Development of Kompetitive Allele Specific PCR markers for identification of persimmon varieties using genotyping-by-sequencing

BACKGROUND: Persimmon (Diospyros kaki Thunb.) is the most widely cultivated species of the genus Diospyros. In this study, genetic diversity and variations in persimmon genotypes were investigated using single nucleotide polymorphism (SNP) markers identified by genotyping-by-sequencing (GBS) analysis. RESULTS: Ninety-five persimmon accessions grown in the Pear Research Institute, National Institute Horticultural and Herbal Science, were sequenced using the Illumina Hiseq2500 platform and polymorphic SNPs were detected to develop molecular markers. These reliable SNPs were analyzed using the Kompetitive Allele Specific PCR (KASP) assay to discriminate among persimmon genotypes. GBS generated a total of 447,495,724 trimmed reads, of which 89.7% were raw reads. After demultiplexing and sequence quality trimming, 108,876,644 clean reads were mapped to the reference transcriptome. An average of 1,146,070 genotype reads were mapped. Filtering of raw SNPs in each sample led to selection of a total of 1,725,401 high-quality SNPs. The number of homozygous and heterozygous SNPs ranged from 1,933 to 6,834 and from 846 to 5,927, respectively. CONCLUSIONS: Of the 49 SNPs selected for development of an identification system for persimmons, 15 SNPs were used in the KASP assay to analyze 32 persimmon accessions. These KASP markers discriminated among all accessions.

Guidelines for Cardiovascular Magnetic Resonance Imaging from the Korean Society of Cardiovascular Imaging-Part 3: Perfusion, Delayed Enhancement, and T1- and T2 Mapping.

This document is the third part of the guidelines for the protocol, the interpretation and post-processing of cardiac magnetic resonance (CMR) studies. These consensus recommendations have been developed by the Consensus Committee of the Korean Society of Cardiovascular Imaging to standardize the requirements for image interpretation and post-processing of CMR. This third part of the recommendations describes tissue characterization modules, including perfusion, late gadolinium enhancement, and T1- and T2 mapping. Additionally, this document provides guidance for visual and quantitative assessment consisting of "What-to-See," "How-To," and common pitfalls for the analysis of each module. The Consensus Committee hopes that this document will contribute to the standardization of image interpretation and post-processing of CMR studies.

Guidelines for Cardiovascular Magnetic Resonance Imaging from the Korean Society of Cardiovascular Imaging-Part 2: Interpretation of Cine, Flow, and Angiography Data.

Cardiovascular magnetic resonance imaging (CMR) is expected to be increasingly used in Korea due to technological advances and the expanded national insurance coverage of CMR assessments. For improved patient care, proper acquisition of CMR images as well as their accurate interpretation by well-trained personnel are equally important. In response to the increased demand for CMR, the Korean Society of Cardiovascular Imaging (KOSCI) has issued interpretation guidelines in conjunction with the Korean Society of Radiology. KOSCI has also created a formal Committee on CMR guidelines to create updated practices. The members of this committee review previously published interpretation guidelines and discuss the patterns of CMR use in Korea.

Guideline for Cardiovascular Magnetic Resonance Imaging from the Korean Society of Cardiovascular Imaging-Part 1: Standardized Protocol.

Cardiac magnetic resonance (CMR) imaging is widely used in many areas of cardiovascular disease assessment. This is a practical, standard CMR protocol for beginners that is designed to be easy to follow and implement. This protocol guideline is based on previously reported CMR guidelines and includes sequence terminology used by vendors, essential MR physics, imaging planes, field strength considerations, MRI-conditional devices, drugs for stress tests, various CMR modules, and disease/symptom-based protocols based on a survey of cardiologists and various appropriate-use criteria. It will be of considerable help in planning and implementing tests. In addressing CMR usage and creating this protocol guideline, we particularly tried to include useful tips to overcome various practical issues and improve CMR imaging. We hope that this document will continue to standardize and simplify a patient-based approach to clinical CMR and contribute to the promotion of public health.

Practice Pattern of Transthoracic Needle Biopsy: 2016 Survey in the Members of Korean Society of Thoracic Radiology.

OBJECTIVE: To assess the current practice patterns of radiologists who perform transthoracic needle biopsy (TNB). MATERIALS AND METHODS: An email survey of 71 questions on TNB was sent to 240 members of the Korean Society of Thoracic Radiology. The answers to multiple-choice questions (n = 56) were analyzed. RESULTS: Of 60 respondents, 45% had 10 or more years of experience in chest radiology, and 70% had 5 or more years of experience in TNB. For the question on the most frequently used diagnostic method for lesions with high probability of being resectable-stage lung cancer, 70% of respondents answered that TNB is initially used, with or without bronchoscopy. In patients at high-risk of TNB-related complications, the proportion of the respondents who consistently declined TNB was only 5%. The number of rebiopsies was said to be increased; molecular analysis for an established target therapy (43.6%) and clinical trial of a new drug (28.2%) were the two most common reasons for it. The most popular needle type was the coaxial cutting needle (55%), and the popular guiding modality was conventional computed tomography (CT) (56.7%). In addition, 15% of respondents have encountered air embolism. CONCLUSION: Despite high variation in how TNB is being performed in Korea, some patterns were noted. It is common for patients with resectable-stage lung cancer to undergo TNB prior to surgery. Rebiopsy is now more common than before, with personalized medicine as the most important reason for it. The most popular type of needle is the coaxial system; the most popular modality for guidance is still CT.

Characterization of a F280N variant of L-arabinose isomerase from Geobacillus thermodenitrificans identified as a D-galactose isomerase.

The double-site variant (C450S-N475K) L-arabinose isomerase (L-AI) from Geobacillus thermodenitrificans catalyzes the isomerization of D-galactose to D-tagatose, a functional sweetener. Using a substrate-docking homology model, the residues near to D-galactose O6 were identified as Met186, Phe280, and Ile371. Several variants obtained by site-directed mutagenesis of these three residues were analyzed, and a triple-site (F280N) variant enzyme exhibited the highest activity for D-galactose isomerization. The k cat/K m of the triple-site variant enzyme for D-galactose was 2.1-fold higher than for L-arabinose, whereas the k cat/K m of the double-site variant enzyme for L-arabinose was 43.9-fold higher than for D-galactose. These results suggest that the triple-site variant enzyme is a D-galactose isomerase. The conversion rate of D-galactose to D-tagatose by the triple-site variant enzyme was approximately 3-fold higher than that of the double-site variant enzyme for 30 min. However, the conversion yields of L-arabinose to L-ribulose by the triple-site and double-site variant enzymes were 10.6 and 16.0 % after 20 min, respectively. The triple-site variant enzyme exhibited increased specific activity, turnover number, catalytic efficiency, and conversion rate for D-galactose isomerization compared to the double-site variant enzyme. Therefore, the amino acid at position 280 determines the substrate specificity for D-galactose and L-arabinose, and the triple-site variant enzyme has the potential to produce D-tagatose on an industrial scale.

γ-Dodecelactone production from safflower oil via 10-hydroxy-12(Z)-octadecenoic acid intermediate by whole cells of Candida boidinii and Stenotrophomonas nitritireducens.

Candida boidinii was selected as a γ-dodecelactone producer because of the highest production of γ-dodecelactone from 10-hydroxy-12(Z)-octadecenoic acid among the 11 yeast strains tested. Under the reaction conditions of pH 5.5 and 25 °C with 5 g/L 10-hydroxy-12(Z)-octadecenoic acid and 30 g/L cells, whole C. boidinii cells produced 2.1 g/L γ-dodecelactone from 5 g/L 10-hydroxy-12(Z)-octadecenoic acid after 6 h, with a conversion yield of 64% (mol/mol) and a volumetric productivity of 350 mg/L/h. The production of γ-dodecelactone from safflower oil was performed by lipase hydrolysis reaction and two-step whole-cell biotransformation using Stenotrophomonas nitritireducens and C. boidinii. γ-Dodecelactone at 1.88 g/L was produced from 7.5 g/L safflower oil via 5 g/L 10-hydroxy-12(Z)-octadecenoic acid intermediate by these reactions after 8 h of reaction time, with a volumetric productivity of 235 mg/L/h and a conversion yield of 25% (w/w). To the best of the authors' knowledge, this is the highest volumetric productivity and conversion yield reported to date for the production of γ-lactone from natural oils.