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In this study, the complete mitochondrial genome of Norwegian skates imported to Korea was sequenced with a circular molecule of 17,121 bp, which consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNA genes, and a control region (D-loop). And among these sequences, 193 bp sequence in the D-loop of the genus Raja suggested the possibility of being used as a genetic marker for classification of Raja and Dipturus species. The BI phylogenetic tree by using the nucleotide sequences of 13 PCGs from 15 available mitogenomes of family Rajidae confirmed also that Norwegian skates imported to Korea form a group with Raja brachyura species with high branch value, and that this was a species of Raja brachyura. As above, these results would be expected to provide for the further understanding on the phylogenetic relationship, taxonomic classification and phylogeography of the family Rajidae.

The complete mitogenome of Sardinella zunasi was determined by next-generation sequencing. The S. zunasi mitogenome was a circular 16,307 bp molecule that contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region (D-loop). The gene arrangement was consistent with other Sardinella mitogenomes. The phylogenetic relationships of 29 Clupeoidei species based on 13 protein-coding genes from the available mitogenomes were analyzed. Sardinella zunasi clustered with Sardinella among Clupeidae, suggesting a closer relationship with this genus. These results will be useful for understanding the phylogenetic relationships, taxonomic classification, and phylogeography of the genus Sardinella relative to other genera of Clupeoidei.

Purpose: This study investigated which body position is more useful for visualizing subphrenic hepatocellular carcinomas (HCCs) during ultrasonography (US) examinations. Methods: This prospective study was approved by the institutional review board and written informed consent was obtained from all patients. Twenty consecutive patients with a single subphrenic HCC (treatment-naïve, 1 to 3 cm) underwent a US examination for planning radiofrequency ablation. The examinations were done by one of three radiologists and the patients were examined in four different body positions-supine, right posterior oblique (RPO), left lateral decubitus (LLD), and semi-erect-by being positioned on a tilted table. The visibility of the index tumor was prospectively assessed using a 4-point scale. Needle insertion was considered to be technically feasible if the visibility score was lower than 2. The visibility score and technical feasibility were compared using the Wilcoxon signed rank test and the McNemar test, respectively, for pairwise comparisons between different body positions. Results: The visibility score was significantly lower in the semi-erect position (median, 2; interquartile range, 1 to 2.75) than in the supine (3, 2 to 4), RPO (3, 2 to 4), and LLD (4, 3.25 to 4) positions (P=0.007, P=0.005, and P=0.001, respectively). The technical feasibility of needle insertion was also significantly higher in the semi-erect position (75%, 15/20) than in the supine (45%, 9/45), RPO (35%, 7/20), and LLD (20%, 4/20) positions (P=0.031, P=0.021, and P=0.001, respectively). Conclusion: The semi-erect position is more useful for the visualization of subphrenic HCCs than the supine, RPO, or LLD positions. [ABSTRACT FROM AUTHOR]

Stomach cancer: DNA methylation of hormone receptor genes A sequencing study reveals abnormal changes to DNA that set the stage for stomach cancer development. DNA methylation, the addition of methyl groups to alter DNA activity, is often disrupted in human cancers. Yong Sung Kim at the Korea Research Institute of Bioscience and Biotechnology (KRIBB) in Daejeon, South Korea, and co-workers used sequencing technogy to identify critical methylation changes in stomach epithelial cells, intestinal metaplasia lesion and tumor cells during early-stage gastric cancer. The team found 3,035 abnormally methylated DNA regions related to the expression of particular genes. Further analysis identified six hormone receptor genes directly involved with stomach acid secretion, whose altered expression was linked to over-methylated DNA regions. Loss of function within these six genes may lead to gastric cancer, and their expression levels could be valuable biomarkers for the disease.

Purpose: This study aimed to evaluate the incidence and severity of biliary complications after treating periductal hepatocellular carcinomas (HCCs) using either cryoablation (CA) or radiofrequency ablation (RFA) and assess independent risk factors for biliary complications after treatment. Materials and methods: Between July 2008 and August 2018, 949 patients with treatment-naïve HCCs underwent either RFA or CA in our institution. Of these, patients with multiple HCCs, tumors equal to or larger than 3 cm or smaller than 1 cm, and tumors with non-periductal locations were excluded. Finally, 31 patients and 25 patients were included in the RFA group and the CA group, respectively. The incidence and severity of biliary complications were compared between the RFA and CA groups. The risk factors for biliary complications were assessed using univariable and multivariable logistic regression analyses using the following variables: age, sex, tumor size, Child–Pugh score, tumor location (peripheral duct versus central duct), ablation method (RFA versus CA), the number of applicators, ablation time, and ablation volume. Results: The incidence and severity of biliary complications were significantly higher in the RFA group than in the CA group (p ¼ 0.007 and p ¼ 0.002, respectively). In univariable and multivariable analyses, the ablation method was an independent risk factor for biliary complications (p ¼ 0.004 and 0.013, respectively). Conclusions: The incidence and severity of biliary complications after treating HCCs abutting the bile duct are lower in CA than RFA, demonstrating that CA is safer than RFA for ablating small periductal HCCs. [ABSTRACT FROM AUTHOR]

Purpose: To evaluate the clinical utility of percentage of serum prostate-specific antigen (proPSA) to free PSA (%p2PSA) and the prostate health index (PHI) for predicting aggressive pathological outcomes of radical prostatectomy (RP) in Korean males. Materials and Methods: This prospective observational multicenter study included 160 Korean males who consecutively underwent RP. The predictive utility of preoperative %p2PSA and PHI for predicting the following pathological outcomes of RP including pT3 disease, pathologic Gleason sum =7, and Gleason sum upgrading was investigated using multivariate and decision-curve analyses. Results: The PHI and %p2PSA levels were significantly higher in patients with pT3 disease, pathologic Gleason sum =7, and Gleason sum upgrading. On univariate analysis, PHI was an accurate predictor of pT3 disease, pathologic Gleason sum =7, and Gleason sum upgrading. Multivariate and decision curve analyses revealed that inclusion of PHI to a base multivariate model including total PSA, percentage free PSA, PSA density, percentage of positive biopsy core, biopsy Gleason sum, and clinical stage factors significantly increased its predictive accuracy; %p2PSA showed a similar result. However, PHI was a more valuable predictor of pathological outcomes of RP. Conclusions: This study revealed PHI and %p2PSA as preoperative biomarkers of pathological outcomes in Korean males who underwent RP for prostate cancer. [ABSTRACT FROM AUTHOR]

Asthma, a heterogeneous disease of the airways, is common around the world, but little is known about the molecular mechanisms underlying the interactions between DNA methylation and gene expression in relation to this disease. The seeds of Descurainia sophia are traditionally used to treat coughs, asthma and edema, but their effects on asthma have not been investigated by multi-omics analysis. We undertook this study to assess the epigenetic effects of ethanol extract of D. sophia seeds (DSE) in an ovalbumin (OVA)-induced mouse model of asthma. We profiled genome-wide DNA methylation by Methyl-seq and characterized the transcriptome by RNA-seq in mouse lung tissue under three conditions: saline control, OVA-induced, and DSE-treated. In total, 1995 differentially methylated regions (DMRs) were identified in association with anti-asthmatic effects, most in promoter and coding regions. Among them, 25 DMRs were negatively correlated with the expression of the corresponding 18 genes. These genes were related to development of the lung, respiratory tube and respiratory system. Our findings provide insights into the anti-asthmatic effects of D. sophia seeds and reveal the epigenetic targets of anti-inflammatory processes in mice.

Demonstrates the power of a tagged library approach for efficient forward chemical genetics, especially by expediting the connection of a hit compound to the affinity matrix by incorporating a linker directly to the library compounds prior to phenotypic screening. Design of tagged library that is based on a triazine scaffold; Novel small-molecule inhibitors for several ribosomal accessory proteins or their complex as the target.

Focuses on a novel microtubule destabilizing entity from orthogonal synthesis of Triazine library and Zebrafish embryo screening. Contribution of microtubule functionality in the design of anticancer drugs; Induction of similar morphological changes; Development of straight forward solid phase synthetic pathway.

Strain IMCC2047 was isolated from the Yellow Sea using dilution-to-extinction culturing. The strain was shown to occupy a distinct phylogenetic position within the Gammaproteobacteria. Here we present the genome sequence of strain IMCC2047, which harbors genes for various metabolic pathways, including proteorhodopsin and ribulose bisphosphate carboxylase. [ABSTRACT FROM AUTHOR]

Strain IMCC9480 is a novel member of the family Oxalobacteraceae of the Betaproteobacteria, isolated from the Arctic Ocean by dilution-to-extinction culturing. Here we present the draft genome sequence of strain IMCC9480. The genome is predicted to contain genes for xanthorhodopsin, retinoid biosynthesis, carbon monoxide dehydrogenase, and C1 metabolism [ABSTRACT FROM AUTHOR]