Now showing items 1-20 of 4087

    • 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)
    • Absence of cGAS-mediated type I IFN responses in HIV-1-infected T cells.

      Elsner, Carina; Ponnurangam, Aparna; Kazmierski, Julia; Zillinger, Thomas; Jansen, Jenny; Todt, Daniel; Döhner, Katinka; Xu, Shuting; Ducroux, Aurélie; Kriedemann, Nils; et al. (2020-07-24)
      The DNA sensor cGAS catalyzes the production of the cyclic dinucleotide cGAMP, resulting in type I interferon responses. We addressed the functionality of cGAS-mediated DNA sensing in human and murine T cells. Activated primary CD4+ T cells expressed cGAS and responded to plasmid DNA by upregulation of ISGs and release of bioactive interferon. In mouse T cells, cGAS KO ablated sensing of plasmid DNA, and TREX1 KO enabled cells to sense short immunostimulatory DNA. Expression of IFIT1 and MX2 was downregulated and upregulated in cGAS KO and TREX1 KO T cell lines, respectively, compared to parental cells. Despite their intact cGAS sensing pathway, human CD4+ T cells failed to mount a reverse transcriptase (RT) inhibitor-sensitive immune response following HIV-1 infection. In contrast, infection of human T cells with HSV-1 that is functionally deficient for the cGAS antagonist pUL41 (HSV-1ΔUL41N) resulted in a cGAS-dependent type I interferon response. In accordance with our results in primary CD4+ T cells, plasmid challenge or HSV-1ΔUL41N inoculation of T cell lines provoked an entirely cGAS-dependent type I interferon response, including IRF3 phosphorylation and expression of ISGs. In contrast, no RT-dependent interferon response was detected following transduction of T cell lines with VSV-G-pseudotyped lentiviral or gammaretroviral particles. Together, T cells are capable to raise a cGAS-dependent cell-intrinsic response to both plasmid DNA challenge or inoculation with HSV-1ΔUL41N. However, HIV-1 infection does not appear to trigger cGAS-mediated sensing of viral DNA in T cells, possibly by revealing viral DNA of insufficient quantity, length, and/or accessibility to cGAS.
    • Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge.

      Kohn, T; Wiegand, S; Boedeker, C; Rast, P; Heuer, A; Jetten, M S M; Schüler, M; Becker, S; Rohde, C; Müller, R-W; et al. (2019-10-11)
      The microbiome of freshwater sponges is rarely studied, and not a single novel bacterial species has been isolated and subsequently characterized from a freshwater sponge to date. A previous study showed that 14.4% of the microbiome from Ephydatia fluviatilis belong to the phylum Planctomycetes. Therefore, we sampled an Ephydatia sponge from a freshwater lake and employed enrichment techniques targeting bacteria from the phylum Planctomycetes. The obtained strain spb1T was subject to genomic and phenomic characterization and found to represent a novel planctomycetal species proposed as Planctopirus ephydatiae sp. nov. (DSM 106606 = CECT 9866). In the process of differentiating spb1T from its next relative Planctopirus limnophila DSM 3776T, we identified and characterized the first phage - Planctopirus phage vB_PlimS_J1 - infecting planctomycetes that was only mentioned anecdotally before. Interestingly, classical chemotaxonomic methods would have failed to distinguish Planctopirus ephydatiae strain spb1T from Planctopirus limnophila DSM 3776T. Our findings demonstrate and underpin the need for whole genome-based taxonomy to detect and differentiate planctomycetal species.
    • Tofacitinib Loaded Squalenyl Nanoparticles for Targeted Follicular Delivery in Inflammatory Skin Diseases.

      Christmann, Rebekka; Ho, Duy-Khiet; Wilzopolski, Jenny; Lee, Sangeun; Koch, Marcus; Loretz, Brigitta; Vogt, Thomas; Bäumer, Wolfgang; Schaefer, Ulrich F; Lehr, Claus-Michael (2020-11-24)
      Tofacitinib (TFB), a Janus kinase inhibitor, has shown excellent success off-label in treating various dermatological diseases, especially alopecia areata (AA). However, TFB's safe and targeted delivery into hair follicles (HFs) is highly desirable due to its systemic adverse effects. Nanoparticles (NPs) can enhance targeted follicular drug delivery and minimize interfollicular permeation and thereby reduce systemic drug exposure. In this study, we report a facile method to assemble the stable and uniform 240 nm TFB loaded squalenyl derivative (SqD) nanoparticles (TFB SqD NPs) in aqueous solution, which allowed an excellent loading capacity (LC) of 20%. The SqD NPs showed an enhanced TFB delivery into HFs compared to the aqueous formulations of plain drug in an ex vivo pig ear model. Furthermore, the therapeutic efficacy of the TFB SqD NPs was studied in a mouse model of allergic dermatitis by ear swelling reduction and compared to TFB dissolved in a non-aqueous mixture of acetone and DMSO (7:1 v/v). Whereas such formulation would not be acceptable for use in the clinic, the TFB SqD NPs dispersed in water illustrated a better reduction in inflammatory effects than plain TFB's aqueous formulation, implying both encouraging good in vivo efficacy and safety. These findings support the potential of TFB SqD NPs for developing a long-term topical therapy of AA.
    • Associations between gut microbiota and genetic risk for rheumatoid arthritis in the absence of disease: a cross-sectional study.

      Wells, Philippa M; Adebayo, Adewale S; Bowyer, Ruth C E; Freidin, Maxim B; Finckh, Axel; Strowig, Till; Lesker, Till Robin; Alpizar-Rodriguez, Deshire; Gilbert, Benoit; Kirkham, Bruce; et al. (2020-06-25)
      We found that presence of Prevotella spp were positively associated with the rheumatoid arthritis PRS in TwinsUK participants (q<1 × 10-7). This finding was validated in SCREEN-RA participants (n=133) carrying established shared epitope risk alleles (q=0·0011). We also found an association between Prevotella spp and presence of preclinical rheumatoid arthritis phases (q=0·021).
    • Modelling collective cell motion: are on- and off-lattice models equivalent?

      Nava-Sedeño, Josué Manik; Voß-Böhme, Anja; Hatzikirou, Haralampos; Deutsch, Andreas; Peruani, Fernando (2020-07-27)
    • Discovery and validation of a personalized risk predictor for incident tuberculosis in low transmission settings.

      Gupta, Rishi K; Calderwood, Claire J; Yavlinsky, Alexei; Krutikov, Maria; Quartagno, Matteo; Aichelburg, Maximilian C; Altet, Neus; Diel, Roland; Dobler, Claudia C; Dominguez, Jose; et al. (2020-10-19)
    • Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology.

      Wiegand, Sandra; Jogler, Mareike; Boedeker, Christian; Pinto, Daniela; Vollmers, John; Rivas-Marín, Elena; Kohn, Timo; Peeters, Stijn H; Heuer, Anja; Rast, Patrick; et al. (2019-11-18)
    • Cows selected for divergent mastitis susceptibility display a differential liver transcriptome profile after experimental Staphylococcus aureus mammary gland inoculation

      Heimes, A.; Brodhagen, J.; Weikard, R.; Becker, D.; Meyerholz, M. M.; Petzl, W.; Zerbe, H.; Schuberth, H. J.; Hoedemaker, M.; Schmicke, M.; et al. (Elsevier, 2020-07-01)
      Infection and inflammation of the mammary gland, and especially prevention of mastitis, are still major challenges for the dairy industry. Different approaches have been tried to reduce the incidence of mastitis. Genetic selection of cows with lower susceptibility to mastitis promises sustainable success in this regard. Bos taurus autosome (BTA) 18, particularly the region between 43 and 59 Mb, harbors quantitative trait loci (QTL) for somatic cell score, a surrogate trait for mastitis susceptibility. Scrutinizing the molecular bases hereof, we challenged udders from half-sib heifers having inherited either favorable paternal haplotypes for somatic cell score (Q) or unfavorable haplotypes (q) with the Staphylococcus aureus pathogen. RNA sequencing was used for an in-depth analysis of challenge-related alterations in the hepatic transcriptome. Liver exerts highly relevant immune functions aside from being the key metabolic organ. Hence, a holistic approach focusing on the liver enabled us to identify challenge-related and genotype-dependent differentially expressed genes and underlying regulatory networks. In response to the S. aureus challenge, we found that heifers with Q haplotypes displayed more activated immune genes and pathways after S. aureus challenge compared with their q half-sibs. Furthermore, we found a significant enrichment of differentially expressed loci in the genomic target region on BTA18, suggesting the existence of a regionally acting regulatory element with effects on a variety of genes in this region. © 2020 American Dairy Science Association
    • C19orf66 is an interferon-induced inhibitor of HCV replication that restricts formation of the viral replication organelle

      Kinast, Volker; Plociennikowska, Agnieszka; Anggakusuma; Bracht, Thilo; Todt, Daniel; Brown, Richard J.P.; Boldanova, Tujana; Zhang, Yudi; Brüggemann, Yannick; Friesland, Martina; et al. (Elsevier, 2020-04-12)
      Background & Aims HCV is a positive-strand RNA virus that primarily infects human hepatocytes. Recent studies have reported that C19orf66 is expressed as an interferon (IFN)-stimulated gene; however, the intrinsic regulation of this gene within the liver as well as its antiviral effects against HCV remain elusive. Methods Expression of C19orf66 was quantified in both liver biopsies and primary human hepatocytes, with or without HCV infection. Mechanistic studies of the potent anti-HCV phenotype mediated by C19orf66 were conducted using state-of-the-art virological, biochemical and genetic approaches, as well as correlative light and electron microscopy and transcriptome and proteome analysis. Results Upregulation of C19orf66 mRNA was observed in both primary human hepatocytes upon HCV infection and in the livers of patients with chronic hepatitis C (CHC). In addition, pegIFNα/ribavirin therapy induced C19orf66 expression in patients with CHC. Transcriptomic profiling and whole cell proteomics of hepatoma cells ectopically expressing C19orf66 revealed no induction of other antiviral genes. Expression of C19orf66 restricted HCV infection, whereas CRIPSPR/Cas9 mediated knockout of C19orf66 attenuated IFN-mediated suppression of HCV replication. Co-immunoprecipitation followed by mass spectrometry identified a stress granule protein-dominated interactome of C19orf66. Studies with subgenomic HCV replicons and an expression system revealed that C19orf66 expression impairs HCV-induced elevation of phosphatidylinositol-4-phosphate, alters the morphology of the viral replication organelle (termed the membranous web) and thereby targets viral RNA replication. Conclusion C19orf66 is an IFN-stimulated gene, which is upregulated in hepatocytes within the first hours post IFN treatment or HCV infection in vivo. The encoded protein possesses specific antiviral activity against HCV and targets the formation of the membranous web. Our study identifies C19orf66 as an IFN-inducible restriction factor with a novel antiviral mechanism that specifically targets HCV replication.
    • Critical Role of Zur and SmtB in Zinc Homeostasis of Mycobacterium smegmatis.

      Goethe, Elke; Laarmann, Kristin; Lührs, Janita; Jarek, Michael; Meens, Jochen; Lewin, Astrid; Goethe, Ralph (2020-04-21)
      Zinc homeostasis is crucial for bacterial cells, since imbalances affect viability. However, in mycobacteria, knowledge of zinc metabolism is incomplete. Mycobacterium smegmatis (MSMEG) is an environmental, nonpathogenic Mycobacterium that is widely used as a model organism to study mycobacterial metabolism and pathogenicity. How MSMEG maintains zinc homeostasis is largely unknown. SmtB and Zur are important regulators of bacterial zinc metabolism. In mycobacteria, these regulators are encoded by an operon, whereas in other bacterial species, SmtB and Zur are encoded on separate loci. Here, we show that the smtB-zur operon is consistently present within the genus Mycobacterium but otherwise found only in Nocardia, Saccharothrix, and Corynebacterium diphtheriae By RNA deep sequencing, we determined the Zur and SmtB regulons of MSMEG and compared them with transcriptional responses after zinc starvation or excess. We found an exceptional genomic clustering of genes whose expression was strongly induced by zur deletion and zinc starvation. These genes encoded zinc importers such as ZnuABC and three additional putative zinc transporters, including the porin MspD, as well as alternative ribosomal proteins. In contrast, only a few genes were affected by deletion of smtB and zinc excess. The zinc exporter ZitA was most prominently regulated by SmtB. Moreover, transcriptional analyses in combination with promoter and chromatin immunoprecipitation assays revealed a special regulation of the smtB-zur operon itself: an apparently zinc-independent, constitutive expression of smtB-zur resulted from sensitive coregulation by both SmtB and Zur. Overall, our data revealed yet unknown peculiarities of mycobacterial zinc homeostasis.IMPORTANCE Zinc is crucial for many biological processes, as it is an essential cofactor of enzymes and a structural component of regulatory and DNA binding proteins. Hence, all living cells require zinc to maintain constant intracellular levels. However, in excess, zinc is toxic. Therefore, cellular zinc homeostasis needs to be tightly controlled. In bacteria, this is achieved by transcriptional regulators whose activity is mediated via zinc-dependent conformational changes promoting or preventing their binding to DNA. SmtB and Zur are important antagonistically acting bacterial regulators in mycobacteria. They sense changes in zinc concentrations in the femtomolar range and regulate transcription of genes for zinc acquisition, storage, and export. Here, we analyzed the role of SmtB and Zur in zinc homeostasis in Mycobacterium smegmatis Our results revealed novel insights into the transcriptional processes of zinc homeostasis in mycobacteria and their regulation.
    • An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria.

      Elliott, Alysha G; Huang, Johnny X; Neve, Søren; Zuegg, Johannes; Edwards, Ingrid A; Cain, Amy K; Boinett, Christine J; Barquist, Lars; Lundberg, Carina Vingsbo; Steen, Jason; et al. (2020-06-23)
      Peptide antibiotics are an abundant and synthetically tractable source of molecular diversity, but they are often cationic and can be cytotoxic, nephrotoxic and/or ototoxic, which has limited their clinical development. Here we report structure-guided optimization of an amphipathic peptide, arenicin-3, originally isolated from the marine lugworm Arenicola marina. The peptide induces bacterial membrane permeability and ATP release, with serial passaging resulting in a mutation in mlaC, a phospholipid transport gene. Structure-based design led to AA139, an antibiotic with broad-spectrum in vitro activity against multidrug-resistant and extensively drug-resistant bacteria, including ESBL, carbapenem- and colistin-resistant clinical isolates. The antibiotic induces a 3–4 log reduction in bacterial burden in mouse models of peritonitis, pneumonia and urinary tract infection. Cytotoxicity and haemolysis of the progenitor peptide is ameliorated with AA139, and the ‘no observable adverse effect level’ (NOAEL) dose in mice is ~10-fold greater than the dose generally required for efficacy in the infection models
    • Targeting zonulin and intestinal epithelial barrier function to prevent onset of arthritis.

      Tajik, Narges; Frech, Michael; Schulz, Oscar; Schälter, Fabian; Lucas, Sébastien; Azizov, Vugar; Dürholz, Kerstin; Steffen, Franziska; Omata, Yasunori; Rings, Andreas; et al. (Springer Nature, 2020-04-24)
      Gut microbial dysbiosis is associated with the development of autoimmune disease, but the mechanisms by which microbial dysbiosis affects the transition from asymptomatic autoimmunity to inflammatory disease are incompletely characterized. Here, we identify intestinal barrier integrity as an important checkpoint in translating autoimmunity to inflammation. Zonulin family peptide (zonulin), a potent regulator for intestinal tight junctions, is highly expressed in autoimmune mice and humans and can be used to predict transition from autoimmunity to inflammatory arthritis. Increased serum zonulin levels are accompanied by a leaky intestinal barrier, dysbiosis and inflammation. Restoration of the intestinal barrier in the pre-phase of arthritis using butyrate or a cannabinoid type 1 receptor agonist inhibits the development of arthritis. Moreover, treatment with the zonulin antagonist larazotide acetate, which specifically increases intestinal barrier integrity, effectively reduces arthritis onset. These data identify a preventive approach for the onset of autoimmune disease by specifically targeting impaired intestinal barrier function.
    • Methylation of Salmonella Typhimurium flagella promotes bacterial adhesion and host cell invasion.

      Horstmann, Julia A; Lunelli, Michele; Cazzola, Hélène; Heidemann, Johannes; Kühne, Caroline; Steffen, Pascal; Szefs, Sandra; Rossi, Claire; Lokareddy, Ravi K; Wang, Chu; et al. (2020-04-24)
      The long external filament of bacterial flagella is composed of several thousand copies of a single protein, flagellin. Here, we explore the role played by lysine methylation of flagellin in Salmonella, which requires the methylase FliB. We show that both flagellins of Salmonella enterica serovar Typhimurium, FliC and FljB, are methylated at surface-exposed lysine residues by FliB. A Salmonella Typhimurium mutant deficient in flagellin methylation is outcompeted for gut colonization in a gastroenteritis mouse model, and methylation of flagellin promotes bacterial invasion of epithelial cells in vitro. Lysine methylation increases the surface hydrophobicity of flagellin, and enhances flagella-dependent adhesion of Salmonella to phosphatidylcholine vesicles and epithelial cells. Therefore, posttranslational methylation of flagellin facilitates adhesion of Salmonella Typhimurium to hydrophobic host cell surfaces, and contributes to efficient gut colonization and host infection.
    • Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms.

      Le, Philipp; Kunold, Elena; Macsics, Robert; Rox, Katharina; Jennings, Megan C; Ugur, Ilke; Reinecke, Maria; Chaves-Moreno, Diego; Hackl, Mathias W; Fetzer, Christian; et al. (2020-02)
    • Tcf1 cells are required to maintain the inflationary T cell pool upon MCMV infection.

      Welten, Suzanne P M; Yermanos, Alexander; Baumann, Nicolas S; Wagen, Franziska; Oetiker, Nathalie; Sandu, Ioana; Pedrioli, Alessandro; Oduro, Jennifer D; Reddy, Sai T; Cicin-Sain, Luka; et al. (Springer Nature, 2020-05-08)
      Cytomegalovirus-based vaccine vectors offer interesting opportunities for T cell-based vaccination purposes as CMV infection induces large numbers of functional effector-like cells that accumulate in peripheral tissues, a process termed memory inflation. Maintenance of high numbers of peripheral CD8 T cells requires continuous replenishment of the inflationary T cell pool. Here, we show that the inflationary T cell population contains a small subset of cells expressing the transcription factor Tcf1. These Tcf1+ cells resemble central memory T cells and are proliferation competent. Upon sensing viral reactivation events, Tcf1+ cells feed into the pool of peripheral Tcf1- cells and depletion of Tcf1+ cells hampers memory inflation. TCR repertoires of Tcf1+ and Tcf1- populations largely overlap, with the Tcf1+ population showing higher clonal diversity. These data show that Tcf1+ cells are necessary for sustaining the inflationary T cell response, and upholding this subset is likely critical for the success of CMV-based vaccination approaches.