BackgroundThoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes.ResultsWe present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not match any current equine gene model. We also identified 189,973 single nucleotide variations (SNVs) from the sequences aligned against the horse reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases. Using differential expression analysis, we further identified a number of exercise-regulated genes: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle. Six of 28 previously-known exercise-related genes were over-expressed in the muscle after exercise. Among the differentially expressed genes, there were 91 transcription factor-encoding genes, which included 56 functionally unknown transcription factor candidates that are probably associated with an early regulatory exercise mechanism. In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.ConclusionThe first sequencing-based horse transcriptome data, extensive analyses results, deferentially expressed genes before and after exercise, and candidate genes that are related to the exercise are provided in this study.

BackgroundStomach cancer is the third deadliest among all cancers worldwide. Although incidence of the intestinal-type gastric cancer has decreased, the incidence of diffuse-type is still increasing and its progression is notoriously aggressive. There is insufficient information on genome variations of diffuse-type gastric cancer because its cells are usually mixed with normal cells, and this low cellularity has made it difficult to analyze the genome.ResultsWe analyze whole genomes and corresponding exomes of diffuse-type gastric cancer, using matched tumor and normal samples from 14 diffuse-type and five intestinal-type gastric cancer patients. Somatic variations found in the diffuse-type gastric cancer are compared to those of the intestinal-type and to previously reported variants. We determine the average exonic somatic mutation rate of the two types. We find associated candidate driver genes, and identify seven novel somatic mutations in CDH1, which is a well-known gastric cancer-associated gene. Three-dimensional structure analysis of the mutated E-cadherin protein suggests that these new somatic mutations could cause significant functional perturbations of critical calcium-binding sites in the EC1-2 junction. Chromosomal instability analysis shows that the MDM2 gene is amplified. After thorough structural analysis, a novel fusion gene TSC2-RNF216 is identified, which may simultaneously disrupt tumor-suppressive pathways and activate tumorigenesis.ConclusionsWe report the genomic profile of diffuse-type gastric cancers including new somatic variations, a novel fusion gene, and amplification and deletion of certain chromosomal regions that contain oncogenes and tumor suppressors.

DNA-based data storage has emerged as a promising method to satisfy the exponentially increasing demand for information storage. However, practical implementation of DNA-based data storage remains a challenge because of the high cost of data writing through DNA synthesis. Here, we propose the use of degenerate bases as encoding characters in addition to A, C, G, and T, which augments the amount of data that can be stored per length of DNA sequence designed (information capacity) and lowering the amount of DNA synthesis per storing unit data. Using the proposed method, we experimentally achieved an information capacity of 3.37 bits/character. The demonstrated information capacity is more than twice when compared to the highest information capacity previously achieved. The proposed method can be integrated with synthetic technologies in the future to reduce the cost of DNA-based data storage by 50%.

DNA nanostructure-based mechanical systems that control the distance between elements of interest have demonstrated great potential for various applications, including nanoplasmonic systems, molecular reactors, and other nanotechnology platforms. However, previously reported systems could not collectively manipulate a 2D or 3D nanoscale network of elements to various forms in multiple stages. A reconfigurable DNA accordion rack structure is introduced that is a DNA beam lattice that changes its conformation with a small amount of short-length DNA locks as the controlling input. The lattice shape of the 2D DNA accordion rack and the diameter and the height of the 3D DNA nanotubular structure made of the DNA accordion rack could be controlled. Furthermore, by sequentially repeating the detachment and the attachment of the different DNA locks using strand displacement, the shape reconfiguration was repeatedly carried out.

Background and ObjectivesTo investigate age-specific and sex-specific distributions of blood cholesterol in the general Korean population.Subjects and MethodsWe analyzed data for 8284 men and 9246 women aged ≥10 years who participated in the fifth (2010-2012) Korea National Health and Nutrition Examination Survey. Age-specific means, medians, and selected percentiles were calculated for men, premenopausal women, and postmenopausal women.ResultsMedian total cholesterol (TC) level increased with age across all age groups, from 147 to 196 mg/dL in males and from 159 to 210 mg/dL in females. Triglyceride (TG) levels increased with age in females; however, in males, TG levels rapidly increased during young adulthood, peaked at 50-54 years, and then decreased. High density lipoprotein-cholesterol (HDL-C) levels were higher in females than in males and decreased with increasing age in both males and females. Low density lipoprotein-cholesterol (LDL-C) levels increased with age across all age groups, from 89 to 127 mg/dL in males and from 82 to 113 mg/dL in females. Lipoprotein-cholesterol fraction (TC/HDL-C, LDL-C/HDL-C, TG/HDL-C, non-HDL-C) levels increased with age in females, but increased more rapidly in males during young adulthood and decreased after middle age.ConclusionBlood cholesterol levels and lipoprotein-cholesterol fractions present different distributions by age, sex, and menopausal status.

DNA‐based data storage has attracted attention because of its higher physical density of the data and longer retention time than those of conventional digital data storage. However, previous DNA‐based data storage lacked index features and the data quality of storage after a single access was not preserved, obstructing its industrial use. Here, DNA micro‐disks, QR‐coded micro‐sized disks that harbor data‐encoded DNA molecules for the efficient management of DNA‐based data storage, are proposed. The two major features that previous DNA‐based data‐storage studies could not achieve are demonstrated. One feature is accessing data items efficiently by indexing the data‐encoded DNA library. Another is achieving write‐once–read‐many (WORM) memory through the immobilization of DNA molecules on the disk and their enrichment through in situ DNA production. Through these features, the reliability of DNA‐based data storage is increased by allowing selective and multiple accession of data‐encoded DNA with lower data loss than previous DNA‐based data storage methods.

Aim To identify the factors affecting fear, anxiety and depressive symptoms among frontline nurses working with COVID‐19 patients or are in charge of COVID‐19 screening in Korea. Background Nurses are at a higher risk of COVID‐19 infection because they are in closer, longer‐duration contact with patients. These situations can negatively affect the mental health of nurses. Methods This study analysed data from COVID‐19 module in the Korean Nurses’ Health Study. Data from 906 participants were analysed. To identify the factors influencing mental health, descriptive statistics, Pearson’s correlation and hierarchical multiple regression analyses were performed. Results Caring for patients who are COVID‐19‐positive increased levels of fear, anxiety and depressive symptoms of nurses. The hospital safety climate influenced mental well‐being among nurses. Conclusion Caring for patients with COVID‐19 had a negative impact on fear, anxiety and depressive symptoms. However, the higher was the perceived hospital safety climate, the lower were the nurses’ psychological symptoms. Further research on the mental health of nurses is warranted. Implications for nursing and health policy Institutions should manage human resources to enable periodic rotation of nurses’ work and working periods related to COVID‐19. In addition, hospital managers should provide sufficient personal protective equipment, related education, and safety climate.

Background/AimsSleep duration affects health in various ways. The objective of this study was to investigate the associations of sleep duration with chronic kidney disease (CKD) in a Korean adult population.MethodsThis cross-sectional analysis was conducted for total of 1,360 participants who completed baseline health examinations for the Korean Genome and Epidemiology Study-Kangwha study in 2010 to 2011. Sleep habits were measured by an interviewer-assisted questionnaire. Sleep duration was calculated based on the number of hours per day participants had slept over the past 1 year. CKD was defined as either proteinuria or estimated glomerular filtration rate (eGFR) < 60 mL/min/1.73 m2. Multiple logistic regression models were applied to examine associations between sleep duration and CKD.ResultsWomen with very long sleep duration (≥ 9 hours/day) were at significantly increased odds for having high serum creatinine (odds ratio [OR], 2.936; 95% confidence interval [CI], 1.176 to 7.326), low eGFR (OR, 3.320; 95% CI, 1.372 to 8.034), and CKD (OR, 3.112; 95% CI, 1.315 to 7.363), compared those with a typical sleep duration (7 to < 8 hours/day), after adjusting for sociodemographic status, socioeconomic status, health behaviors, comorbidities, and sleep quality. Among women, for every 1 hour increase in sleep duration per day, there was a 24.6% increase in the presence of CKD (OR, 1.246; 95% CI, 1.019 to 1.523). However, among men, sleep duration was not significantly associated with CKD.ConclusionsVery long sleep duration was independently associated with a higher prevalence of CKD among Korean women. Gender may influence this association.