• Genomics & Informatics
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• v.3 no.3
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• pp.53-62
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• 2005

MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the 'tight' tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.

• Parasites, Hosts and Diseases
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• v.51 no.1
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• pp.1-8
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• 2013

Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.

• Journal of Ginseng Research
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• v.45 no.5
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• pp.599-609
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• 2021

Ginseng has long been considered as an herbal medicine. Recent data suggest that ginseng has antiinflammatory properties and can improve learning- and memory-related function in the central nervous system (CNS) following the development of CNS neuroinflammatory diseases such as Alzheimer's disease, cerebral ischemia, and other neurological disorders. In this review, we discuss the role of ginseng in the neurovascular unit, which is composed of endothelial cells surrounded by astrocytes, pericytes, microglia, neural stem cells, oligodendrocytes, and neurons, especially their blood-brain barrier maintenance, anti-inflammatory effects and regenerative functions. In addition, cell-cell communication enhanced by ginseng may be attributed to regeneration via induction of neurogenesis and angiogenesis in CNS diseases. Thus, ginseng may have therapeutic potential to exert cognitive improvement in neuroinflammatory diseases such as stroke, traumatic brain injury, multiple sclerosis, Parkinson's disease, and Alzheimer's disease.

• Journal of Species Research
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• v.10 no.1
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• pp.46-56
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• 2021

Diatoms have been used in examining water quality and environmental change in freshwater systems. Here, we analyzed molecular profiling of seasonal diatoms in the Han River, Korea, using the hypervariable region of 18S V1-V3 rRNA and pyrosequencing. Physicochemical data, such as temperature, DO, pH, and nutrients showed the typical seasonal pattern in a temperate region. In addition, cell counts and chlorophyll-a, were recorded at high levels in spring compared to other seasons, due to the diatom bloom. Metagenomic analysis showed a seasonal variation in the phytoplankton community composition, with diatoms as the most frequently detected in spring (83.8%) and winter (69.7%). Overall, diatom genera such as Stephanodiscus, Navicula, Cyclotella, and Discostella were the most frequent in the samples. However, a large number of unknown Thalassiosirales diatoms were found in spring (35.5%) and winter (36.3%). Our molecular profiling revealed a high number of diatom taxa compared to morphological observation. This is the first study of diatoms in the Han River using molecular approaches, providing a valuable reference for future study on diatoms-basis environmental molecular monitoring and ecology.

• BMB Reports
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• v.55 no.12
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• pp.639-644
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• 2022

Serine-arginine-rich splicing factors (SRSFs) are members of RNA processing proteins in the serine-arginine-rich (SR) family that could regulate the alternative splicing of the human immunodeficiency virus-1 (HIV-1). Whether SRSF9 has any effect on HIV-1 regulation requires elucidation. Here, we report for the first time the effects and mechanisms of SRSF9 on HIV-1 regulation. The overexpression of SRSF9 inhibits viral production and infectivity in both HEK293T and MT-4 cells. Deletion analysis of SRSF9 determined that the RNA regulation motif domain of SRSF9 is important for anti-HIV-1 effects. Furthermore, overexpression of SRSF9 increases multiple spliced forms of viral mRNA, such as Vpr mRNA. These data suggest that SRSF9 overexpression inhibits HIV-1 production by inducing the imbalanced HIV-1 mRNA splicing that could be exploited further for a novel HIV-1 therapeutic molecule.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2007.11a
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• pp.19-27
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• 2007

An important potential of metabolomics-based approach is the possibility to develop fingerprints of diseases or cellular responses to classes of compounds with known common biological effect. Such fingerprints have the potential to allow classification of disease states or compounds, to provide mechanistic information on cellular perturbations and pathways and to identify biomarkers specific for disease severity and drug efficacy. Metabolic profiles of biological fluids contain a vast array of endogenous metabolites. Changes in those profiles resulting from perturbations of the system can be observed using analytical techniques, such as NMR and MS. $^1H$ NMR was used to generate a molecular fingerprint of serum or urinary sample, and then pattern recognition technique was applied to identity molecular signatures associated with the specific diseases or drug efficiency. Several metabolites that differentiate disease samples from the control were thoroughly characterized by NMR spectroscopy. We investigated the metabolic changes in human normal and clinical samples using $^1H$ NMR. Spectral data were applied to targeted profiling and spectral binning method, and then multivariate statistical data analysis (MVDA) was used to examine in detail the modulation of small molecule candidate biomarkers. We show that targeted profiling produces robust models, generates accurate metabolite concentration data, and provides data that can be used to help understand metabolic differences between healthy and disease population. Such metabolic signatures could provide diagnostic markers for a disease state or biomarkers for drug response phenotypes.

• The Bulletin of The Korean Astronomical Society
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• v.42 no.2
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• pp.79.2-79.2
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• 2017

To dynamically and chemically understand how filaments, dense cores, and stars form under different environments, we are conducting a systematic mapping survey of nearby molecular clouds using the TRAO 14 m telescope with high ($N_2H^+$ 1-0, $HCO^+$ 1-0, SO 32-21, and $NH_2D$ v=1-0) and low ($^{13}CO$ 1-0, $C^{18}O$ 1-0) density tracers. The goals of this survey are to obtain the velocity distribution of low dense filaments and their dense cores for the study of their origin of the formation, to understand whether the dense cores form from any radial accretion or inward motions toward dense cores from their surrounding filaments, and to study the chemical differentiation of the filaments and the dense cores. Until the 2017A season, the real OTF observation time is ~760 hours. We have almost completed mapping observation with four molecular lines ($^{13}CO$ 1-0, $C^{18}O$ 1-0, $N_2H^+$ 1-0, and $HCO^+$ 1-0) on the six regions of molecular clouds (L1251 of Cepheus, Perseus West, Polaris South, BISTRO region of Serpens, California, and Orion B). The cube data for $^3CO$ and $C^{18}O$ lines were obtained for a total of 6 targets, 57 tiles, 676 maps, and $7.1deg^2$. And $N_2H^+$ and $HCO^+$ data were added for $2.2deg^2$ of dense regions. All OTF data were regridded to a cell size of 44 by 44 arcseconds. The $^{13}CO$ and $C^{18}O$ data show the RMS noise level of about (0.1-0.2) K and $N_2H^+$ and $HCO^+$ data show about (0.07-0.2) K at the velocity resolution of 0.06 km/s. Additional observations will be made on some regions that have not reached the noise level for analysis. To identify filaments, we are using and testing programs (DisPerSE, Dendrogram, FIVE) and visual inspection for 3D image of cube data. A basic analysis of the physical and chemical properties of each filament is underway.

• The Bulletin of The Korean Astronomical Society
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• v.42 no.1
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• pp.32.1-32.1
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• 2017

To dynamically and chemically understand how filaments, dense cores, and stars form under different environments, we are conducting a systematic mapping survey of nearby molecular clouds using the TRAO 14 m telescope with high ($N_2H^+$ 1-0, $HCO^+$ 1-0, SO 32-21, and $NH_2D$ v=1-0) and low ($^{13}CO$ 1-0, $C^{18}O$ 1-0) density tracers. The goals of this survey are to obtain the velocity distribution of low dense filaments and their dense cores for the study of their origin of the formation, to understand whether the dense cores form from any radial accretion or inward motions toward dense cores from their surrounding filaments, and to study the chemical differentiation of the filaments and the dense cores. Until Feb. 2017, the real OTF observation time is 460 hours. We have almost completed mapping observation with four molecular lines ($^{13}CO$ 1-0, $C^{18}O$ 1-0, $N_2H^+$ 1-0, and $HCO^+$ 1-0) on the five regions of molecular clouds (L1251 of Cepheus, Perseus west, Polaris south, BISTRO region of Serpense, California, and Orion B). The maps of a total area of $7.38deg^2$ for both $^{13}CO$ and $C^{18}O$ lines and $2.19deg^2$ for both $N_2H^+$ and $HCO^+$ lines were obtained. All OTF data were regridded to a cell size of 22 by 22 arcseconds. The $^{13}CO$ and $C^{18}O$ data show the RMS noise level of about 0.22 K and $N_2H^+$ and $HCO^+$ data show about 0.14 K at the velocity resolution of 0.06 km/s. Additional observations will be made on some regions that have not reached the noise level for analysis. We are refining the process for a massive amount of data and the data reduction and analysis are underway. This presentation introduces the overall progress from observations to data processing and the initial analysis results to date.

• Molecules and Cells
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• v.20 no.1
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• pp.151-156
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• 2005

The phylogeny and geography of the medaka (Oryzias latipes) populations of Korea were investigated by analyzing sequence data for the mitochondrial control region. From the 41 haplotypes including 25 Korean haplotypes detected in 64 Korean specimens and data for the Japanese and Chinese populations, phylogenetic and nested clade analyses were executed to examine the phylogeny of haplogroups and the relation of the genetic architecture of the haplotypes to the historical geography of the Korean medaka fish. The analyses suggest that there are two very distinct lineages of Korean medaka, and that these result from reproductive isolation mechanisms due to geographic barriers. The southeastern lineage has experienced recent range expansion to the western region. The northwestern lineage, sister to Chinese populations, showed evidence of internal range expansion with shared haplotypes.

• Journal of The Korean Astronomical Society
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• v.35 no.4
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• pp.187-196
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• 2002

A spectral line survey is performed from 159.7 to 164.7 GHz toward Orion-KL, as an extension of our previous line survey from 138.3 to 150.7 GHz with the same 14 m radio telescope of Taeduk Radio Astronomy Observatory. Typical system temperatures were 260 - 1000 K to achieve a sensitivity of about 0.02 - 0.04 K in TA unit. A total of 63 line spectra are detected in this survey. Among them, 54 lines lines are found to be the first detections towards an astronomical source and only 9 spectral lines have been previously identified from other observations. Forty-eight of 54 lines are believed to be from the known transitions of the known molecules, while 6 lines are 'unidentified'. All detected lines are found to be from a total of 10 molecular species and their isotopic variants. The molecular species with most numerous detected transitions are $HCOOCH_3$ (22), followed by $CH_3OCH_3$ (7), $C_2H_5CN$ (7), and $SO_2$ (6). The LTE rotation diagram analysis using all homogeneous data with those from previous survey gives more reliable determination of physical quantities. The derived values of the rotation temperatures and column densities for $HCOOCH_3$, $CH_3OCH_3$, and $SO_2$ are are 75 $\~$ 197 K and $1.5 {\~}18 {\times} 10^{15}\;cm^{-2}$, respectively.