• Journal of the Institute of Electronics Engineers of Korea CI
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• v.49 no.2
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• pp.123-133
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• 2012

This paper discuss about DNA watermarking using coding DNA sequence (CDS) for the authentication, the privacy protection, or the prevention of illegal copy and mutation of DNA sequence and propose a DNA watermarking scheme with the mutation robustness and the animo acid preservation. The proposed scheme selects a number of codons at the regular singularity in coding regions for the embedding target and embeds the watermark for watermarked codons and original codons to be transcribed to the same amino acids. DNA base sequence is the string of 4 characters, {A,G,C,T} ({A,G,C,U} in RNA). We design the codon coding table suitable to watermarking signal processing and transform the codon sequence to integer numerical sequence by this table and re-transform this sequence to floating numerical sequence of circular angle. A codon consists of a consecutive of three bases and 64 codons are transcribed to one from 20 amino acids. We substitute the angle of selected codon to one among the angle range with the same animo acid, which is determined by the watermark bit and the angle difference of adjacent codons. From in silico experiment by using HEXA and ANG sequences, we verified that the proposed scheme is more robust to silent and missense mutations than the conventional scheme and preserve the amino acids of the watermarked codons.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2022.05a
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• pp.273-275
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• 2022

The use of drugs by pregnant women poses a potential risk to the fetus. Therefore, it is essential to classify drugs that pregnant women should prohibit. However, the fetal toxicity of most drugs has not been identified. This takes a lot of time and cost. In silico approaches, such as virtual screening, can identify compounds that may present a high risk to the fetus for a wide range of compounds at the low cost and time. We collected class information of each drug from the hazard classification lists for prescribing drugs in pregnancy by the government of Korea and Australia. Using the structural and chemical features of each drug, various machine learning models were constructed to predict fetal toxicity of drugs. For all models, the quantitative performance evaluation was performed. Based on the attention algorithm, important molecular substructures of compounds were identified in the process of predicting the fetal toxicity of the drug by the proposed model. From the results, we confirmed that drugs with a high risk of fetal toxicity can be predicted for a wide range of compounds by machine learning. This study can be used as a pre-screening tool for fetal toxicity predictions, as it provides key molecular substructures associated with the fetal toxicity of compounds.

• Journal of Life Science
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• v.29 no.2
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• pp.181-190
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• 2019

The purpose of this study was to acquire the active compounds of Anisi stellati fructus (ASF) and to analyze the genes and diseases it targets, focusing on its antibacterial effects using a system pharmacological analysis approach. Active compounds of ASF were obtained through the Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database and Analysis Platform. This contains the pharmacokinetic properties of active compounds and related drug-target-disease networks, which is a breakthrough in silico approach possible at the network level. Gene information of targets was gathered from the UnitProt Database, and gene ontology analysis was performed using the David 6.8 Gene Functional Classification Tool. A total of 201 target genes were collected, which corresponded to the nine screened active compounds, and 47 genes were found to act on biological processes related to antimicrobial activity. The representative active compounds involved in antibacterial action were luteolin, kaempferol, and quercetin. Among their targets, Chemokine ligand2, Interleukin-10, Interleukin-6, and Tumor Necrosis Factor were associated with more than three antimicrobial biological processes. This study has provided accurate evidence while saving time and effort to select future laboratory research materials. The data obtained has provided important data for infection prevention and treatment strategies.

• Journal of Microbiology and Biotechnology
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• v.33 no.7
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• pp.909-914
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• 2023

While searching for the bacteria which are responsible for degradation of pesticide in soybean field soil, a novel bacterial strain, designated 5-5^T, was isolated. The cells of the strain were Gram-staining-positive, aerobic and non-motile rods. Growth occurred at 10-42℃ (optimum, 30℃), pH 5.5-9.0 (optimum, pH 7.0-7.5), and 0-2% (w/v) NaCl (optimum, 1%). The predominant fatty acids were C_15:0 anteiso, C_17:0 anteiso, and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The predominant menaquinone was MK-9 (H₂). Diphosphatidylglycerol, glycolipids, phosphatidylinositol, and phosphatidylglycerol were the major polar lipids. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 5-5^T is a member of the genus Sinomonas and its closest relative is Sinomonas humi MUSC 117^T, sharing a genetic similarity of 98.4%. The draft genome of strain 5-5^T was 4,727,205 bp long with an N50 contig of 4,464,284 bp. Genomic DNA G+C content of strain 5-5^T was68.0 mol%. The average nucleotide identity (ANI) values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 87.0, and 84.3 % respectively. In silico DNA-DNA hybridization values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 32.5% and 27.9% respectively. Based on the ANI and in silico DNA-DNA hybridization analyses, the 5-5^T strain was considered as novel species belonging to the genus Sinomonas. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain 5-5^T represents a novel speciesof the genus Sinomonas, for which the name Sinomonas terrae sp. nov. is proposed. The type strain is 5-5^T (=KCTC 49650^T =NBRC 115790^T).

• Genomics & Informatics
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• v.8 no.2
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• pp.70-75
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• 2010

Asp66his, Asp54Lys, and Asp50Asn are mutations in connexin 26 that are observed in the clinic and give rise to autosomal dominant syndromes. They are the result of point mutations in the human gap junction ${\beta}-2$ gene. In order to investigate the structural mechanism of Bart-Pumphrey Syndrome, Keratitis-Ichthyosis-Deafness Syndrome, and Vohwinkel Syndrome, homology modeling was carried out. Asp66 has direct contact with Asn62 by two hydrogen bonds in the wild-type protein, and in Asp66His, the biggest change observed is a tremendous energy increase caused by hydrogen bond breakage to Asn62. Shifts in the side chain and new hydrogen bond formation are observed for Lys54 compared to the wild-type protein (Asn54) and result in closer contact to Val84. Asp50Asn causes a significant decrease in bond energy, and residual charge reversal repels the ion and metabolites and, hence, inhibits their transportation. Such perturbations are likely to be a factor contributing to abnormal functioning of ion channels, resulting cell death and disease.

• Journal of Microbiology and Biotechnology
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• v.21 no.2
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• pp.136-146
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• 2011

This study provides first-hand proteomic data on the survival strategy of Anabaena sp. PCC 7120 when subjected to long-term iron-starvation conditions. 2D-gel electrophoresis followed by MALDI-TOF/MS analysis of iron-deficient Anabaena revealed significant and reproducible alterations in ten proteins, of which six are associated with photosynthesis and respiration, three with the antioxidative defense system, and the last, hypothetical protein all1861, conceivably connected with iron homeostasis. Iron-starved Anabaena registered a reduction in growth, photosynthetic pigments, PSI, PSII, whole-chain electron transport, carbon and nitrogen fixation, and ATP and NADPH content. The kinetics of hypothetical protein all1861 expression, with no change in expression until day 3, maximum expression on the $7^{th}$ day, and a decline in expression from the $15^{th}$ day onward, coupled with in silico analysis, suggested its role in iron sequestration and homeostasis. Interestingly, the up-regulated FBP-aldolase, Mn/Fe-SOD, and all1861 all appear to assist the survival of Anabeana subjected to iron-starvation conditions. Furthermore, the $N_2$-fixation capabilities of the iron-starved Anabaena encourage us to recommend its application as a biofertilizer, particularly in iron-limited paddy soils.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.779-784
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• 2013

Leptospirosis is a worldwide zoonosis of global concern caused by Leptospira interrogans. The availability of ligand libraries has facilitated the search for novel drug targets using chemogenomics approaches, compared with the traditional method of drug discovery, which is time consuming and yields few leads with little intracellular information for guiding target selection. Recent subtractive genomics studies have revealed the putative drug targets in peptidoglycan biosynthesis pathways in Leptospira interrogans. Aligand library for the murD ligase enzyme in the peptidoglycan pathway has also been identified. Our approach in this research involves screening of the pre-existing ligand library of murD with related protein family members in the putative drug target assembly in the peptidoglycan biosynthesis pathway. A chemogenomics approach has been implemented here, which involves screening of known ligands of a protein family having analogous domain architecture for identification of leads for existing druggable protein family members. By means of this approach, one murC and one murF inhibitor were identified, providing a platform for developing an anti-leptospirosis drug targeting the peptidoglycan biosynthesis pathway. Given that the peptidoglycan biosynthesis pathway is exclusive to bacteria, the in silico identified mur ligase inhibitors are expected to be broad-spectrum Gram-negative inhibitors if synthesized and tested in in vitro and in vivo assays.

• Journal of Microbiology and Biotechnology
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• v.23 no.12
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• pp.1683-1690
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• 2013

The cyclic AMP receptor protein (CRP) homolog, GlxR, controls the expression of several genes involved in the regulation of diverse physiological processes in Corynebacterium glutamicum. In silico analysis has revealed the presence of glxR binding sites upstream of genes ptsG, adhA, and ald, encoding glucose-specific phosphotransferase system protein, alcohol dehydrogenase (ADH), and acetaldehyde dehydrogenase (ALDH), respectively. However, the involvement of the GlxR-cAMP complex on the expression of these genes has been explored only in vitro. In this study, the expressions of ptsG, adhA, and ald were analyzed in detail using an adenylate cyclase gene (cyaB) deletion mutant and glxR deletion mutant. The specific activities of ADH and ALDH were increased in both the mutants in glucose and glucose plus ethanol media, in contrast to the wild type. In accordance, the promoter activities of adhA and ald were derepressed in the cyaB mutant, indicating that glxR acts as a repressor of adhA. Similarly, both the mutants exhibited derepression of ptsG regardless of the carbon source. These results confirm the involvement of GlxR on the expression of important carbon metabolic genes; adhA, ald, and ptsG.

• Korean Journal of Metals and Materials
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• v.50 no.1
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• pp.45-51
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• 2012

Thermodynamics of carbon in manganese alloy melts is important in manufacturing low carbon ferromanganese and silico-manganese alloys. In order to predict the carbon solubility in liquid $Mn-Si-Fe-C_{sat}$ alloys as a function of melt composition and temperature, thermodynamic interactions among carbon, silicon and iron in carbon saturated liquid manganese should be known. In the present study, the effects of silicon and iron on the carbon solubility in Mn-Si, Mn-Fe and Mn-Si-Fe melts were measured in the temperature range from 1673 to 1773 K. The carbon solubility decreases significantly as silicon and iron contents increase in liquid manganese alloy. The interaction parameters among carbon, silicon and iron in carbon saturated liquid manganese were determined from the carbon solubility data and the Lupis' relation for the interaction coefficient at constant activity.

• Toxicological Research
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• v.32 no.3
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• pp.259-267
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• 2016

Animal testing was used traditionally in the cosmetics industry to confirm product safety, but has begun to be banned; alternative methods to replace animal experiments are either in development, or are being validated, worldwide. Research data related to test substances are critical for developing novel alternative tests. Moreover, safety information on cosmetic materials has neither been collected in a database nor shared among researchers. Therefore, it is imperative to build and share a database of safety information on toxicological mechanisms and pathways collected through in vivo, in vitro, and in silico methods. We developed the CAMSEC database (named after the research team; the Consortium of Alternative Methods for Safety Evaluation of Cosmetics) to fulfill this purpose. On the same website, our aim is to provide updates on current alternative research methods in Korea. The database will not be used directly to conduct safety evaluations, but researchers or regulatory individuals can use it to facilitate their work in formulating safety evaluations for cosmetic materials. We hope this database will help establish new alternative research methods to conduct efficient safety evaluations of cosmetic materials.