Correction: Increasing Fusobacterium infections with Fusobacterium varium, an emerging pathogen.

[This corrects the article DOI: 10.1371/journal.pone.0266610.].

Complete genome sequence of a novel species of Brevundimonas (strain NIBR10).

The complete genome sequence of strain NIBR10 was sequenced using PacBio RS II (Pacific Biosciences) sequencing platform. The 4,006,378-bp genome has a G + C content of 66.89% and around 3,832 coding sequences. Genomic data will provide valuable research for natural taxonomy and comparative genomics of the genus Brevundimonas.

Complete Genome Sequence of Phenylobacterium Strain NIBR 498073, Isolated from the Sediment of a Tidal Flat.

We report the complete genome sequence of Phenylobacterium sp. strain NIBR 498073. The sample was isolated from sediment from a tidal flat in Incheon, South Korea. The whole genome consists of one circular chromosome of 4,289,989 bp, and annotation using PGAP predicted 4,160 protein coding genes, 47 tRNAs, 6 rRNAs, and 3 noncoding RNAs.

Construction of the Whole Genome of Brevundimonas sp. Strain NIBR11: An Exploration of Bacteria Isolated from Algae in the Nakdong River.

We report the genome sequence of Brevundimonas sp. strain NIBR11. Strain NIBR11 was isolated from algae collected from the Nakdong River. The assembled contig contains 3,123 coding sequences (CDSs), 6 rRNA genes, 48 tRNA genes, 1,623 genes for hypothetical proteins, and 109 genes for proteins with putative functions.

Complete Genome Sequence of Caulobacter sp. (Strain NIBR1757) Isolated from Lake Chungju in South Korea.

Here, we report the complete genome sequence of strain NIBR1757, isolated from the water of Lake Chungju in South Korea. The assembled genome consists of 4,185 coding sequences (CDSs), 6 rRNAs, and 51 tRNAs. Comparative 16S rRNA gene sequence studies and GTDB-Tk analysis show that this strain belongs to the genus Caulobacter.

Complete Genome Sequence of Sphingomonas sp. Strain NIBR02145.

Sphingomonas sp. strain NIBR02145 is a putative chemoheterotrophic strain that was isolated from soil in Wando-gun, Republic of Korea. The NIBR02145 genome was sequenced with PacBio next-generation sequencing technology. The 5,010,245-bp circular genome has a GC content of 66.79% and harbors 4,561 coding sequences, 6 rRNAs, and 52 tRNAs.

Exposure to COVID-19 Infection and Mortality Rates Among People With Disabilities in South Korea.

BACKGROUND: With the delayed eradication of coronavirus disease 2019 (COVID-19), people with disabilities, a socially vulnerable class of individuals, face aggravated hardships caused by a pause in support services and lack of care due to stricter social distancing policies combined with the challenges of their disabilities. Given this background, we aim to investigate COVID-19 infection and mortality rates among people with disabilities, who face heightened physical and mental health threats amidst the COVID-19 pandemic. METHODS: Gender, age, health insurance premiums, the Charlson Comorbidity Index (CCI), the severity of the disability, and the type of disability were compared among people with disabilities who had been infected with or died from COVID-19 using the nationally representative National Health Insurance Service (NHIS)-COVID-19 database (DB). RESULTS: We found that the COVID-19 infection rate was higher among those with low income, those with severe disability, and those with "other" disabilities (ie, speech disabilities, hepatic dysfunction, respiratory dysfunction, facial disfigurement, intestinal fistular/urinary disability, epilepsy, intellectual disability, autistic disorder, and mental disorders). The mortality rate was markedly higher (ie, 15.90 times higher, odds ratio [OR]: 15.90, 95% confidence interval [CI]: 6.16 - 41.06) among people aged 80 years or older as compared with those aged 60 years or younger. The odds for mortality were 2.49 times higher (OR: 2.49, 95% CI: 1.33 - 4.64) among people with severe disabilities as compared with mild disabilities. CONCLUSION: Among people with disabilities, we found that COVID-19 infection rates differed according to income level, severity of the disability, and disability type, while the COVID-19 mortality rates differed according to age and severity of the disability.

Complete Genome Sequence of Flavobacterium sediminilitoris YSM-43T, Isolated from Tidal Sediment in Yeosu.

Here, we report the complete genome sequence of Flavobacterium sediminilitoris YSM-43T, isolated from a tidal flat in Yeosu, Republic of Korea. The whole genome consists of one circular chromosome of 3,913,692 bp. A total of 3,599 genes were predicted, comprising 3,537 coding DNA sequences (CDSs), 50 tRNAs, 9 rRNAs, and 3 noncoding RNAs (ncRNAs).

Increasing Fusobacterium infections with Fusobacterium varium, an emerging pathogen.

Infections caused by Fusobacterium species are rare; however serious infections with complications or mortality may occur occasionally. We conducted a retrospective study to investigate the clinical features of patients with Fusobacterium infections and the differences between infections caused by the species F. necrophorum, F. nucleatum, and F. varium. Additionally, we attempted to identify risk factors for Fusobacterium-associated mortality. This study included all patients at a large tertiary care teaching hospital in South Korea with Fusobacterium infections from January 2006 to April 2021. Demographic, clinical, laboratory, and outcome data were analyzed. Multiple logistic regression analysis was performed to assess the risk factors for in-hospital mortality associated with F. nucleatum and F. varium infections. We identified 272 patients with Fusobacterium infections during the study period. The number of Fusobacterium cases has increased recently, with F. varium infections markedly increasing since 2016 and causing a significant proportion of infections. Patients with F. varium infections were older and had a higher proportion of nosocomial infections than the other groups. The F. nucleatum and F. varium groups showed higher in-hospital mortality than the F. necrophorum group. Through logistic regression analysis, APACHE II score and serum albumin level were considered risk factors for in-hospital mortality. APACHE II score was positively correlated with age, red cell distribution width, and serum blood urea nitrogen, and negatively correlated with serum albumin level. Infections caused by Fusobacterium species are increasing. F. varium causes a significant proportion of severe infections.

Comparing Treatment Outcomes of Ampicillin-Sulbactam, Other ß-Lactams, and Vancomycin in Blood Culture-Negative Infective Endocarditis.

Selection of proper antibiotics for blood culture-negative infective endocarditis (BCNIE) is difficult due to limited data on antibiotic regimens for BCNIE in existing literature. The aim of this study was to compare ampicillin-sulbactam, other ß-lactams antibiotics, and vancomycin among patients with BCNIE to determine the proper antibiotic regimens. This retrospective study included adult patients with BCNIE admitted to Severance Hospital from November 2005 to August 2017. Patients were classified into three groups as, treated with ampicillin-sulbactam, other ß-lactams, and vancomycin. The primary outcome was 1-year all-cause mortality. A total of 74 cases with BCNIE were enrolled in this study. There were no statistically significant differences in clinical characteristics between the three groups. One-year mortality did not significantly differ between the study groups either. Further, in-hospital mortality, 28-day mortality and overall mortality showed no difference. However, Cox-regression analysis showed nosocomial infective endocarditis as an independent risk factor and a protective effect of surgery on 1-year mortality. This study showed no clear difference in the outcomes of BCNIE as per the antibiotic therapy but suggested the beneficial effect of surgical treatment. With increasing global concern of antimicrobial resistance, it might be reasonable to select ampicillin-sulbactam-based antibiotic therapy while actively considering surgical treatment in BCNIE.

Anti-Inflammatory and Anti-Diabetic Effect of Black Soybean Anthocyanins: Data from a Dual Cooperative Cellular System.

Obesity is characterized by elevated infiltration of macrophages into adipose tissue, leading to the development of insulin resistance. The black soybean seed coat is a rich source of anthocyanins with antioxidative and anti-inflammatory activities. This study investigated the effects of black soybean anthocyanin extract (BSAn) on obesity-induced oxidative stress, the inflammatory response, and insulin resistance in a coculture system of hypertrophied 3T3-L1 adipocytes and RAW264 macrophages. Coculture of adipocytes with macrophages increased the production of reactive oxygen species and inflammatory mediators and cytokines (NO, MCP-1, PGE2, TNFα, and IL-6) and the release of free fatty acids but reduced anti-inflammatory adiponectin secretion. BSAn treatment (12.5, 25, 50, and 100 µg/mL) alleviated the coculture-induced changes (p < 0.001) and inhibited coculture-induced activation of JNK and ERK signaling (p < 0.01). BSAn also blocked the migration of RAW264.7 macrophages toward 3T3-L1 adipocytes. In addition, treatment with BSAn increased PPARγ expression and glucose uptake in response to insulin in hypertrophied 3T3-L1 adipocyte and RAW264.7 macrophage coculture (p < 0.01). These results demonstrate that BSAn attenuates inflammatory responses and improves adipocyte metabolic function in the coculture of hypertrophied 3T3-L1 adipocytes and RAW264.7 macrophages, suggesting the effectiveness of BSAn for obesity-induced insulin resistance.

Phylogenetic and evolutionary analysis of foot-and-mouth disease virus A/ASIA/Sea-97 lineage.

Foot-and-mouth disease virus (FMDV) A/ASIA/Sea-97 is a predominant lineage in Southeast Asia and East Asia. However, Sea-97 lineage has not been well studied since its first outbreak in Thailand in 1997. Thus, we conducted phylogenetic and evolutionary analysis of Sea-97 using 224 VP1 sequences of FMDV A/ASIA during 1960 and 2018. Phylogenetic analysis revealed that Sea-97 lineage can be classified into five groups (G1-G5). After the emergence of G2 from G1, the genetic diversity of Sea-97 increased sharply, causing divergence into G3, G4 and G5. During this evolutionary process, Sea-97 lineage, which was initially found only in some countries in Southeast Asia, gradually spread to East Asia. The evolution rate of this lineage was estimated to be 1.2 × 10-2 substitutions/site/year and there were many differences in amino acid residues compared to vaccine strain. Substitutions at antigenically important sites may affect the efficacy of the vaccine, suggesting the need for appropriate vaccine strains. Our results could provide meaningful information to understand comprehensive characteristic of Sea-97 lineage.

[Types of Perception toward Ethical Issues in Perioperative Nurses: Q-Methodological Approach].

PURPOSE: This study was aimed at identifying the types of perceptions of ethical issues among perioperative nurses. METHODS: Q-methodology focusing on individual subjectivity was used with data collected in November 2016. Thirty-four Q-statements were selected and scored by the 35 participants on a 9-point scale with normal distribution. Participants were perioperative nurses working in advanced general hospitals and general hospitals. The data were analyzed using the PC-QUANL program. RESULTS: total of 35 perioperative nurses were classified into 4 factors based on the following viewpoints: self-centered (type 1), onlooking and avoiding (type 2), patient-centered (type 3), and problem-centered (type 4). The 4 factors accounted for 57.84% of the total variance. Individual contributions of factors 1, 2, 3, and 4 were 41.80%, 7.18%, 5.20%, and 3.66%, respectively. CONCLUSION: The major contribution of this study is the clarification of perioperative nurses' subjective perceptions of ethical issues. These findings can be used in formulating effective strategies for nursing educators, professional nurses, and nursing administrators to improve ethical decision-making abilities and to perform ethical nursing care by the appropriate management of ethical issues in everyday nursing practice.

Black soybean anthocyanins attenuate inflammatory responses by suppressing reactive oxygen species production and mitogen activated protein kinases signaling in lipopolysaccharide-stimulated macrophages.

BACKGROUND/OBJECTIVES: Oxidative stress is closely related with inflammation and development of many diseases. Black soybean seed coat contains high amount of anthocyanins, which are well-known for free radical scavenging activities. This study investigated inflammatory response and action mechanism of black soybean anthocyanins with regard to antioxidant activity in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells. MATERIALS/METHODS: RAW 264.7 cells were treated with anthocyanins extracted from black soybean seed coats in a concentration range of 12.5 to 100 µg/mL. The production of reactive oxygen species (ROS), secretion of pro-inflammatory mediators and cytokines, and the signaling in the mitogen activated protein kinases (MAPKs) pathway were examined. RESULTS: Black soybean anthocyanins significantly decreased LPS-stimulated production of ROS, inflammatory mediators such as nitric oxide (NO) and prostaglandin E2, and pro-inflammatory cytokines, including tumor necrosis factor α and interleukin-6, in a dose-dependent manner without cytotoxicity (P < 0.001). Black soybean anthocyanins downregulated the expression of inducible NO synthase and cyclooxygenase-2 in LPS-stimulated RAW 264.7 cells (P < 0.001). Moreover, black soybean anthocyanins inhibited LPS-induced phosphorylation of MAPKs, including extracellular signal-regulated kinase, c-Jun N-terminal kinase, and p38 (P < 0.001). CONCLUSION: These results suggest that black soybean anthocyanins exert anti-inflammatory activity by inhibiting ROS generation and subsequent MAPKs signaling, thereby inhibiting inflammatory responses.

The Genetic Origin of Short Tail in Endangered Korean Dog, DongGyeongi.

The tail of many animal species is responsible for various physiological functions. The functional importance of tail may have brought tail-loss to attention in many evolutionary and developmental studies. To provide a better explanation for the loss of tail, the current study aims to identify the evolutionary history and putative causal variants for the short tail in DongGyeongi (DG), an endangered dog breed, which is also the only dog in Korea that possesses a short tail. Whole genome sequencing was conducted on 22 samples of DG, followed by an investigation of population stratification with 10 other dog breeds. The genotypes, selective sweep and demography of DG were also investigated. As a result, we discovered the unique genetic structure of DG and suggested two possible ways in which the short tail phenotype developed. Moreover, this study suggested that selective sweep genes, ANKRD11 and ACVR2B may contribute to the reduction in tail length, and non-synonymous variant in the coding sequence of T gene and the CpG island variant of SFRP2 gene are the candidate causal variants for the tail-loss.

Status of dosage compensation of X chromosome in bovine genome.

Dosage compensation system with X chromosome upregulation and inactivation have evolved to overcome the genetic imbalance between sex chromosomes in both male and female of mammals. Although recent development of chromosome-wide technologies has allowed us to test X upregulation, discrete data processing and analysis methods draw disparate conclusions. A series of expression studies revealed status of dosage compensation in some species belonging to monotremes, marsupials, rodents and primates. However, X upregulation in the Artiodactyla order including cattle have not been studied yet. In this study, we surveyed the genome-wide transcriptional upregulation in X chromosome in cattle RNA-seq data using different gene filtration methods. Overall examination of RNA-seq data revealed that X chromosome in the pituitary gland expressed more genes than in other peripheral tissues, which was consistent with the previous results observed in human and mouse. When analyzed with globally expressed genes, a median X:A expression ratio was 0.94. The ratio of 1-to-1 ortholog genes between chicken and mammals, however, showed considerable reduction to 0.68. These results indicate that status of dosage compensation for cattle is not deviated from those found in rodents and primate, and this is consistent with the evolutionary history of cattle.

Risk factors for delayed post-polypectomy bleeding.

BACKGROUND/AIMS: Among the many complications that can occur following therapeutic endoscopy, bleeding is the most serious, which occurs in 1.0-6.1% of all colonoscopic polypectomies. The aim of this study was to identify risk factors of delayed post-polypectomy bleeding (PPB). METHODS: We retrospectively reviewed the data of patients who underwent colonoscopic polypectomy between January 2003 and December 2012. We compared patients who experienced delayed PPB with those who did not. The control-to-patient ratio was 3:1. The clinical data analyzed included polyp size, number, location, and shape, patient' body mass index (BMI), preventive hemostasis, and endoscopist experience. RESULTS: Of 1,745 patients undergoing colonoscopic polypectomy, 21 (1.2%) experienced significant delayed PPB. We selected 63 age- and sex-matched controls. Multivariate logistic regression analysis showed that polyps >10 mm (odds ratio [OR], 2.605; 95% confidence interval [CI], 1.035-4.528; P=0.049), a pedunculated polyp (OR, 3.517; 95% CI, 1.428-7.176; P=0.045), a polyp located in the right hemicolon (OR, 3.10; 95% CI, 1.291-5.761; P=0.013), and a high BMI (OR, 3.681; 95% CI, 1.876-8.613; P=0.013) were significantly associated with delayed PPB. CONCLUSIONS: Although delayed PPB is a rare event, more caution is needed during colonoscopic polypectomies performed in patients with high BMI or large polyps, pedunculated polyps, or polyps located in the right hemicolon.

Morphological effects of mitomycin C on urothelial responses to experimentally-induced urethral stricture in rats.

OBJECTIVES: To analyze the urothelial responses to mitomycin C treatment after urethral injury in rats, as the urothelium might play a role in the pathogenesis of urethral stricture. METHODS: Male Sprague-Dawley rats were divided into four groups (n = 5/group): negative control, positive control without further treatment, experimental control treated with sodium hyaluronate and sodium carboxymethylcellulose, and experimental treated with mitomycin C after internal urethrotomy. RESULTS: Compared with negative controls, positive controls showed a significant increase in cell proliferation and DNA damage accompanied by a considerable decrease in DNA repair in the urothelium, which resulted in urethral stricture. Experimental controls showed a significant increase in cell proliferation, DNA damage and DNA repair compared with negative controls. The mitomycin C-treated group showed a significant decrease in cell proliferation and DNA damage, but a considerable increase in DNA repair compared with the positive and experimental control groups. DNA damage was immediately increased after urethral injury, but DNA repair and cell proliferation showed belated and upregulated expression after mitomycin C treatment. CONCLUSIONS: Mitomycin C could induce healthy re-epithelialization without severe damage in the urothelium. This finding might support the possibility of using mitomycin C as an adjuvant therapy for urethral strictures, and it might also suggest a urothelial role in the process of urethral stricture after urethral injury.

Ursolic acid isolated from guava leaves inhibits inflammatory mediators and reactive oxygen species in LPS-stimulated macrophages.

Psidium guajava (guava) leaves have been frequently used for the treatment of rheumatism, fever, arthritis and other inflammatory conditions. The purpose of this study was to identify major anti-inflammatory compounds from guava leaf extract. The methanol extract and its hexane-, dichloromethane-, ethylacetate-, n-butanol- and water-soluble phases derived from guava leaves were evaluated to determine their inhibitory activity on nitric oxide (NO) production by RAW 264.7 cells stimulated with lipopolysaccharide (LPS). The methanol extract decreased NO production in a dose-dependent manner without cytotoxicity at a concentration range of 0-100 µg/mL. The n-butanol soluble phase was the most potent among the five soluble phases. Four compounds were isolated by reversed-phase HPLC from the n-butanol soluble phase and identified to be avicularin, guaijaverin, leucocyanidin and ursolic acid by their NMR spectra. Among these compounds, ursolic acid inhibited LPS-induced NO production in a dose-dependent manner without cytotoxity at a concentration range of 1-10 µM, but the other three compounds had no effect. Ursolic acid also inhibited LPS-induced prostaglandin E2 production. A western blot analysis showed that ursolic acid decreased the LPS-stimulated inducible nitric oxide synthase and cyclooxygenase protein levels. In addition, ursolic acid suppressed the production of intracellular reactive oxygen species in LPS-stimulated RAW 264.7 cells, as measured by flow cytometry. Taken together, these results identified ursolic acid as a major anti-inflammatory compound in guava leaves.

Apurinic/apyrimidinic endonuclease 1 on aging-associated deteriorations in rat kidneys.

We have reported a possible involvement of apurinic/apyrimidinic endonuclease 1 (APE1), one of the DNA repair pathways, in various nephropathy models and found that there is a close connection between APE1 and p53-dependent apoptosis. Therefore, we investigated the changes of APE in aging rat kidney since aging is the consequence of increased susceptibility to apoptosis and impaired repair. Characteristics of chronological aging were compared among 6-, 24- and 28-month-old male Sprague-Dawley rats. Serum blood urea nitrogen and creatinine were measured for renal function. Western blot assay was compared for p53, bax, cleaved caspase 3, rH2AX, and APE1. Immunohistochemical staining of 8-hydroxy-2'-deoxyguanosine (8-OHdG) and APE1 was performed. Cellular senescence was checked by beta-galactosidase staining. Compared with young rats, aged rats showed significant increase in creatinine level with cellular senescence in the proximal convoluted tubules confirmed by beta-galactosidase staining. All the checked variables were significantly increased with aging: 1) increased p53, bax, and caspase 3 may activate the apoptotic pathway, 2) increased rH2AX and 8-OHdG immunolocalization in the proximal convoluted tubules might mean augmented DNA damage, and 3) increased APE1 might be caused by the immunoreactivity in the distal convoluted tubules while decreased in the proximal convoluted tubules. These results suggested that APE1 might have little protective effects on p53-dependent apoptosis irrespective of DNA repair activities in aged renal proximal tubules. Therefore, researchers should use older animals than 24-month-old rats in future studies for investigating the relationship between the apoptosis and DNA repair in the aging kidneys.