Complete genome sequence and comparative analysis of Streptomyces seoulensis, a pioneer strain of nickel superoxide dismutase

Jihoon Shin,Shinae Park,Jung‑Shin Lee,Eun‑Jin Lee,Hong‑Duk Youn 한국유전학회 2020 Genes & Genomics Vol.42 No.3

Background Streptomyces seoulensis has contributed to the discovery and initiation of extensive research into nickel superoxide dismutase (NiSOD), a unique type of superoxide dismutase found in actinomycetes. Still so far, there is no information about whole genome sequence of this strain. Objective To investigate complete genome sequence and perform bioinformatic analyses for genomic functions related with nickel-associated genes. Methods DNA was extracted using the Wizard Genomic DNA Purification Kit then sequenced using a Pacific Biosciences SMRT cell 8Pac V3 DNA Polymerase Binding Kit P6 with the PacBiov2 RSII platform. We assembled the PacBio longreads with the HGAP3 pipeline. Results We obtained complete genome sequence of S. seoulensis, which comprises a 6,339,363 bp linear chromosome. While analyzing the genome to annotate the genomic function, we discovered the nickel-associated genes. We observed that the sodN gene encoding for NiSOD is located adjacent to the sodX gene, which encodes for the nickel-type superoxide dismutase maturation protease. In addition, several nickel-associated genes and gene clusters-nickel-responsive regulator, nickel uptake transporter, nickel–iron [NiFe]-hydrogenase and other putative genes were also detected. Strain specific genes were discovered through a comparative analysis of S. coelicolor and S. griseus. Further bioinformatic analyses revealed that this strain encodes at least 22 putative biosynthetic gene clusters, thereby implying that S. seoulensis has the potential to produce novel bioactive compounds. Conclusion We annotated the genome and determined nickel-associated genes and gene clusters and discovered biosynthetic gene clusters for secondary metabolites implying that S. seoulensis produces novel types of bioactive compounds.

Keyword-based mobile semantic search using mobile ontology

Shin, Sangjin,Ko, Jihoon,Eom, Sungkwang,Song, Minjae,Shin, Dong-Hoon,Lee, Kyong-Ho SAGE Publications 2015 JOURNAL OF INFORMATION SCIENCE Vol.41 No.2

<P>A large volume of mobile data is being generated and shared among mobile devices such as smartphones. Most of the mobile platforms provide a user with a keyword-based full text search (FTS) in order to search for mobile data. However, FTS only returns the data corresponding to the keywords given by users as results without considering a user’s query intention. To overcome this limitation, we propose a semantically enhanced keyword-based search method. Although there are various semantic search techniques, it is hard to apply existing methods to mobile devices just as they are. This is caused by the characteristics of mobile devices such as isolated database structures and limited computing resources. To enable semantic search on mobile devices, we also propose a lightweight mobile ontology. Experimental results from the prototype implementation of the proposed method show that the proposed method provides a better user experience than the conventional FTS and returns accurate search results in an acceptable response time.</P>

Application of exergy analysis for improving energy efficiency of natural gas liquids recovery processes

Shin, Jihoon,Yoon, Sekwang,Kim, Jin-Kuk Elsevier 2015 Applied thermal engineering Vol.75 No.-

<P><B>Abstract</B></P> <P>Thermodynamic analysis and optimization method is applied to provide design guidelines for improving energy efficiency and cost-effectiveness of natural gas liquids recovery processes. Exergy analysis is adopted in this study as a thermodynamic tool to evaluate the loss of exergy associated with irreversibility in natural gas liquids recovery processes, with which conceptual understanding on inefficient design feature or equipment can be obtained. Natural gas liquids processes are modeled and simulated within UniSim<SUP>®</SUP> simulator, with which detailed thermodynamic information are obtained for calculating exergy loss. The optimization framework is developed by minimizing overall exergy loss, as an objective function, subject to product specifications and engineering constraints. The optimization is carried out within MATLAB<SUP>®</SUP> with the aid of a stochastic solver based on genetic algorithms. The process simulator is linked and interacted with the optimization solver, in which optimal operating conditions can be determined. A case study is presented to illustrate the benefit of using exergy analysis for the design and optimization of natural gas liquids processes and to demonstrate the applicability of design method proposed in this paper.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Application of exergy analysis for natural gas liquids (NGL) recovery processes. </LI> <LI> Minimization of exergy loss for improving energy efficiency. </LI> <LI> A systematic optimization framework for the design of NGL recovery processes. </LI> </UL> </P>

Lagrangian Stochastic Modeling of Stratified Atmospheric Boundary Layer

Jihoon Shin,Jong-Jin Baik 한국기상학회 2023 한국기상학회 학술대회 논문집 Vol.2023 No.11

Differentiation of Glycan Diversity with Serial Affinity Column Set (SACS)

( Jihoon Shin ),( Wonryeon Cho ) 한국질량분석학회 2016 Mass spectrometry letters Vol.7 No.3

Targeted glycoproteomics is an effective way to discover disease-associated glycoproteins in proteomics and serial affinity chromatography (SAC) using lectin and glycan-targeting antibodies shows glycan diversity on the captured glycoproteins. This study suggests a way to determine glycan heterogeneity and structural analysis on the post-translationally modified proteins through serial affinity column set (SACS) using four Lycopersicon esculentum lectin (LEL) columns. The great advantage of this method is that it differentiates between glycoproteins on the basis of their binding affinity. Through this study, some proteins were identified to have glycoforms with different affinity on a single glycoprotein. It will be particularly useful in determining biomarkers in which the disease-specific feature is a unique glycan, or a group of glycans.

Evaluation of temperature effects on brake wear particles using clustered heatmaps

Jihoon Shin,Inhyeok Yim,Soon-Bark Kwon,Sechan Park,Min-soo Kim,YoonKyung Cha 대한환경공학회 2019 Environmental Engineering Research Vol.24 No.4

Temperature effects on the generation of brake wear particles from railway vehicles were generated, with a particular focus on the generation of ultrafine particles. A real scale brake dynamometer test was repeated five times under low and high initial temperatures of brake discs, respectively, to obtain generalized results. Size distributions and temporal patterns of wear particles were analyzed through visualization using clustered heatmaps. Our results indicate that high initial temperature conditions promote the generation of ultrafine particles. While particle concentration peaked within the range of fine sized particles under both low and high initial temperature, an additional peak occurred within the range of ultrafine sized particles only under high initial temperature. The timing of peak occurrence also differed between low and high initial temperature conditions. Under low initial temperature fine sized particles were generated intensively at the latter end of braking, whereas under high initial temperature both fine and ultrafine particles were generated more dispersedly along the braking period. The clustered correlation heatmap divided particle sizes into two groups, within which generation timing and concentration of particles were similar. The cut-off point between the two groups was approximately 100 nm, confirming that the governing mechanisms for the generation of fine particles and ultrafine particles are different.

Loss of Potential Biomarker Proteins Associated with Abundant Proteins during Abundant Protein Removal in Sample Pretreatment

Shin, Jihoon,Lee, Jinwook,Cho, Wonryeon Korean Society for Mass Spectrometry 2018 Mass spectrometry letters Vol.9 No.2

Capture of non-glycoproteins during lectin affinity chromatography is frequently observed, although it would seem to be anomalous. In actuality, lectin affinity chromatography works at post-translational modification (PTM) sites on a glycoprotein which is not involved in protein-protein interactions (PPIs). In this study, serial affinity column set (SACS) using lectins followed by proteomics methods was used to identify PPI mechanisms of captured proteins in human plasma. MetaCore, STRING, Ingenuity Pathway Analysis (IPA), and IntAct were individually used to elucidate the interactions of the identified abundant proteins and to obtain the corresponding interaction maps. The abundant non-glycoproteins were captured with the binding to the selected glycoproteins. Therefore, depletion process in sample pretreatment for abundant protein removal should be considered with more caution because it may lose precious disease-related low abundant proteins through PPIs of the removed abundant proteins in human plasma during the depletion process in biomarker discovery. Glycoproteins bearing specific glycans are frequently associated with cancer and can be specifically isolated by lectin affinity chromatography. Therefore, SACS using Lycopersicon esculentum lectin (LEL) can also be used to study disease interactomes.

Lagrangian Stochastic Modeling of Stratified Atmospheric Boundary Layer

Jihoon Shin,Jong-Jin Baik 한국기상학회 2023 한국기상학회 학술대회 논문집 Vol.2023 No.10

Differentiation of Glycan Diversity with Serial Affinity Column Set (SACS)

Shin, Jihoon,Cho, Wonryeon Korean Society for Mass Spectrometry 2016 Mass spectrometry letters Vol.2 No.2

Targeted glycoproteomics is an effective way to discover disease-associated glycoproteins in proteomics and serial affinity chromatography (SAC) using lectin and glycan-targeting antibodies shows glycan diversity on the captured glycoproteins. This study suggests a way to determine glycan heterogeneity and structural analysis on the post-translationally modified proteins through serial affinity column set (SACS) using four Lycopersicon esculentum lectin (LEL) columns. The great advantage of this method is that it differentiates between glycoproteins on the basis of their binding affinity. Through this study, some proteins were identified to have glycoforms with different affinity on a single glycoprotein. It will be particularly useful in determining biomarkers in which the disease-specific feature is a unique glycan, or a group of glycans.

Poly(lactide) Architectures for Elastomeric, Toughening, Degradable, and Flexible

Jihoon Shin(신지훈) 한국고분자학회 2022 한국고분자학회 학술대회 연구논문 초록집 Vol.47 No.1