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

Jeong, Minwoo / Jeon, Hayoung / Shin, Donghyuk

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
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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: Effect of N doping on the microstructure and dry etch properties of amorphous carbon deposited with a DC sputtering system.

Kim, Sungtae / Jeong, Min-Woo / Kim, Kuntae / Kim, Ung-Gi / Kim, Miyoung / Lee, So-Yeon / Joo, Young-Chang

RSC advances

2023 Volume 13, Issue 3, Page(s) 2131–2139

Abstract: The importance of developing a hardmask with excellent performance, and physical and chemical properties to utilize in long-term etching is spotlighted due to the acceleration of development in high-density semiconductors. To develop such a hardmask, ... ...

Abstract	The importance of developing a hardmask with excellent performance, and physical and chemical properties to utilize in long-term etching is spotlighted due to the acceleration of development in high-density semiconductors. To develop such a hardmask, amorphous carbon hardmasks doped with various concentrations of N were fabricated with a DC magnetron sputtering system using varying inert gas (Ar to N
Language	English
Publishing date	2023-01-12
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d2ra06808g
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Book ; Online: Connecting Low-Loss Subspace for Personalized Federated Learning

Hahn, Seok-Ju / Jeong, Minwoo / Lee, Junghye

2021

Abstract: Due to the curse of statistical heterogeneity across clients, adopting a personalized federated learning method has become an essential choice for the successful deployment of federated learning-based services. Among diverse branches of personalization ... ...

Abstract	Due to the curse of statistical heterogeneity across clients, adopting a personalized federated learning method has become an essential choice for the successful deployment of federated learning-based services. Among diverse branches of personalization techniques, a model mixture-based personalization method is preferred as each client has their own personalized model as a result of federated learning. It usually requires a local model and a federated model, but this approach is either limited to partial parameter exchange or requires additional local updates, each of which is helpless to novel clients and burdensome to the client's computational capacity. As the existence of a connected subspace containing diverse low-loss solutions between two or more independent deep networks has been discovered, we combined this interesting property with the model mixture-based personalized federated learning method for improved performance of personalization. We proposed SuPerFed, a personalized federated learning method that induces an explicit connection between the optima of the local and the federated model in weight space for boosting each other. Through extensive experiments on several benchmark datasets, we demonstrated that our method achieves consistent gains in both personalization performance and robustness to problematic scenarios possible in realistic services. Comment: Appears at ACM SIGKDD 2022. Code available at http://github.com/vaseline555/SuPerFed
Keywords	Computer Science - Machine Learning ; Computer Science - Artificial Intelligence
Subject code	006
Publishing date	2021-09-15
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data.

Kim, Yujin / Jeong, Minwoo / Koh, In Gyeong / Kim, Chanhee / Lee, Hyeji / Kim, Jae Hyun / Yurko, Ronald / Kim, Il Bin / Park, Jeongbin / Werling, Donna M / Sanders, Stephan J / An, Joon-Yong

medRxiv : the preprint server for health sciences

2024

Abstract: Variants in cis-regulatory elements link the noncoding genome to human brain pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a ... ...

Abstract	Variants in cis-regulatory elements link the noncoding genome to human brain pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS) employs both whole-genome sequencing and user-provided functional data to enhance noncoding variant analysis, with a faster and more efficient execution of the CWAS workflow. Here, we used single-nuclei assay for transposase-accessible chromatin with sequencing to facilitate CWAS-guided noncoding variant analysis at cell-type specific enhancers and promoters. Examining autism spectrum disorder whole-genome sequencing data (n = 7,280), CWAS-Plus identified noncoding
Language	English
Publishing date	2024-04-15
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.15.24305828
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Article: Bonding structure and etching characteristics of amorphous carbon for a hardmask deposited by DC sputtering

Lee, So-Yeon / Jang, Kyung-Tae / Jeong, Min-Woo / Joo, Young-Chang / Kim, Kuntae / Kim, Miyoung / Kim, Sungtae / Lee, Gun-Do / Park, Hwanyeol

Carbon. 2019 Dec., v. 154

2019

Abstract: An amorphous carbon hardmask was fabricated by DC sputtering to evaluate the etching characteristics for semiconductor microstructure patterning. The bonding structure of the carbon films deposited by sputtering was modified by the DC sputtering ... ...

Abstract	An amorphous carbon hardmask was fabricated by DC sputtering to evaluate the etching characteristics for semiconductor microstructure patterning. The bonding structure of the carbon films deposited by sputtering was modified by the DC sputtering conditions and the deposition pressure. In the case of a low-pressure deposition process, an sp3-bonding-rich amorphous carbon film was fabricated and had excellent etching resistance. On the other hand, during the high-pressure deposition process, an sp2-bonding-rich amorphous carbon film was fabricated and had poor etching resistance. To understand the degradation process of the carbon hardmask induced by the penetration of fluorine ions into the film during dry etching, the phenomenon of fluorine penetration into the film and the interaction between fluorine and the carbon bonds were studied by density functional theory (DFT). Through the DFT calculations, it is unveiled that the energy barrier for the migration of a fluorine atom through the sp3 bonding path is much larger than that of a fluorine atom through the sp2 bonding path in amorphous carbon.
Keywords	carbon ; density functional theory ; energy ; fluorine ; ions ; microstructure ; semiconductors
Language	English
Dates of publication	2019-12
Size	p. 277-284.
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0008-6223
DOI	10.1016/j.carbon.2019.08.013
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Natural language dialog systems and intelligent assistants

Jeong, Minwoo / Kim, Hong Kook / Kim, Ji-Hwan / Lee, Gary Geunbae

2015

Author's details	Gary Geunbae Lee, Hong Kook Kim, Minwoo Jeong, Ji-Hwan Kim, editors
Keywords	Human-computer interaction ; Human-robot interaction ; Natural language processing (Computer science)
Language	English
Size	Online-Ressource (x, 275 pages)
Publisher	Springer
Publishing place	Cham
Document type	Book ; Online
Note	Includes bibliographical references and index
ISBN	3319192914 ; 9783319192901 ; 9783319192918 ; 3319192906
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: New pathway for the formation of metallic cubic phase Ge-Sb-Te compounds induced by an electric current.

Park, Yong-Jin / Cho, Ju-Young / Jeong, Min-Woo / Na, Sekwon / Joo, Young-Chang

Scientific reports

2016 Volume 6, Page(s) 21466

Abstract: The novel discovery of a current-induced transition from insulator to metal in the crystalline phase of Ge2Sb2Te5 and GeSb4Te7 have been studied by means of a model using line-patterned samples. The resistivity of cubic phase Ge-Sb-Te compound was ... ...

Abstract	The novel discovery of a current-induced transition from insulator to metal in the crystalline phase of Ge2Sb2Te5 and GeSb4Te7 have been studied by means of a model using line-patterned samples. The resistivity of cubic phase Ge-Sb-Te compound was reduced by an electrical current (~1 MA/cm(2)), and the final resistivity was determined based on the stress current density, regardless of the initial resistivity and temperature, which indicates that the conductivity of Ge-Sb-Te compound can be modulated by an electrical current. The minimum resistivity of Ge-Sb-Te materials can be achieved at high kinetic rates by applying an electrical current, and the material properties change from insulating to metallic behavior without a phase transition. The current-induced metal transition is more effective in GeSb4Te7 than Ge2Sb2Te5, which depends on the intrinsic vacancy of materials. Electromigration, which is the migration of atoms induced by a momentum transfer from charge carriers, can easily promote the rearrangement of vacancies in the cubic phase of Ge-Sb-Te compound. This behavior differs significantly from thermal annealing, which accompanies a phase transition to the hexagonal phase. This result suggests a new pathway for modulating the electrical conductivity and material properties of chalcogenide materials by applying an electrical current.
Language	English
Publishing date	2016-02-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep21466
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Article ; Online: HnRNP A1 phosphorylated by VRK1 stimulates telomerase and its binding to telomeric DNA sequence.

Choi, Yoon Ha / Lim, Jong-Kwan / Jeong, Min-Woo / Kim, Kyong-Tai

Nucleic acids research

2012 Volume 40, Issue 17, Page(s) 8499–8518

Abstract: The telomere integrity is maintained via replication machinery, telomere associated proteins and telomerase. Many telomere associated proteins are regulated in a cell cycle-dependent manner. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), a single- ...

Abstract	The telomere integrity is maintained via replication machinery, telomere associated proteins and telomerase. Many telomere associated proteins are regulated in a cell cycle-dependent manner. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), a single-stranded oligonucleotide binding protein, is thought to play a pivotal role in telomere maintenance. Here, we identified hnRNP A1 as a novel substrate for vaccinia-related kinase 1 (VRK1), a cell cycle regulating kinase. Phosphorylation by VRK1 potentiates the binding of hnRNP A1 to telomeric ssDNA and telomerase RNA in vitro and enhances its function for telomerase reaction. VRK1 deficiency induces a shortening of telomeres with an abnormal telomere arrangement and activation of DNA-damage signaling in mouse male germ cells. Together, our data suggest that VRK1 is required for telomere maintenance via phosphorylation of hnRNP A1, which regulates proteins associated with the telomere and telomerase RNA.
MeSH term(s)	Animals ; Base Sequence ; Binding Sites ; Cell Cycle/genetics ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/metabolism ; HeLa Cells ; Heterogeneous Nuclear Ribonucleoprotein A1 ; Heterogeneous-Nuclear Ribonucleoprotein Group A-B/chemistry ; Heterogeneous-Nuclear Ribonucleoprotein Group A-B/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Male ; Mice ; Phosphorylation ; Protein-Serine-Threonine Kinases/deficiency ; Protein-Serine-Threonine Kinases/metabolism ; RNA/metabolism ; Spermatogonia/metabolism ; Telomerase/metabolism ; Telomere/chemistry ; Telomere/metabolism ; Telomere Homeostasis
Chemical Substances	DNA, Single-Stranded ; Heterogeneous Nuclear Ribonucleoprotein A1 ; Heterogeneous-Nuclear Ribonucleoprotein Group A-B ; Hnrnpa1 protein, mouse ; Intracellular Signaling Peptides and Proteins ; hnRNPA1 protein, human ; telomerase RNA ; RNA (63231-63-0) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; VRK1 protein, human (EC 2.7.11.1) ; Vrk1 protein, mouse (EC 2.7.11.1) ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2012-06-26
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/gks634
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Zs.A 1067: Show issues

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Article ; Online: Mitogen-activated protein kinase phosphatase 2 regulates histone H3 phosphorylation via interaction with vaccinia-related kinase 1.

Jeong, Min-Woo / Kang, Tae-Hong / Kim, Wanil / Choi, Yoon Ha / Kim, Kyong-Tai

Molecular biology of the cell

2012 Volume 24, Issue 3, Page(s) 373–384

Abstract: Mitogen-activated protein kinase phosphatase 2 (MKP2) is a member of the dual-specificity MKPs that regulate MAP kinase signaling. However, MKP2 functions are still largely unknown. In this study, we showed that MKP2 could regulate histone H3 ... ...

Abstract	Mitogen-activated protein kinase phosphatase 2 (MKP2) is a member of the dual-specificity MKPs that regulate MAP kinase signaling. However, MKP2 functions are still largely unknown. In this study, we showed that MKP2 could regulate histone H3 phosphorylation under oxidative stress conditions. We found that MKP2 inhibited histone H3 phosphorylation by suppressing vaccinia-related kinase 1 (VRK1) activity. Moreover, this regulation was dependent on the selective interaction with VRK1, regardless of its phosphatase activity. The interaction between MKP2 and VRK1 mainly occurred in the chromatin, where histones are abundant. We also observed that the protein level of MKP2 and its interaction with histone H3 increased from G1 to M phase during the cell cycle, which is similar to the VRK1 profile. Furthermore, MKP2 specifically regulated the VRK1-mediated histone H3 phosphorylation at M phase. Taken together, these data suggest a novel function of MKP2 as a negative regulator of VRK1-mediated histone H3 phosphorylation.
MeSH term(s)	Cell Division ; Chromatin/enzymology ; Dual-Specificity Phosphatases/metabolism ; HeLa Cells ; Histones/metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Intracellular Signaling Peptides and Proteins/metabolism ; Mitogen-Activated Protein Kinase Phosphatases/metabolism ; Oxidative Stress ; Phosphorylation ; Protein Processing, Post-Translational ; Protein Transport ; Protein-Serine-Threonine Kinases/metabolism
Chemical Substances	Chromatin ; Histones ; Intracellular Signaling Peptides and Proteins ; Hydrogen Peroxide (BBX060AN9V) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; VRK1 protein, human (EC 2.7.11.1) ; Mitogen-Activated Protein Kinase Phosphatases (EC 3.1.3.16) ; DUSP4 protein, human (EC 3.1.3.48) ; Dual-Specificity Phosphatases (EC 3.1.3.48)
Language	English
Publishing date	2012-12-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E12-06-0456
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Zs.A 2853: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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