This is the institutional Repository of the Helmholtz Centre for Infection Research in Braunschweig/Germany (HZI), the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken/Germany, the TWINCORE Zentrum für Exprerimentelle und Klinische Infektionsforschung, Hannover/Germany,Helmholtz-Institut für RNA-basierte Infektionsforschung (HIRI), Würzburg/Germany, Braunschweig Integrated Centre for Systems biology (BRICS), Centre for Structural Systems Biology (CSSB) the Study Centre Hannover, Hannover/Germany and the Centre for Individualised Infection Medicine (CiiM).

 

  • POTATO: Automated pipeline for batch analysis of optical tweezers data

    Buck, Stefan; Pekarek, Lukas; Caliskan, Neva; Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, GermanyMedical Faculty, Julius-Maximilians University Würzburg, Würzburg, Germany (Elsevier, 2022-08-02)
    Optical tweezers are a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein-nucleic acid interactions, and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (practical optical tweezers analysis tool). POTATO automatically processes the high-frequency raw data generated by force-ramp experiments and identifies (un)folding events using predefined parameters. After segmentation of the force-distance trajectories at the identified (un)folding events, sections of the curve can be fitted independently to a worm-like chain and freely jointed chain models, and the work applied on the molecule can be calculated by numerical integration. Furthermore, the tool allows plotting of constant force data and fitting of the Gaussian distance distribution over time. All these features are wrapped in a user-friendly graphical interface, which allows researchers without programming knowledge to perform sophisticated data analysis. -(c) 2022 Biophysical Society
  • Bacteria as genetically programmable producers of bioactive natural products

    Hug, Joachim J.; Krug, Daniel; Müller, Rolf (2020-04-01)
  • Repositories for Taxonomic Data: Where We Are and What is Missing.

    Miralles, Aurélien; Bruy, Teddy; Wolcott, Katherine; Scherz, Mark D; Begerow, Dominik; Beszteri, Bank; Bonkowski, Michael; Felden, Janine; Gemeinholzer, Birgit; Glaw, Frank; et al. (2020-11-01)
  • A dynamic CD2-rich compartment at the outer edge of the immunological synapse boosts and integrates signals.

    Demetriou, Philippos; Abu-Shah, Enas; Valvo, Salvatore; McCuaig, Sarah; Mayya, Viveka; Kvalvaag, Audun; Starkey, Thomas; Korobchevskaya, Kseniya; Lee, Lennard Y W; Friedrich, Matthias; et al. (2020-09-14)
    The CD2-CD58 recognition system promotes adhesion and signaling and counters exhaustion in human T cells. We found that CD2 localized to the outer edge of the mature immunological synapse, with cellular or artificial APC, in a pattern we refer to as a 'CD2 corolla'. The corolla captured engaged CD28, ICOS, CD226 and SLAM-F1 co-stimulators. The corolla amplified active phosphorylated Src-family kinases (pSFK), LAT and PLC-γ over T cell receptor (TCR) alone. CD2-CD58 interactions in the corolla boosted signaling by 77% as compared with central CD2-CD58 interactions. Engaged PD-1 invaded the CD2 corolla and buffered CD2-mediated amplification of TCR signaling. CD2 numbers and motifs in its cytoplasmic tail controlled corolla formation. CD8+ tumor-infiltrating lymphocytes displayed low expression of CD2 in the majority of people with colorectal, endometrial or ovarian cancer. CD2 downregulation may attenuate antitumor T cell responses, with implications for checkpoint immunotherapies.
  • Cell-substrate adhesion drives Scar/WAVE activation and phosphorylation by a Ste20-family kinase, which controls pseudopod lifetime.

    Singh, Shashi Prakash; Thomason, Peter A; Lilla, Sergio; Schaks, Matthias; Tang, Qing; Goode, Bruce L; Machesky, Laura M; Rottner, Klemens; Insall, Robert H (2020-08-03)

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