• Genomics & Informatics
• /
• v.20 no.2
• /
• pp.17.1-17.11
• /
• 2022

Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.

• Mycobiology
• /
• v.50 no.1
• /
• pp.79-85
• /
• 2022

Strawberries are a popular economic crop, and one of the major plantations and exporting countries is Korea in the world. The Fusarium oxysporum species complex (FOSC) is a soil-borne pathogen with genetic diversity, resulting in wilt disease in various crops. In Korea, strawberries wilt disease was first reported in the 1980s due to the infection of FOSC, causing significant economic damage every year. The causal agent, F. oxysporum f. sp. fragariae, is a soil-borne pathogen with a characteristic of FOSC that is difficult to control chemically and mutates easily. This study obtained genetic polymorphism information that was based on AFLP, of F. oxysporum f. sp. fragariae 91 strains, which were isolated from strawberry cultivation sites in Gyeongsangnam-do and Chungcheongnam-do, and compared strains information, which was the isolated location, host variety, response to chemical fungicide, and antagonistic bacteria, and mycelium phenotype. As a result, AFLP phylogeny found that two groups were mainly present, and group B was present at a high frequency in Gyeongsangnam-do. Group B proved less sensitive to tebuconazole than group A through Student's t-test. In addition, the fractions pattern of AFLP was calculated by comparing the strain information using PCA and PERMANOVA, and the main criteria were separated localization and strawberry varieties (PERMANOVA; p< 0.05). And tebuconazole was different with weak confidence (PERMANOVA; p< 0.10). This study suggests that the F. oxysporum f. sp. fragariae should be continuously monitored and managed, including group B, which is less chemically effective.

• Journal of Periodontal and Implant Science
• /
• v.53 no.5
• /
• pp.362-375
• /
• 2023

Purpose: The aim of this study was to investigate the relationships between gingival thickness (GT) and keratinized gingiva width (KGW), papilla height (PH), and crown ratio (CR) by employing transgingival probing and an intraoral scanner (IOS). Methods: This cross-sectional study examined 360 maxillary anterior teeth from 60 patients. GT was assessed using transgingival probing with an endodontic spreader. KGW, CR, and PH were measured using an IOS. One-way analysis of variance, the Student's t-test, and Spearman correlation coefficients were employed for statistical analysis. Results: Higher GT was significantly associated with thinner KGW in the central region (P=0.019). There was no statistically significant difference in GT between teeth (P=0.06). PH was lower in lateral teeth than in canines (P=0.047), with a PH of 2.99 mm in lateral teeth. The KGW was narrower in canines than in central teeth (P=0.007). A moderate correlation was observed between KGW and PH in the central region (P=0.01), while a weak negative correlation was found between KGW and CR (P=0.043). Conclusions: A moderate negative correlation was found between GT and KGW, as well as between PH and KGW in central teeth. In contrast, a weak negative correlation existed between CR and KGW. The PH (2.99 mm) was lower in lateral teeth than in canines. The traditional paradigm, which suggests a positive correlation between KGW and GT, was reevaluated by measuring KGW using an IOS.

• Journal of Life Science
• /
• v.20 no.10
• /
• pp.1549-1555
• /
• 2010

Streptococcus suis is a worldwide pathogen of a variety of porcine infection and has also been described as a pathogen for humans. We studied biochemical characteristics, antimicrobial susceptibility, and identification of polymerase chain reaction (PCR) of S. suis isolated from diseased pigs in Gyeongbuk province from 2004 to 2009. Sixty-one isolates were identified as S. suis by biochemical characteristics and PCR from 40 farms. The biochemical characteristics of S. suis isolates were production of VP-negative, hippurate, esculin, and arginine decarboxylase-positive, and fermentation of carbohydrate was variable lactose, trehalose, inulin, and raffinose, which was typeable 11 phenotype. In an antimicrobial susceptibility test, the majority of isolates were highly susceptible to amoxicillin/clavulanic acid, ampicillin, cephalothin, cefoperazone and florfenicol, while being highly resistant to streptomycin, kanamycin, amikacin, neomycin, erythromycin, clindamycin, and tetracycline. The isolates were divided into 11 phenotypes of biochemistry. By using PCR, the 16S-rRNA gene DNA fragment was detected at 304 bp from all of isolates. These results may provide the basic information needed to establish strategies for the prevention of S. suis infection in pigs.

• Korean Journal of Ecology and Environment
• /
• v.46 no.3
• /
• pp.360-366
• /
• 2013

This study was it conducted on effluent or river water close to discharge locations from a treatment plant, which were analyzed for the presence, phenotype and antibiotic resistance rates of Vancomycin Resistant Enterococci (VRE). The test results for isolation and identification of Enterococcus spp. showed that they all were VRE positive, with a total of 32 strains detected. Multiplex PCR was conducted for 32 strains, each of which were identified as E. faecium, and the results indicated that they were all confirmed as VRE, corresponding to the Van A phenotype. The results of E. faecium concentrations measured at various locations indicated that they were, on average, higher at the location of sewage treatment plants. The frequency of positive tests as well as the number of colonies was higher downstream of treatment plants. The minimum inhibitory concentration was inspected for 26 strains of discharged water samples from sewage water treatment plants, and 6 strains of river samples. Out of 19 antibiotics, 14 and 5 species showed resistance and sensitivity, respectively.

• Journal of Life Science
• /
• v.15 no.4 s.71
• /
• pp.553-560
• /
• 2005

The stf (Salmonella typhimurium fimbriae) operon consisting of stfA(CDEFG assumes to encode putative fimbriae. The complete stf operon is existed in S. typhimurium and S. choleraesuis, whereas it is absent in S. typhi. Analyses of the amino acid residues between major subunit StfA of the Stf fimbriae and those of known other fimbriaes suggested that Stf belongs to class I type fimbriae. Through comparison of StfD chaperone with the other fimbrial chaperones, and of C-terminus in subunits of Stf fimbriae, it belongs to FGS (with a short Fl-G1 loop) subfamily. In order to investigate the expression of stf operon, we have constructed a Salmonella strain containing a chromosomal stfA::lacZYA transcriptional fusion, resulting in S. typhimurium $_X8532$. The strain $_X8532$ lacked the expression of \beta-galactosidase$ under normal culture conditions. However, with longer incubation time of the S. typhimurium $_X8532$, we have isolated 21 individual strains exhibiting $Lac^+$ phenotype. $Lac^+$ phenotype was appeared as approximately 0.03 frequency per generation. All isolates expressed lacZ constitutively in the various environmental conditions. Various global regulatory proteins including RpoS, OmpR, and CpxR were not involved in the regulation of the stf operon. A S. typhimurium $_X8661$ mutant lacking stfAC function attenuated 6.7 folds more than that of wild type $_X3761$ in the mouse virulence test, suggesting in the somehow involved in the Salmonella pathogenesis.

• Pediatric Infection and Vaccine
• /
• v.27 no.3
• /
• pp.147-157
• /
• 2020

Purpose: We investigated the trend of antibiotic susceptibility of Haemophilus influenzae over 5 consecutive years. Methods: We analyzed the antibiotic susceptibility of H. influenzae isolated from children aged <18 years, who were admitted to the Asan Medical Center Children's Hospital from March 2014 to April 2019. Antibiotic susceptibility of H. influenzae was determined by the disk diffusion test according to the European Committee on Antimicrobial Susceptibility Testing guidelines. Results: Excluding duplicates, 69 isolates were obtained over the past 5 years. The median age of the patients was 5 years (range, 2.8-8.6 years). The antibiotic susceptibility patterns were as follows: ampicillin (AMP)-susceptible/amoxicillin-clavulanate (AMC)-susceptible (AS/ACS; n=15 [21.7%]), AMP-resistant/AMC-susceptible (AR/ACS; n=21 [30.4%]), and AMP-resistant/AMC-resistant (AR/ACR; n=33 [47.8%]). The prevalence of isolates with AR/ACR phenotype tended to increase from 42.1% in 2014-2015 to 54.5% in 2018-2019 (P=0.342). Compared to 2014-2015, the resistance rates to cefuroxime and ceftriaxone in 2018-2019 increased from 31.6% to 77.3% and from 0.0% to 59.1%, respectively (P=0.003 and P<0.001, respectively). Conclusions: Over the last 5 years, H. influenzae isolates with AR/ACR phenotype and ceftriaxone resistance were frequently observed at our institute. The incidence of resistance to cefuroxime and ceftriaxone has increased significantly.

• Journal of Life Science
• /
• v.31 no.12
• /
• pp.1072-1078
• /
• 2021

The oral pathogen Streptococcus mutans is considered a major causative agent of dental caries in humans. The use of dental hygiene products, including toothpaste and mouthwash, is used for caries control. However, food intake can lead to the recurrence of oral microorganisms. This study aimed to explore why this bacterium dies so quickly during prolonged incubation and to assess whether this growth characteristic is closely associated with the secretion of metabolic products. Notably, the number of live S. mutans cells rapidly declined after 24 hr during the entire period tested, whereas the number of Escherichia coli cells, an indicator strain, remained steady over the same period. To test whether the S. mutans supernatants contained possible signals that accelerated the death of neighbor cells, we obtained the individual supernatants at the above time points. Following pH neutralization, the cells in which the supernatant was supplemented with glucose grew well. However, pH adjustment alone could not fully recover cell growth in conditions in which the supernatant was supplemented, with or without glucose. These phenotypes of S. mutans may be associated with signaling, not only resulting from nutrient depletion. The findings on the survival phenotype of S. mutans provide new insights into cell-cell communication in the biology of this bacterium.

• Communications for Statistical Applications and Methods
• /
• v.16 no.3
• /
• pp.397-408
• /
• 2009

The development of microarray technology makes possible to analyse many thousands of genes simultaneously. While it is important to test each gene whether it shows changes in expression associated with a phenotype, human diseases are thought to occur through the interactions of multiple genes within a same functional cafe-gory. Recent research interests aims to directly test the behavior of sets of functionally related genes, instead of focusing on single genes. Gene set enrichment analysis(GSEA), significance analysis of microarray to gene-set analysis(SAM-GS) and parametric analysis of gene set enrichment(PAGE) have been applied widely as a tool for gene-set analyses. We describe their problems and propose an alternative method using a parametric analysis by adopting normal score transformation of gene expression values. Performance of the newly derived method is compared with previous methods on three real microarray datasets.

• Tuberculosis and Respiratory Diseases
• /
• v.81 no.3
• /
• pp.228-232
• /
• 2018

Background: Chronic bronchitis (CB) is an important phenotype in chronic obstructive pulmonary disease (COPD). The purpose of this study is to evaluate different pattern of COPD assessment test (CAT) score between CB and non-CB patients. Methods: Patients were recruited from 45 centers in Korea, as part of the Korean COPD Subgroup Study cohort. CB was defined when sputum continued for at least 3 months. Results: Total 958 patients with COPD were eligible for analysis. Among enrolled patients, 328 (34.2%) were compatible with CB. The CAT score was significantly higher in patients with CB than non-CB, and each component of CAT score showed a similar result. CB was significantly associated with CAT score when adjusted with age, sex, modified Medical Research Council, and post-bronchodilator forced expiratory volume in 1 second. Each component of CAT score between patients with CB and non-CB showed different pattern according to Global Initiative for Chronic Obstructive Lung Disease grade. Conclusion: CAT score is significantly higher in patients with CB than non-CB. Each component of CAT score was significantly different between two groups.