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.

Genetically, Dietary Sodium Intake Is Causally Associated with Salt-Sensitive Hypertension Risk in a Community-Based Cohort Study: a Mendelian Randomization Approach.

PURPOSE OF REVIEW: Excessive dietary salt intake is associated with an increased risk of hypertension. Salt sensitivity, i.e., an elevation in blood pressure in response to high dietary salt intake, has been associated with a high risk of cardiovascular disease and mortality. We investigated whether a causal association exists between dietary sodium intake and hypertension risk using Mendelian randomization (MR). RECENT FINDINGS: We performed an MR study using data from a large genome-wide association study comprising 15,034 Korean adults in a community-based cohort study. A total of 1282 candidate single nucleotide polymorphisms associated with dietary sodium intake, such as rs2960306, rs4343, and rs1937671, were selected as instrumental variables. The inverse variance weighted method was used to assess the evidence for causality. Higher dietary sodium intake was associated with salt-sensitive hypertension risk. The variants of SLC8E1 rs2241543 and ADD1 rs16843589 were strongly associated with increased blood pressure. In the logistic regression model, after adjusting for age, gender, smoking, drinking, exercise, and body mass index, the GRK4 rs2960306TT genotype was inversely associated with hypertension risk (OR, 0.356; 95% CI, 0.236-0.476). However, the 2350GG genotype (ACE rs4343) exhibited a 2.11-fold increased hypertension risk (OR, 2.114; 95% CI, 2.004-2.224) relative to carriers of the 2350AA genotype, after adjusting for confounders. MR analysis revealed that the odds ratio for hypertension per 1 mg/day increment of dietary sodium intake was 2.24 in participants with the PRKG1 rs12414562 AA genotype. Our findings suggest that dietary sodium intake may be causally associated with hypertension risk.

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.

Proinflammatory cytokine IL-1 ß polymorphisms in sudden sensorineural hearing loss.

The cause and pathogenesis of sudden sensorineural hearing loss (SSNHL) remain unknown. IL-1ß is one of the most powerful inflammatory cytokines. The aim of this study was to evaluate the relationships between interleukin-1 ß (IL-1ß) gene polymorphisms (-511 C/T and +3953 C/T) in patients with SSNHL. One hundred two patients affected by SSNHL and 595 controls were genotyped for IL-1ß gene polymorphisms. The polymorphisms were analyzed by polymerase chain reaction amplification and DNA fragment separation via electrophoresis. Compared to controls, the IL-1ß (+3953) T allele increased the relative risk of SSNHL in subjects with IL-1ß (-511) TT genotype (p = 0.022, OR = 9.111, 95% CI = 1.441-57.618). In this study, polymorphisms in the IL-1ß -511 and IL-1ß +3953 loci were assessed for evidence of association with SSNHL. From this assessment, a significant difference in carriage of both the IL-1ß -511 T allele and the IL-1ß +3953 T allele was observed between SSNHL and controls. This suggests that the IL-1ß -511 and +3953 loci may play an important role in the etiopathogenesis of SSNHL.

Resorption of labial bone in maxillary anterior implant.

PURPOSE: The purpose of this study was to evaluate the amount of resorption and thickness of labial bone in anterior maxillary implant using cone beam computed tomography with Hitachi CB Mercuray (Hitachi, Medico, Tokyo, Japan). MATERIALS AND METHODS: Twenty-one patients with 26 implants were followed-up and checked with CBCT. 21 OSSEOTITE NT® (3i/implant Innovations, Florida, USA) and 5 OSSEOTITE® implants (3i/implant Innovations, Florida, USA) were placed at anterior region and they were positioned vertically at the same level of bony scallop of adjacent teeth. Whenever there was no lesion or labial bone was intact, immediate placement was tried as possible as it could be. Generated bone regeneration was done in the patients with the deficiency of hard tissue using Bio-Oss® (Geistlich, Wolhusen, Switzerland) and Bio-Gide® (Geistlich, Wolhusen, Switzerland). Second surgery was done in 6 months after implant placement and provisionalization was done for 3 months. Definite abutment was made of titanium abutment with porcelain, gold and zirconia, and was attached after provisionalization. Two-dimensional slices were created to produce sagittal, coronal, axial and 3D by using OnDemand3D (Cybermed, Seoul, Korea). RESULTS: The mean value of bone resorption (distance from top of implant to labial bone) was 1.32 ± 0.86 mm and the mean thickness of labial bone was 1.91 ± 0.45 mm. CONCLUSION: It is suggested that the thickness more than 1.91 mm could reduce the amount and incidence of resorption of labial bone in maxillary anterior implant.

Steroid combination therapy and detoxification enzyme gene polymorphisms in sudden sensorineural hearing loss patients.

OBJECTIVE: The purpose of this study was to evaluate the relations among the combined therapy with steroid and the detoxification enzyme gene polymorphisms in patients with sudden sensorineural hearing loss (SSNHL). The pathogenetic mechanism of inner ear dysfunction could involve an increase in lipid peroxidation and a decrease in cellular antioxidant defense. Glutathione S-transferases (GSTs) and cytochrome P450 (CYP) belong to a system of detoxification and antioxidant enzymes that have been demonstrated in the inner ear. STUDY DESIGN: A prospective study in patients with SSNHL. PATIENTS AND METHODS: All 441 subjects were genotyped for GSTM1, GSTT1, and CYP1A1 polymorphisms. The polymorphisms were analyzed by polymerase chain reaction amplification, restriction enzyme digestion, and deoxyribonucleic acid fragment separation by electrophoresis. RESULTS: No significant difference was observed between SSNHL patients and controls in 3 polymorphisms. However, the prevalence of the partial recovery group in patients with the CC genotype of CYP1A1 (22%) was higher than that in the complete recovery (7.4%) or no recovery group (12.5%) for the subjects classified according to modified Siegel's criteria but were not statistically significant. CONCLUSION: This is the first approach to analyze gene polymorphism and efficacy of clinical treatment of patients with SSNHL, although the observations do not confirm the effect of the GSTM1/T1 and CYP1A1 genotypes as a risk factor for SSNHL.