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.

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.

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

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

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

( Jihoon Shin ),( Hong-duk Youn ) 생화학분자생물학회 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]

Kinetic Trans-Assembly of DNA Nanostructures

Shin, Jihoon,Kim, Junghoon,Park, Sung Ha,Ha, Tai Hwan American Chemical Society 2018 ACS NANO Vol.12 No.9

<P>The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic paradigms of DNA nanotechnology, we present a rationally designed synthetic platform that functions in an analogous manner to create complex DNA nanostructures. Starting from one type of DNA nanostructure, DNA strand displacement circuits were designed to interact and pass along the information encoded in the initial structure to mediate the self-assembly of a different type of structure, the final output structure depending on the type of circuit triggered. Using this concept of a DNA structure “trans-assembling” a different DNA structure through nonlocal strand displacement circuitry, four different schemes were implemented. Specifically, 1D ladder and 2D double-crossover (DX) lattices were designed to kinetically trigger DNA circuits to activate polymerization of either ring structures or another type of DX lattice under enzyme-free, isothermal conditions. In each scheme, the desired multilayer reaction pathway was activated, among multiple possible pathways, ultimately leading to the downstream self-assembly of the correct output structure.</P> [FIG OMISSION]</BR>

Lagrangian Stochastic Modeling of Stratified Atmospheric Boundary Layer

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

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.

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.

Global Simulation of Madden-Julian Oscillation with Stochastic Unified Convection Scheme

Jihoon Shin,Jong-Jin Baik 한국기상학회 2023 한국기상학회 학술대회 논문집 Vol.2023 No.4