Epigenetic Methylation Changes in Pregnant Women: Bisphenol Exposure and Atopic Dermatitis

Bisphenol is a chemical substance widely used in plastic products and food containers. In this study, we observed a relationship between DNA methylation and atopic dermatitis (AD) in the peripheral blood mononuclear cells (PBMCs) of pregnant women exposed to bisphenol A (BPA) and its alternatives, bisphenol S (BPS) and bisphenol F (BPF). DNA methylation is an epigenetic mechanism that regulates gene expression, which can be altered by environmental factors, and affects the onset and progression of diseases. We found that genes belonging to the JAK-STAT and PI3K-AKT signaling pathways were hypomethylated in the blood of pregnant women exposed to bisphenols. These genes play important roles in skin barrier function and immune responses, and may influence AD. Therefore, we suggest that not only BPA, but also BPS and BPF, which are used as alternatives, can have a negative impact on AD through epigenetic mechanisms.

Stratum corneum lipid and cytokine biomarkers at age 2 months predict the future onset of atopic dermatitis

BACKGROUND

Atopic dermatitis (AD) commonly occurs in children and can progress into severe phenotypes or atopic march, causing significant impairment in quality of life. It is important to find early biomarkers of future onset of AD before any clinical manifestations.

OBJECTIVE

We sought to find early predictors of future onset of AD in skin stratum corneum (SC).

METHODS

Skin tape strips were collected from the forearm of newborns (n = 111) with and without family history of atopic diseases at the age of 2 months before any signs of clinical AD. Children were clinically monitored until they reached age 2 years to ensure the presence or absence of AD. Skin tape strips were subjected to lipidomic analyses by the liquid chromatography electrospray ionization tandem mass spectrometry and cytokine determination by Meso Scale Discovery U-Plex assay.

RESULTS

Overall, 22 of 74 (29.7%) and 5 of 37 (13.5%) infants developed AD in the risk group and the control group, respectively. In the SC of future AD children, protein-bound ceramides were decreased (P < .001), whereas unsaturated sphingomyelin species (P < .0001) and "short-chain" nonhydroxy fatty acid sphingosine and alpha-hydroxy fatty acid sphingosine ceramides were elevated (P < .01 and .05, respectively) as compared with healthy children. Thymic stromal lymphopoietin and IL-13 levels were increased in the SC of future AD subjects (by 74.5% and 78.3%, P = .0022 and P < .0001, respectively). Multivariable logistic regression analysis revealed strong AD predicting power of the combination of family history, type 2 cytokines, and dysregulated lipids, with an odds ratio reaching 54.0 (95% CI, 9.2-317.5).

CONCLUSIONS

Noninvasive skin tape strip analysis at age 2 months can identify asymptomatic children at risk of future AD development with a high probability.

Cerebral venous thrombosis after ChAdOx1 nCoV-19 vaccination: a systematic review

OBJECTIVE

To perform a systematic review of case reports or case series regarding thrombosis with thrombocytopenia syndrome (TTS) and cerebral venous thrombosis (CVT) related to ChAdOx1 nCoV-19 vaccination to address the clinical features, laboratory findings, treatment modalities, and prognosis related with CVT.

SUBJECTS AND METHODS

We included 64 TTS patients from 19 articles, 6 case series and 13 case reports, in which thrombosis occurred after the first dose of ChAdOx1 nCoV-19 vaccination published up to 30 June 2021 in Embase, ePubs, Medline/PubMed, Scopus, and Web of Science databases.

RESULTS

Of the 64 TTS patients, 38 (59.3%) had CVT. Patients with CVT were younger (median 36.5 vs. 52.5 years, p<0.001), had lower fibrinogen levels (130 vs. 245 mg/dL, p=0.008), had more frequent history of intracerebral hemorrhage (ICH), and had higher mortality rate (48.6% vs. 19.2%, p=0.020) than that of patients without CVT. In multivariable analysis, the possibility of presence of CVT was higher in younger age groups [odd ratio (OR): 0.91, 95% confidence interval (CI): (0.86-0.97, p<0.001)] and those with accompanying intracerebral hemorrhage (ICH) (OR: 13.60, 95% CI (1.28-144.12, p=0.045).

CONCLUSIONS

Our study demonstrated that CVT related to ChAdOx1 nCoV-19 vaccination was associated with younger age, low levels of fibrinogen, presence of ICH and more frequent mortality compared to those of non-CVT. If TTS occurs after ChAdOx1 nCoV-19 vaccination, the presence of CVT in patients with young age or ICH should be considered.

Analysis of multi-omics data on the relationship between epigenetic changes and nervous system disorders caused by exposure to environmentally harmful substances

Environmentally hazardous substances and exposure to these can cause various diseases. Volatile organic compounds can easily evaporate into the atmosphere, thereby exerting toxic effects through either the skin or respiratory tract exposures. Toluene, a neurotoxin, has been widely used in various industries. However, it has a detrimental effect on the nervous system (such as hallucinations or memory impairment), while data on the mechanism underlaying its harmful effects remain limited. Therefore, this study investigates the effect of toluene on the nervous system via epigenetic and genetic changes of toluene-exposed individuals. We identified significant epigenetic changes and confirmed that the affected abnormally expressed genes negatively influenced the nervous system. In particular, we confirmed that the miR-15 family, upregulated by toluene, downregulated ABL2, which could affect the R as signaling pathway resulting in neuronal structural abnormalities. Our study suggests that miR-15a-5p, miR-15b-5p, miR-16-5p, miR-301a-3p, and lncRNA NEAT1 may represent effective epigenomic markers associated with neurodegenerative diseases caused by toluene.

Application of droplet digital PCR method for DNA methylation-based age prediction from saliva

The recent studies reported that DNA methylation markers show changes with age, and expected that the DNA methylation markers can be effectively used for estimation of age in forensic genetics. In this study, we applied droplet digital PCR (ddPCR) method to investigate the DNA methylation pattern in the CpG sites, and we constructed an age prediction model based on the ddPCR method. The ddPCR is capable of highly sensitive quantitation of nucleic acid and detection of sequence variations in gene by separating the sample into large number of partitions and clonally amplifying nucleic acids in each partition. We extracted DNA from saliva samples collected from several age groups. The DNA was bisulfite converted and subjected to ddPCR using specifically designed primers and probes. The methylation ratio of each sample was calculated and correlation between the methylation ratio and the chronological age was analyzed. In the results, methylated DNA ratio at the 4 CpG sites (cg14361627, cg14361627, cg08928145 and cg07547549) showed strong correlation with chronological age. Percent-methylation values at 4 CpG markers and chronological ages of the 76 individuals were analyzed by multiple regression analysis, and we constructed an age prediction model. We observed a strong correlation (Spearman's rho = 0.922) between predicted and chronological ages of 76 individuals with a MAD from chronological age of 3.3 years. Collectively, the result in this study showed the potential applicability of ddPCR to predict age from saliva.

Prenatal Exposure to Heavy Metals Affects Gestational Age by Altering DNA Methylation Patterns

Environmental exposure is known to have toxic effects. Maternal environmental exposure not only affects mothers but also their fetuses in utero, which may interrupt their early development. Preterm birth, one of the outcomes of prenatal exposure, is a significant factor in lifelong health risks. To understand the effects of prenatal exposome on preterm birth, we studied the association between maternal and prenatal heavy metal exposure and gestational age, using resources from the MOthers' and Children's Environmental Health (MOCEH) study in South Korea. Additionally, a methylation assay was performed to analyze epigenetic mediation using genomic DNA derived from the cord blood of 384 participants in the MOCEH study. The results suggest that maternal cadmium exposure is associated with a decrease in gestational age through an alteration in DNA methylation at a specific CpG site, cg21010642. The CpG site was annotated to a gene involved in early embryonic development. Therefore, irregular methylation patterns at this site may contribute to premature birth by mediating irregular biological mechanisms.

Integrated analysis of multi-omics data on epigenetic changes caused by combined exposure to environmental hazards

Humans are easily exposed to environmentally hazardous factors in industrial sites or daily life. In addition, exposure to various substances and not just one harmful substance is common. However, research on the effects of combined exposure on humans is limited. Therefore, this study examined the effects of combined exposure to volatile organic compounds (VOCs) on the human body. We separated 193 participants into four groups according to their work-related exposure (nonexposure, toluene exposure, toluene and xylene exposure, and toluene, ethylbenzene, and xylene exposure). We then identified the methylation level and long noncoding RNA (lncRNA) levels by omics analyses, and performed an integrated analysis to examine the change of gene expression. Thereafter, the effects of combined exposure to environmental hazards on the human body were investigated and analyzed. Exposure to VOCs was found to negatively affect the development and maintenance of the nervous system. In particular, the MALAT1 lncRNA was found to be significantly reduced in the complex exposure group, and eight genes were significantly downregulated by DNA hypermethylation. The downregulation of these genes could cause a possible decrease in the density of synapses as well as the number and density of dendrites and spines. In summary, we found that increased combined exposure to environmental hazards could lead to additional epigenetic changes, and consequently abnormal dendrites, spines, and synapses, which could damage motor learning or spatial memory. Thus, lncRNA MALAT1 or FMR1 could be novel biomarkers of neurotoxicity to identify the negative health effects of VOC complex exposure.

Transcriptome dynamics of alternative splicing events revealed early phase of apoptosis induced by methylparaben in H1299 human lung carcinoma cells

Methylparaben is most frequently used as an antimicrobial preservative in pharmaceuticals and foods. Methylparaben has been subjected to toxicological studies owing to the increasing concern regarding its possible impact on the environment and human health. However, the cytotoxicity and underlying mechanisms of methylparaben exposure in human lung cells have not been explored. Here, we investigated the effect of methylparaben on cell cycle, apoptotic pathways, and changes in the transcriptome profiles in human lung cells. Our results demonstrate that treatment with methylparaben causes inhibition of cell growth. In addition, methylparaben induced S- and G2/M-phase arrest as a result of enhanced apoptosis. Transcriptome analysis using RNA-seq revealed that mRNA expression of ER stress- and protein misfolding-related gene sets was upregulated in methylparaben-treated group. RNA splicing- and maturation-related gene sets were significantly down-regulated by methylparaben treatment. Interestingly, RNA-seq analysis at the transcript level revealed that alternative splicing events, especially retained intron, were markedly changed by a low dose of methylparaben treatment. Altogether, these data show that methylparaben induces an early phase of apoptosis through cell cycle arrest and downregulation of mRNA maturation.

Design, Fabrication, and Testing of a Microfluidic Device for Thermotaxis and Chemotaxis Assays of Sperm

Infertile couples needing assisted reproduction are increasing, so a fundamental understanding of motile sperm migration is required. This paper presents an advanced microfluidic device for sperm motion analysis utilizing chemotaxis and thermotaxis simultaneously for the first time. The proposed device is a transparent polydimethylsiloxane- and glass-based microfluidic chip system providing a low-cost, useful, and disposable platform for sperm analysis. The concentration gradient of the chemoattractant (acetylcholine) and the temperature difference are formed along the microchannel. The temperature gradient is generated and controlled by a microheater and microsensor. Thermotactic and chemotactic responses of mouse sperm were examined using the proposed device. Experimental results show that motile mouse sperm are attracted more sensitively under integrated conditions of chemotaxis and thermotaxis rather than individual conditions of chemotaxis and thermotaxis. This sperm analysis device is expected to be a useful tool for the study of mammalian sperm migration and the improvement of artificial insemination techniques.

PPARα-Target Gene Expression Requires TIS21/BTG2 Gene in Liver of the C57BL/6 Mice under Fasting Condition

The TIS21/BTG2/PC3 gene belongs to the antiproliferative gene (APRO) family and exhibits tumor suppressive activity. However, here we report that TIS21 controls lipid metabolism, rather than cell proliferation, under fasting condition. Using microarray analysis, whole gene expression changes were investigated in liver of TIS21 knockout (TIS21-KO) mice after 20 h fasting and compared with wild type (WT). Peroxisome proliferator-activated receptor alpha (PPARα) target gene expression was almost absent in contrast to increased lipid synthesis in the TIS21-KO mice compared to WT mice. Immunohistochemistry with hematoxylin and eosin staining revealed that lipid deposition was focal in the TIS21-KO liver as opposed to the diffuse and homogeneous pattern in the WT liver after 24 h starvation. In addition, cathepsin E expression was over 10 times higher in the TIS21-KO liver than that in the WT, as opposed to the significant reduction of thioltransferase in both adult and fetal livers. At present, we cannot account for the role of cathepsin E. However, downregulation of glutaredoxin 2 thioltransferase expression might affect hypoxic damage in the TIS21-KO liver. We suggest that the TIS21/BTG2 gene might be essential to maintain energy metabolism and reducing power in the liver under fasting condition.

Metronome vs. Popular Song: A Comparison of Long-Term Retention of Chest Compression Skills after Layperson Training for Cardiopulmonary Resuscitation

Introduction

Long-term retention of cardiopulmonary resuscitation (CPR) skill is challenging for layperson trainees. This study compared the long-term retention of chest compression skills after either metronome-guided (MG) or popular song-guided (PG) CPR training.

Methods

This was a prospective randomised simulation trial. Untrained laypersons were randomly allocated to MG (n=61) or PG (n=68) groups at CPR training sessions. After CPR training, each participant performed 5-cycle CPR using a manikin with a Skill-Reporter™ immediately and six months afterwards.

Results

Immediately after training, the mean compression rate (MCR) was slightly higher in the PG than the MG group (107.4 vs. 102.2/min; p<0.0001), but there was no significant difference in the proportions of participants with an appropriate chest compression rate (100-120/min) (PSACCR) between the MG and PG (53/61 (86.9%) vs. 65/68 (95.6%); p=0.114). Six months later, MCR was faster in the MG than the PG (124.8 vs. 110.0/min; p<0.0001), and PSACCR in the PG was higher than that in the MG (62/68 (91.2%) vs. 25/61 (41.0%); p<0.0001). In both tests, there were no significant differences in other chest compression parameters of between the two groups, except for a minimal difference in incomplete chest release.

Conclusion

CPR training using a popular song is more effective than metronome-guided training in helping laypersons to maintain recommended compression rates after 6 months. (Hong Kong j.emerg.med. 2016;23:145-152)

Holiday Fast-Track Reduced Medical Cost and Length of Emergency Department Stay: Preliminary Report from a Single Secondary Care Hospital

Introduction

The aims of this study were to compare the effect of a Holiday Fast-Track (HFT) unit on medical costs and emergency department (ED) length of stay (LOS) associated with low acuity patients attended during the same timeframe in two consecutive years in a single secondary care hospital ED.

Methods

Two groups (non-HFT vs. HFT), before and after the fast-track unit was implemented, were compared. The HFT unit was operated to improve the flow of low acuity patients, which were defined as the patients classified as level 4 or 5 by the modified Canadian Triage and Acuity Scale. Data were collected from March 1 to April 30, 2011 for the non-HFT group and during the same period in 2012 for the HFT group.

Results

A total of 894 (431 for non-HFT period and 463 for HFT period) patients of acuity level 4 or 5 visited the ED during the study period. Compared to the non-HFT group, the ED LOS of the HFT group decreased by 27 min and 3.5 min in the patients with acuity levels 4 and 5, respectively (p=0.005 and p=0.003, respectively). Furthermore, total medical costs and laboratory fees were also reduced significantly in the HFT group (p<0.001, p=0.038). However, there was no difference in the other variables between those two groups.

Conclusions

The HFT system decreases the medical costs and LOS in low acuity patients visiting the ED of a secondary care hospital. (Hong Kong j.emerg.med. 2015;22:84-92)

Cucumber Plants Baited with Methyl Salicylate Accelerates Scymnus (Pullus) sodalis (Coleoptera: Coccinellidae) Visiting to Reduce Cotton Aphid (Hemiptera: Aphididae) Infestation

The cotton aphid, Aphis gossypii (Glover) (Hemiptera: Aphididae), is a major pest of many crops worldwide and a major cucumber plant pest in Taiwan. Because cotton aphids rapidly develop insecticide resistance and because of the insecticide residue problem, a safe and sustainable method is required to replace conventional chemical control methods. Methyl salicylate (MeSA), a herbivore-induced plant volatile, has been shown to affect aphids' behavior and attract the natural enemies of aphids for reducing their population. Therefore, this study examined the direct effects of MeSA on cotton aphids' settling preference, population development, and attractiveness to natural enemies. The efficiency of using MeSA and the commercial insecticide pymetrozine for reducing the cotton aphid population in laboratory and outdoor cucumber plant pot was also examined. The results showed no difference in winged aphids' settling preference and population development between the MeSA and blank treatments. Cucumber plants infested with cotton aphids and baited with 0.1% or 10% MeSA contained significantly higher numbers of the natural enemy of cotton aphids, namely Scymnus (Pullus) sodalis (Weise) (Coleoptera: Coccinellidae), and MeSA-treated cucumber plants contained a lower number of aphids. Significantly lower cotton aphid numbers were found on cucumber plants within a 10-m range of MeSA application. In addition, fruit yield showed no difference between the MeSA and pymetrozine treatments. According to our findings, 0.1% MeSA application can replace insecticides as a cotton aphid control tool. However, large-scale experiments are necessary to confirm its efficiency and related conservation biological control strategies before further use.

Effect of relative humidity on preeclampsia

PURPOSE OF INVESTIGATION

The authors aimed to determine the relationship between meteorological variables and hypertension in pregnancy by using data from a national weather database.

MATERIALS AND METHODS

For this population-based observational study, the database of the Korea National Health Insurance (KNHI) Claims of the Health Insurance Review and Assessment Service (HIRA) and Korea Meteorological Administration was used. The 48,275 women with preeclampsia among 2,495,383 women who gave birth were included. Monthly meteorological factors and preeclampsia prevalence for five years were statistically analyzed.

RESULTS

Among temperature, relative humidity, sunlight duration, and rainfall, only relative humidity had a significant inverse correlation with the preeclampsia prevalence (p < 0.001). The other meteorological factors were not associated with preeclampsia.

CONCLUSION

Relative humidity may be a significant factor for of the development of preeclampsia. Further monitoring of weather parameters during the entire pregnancy period may be the best method for verifying the present results in the development of preeclampsia.

A study of the dietary intakes by the pre-pregnancy body mass index in pregnant women

The authors analyzed the difference in weight gain and nutrition, according to the BMI before pregnancy. They divided 91 subjects into BMI group I (normal weight) and BMI group 2 (overweight) before pregnancy. In general, the BMI before pregnancy did not influence weight gain but, in the BMI group 2, the intakes of all of cholesterol, total fatty acids, vitamin B 12, iron, and copper were significantly higher. Neither group exhibited sufficient intake of vitamin B 1, vitamin B2, niacin, vitamin B6, folic acid, calcium, magnesium, iron, or zinc. Pre-pregnancy weight management and nutrition during pregnancy is very important.

Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis

Volatile organic compounds (VOCs) can be easily taken up by humans, leading to various diseases, such as respiratory system and central nervous system disorders. Environmental risk assessment is generally conducted using traditional tests, which may be time-consuming and technically challenging. Therefore, analysis of the effects of VOCs, such as toluene, ethylbenzene, and xylene, may be improved by use of novel, high-throughput methods, such as microarray analysis. In this study, we examined the effects of VOCs exposure in humans on gene expression and methylation using microarray analysis. We recruited participants who had short-term exposure, long-term exposure, or no exposure. We then analyzed changes in gene expression in blood samples from these participants. A total of 866 genes were upregulated, while 366 genes were downregulated in the short-term exposure group. Similarly, in the long-term exposure group, a total of 852 and 480 genes were up- or downregulated, respectively. Hierarchical clustering analysis was used to divide the clustered genes into nine clusters to investigate the expression of variations in accordance with the exposure period. And the methylation microarray was performed at the same time to see whether this expression variation is related to the epigenetic study. Finally, we have 5 genes that were upregulated and 12 genes that were downregulated, gradually and respectively, so these genes are expected to function as biomarkers of the duration of exposure to VOCs. Further research is required to determine the time-dependent effects of VOCs on epigenetic regulation of gene expression. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1563-1570, 2016.

High specific genotyping method using short target probe and helper probe

Differentiating 1-bp differences using real-time PCR often leads to false-positive results. Therefore, we developed a fluorescence melting curve analysis (FMCA) method with a short target probe and helper probe labeled with a fluorophore and quencher, respectively. This fluorophore and quencher were designed to be near each other when the probes were hybridized to template DNA. The target probe was designed with a shorter length to facilitate a dramatic shift in melting temperature (Tm) upon encountering mismatched hybridization. In FMCA, when the temperature approached the target probe Tm, the target probe would begin to denature from the template DNA, and at the target probe Tm, the fluorescence signal increased markedly. Here, we examined 1-bp differences using the developed method with mitochondrial DNA from Larimichthys polyactis and Larimichthys crocea. Application of this method permitted specific genotype identification for all cases with no cross-reactivity, even when both templates were added to the same tube.

Accumulation and temporal changes of PCDD/Fs and dioxin-like PCBs in finless porpoises (Neophocaena asiaeorientalis) from Korean coastal waters: Tracking the effectiveness of regulation

Temporal trend studies are useful to evaluate the effectiveness of regulations on local pollutants. The emission of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (PCBs) has been regulated by the Korean government in accordance with the Stockholm Convention. The accumulation and temporal trends of PCDD/Fs and dioxin-like PCBs were investigated in finless porpoises (Neophocaena asiaeorientalis) collected in Korean waters. Median concentrations of PCDDs, PCDFs, non-ortho PCBs, and mono-ortho PCBs were 1.0, 1.1, 0.1, and 1.8pgTEQ/g lipid weight, respectively, which were lower than threshold values for marine mammals. Age- and sex-dependent accumulation patterns were found for PCDFs and DL-PCBs. Temporal trends in finless porpoises collected between 2003 and 2010 showed significant reduction rates of 57%, 54%, 69%, and 60% for PCDDs, PCDFs, non-ortho PCBs, and mono-ortho PCBs, respectively. Our results suggest that the regulations on dioxin-like contaminants have been effective for marine mammals in Korea.

Association analysis of toluene exposure time with high-throughput mRNA expressions and methylation patterns using in vivo samples

The emission of volatile organic compounds (VOCs) resulting from outdoor air pollution can contribute to major public health problems. However, there has been limited research on the health effects in humans from the inhalation of VOCs. Therefore, this study conducted an in vivo analysis of the effects of toluene, one of the most commonly used chemicals in many industries, on gene expression and methylation over time using the high-throughput technique of microarray analysis. We separated participants into three groups (control, short-term exposure, and long-term exposure) to investigate the influence of toluene exposure time on gene expression. We then comprehensively analyzed and investigated the correlation between variations in gene expression and the occurrence of methylation. Twenty-six genes were upregulated and hypomethylated, while 32 genes were downregulated and hypermethylated. The pathways of these genes were confirmed to be associated with cell survival and the immune system. Based on our findings, these genes can help predict the effects of time-dependent exposure to toluene on human health. Thus, observations from our data may have implications for the identification of biomarkers of toluene exposure.

Compound EGFR mutation is frequently detected with co-mutations of actionable genes and associated with poor clinical outcome in lung adenocarcinoma

Compound EGFR mutations, defined as double or multiple mutations in the EGFR tyrosine kinase domain, are frequently detected with advances in sequencing technology but its clinical significance is unclear. This study analyzed 61 cases of EGFR mutation positive lung adenocarcinoma using next-generation sequencing (NGS) based repeated deep sequencing panel of 16 genes that contain actionable mutations and investigated clinical implication of compound EGFR mutations. Compound EGFR mutation was detected in 15 (24.6%) of 61 cases of EGFR mutation-positive lung adenocarcinoma. The majority (12/15) of compound mutations are combination of the atypical mutation and typical mutations such as exon19 deletion, L858R or G719X substitutions, or exon 20 insertion whereas 3 were combinations of rare atypical mutations. The patients with compound mutation showed shorter overall survival than those with simple mutations (83.7 vs. 72.8 mo; P = 0.020, Breslow test). Among the 115 missense mutations discovered in the tested genes, a few number of actionable mutations were detected irrelevant to the subtype of EGFR mutations, including ALK rearrangement, BCL2L11 intron 2 deletion, KRAS c.35G>A, PIK3CA c.1633G>A which are possible target of crizotinib, BH3 mimetics, MEK inhibitors, and PI3K-tyrosine kinase inhibitors, respectively. 31 missense mutations were detected in the cases with simple mutations whereas 84 in those with compound mutation, showing that the cases with compound missense mutation have higher burden of missense mutations (P = 0.001, independent sample t-test). Compound EGFR mutations are detected at a high frequency using NGS-based repeated deep sequencing. Because patients with compound EGFR mutations showed poor clinical outcomes, they should be closely monitored during follow-up.

Genetic heterogeneity of actionable genes between primary and metastatic tumor in lung adenocarcinoma

BACKGROUND

Biopsy for lung cancer diagnosis is usually done at a single site. But it is unclear that genetic information at one biopsy site represents that of other lesions and is sufficient for therapeutic decision making.

METHODS

Non-synonymous mutations and insertions/deletions of 16 genes containing actionable mutations, and intron 2 deletion polymorphism of Bcl2-like11 were analyzed in 41 primary tumor and metastatic lymph node (L/N) matched, pStage IIA ~ IIIA non-small cell lung cancer (NSCLC) samples using a next generation sequencing based technique.

RESULTS

A total of 249 mutations, including 213 non-synonymous mutations, 32 deletions, and four insertions were discovered. There was a higher chance of discovering non-synonymous mutations in the primary tumors than in the metastatic L/N (138 (64.8%) vs. 75 (35.2%)). In the primary tumors, 106 G > A:C > T transitions (76.8%) of 138 non-synonymous mutations were detected, whereas in the metastatic L/N, 44 (58.7%) of 75 were discovered. A total 24 (11.3%) out of 213 non-synonymous mutations were developed in the context of APOBEC signature. Of those, 21 (87.5%) was detected in the primary tumors and 4 (16.7%) was detected in the metastatic L/N. When the mutation profiles between primary tumor and metastatic L/N were compared, 13 (31.7%) of 41 cases showed discrepant mutation profile. There were no statistically significant differences in disease free survival and overall survival between groups showing identical mutation profiles and those with discrepancy between primary and metastatic L/N.

CONCLUSIONS

Genetic heterogeneity between the primary and L/N metastatic lesions is not infrequent finding to consider when interpreting genomic data based on the result of one site inspection. A large prospective study may be needed to evaluate the impact of genetic heterogeneity on the clinical outcomes of NSCLC patients.

Differentiation of Scomber japonicus from Scomber scombrus by using a single locked nucleic acid probe

Mackerel is marketed at prices according to the species type, Scomber japonicus and Scomber scombrus. Distinguishing these two species with the naked eye is difficult, and their differentiation becomes more difficult after they are processed by cooking, thereby leading to counterfeiting issues. Thus, in this study, we developed a method to differentiate S. japonicus from S. scombrus by detecting polymorphisms in mitochondrial 16 s rRNA gene by using fluorescence melting curve analysis and locked nucleic acid probes. Our method could distinguish S. japonicus from S. scombrus in a single experiment by using a single probe. The probes developed matched exactly with S. japonicus and had a melting temperature of 64 °C. However, the probes were mismatched with S. scombrus, resulting in a lower melting temperature of 46 °C. The high specificity of the locked nucleic acid probes resulted in this large difference in the melting temperatures.

Use of vertebral body units to locate the cavoatrial junction for optimum central venous catheter tip positioning

BACKGROUND

Central venous catheter (CVC) placement plays an important role in clinical practice; however, optimal positioning of the CVC tip remains a controversial issue. The objective of this study was to evaluate the use of vertebral body unit (VBUs), to locate the cavoatrial junction (CAJ), for optimal CVC tip placement based on chest radiography (CXR) using the carina as a landmark.

METHODS

524 patients who underwent coronary computed tomographic angiography (CTA) and CXR were included. The position of the CAJ was identified using VBUs, and the efficacy of VBUs for locating the CAJ with the carina as a landmark was analysed using multiple regression analysis. A VBU was defined as the distance between two adjacent vertebral bodies, including the inter-vertebral disk space.

RESULTS

The mean (sd) distance from the carina to the superior CAJ was 54.3 (9.7) mm on CTA; the mean distance in VBUs at the level of the carina was 21.4 (1.7) mm on CTA and 22.6 (2.1) mm on CXR. The mean CAJ position was 2.5 VBUs below the carina on CTA and 2.4 VBUs below on CXR with 95% limits of agreement between -0.6 and +0.3.

CONCLUSIONS

The position of the CVC tip in relation to the carina can be described using the thoracic spine as an internal ruler, and the position of the CAJ in adults was reliably estimated to be 2.4 VBUs below the carina.

CLINICAL TRIAL REGISTRATION

KCT0001319.

Multiplex genotyping based on the melting temperature of a single locked nucleic acid probe

Locked nucleic acid (LNA) is a modified RNA nucleotide that can be incorporated at specific positions to generate probes with the desired length, melting temperature (TM), and specificity. Here, we describe a method of multiplex genotyping based on dramatic shifts in the TM of a single dual-labeled LNA probe. Using this method, two varieties of the hairtail fish Trichiurus lepturus can be distinguished from each other, as well as from Trichiurus japonicus, based on a 1- to 2-bp difference in a fragment of mitochondrial cytochrome oxidase subunit 1. The shift in TM was 15 °C for a 1-bp mismatch and 27 °C for a 2-bp mismatch, indicating remarkable specificity. We anticipate that the method will be widely useful in applications such as species identification that require accurate, multiplex, and efficient detection of DNA polymorphisms.

Genotyping of velvet antlers for identification of country of origin using mitochondrial DNA and fluorescence melting curve analysis with locked nucleic acid probes

Velvet antlers are used medicinally in Asia and possess various therapeutic effects. Prices are set according to the country of origin, which is unidentifiable to the naked eye, and therefore counterfeiting is prevalent. Additionally, antlers of the Canadian elk, which can generate chronic wasting disease, are prevalently smuggled and distributed in the market. Thus, a method for identifying the country of origin of velvet antlers was developed, using polymorphisms in mitochondrial DNA, fluorescence melting curve analysis and analysis of locked nucleic acids (LNA). This combined method is capable of identifying five genotypes of velvet antlers in a single experiment using two probes. It also has advantages in multiplexing, simplicity and efficiency in genotyping, when compared to real-time PCR or microarrays. The developed method can be used to improve identification rates in the velvet antler market and, by extension, research based on polymorphisms in DNA sequences.

Utility of Stable Isotope and Cytochrome Oxidase I Gene Sequencing Analyses in Inferring Origin and Authentication of Hairtail Fish and Shrimp

Mislabeling of fishery products continues to be a serious threat to the global market. Consequently, there is an urgent necessity to develop tools for authenticating and establishing their true origin. This investigation evaluates the suitability of stable isotopes and cytochrome oxidase I (COI) sequencing in identifying and tracing the origin of hairtail fish and shrimp. By use of COI sequencing, the hairtail fish samples were identified as Trichiurus japonicus and Trichiurus lepturus, while the shrimp samples were identified as Pandalus borealis, Marsupenaeus japonicus, Fenneropenaeus chinensis, Litopenaeus vannamei, Penaeus monodon, and Solenocera crassicornis. Linear discriminant analysis (LDA) of stable isotopes further categorized the individuals of the same species based on the country of origin. Natural and farmed shrimp (from the same country) were distinctly differentiated on the basis of stable isotope values. Therefore, these two methods could be cooperatively utilized to identify and authenticate fishery products, the utilization of which would enhance transparency and fair trade.

Fluorescence melting curve analysis using self-quenching dual-labeled peptide nucleic acid probes for simultaneously identifying multiple DNA sequences

Previous fluorescence melting curve analysis (FMCA) used intercalating dyes, and this method has restricted application. Therefore, FMCA methods such as probe-based FMCA and molecular beacons were studied. However, the usual dual-labeled probes do not possess adequate fluorescence quenching ability and sufficient specificity, and molecular beacons with the necessary stem structures are hard to design. Therefore, we have developed a peptide nucleic acid (PNA)-based FMCA method. PNA oligonucleotide can have a much higher melting temperature (Tm) value than DNA. Therefore, short PNA probes can have adequate Tm values for FMCA, and short probes can have higher specificity and accuracy in FMCA. Moreover, dual-labeled PNA probes have self-quenching ability via single-strand base stacking, which makes PNA more favorable. In addition, this method can facilitate simultaneous identification of multiple DNA templates. In conventional real-time polymerase chain reaction (PCR), one fluorescence channel can identify only one DNA template. However, this method uses two fluorescence channels to detect three types of DNA. Experiments were performed with one to three different DNA sequences mixed in a single tube. This method can be used to identify multiple DNA sequences in a single tube with high specificity and high clarity.

Concentrative nucleoside transporter 3 as a prognostic indicator for favorable outcome of t(8;21)-positive acute myeloid leukemia patients after cytarabine-based chemotherapy

Although acute myeloid leukemia (AML) exhibits diverse responses to chemotherapy, patients harboring the t(8;21) translocation are part of a favorable risk group. However, the reason why this subgroup is more responsive to cytarabine-based therapy has not been elucidated. In the present study, we analyzed expression levels of cytarabine metabolism-related genes in patients diagnosed with AML with or without t(8;21) and investigated their correlation with clinical outcomes after cytarabine-based therapy. Among the 8 genes studied, expression of the concentrative nucleoside transporter 3 (CNT3) gene was significantly higher in t(8;21)-positive patients compared to the others in the test population and the validation cohort (P<0.001 in Mann-Whitney U test; P<0.002 in Pearson's correlation analysis). Additionally, in both multivariate and univariate analyses, t(8;21)-positive patients categorized in a higher CNT3 expression tertile had longer disease-free survival [hazard ratio (HR), 0.117; 95% confidence interval (CI), 0.025-0.557; P=0.008] and overall survival (HR, 0.062; 95% CI, 0.007-0.521; P=0.010) compared to t(8;21)-positive patients in a lower CNT3 expression tertile. Notably, these trends did not occur in t(8;21)-negative patients. Our results demonstrate that CNT3 expression is associated with overall favorable outcomes and is predictive of clinical outcomes in AML patients with t(8;21). This suggests that CNT3 expression can be used to optimize treatment strategies for AML patients.

Application of fluorescence melting curve analysis for dual DNA detection using single peptide nucleic acid probe

Peptide nucleic acid (PNA) is an artificially synthesized polymer. PNA oligomers show greater specificity in binding to complementary DNAs. Using this PNA, fluorescence melting curve analysis (FMCA) for dual detection was established. Genomic DNA of Mycoplasma fermentans and Mycoplasma hyorhinis was used as a template DNA model. By using one PNA probe, M. fermentans and M. hyorhinis could be detected and distinguished simultaneously in a single tube. The developed PNA probe is a dual-labeled probe with fluorescence and quencher dye. The PNA probe perfectly matches the M. fermentans 16s rRNA gene, with a melting temperature of 72°C. On the other hand, the developed PNA probe resulted in a mismatch with the 16s rRNA gene of M. hyorhinis, with a melting temperature of 44-45°C. The melting temperature of M. hyorhinis was 27-28°C lower than that of M. fermentans. Due to PNA's high specificity, this larger melting temperature gap is easy to create. FMCA using PNA offers an alternative method for specific DNA detection.

Efficient production of transgenic melon via Agrobacterium-mediated transformation

Oriental melon (Cucumis melo L. var. makuwa) is an important fruit for human consumption. However, this plant species is one of the most recalcitrant to genetic transformation. The lack of an efficient in vitro system limits the development of a reproducible genetic transformation protocol for Oriental melon. In this study, an efficient transgenic production method for Agrobacterium-mediated transformation using cotyledon explants of Oriental melon was developed. Cotyledon explants were pre-cultivated for two days in the dark, and the optimal conditions for transformation of melon were determined to be a bacteria concentration of OD600 0.6, inoculation for 30 min, and two days of co-cultivation. Transgenic melon plants were produced from kanamycin-resistant shoots. A total of 11 independent transgenic plants were regenerated with a transformation efficiency of 0.8% of the inoculated explants. The transgenic plants were phenotypically normal and fully fertile, which might be a consequence of the co-cultivation time.

Development of electrochemical microbiochip for the biological diagnosis of Neisseria gonorrhoeae

A sexually transmitted disease is an illness that has a high probability of transmission between humans or animals who have sexual contact. Our research is based on the development of a microbiochip for Neisseria gonorrhoeae (N.G.). In our study, we have employed fusion technology between microarray technology and a microfluidic system for quantitative analysis of N.G. A great deal of attention has been focused on electrochemical detection by using a DNA probe, which is a specific DNA sequence and binds to a target biomolecule, because of high affinity, ease of usage, and fast measurement. The microbiochip consisted of two electrode systems and microchannel based PDMS. Our detection principles use electrochemical detection. Consequently, our microbiochip detected 5 ng/mL of N.G. and the correlation rate was over 0.95. We can produce a microbiochip, which could bind to a DNA probe and detect sample of interest. We expect that our electrobiochemical chip will be used for the development of a portable device.

Development of a DNA microarray for species identification of quarantine aphids

BACKGROUND

Aphid pests are being brought into Korea as a result of increased crop trading. Aphids exist on growth areas of plants, and thus plant growth is seriously affected by aphid pests. However, aphids are very small and have several sexual morphs and life stages, so it is difficult to identify species on the basis of morphological features. This problem was approached using DNA microarray technology.

RESULTS

DNA targets of the cytochrome c oxidase subunit I gene were generated with a fluorescent dye-labelled primer and were hybridised onto a DNA microarray consisting of specific probes. After analysing the signal intensity of the specific probes, the unique patterns from the DNA microarray, consisting of 47 species-specific probes, were obtained to identify 23 aphid species. To confirm the accuracy of the developed DNA microarray, ten individual blind samples were used in blind trials, and the identifications were completely consistent with the sequencing data of all individual blind samples.

CONCLUSION

A microarray has been developed to distinguish aphid species. DNA microarray technology provides a rapid, easy, cost-effective and accurate method for identifying aphid species for pest control management.

Use of antimicrobial agents in aquaculture

The aquaculture industry has grown dramatically, and plays an important role in the world's food supply chain. Antimicrobial resistance in bacteria associated with food animals receives much attention, and drug use in aquaculture is also an important issue. There are many differences between aquatic and terrestrial management systems, such as the methods used for administration of drugs. Unique problems are related to the application of drugs in aquatic environments. Residual drugs in fish products can affect people who consume them, and antimicrobials released into aquatic environments can select for resistant bacteria. Moreover, these antimicrobial-resistant bacteria, or their resistance genes, can be transferred to humans. To decrease the risks associated with the use of antimicrobials, various regulations have been developed. In addition, it is necessary to prevent bacterial diseases in aquatic animals by vaccination, to improve culture systems, and to monitor the amount of antimicrobial drugs used and the prevalence of antimicrobial-resistant bacteria.