Analysis of Whole Transcriptome Sequencing Data: Workflow and Software

RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification.

Sequence Generation and Genotyping of 15 Autosomal STR Markers Using Next Generation Sequencing / 대한법의학회지

Recently, next generation sequencing (NGS) has received attention as the ultimate genotyping method to overcome the limitations of capillary electrophoresis (CE)-based short tandem repeat (STR) analysis, such as the limited number of STR loci that can be measured simultaneously using fluorescent-labeled primers and the maximum size of STR amplicons. In this study, we analyzed 15 autosomal STR markers via the NGS method and evaluated their effectiveness in STR analysis. Using male and female standard DNA as single-sources and their 1:1 mixture, we sequentially generated sample amplicons by the multiplex polymerase chain reaction (PCR) method, constructed DNA libraries by ligation of adapters with a multiplex identifier (MID), and sequenced DNA using the Roche GS Junior Platform. Sequencing data for each sample were analyzed via alignment with pre-built reference sequences. Most STR alleles could be determined by applying a coverage threshold of 20% for the two single-sources and 10% for the 1:1 mixture. The structure of the STR in each allele was accurately determined by examining the sequences of the target STR region. The mixture ratio of the mixed sample was estimated by analyzing the coverage ratios between assigned alleles at each locus and the reference/variant ratios from the observed sequence variations. In conclusion, the experimental method used in this study allowed the successful generation of NGS data. In addition, the NGS data analysis protocol enables accurate STR allele call and repeat structure determination at each locus. Therefore, this approach using the NGS system will be helpful to interpret and analysis the STR profiles from singe-source and even mixed samples in forensic investigation.

Analysis of Kinship Index Distributions in Koreans Using Simulated Autosomal STR Profiles / 대한법의학회지

Kinship testing in forensic casework is largely based on a likelihood ratio (LR) approach with short tandem repeat (STR) markers; however, in order to efficiently identify potential relatives in a specific population, the threshold values for kinship prediction should be determined by analyzing the kinship index distributions of the population in question. In this study, 250,000 DNA profiles were simulated using allele frequencies at 20 autosomal STR loci in Koreans, then the LRs were calculated for true close relatives and unrelated pairs. The LR distributions in related and unrelated pairs under a given relationship were compared in 2 sets of 13 Combined DNA Index System (CODIS) and 20 STR profiles. Using 13 CODIS STRs, true relatives in parent/child and full-sibling relationships were sufficiently discriminated from unrelated pairs with LR thresholds of 1,000 and 100, respectively. However, the CODIS STRs lacked the discriminatory power to differentiate between related and unrelated pairs in uncle/nephew and first cousin relationships due to high false-positive and false-negative rates with a LR threshold of 10. Increasing the number of STR loci to 20 increased discrimination of close relatives, but high false results remained in uncle/nephew and first cousin relationships. The kinship index data from this study will help make decisions on various kinship testing and familial searching in Koreans.

Web-based Y-STR Database for Haplotype Frequency Estimation and Kinship Index Calculation / 대한법의학회지

We developed a web-based Y chromosomal short tandem repeat (Y-STR) database (ySTRmanager, http://ystrmanager.yonsei.ac.kr) to facilitate calculation of Y-STR haplotype frequency estimates for random matches and kinship indices for various relationship levels. The ySTRmanager database provides 3 functions: (i) Y-STR haplotype search, (ii) kinship index calculation, and (iii) user database configuration. The Y-STR haplotype search function allows researchers to retrieve Y-STR haplotypes that meet queried Y-STR allele, Y-haplogroup affiliation, and/or sample information from a selected population in the open database, which consists of 12-17 Y-STR loci. The number of matches in a selected population, haplotype frequency estimator, and detailed results for matched and neighbor haplotypes are displayed as a set of search results. The kinship index calculation function provides kinship indices of 2 input Y-STR haplotypes for the relationship represented by the number of meioses, with consideration of target population and mutation rate of each Y-STR. In addition, ySTRmanager allows registered users to configure their own database to store and analyze Y-STR haplotype and/or mutation rate data. The stored Y-STR data can be used in the search function and in the analysis to obtain forensic statistical values. The ySTRmanager will be a useful system to analyze and manage Y-STR data in the practice of forensic genetics.

A survey on the use of composite resin in Class II restoration in Korea / 대한치과보존학회지

The purpose of this study was to assess the current materials, methods and difficulties according to the year of licence and educational background of Korean dentists in Class II direct composite resin restorations. Total 17 questions were included in the questionnaire. Questions were broadly divided into two parts; first, operator's information, and second, the materials and methods used in Class II posterior composite restoration. The questionnaire was sent to dentists enrolled in Korean Dental Association via e-mail. Total 12,193 e-mails were distributed to dentists, 2,612 e-mails were opened, and 840 mails (32.2%) were received from respondents. The data was statically analyzed by chi-square test using SPSS(v. 12.0.1, SPSS Inc, Chicago, IL, USA). Male dentists among respondents was 79%. 60.3% of the respondents acquired their licences recently (1998-2007), and 77% practiced in private offices. 83.4% have acquired their knowledge through school lectures, conferences and seminars. For the Class II restorations, gold inlays were preferred by 65.7% of respondents, while direct composite resin restorations were used by 12.1% amalgam users were only 4.4% of respondents. For the restorative technique, 74.4% of respondents didn't use rubber dam as needed. For the matrix, mylar strip (53.4%), metal matrix (33.8%) and Palodent system (6.5%) were used. 99.6% of respondents restored the Class II cavity by incremental layering. Obtaining of the tight interproximal contact was considered as the most difficult procedure (57.2%) followed by field isolation (21%). Among various bonding systems, 22.6% of respondents preferred SE Bond and 20.2% used Single Bond. Z-250 was used most frequently among a variety of composite resins.

A study on transportation of apical foramen after overinstrumentation by ProFile(R), ProTaper(TM) and K3TM in simulated canals with different curvatures / 대한치과보존학회지

This study was done to evaluate transportation of the apical foramen after 0.5 mm overinstrumentation by ProFile, ProTaper and K3 in simulated resin root canal. Sixty simulated resin root canal with a curvature of J and S-shape were divided into two groups. Each group consisted of three subgroups with 10 blocks according to the instruments used: ProFile(R), ProTaper(TM), and K3TM. Simulated resin root canal was prepared by ProFile, ProTaper and K3 with 300 rpm by the crown-down preparation technique. Pre- and post-instrumentation apical foramen images were overlapped and recorded with Image-analyzing microscope 100X (Camcope, Sometech Inc, Korea). The amounts of difference in width and dimension on overlapped images were measured after reference points were determined by Image Analysis program (Image-Pro(R) Express, Media Cybernetic, USA). Data were analyzed using Kruskal-Wallis and Mann-Whitney U-test. The results suggest that ProFile showed significantly less canal transportation and maintained original apical foramen shape better than K3 and ProTaper.

Pulp response of mineral trioxide aggregate, calcium sulfate or calcium hydroxide / 대한치과보존학회지

This study was performed to verify the possibility of MTA and calcium sulfate as a pulp capping agent through comparing the dental pulp response in dogs after capping with MTA, calcium sulfate, and calcium hydroxide. 24 teeth of 2 dogs, 8 month old, were used in this study. Under general anesthesia, cervical cavities were prepared and pulp was exposed with sterilized #2 round bur in a high speed handpiece. MTA, calcium hydroxide, and calcium sulfate were applied on the exposed pulp. Then the coronal openings were sealed with IRM and light-cured composite. Two months after treatment, the animals were sacrificed. The extracted teeth were fixed in 10% neutral-buffered formalin solution and were decalcified in formic acid-sodium citrate. They were prepared for histological examination in the usual manner. The sections were stained with haematoxylin and eosin. In MTA group, a hard tissue bridges formation and newly formed odontoblasts layer was observed. There was no sign of pulp inflammatory reaction in pulp tissue. In calcium hydroxide group, there was no odontoblast layer below the dentin bridge. In pulpal tissue, chronic inflammatory reaction with variable intensity and extension occurred in all samples. In calcium sulfate group, newly formed odontoblast layer was observed below the bridge. Mild chronic inflammation with a few neutrophil infiltrations was observed on pulp tissue. These results suggest that MTA is more biocompatible on pulp tissue than calcium hydroxide or calcium sulfate.

Molecular Analysis of Isoleucyl-tRNA Synthetase Mutations in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus with Low-Level Mupirocin Resistance

Emergence and spread of low-level mupirocin resistance in staphylococci have been increasingly reported in recent years. The aim of this study was to characterize missense mutations within the chromosomal isoleucyl-tRNA synthetase gene (ileS) among clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) with low-level mupirocin resistance. A total of 20 isolates of MRSA with low-level mupirocin resistance (minimal inhibitory concentration, 16-64 microgram/mL) were collected from 79 patients in intensive care units for six months. The isolates were analyzed for isoleucyl-tRNA synthetase (IleS) mutations that might affect the binding of mupirocin to the three-dimensional structure of the S. aureus IleS enzyme. All isolates with low-level mupirocin resistance contained the known V588F mutation affecting the Rossman fold, and some of them additionally had previously unidentified mutations such as P187F, K226T, F227L, Q612H, or V767D. Interestingly, Q612H was a novel mutation that was involved in stabilizing the conformation of the catalytic loop containing the KMSKS motif. In conclusion, this study confirms that molecular heterogeneity in ileS gene is common among clinical MRSA isolates with low-level mupirocin resistance, and further study on clinical mutants is needed to understand the structural basis of low-level mupirocin resistance.

A comparative study of the canal configuration after shaping by protaper rotary and hand files in resin simulated canals / 대한치과보존학회지

The purpose of this study was to compare the canal configuration after shaping by ProTaper rotary files and ProTaper hand files in resin simulated canals. Forty resin simulated canals with a curvature of J-shape and S-shape were divided into four groups by 10 blocks each. Simulated root canals in resin block were prepared by ProTaper rotary files and ProTaper hand files using a crown-down pressureless technique. All simulated canals were prepared up to size #25 file at end-point of preparation. Pre- and post-instrumentation images were recorded with color scanner. Assessment of canal shape was completed with an image analysis program. Measurements were made at 0, 1, 2, 3, 4, 5, 6 and 7 mm from the apex. At each level, outer canal width, inner canal width, total canal width, and amount of transportation from original axis were recorded. Instrumentation time was recorded. The data were analyzed statistically using independent t-test. The result was that ProTaper hand files cause significantly less canal transportation from original axis of canal body and maintain original canal configuration better than ProTaper rotary files, however ProTaper hand files take more shaping time.

Angiolymphoid hyperplasia with eosinophilia:a case report

No abstract available.

A case of Aicardi syndrome with cleft lip and palate

A case of Aicardi syndrome with cleft lip and palate was experienced at the Department of Pediatrics, College of Medicine, Hallym University, and the patient's infantile spasm was treated with ACTH. In previous studies, four cases of Aicardi syndrome accompanied by cleft lip and palate were reported. We present the fifth case of Aicardi syndrome with cleft lip and palate in the world. Thus, facial clefts may be found as an occasional manifestation of Aicardi syndrome.