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Article: Editorial: Protein homeostasis in host-pathogen interactions.

Yeom, Jinki / Shin, Donghyuk / Qiao, Yuan

2023 Volume 13, Page(s) 1115857

Language	English
Publishing date	2023-01-04
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.1115857
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ubiquitin-regulating effector proteins from Legionella.

Jeong, Minwoo / Jeon, Hayoung / Shin, Donghyuk

BMB reports

2022 Volume 55, Issue 7, Page(s) 316–322

Abstract: Ubiquitin is relatively modest in size but involves almost entire cellular signaling pathways. The primary role of ubiquitin is maintaining cellular protein homeostasis. Ubiquitination regulates the fate of target proteins using the proteasome- or ... ...

Abstract	Ubiquitin is relatively modest in size but involves almost entire cellular signaling pathways. The primary role of ubiquitin is maintaining cellular protein homeostasis. Ubiquitination regulates the fate of target proteins using the proteasome- or autophagymediated degradation of ubiquitinated substrates, which can be either intracellular or foreign proteins from invading pathogens. Legionella, a gram-negative intracellular pathogen, hinders the host-ubiquitin system by translocating hundreds of effector proteins into the host cell's cytoplasm. In this review, we describe the current understanding of ubiquitin machinery from Legionella. We summarize structural and biochemical differences between the host-ubiquitin system and ubiquitin-related effectors of Legionella. Some of these effectors act much like canonical host-ubiquitin machinery, whereas others have distinctive structures and accomplish non-canonical ubiquitination via novel biochemical mechanisms. [BMB Reports 2022; 55(7): 316-322].
MeSH term(s)	Bacterial Proteins/metabolism ; Legionella/metabolism ; Legionella pneumophila/metabolism ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Bacterial Proteins ; Ubiquitin
Language	English
Publishing date	2022-06-24
Publishing country	Korea (South)
Document type	News ; Review
ZDB-ID	2410389-5
ISSN	1976-670X ; 1976-6696
ISSN (online)	1976-670X
ISSN	1976-6696
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural insights into ubiquitin chain cleavage by

Kang, Sangwoo / Kim, Gyuhee / Choi, Minhyeong / Jeong, Minwoo / van der Heden van Noort, Gerbrand J / Roh, Soung-Hun / Shin, Donghyuk

Life science alliance

2023 Volume 6, Issue 7

Abstract: Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. ...

Abstract	Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system.
MeSH term(s)	Female ; Humans ; Ubiquitin/metabolism ; Polyubiquitin/chemistry ; Polyubiquitin/metabolism ; Legionella/metabolism ; Deubiquitinating Enzymes/genetics ; Deubiquitinating Enzymes/metabolism ; Ovarian Neoplasms/genetics
Chemical Substances	Ubiquitin ; Polyubiquitin (120904-94-1) ; Deubiquitinating Enzymes (EC 3.4.19.12)
Language	English
Publishing date	2023-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202201876
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Article ; Online: Design of synthetic promoters for cyanobacteria with generative deep-learning model.

Seo, Euijin / Choi, Yun-Nam / Shin, Ye Rim / Kim, Donghyuk / Lee, Jeong Wook

Nucleic acids research

2023 Volume 51, Issue 13, Page(s) 7071–7082

Abstract: Deep generative models, which can approximate complex data distribution from large datasets, are widely used in biological dataset analysis. In particular, they can identify and unravel hidden traits encoded within a complicated nucleotide sequence, ... ...

Abstract	Deep generative models, which can approximate complex data distribution from large datasets, are widely used in biological dataset analysis. In particular, they can identify and unravel hidden traits encoded within a complicated nucleotide sequence, allowing us to design genetic parts with accuracy. Here, we provide a deep-learning based generic framework to design and evaluate synthetic promoters for cyanobacteria using generative models, which was in turn validated with cell-free transcription assay. We developed a deep generative model and a predictive model using a variational autoencoder and convolutional neural network, respectively. Using native promoter sequences of the model unicellular cyanobacterium Synechocystis sp. PCC 6803 as a training dataset, we generated 10 000 synthetic promoter sequences and predicted their strengths. By position weight matrix and k-mer analyses, we confirmed that our model captured a valid feature of cyanobacteria promoters from the dataset. Furthermore, critical subregion identification analysis consistently revealed the importance of the -10 box sequence motif in cyanobacteria promoters. Moreover, we validated that the generated promoter sequence can efficiently drive transcription via cell-free transcription assay. This approach, combining in silico and in vitro studies, will provide a foundation for the rapid design and validation of synthetic promoters, especially for non-model organisms.
MeSH term(s)	Deep Learning ; Promoter Regions, Genetic ; Synechocystis/genetics ; Neural Networks, Computer
Language	English
Publishing date	2023-05-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad451
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Article ; Online: Minimization of Torque Deviation of Cylinder Deactivation Engine through 48V Mild-Hybrid Starter-Generator Control.

Shin, Hyunki / Jung, Donghyuk / Han, Manbae / Hong, Seungwoo / Han, Donghee

Sensors (Basel, Switzerland)

2021 Volume 21, Issue 4

Abstract: Cylinder deactivation (CDA) is an effective technique to improve fuel economy in spark ignition (SI) engines. This technique enhances volumetric efficiency and reduces throttling loss. However, practical implementation is restricted due to torque ... ...

Abstract	Cylinder deactivation (CDA) is an effective technique to improve fuel economy in spark ignition (SI) engines. This technique enhances volumetric efficiency and reduces throttling loss. However, practical implementation is restricted due to torque fluctuations between individual cylinders that cause noise, vibration, and harshness (NVH) issues. To ease torque deviation of the CDA, we propose an in-cylinder pressure based 48V mild-hybrid starter-generator (MHSG) control strategy. The target engine realizes CDA with a specialized engine configuration of separated intake manifolds to independently control the airflow into the cylinders. To handle the complexity of the combined CDA and mild-hybrid system, GT-POWER simulation environment was integrated with a SI turbulent combustion model and 48V MHSG model with actual part specifications. The combustion model is essential for in-cylinder pressure-based control; thus, it is calibrated with actual engine experimental data. The modeling results demonstrate the precise accuracy of the engine cylinder pressures and of quantities such as MAF, MAP, BMEP, and IMEP. The proposed control algorithm also showed remarkable control performance, achieved by instantaneous torque calculation and dynamic compensation, with a 99% maximum reduction rate of engine torque deviation under target CDA operations.
Language	English
Publishing date	2021-02-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s21041432
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Article: Polyphenols Coordinated with Cu (II) in an Aqueous System Build Ion-Channel Coatings on Hair Surfaces.

Jin, Lei / Yun, Daemyoung / Zhang, Wei / Lee, Jinsung / Shin, Hongchul / Kim, Donghyuk / Kang, Tae-Bong / Won, Hyung-Sik / Jang, Hohyoun / Kim, Whangi

Materials (Basel, Switzerland)

2023 Volume 16, Issue 4

Abstract: Recently, developments in the field of cosmetics have led to a renewed interest in hair dyeing. However, damage to the hair during the dyeing process has increased hesitation in attempting hair dyeing. As a result, hair dyes with minimal side effects ... ...

Abstract	Recently, developments in the field of cosmetics have led to a renewed interest in hair dyeing. However, damage to the hair during the dyeing process has increased hesitation in attempting hair dyeing. As a result, hair dyes with minimal side effects have been in constant demand, and are being developed. In this study, natural-extract polyphenols, pyrogallol, and gallic acid are coordinated by CuCl
Language	English
Publishing date	2023-02-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma16041333
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Article: Genome sequence of the potential probiotic eukaryote

Hwang, Junsang / Bang, Ina / Kim, Donghyuk / Shin, Seung Chul / Chin, Young-Wook / Kim, Tae-Wan / Kim, Hyo Jin

3 Biotech

2020 Volume 10, Issue 4, Page(s) 185

Abstract: Saccharomyces ... ...

Abstract	Saccharomyces cerevisiae
Language	English
Publishing date	2020-03-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-020-02174-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis.

Park, Hong-Tae / Lee, Sang-Mok / Ko, Seyoung / Kim, Suji / Park, Hyun-Eui / Shin, Min-Kyoung / Kim, Donghyuk / Yoo, Han Sang

Veterinary research

2022 Volume 53, Issue 1, Page(s) 71

Abstract: Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing ... ...

Abstract	Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host-pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host-pathogen interactions.
MeSH term(s)	Animals ; Arginine/metabolism ; Humans ; Mycobacterium avium subsp. paratuberculosis ; Paratuberculosis/microbiology ; RNA-Seq/veterinary ; THP-1 Cells
Chemical Substances	Arginine (94ZLA3W45F)
Language	English
Publishing date	2022-09-13
Publishing country	England
Document type	Journal Article
ZDB-ID	1146298-x
ISSN	1297-9716 ; 0928-4249
ISSN (online)	1297-9716
ISSN	0928-4249
DOI	10.1186/s13567-022-01089-y
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Article: Alpha-2-Macroglobulin as a New Promising Biomarker Improving the Diagnostic Sensitivity of Bovine Paratuberculosis.

Park, Hyun-Eui / Park, Jin-Sik / Park, Hong-Tae / Choi, Jeong-Gyu / Shin, Jeong-Ih / Jung, Myunghwan / Kang, Hyung-Lyun / Baik, Seung-Chul / Lee, Woo-Kon / Kim, Donghyuk / Yoo, Han Sang / Shin, Min-Kyoung

Frontiers in veterinary science

2021 Volume 8, Page(s) 637716

Abstract: Johne's disease (JD) is a chronic granulomatous enteritis of ruminants caused ... ...

Abstract	Johne's disease (JD) is a chronic granulomatous enteritis of ruminants caused by
Language	English
Publishing date	2021-03-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2021.637716
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Article ; Online: An analysis of the impact of product recall on stock prices based on Google trend search counts

Kim, Ahyun / Lee, Sang Gun / Shin, Donghyuk

2020

Abstract: Purpose: Recall can have a critical impact on a companys image and reputation, and is one of the biggest issues for customers. In this study, we take the Event Study approach to analyze the impact of recall on corporate stock prices. In previous works, ... ...

Abstract	Purpose: Recall can have a critical impact on a companys image and reputation, and is one of the biggest issues for customers. In this study, we take the Event Study approach to analyze the impact of recall on corporate stock prices. In previous works, conflicting conclusions were drawn depending on the recall case and data collection process. Design/methodology/approach: To alleviate such issues, we utilize data as a more objective Google Trends. Specifically, we study the effects of product recall on stock prices from multiple aspects including (1) Google Trend search volume, (2) type of recall, (3) industry category, and (4) by country. Findings: Though we find that recall does not have a statistically significant effect on company share prices, we identified that recalls of companies with high search volume has a greater impact than those with low search volume. We also find that involuntary recalls have a greater impact than voluntary recalls, and non-automobile industries have a greater impact than the automobile industry. Research limitations/implications: The limitation of the research is that Google cannot accurately represent the world. It may not be fully reflected because there are countries that cannot use Google due to lack of IT infrastructure or government regulations. Also, it is not possible to know exactly when the information will leak when an event occurs. This is because if information had already leaked through peoples oral traditions before it spread to the news, its influence would be reduced. Originality/value: For studies using traditional event studies, the choice of events was very likely to be chosen according to the choice of researchers. This study is significant in that it tried to solve this problem with Google Trends and investigated all the data mentioned on the Internet except for countries that could not access Google due to lack of government regulations or IT infrastructure.
Keywords	ddc:650 ; Google trend ; Product recall ; Event study ; Automobile ; Non-Automobile
Subject code	306
Language	English
Publisher	Seoul: People & Global Business Association (P&GBA)
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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