Association of IGF1R polymorphisms with kidney function-related traits.

BACKGROUND: Unimpaired kidney function is important for maintaining a healthy state of homeostasis in the body. A genome-wide association study (GWAS) conducted on kidney function-associated traits and novel loci of Japanese subjects found that insulin-like-growth factor 1 receptor (IGF1R) gene variants associated with replication were responsible for all three kinds of kidney functions and satisfied the Bonferroni significance level. OBJECTIVE: This study aimed to investigate whether a comparable relationship exists in the Korean population. METHOD: This study replicated three SNPs (rs28657002, rs10794486, and rs4966025) and conducted a linear regression analysis between 46 SNPs in the IGF1R gene and three kidney function-related traits, namely blood urea nitrogen (BUN), creatinine, and estimated glomerular filtration rate (eGFR) in Koreans. RESULTS: The IGF1R gene was found to be replicated with a significant correlation in Koreans and was extended to the entire gene region to confirm its association with kidney-related functions. Three SNPs in IGF1R were replicated (rs28657002, BUN, P = 3.39 × 10-4; rs10794486, creatinine, P = 5.79 × 10-6; rs4966025, eGFR, P = 1.57 × 10-5) and five SNPs (rs28657002, rs10794486, rs4966025, rs12439557, and rs11247372) showed common significance among the three traits. Additionally, two significant SNPs (rs11857366 and rs28657002) showed the potential to affect IGF1R expression. CONCLUSIONS: The results suggest that genetic polymorphisms in the IGF1R replicated previous studies and could affect kidney function. The results of this study will further enhance our understanding of how genetic differences in individuals affect kidney function-related traits.

Interaction between ALDH2 rs671 and life habits affects the risk of hypertension in Koreans: A STROBE observational study.

ABSTRACT: Aldehyde dehydrogenase-2 (ALDH2) is associated with the risk of hypertension, and the effects of lifestyle factors on blood pressure vary according to genotype. Among the Han Chinese, the risk of hypertension is lower in the group with the rs671 A allele than in the group with the G allele, and there is a significant association between the frequency of fried food consumption and hypertension. However, the A allele significantly increases the risk of hypertension with increased fried food intake. This study aimed to investigate the effect of the relationship between ALDH2 polymorphism and complex lifestyle habits (fried food consumption and exercise) on hypertension.rs671 polymorphisms of ALDH2 were examined using Korean genome and epidemiology data from 8157 hypertensive cases and 9550 controls. Further, we investigated whether the A allele is protective against hypertension in Koreans and explored the effect of the combination of fried food intake and exercise habits on hypertension by genotype.The genotype frequencies of rs671, which is specific to East Asia, were 2.51% AA, 26.66% GA, and 70.83% GG in the Korean population. The group with inactive aldehyde dehydrogenase-2 had a low odds ratio [OR = 0.75 (95% CI:0.69-0.80), P = 4.35 × 10-14] of hypertension, and low metabolism of acetaldehyde. Subjects carrying the A allele exhibited an increased risk of hypertension with increased fried food intake without exercise [OR = 2.256 (95% CI:1.094-4.654), P = .028].ALDH2 polymorphism and complex lifestyle habits (fried food consumption and exercise) are associated with the risk of hypertension. Further, the A allele is associated with a low risk of hypertension, but it increases the risk of hypertension as fried food intake without exercise increases.

Tuberculosis risk is associated with genetic polymorphisms in the LRP2, CUBN, and VDR genes.

BACKGROUND: Vitamin D (Vit. D) is used extensively during tuberculosis treatment. Low levels of serum Vit. D increase the risk of active tuberculosis development. Altered expression of the proteins involved in Vit. D metabolism impairs cathelicidin production, thereby increasing the host susceptibility to tuberculosis. OBJECTIVE: We are trying to investigate whether single nucleotide polymorphisms (SNPs) in LRP2, CUBN, and VDR genes could affect tuberculosis development. METHODS: We included participants of the Korean Association Resource (KARE), part of the Korean Genome and Epidemiology Study (KoGES), and used their recorded data. A total of 8840 people (4182 men and 4658 women) were eligible subjects. The 5-kb regions from the ends of transcripts of GC, LRP2, CUBN, and VDR genes were amplified to select 13, 47, 70, and 15 SNPs, respectively. For association analysis and statistical analysis, PLINK version 1.07 and PASW Statistics version 18.0 were used. RESULTS: Significant correlation was observed in 11, 2, and 1 SNPs in LRP2, CUBN, and VDR genes. The effect of rs6747692 of LRP2 on transcription factor binding was confirmed using RegulomeDB. We confirmed that rs2239182 of VDR is located in the genomic eQTL region and can affect transcription factor binding and gene expression. CONCLUSIONS: Genetic polymorphisms in genes encoding proteins involved in Vit. D metabolism influence immune system components. Therefore, such polymorphisms may influence the susceptibility to Mycobacterium tuberculosis invasion and alter the defense mechanisms against Mycobacterium tuberculosis infection. The correlation between genetic variation and tuberculosis development can provide new guidelines for the management of tuberculosis.

Evaluation of organic migration and biomass formation on polymeric components in a point-of-use water dispenser.

To minimize the aesthetic and hygienic concerns regarding tap water (e.g., odor, taste, suspended solids, and microorganisms), point-of-use (POU) water dispensers and filters are used in households worldwide. However, the POU water dispenser itself can adversely impact water quality. This study investigated the bacterial growth through a POU water dispenser fed with chlorinated tap water; specifically, the heterotrophic plate count increased from 0.01 to 20.01 × 103 of colony-forming units per ml. The BioMig test, which evaluates the biostability of polymeric materials based on the migration potential and the biofilm formation potential, was firstly applied for the water dispenser system. Organic migration and biofilm formation varied by the polymer type used in the water dispenser components (e.g., tubing, fittings, and reservoir). Assimilable organic carbon migration in cold water (23 ±â€¯2 °C) was better correlated with the biofilm formation potential (R = 0.93) than that of warm water (60 ±â€¯2 °C) migration (R = 0.62). The most problematic test material was silicone based on assimilable organic carbon migration and biofilm formation, whereas approved materials such as polyethylene and polyvinyl chloride were relatively stable. Polymeric component examination of an actual POU water dispenser revealed highly accumulated biofilms on the silicone tube used in the device (118 × 103 CFU cm-2). The use of polymers with high biofilm formation should be minimized in water dispensers, whereas approved polymeric components contribute to biological stability in the dispensed drinking water.

Association between CD53 genetic polymorphisms and tuberculosis cases.

BACKGROUND: Tetraspanin proteins are expressed in various immune cells, and they play an important role in tuberculosis formation. CD53 is a protein in the tetraspanin family that is expressed in many white blood cells. In particular, it plays an important role in cytokine regulation and interaction between natural killer (NK) cells and antigen-presenting cells (APCs). OBJECTIVES: The purpose of this study was to investigate whether the single nucleotide polymorphisms (SNPs) difference of CD53 gene could affect TB case. METHODS: In this study, we investigated the effects of genetic polymorphism of CD53 on the pathogenesis of tuberculosis based on Korean Association Resource (KARE) data. Logistic regression analysis was used to determine the effect of SNPs of the CD53 gene on tuberculosis in TB cases and control groups. We also examined the effect of SNPs on tuberculosis in gene expression. RESULTS: Eight SNPs of CD53 were found to be associated with TB case. The SNP showing the greatest significance in this association was rs4839583 (odds ratio = 0.83, 95% confidence interval 0.72-0.96, p = 0.010). These genetic variants might be involved in cytokine regulation through the Jun pathway, and are thought to affect the immune responses and pathogenesis of TB. DISCUSSION: CD53 is a type of tetraspanin that is expressed on various immune cells. In this study, we identified eight statistically significant SNPs in CD53 gene, confirming that it could be involved in the regulation of CD53 gene expression. CONCLUSION: Associations between genetic variants and tuberculosis facilitated better understanding of the differences in the incidence of tuberculosis in various populations.

Prevalence of human Norovirus by genotype in contaminated groundwater in Korea over the last decade (2007-2016).

This study investigated the occurrence of human Norovirus (HuNoV) by genotype in 1,486 groundwater samples collected from 843 groundwater wells suspected of contamination during 2007-2016, in South Korea. We identified and genotyped 186 HuNoV sequences in 178 HuNoV-positive samples using the RIVM-NoroNet norovirus genotyping tool (NGT) and phylogenetic tree analysis based on RIVM-NoroNet reference sequences. HuNoV GII was more prevalent than GI. The major genotypes detected were HuNoV GII.4 (43.0%), GII.22 (15.6%), GI.5 (10.2%), and GI.1 (8.6%); several genotypes accounted for < 5.0% of all HuNoVs, including GII.17, GI.6, GI.4, GII.6, GI.8, GII.3, GII.13, GI.3, GI.7, GI.2, GI.9, GII.1, GII.8, and GII.10. The prevalence of HuNoVs and number of genotypes detected has drastically decreased over the last decade. HuNoV GII.17, the emerging genotype worldwide including Europe and Asia, appeared in Korean groundwater from 2010, dominated in 2013-2014, and continued to be observed. HuNoV GII.4, the major type occurred last decade from Korean groundwater except 2013-2014, continued to be detected and prevalent similar to HuNoV GII.17 in 2016.

Monitoring of Noxious Protozoa for Management of Natural Water Resources.

Waterborne parasitic protozoa, particularly Giardia lamblia and Cryptosporidium spp., are common causes of diarrhea and gastroenteritis worldwide. The most frequently identified source of infestation is water, and exposure involves either drinking water or recreation in swimming pools or natural bodies of water. In practice, studies on Cryptosporidium oocysts and Giardia cysts in surface water are challenging owing to the low concentrations of these microorganisms because of dilution. In this study, a 3-year monitoring of Cryptosporidium parvum, Giardia lamblia, and Naegleria fowleri was conducted from August 2014 to June 2016 at 5 surface water sites including 2 lakes, 1 river, and 2 water intake plants. A total of 50 water samples of 40 L were examined. Cryptosporidium oocysts were detected in 22% of samples and Giardia cysts in 32%. Water at the 5 sampling sites was all contaminated with Cryptosporidium oocysts (0-36/L), Giardia cysts (0-39/L), or both. The geometric mean concentrations of Cryptosporidium and Giardia were 1.14 oocysts/L and 4.62 cysts/L, respectively. Thus, effective monitoring plans must take into account the spatial and temporal parameters of contamination because they affect the prevalence and distribution of these protozoan cysts in local water resources.

Nocardioides suum sp. nov. isolated from the air environment in an indoor pig farm.

A bacterial strain PBT33-2T was isolated from the air environment in an indoor pig farm. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PBT33-2T belonged to the genus Nocardioides in the phylum Actinobacteria, and was most closely related to Nocardioides daphnia D287T in a maximum-likelihood and neighbor-joining phylogenetic trees. Strain PBT33-2T shared 95.3% sequence identity with N. daphnia D287T. However, the highest sequence similarity was shown with N. sediminis MSL-01T (96.0%). It had less than 96.0% sequence identities with other type species of the genus Nocardioides. Strain PBT-33-2T grew at 15-45°C (optimum 20-35°C), pH 5.0-11.0 (optimum pH 7.0) and 0-4.0% (w/v) NaCl (optimum 0%). The major fatty acid and quinone were iso-C16:0 and MK-8, and the DNA G+C content of strain PBT33-2T was 69.3 mol%. On the basis of poly-phasic results, strain PBT33-2T represents a novel species of the genus Nocardioides, for which the name Nocardioides suum sp. nov. is proposed. Its type strain is PBT33-2T (=KCTC 39558T =DSM 102833T).

Long term results from a prospective database on high dose rate (HDR) interstitial brachytherapy for primary cervical carcinoma.

OBJECTIVE: Present long-term outcomes in primary cervical cancer treated with external beam and high dose rate interstitial brachytherapy. METHODS: High dose rate (HDR) interstitial (IS) brachytherapy (BT) and external beam (EBRT) were administered from 1992 to 2009 to 315 patients who were unsuitable for intracavitary (IC) BT alone. Histology was 89% squamous cell, 8% adenocarcinoma, and 3% adenosquamous. FIGO stage was I-14%, II-47%, III-34%, and IVA-5%. Median tumor size was 6cm. Lymph node metastases were 26% pelvic and 9.5% para-aortic. Treatment planning was 49% 2D and 51% 3D-CT. The mean doses were central EBRT EQD210 37.3±4.3Gy (sidewall 49.2±3.6Gy) and HDR EQD210 42.3±5.3Gy (nominal 5.4Gy×6 fractions using a mean of 24 catheters and 1 tandem). Total EQD210 mean target dose was 79.5±5.4Gy. Standardized planned dose constraints were ICRU points or D0.1cc bladder 80%, rectum 75% and urethra 90% of the HDR dose per fraction. Morbidity assessment was CTCAEv3. Median and mean follow-up were 50 and 61months (3-234). RESULTS: The 10-year actuarial local control was 87%, regional control 84%, and loco-regional control 77%. Distant metastasis free survival was 66%, cause specific survival 56%, disease free survival 54%, and overall survival 40%. The rates of late grade GU and GI toxicities were 4.8% G3 and 5.4% G4. CONCLUSIONS: Template-guided interstitial can be safely performed to successfully deliver high radiation dose to locally advanced cervix cancer and avoid excessive dose and injury to adjacent vital pelvic organs. We achieved high tumor control with low morbidity in patients who were poor candidates for intracavitary brachytherapy.

Detection of circulating tumor cell-specific markers in breast cancer patients using the quantitative RT-PCR assay.

BACKGROUND: Breast cancer is a highly prevalent disease among women worldwide. While the expression of certain proteins within breast cancer tumors is used to determine the prognosis and select therapies, additional markers need to be identified. Circulating tumor cells (CTCs) are constituent cells that have detached from a primary tumor to circulate in the bloodstream. CTCs are considered the main source of breast cancer metastases; therefore, detection of CTCs could be a promising diagnostic method for metastatic breast cancer. METHODS: In this study, the CircleGen CTC RT-qDx assay was used to analyze the mRNA expression levels of six CTC-specific markers including EpCAM, CK19, HER2, Ki67, hTERT, and vimentin with a total of 692 peripheral whole blood samples from 221 breast cancer patients and 376 healthy individuals. RESULTS: This assay showed high specificity with multiple markers; none of the healthy controls were detected positive, whereas 21.7 and 14 % of breast cancer patients were positive for EpCAM and CK19, respectively. Of the 221 breast cancer patients, 84 (38 %), 46 (20.8 %), 83 (37.6 %), and 39 (17.6 %) were positively for HER2, Ki67, hTERT, and vimentin mRNA, respectively. Of the 84 patients who were HER2 positive, nine (4 %) were also positive for EpCAM, CK19, Ki67, hTERT, and vimentin. Of the 139 breast cancer patients who were HER2 negative, 65 (29.1 %) were negative for EpCAM, CK19, Ki67, hTERT, and vimentin. Furthermore, the EpCAM-positive population decreased from 21.5 to 8.3 % after completion of anti-tumor treatment (TP4). Similarly, the CK19, HER2, hTERT, and vimentin positives also decreased from 13.9 to 9.5 %, from 37.7 to 21.4 %, from 37.2 to 33.3 %, and from 17.5 to 14.3 %, respectively, after completion of anti-tumor treatment. In contrast, the Ki67 positives increased from 20.6 to 41.7 % after completion of anti-tumor treatment. CONCLUSIONS: mRNA overexpression of six CTC-specific markers was detected by the CircleGen CTC RT-qDx assay with high specificity, and the obtained mRNA expression levels of CTC-specific markers might provide useful criteria to select appropriate anti-tumor treatment for breast cancer patients.

Quantitative RT-PCR assay of HER2 mRNA expression in formalin-fixed and paraffin-embedded breast cancer tissues.

Detection of human epidermal growth factor receptor 2 gene (HER2, also known as erbB2) expression is a preparatory process to decide a treatment strategy for breast cancer patients. 20-30% of breast cancer patients have HER2 overexpression, and they usually show poor recovery rate. For detection of HER2 expression, immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) methods are conventionally used. Although these methods are accurate and reliable, their time-consuming process and high cost need a concise method with high sensitivity and accuracy. As a complementary method to the current IHC/FISH standard techniques, PCR-based methods have been developed. Here we employed a quantitative PCR method to detect HER2 expression in one hundred ninety nine formalin-fixed and paraffin-embedded (FFPE) breast cancer tissue samples from the patients treated over two years at the Yonsei University Severance Hospital, Republic of Korea. Relative expression of HER2 mRNA in the FFPE samples was analyzed using a quantitative RT-PCR (RT-qPCR) method and the obtained HER2 expression levels were compared with those from IHC/FISH methods. Our results show that the RT-qPCR method was highly concordant with IHC/FISH methods for detecting HER2 expression. Overall sensitivity and specificity of the BrightGen HER2 RT-qDx assay kit (Syantra, Calgary, Canada), which is a kit we used for RT-qPCR analyses, were 93.0% and 89.8% (P < 0.0001), respectively. The diagnostic cut-off value of HER2 RT-qDx for the clinical samples was determined by likelihood ratio, among which the highest likelihood ratio of relative HER2 mRNA levels was over 105.5 (AUC = 0.9466) with the highest sensitivity and specificity. Our study indicates that quantification of HER2 mRNA expression with the RT-qPCR could be an alternative method of conventional IHC/FISH methods.

Evaluation of BrightGen HR RT-qDx assay to detect nuclear receptors mRNA overexpression in FFPE breast cancer tissue samples for selection of tamoxifen therapy.

Breast cancer is a significant cause of death in women. Estrogen receptor (ER) and progesterone receptor (PR) are important prognostic factors indicating higher recovery rate in the breast cancer patients. Currently, immunohistochemical (IHC) staining is a conventional method to identify expression of ER and PR. If a breast cancer patient expresses ER or PR, a chemotherapy with estrogen inhibitors such as tamoxifen is supposed to be effective. Although IHC staining is a reliable method, it may not a useful method for continuous monitoring of ER and PR expression changes in multiple breast cancer patients. In the present study, we evaluated an alternative method of IHC for detection of ER and PR expression. A quantitative RT-PCR method called 'the BrightGen HR RT-qDx assay' was employed to detect mRNA expression of the nuclear receptors in 199 formalin-fixed paraffin-embedded (FFPE) breast cancer tissue samples. Among the ER/PR positive samples by IHC, 83 were determined positive and 16 were determined negative for the nuclear receptor mRNA by the quantitative RT-PCR method. Among the ER/PR negative samples by IHC, 37 were determined negative and 2 were determined positive by the quantitative RT-PCR method. The overall sensitivity and specificity of the quantitative RT-PCR method were 83.8% and 94.8% (P = 0.0026), respectively. We also optimized the quantitative RT-PCR method by setting up the diagnostic cut-off value using the likelihood ratio. The highest likelihood ratio was when the expression levels of the relative nuclear receptor mRNA passed 103.3 at which sensitivity and specificity was highest. These data suggest that BrightGen HR RT-qDx assay could be an alternative method for detection of the prognostic factors of nuclear receptors expressed in breast cancer patients for providing essential information for therapeutic application of tamoxifen.

Detection of circulating tumor cells in patients with breast cancer using the quantitative RT-PCR assay for monitoring of therapy efficacy.

Circulating tumor cells (CTCs) are an independent prognostic factor for patients with breast cancer. However, the role of CTCs in early breast cancer management is not yet clearly defined. The aim of this study was to isolate and characterize CTCs in blood sample of a breast cancer patient as a biomarker for monitoring treatments efficacy. In this study, 692 blood samples from 221 breast cancer patients and 376 healthy individuals was used to detect CTCs with multiple markers including epithelial cell adhesion molecule (EpCAM), cytokeratin (CK) 19, human epidermal growth factor (HER) 2, Ki67, human telomerase reverse transcriptase (hTERT), and vimentin using quantitative reverse transcription PCR (RT-qPCR). A total of 153 (69.2%) blood samples of 221 patients with breast cancer were found to be positive for at least one of the cancer-associated marker gene before treatment. After chemotherapy, no CTCs were found in 28 (33.3%) of the 84 blood samples analyzed for the presence of CTCs using the RT-qPCR, whereas 56 (66.7%) blood samples were still found to be positive for at least one of the markers. After completing the therapy, the CTC positivity rate decreased to 7 (20.6%) in the neoadjuvant group, whereas this increased to 7 (14%) cases in the adjuvant group. There was no statistically significant relationship between TNM stage and detection of CTC-related markers. Data from this study suggest that RT-qPCR assay for the detection of CTC markers might be useful in selecting appropriate therapeutics and for monitoring treatment efficacy in breast cancer patients.

Evaluation of a quantitative RT-PCR assay to detect HER2 mRNA overexpression for diagnosis and selection of trastuzumab therapy in breast cancer tissue samples.

Breast cancer patients who have a positive result for HER2 overexpression are commonly treated with Herceptin, a HER2-targeted therapy. In the present study, the BrightGen HER2 RT-qDx (Syantra, Calgary, Canada), which is based on a one-tube nested RT-qPCR method that detects HER2 mRNA overexpression, was clinically evaluated in a total of 237 formalin-fixed paraffin-embedded (FFPE) tissue samples from breast cancer patients. Among the 38 HER2 positive samples, which were determined via IHC/FISH methods, 13 samples out of 16 (81.3%) that were IHC2+/FISH+ and 22 samples out of 22 (100%) that were IHC3+ have been decided positive for HER2 expression via the RT-qPCR method. The true positivity and false positivity results for the RT-qPCR were 92% (35/38) and 2% (1/65), respectively. The concordance between RT-qPCR and IHC results and RT-qPCR and IHC/FISH was 87.2% and 92.1%, respectively. Conclusively, the BrightGen HER2 RT-qDx may be a reliable and convenient method that can supplement traditional IHC and FISH methods for efficient use of trastuzumab.

Comparison of the performance of the NucliSENS EasyQ HPV E6/E7 mRNA assay and HPV DNA chip for testing squamous cell lesions of the uterine cervix.

This study aims to evaluate the clinical performance of the NucliSENS EasyQ assay and compare it with HPV DNA genotyping for the detection of high-grade squamous intraepithelial lesions (HSIL) and cancer in a Korean population. In 188 total thin prep samples, the remaining fluid after cytology slide preparation was tested with Goodgene HPV DNA chips and the NucliSENS EasyQ HPV E6/E7 messenger RNA (mRNA) assay. The sensitivity and specificity of each test were calculated with HSIL and squamous cell carcinoma (SCC) as the disease endpoint. Out of the 188 samples, 139 (74%) were positive for DNA of 14 HPV types, while 57 (30%) cases were positive for E6/E7 mRNA. The DNA test was positive in cytology cases of SCC, HSIL, and atypical squamous cell. The mRNA test yielded results of 75%, 74%, 60%, 56%, and 29% positivity in abnormal cytology cases of SCC, HSIL, atypical squamous cells - cannot exclude HSIL, atypical squamous cells of undetermined significance, and low-grade squamous intraepithelial lesion, respectively. In normal cytology cases, the positivity rates were 9% and 53% for the mRNA and DNA tests, respectively. For detection of HSIL and SCC, the sensitivity of the mRNA test was 74.36% and that of the DNA test was 100%, while the specificities of the tests were 85% and 40.83%, respectively. These findings suggest that the HPV E6/E7 mRNA assay can overcome the shortcoming of low specificity of DNA assays for clinical detection of high-grade cervical lesions and malignancies.

Mycobacterium tuberculosis-induced expression of granulocyte-macrophage colony stimulating factor is mediated by PI3-K/MEK1/p38 MAPK signaling pathway.

Members of the colony stimulating factor cytokine family play important roles in macrophage activation and recruitment to inflammatory lesions. Among them, granulocyte-macrophage colony stimulating factor (GM-CSF) is known to be associated with immune response to mycobacterial infection. However, the mechanism through which Mycobacterium tuberculosis (MTB) affects the expression of GM-CSF is poorly understood. Using PMA-differentiated THP-1 cells, we found that MTB infection increased GM-CSF mRNA expression in a dosedependent manner. Induction of GM-CSF mRNA expression peaked 6 h after infection, declining gradually thereafter and returning to its basal levels at 72 h. Secretion of GM-CSF protein was also elevated by MTB infection. The increase in mRNA expression and protein secretion of GM-CSF caused by MTB was inhibited in cells treated with inhibitors of p38 MAPK, mitogen-activated protein kinase kinase (MEK-1), and PI3-K. These results suggest that up-regulation of GM-CSF by MTB is mediated via the PI3-K/MEK1/p38 MAPK-associated signaling pathway.

Response of fish communities to various environmental variables across multiple spatial scales.

A better understanding of the relative importance of different spatial scale determinants on fish communities will eventually increase the accuracy and precision of their bioassessments. Many studies have described the influence of environmental variables on fish communities on multiple spatial scales. However, there is very limited information available on this topic for the East Asian monsoon region, including Korea. In this study, we evaluated the relationship between fish communities and environmental variables at multiple spatial scales using self-organizing map (SOM), random forest, and theoretical path models. The SOM explored differences among fish communities, reflecting environmental gradients, such as a longitudinal gradient from upstream to downstream, and differences in land cover types and water quality. The random forest model for predicting fish community patterns that used all 14 environmental variables was more powerful than a model using any single variable or other combination of environmental variables, and the random forest model was effective at predicting the occurrence of species and evaluating the contribution of environmental variables to that prediction. The theoretical path model described the responses of different species to their environment at multiple spatial scales, showing the importance of altitude, forest, and water quality factors to fish assemblages.

c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (p38 MAPK) are involved in Mycobacterium tuberculosis-induced expression of Leukotactin-1.

Leukotactin(Lkn)-1 is a CC chemokine and is upregulated in macrophages in response to Mycobacterium tuberculosis (MTB) infection. We investigated whether mitogen-activated protein kinases (MAPKs) are involved in MTB-induced expression of Lkn-1. The up-regulation of Lkn-1 by infection with MTB was inhibited in cells treated with inhibitors specific for JNK (SP600125) or p38 MAPK (SB202190). Since the up-regulation of Lkn-1 by MTB has been reported to be mediated by the PI3-K/PDK1/Akt signaling, we examined whether JNK and/or p38 MAPK are also involved in this signal pathway. MTB-induced Akt phosphorylation was blocked by treatment with JNK- or p38 MAPK-specific inhibitors implying that p38 and JNK are upstream of Akt. In addition, treatment with the PI3-K-specific inhibitor inhibited MTB-stimulated activation of JNK or p38 MAPK implying that PI3-K is upstream of JNK and p38 MAPK. These results collectively suggest that JNK and p38 MAPK are involved in the signal pathway responsible for MTB-induced up-regulation of Lkn-1.

REBA HPV-ID® for efficient genotyping of human papillomavirus in clinical samples from Korean patients.

This study was conducted to evaluate the overall performance of a reverse blot hybridization-based assay, REBA HPV-ID® (Molecules and Diagnostics, Wonju, Korea) for genotyping human papillomaviruses (HPV). HPV Genotyping on 356 specimens examined cytologically was performed using the REBA HPV-ID®, and its results were compared with those obtained using the MyHPV DNA Chip® (Mygene, Seoul, Korea), DNA chip-based HPV genotyping assay. The results from this study showed that the positivity rate of the REBA HPV-ID® for abnormal cytological samples was higher (80.9%) than that of the MyHPV DNA chip (69.8%). In addition, the REBA HPV-ID® positivity rate with normal cytological samples was higher (64.4%) than that obtained using DNA chips (34.4%). Subsequently, sequence analysis was performed with specimens that generated conflicting test results. Sequence analysis confirmed that the specimens which were positive by REBA HPV-ID® did indeed contain HPV sequences. The results of this study suggest that the REBA HPV-ID® is a sensitive test for genotyping HPV of clinical specimens.

Improved rapid molecular diagnosis of multidrug-resistant tuberculosis using a new reverse hybridization assay, REBA MTB-MDR.

Rapid diagnosis of multidrug-resistant tuberculosis (MDR-TB) is essential for the prompt initiation of effective second-line therapy to improve treatment outcome and limit transmission of this obstinate disease. A variety of molecular methods that enable the rapid detection of mutations implicated in MDR-TB have been developed. The sensitivity of the methods is dependent, in principle, on the repertoire of mutations being detected, which is typically limited to mutations in the genes rpoB, katG and the promoter region of inhA. In this study, a new reverse hybridization assay, REBA MTB-MDR (M&D), that probes mutations in the oxyR-ahpC intergenic region, in addition to those in rpoB, katG and the inhA promoter region, was evaluated. A set of 240 Mycobacterium tuberculosis clinical isolates from patients receiving retreatment regimens was subjected to conventional phenotypic drug-susceptibility testing (DST) and the REBA MTB-MDR assay. The nucleotide sequences of the loci known to be involved in drug resistance were determined for comparison. In brief, the results showed that the REBA MTB-MDR assay efficiently recognized nucleotide changes in the oxyR-ahpC intergenic region as well as those in rpoB, katG and the inhA promoter region with higher sensitivity, resulting in an 81.0 % detection rate for isoniazid resistance. Inclusion of the oxyR-ahpC intergenic region in the REBA MTB-MDR assay improved the overall sensitivity of molecular DST for MDR-TB from 73.1 to 79.9 %.