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.

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.

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.

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.

Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq.

Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.

Genome-wide DNA Methylation Profiles of Small Intestine and Liver in Fast-growing and Slow-growing Weaning Piglets.

Although growth rate is one of the main economic traits of concern in pig production, there is limited knowledge on its epigenetic regulation, such as DNA methylation. In this study, we conducted methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) to compare genome-wide DNA methylation profile of small intestine and liver tissue between fast- and slow-growing weaning piglets. The genome-wide methylation pattern between the two different growing groups showed similar proportion of CpG (regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence) coverage, genomic regions, and gene regions. Differentially methylated regions and genes were also identified for downstream analysis. In canonical pathway analysis using differentially methylated genes, pathways (triacylglycerol pathway, some cell cycle related pathways, and insulin receptor signaling pathway) expected to be related to growth rate were enriched in the two organ tissues. Differentially methylated genes were also organized in gene networks related to the cellular development, growth, and carbohydrate metabolism. Even though further study is required, the result of this study may contribute to the understanding of epigenetic regulation in pig growth.

Efficacious rat model displays non-toxic effect with Korean beechwood creosote: a possible antibiotic substitute.

Wood creosote, an herbal anti-diarrheal and a mixture of major volatile compounds, was tested for its non-toxicological effects, using a rat model, with the objective to use the creosote as an antibiotic substitute. A total of 30 Sprague-Dawley rats were studied to form five groups with 6 rats each. Korea beechwood creosote was supplemented into three test groups with 0.03 g/kg, 0.07 g/kg and 0.1 g/kg body weight/day without antibiotic support, along with a positive control of Apramycin sulphate (at 0.5% of the daily feed) and a negative control. Korean beechwood creosote supplementation showed no negative effect on the body weight gain in comparison to the negative and the positive control groups and the feed conversion ratio was also comparable with that of the control groups. The clinical pathology parameters studied were also under the umbrella of normal range, including liver specific enzymes, blood glucose, total protein, blood urea nitrogen (BUN), which indicated no toxic effect of creosote at the given doses. The non-hepatotoxic effect was also confirmed using hepatic damage specific molecular markers like Tim-p1, Tim-p2 and Tgf-ß1. The results suggested that Korean beechwood may be used as antibiotic substitute in weanling pigs feed without any toxic effect on the body. Although the antimicrobial properties of creosote were not absolutely similar to those of apramycin sulphate, they were comparable.

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

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

Status of bovine mastitis and associated risk factors in subtropical Jeju Island, South Korea.

The present investigation was carried out to study the prevalence of mastitis in 136 Holstein cows from a subtropical province of South Korea. Out of 527 milk samples studied, 22.6 % were found positive for mastitis. On animal level, prevalence was estimated at 55.2 %. Late lactating cows were at higher risk for mastitis development as compared to those in early and mid lactations. The study revealed that the risk of an increase in somatic cell count (SSC) and mastitis increased with advanced age and in animals with higher parity. The highest infection rate of 71.4 % was found in the age group >9 years followed by cows with higher than fifth parity (65.5 %). On severity and quarter basis, cows of <3 years of age had higher occurrence (12.5 %) of severe mastitis. From the present study, it may be concluded that a positive relationship exists between increased prevalence of mastitis and high SCC and the advance in age and parity of Holstein cows.

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 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.

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.

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.

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.

Characterization and application of oviductal epithelial cells in vitro in Gallus domesticus.

Chicken oviductal epithelium produces large quantities of egg white protein in daily cycles. In this study, we cultured and characterized oviductal epithelial cells (OECs) from juvenile (10-wk-old) chickens and from actively laying (30-wk-old) hens. The juvenile OECs were maintained over passage 25 and were positive for toluidine blue, lectin-ConA, HPA, UEA-1, WFA, WGA, anti-OVA, anti-ESR1, and anti-PGR, whereas the adult OECs were cultured over passage 6 and were positive for toluidine blue, periodic acid-Schiff, lectin-ConA, WFA, WGA, anti-OVA, anti-ESR1, and anti-PGR. To investigate the optimal concentration of steroid hormones for inducing egg white protein genes in vitro, we examined the effects of estrogen, diethylstilbestrol, progesterone, and corticosterone on OECs. Results showed that oviduct-specific levels of avidin, ovalbumin, ovomucin, lysozyme, ESR1, and PGR gene expression were significantly elevated in steroid hormone-treated OECs compared with those of untreated cells (P < 0.05). Ovalbumin protein was also secreted into culture medium from hormone-treated OECs. In addition, to examine the application of OECs for avian transgenesis, we introduced human thrombopoietin (THPO)-expressing lentiviral vector controlled by a 3.5-kb ovalbumin promoter into cultured OECs, and THPO expression was significantly induced with diethylstilbestrol or progesterone in juvenile OECs (P < 0.05) and in adult OECs (P < 0.05). In conclusion, these data demonstrate the potential of cultured OECs as a model system for providing a better understanding of the regulation of gene expression and for the production of an avian transgenic bioreactor.

Structural and histological characterization of oviductal magnum and lectin-binding patterns in Gallus domesticus.

BACKGROUND: Although chicken oviduct is a useful model and target tissue for reproductive biology and transgenesis, little is known because of the highly specific hormonal regulation and the lack of fundamental researches, including lectin-binding activities and glycobiology. Because lectin is attached to secreted glycoproteins, we hypothesized that lectin could be bound to secretory egg-white proteins, and played a crucial role in the generation of egg-white protein in the oviduct. Hence, the purpose of this study was to investigate the structural, histological and lectin-binding characteristics of the chicken oviductal magnum from juvenile and adult hens. METHODS: The oviductal magnums from juvenile and adult hens were prepared for ultrastructural analysis, qRT-PCR and immunostaining. Immunohistochemistry of anti-ovalbumin, anti-ESR1 and anti-PGR, and mRNA expression of egg-white genes and steroid hormone receptor genes were evaluated. Lectin histochemical staining was also conducted in juvenile and adult oviductal magnum tissues. RESULTS: The ultrastructural analysis showed that ciliated cells were rarely developed on luminal surface in juvenile magnum, but not tubular gland cells. In adult magnum, two types of epithelium and three types of tubular gland cells were observed. qRT-PCR analysis showed that egg-white genes were highly expressed in adult oviduct compared with the juvenile. However, mRNA expressions of ESR1 and PGR were considerably higher in juvenile oviduct than adult (P < 0.05). The immunohistochemical analysis showed that anti-ovalbumin antibody was detected in adult oviduct not in juvenile, unlikely anti-ESR1 and anti-PGR antibodies that were stained in both oviducts. In histological analysis, Toluidine blue was stained in juvenile and adult oviductal epithelia, and adult tubular glands located in the outer layer of oviductal magnum. In contrast, PAS was positive only in adult oviductal tubular gland. Lectins were selectively bound to oviductal epithelium, stroma, and tubular gland cells. Particularly, lectin-ConA and WGA were bound to electron-dense secretory granules in tubular gland. CONCLUSIONS: The observation of ultrastructural analysis, mRNA expression, immunohistochemistry and lectin staining showed structural and physiological characterization of juvenile and adult oviductal magnum. Consequently, oviduct study could be helped to in vitro culture of chicken oviductal cells, to develop epithelial or tubular gland cell-specific markers, and to understand female reproductive biology and endocrinology.