evaluate the insecticidal activity of Cry proteins from IMBL-B9, cry gene-sourced recombinant Bt strains were constructed. These strains have insecticidal activity and synergic action against lepidopteran pests. CONCLUSION: In this study, a novel Bt kurstaki IMBL-B9 strain was isolated and this could be useful for the development of new bio-insecticide or cry gene-based recombinant products as an alternative solution against lepidopterans, including Noctuidae and Plutellidae. © 2022 Society of Chemical Industry.

Targeting senescent retinal pigment epithelial cells facilitates retinal regeneration in mouse models of age-related macular degeneration.

Although age-related macular degeneration (AMD) is a multifactorial disorder with angiogenic, immune, and inflammatory components, the most common clinical treatment strategies are antiangiogenic therapies. However, these strategies are only applicable to neovascular AMD, which accounts for less than 20% of all AMD cases, and there are no FDA-approved drugs for the treatment of dry AMD, which accounts for ~ 80% of AMD cases. Here, we report that the elimination of senescent cells is a potential novel therapeutic approach for the treatment of all types of AMD. We identified senescent retinal pigment epithelium (RPE) cells in animal models of AMD and determined their contributions to retinal degeneration. We further confirmed that the clearance of senescent RPE cells with the MDM2-p53 inhibitor Nutlin-3a ameliorated retinal degeneration. These findings provide new insights into the use of senescent cells as a therapeutic target for the treatment of AMD.

Genetic Differences between Physical Injury Patients With and Without Post-traumatic Syndrome: Focus on Secondary Findings and Potential Variants Revealed by Whole Exome Sequencing.

Objective: Sudden traumatic physical injuries often cause psychological distress, which may be associated with chronic disability. Although considerable effort has been expended to identify genetic predictors of post-traumatic stress disorder (PTSD) after traumatic events, genetic predictors of psychological distress in response to severe physical injuries have been yet to be elucidated using whole exome sequencing (WES). Here, the genetic architecture of post-traumatic syndrome (PTS), which encompasses a broad range of psychiatric disorders after traumatic events including depression, anxiety disorder, acute stress disorder, and PTSD, was explored using WES in severely physically injured patients, focusing on secondary findings and potential PTS-related variants. Methods: In total, 141 severely physically injured patients were consecutively recruited, and PTS was evaluated within 1 month of the injury. Secondary findings were analyzed according to PTS status. To identify PTS-related variants, genome-wide association analyses and the optimal sequencing kernel association test were performed. Results: Of the 141 patients, 88 (62%) experienced PTS. There were 108 disease-causing variants in severely physically injured patients. As secondary findings, the stress- and inflammation-related signaling pathways were enriched in the PTS patients, while the glucose metabolism pathway was enriched in those without PTS. However, no significant PTS-related variants were identified. Conclusion: Our findings suggest that genetic alterations in stress and inflammatory pathways might increase the likelihood of PTS immediately after severe physical injury. Future studies with larger samples and longitudinal designs are needed.

Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle.

Horses have been studied for exercise function rather than food production, unlike most livestock. Therefore, the role and characteristics of tissue landscapes are critically understudied, except for certain muscles used in exercise-related studies. In the present study, we compared RNA-Seq data from 18 Jeju horse skeletal muscles to identify differentially expressed genes (DEGs) between tissues that have similar functions and to characterize these differences. We identified DEGs between different muscles using pairwise differential expression (DE) analyses of tissue transcriptome expression data and classified the samples using the expression values of those genes. Each tissue was largely classified into two groups and their subgroups by k-means clustering, and the DEGs identified in comparison between each group were analyzed by functional/pathway level using gene set enrichment analysis and gene level, confirming the expression of significant genes. As a result of the analysis, the differences in metabolic properties like glycolysis, oxidative phosphorylation, and exercise adaptation of the groups were detected. The results demonstrated that the biochemical and anatomical features of a wide range of muscle tissues in horses could be determined through transcriptome expression analysis, and provided proof-of-concept data demonstrating that RNA-Seq analysis can be used to classify and study in-depth differences between tissues with similar properties.

Bioinformatics services for analyzing massive genomic datasets.

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.

Genome-wide association and epistatic interactions of flowering time in soybean cultivar.

Genome-wide association studies (GWAS) have enabled the discovery of candidate markers that play significant roles in various complex traits in plants. Recently, with increased interest in the search for candidate markers, studies on epistatic interactions between single nucleotide polymorphism (SNP) markers have also increased, thus enabling the identification of more candidate markers along with GWAS on single-variant-additive-effect. Here, we focused on the identification of candidate markers associated with flowering time in soybean (Glycine max). A large population of 2,662 cultivated soybean accessions was genotyped using the 180k Axiom® SoyaSNP array, and the genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and flowering time. A total of 93 significant SNP markers were detected within 59 significant genes, including E1 and E3, which are the main determinants of flowering time. Based on the GWAS results, multilocus epistatic interactions were examined between the significant and non-significant SNP markers. Two significant and 16 non-significant SNP markers were discovered as candidate markers affecting flowering time via interactions with each other. These 18 candidate SNP markers mapped to 18 candidate genes including E1 and E3, and the 18 candidate genes were involved in six major flowering pathways. Although further biological validation is needed, our results provide additional information on the existing flowering time markers and present another option to marker-assisted breeding programs for regulating flowering time of soybean.

Dissection of soybean populations according to selection signatures based on whole-genome sequences.

BACKGROUND: Domestication and improvement processes, accompanied by selections and adaptations, have generated genome-wide divergence and stratification in soybean populations. Simultaneously, soybean populations, which comprise diverse subpopulations, have developed their own adaptive characteristics enhancing fitness, resistance, agronomic traits, and morphological features. The genetic traits underlying these characteristics play a fundamental role in improving other soybean populations. RESULTS: This study focused on identifying the selection signatures and adaptive characteristics in soybean populations. A core set of 245 accessions (112 wild-type, 79 landrace, and 54 improvement soybeans) selected from 4,234 soybean accessions was re-sequenced. Their genomic architectures were examined according to the domestication and improvement, and accessions were then classified into 3 wild-type, 2 landrace, and 2 improvement subgroups based on various population analyses. Selection and gene set enrichment analyses revealed that the landrace subgroups have selection signals for soybean-cyst nematode HG type 0 and seed development with germination, and that the improvement subgroups have selection signals for plant development with viability and seed development with embryo development, respectively. The adaptive characteristic for soybean-cyst nematode was partially underpinned by multiple resistance accessions, and the characteristics related to seed development were supported by our phenotypic findings for seed weights. Furthermore, their adaptive characteristics were also confirmed as genome-based evidence, and unique genomic regions that exhibit distinct selection and selective sweep patterns were revealed for 13 candidate genes. CONCLUSIONS: Although our findings require further biological validation, they provide valuable information about soybean breeding strategies and present new options for breeders seeking donor lines to improve soybean populations.

Oncogenic KRAS Sensitizes Lung Adenocarcinoma to GSK-J4-Induced Metabolic and Oxidative Stress.

Genetic and epigenetic changes (e.g., histone methylation) contribute to cancer development and progression, but our understanding of whether and how specific mutations affect a cancer's sensitivity to histone demethylase (KDM) inhibitors is limited. Here, we evaluated the effects of a panel of KDM inhibitors on lung adenocarcinomas (LuAC) with various mutations. Notably, LuAC lines harboring KRAS mutations showed hypersensitivity to the histone H3K27 demethylase inhibitor GSK-J4. Specifically, GSK-J4 treatment of KRAS mutant-containing LuAC downregulated cell-cycle progression genes with increased H3K27me3. In addition, GSK-J4 upregulated expression of genes involved in glutamine/glutamate transport and metabolism. In line with this, GSK-J4 reduced cellular levels of glutamate, a key source of the TCA cycle intermediate α-ketoglutarate (αKG) and of the antioxidant glutathione, leading to reduced cell viability. Supplementation with an αKG analogue or glutathione protected KRAS-mutant LuAC cells from GSK-J4-mediated reductions in viability, suggesting GSK-J4 exerts its anticancer effects by inducing metabolic and oxidative stress. Importantly, KRAS knockdown in mutant LuAC lines prevented GSK-J4-induced decrease in glutamate levels and reduced their susceptibility to GSK-J4, whereas overexpression of oncogenic KRAS in wild-type LuAC lines sensitized them to GSK-J4. Collectively, our study uncovers a novel association between a genetic mutation and KDM inhibitor sensitivity and identifies the underlying mechanisms. This suggests GSK-J4 as a potential treatment option for cancer patients with KRAS mutations. SIGNIFICANCE: This study not only provides a novel association between KRAS mutation and GSK-J4 sensitivity but also demonstrates the underlying mechanisms, suggesting a potential use of GSK-J4 in cancer patients with KRAS mutations.