• Korean Journal of Clinical Laboratory Science
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• v.52 no.3
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• pp.229-236
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• 2020

Sixty-five molds isolated from clinical specimens were included in this study. All the isolates were molds that could be identified morphologically, strains that are difficult to identify because of morphological similarities, and strains that require species-level identification. PCR and direct sequencing were performed to target the internal transcribed spacer (ITS) region, the D1/D2 region, and the β-tubulin gene. Comparative sequence analysis using the GenBank database was performed using the basic local alignment search tool (BLAST) algorithm. The fungi identified morphologically to the genus level were 67%. Sequencing analysis was performed on 62 genera and species level of the 65 strains. Discrepancies were 14 (21.5%) of the 65 strains between the results of phenotypic and molecular identification. B. dermatitidis, T. marneffei, and G. argillacea were identified for the first time in Korea using the DNA sequencing method. Morphological identification is a very useful method in terms of the reporting time and costs in cases of frequently isolated and rapid growth, such as Aspergillus. When molecular methods are employed, the cost and clinical significance should be considered. On the other hand, the molecular identification of molds can provide fast and accurate results.

• Genomics & Informatics
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• v.6 no.1
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• pp.18-28
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency $\geq$ 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

• Journal of Animal Science and Technology
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• v.58 no.4
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• pp.14.1-14.9
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• 2016

Background: Peroxisome proliferator-activated receptor gamma (PPARG), CCAAT/enhancer binding protein alpha (CEBPA) and retinoid X receptor alpha (RXRA) are nuclear transcription factors that play important roles in regulation of adipogenesis and fat deposition. The objectives of this study were to characterise the variability of these three candidate genes in a mixed sample panel composed of several cattle breeds with different meat quality, validate single nucleotide polymorphisms (SNPs) in a local crossbred population (Angus - Hereford - Limousin) and evaluate their effects on meat quality traits (backfat thickness, intramuscular fat content and fatty acid composition), supporting the association tests with bioinformatic predictive studies. Results: Globally, nine SNPs were detected in the PPARG and CEBPA genes within our mixed panel, including a novel SNP in the latter. Three of these nine, along with seven other SNPs selected from the Single Nucleotide Polymorphism database (SNPdb), including SNPs in the RXRA gene, were validated in the crossbred population (N = 260). After validation, five of these SNPs were evaluated for genotype effects on fatty acid content and composition. Significant effects were observed on backfat thickness and different fatty acid contents (P < 0.05). Some of these SNPs caused slight differences in mRNA structure stability and/or putative binding sites for proteins. Conclusions: PPARG and CEBPA showed low to moderate variability in our sample panel. Variations in these genes, along with RXRA, may explain part of the genetic variation in fat content and composition. Our results may contribute to knowledge about genetic variation in meat quality traits in cattle and should be evaluated in larger independent populations.

• Journal of Society of Preventive Korean Medicine
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• v.21 no.2
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• pp.1-13
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• 2017

Objectives : This paper serves to explore current trends of systems biology in Traditional Chinese Medicine (TCM) and examine how it may influence the Traditional Korean medicine. Methods : Literature review method was collectively used to classify Introduction to systems biology, diagnosis and syndrome classification of systems biology in TCM perspective, physiotherapy including acupuncture, herbs and formula functions, TCM systems biology, and directions of academic development. Results : The term 'Systems biology' is coined as a combination of systems science and biology. It is a field of study that tries to understand living organism by establishing a theory based on an ideal model that analyzes and predicts the desired output with understanding of interrelationships and dynamics between variables. Systems biology has an integrated and multi-dimensional nature that observes the interaction among the elements constructing the network. The current state of systems biology in TCM is categorized into 4 parts: diagnosis and syndrome, physical therapy, herbs and formulas and academic development of TCM systems biology and its technology. Diagnosis and syndrome field is focusing on developing TCM into personalized medicine by clarifying Kidney yin deficiency patterns and metabolic differences among five patterns of diabetes and analyzing plasma metabolism and biomarkers of coronary heart disease patients. In the field of physical therapy such as acupuncture and moxibustion, researchers discovered the effect of stimulating acupoint ST40 on gene expression and the effects of acupuncture on treating functional dyspepsia and acute ischemic stroke. Herbs and formulas were analyzed with TCM network pharmacology. The therapeutic mechanisms of Si Wu Tang and its series formulas are explained by identifying potential active substances, targets and mechanism of action, including metabolic pathways of amino acid and fatty acid. For the academic development of TCM systems biology and its technology, it is necessary to integrate massive database, integrate pharmacokinetics and pharmacodynamics, as well as systems biology. It is also essential to establish a platform to maximize herbal treatment through accumulation of research data and diseases-specific, or drug-specific network combined with clinical experiences, and identify functions and roles of molecules in herbs and conduct animal-based studies within TCM frame. So far, few literature reviews exist for systems biology in traditional Korean medicine and they merely re-examine known efficacies of simple substances, herbs and formulas. For the future, it is necessary to identify specific mechanisms of working agents and targets to maximize the effects of traditional medicine modalities. Conclusions : Systems biology is widely accepted and studied in TCM and already advanced into a field known as 'TCM systems biology', which calls for the study of incorporating TCM and systems biology. It is time for traditional Korean medicine to acknowledge the importance of systems biology and present scientific basis of traditional medicine and establish the principles of diagnosis, prevention and treatment of diseases. By doing so, traditional Korean medicine would be innovated and further developed into a personalized medicine.

• Journal of Sasang Constitutional Medicine
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• v.22 no.1
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• pp.34-40
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• 2010

1. Objectives: Leptin is ob-gene originated hormone that is concerned with energy metabolism, obesity and asthma which features are supposed to related with Sasangin's 4 viscera physiological theory of Sasang constitutional medicine(SCM). This study aims to investigate whether serum leptin concentration is associated with Sasangin. 2. Methods: Two Way ANOVA analysis was used on the constitution and serum leptin concentration corresponding with BMI among 1054 cases drawn from the Constitutional Information Bank, which was a database with clinically confirmed constitution cases collected from 21 oriental medical institutes in Korea starting from November 2007 to May 2009. The measurement of serum leptin concentration is implemented through radioimmunoassay by request to SCL. 3. Results: Male subjects showed notable difference(p=0.033) in the comparison between constitution and serum leptin concentration corresponding to BMI levels. Tae-eumins showed the highest serum leptin concentration levels in the normal and overweight groups, followed by Soyangin and Soeumin. As the groups changed from overweight to obese, there was an interaction phenomenon in the order of serum leptin concentration levels(p=0.040). As a result, Soeumins showed the highest serum leptin concentration levels and Tae-eumins and Soyangins followed in place. Female subjects did not show statistically notable differences in comparison between constitution and serum leptin concentration corresponding to BMI levels(p=0.239). Serum leptin concentration levels among overweight and obese groups, resulted in the order of Soeumins, Tae-eumins, and Soyangins. But in the as groups changed from overweight to normal the order resulted in Tae-eumin, Soyangin, and Soeumin(p=0.660). 4. Conclusion: Due to a number of limitations in this study, the examination of the relation between constitution and leptin, a main hormone responsible for the digestion, appetite, and energy metabolism, resulted to be uncertain. But statistically notable differences were confirmed in male Tae-eumins with the consideration of BMI. Further examination of the relation between constitution and leptin is necessary through prospective studies with the restriction of confusion variables in the future.

• Journal of Ginseng Research
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• v.38 no.4
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• pp.278-288
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• 2014

Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

• Korean Journal of Microbiology
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• v.46 no.2
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• pp.213-218
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• 2010

Lactate dehydrogenases (LDHs) have been highly focused for long time, due to their important roles in biochemical and metabolic pathways of cells. On the basis of genome-wide searching results, three putative LDH genes from Bacillus cereus ATCC 14579 genome have been PCR-amplified, cloned, and well-expressed in E. coli. All three BcLDH isozymes are supposed to share highly conserved catalytic amino acid residues in common $NAD^+$-dependent LDHs. Meanwhile, BcLDH1 consisting of 314 amino acids shares 86 and 49% of identities with BcLDH2 and 3, respectively. Interestingly, only BcLDH1 showed the converting activities between L-lactate and pyruvate in the presence of $NAD^+$ coenzyme, while the other isozymes are likely to have almost no activity. As a result, it was revealed that BcLDH1 can be a typical $NAD^+$-dependent L-lactate-specific dehydrogenase.

• Journal of Life Science
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• v.25 no.3
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• pp.323-328
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• 2015

The study of microbial diversity and richness in soil samples from a volcanic island named Ulleungdo, located east of South Korea. The soil bacterial communities on the Ulleungdo were analyzed using pyrosequencing method based on 16S rRNA gene. There were 1,613 operational taxonomic units (OUT) form soil sample. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. Proteobacteria was the most dominant phylum with 48.28%, followed by acidobacteria (26.30%), actionbacteria (6.89%), Chloroflexi (4.58), Planctomycetes (4.56%), Nitrospirae (1.83%), Bacteroidetes (1.51%), Verrucomicrobia (1.48%), and Gemmatimonadetes (1.11%). α-proteobacteria was the most dominant class with 36.07% followed by Acidobacteria_c (10.65%), Solibacteres (10.64%), δ-proteobacteria (4.42%), γ-proteobacteria (4.29%), Planctomycetacia (4.16%), Actinobacteria_c (4.00%), Betaproteobacteria (3.50%), EU686603_c (2.97%), Ktedonobacteria (2.91%), Acidimicrobiia (1.32%), Verrucomicrobiae (1.27%), Gemmatimonadetes_c (1.11%), Sphingobacteria (1.09%), and GU444092_c (1.06%). Bradyrhizobiaceae was the most dominant family with 22.83% followed by Acidobacteriaceae (10.62%), EU445199_f (5.72%), Planctomycetaceae (4.03%), Solibacteraceae (3.63%), FM209092_f (3.58%), Steroidobacter_f (2.81%), EU686603_f (2.73%), Hyphomicrobiaceae (2.33%), Ktedonobacteraceae (1.75%), AF498716_f (1.46%), Rhizomicrobium_f (1.03%), and Mycobacteriaceae (1.01%). Differences in the diversity of bacterial communities have more to do with geography than the impact on environmental factors and also the type of vegetation seems to affect the diversity of bacterial communities.

• Korean Journal of Microbiology
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• v.41 no.4
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• pp.262-268
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• 2005

Intoxication of murine macrophages (RAW 264.7) with the anthrax lethal toxin (LeTx 100 ng/ml) results in profound alterations in the host cell gene expression. The role of LeTx in mediating these effects is unknown, largely due to the difficulty in identifying and assigning function to individual proteins. In this study, we have used two-dimensional polyacrylamide gel electrophoresis to analyze the protein profile of murine macrophages treated with the LeTx, and have coupled this to protein identification using MALDI-TOF mass spectrometry. Interpretation of the peptide mass fingerprint data has relied primarily on the ProFound database. Among the differentially expressed spots, cleaved mitogen-activated protein kinase kinase (Mek1) and glucose-6-phosphate dehydrogenase were increased in the LeTx treated macrophages. Mek1 acts as a negative element in the signal transduction pathway, and G6PD plays the role for the protection of the cells from the hyper-production of active oxygen. Our results suggest that this proteomic approach is a useful tool to study protein expression in intoxicated macrophages and will contribute to the identification of a putative substrate for LeTx.

• Journal of Oriental Neuropsychiatry
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• v.19 no.1
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• pp.125-146
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• 2008

Objectives : The purpose of this study is to suggest for the following experimental study of dementia by reviewing recent oriental medicine journals that have been published since 2000. Methods: We have investigated various types of studies in relation to dementia through 90 articles that have been published from 2000 to 2007 in recent oriental medicine journals were registered Korea research foundation. Results and Conclusions : 1. Since 2000, 88 articles in relation to dementia have been published and almost of them are herbal medicine-centered studies. Also they show a tendency to increase every year. The journal of oriental neuropsychiatry carries the highest number of studies in relation to dementia. 2. According to the experimental paper, there are 30 cases of using herb simplexes, 48 cases of herb-combined prescription, and 10 cases of other ways. Especially 7 cases of using herb-combined prescription relation to Sasang constitution are all for the Taeumin. 3. There are 85 cases of Animal and cellular experimental, 60 cases of using pathologic model induced cytotoxic activity, a case of using L-NAME, 3 cases of 192 saporin, 4 cases of ibotenic acid, 10 cases of focal cerebral ischemia, 3 cases of alcohol-administered, and one case of natural degradation. 4. Moms water maze, Radial arm maze Passive avoidance learning model were using for examining learning and memory of model animal 5. We propose that following studies of dementia are to he investigated of the applied method of using siRNA with tranceduced gene, sample preparation by water-soaking, oriental medical diagnosis, standardization of differentiating symptom and herb simplexes, building the database by classified prescriptions, and experiment model which are based on precise examining mechanism with cell line as like mouse H19-7 hippocampus, rat HT22 hippocampus, astrocyte, microglia, using the model of animals at APP, PS1, BACE, CT99/PS1, APOE4, Tau, APP/PSI/Tau