Method to minimize ozone effect on Cy5 fluorescent intensity in DNA microarrays.

Cyanine 5 (Cy5) is an established fluorescent dye in microarray analysis. It is degraded rapidly when exposed to atmospheric ozone during post-hybridization washes, which leads to loss of fluorescent intensity. To minimize this undesirable effect, we coated microarray slides with sodium dodecyl sulfate (SDS) solution at post-hybridization washes. The fluorescent intensities on coated slides were more stable than those on uncoated slide. We also performed the microarrays with SDS solution for a year to check the solution's effectiveness along with seasonal changes of atmospheric ozone level. Consistent results in microarray analysis were obtained using Cy5 dye under atmospheric ozone.

Kinetic and competitive effects of sorption on multi-element migration through crushed granite and biotite gneiss in Ca-HCO3-SO4 type groundwater.

Crystalline rock is used as the host rock for the disposal of high-level radioactive waste. Two cationic elements (Cs(I) and Ni(II)) and three anionic elements (Se(IV/VI), Mo(VI), and U(VI)) were selected to comprehensively evaluate the sorption behaviors of these radionuclides on crystalline granite and biotite gneiss. The anionic elements showed weak sorption (log Kd (L·kg-1) < 1) and little competition effect, while the cationic elements (log Kd (L·kg-1) = 2-3) showed clear competition (18-98% in Kd values) even at low concentrations. Analysis by pseudo-second-order kinetics showed that Cs(I) sorbed at similar rates on both rocks (20% faster on biotite gneiss), but Ni(II) sorbed 190% faster on biotite gneiss than on granite. That is why the retardation factors for Cs(I) and Ni(II) were reversed in the biotite gneiss column compared to their distribution coefficients. Therefore, the sorption kinetics cannot be neglected in groundwater systems with high flow rates. In the desorption column test, the retardation followed the order of the distribution coefficient. The desorption column test revealed that the distribution coefficient determines the strength of sorption on crystalline rocks.

Risk factors for cytological progression in HPV 16 infected women with ASC-US or LSIL: The Korean HPV cohort.

OBJECTIVE: This study was to identify the risk factors for cytological progression in women with atypical squamous cells of undetermined significance (ASC-US) or low-grade squamous intraepithelial lesions (LSIL). METHODS: We analyzed data from women infected with the human papillomavirus (HPV) who participated in the Korean HPV cohort study. The cohort recruited women aged 20-60 years with abnormal cervical cytology (ASC-US or LSIL) from April 2010. All women were followed-up at every 6-month intervals with cervical cytology and HPV DNA testing. RESULTS: Of the 1,158 women included, 654 (56.5%) and 504 (43.5%) women showed ASC-US and LSIL, respectively. At the time of enrollment, 143 women tested positive for HPV 16 (85 single and 58 multiple infections). Cervical cytology performed in the HPV 16-positive women showed progression in 27%, no change in 23%, and regression in 50% of the women at the six-month follow-up. The progression rate associated with HPV 16 infection was higher than that with infection caused by other HPV types (relative risk [RR], 1.75; 95% confidence interval [CI], 1.08-2.84; P=0.028). The cytological progression rate in women with persistent HPV 16 infection was higher than that in women with incidental or cleared infections (P<0.001). Logistic regression analysis showed a significant relationship between cigarette smoking and cytological progression (RR, 4.15; 95% CI, 1.01-17.00). CONCLUSION: The cytological progression rate in HPV 16-positive women with ASC-US or LSIL is higher than that in women infected with other HPV types. Additionally, cigarette smoking may play a role in cytological progression.

Effects of infections with five sexually transmitted pathogens on sperm quality.

OBJECTIVE: This study investigated the prevalence of infections with human papillomavirus, Chlamydia trachomatis, Ureaplasma urealyticum, Mycoplasma hominis, and Mycoplasma genitalium in the semen of Korean infertile couples and their associations with sperm quality. METHODS: Semen specimens were collected from 400 men who underwent a fertility evaluation. Infection with above five pathogens was assessed in each specimen. Sperm quality was compared in the pathogen-infected group and the non-infected group. RESULTS: The infection rates of human papillomavirus, C. trachomatis, U. urealyticum, M. hominis, and M. genitalium in the study subjects were 1.57%, 0.79%, 16.80%, 4.46%, and 1.31%, respectively. The rate of morphological normality in the U. urealyticum-infected group was significantly lower than in those not infected with U. urealyticum. In a subgroup analysis of normozoospermic samples, the semen volume and the total sperm count in the pathogen-infected group were significantly lower than in the non-infected group. CONCLUSION: Our results suggest that infection with U. urealyticum alone and any of the five sexually transmitted infections are likely to affect sperm morphology and semen volume, respectively.

Combined SYBR Green real-time polymerase chain reaction and microarray method for the simultaneous determination of human papillomavirus loads and genotypes.

OBJECTIVE: The aim of this study was to describe the principle of the Cheil HPV DNA Chip assay and evaluate its accuracy. In order to quantify the human papillomavirus (HPV) load and identify HPV genotypes simultaneously, this assay combined the two methods: SYBR Green quantitative real-time polymerase chain reaction (PCR) and DNA microarray. METHODS: We designed novel consensus primer sets that target the conserved region of the HPV L1 gene for quantifying and detecting a broad range of HPV types by quantitative real-time PCR. Subsequently, using the PCR products, DNA microarray was performed with 36 HPV type-specific probes. To validate this method, direct sequencing and correlation analysis among HPV genotype, viral load, and cytological abnormality was performed by Cohen's kappa values, two-sided McNemar chi-square test, Kruskal-Wallis test, and odds ratios. RESULTS: The kappa value of the Cheil HPV DNA Chip was 0.963 (95% confidence interval, 0.919 to 0.98), which was significantly higher than the value of 0.527 (95% confidence interval, 0.447 to 0.59) obtained using a conventional HPV DNA Chip. HPV16 (χ2=62.28, P<0.01), HPV33 (χ2=7.18, P<0.01), and HPV58 (χ2=9.52, P<0.01), which are classified as high-risk HPVs, were detected at significant levels in samples with high-grade lesions. And viral loads tended to be higher in groups with high odds ratios. CONCLUSION: The Cheil HPV DNA Chip is an effective diagnostic assay for simultaneously detecting HPV genotypes and loads in cervical samples.

The Impact of High-Risk HPV Genotypes Other Than HPV 16/18 on the Natural Course of Abnormal Cervical Cytology: A Korean HPV Cohort Study.

PURPOSE: The purpose of this study is to evaluate the impact of high-risk human papillomaviruses (HPVs) other than HPV 16/18 on the natural course of atypical squamous cells of undetermined significance (ASC-US) or low-grade squamous intraepithelial lesion (LSIL). MATERIALS AND METHODS: The study population was derived from the Korean HPV cohort (2010-2014). Women aged 20 to 60 who satisfied the criteria of having both HPV infection and abnormal cervical cytology of either ASC-US or LSIL were recruited from five institutions nationwide. Enrolled patients underwent cervical cytology and HPV DNA testing every 6 months. RESULTS: A total of 1,158 patients were enrolled. The 10 most common HPV types were HPV 16 (12.3%), 58 (10.0%), 56 (8.8%), 53 (8.4%), 52 (7.7%), 39 (6.2%), 18 (6.0%), 51 (5.7%), 68 (5.1%), and 66 (4.6%). Among these patients, 636 women were positive for high-risk HPVs other than HPV 16 or 18, and 429 women were followed for more than 6 months. Cytology evaluations showed progression in 15.3% of women, no change in 22.6%, and regression in 62.1% of women at 12 months. In cases of HPV 58 single infection, a more highly significant progression rate, compared to other high-risk types, was observed at 6 months (relative risk [RR], 3.3; 95% confidence interval [CI], 2.04 to 5.30; p < 0.001) and 12 months (RR, 5.03; 95% CI, 2.56 to 9.91; p < 0.001). CONCLUSION: HPV genotypes numbered in the 50s were frequent in Korean women with ASC-US and LSIL. HPV 58 was the second most common type, with a high progression rate of cervical cytology.

Clearance of persistent HPV infection and cervical lesion by therapeutic DNA vaccine in CIN3 patients.

Here, we demonstrate that electroporation-enhanced immunization with a rationally designed HPV DNA vaccine (GX-188E), preferentially targeting HPV antigens to dendritic cells, elicits a significant E6/E7-specific IFN-γ-producing T-cell response in all nine cervical intraepithelial neoplasia 3 (CIN3) patients. Importantly, eight out of nine patients exhibit an enhanced polyfunctional HPV-specific CD8 T-cell response as shown by an increase in cytolytic activity, proliferative capacity and secretion of effector molecules. Notably, seven out of nine patients display complete regression of their lesions and viral clearance within 36 weeks of follow up. GX-188E administration does not elicit serious vaccine-associated adverse events at all administered doses. These findings indicate that the magnitude of systemic polyfunctional CD8 T-cell response is the main contributing factor for histological, cytological and virological responses, providing valuable insights into the design of therapeutic vaccines for effectively treating persistent infections and cancers in humans.

Luminescence properties and compositions of contaminating inorganic minerals separated from gamma-irradiated fresh and white ginsengs from different areas.

Gamma-irradiation (0-7 kGy) of ginseng is permitted in Korea for the purpose of microbial decontamination; with strict labeling, traceability and monitoring requirements. An identification study was conducted to determine the photostimulated-luminescence (PSL) and thermoluminescence (TL) properties of gamma-irradiated fresh and white ginsengs cultivated in different areas. Dosedependent PSL-based screening was possible for white ginseng samples; however, inappropriate results from non-irradiated fresh ginseng samples were obtained, showing intermediate (700 to 5,000) or positive (T2 >5,000, irradiated) PSL counts due to the abundance of minerals on the surfaces of the samples. TL analysis of separated minerals from all non-irradiated samples gave TL glow curves of low intensity with a maximum peak after 300℃. However, well-defined irradiation-specific (high intensity with a maximum peak at about 200℃) glow curves were observed for all the irradiated samples, regardless of their type and origins. TL ratios (first glow curve /second glow curve) were also determined to confirm the irradiated (>0.1) and non-irradiated (<0.1) results. SEM-EDX (scanning electron microscope-energy dispersive X-ray) and XRD (X-ray diffraction) spectroscopic analyses showed that feldspar and quartz minerals were the main source for the typical radiation-specific luminescence properties.

The monetary value of the man-mSv for Korean NPP radiation workers assessed by the radiation aversion factor.

The monetary value of the man-mSv for operators of Korean nuclear power plants (NPPs) was calculated using a radiation aversion factor based on a survey of NPP workers. Initially, the life expectancy in the population is 79.4 y, the average age of cancer occurrence is 60 y, the average annual wage for an electric worker is 56 000 $ y(-1) and the nominal risk coefficient induced by radiation is 4.2E(-5) mSv were used to evaluate the basic monetary value (α(base)) resulting in 45.6 $ mSv(-1). To investigate the degree of radiation aversion, the subject of the investigation was selected as the working radiation workers in 10 NPPs in Korea (Kori 1-2, Yeonggwang 1-3, Ulchin 1-3 and Wolseong 1-2). In August 2010, with the cooperation of KHNP and partner companies, a total of 2500 survey questionnaires to 10 NPPs (or 250 surveys to each NPP) were distributed to currently employed radiation workers. From these, 2157 responses were obtained between August and October 2010. The assessed radiation aversion factor and the monetary value of the man-mSv from the calculated radiation aversion factor were 1.26 and ∼50 $ in the 0-1 mSv range, 1.38 and ∼200 $ in the 1-5 mSv range, 1.52 and ∼1000 $ in the 5-10 mSv range, 1.65 and ∼4000 $ in the 10-20 mSv range and 1.74 and ∼8500 $ >20 mSv.