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  1. Article ; Online: Antibacterial Neutrophil Effector Response: Ex Vivo Quantification of Regulated Cell Death Associated with Extracellular Trap Release.

    Schweizer, Tiziano A / Hertegonne, Sanne / Vulin, Clément / Zinkernagel, Annelies S / Mairpady Shambat, Srikanth

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2674, Page(s) 235–250

    Abstract: Regulated cell death (RCD) and the concomitant release of extracellular traps by neutrophils (NETs) constitute an important antibacterial effector response. Usually, the dynamic processes of RCD and NETs release are assessed independently of each other ... ...

    Abstract Regulated cell death (RCD) and the concomitant release of extracellular traps by neutrophils (NETs) constitute an important antibacterial effector response. Usually, the dynamic processes of RCD and NETs release are assessed independently of each other by either unspecific or time-consuming methods. Here, we describe a flow cytometry-based high-throughput analysis method incorporating neutrophil RCD and NETs release with visual live-imaging conformation upon ex vivo bacterial challenge. This combined approach allows to quantify and closely follow the kinetics of the dynamic neutrophil effector response towards bacterial infection.
    MeSH term(s) Neutrophils/metabolism ; Extracellular Traps/metabolism ; Regulated Cell Death ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Flow Cytometry/methods
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-05-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3243-7_16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system.

    Rodríguez-Verdugo, Alejandra / Vulin, Clément / Ackermann, Martin

    Ecology letters

    2019  Volume 22, Issue 5, Page(s) 838–846

    Abstract: Species interactions change when the external conditions change. How these changes affect microbial community properties is an open question. We address this question using a two-species consortium in which species interactions change from exploitation ... ...

    Abstract Species interactions change when the external conditions change. How these changes affect microbial community properties is an open question. We address this question using a two-species consortium in which species interactions change from exploitation to competition depending on the carbon source provided. We built a mathematical model and calibrated it using single-species growth measurements. This model predicted that low frequencies of change between carbon sources lead to species loss, while intermediate and high frequencies of change maintained both species. We experimentally confirmed these predictions by growing co-cultures in fluctuating environments. These findings complement more established concepts of a diversity peak at intermediate disturbance frequencies. They also provide a mechanistic understanding for how the dynamics at the community level emerges from single-species behaviours and interspecific interactions. Our findings suggest that changes in species interactions can profoundly impact the ecological dynamics and properties of microbial systems.
    MeSH term(s) Carbon ; Ecology ; Models, Theoretical
    Chemical Substances Carbon (7440-44-0)
    Language English
    Publishing date 2019-02-21
    Publishing country England
    Document type Letter
    ZDB-ID 1441608-6
    ISSN 1461-0248 ; 1461-023X
    ISSN (online) 1461-0248
    ISSN 1461-023X
    DOI 10.1111/ele.13241
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The rate of environmental fluctuations shapes ecological dynamics in a two‐species microbial system

    Rodríguez‐Verdugo, Alejandra / Vulin, Clément / Ackermann, Martin

    Ecology letters. 2019 May, v. 22, no. 5

    2019  

    Abstract: Species interactions change when the external conditions change. How these changes affect microbial community properties is an open question. We address this question using a two‐species consortium in which species interactions change from exploitation ... ...

    Abstract Species interactions change when the external conditions change. How these changes affect microbial community properties is an open question. We address this question using a two‐species consortium in which species interactions change from exploitation to competition depending on the carbon source provided. We built a mathematical model and calibrated it using single‐species growth measurements. This model predicted that low frequencies of change between carbon sources lead to species loss, while intermediate and high frequencies of change maintained both species. We experimentally confirmed these predictions by growing co‐cultures in fluctuating environments. These findings complement more established concepts of a diversity peak at intermediate disturbance frequencies. They also provide a mechanistic understanding for how the dynamics at the community level emerges from single‐species behaviours and interspecific interactions. Our findings suggest that changes in species interactions can profoundly impact the ecological dynamics and properties of microbial systems.
    Keywords carbon ; coculture ; mathematical models ; microbial communities ; prediction
    Language English
    Dates of publication 2019-05
    Size p. 838-846.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note LETTER
    ZDB-ID 1441608-6
    ISSN 1461-0248 ; 1461-023X
    ISSN (online) 1461-0248
    ISSN 1461-023X
    DOI 10.1111/ele.13241
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2005/709: Show issues

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  4. Article ; Online: Author Correction: Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application.

    Bär, Julian / Boumasmoud, Mathilde / Kouyos, Roger D / Zinkernagel, Annelies S / Vulin, Clément

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 6050

    Language English
    Publishing date 2021-03-09
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-85033-8
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  5. Article ; Online: Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application.

    Bär, Julian / Boumasmoud, Mathilde / Kouyos, Roger D / Zinkernagel, Annelies S / Vulin, Clément

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 16084

    Abstract: Populations of genetically identical bacteria are phenotypically heterogeneous, giving rise to population functionalities that would not be possible in homogeneous populations. For instance, a proportion of non-dividing bacteria could persist through ... ...

    Abstract Populations of genetically identical bacteria are phenotypically heterogeneous, giving rise to population functionalities that would not be possible in homogeneous populations. For instance, a proportion of non-dividing bacteria could persist through antibiotic challenges and secure population survival. This heterogeneity can be studied in complex environmental or clinical samples by spreading the bacteria on agar plates and monitoring time to growth resumption in order to infer their metabolic state distribution. We present ColTapp, the Colony Time-lapse application for bacterial colony growth quantification. Its intuitive graphical user interface allows users to analyze time-lapse images of agar plates to monitor size, color and morphology of colonies. Additionally, images at isolated timepoints can be used to estimate lag time. Using ColTapp, we analyze a dataset of Staphylococcus aureus time-lapse images including populations with heterogeneous lag time. Colonies on dense plates reach saturation early, leading to overestimation of lag time from isolated images. We show that this bias can be corrected by taking into account the area available to each colony on the plate. We envision that in clinical settings, improved analysis of colony growth dynamics may help treatment decisions oriented towards personalized antibiotic therapies.
    MeSH term(s) Agar ; Algorithms ; Bacterial Load/methods ; Bacterial Load/statistics & numerical data ; Colony Count, Microbial/methods ; Colony Count, Microbial/statistics & numerical data ; Humans ; Image Processing, Computer-Assisted/methods ; Image Processing, Computer-Assisted/statistics & numerical data ; Software ; Staphylococcus aureus/cytology ; Staphylococcus aureus/growth & development ; Time-Lapse Imaging ; User-Computer Interface
    Chemical Substances Agar (9002-18-0)
    Language English
    Publishing date 2020-09-30
    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/s41598-020-72979-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: C-di-AMP levels modulate

    Dengler Haunreiter, Vanina / Tarnutzer, Andrea / Bär, Julian / von Matt, Manuela / Hertegonne, Sanne / Andreoni, Federica / Vulin, Clément / Künzi, Lisa / Menzi, Carmen / Kiefer, Patrick / Christen, Philipp / Vorholt, Julia A / Zinkernagel, Annelies S

    Microbiology spectrum

    2023  Volume 11, Issue 6, Page(s) e0278823

    Abstract: Importance: Antibiotic resistance and tolerance are substantial healthcare-related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di- ... ...

    Abstract Importance: Antibiotic resistance and tolerance are substantial healthcare-related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di-AMP), have recently been associated with resistance to beta-lactam antibiotics in clinical
    MeSH term(s) Humans ; Staphylococcus aureus/metabolism ; Methicillin-Resistant Staphylococcus aureus/genetics ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Staphylococcal Infections/drug therapy ; Staphylococcal Infections/metabolism ; Cell Wall/metabolism ; Methicillin Resistance ; Oxidative Stress ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests
    Chemical Substances cyclic diadenosine phosphate ; Anti-Bacterial Agents ; Bacterial Proteins
    Language English
    Publishing date 2023-11-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.02788-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Serine-threonine phosphoregulation by PknB and Stp contributes to quiescence and antibiotic tolerance in

    Huemer, Markus / Mairpady Shambat, Srikanth / Hertegonne, Sanne / Bergada-Pijuan, Judith / Chang, Chun-Chi / Pereira, Sandro / Gómez-Mejia, Alejandro / Van Gestel, Lies / Bär, Julian / Vulin, Clément / Pfammatter, Sibylle / Stinear, Timothy P / Monk, Ian R / Dworkin, Jonathan / Zinkernagel, Annelies S

    Science signaling

    2023  Volume 16, Issue 766, Page(s) eabj8194

    Abstract: Staphylococcus ... ...

    Abstract Staphylococcus aureus
    MeSH term(s) Animals ; Mice ; Humans ; Staphylococcus aureus/genetics ; Anti-Bacterial Agents/pharmacology ; Protein Serine-Threonine Kinases/metabolism ; Phosphorylation ; Phosphoprotein Phosphatases/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism
    Chemical Substances Anti-Bacterial Agents ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Phosphoprotein Phosphatases (EC 3.1.3.16) ; Bacterial Proteins
    Language English
    Publishing date 2023-01-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2417226-1
    ISSN 1937-9145 ; 1945-0877
    ISSN (online) 1937-9145
    ISSN 1945-0877
    DOI 10.1126/scisignal.abj8194
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  8. Article ; Online: Observing Nutrient Gradients, Gene Expression and Growth Variation Using the "Yeast Machine" Microfluidic Device.

    Marinkovic, Zoran S / Vulin, Clément / Acman, Mislav / Song, Xiaohu / Di Meglio, Jean Marc / Lindner, Ariel B / Hersen, Pascal

    Bio-protocol

    2020  Volume 10, Issue 13, Page(s) e3668

    Abstract: The natural environment of microbial cells like bacteria and yeast is often a complex community in which growth and internal organization reflect morphogenetic processes and interactions that are dependent on spatial position and time. While most of ... ...

    Abstract The natural environment of microbial cells like bacteria and yeast is often a complex community in which growth and internal organization reflect morphogenetic processes and interactions that are dependent on spatial position and time. While most of research is performed in simple homogeneous environments (
    Language English
    Publishing date 2020-07-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.3668
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  9. Article ; Online: Wide lag time distributions break a trade-off between reproduction and survival in bacteria.

    Moreno-Gámez, Stefany / Kiviet, Daniel J / Vulin, Clément / Schlegel, Susan / Schlegel, Kim / van Doorn, G Sander / Ackermann, Martin

    Proceedings of the National Academy of Sciences of the United States of America

    2020  Volume 117, Issue 31, Page(s) 18729–18736

    Abstract: Many microorganisms face a fundamental trade-off between reproduction and survival: Rapid growth boosts population size but makes microorganisms sensitive to external stressors. Here, we show that starved bacteria encountering new resources can break ... ...

    Abstract Many microorganisms face a fundamental trade-off between reproduction and survival: Rapid growth boosts population size but makes microorganisms sensitive to external stressors. Here, we show that starved bacteria encountering new resources can break this trade-off by evolving phenotypic heterogeneity in lag time. We quantify the distribution of single-cell lag times of populations of starved
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Biological Evolution ; Drug Resistance, Bacterial ; Escherichia coli/genetics ; Escherichia coli/physiology ; Microbial Viability ; Models, Biological ; Phenotype ; Single-Cell Analysis
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2020-07-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2003331117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Prolonged bacterial lag time results in small colony variants that represent a sub-population of persisters.

    Vulin, Clément / Leimer, Nadja / Huemer, Markus / Ackermann, Martin / Zinkernagel, Annelies S

    Nature communications

    2018  Volume 9, Issue 1, Page(s) 4074

    Abstract: Persisters are a subpopulation of bacteria that are not killed by antibiotics even though they lack genetic resistance. Here we provide evidence that persisters can manifest as small colony variants (SCVs) in clinical infections. We analyze growth ... ...

    Abstract Persisters are a subpopulation of bacteria that are not killed by antibiotics even though they lack genetic resistance. Here we provide evidence that persisters can manifest as small colony variants (SCVs) in clinical infections. We analyze growth kinetics of Staphylococcus aureus sampled from in vivo conditions and in vitro stress conditions that mimic growth in host compartments. We report that SCVs arise as a result of a long lag time, and that this phenotype emerges de novo during the growth phase in various stress conditions including abscesses and acidic media. We further observe that long lag time correlates with antibiotic usage. These observations suggest that treatment strategies should be carefully tailored to address bacterial persisters in clinics.
    MeSH term(s) Abscess/microbiology ; Animals ; Anti-Bacterial Agents ; Cell Proliferation ; Humans ; Mice ; Middle Aged ; Staphylococcus aureus/drug effects ; Staphylococcus aureus/growth & development ; Stress, Physiological
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2018-10-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-018-06527-0
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