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.

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>

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.

Parameterization of Stochastically Entraining Convection Using Machine Learning Technique

Jihoon Shin,Jong-Jin Baik 한국기상학회 2021 한국기상학회 학술대회 논문집 Vol.2021 No.10

The mixing between cumulus clouds and nearby environment is one of the largest sources of uncertainty in climate modeling. The air mass flux crosses into a cloud is called the entrainment and out of a cloud is called the detrainment. A stochastic mixing model with a machine learning technique is proposed for mass flux convection schemes. The model consists of the stochastic differential equations (SDEs) for the fractional entrainment rate, fractional detrainment rate, fractional dilution rate, and vertical acceleration. Unknowns in SDEs are parameterized using a deep neural network with the inputs of cloud and environment properties. The deep neural network is found to predict entrainment and detrainment rates better than previously proposed parameterizations. The new mixing model is implemented in a unified convection scheme (UNICON) and tested in a single-column mode for two marine shallow convection cases. It is shown that the simulations with the new mixing model produce realistic mean and variance of various convective updraft properties and that the appropriate amount of stochasticity is generated. Consistently accurate simulations of updraft mass fluxes and moist conserved variables reduce model errors in the original UNICON. Additional sensitivity simulations enabling or disabling the stochasticity in mixing and initialization suggest that most of the cloud variabilities are generated from the mixing process.

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>

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.

Degradable Poly(lactide) Architectures for Vehicle Applications

Jihoon Shin(신지훈) 한국고분자학회 2021 한국고분자학회 학술대회 연구논문 초록집 Vol.46 No.1

Poly(lactide) (PLA) is a renewable, degradable and compostable thermoplastic with mechanical properties similar to poly(styrene). Unfortunately, PLA is inherently brittle and possesses poor melt strength. In particular, the brittle nature of PLA limits its current utility to disposable packing. Melt blends of PLA and a rubbery material can rubber toughen the plastic. Current efforts explore using block and graft copolymers with a majority PLA block and minority rubbery block that phase separate on the nanometer length scale to rubber toughen PLA. Careful molecular design is needed to obtain the desired phase separation on nanometer length scale. To achieve these hierarchically structured, tough, and sustainable, and degradable materials, controlled polymerization, post-polymerization functionalization, and coupling chemistries need to be developed. These methods will not only benefit the field of tough sustainable plastics but other areas of polymer chemistry.

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.

Lagrangian Stochastic Modeling of Stratified Atmospheric Boundary Layer

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

Artificial DNA Lattice Fabrication by Noncomplementarity and Geometrical Incompatibility

Shin, Jihoon,Kim, Junghoon,Amin, Rashid,Kim, Seungjae,Kwon, Young Hun,Park, Sung Ha American Chemical Society 2011 ACS NANO Vol.5 No.6

<P>Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson–Crick base-pairing rules between complementary base sequences. Second, the geometrical compatibility of the DNA oligonucleotide must match for lattices to form. Here we present a fabrication scheme of DNA nanostructures with noncomplementary and/or geometrically incompatible DNA oligonucleotides, which contradicts conventional DNA structure creation rules. Quantitative analyses of DNA lattice sizes were carried out to verify the unfavorable binding occurrences, which correspond to errors in algorithmic self-assembly. Further studies of these types of bindings may shed more light on the exact mechanisms at work in the self-assembly of DNA nanostructures.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancac3/2011/ancac3.2011.5.issue-6/nn201312g/production/images/medium/nn-2011-01312g_0004.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/nn201312g'>ACS Electronic Supporting Info</A></P>