CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.

Motivation: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin accessibility from MAPit-BGS and NOMe-seq. Results: In this article, we present CAME (Chromatin Accessibility and Methylation), a seed-extension based approach that identifies chromatin accessibility from NOMe-seq. The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data, and the results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods. Availability and Implementation: CAME is implemented in java and the program is freely available online at http://sourceforge.net/projects/came/. Contacts: jechoi@gru.edu or khryu@dblab.chungbuk.ac.kr. Supplementary information: Supplementary data are available at Bioinformatics online.

A comparative pilot study of symptom improvement before and after phototherapy in Korean patients with perennial allergic rhinitis.

Although allergic rhinitis is not life threatening, it significantly influences the quality of a patient's life. This study is intended to evaluate the safety and efficacy of phototherapy with low-level energy of a 650 nm laser irradiation system in perennial allergic rhinitis patients. This clinical trial was an open-label, single-center study with 42 perennial allergic rhinitis subjects. Following laser irradiation in the nasal cavity with a laser irradiation system, the efficacy at weeks 1 through 4 was determined. The symptoms were scored with four parameters (nasal obstruction, rhinorrhea, sneezing and itching) before and after illumination of the laser, and the total score was recorded. A survey of Rhinoconjunctivitis Quality of Life Questionnaire (RQLQ) was conducted by patients before and after treatment. Following treatment, significant improvement in the clinical symptoms of nasal obstruction (P < 0.001), rhinorrhea (P = 0.005), sneezing (P = 0.001) and itching (P = 0.003) was reported by 68% of perennial allergic rhinitis patients. The overall RQLQ scores significantly improved by 45% from the baseline with the treatment after 4 weeks. These results indicate that phototherapy is an effective modality for treating perennial allergic rhinitis and is another option in the steroid-free management of immune-mediated mucosal diseases.

Serum adipocyte fatty acid-binding protein levels are independently associated with sarcopenic obesity.

AIMS: Adipocyte fatty acid-binding protein (A-FABP) plays a key role in obesity-related insulin resistance and inflammation which may be involved in the pathogenesis of sarcopenic obesity (SO). This study examined the association of SO with serum A-FABP levels in Korean adults. METHODS: Two hundred ninety eight adults aged 20-70 years were examined using dual X-ray absorptiometry and computed tomography and measuring serum A-FABP levels. Sarcopenia was defined as the appendicular skeletal muscle mass (ASM) divided by weight (%) of <1 SD below the mean values of young adults in both sexes. Obesity was defined as visceral fat area (VFA) ≥ 100 cm(2). RESULTS: Serum A-FABP levels were higher in groups with SO compared to non-SO groups in both men and women. In the unadjusted model, serum A-FABP levels were positively associated with VFA and negatively associated with ASM/weight. Even after adjusting for possible confounding factors, ASM/weight was found to be independently and negatively associated with serum A-FABP levels. In addition, multiple logistic regression analysis showed that increased serum levels of A-FABP were independently associated with the presence of SO. CONCLUSIONS: The present findings indicate that serum A-FABP levels may be valuable markers of the presence of SO.

Elevated A1C is associated with impaired early-phase insulin secretion rather than insulin resistance in Koreans at high risk for developing diabetes.

The purpose of this study is to examine the association of A1C with beta-cell dysfunction, insulin resistance, and cardiovascular risk factors in Koreans with the relatively high risk for the future development of diabetes. This cross-sectional study recruited subjects from the pre-diabetic cohort of the Korea National Diabetes Program. Among study subjects (n = 616) aged 21-77 years with a history of hyperglycemia (fasting plasma glucose (FPG) ≥ 5.5 mmol/mL), analyses were conducted on 504 participants (296 women, 208 men) except for subjects with FPG ≥ 7.0 mmol/L or 120-min post-challenge plasma glucose ≥ 11.1 mmol/L or A1C ≥ 6.5 %. For insulin sensitivity and ß-cell function classified by the categories of A1C levels, ∆Ins(30-0)/∆Glu(30-0) was lower in the highest quartile group than other groups. Although there was no significant difference in HOMA-IR according to the A1C categories, even lowest A1C group (≤ 5.3 %) already included many subjects with abnormal glucose tolerance. A1C showed a significant association with hsCRP, number of metabolic syndrome (MetS) components and ∆Ins(30-0)/∆Glu(30-0) after adjusting for age, gender, BMI, and medications whereas HOMA-IR was insignificantly associated with A1C. Stepwise regression analysis for A1C showed that A1C is independently and negatively associated with ∆Ins(30-0)/∆Glu(30-0), and positively associated with hsCRP. Our study showed that higher A1C was associated with impaired early-phase insulin secretion, MetS, and low grade inflammation in Koreans with the relatively high risk for the future development of diabetes.