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  1. Article ; Online: Microbiology: How to Bridge Mechanisms and Phenomenology.

    Jun, Suckjoon

    Journal of molecular biology

    2020  Volume 432, Issue 21, Page(s) 5735

    MeSH term(s) Bacteria/cytology ; Bacteria/genetics ; Bacteria/growth & development ; Bacterial Infections/microbiology ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Humans ; Models, Biological ; RNA, Bacterial/genetics ; Transcriptional Activation
    Chemical Substances DNA, Bacterial ; RNA, Bacterial
    Language English
    Publishing date 2020-08-07
    Publishing country England
    Document type Editorial ; Introductory Journal Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2020.08.001
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
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  2. Article ; Online: Bacterial Replication Initiation as Precision Control by Protein Counting.

    Fu, Haochen / Xiao, Fangzhou / Jun, Suckjoon

    PRX life

    2023  Volume 1, Issue 1

    Abstract: Balanced biosynthesis is the hallmark of bacterial cell physiology, where the concentrations of stable proteins remain steady. However, this poses a conceptual challenge to modeling the cell-cycle and cell-size controls in bacteria, as prevailing ... ...

    Abstract Balanced biosynthesis is the hallmark of bacterial cell physiology, where the concentrations of stable proteins remain steady. However, this poses a conceptual challenge to modeling the cell-cycle and cell-size controls in bacteria, as prevailing concentration-based eukaryote models are not directly applicable. In this study, we revisit and significantly extend the initiator-titration model, proposed 30 years ago, and we explain how bacteria precisely and robustly control replication initiation based on the mechanism of protein copy-number sensing. Using a mean-field approach, we first derive an analytical expression of the cell size at initiation based on three biological mechanistic control parameters for an extended initiator-titration model. We also study the stability of our model analytically and show that initiation can become unstable in multifork replication conditions. Using simulations, we further show that the presence of the conversion between active and inactive initiator protein forms significantly represses initiation instability. Importantly, the two-step Poisson process set by the initiator titration step results in significantly improved initiation synchrony with
    Language English
    Publishing date 2023-08-28
    Publishing country United States
    Document type Journal Article
    ISSN 2835-8279
    ISSN (online) 2835-8279
    DOI 10.1103/prxlife.1.013011
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  3. Article: Replication initiation in bacteria: precision control based on protein counting.

    Fu, Haochen / Xiao, Fangzhou / Jun, Suckjoon

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Balanced biosynthesis is the hallmark of bacterial cell physiology, where the concentrations of stable proteins remain steady. However, this poses a conceptual challenge to modeling the cell-cycle and cell-size controls in bacteria, as prevailing ... ...

    Abstract Balanced biosynthesis is the hallmark of bacterial cell physiology, where the concentrations of stable proteins remain steady. However, this poses a conceptual challenge to modeling the cell-cycle and cell-size controls in bacteria, as prevailing concentration-based eukaryote models are not directly applicable. In this study, we revisit and significantly extend the initiator-titration model, proposed thirty years ago, and explain how bacteria precisely and robustly control replication initiation based on the mechanism of protein copy-number sensing. Using a mean-field approach, we first derive an analytical expression of the cell size at initiation based on three biological mechanistic control parameters for an extended initiator-titration model. We also study the stability of our model analytically and show that initiation can become unstable in multifork replication conditions. Using simulations, we further show that the presence of the conversion between active and inactive initiator protein forms significantly represses initiation instability. Importantly, the two-step Poisson process set by the initiator titration step results in significantly improved initiation synchrony with
    Language English
    Publishing date 2023-07-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.26.542547
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Chromosome, cell cycle, and entropy.

    Jun, Suckjoon

    Biophysical journal

    2015  Volume 108, Issue 4, Page(s) 785–786

    MeSH term(s) Cell Nucleus/ultrastructure ; Chromosome Segregation/physiology ; Chromosomes, Bacterial/physiology ; DNA, Bacterial/chemistry ; DNA, Superhelical/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Hardness/physiology ; Hardness Tests/instrumentation ; Models, Biological ; Organelles/ultrastructure ; Polymers/chemistry
    Chemical Substances DNA, Bacterial ; DNA, Superhelical ; Polymers
    Language English
    Publishing date 2015-02-17
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2014.12.032
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: Show issues Location:
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    Zs.MO 2: Show issues

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  5. Article: Quantitative Examination of Five Stochastic Cell-Cycle and Cell-Size Control Models for

    Le Treut, Guillaume / Si, Fangwei / Li, Dongyang / Jun, Suckjoon

    Frontiers in microbiology

    2021  Volume 12, Page(s) 721899

    Abstract: We examine five quantitative models of the cell-cycle and cell-size control ... ...

    Abstract We examine five quantitative models of the cell-cycle and cell-size control in
    Language English
    Publishing date 2021-10-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.721899
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  6. Article ; Online: Promoting an "Auteur Theory" for Young Scientists: Preserving Excitement and Creativity ….

    Desai, Arshad / Jun, Suckjoon

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2018  Volume 40, Issue 11, Page(s) e1800147

    MeSH term(s) Biomedical Research/education ; Biomedical Research/methods ; Creativity ; Humans ; Science/education ; Science/methods
    Language English
    Publishing date 2018-09-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.201800147
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    Zs.A 2024: 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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  7. Article ; Online: Tools and methods for high-throughput single-cell imaging with the mother machine.

    Thiermann, Ryan / Sandler, Michael / Ahir, Gursharan / Sauls, John T / Schroeder, Jeremy / Brown, Steven / Le Treut, Guillaume / Si, Fangwei / Li, Dongyang / Wang, Jue D / Jun, Suckjoon

    eLife

    2024  Volume 12

    Abstract: Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells ... ...

    Abstract Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning-based segmentation, 'what you put is what you get' (WYPIWYG) - that is, pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother machine-based high-throughput imaging and analysis methods in their research.
    MeSH term(s) Female ; Humans ; Mothers ; Image Processing, Computer-Assisted ; Microscopy ; Culture ; Research Personnel
    Language English
    Publishing date 2024-04-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.88463
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  8. Article: Tools and methods for high-throughput single-cell imaging with the mother machine.

    Thiermann, Ryan / Sandler, Michael / Ahir, Gursharan / Sauls, John T / Schroeder, Jeremy W / Brown, Steven D / Le Treut, Guillaume / Si, Fangwei / Li, Dongyang / Wang, Jue D / Jun, Suckjoon

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells ... ...

    Abstract Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely-used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning based segmentation, "what you put is what you get" (WYPIWYG) - i.e., pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother-machine-based high-throughput imaging and analysis methods in their research.
    Language English
    Publishing date 2024-02-05
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.27.534286
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: A Fundamental Unit of Cell Size in Bacteria.

    Jun, Suckjoon / Rust, Michael J

    Trends in genetics : TIG

    2017  Volume 33, Issue 7, Page(s) 433–435

    Abstract: A new study clarifies a relationship between growth, gene expression, and cell size in cyanobacteria. Quite unexpectedly, cyanobacteria and Escherichia coli appear to share an invariance principle to coordinate growth and chromosome replication. This ... ...

    Abstract A new study clarifies a relationship between growth, gene expression, and cell size in cyanobacteria. Quite unexpectedly, cyanobacteria and Escherichia coli appear to share an invariance principle to coordinate growth and chromosome replication. This principle allows quantitative predictions of cell size across a range of growth conditions in both organisms.
    MeSH term(s) Cell Size ; Chromosomes, Bacterial ; Cyanobacteria/genetics ; Escherichia coli/genetics
    Language English
    Publishing date 2017
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2017.05.001
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  10. Article: Protocol for Construction of a Tunable CRISPR Interference (tCRISPRi) Strain for

    Li, Xin-Tian / Sou, Cindy / Jun, Suckjoon

    Bio-protocol

    2017  Volume 7, Issue 19

    Abstract: We present a protocol for construction of tunable CRISPR interference (tCRISPRi) strains ... ...

    Abstract We present a protocol for construction of tunable CRISPR interference (tCRISPRi) strains for
    Language English
    Publishing date 2017-10-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.2574
    Database MEDical Literature Analysis and Retrieval System OnLINE

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