YongJu Ahn - Academia.edu (original) (raw)

Papers by YongJu Ahn

Research paper thumbnail of Epigenome-wide Association Study for Tic Disorders in Children: A Preliminary Study in Korean Population

Objective: Tic disorders can affect the quality of life in both childhood and adolescence. Many f... more Objective: Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are involved in the etiology of tic disorders, and the genetic and epigenetic factors of tic disorders are considered complex and heterogeneous. Methods: In this study, the differentially methylated regions (DMRs) between normal controls (n = 24; aged 6−15; 7 females) and patients with tic disorders (n = 16; aged 6−15; 5 females) were analyzed. We performed an epigenome-wide association study of tic disorders in Korean children. The tics were assessed using Yale Global Tic Severity Scale. The DNA methylation data consisted of 726,945 cytosine phosphate guanine (CpG) sites, assessed using the Illumina Infinium MethylationEPIC (850k) BeadChip. The DNA methylation data of the 40 participants were retrieved, and DMRs between the four groups based on sex and tic disorder were identified. From 28 male and 16 female samples, 37 and 38 DMRs were identified, respectively. We analyzed the enriched terms and visualized the network, heatmap, and upset plot. Results: In male, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed hypomethylated patterns in the ligand, receptor, and second signal transductors of the PI3K-Akt and MAPK signaling pathway (most cells were indicated as green color), and in female, the opposite patterns were revealed (most cells were indicated as red color). Five mental disorder-related enriched terms were identified in the network analysis. Conclusion: Here, we provide insights into the epigenetic mechanisms of tic disorders. Abnormal DNA methylation patterns are associated with mental disorder-related symptoms.

Research paper thumbnail of Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature

Young-Do nam 1,5* the gut microbiome is related to various host health conditions through metabol... more Young-Do nam 1,5* the gut microbiome is related to various host health conditions through metabolites produced by microbiota. Investigating their relationships involves association analysis of the population-level microbiome and metabolome data, which requires the appropriate collection, handling, and storage of specimens. Simplification of the specimen handling processes will facilitate such investigations. As a pilot study for population-level studies, we collected the fecal samples from three volunteers and tested whether a single sample collection procedure, particularly using OMNIgene-GUT, can be used to reliably obtain both microbiome and metabolome data. We collected fecal samples from three young and healthy Korean adults, stored them at room temperature with and without OMNIgene-GUT solution up to three weeks, and analyzed their microbiome and metabolite profiles. We found that the microbiome profiles were stably maintained in OMNIgene-GUT solution for 21 days, and the abundance relationships among metabolites were well preserved, although their absolute abundances slightly varied over time. Our results show that a single sampling procedure suffices to obtain a fecal sample for collecting gut microbiome and gut metabolome data of an individual. We expect that the health effects of gut microbiome via fecal metabolites can be further understood by increasing the sampling size to the population level.

Research paper thumbnail of The opposite patterns of DNA methylation between female and male children from tic disorders by a case-control study

Research Square (Research Square), Oct 31, 2022

Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are ... more Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are involved in the etiology of tic disorders, and the genetic and epigenetic factors of tic disorders are considered complex and heterogeneous. In this study, the differentially methylated regions (DMRs) between normal controls (n = 24; aged 6-15; 7 females) and patients with tic disorders (n = 16; aged 6-15; 5 females) were analyzed. We performed an epigenome-wide association study (EWAS) of tic disorders in Korean children. The severity of the tics was measured using a self-report version of the YGTSS. The DNA methylation data consisted of 726,945 CpG sites, assessed using the Illumina In nium MethylationEPIC (850k) BeadChip. The DNA methylation data of the 40 participants were retrieved, and DMRs between the four groups based on sex and tic disorder were identi ed. From 28 male and 16 female samples, 37 and 38 DMRs were identi ed, respectively. We analyzed the enriched terms and visualized the network, heatmap, and upset plot. In male, KEGG enrichment analysis revealed hypomethylated patterns in the ligand, receptor, and second signal transductors of the MAPK, Ras, Rap1, and PI3K-Akt signaling pathway, and in female, the opposite patterns were revealed. Five mental disorder-related enriched terms were identi ed in the network analysis. Here, we provide insights into the epigenetic mechanisms of tic disorders. Abnormal DNA methylation patterns are associated with mental disorder-related symptoms.

Research paper thumbnail of A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data

Microorganisms, Jan 30, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Research paper thumbnail of Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans

Journal of Oral Microbiology

Research paper thumbnail of A Real-Time Detection Device for the Rapid Quantification of Skin Casual Sebum Using the Oil Red O Staining Method

Sensors

The human skin sebum suggests that it (along with other epidermal surface lipids) plays a role in... more The human skin sebum suggests that it (along with other epidermal surface lipids) plays a role in skin barrier formation, the moderation of cutaneous inflammation, and antimicrobial defense. Various methods have been developed for collecting and measuring skin sebum. We tested methods of detection using “color intensity”, by staining the skin casual sebum. This process was conducted in three steps; first, the selection of materials for sebum collection; second, staining the collected sebum; third, the development of a device that can measure the level of stained sebum. A plastic film was used to effectively collect sebum that increased with the replacement time of the sebum. In addition, the collected sebum was stained with Oil Red O (ORO) and checked with RGB; as a result, the R2 value was higher than 0.9. It was also confirmed that the correlation value was higher than 0.9 in the comparison result with Sebumeter®, which is a common standard technology. Finally, it was confirmed th...

Research paper thumbnail of Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans

Journal of Oral Microbiology, Mar 3, 2023

Research paper thumbnail of The Effects of Household Economic Variables and Work Satisfaction on Marital Satisfaction of Working Married Women

Research paper thumbnail of Evaluation of an effective detection and quantification method for particular microorganisms by comparing NGS-based metagenome profiling data

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to ... more Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been activated, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) are still of considerable technique in detecting and quantifying bacteria associated with the human mouth, nasal cavity, and pharynx due to analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis of identifying for five bacterial genera proportions (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primer, targeting the particular gene of eac...

Research paper thumbnail of Author Correction: Association between the relative abundance of gastric microbiota and the risk of gastric cancer: a case-control study

Research paper thumbnail of Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study

Scientific Reports

The gut microbiome is related to various host health conditions through metabolites produced by m... more The gut microbiome is related to various host health conditions through metabolites produced by microbiota. Investigating their relationships involves association analysis of the population-level microbiome and metabolome data, which requires the appropriate collection, handling, and storage of specimens. Simplification of the specimen handling processes will facilitate such investigations. As a pilot study for population-level studies, we collected the fecal samples from three volunteers and tested whether a single sample collection procedure, particularly using OMNIgene-GUT, can be used to reliably obtain both microbiome and metabolome data. We collected fecal samples from three young and healthy Korean adults, stored them at room temperature with and without OMNIgene-GUT solution up to three weeks, and analyzed their microbiome and metabolite profiles. We found that the microbiome profiles were stably maintained in OMNIgene-GUT solution for 21 days, and the abundance relationship...

Research paper thumbnail of Association between the relative abundance of gastric microbiota and the risk of gastric cancer: a case-control study

Scientific Reports

The human gut hosts a diverse community of bacteria referred to as the gut microbiome. We investi... more The human gut hosts a diverse community of bacteria referred to as the gut microbiome. We investigated the association between the relative abundance of gastric microbiota and gastric cancer (GC) risk in a Korean population. The study participants included 268 GC patients and 288 controls. DNA was extracted from gastric biopsies, and 16S rRNA gene analysis was performed. Unconditional logistic regression models were used to observe the associations. Of the participants, those who had the highest level (highest tertile) of relative Helicobacter pylori and Propionibacterium acnes abundances showed a significantly higher risk for GC after adjusting for potential confounding variables (odds ratio (OR) = 1.86, 95% confidence interval (CI) = 1.17–2.97, p for trend = 0.017 and OR = 4.77, 95% CI = 2.94–7.74, p for trend <0.001, respectively). Subjects who carried Prevotella copri had a significantly higher risk of GC than noncarriers (OR = 2.54, 95% CI = 1.42–4.55, p for trend = 0.002). ...

Research paper thumbnail of A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis

Background: Accurate classification into genotypes is critical in understanding evolution of dive... more Background: Accurate classification into genotypes is critical in understanding evolution of divergent viruses. Here we report a new approach, MuLDAS, which classifies a query sequence based on the statistical genotype models learned from the known sequences. Thus, MuLDAS utilizes full spectra of well characterized sequences as references, typically of an order of hundreds, in order to estimate the significance of each genotype assignment. Results: MuLDAS starts by aligning the query sequence to the reference multiple sequence alignment and calculating the subsequent distance matrix among the sequences. They are then mapped to a principal coordinate space by multidimensional scaling, and the coordinates of the reference sequences are used as features in developing linear discriminant models that partition the space by genotype. The genotype of the query is then given as the maximum a posteriori estimate. MuLDAS tests the model confidence by leave-one-out cross-validation and also provides some heuristics for the detection of 'outlier' sequences that fall far outside or in-between genotype clusters. We have tested our method by classifying HIV-1 and HCV nucleotide sequences downloaded from NCBI GenBank, achieving the overall concordance rates of 99.3% and 96.6%, respectively, with the benchmark test dataset retrieved from the respective databases of Los Alamos National Laboratory. Conclusions: The highly accurate genotype assignment coupled with several measures for evaluating the results makes MuLDAS useful in analyzing the sequences of rapidly evolving viruses such as HIV-1 and HCV. A web-based genotype prediction server is available at http://www.muldas.org/MuLDAS/.

Research paper thumbnail of GTVseq: A Web-based Genotyping Tool for Viral Sequences

Genomics & …, 2008

Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on... more Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on the viral genome sequences including HIV-1, HIV-2, HBV, HCV, HTLV-1, HTLV-2, poliovirus, enterovirus, flavivirus, Hantavirus, and rotavirus. GTVseq produces alternative and additive genotype information for the query viral sequences based on two different, but related, scoring methods. The genotype information produced is reported in a graphical manner for the reference genotype matches and each graphical output is linked to the detailed sequence alignments between the query and the matched reference sequences. GTVseq also reports the potential 'repeats' and/or 'recombination' sequence region in a separated window. GTVseq does not replace completely other well-known genotyping tools such as NCBI's virus sequence genotyping tool (http://www.ncbi. nlm.nih.gov/projects/genotyping/formpage.cgi), but provides additional information useful in the confirmation or for further investigation of the genotype(s) for the newly isolated viral sequences.

Research paper thumbnail of Epigenome-wide Association Study for Tic Disorders in Children: A Preliminary Study in Korean Population

Objective: Tic disorders can affect the quality of life in both childhood and adolescence. Many f... more Objective: Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are involved in the etiology of tic disorders, and the genetic and epigenetic factors of tic disorders are considered complex and heterogeneous. Methods: In this study, the differentially methylated regions (DMRs) between normal controls (n = 24; aged 6−15; 7 females) and patients with tic disorders (n = 16; aged 6−15; 5 females) were analyzed. We performed an epigenome-wide association study of tic disorders in Korean children. The tics were assessed using Yale Global Tic Severity Scale. The DNA methylation data consisted of 726,945 cytosine phosphate guanine (CpG) sites, assessed using the Illumina Infinium MethylationEPIC (850k) BeadChip. The DNA methylation data of the 40 participants were retrieved, and DMRs between the four groups based on sex and tic disorder were identified. From 28 male and 16 female samples, 37 and 38 DMRs were identified, respectively. We analyzed the enriched terms and visualized the network, heatmap, and upset plot. Results: In male, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed hypomethylated patterns in the ligand, receptor, and second signal transductors of the PI3K-Akt and MAPK signaling pathway (most cells were indicated as green color), and in female, the opposite patterns were revealed (most cells were indicated as red color). Five mental disorder-related enriched terms were identified in the network analysis. Conclusion: Here, we provide insights into the epigenetic mechanisms of tic disorders. Abnormal DNA methylation patterns are associated with mental disorder-related symptoms.

Research paper thumbnail of Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature

Young-Do nam 1,5* the gut microbiome is related to various host health conditions through metabol... more Young-Do nam 1,5* the gut microbiome is related to various host health conditions through metabolites produced by microbiota. Investigating their relationships involves association analysis of the population-level microbiome and metabolome data, which requires the appropriate collection, handling, and storage of specimens. Simplification of the specimen handling processes will facilitate such investigations. As a pilot study for population-level studies, we collected the fecal samples from three volunteers and tested whether a single sample collection procedure, particularly using OMNIgene-GUT, can be used to reliably obtain both microbiome and metabolome data. We collected fecal samples from three young and healthy Korean adults, stored them at room temperature with and without OMNIgene-GUT solution up to three weeks, and analyzed their microbiome and metabolite profiles. We found that the microbiome profiles were stably maintained in OMNIgene-GUT solution for 21 days, and the abundance relationships among metabolites were well preserved, although their absolute abundances slightly varied over time. Our results show that a single sampling procedure suffices to obtain a fecal sample for collecting gut microbiome and gut metabolome data of an individual. We expect that the health effects of gut microbiome via fecal metabolites can be further understood by increasing the sampling size to the population level.

Research paper thumbnail of The opposite patterns of DNA methylation between female and male children from tic disorders by a case-control study

Research Square (Research Square), Oct 31, 2022

Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are ... more Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are involved in the etiology of tic disorders, and the genetic and epigenetic factors of tic disorders are considered complex and heterogeneous. In this study, the differentially methylated regions (DMRs) between normal controls (n = 24; aged 6-15; 7 females) and patients with tic disorders (n = 16; aged 6-15; 5 females) were analyzed. We performed an epigenome-wide association study (EWAS) of tic disorders in Korean children. The severity of the tics was measured using a self-report version of the YGTSS. The DNA methylation data consisted of 726,945 CpG sites, assessed using the Illumina In nium MethylationEPIC (850k) BeadChip. The DNA methylation data of the 40 participants were retrieved, and DMRs between the four groups based on sex and tic disorder were identi ed. From 28 male and 16 female samples, 37 and 38 DMRs were identi ed, respectively. We analyzed the enriched terms and visualized the network, heatmap, and upset plot. In male, KEGG enrichment analysis revealed hypomethylated patterns in the ligand, receptor, and second signal transductors of the MAPK, Ras, Rap1, and PI3K-Akt signaling pathway, and in female, the opposite patterns were revealed. Five mental disorder-related enriched terms were identi ed in the network analysis. Here, we provide insights into the epigenetic mechanisms of tic disorders. Abnormal DNA methylation patterns are associated with mental disorder-related symptoms.

Research paper thumbnail of A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data

Microorganisms, Jan 30, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Research paper thumbnail of Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans

Journal of Oral Microbiology

Research paper thumbnail of A Real-Time Detection Device for the Rapid Quantification of Skin Casual Sebum Using the Oil Red O Staining Method

Sensors

The human skin sebum suggests that it (along with other epidermal surface lipids) plays a role in... more The human skin sebum suggests that it (along with other epidermal surface lipids) plays a role in skin barrier formation, the moderation of cutaneous inflammation, and antimicrobial defense. Various methods have been developed for collecting and measuring skin sebum. We tested methods of detection using “color intensity”, by staining the skin casual sebum. This process was conducted in three steps; first, the selection of materials for sebum collection; second, staining the collected sebum; third, the development of a device that can measure the level of stained sebum. A plastic film was used to effectively collect sebum that increased with the replacement time of the sebum. In addition, the collected sebum was stained with Oil Red O (ORO) and checked with RGB; as a result, the R2 value was higher than 0.9. It was also confirmed that the correlation value was higher than 0.9 in the comparison result with Sebumeter®, which is a common standard technology. Finally, it was confirmed th...

Research paper thumbnail of Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans

Journal of Oral Microbiology, Mar 3, 2023

Research paper thumbnail of The Effects of Household Economic Variables and Work Satisfaction on Marital Satisfaction of Working Married Women

Research paper thumbnail of Evaluation of an effective detection and quantification method for particular microorganisms by comparing NGS-based metagenome profiling data

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to ... more Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been activated, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) are still of considerable technique in detecting and quantifying bacteria associated with the human mouth, nasal cavity, and pharynx due to analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis of identifying for five bacterial genera proportions (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primer, targeting the particular gene of eac...

Research paper thumbnail of Author Correction: Association between the relative abundance of gastric microbiota and the risk of gastric cancer: a case-control study

Research paper thumbnail of Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study

Scientific Reports

The gut microbiome is related to various host health conditions through metabolites produced by m... more The gut microbiome is related to various host health conditions through metabolites produced by microbiota. Investigating their relationships involves association analysis of the population-level microbiome and metabolome data, which requires the appropriate collection, handling, and storage of specimens. Simplification of the specimen handling processes will facilitate such investigations. As a pilot study for population-level studies, we collected the fecal samples from three volunteers and tested whether a single sample collection procedure, particularly using OMNIgene-GUT, can be used to reliably obtain both microbiome and metabolome data. We collected fecal samples from three young and healthy Korean adults, stored them at room temperature with and without OMNIgene-GUT solution up to three weeks, and analyzed their microbiome and metabolite profiles. We found that the microbiome profiles were stably maintained in OMNIgene-GUT solution for 21 days, and the abundance relationship...

Research paper thumbnail of Association between the relative abundance of gastric microbiota and the risk of gastric cancer: a case-control study

Scientific Reports

The human gut hosts a diverse community of bacteria referred to as the gut microbiome. We investi... more The human gut hosts a diverse community of bacteria referred to as the gut microbiome. We investigated the association between the relative abundance of gastric microbiota and gastric cancer (GC) risk in a Korean population. The study participants included 268 GC patients and 288 controls. DNA was extracted from gastric biopsies, and 16S rRNA gene analysis was performed. Unconditional logistic regression models were used to observe the associations. Of the participants, those who had the highest level (highest tertile) of relative Helicobacter pylori and Propionibacterium acnes abundances showed a significantly higher risk for GC after adjusting for potential confounding variables (odds ratio (OR) = 1.86, 95% confidence interval (CI) = 1.17–2.97, p for trend = 0.017 and OR = 4.77, 95% CI = 2.94–7.74, p for trend <0.001, respectively). Subjects who carried Prevotella copri had a significantly higher risk of GC than noncarriers (OR = 2.54, 95% CI = 1.42–4.55, p for trend = 0.002). ...

Research paper thumbnail of A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis

Background: Accurate classification into genotypes is critical in understanding evolution of dive... more Background: Accurate classification into genotypes is critical in understanding evolution of divergent viruses. Here we report a new approach, MuLDAS, which classifies a query sequence based on the statistical genotype models learned from the known sequences. Thus, MuLDAS utilizes full spectra of well characterized sequences as references, typically of an order of hundreds, in order to estimate the significance of each genotype assignment. Results: MuLDAS starts by aligning the query sequence to the reference multiple sequence alignment and calculating the subsequent distance matrix among the sequences. They are then mapped to a principal coordinate space by multidimensional scaling, and the coordinates of the reference sequences are used as features in developing linear discriminant models that partition the space by genotype. The genotype of the query is then given as the maximum a posteriori estimate. MuLDAS tests the model confidence by leave-one-out cross-validation and also provides some heuristics for the detection of 'outlier' sequences that fall far outside or in-between genotype clusters. We have tested our method by classifying HIV-1 and HCV nucleotide sequences downloaded from NCBI GenBank, achieving the overall concordance rates of 99.3% and 96.6%, respectively, with the benchmark test dataset retrieved from the respective databases of Los Alamos National Laboratory. Conclusions: The highly accurate genotype assignment coupled with several measures for evaluating the results makes MuLDAS useful in analyzing the sequences of rapidly evolving viruses such as HIV-1 and HCV. A web-based genotype prediction server is available at http://www.muldas.org/MuLDAS/.

Research paper thumbnail of GTVseq: A Web-based Genotyping Tool for Viral Sequences

Genomics & …, 2008

Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on... more Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on the viral genome sequences including HIV-1, HIV-2, HBV, HCV, HTLV-1, HTLV-2, poliovirus, enterovirus, flavivirus, Hantavirus, and rotavirus. GTVseq produces alternative and additive genotype information for the query viral sequences based on two different, but related, scoring methods. The genotype information produced is reported in a graphical manner for the reference genotype matches and each graphical output is linked to the detailed sequence alignments between the query and the matched reference sequences. GTVseq also reports the potential 'repeats' and/or 'recombination' sequence region in a separated window. GTVseq does not replace completely other well-known genotyping tools such as NCBI's virus sequence genotyping tool (http://www.ncbi. nlm.nih.gov/projects/genotyping/formpage.cgi), but provides additional information useful in the confirmation or for further investigation of the genotype(s) for the newly isolated viral sequences.