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.

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.

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.

COVID-19, Obesity, and GRP78: Unraveling the Pathological Link

Jihoon Shin,Iichiro Shimomura 대한비만학회 2023 Journal of obesity & metabolic syndrome Vol.32 No.3

The coronavirus disease 2019 (COVID-19) pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an unprecedented global surge in infections and fatalities. Notably, obesity has emerged as an important susceptibility factor for COVID-19; however, the pathological mechanisms for this remain poorly understood. Recent studies proposed a role for glucose-regulated protein 78 (GRP78), a protein implicated in both obesity and metabolic syndrome, which may function as a binding partner and/or co-receptor for SARS-CoV-2. Given its crucial involvement in diverse biological processes, GRP78 likely plays a major role in multiple facets of the viral life cycle and the pathology of COVID-19. This perspective review discusses the potential contributions of GRP78 to the dynamics of SARS-CoV-2 infection and pathology, particularly in the context of obesity. The primary objective is to facilitate a deeper understanding of the pathogenesis of COVID-19. Through this exploration, we aim to illuminate the complex interactions underpinning the nexus of COVID-19, obesity, and GRP78, ultimately paving the way for informed therapeutic strategies and preventive measures.

Optimization and Evaluation of Stochastic Unified Convection Using Single-Column Model Simulations at Multiple Observation Sites

Jihoon Shin,Jong-Jin Baik 한국기상학회 2022 한국기상학회 학술대회 논문집 Vol.2022 No.10

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

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

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.

Oct4 resetting by Aurkb-PP1 cell cycle axis determines the identity of mouse embryonic stem cells

( Jihoon Shin ),( Hong-duk Youn ) 생화학분자생물학회(구 한국생화학분자생물학회) 2016 BMB Reports Vol.49 No.10

In embryonic stem cells (ESCs), cell cycle regulation is deeply connected to pluripotency. Especially, core transcription factors (CTFs) which are essential to maintaining the pluripotency transcription programs should be reset during M/G1 transition. However, it remains unknown about how CTFs are governed during cell cycle progression. Here, we describe that the regulation of Oct4 by Aurora kinase b (Aurkb)/protein phosphatase 1 (PP1) axis during the cell cycle is important for resetting Oct4 to pluripotency and cell cycle related target genes in determining the identity of ESCs. Aurkb starts to phosphorylate Oct4(S229) at the onset of G2/M phase, inducing the dissociation of Oct4 from chromatin, whereas PP1 binds Oct4 and dephosphorylates Oct4(S229) during M/G1 transition, which resets Oct4-driven transcription for pluripotency and the cell cycle. Furthermore, Aurkb phosphormimetic and PP1 binding-deficient mutations in Oct4 disrupt the pluripotent cell cycle, lead to the loss of pluripotency in ESCs, and decrease the efficiency of somatic cell reprogramming. Based on our findings, we suggest that the cell cycle is directly linked to pluripotency programs in ESCs. [BMB Reports 2016; 49(10): 527-528]

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>