Hydrothermally treated coral scaffold promotes proliferation of mesenchymal stem cells and enhances segmental bone defect healing

Introduction: Synthetic hydroxyapatite (HAp) scaffolds have shown promising therapeutic outcomes in both animals and patients. In this study, we aim to evaluate the chemical and physical phenotype, biocompatibility, and bone repair effects of hydrothermally treated coral with natural coral and synthetic HAp.Methods: The phase composition, surface pattern, 3D structures, and porosity of the scaffolds were characterized, and cell viability, proliferation, and osteogenic differentiation of mesenchymal stem cells (MSCs) after seeding onto the scaffold were determined. The scaffolds were implanted into rats to assess their bone repair effects using micro-CT analysis, mechanical testing, and histological staining.Results: The results showed that the phase composition, porous structure, and porosity of hydrothermally treated coral were comparable to pure HAp scaffold. While only the natural coral happens to be dominantly calcium carbonate. Higher cell proliferation and osteogenic differentiation potential were observed in the hydrothermally treated coral scaffold compared to natural coral and pure HAp. Histological results also showed increased new bone formation in the hydrothermally treated coral group.Discussion: Overall, our study suggests that hydrothermal modification enhances the cytocompatibility and therapeutic capacity of coral without altering its physical properties, showing superior effectiveness in bone repair to synthetic HAp

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 down-stream analysis of genome data. Bio-Express web service is freely available at https://www. bioexpress.re.kr/. ?? 2020, Korea Genome Organization

Spatio-Temporal Characteristics in the Clearness Index Derived from Global Solar Radiation Observations in Korea

The spatio-temporal characteristics of the clearness index (KT) were investigated using daily global solar irradiance measurements (290–2800 nm) for the period of 2000–2014 at 21 sites in Korea, a complex region in East Asia with a distinct monsoon season and heavy aerosol loading year-round. The annual mean KT value for all sites is 0.46, with values of 0.63 and 0.25 for clear and overcast skies, respectively. The seasonal variations in monthly average KT show a minimum of 0.37 in July at all sites except for Jeju, where the value was 0.29 in January. The maximum value (KT = 0.51) is observed in October, followed by a secondary peak (KT = 0.49) during February–April. The lowest KT value (KT = 0.42) was observed at both the Seoul and Jeju sites, and the highest (KT = 0.48) in the southeastern regions. Increases in average KT exceeding 4% per decade were observed in the middle and southeastern regions, with the maximum (+8% per decade) at the Daegu site. Decreasing trends (<−4% per decade) were observed in the southwestern regions, with the maximum (−7% per decade) at the Mokpo site. Cloud amount, relative humidity, and aerosol optical depth together explained 57% of the variance in daily mean KT values. The contributions of these three variables to variations in KT are 42%, 9% and 6%, respectively. Thus, the variations in KT in Korea can be primarily attributed to the presence of clouds and water vapor, with relatively weak aerosol effects

Spatio-Temporal Characteristics in the Clearness Index Derived from Global Solar Radiation Observations in Korea

The spatio-temporal characteristics of the clearness index (KT) were investigated using daily global solar irradiance measurements (290–2800 nm) for the period of 2000–2014 at 21 sites in Korea, a complex region in East Asia with a distinct monsoon season and heavy aerosol loading year-round. The annual mean KT value for all sites is 0.46, with values of 0.63 and 0.25 for clear and overcast skies, respectively. The seasonal variations in monthly average KT show a minimum of 0.37 in July at all sites except for Jeju, where the value was 0.29 in January. The maximum value (KT = 0.51) is observed in October, followed by a secondary peak (KT = 0.49) during February–April. The lowest KT value (KT = 0.42) was observed at both the Seoul and Jeju sites, and the highest (KT = 0.48) in the southeastern regions. Increases in average KT exceeding 4% per decade were observed in the middle and southeastern regions, with the maximum (+8% per decade) at the Daegu site. Decreasing trends (<−4% per decade) were observed in the southwestern regions, with the maximum (−7% per decade) at the Mokpo site. Cloud amount, relative humidity, and aerosol optical depth together explained 57% of the variance in daily mean KT values. The contributions of these three variables to variations in KT are 42%, 9% and 6%, respectively. Thus, the variations in KT in Korea can be primarily attributed to the presence of clouds and water vapor, with relatively weak aerosol effects

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

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

Hydrodynamic shear stress promotes epithelial-mesenchymal transition by downregulating ERK and GSK3β activities

Abstract Background Epithelial-mesenchymal transition (EMT) occurs in the tumor microenvironment and presents an important mechanism of tumor cell intravasation, stemness acquisition, and metastasis. During metastasis, tumor cells enter the circulation to gain access to distant tissues, but how this fluid microenvironment influences cancer cell biology is poorly understood. Methods and results Here, we present both in vivo and in vitro evidence that EMT-like transition also occurs in circulating tumor cells (CTCs) as a result of hydrodynamic shear stress (+SS), which promotes conversion of CD24middle/CD44high/CD133middle/CXCR4low/ALDH1low primary patient epithelial tumor cells into specific high sphere-forming CD24low/CD44low/CD133high/CXCR4high/ALDH1high cancer stem-like cells (CSLCs) or tumor-initiating cells (TICs) with elevated tumor progression and metastasis capacity in vitro and in vivo. We demonstrate that conversion of CSLCs/TICs from epithelial tumor cells via +SS is dependent on reactive oxygen species (ROS)/nitric oxide (NO) generation, and suppression of extracellular signal-related kinase (ERK)/glycogen synthase kinase (GSK)3β, a mechanism similar to that operating in embryonic stem cells to prevent their differentiation while promoting self-renewal. Conclusion Fluid shear stress experienced during systemic circulation of human breast tumor cells can lead to specific acquisition of mesenchymal stem cell (MSC)-like potential that promotes EMT, mesenchymal-epithelial transition, and metastasis to distant organs. Our data revealed that biomechanical forces appeared to be important microenvironmental factors that not only drive hematopoietic development but also lead to acquisition of CSLCs/TIC potential in cancer metastasis. Our data highlight that +SS is a critical factor that promotes the conversion of CTCs into distinct TICs in blood circulation by endowing plasticity to these cells and by maintaining their self-renewal signaling pathways

The role of the addition of ovarian suppression to tamoxifen in young women with hormone-sensitive breast cancer who remain premenopausal or regain menstruation after chemotherapy (ASTRRA): Study protocol for a randomized controlled trial and progress

Background: Ovarian function suppression (OFS) has been shown to be effective as adjuvant endocrine therapy in premenopausal women with hormone receptor-positive breast cancer. However, it is currently unclear if addition of OFS to standard tamoxifen therapy after completion of adjuvant chemotherapy results in a survival benefit. In 2008, the Korean Breast Cancer Society Study Group initiated the ASTRRA randomized phase III trial to evaluate the efficacy of OFS in addition to standard tamoxifen treatment in hormone receptor-positive breast cancer patients who remain or regain premenopausal status after chemotherapy. Methods: Premenopausal women with estrogen receptor-positive breast cancer treated with definitive surgery were enrolled after completion of neoadjuvant or adjuvant chemotherapy. Ovarian function was assessed at the time of enrollment and every 6 months for 2 years by follicular-stimulating hormone levels and bleeding history. If ovarian function was confirmed as premenopausal status, the patient was randomized to receive 2 years of goserelin plus 5 years of tamoxifen treatment or 5 years of tamoxifen alone. The primary end point will be the comparison of the 5-year disease-free survival rates between the OFS and tamoxifen alone groups. Patient recruitment was finished on March 2014 with the inclusion of a total of 1483 patients. The interim analysis will be performed at the time of the observation of the 187th event. Discussion: This study will provide evidence of the benefit of OFS plus tamoxifen compared with tamoxifen only in premenopausal patients with estrogen receptor-positive breast cancer treated with chemotherapy