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  1. Article ; Online: Where bacteria and eukaryotes meet.

    Chai, Liraz / Shank, Elizabeth A / Zaburdaev, Vasily

    Journal of bacteriology

    2024  Volume 206, Issue 2, Page(s) e0004923

    Abstract: The international workshop "Interdisciplinary life of microbes: from single cells to multicellular aggregates," following a virtual preassembly in November 2021, was held in person in Dresden, from 9 to 13 November 2022. It attracted not only prominent ... ...

    Abstract The international workshop "Interdisciplinary life of microbes: from single cells to multicellular aggregates," following a virtual preassembly in November 2021, was held in person in Dresden, from 9 to 13 November 2022. It attracted not only prominent experts in biofilm research but also researchers from broadly neighboring disciplines, such as medicine, chemistry, and theoretical and experimental biophysics, both eukaryotic and prokaryotic. Focused brainstorming sessions were the special feature of the event and are at the heart of this commentary.
    MeSH term(s) Humans ; Bacteria/genetics ; Biofilms ; Eukaryota/genetics
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/jb.00049-23
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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.50: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  2. Book ; Online ; Thesis: Computational Methods to Find and Rank MHC-I Restricted Tumor-Associated Antigens to Improve Therapeutic Efficacy and Tolerability of Antigen-based Cancer Immunotherapy

    Lischer, Christopher [Verfasser] / Zaburdaev, Vasily [Akademischer Betreuer] / Vera González, Julio [Akademischer Betreuer] / Zaburdaev, Vasily [Gutachter] / Vera González, Julio [Gutachter]

    2024  

    Author's details Christopher Lischer ; Gutachter: Vasily Zaburdaev,  Julio Vera González ; Vasily Zaburdaev,  Julio Vera González
    Keywords Medizin, Gesundheit ; Medicine, Health
    Subject code sg610
    Language English
    Publisher Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
    Publishing place Erlangen
    Document type Book ; Online ; Thesis
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  3. Article ; Online: Periodic ethanol supply as a path toward unlimited lifespan of

    Zhang, Xingyu / Penkov, Sider / Kurzchalia, Teymuras V / Zaburdaev, Vasily

    Frontiers in aging

    2023  Volume 4, Page(s) 1031161

    Abstract: The dauer larva is a specialized stage of worm development optimized for survival under harsh conditions that have been used as a model for stress resistance, metabolic adaptations, and longevity. Recent findings suggest that the dauer larva ... ...

    Abstract The dauer larva is a specialized stage of worm development optimized for survival under harsh conditions that have been used as a model for stress resistance, metabolic adaptations, and longevity. Recent findings suggest that the dauer larva of
    Language English
    Publishing date 2023-09-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 3076785-4
    ISSN 2673-6217 ; 2673-6217
    ISSN (online) 2673-6217
    ISSN 2673-6217
    DOI 10.3389/fragi.2023.1031161
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  4. Article ; Online: Residual cells and nutrient availability guide wound healing in bacterial biofilms.

    Ye, Yusong / Ghrayeb, Mnar / Miercke, Sarah / Arif, Sania / Müller, Susann / Mascher, Thorsten / Chai, Liraz / Zaburdaev, Vasily

    Soft matter

    2024  Volume 20, Issue 5, Page(s) 1047–1060

    Abstract: Biofilms are multicellular heterogeneous bacterial communities characterized by social-like division of labor, and remarkable robustness with respect to external stresses. Increasingly often an analogy between biofilms and arguably more complex ... ...

    Abstract Biofilms are multicellular heterogeneous bacterial communities characterized by social-like division of labor, and remarkable robustness with respect to external stresses. Increasingly often an analogy between biofilms and arguably more complex eukaryotic tissues is being drawn. One illustrative example of where this analogy can be practically useful is the process of wound healing. While it has been extensively studied in eukaryotic tissues, the mechanism of wound healing in biofilms is virtually unexplored. Combining experiments in
    MeSH term(s) Bacteria ; Biofilms ; Biological Transport ; Bacillus ; Wound Healing
    Language English
    Publishing date 2024-01-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d3sm01032e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The shape of pinned forced polymer loops.

    Huang, Wenwen / Zaburdaev, Vasily

    Soft matter

    2018  Volume 15, Issue 8, Page(s) 1785–1792

    Abstract: Loop geometry is a frequent encounter in synthetic and biological polymers. Here we provide an analytical theory to characterize the shapes of polymer loops subjected to an external force field. We show how to calculate the polymer density, gyration ... ...

    Abstract Loop geometry is a frequent encounter in synthetic and biological polymers. Here we provide an analytical theory to characterize the shapes of polymer loops subjected to an external force field. We show how to calculate the polymer density, gyration radius and its distribution. Interestingly, the distribution of the gyration radius shows a non-monotonic behavior as a function of the external force. Furthermore, we analyzed the gyration tensor of the polymer loop characterizing its overall shape. Two parameters called asphericity and the nature of asphericity derived from the gyration tensor, along with the gyration radius, can be used to quantify the shape of polymer loops in theory and experiments.
    Language English
    Publishing date 2018-03-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/c8sm02357c
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  6. Article ; Online: Continuum Theory of Active Phase Separation in Cellular Aggregates.

    Kuan, Hui-Shun / Pönisch, Wolfram / Jülicher, Frank / Zaburdaev, Vasily

    Physical review letters

    2021  Volume 126, Issue 1, Page(s) 18102

    Abstract: Dense cellular aggregates are common in biology, ranging from bacterial biofilms to organoids, cell spheroids, and tumors. Their dynamics, driven by intercellular forces, is intrinsically out of equilibrium. Motivated by bacterial colonies as a model ... ...

    Abstract Dense cellular aggregates are common in biology, ranging from bacterial biofilms to organoids, cell spheroids, and tumors. Their dynamics, driven by intercellular forces, is intrinsically out of equilibrium. Motivated by bacterial colonies as a model system, we present a continuum theory to study dense, active, cellular aggregates. We describe the process of aggregate formation as an active phase separation phenomenon, while the merging of aggregates is rationalized as a coalescence of viscoelastic droplets where the key timescales are linked to the turnover of the active force. Our theory provides a general framework for studying the rheology and nonequilibrium dynamics of dense cellular aggregates.
    MeSH term(s) Fimbriae, Bacterial/physiology ; Models, Biological ; Neisseria gonorrhoeae/cytology
    Language English
    Publishing date 2021-01-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.126.018102
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    In stock of ZB MED Bonn / Germany

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  7. Article ; Online: Unbiased retrieval of frequency-dependent mechanical properties from noisy time-dependent signals.

    Abuhattum, Shada / Kuan, Hui-Shun / Müller, Paul / Guck, Jochen / Zaburdaev, Vasily

    Biophysical reports

    2022  Volume 2, Issue 3, Page(s) 100054

    Abstract: The mechanical response of materials to dynamic loading is often quantified by the frequency-dependent complex modulus. Probing materials directly in the frequency domain faces technical challenges such as a limited range of frequencies, long measurement ...

    Abstract The mechanical response of materials to dynamic loading is often quantified by the frequency-dependent complex modulus. Probing materials directly in the frequency domain faces technical challenges such as a limited range of frequencies, long measurement times, or small sample sizes. Furthermore, many biological samples, such as cells or tissues, can change their properties upon repetitive probing at different frequencies. Therefore, it is common practice to extract the material properties by fitting predefined mechanical models to measurements performed in the time domain. This practice, however, precludes the probing of unique and yet unexplored material properties. In this report, we demonstrate that the frequency-dependent complex modulus can be robustly retrieved in a model-independent manner directly from time-dependent stress-strain measurements. While applying a rolling average eliminates random noise and leads to a reliable complex modulus in the lower frequency range, a Fourier transform with a complex frequency helps to recover the material properties at high frequencies. Finally, by properly designing the probing procedure, the recovery of reliable mechanical properties can be extended to an even wider frequency range. Our approach can be used with many state-of-the-art experimental methods to interrogate the mechanical properties of biological and other complex materials.
    Language English
    Publishing date 2022-03-30
    Publishing country United States
    Document type Journal Article
    ISSN 2667-0747
    ISSN (online) 2667-0747
    DOI 10.1016/j.bpr.2022.100054
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  8. Article ; Online: Amphiphiles Formed from Synthetic DNA-Nanomotifs Mimic the Stepwise Dispersal of Transcriptional Clusters in the Cell Nucleus.

    Tschurikow, Xenia / Gadzekpo, Aaron / Tran, Mai P / Chatterjee, Rakesh / Sobucki, Marcel / Zaburdaev, Vasily / Göpfrich, Kerstin / Hilbert, Lennart

    Nano letters

    2023  Volume 23, Issue 17, Page(s) 7815–7824

    Abstract: Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct ... ...

    Abstract Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and we achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Increasing amphiphile concentrations induce rounding of droplets, prevent droplet fusion, and, at high concentrations, cause full dispersal of droplets. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that the addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of transcriptional cluster formation in biological cells using relatively simple DNA sequence-programmable nanostructures, opening novel ways to control the mesoscopic organization of synthetic nanomaterials.
    MeSH term(s) Animals ; Zebrafish ; Cell Nucleus ; Nanostructures/chemistry ; DNA/chemistry
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-08-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1530-6992
    ISSN (online) 1530-6992
    DOI 10.1021/acs.nanolett.3c01301
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  9. Book ; Online ; Thesis: Planar dielectric antennas for applications in bio-physics

    Morales Inostroza, Luis Esteban Alejandro [Verfasser] / Sandoghdar, Vahid [Akademischer Betreuer] / Fabry, Ben [Gutachter] / Zaburdaev, Vasily [Gutachter] / Sandoghdar, Vahid [Gutachter]

    2023  

    Author's details Luis Esteban Alejandro Morales Inostroza ; Gutachter:  Ben Fabry,  Vasily Zaburdaev,  Vahid Sandoghdar ; Betreuer:  Vahid Sandoghdar
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
    Publishing place Erlangen
    Document type Book ; Online ; Thesis
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  10. Article ; Online: How bacterial cells and colonies move on solid substrates.

    Pönisch, Wolfram / Weber, Christoph A / Zaburdaev, Vasily

    Physical review. E

    2019  Volume 99, Issue 4-1, Page(s) 42419

    Abstract: Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions of multiple ... ...

    Abstract Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions of multiple pili. It was shown experimentally that the substrate motility of Neisseria gonorrhoeae cells can be described as a persistent random walk with a persistence length that exceeds the mean pili length. Moreover, the persistence length increases for a higher number of pili per cell. With the help of a simple, tractable stochastic model, we test whether a tug of war without directional memory can explain the persistent motion of single Neisseria gonorrhoeae cells. While persistent motion of single cells indeed emerges naturally in the model, a tug of war alone is not capable of explaining the motility of microcolonies, which becomes weaker with increasing colony size. We suggest sliding friction between the microcolonies and the substrate as the missing ingredient. While such friction almost does not affect the general mechanism of single cell motility, it has a strong effect on colony motility. We validate the theoretical predictions by using a three-dimensional computational model that includes explicit details of the pili dynamics, force generation, and geometry of cells.
    MeSH term(s) Fimbriae, Bacterial/metabolism ; Models, Biological ; Movement ; Neisseria gonorrhoeae/cytology ; Stochastic Processes
    Language English
    Publishing date 2019-05-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.99.042419
    Database MEDical Literature Analysis and Retrieval System OnLINE

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