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  1. Article ; Online: Abundance of the Membrane Proteome in Yeast Cells Lacking Spc1, a Non-catalytic Subunit of the Signal Peptidase Complex.

    Yim, Chewon / Chung, Yeonji / Son, Sungjoon / Kim, Jeesoo / Kim, Jong-Seo / Kim, Hyun

    The Journal of membrane biology

    2024  

    Abstract: The signal peptidase complex (SPC) mediates processing of signal peptides of secretory precursors. But, recent studies show that the eukaryotic SPC also cleaves internal transmembrane segments of some membrane proteins, and its non-catalytic subunit, ... ...

    Abstract The signal peptidase complex (SPC) mediates processing of signal peptides of secretory precursors. But, recent studies show that the eukaryotic SPC also cleaves internal transmembrane segments of some membrane proteins, and its non-catalytic subunit, Spc1/SPCS1 plays a critical role in this process. To assess the impact of Spc1 on membrane proteostasis, we carried out quantitative proteomics of yeast cells with and without Spc1. Our data show that the abundance of the membrane proteome in yeast cells lacking Spc1 is in general reduced compared to that in wild-type cells, implicating its role in controlling the cellular levels of membrane proteins.
    Language English
    Publishing date 2024-04-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3082-x
    ISSN 1432-1424 ; 0022-2631
    ISSN (online) 1432-1424
    ISSN 0022-2631
    DOI 10.1007/s00232-024-00312-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 613: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  2. Article ; Online: Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle.

    Choi, Yeon / Um, Buyeon / Na, Yongwoo / Kim, Jeesoo / Kim, Jong-Seo / Kim, V Narry

    Molecular cell

    2024  Volume 84, Issue 9, Page(s) 1764–1782.e10

    Abstract: mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse ... ...

    Abstract mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside in human cells, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA binding proteins (RBPs) across ten time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed RBPs with unexpected dynamics: the transcription-export (TREX) complex recruited posttranscriptionally after nuclear export factor 1 (NXF1) binding, challenging the current view of transcription-coupled mRNA export, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of the mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with Gene Ontology (GO) annotations. Our data can be explored at chronology.rna.snu.ac.kr.
    MeSH term(s) Humans ; RNA, Messenger/metabolism ; RNA, Messenger/genetics ; RNA-Binding Proteins/metabolism ; RNA-Binding Proteins/genetics ; Ribonucleoproteins/metabolism ; Ribonucleoproteins/genetics ; Protein Binding ; Nucleocytoplasmic Transport Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/genetics ; HeLa Cells ; Time Factors ; Machine Learning
    Chemical Substances RNA, Messenger ; RNA-Binding Proteins ; Ribonucleoproteins ; Nucleocytoplasmic Transport Proteins ; messenger ribonucleoprotein ; NXF1 protein, human
    Language English
    Publishing date 2024-04-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.03.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 5055: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  3. Article ; Online: Development of clothing-type platforms considering pressure and user satisfaction: focusing on industrial workers who tend to lift loads

    Kim, Yehyoun / Kim, Jeesoo / Lee, Dongyoung / Piao, Jiaoli / Bae, Joonbum / Koo, Sumin Helen

    Textile Research Journal. 2023 May, v. 93, no. 9-10 p.2226-2241

    2023  

    Abstract: The purpose of this study was to develop a clothing-type platform of wearable robots for industrial workers who usually lift loads to prevent accidents and increase their work efficiency. First, fabrics were selected through test analyses of the ... ...

    Abstract The purpose of this study was to develop a clothing-type platform of wearable robots for industrial workers who usually lift loads to prevent accidents and increase their work efficiency. First, fabrics were selected through test analyses of the elongation recovery rate and tensile strength. Second, a suit-type platform embedded with electrostatic clutch band actuators was prototyped and measured the friction force, and a washing dimension change rate of the test with the platform was conducted. Third, clothing pressures were measured after the developed prototype was worn, using an air injection sensor system at nine points and with four motions. Next, subjective clothing pressure and satisfaction surveys were conducted. The study produced four major results: (a) the selected fabrics and the prototype with the electrostatic clutch actuator met the performance requirements; (b) the greatest clothing pressure occurred at the back, back waist, and back knee, where actuators were connected, and the clothing pressure was sufficient for positional stability; (c) the subjective pressure was different in each section from the actual clothing pressure measurement; and (d) participants were satisfied with the developed prototypes, and they showed willingness to purchase them. The results can help developers of wearable robots increase comfort and user satisfaction.
    Keywords air ; consumer satisfaction ; fabrics ; friction ; prototypes ; tensile strength ; waist ; willingness to pay ; Clothing-type ; platform ; soft wearable robot ; clothing pressure ; user satisfaction
    Language English
    Dates of publication 2023-05
    Size p. 2226-2241.
    Publishing place SAGE Publications
    Document type Article ; Online
    ZDB-ID 2209596-2
    ISSN 1746-7748 ; 0040-5175
    ISSN (online) 1746-7748
    ISSN 0040-5175
    DOI 10.1177/00405175221143543
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Super-resolution proximity labeling with enhanced direct identification of biotinylation sites.

    Shin, Sanghee / Lee, Song-Yi / Kang, Myeong-Gyun / Jang, Dong-Gi / Kim, Jeesoo / Rhee, Hyun-Woo / Kim, Jong-Seo

    Communications biology

    2024  Volume 7, Issue 1, Page(s) 554

    Abstract: Promiscuous labeling enzymes, such as APEX2 or TurboID, are commonly used in in situ biotinylation studies of subcellular proteomes or protein-protein interactions. Although the conventional approach of enriching biotinylated proteins is widely ... ...

    Abstract Promiscuous labeling enzymes, such as APEX2 or TurboID, are commonly used in in situ biotinylation studies of subcellular proteomes or protein-protein interactions. Although the conventional approach of enriching biotinylated proteins is widely implemented, in-depth identification of specific biotinylation sites remains challenging, and current approaches are technically demanding with low yields. A novel method to systematically identify specific biotinylation sites for LC-MS analysis followed by proximity labeling showed excellent performance compared with that of related approaches in terms of identification depth with high enrichment power. The systematic identification of biotinylation sites enabled a simpler and more efficient experimental design to identify subcellular localized proteins within membranous organelles. Applying this method to the processing body (PB), a non-membranous organelle, successfully allowed unbiased identification of PB core proteins, including novel candidates. We anticipate that our newly developed method will replace the conventional method for identifying biotinylated proteins labeled by promiscuous labeling enzymes.
    MeSH term(s) Biotinylation ; Humans ; Biotin/chemistry ; Biotin/metabolism ; Proteomics/methods ; Animals ; Staining and Labeling/methods ; Chromatography, Liquid/methods ; Proteome/metabolism ; Mass Spectrometry/methods
    Chemical Substances Biotin (6SO6U10H04) ; Proteome
    Language English
    Publishing date 2024-05-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-024-06112-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: SAVE

    Song, Yeji / Shin, Wonsik / Lee, Junsoo / Kim, Jeesoo / Kwak, Nojun

    Protagonist Diversification with Structure Agnostic Video Editing

    2023  

    Abstract: Driven by the upsurge progress in text-to-image (T2I) generation models, text-to-video (T2V) generation has experienced a significant advance as well. Accordingly, tasks such as modifying the object or changing the style in a video have been possible. ... ...

    Abstract Driven by the upsurge progress in text-to-image (T2I) generation models, text-to-video (T2V) generation has experienced a significant advance as well. Accordingly, tasks such as modifying the object or changing the style in a video have been possible. However, previous works usually work well on trivial and consistent shapes, and easily collapse on a difficult target that has a largely different body shape from the original one. In this paper, we spot the bias problem in the existing video editing method that restricts the range of choices for the new protagonist and attempt to address this issue using the conventional image-level personalization method. We adopt motion personalization that isolates the motion from a single source video and then modifies the protagonist accordingly. To deal with the natural discrepancy between image and video, we propose a motion word with an inflated textual embedding to properly represent the motion in a source video. We also regulate the motion word to attend to proper motion-related areas by introducing a novel pseudo optical flow, efficiently computed from the pre-calculated attention maps. Finally, we decouple the motion from the appearance of the source video with an additional pseudo word. Extensive experiments demonstrate the editing capability of our method, taking a step toward more diverse and extensive video editing.

    Comment: Project website: https://ldynx.github.io/SAVE/
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 004
    Publishing date 2023-12-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Development of a comfort suit-type soft-wearable robot with flexible artificial muscles for walking assistance.

    Piao, Jiaoli / Kim, Minseo / Kim, Jeesoo / Kim, Changhwan / Han, Seunghee / Back, Inryeol / Koh, Je-Sung / Koo, Sumin

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 4869

    Abstract: Anchoring components are added to wearable robots to ensure a stable interaction between the suits and the human body and to minimize the displacement of the suits. However, these components can apply pressure to the body and can cause user ... ...

    Abstract Anchoring components are added to wearable robots to ensure a stable interaction between the suits and the human body and to minimize the displacement of the suits. However, these components can apply pressure to the body and can cause user dissatisfaction, which can decrease willingness to use the suits. Therefore, this study aims to develop a suit-type soft-wearable robot platform for walking assistance by providing comfortable garment pressure to ensure user satisfaction. The first prototype of a wearable robot suit was developed with anchoring components on the shoulders, waist, and thighs based on previous research results. Wear tests were conducted to measure garment pressure depending on posture using pressure sensors, and satisfaction surveys were conducted. The second prototype design was then developed, and performance tests with flexible artificial muscles and a satisfaction survey were conducted. Regarding the first prototype, the participants felt more than normal pressure in the shoulders and relatively less pressure in the thighs and calves. Thus, compared to the first design, the second design ensured a decreased garment pressure and resulted in an improvement of overall user satisfaction. These results can help provide guidance in the development of wearable robots by taking pressure comfort and user satisfaction into consideration.
    MeSH term(s) Humans ; Robotics ; Exoskeleton Device ; Wearable Electronic Devices ; Muscles ; Walking/physiology
    Language English
    Publishing date 2023-03-24
    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/s41598-023-32117-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online: Few-shot Image Generation with Mixup-based Distance Learning

    Kong, Chaerin / Kim, Jeesoo / Han, Donghoon / Kwak, Nojun

    2021  

    Abstract: Producing diverse and realistic images with generative models such as GANs typically requires large scale training with vast amount of images. GANs trained with limited data can easily memorize few training samples and display undesirable properties like ...

    Abstract Producing diverse and realistic images with generative models such as GANs typically requires large scale training with vast amount of images. GANs trained with limited data can easily memorize few training samples and display undesirable properties like "stairlike" latent space where interpolation in the latent space yields discontinuous transitions in the output space. In this work, we consider a challenging task of pretraining-free few-shot image synthesis, and seek to train existing generative models with minimal overfitting and mode collapse. We propose mixup-based distance regularization on the feature space of both a generator and the counterpart discriminator that encourages the two players to reason not only about the scarce observed data points but the relative distances in the feature space they reside. Qualitative and quantitative evaluation on diverse datasets demonstrates that our method is generally applicable to existing models to enhance both fidelity and diversity under few-shot setting. Code is available.

    Comment: ECCV 2022, 27 pages
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 004
    Publishing date 2021-11-23
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Online: Normalization Matters in Weakly Supervised Object Localization

    Kim, Jeesoo / Choe, Junsuk / Yun, Sangdoo / Kwak, Nojun

    2021  

    Abstract: Weakly-supervised object localization (WSOL) enables finding an object using a dataset without any localization information. By simply training a classification model using only image-level annotations, the feature map of the model can be utilized as a ... ...

    Abstract Weakly-supervised object localization (WSOL) enables finding an object using a dataset without any localization information. By simply training a classification model using only image-level annotations, the feature map of the model can be utilized as a score map for localization. In spite of many WSOL methods proposing novel strategies, there has not been any de facto standard about how to normalize the class activation map (CAM). Consequently, many WSOL methods have failed to fully exploit their own capacity because of the misuse of a normalization method. In this paper, we review many existing normalization methods and point out that they should be used according to the property of the given dataset. Additionally, we propose a new normalization method which substantially enhances the performance of any CAM-based WSOL methods. Using the proposed normalization method, we provide a comprehensive evaluation over three datasets (CUB, ImageNet and OpenImages) on three different architectures and observe significant performance gains over the conventional min-max normalization method in all the evaluated cases.

    Comment: Accepted at ICCV 2021. 16 pages, 10 figures
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2021-07-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Identification of a Structurally Dynamic Domain for Oligomer Formation in Rootletin.

    Ko, Donghee / Kim, Jeesoo / Rhee, Kunsoo / Choi, Hee-Jung

    Journal of molecular biology

    2020  Volume 432, Issue 13, Page(s) 3915–3932

    Abstract: Rootletin is the main component of the ciliary rootlet and functions as a centriole linker connecting the two mother centrioles. Despite the functional importance of rootletin, the molecular architecture of the rootletin filament and its assembly ... ...

    Abstract Rootletin is the main component of the ciliary rootlet and functions as a centriole linker connecting the two mother centrioles. Despite the functional importance of rootletin, the molecular architecture of the rootletin filament and its assembly mechanism are poorly understood. Here, we identify the coiled-coil domain 3 (CCD3) of rootletin as the key domain for its cellular function. The crystal structure of the CCD3
    MeSH term(s) Biophysics ; Centrioles/genetics ; Centrioles/ultrastructure ; Crystallography, X-Ray ; Cytoskeletal Proteins/chemistry ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/ultrastructure ; Cytoskeleton/genetics ; Cytoskeleton/ultrastructure ; Humans ; Protein Conformation
    Chemical Substances CROCC protein, human ; Cytoskeletal Proteins
    Language English
    Publishing date 2020-04-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2020.04.012
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: Spc1 regulates the signal peptidase-mediated processing of membrane proteins.

    Yim, Chewon / Chung, Yeonji / Kim, Jeesoo / Nilsson, IngMarie / Kim, Jong-Seo / Kim, Hyun

    Journal of cell science

    2021  Volume 134, Issue 13

    Abstract: Signal peptidase (SPase) cleaves the signal sequences (SSs) of secretory precursors. It contains an evolutionarily conserved membrane protein subunit, Spc1, that is dispensable for the catalytic activity of SPase and whose role remains unknown. In this ... ...

    Abstract Signal peptidase (SPase) cleaves the signal sequences (SSs) of secretory precursors. It contains an evolutionarily conserved membrane protein subunit, Spc1, that is dispensable for the catalytic activity of SPase and whose role remains unknown. In this study, we investigated the function of yeast Spc1. First, we set up an in vivo SPase cleavage assay using variants of the secretory protein carboxypeptidase Y (CPY) with SSs modified in the N-terminal and hydrophobic core regions. When comparing the SS cleavage efficiencies of these variants in cells with or without Spc1, we found that signal-anchored sequences became more susceptible to cleavage by SPase without Spc1. Furthermore, SPase-mediated processing of model membrane proteins was enhanced in the absence of Spc1 and was reduced upon overexpression of Spc1. Spc1 co-immunoprecipitated with proteins carrying uncleaved signal-anchored or transmembrane (TM) segments. Taken together, these results suggest that Spc1 protects TM segments from SPase action, thereby sharpening SPase substrate selection and acting as a negative regulator of the SPase-mediated processing of membrane proteins.
    MeSH term(s) Membrane Proteins/genetics ; Peptide Hydrolases ; Protein Sorting Signals ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins ; Serine Endopeptidases/metabolism
    Chemical Substances Membrane Proteins ; Protein Sorting Signals ; SPC1 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Peptide Hydrolases (EC 3.4.-) ; Serine Endopeptidases (EC 3.4.21.-) ; type I signal peptidase (EC 3.4.21.89)
    Language English
    Publishing date 2021-07-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.258936
    Database MEDical Literature Analysis and Retrieval System OnLINE

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