{"entity": "researcher", "timestamp": "2026-03-17T02:33:29.982Z", "family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "affiliations": ["Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 Centre for Microbial Research (UCMR), Ume\u00e5 University, Ume\u00e5, Sweden. maria.fallman@umu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc"}}, "publications": [{"entity": "publication", "iuid": "bd2469b856a34c23bf93587d768559f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2"}}, "title": "A two-step activation mechanism enables mast cells to differentiate their response between extracellular and invasive enterobacterial infection.", "authors": [{"family": "von Beek", "given": "Christopher", "initials": "C", "orcid": "0000-0001-6310-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ea7730832f4f45ae6583076d90418a.json"}}, {"family": "Fahlgren", "given": "Anna", "initials": "A"}, {"family": "Geiser", "given": "Petra", "initials": "P", "orcid": "0000-0003-2785-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0bf10f41dc4698b19288809bae2dd6.json"}}, {"family": "Di Martino", "given": "Maria Letizia", "initials": "ML", "orcid": "0000-0002-9491-4000", "researcher": {"href": "https://publications.scilifelab.se/researcher/708eae058cb3494f8407574a666a16f0.json"}}, {"family": "Lindahl", "given": "Otto", "initials": "O", "orcid": "0000-0001-7518-9483", "researcher": {"href": "https://publications.scilifelab.se/researcher/78053dd357c3435ba53aff83f06f28a4.json"}}, {"family": "Prensa", "given": "Grisna I", "initials": "GI", "orcid": "0009-0002-7101-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d030d78925948d993999b66e1959acc.json"}}, {"family": "Mendez-Enriquez", "given": "Erika", "initials": "E", "orcid": "0000-0002-2114-2812", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae73474be904a638ec13a8f704a9154.json"}}, {"family": "Eriksson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8945-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/b94e7f542841474d86d53aa48958f870.json"}}, {"family": "Hallgren", "given": "Jenny", "initials": "J", "orcid": "0000-0002-3685-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe8b929dbe60446f96db17a5eb2ba6f3.json"}}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}], "type": "journal article", "published": "2024-01-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "904", "issn-l": "2041-1723"}, "abstract": "Mast cells localize to mucosal tissues and contribute to innate immune defense against infection. How mast cells sense, differentiate between, and respond to bacterial pathogens remains a topic of ongoing debate. Using the prototype enteropathogen Salmonella Typhimurium (S.Tm) and other related enterobacteria, here we show that mast cells can regulate their cytokine secretion response to distinguish between extracellular and invasive bacterial infection. Tissue-invasive S.Tm and mast cells colocalize in the mouse gut during acute Salmonella infection. Toll-like Receptor 4 (TLR4) sensing of extracellular S.Tm, or pure lipopolysaccharide, causes a modest induction of cytokine transcripts and proteins, including IL-6, IL-13, and TNF. By contrast, type-III-secretion-system-1 (TTSS-1)-dependent S.Tm invasion of both mouse and human mast cells triggers rapid and potent inflammatory gene expression and >100-fold elevated cytokine secretion. The S.Tm TTSS-1 effectors SopB, SopE, and SopE2 here elicit a second activation signal, including Akt phosphorylation downstream of effector translocation, which combines with TLR activation to drive the full-blown mast cell response. Supernatants from S.Tm-infected mast cells boost macrophage survival and maturation from bone-marrow progenitors. Taken together, this study shows that mast cells can differentiate between extracellular and host-cell invasive enterobacteria via a two-step activation mechanism and tune their inflammatory output accordingly.", "doi": "10.1038/s41467-024-45057-w", "pmid": "38291037", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10828507"}, {"db": "pii", "key": "10.1038/s41467-024-45057-w"}], "notes": [], "created": "2024-03-21T12:10:55.423Z", "modified": "2024-03-21T12:10:55.804Z"}, {"entity": "publication", "iuid": "4d45ed3127e14888bfb30d089ff84763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d45ed3127e14888bfb30d089ff84763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d45ed3127e14888bfb30d089ff84763"}}, "title": "RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.", "authors": [{"family": "Avican", "given": "Kemal", "initials": "K", "orcid": "0000-0003-0707-2050", "researcher": {"href": "https://publications.scilifelab.se/researcher/84631a1299084ea695653c961e906ff3.json"}}, {"family": "Aldahdooh", "given": "Jehad", "initials": "J"}, {"family": "Togninalli", "given": "Matteo", "initials": "M"}, {"family": "Mahmud", "given": "A K M Firoj", "initials": "AKMF", "orcid": "0000-0002-6541-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6eb0bf023f343359be1914cb9100c0e.json"}}, {"family": "Tang", "given": "Jing", "initials": "J", "orcid": "0000-0001-7480-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1219a45cf6a428c87b6d99369e5f726.json"}}, {"family": "Borgwardt", "given": "Karsten M", "initials": "KM"}, {"family": "Rhen", "given": "Mikael", "initials": "M"}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}], "type": "comparative study", "published": "2021-06-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3282", "issn-l": "2041-1723"}, "abstract": "Bacterial processes necessary for adaption to stressful host environments are potential targets for new antimicrobials. Here, we report large-scale transcriptomic analyses of 32 human bacterial pathogens grown under 11 stress conditions mimicking human host environments. The potential relevance of the in vitro stress conditions and responses is supported by comparisons with available in vivo transcriptomes of clinically important pathogens. Calculation of a probability score enables comparative cross-microbial analyses of the stress responses, revealing common and unique regulatory responses to different stresses, as well as overlapping processes participating in different stress responses. We identify conserved and species-specific 'universal stress responders', that is, genes showing altered expression in multiple stress conditions. Non-coding RNAs are involved in a substantial proportion of the responses. The data are collected in a freely available, interactive online resource (PATHOgenex).", "doi": "10.1038/s41467-021-23588-w", "pmid": "34078900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23588-w"}, {"db": "pmc", "key": "PMC8172932"}], "notes": [], "created": "2021-10-01T09:00:20.445Z", "modified": "2021-12-06T13:46:14.370Z"}, {"entity": "publication", "iuid": "38f9cf370fca43aea73e0146f2e1a8e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38f9cf370fca43aea73e0146f2e1a8e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38f9cf370fca43aea73e0146f2e1a8e6"}}, "title": "Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.", "authors": [{"family": "Mahmud", "given": "A K M Firoj", "initials": "AKMF"}, {"family": "Nilsson", "given": "Kristina", "initials": "K"}, {"family": "Fahlgren", "given": "Anna", "initials": "A"}, {"family": "Navais", "given": "Roberto", "initials": "R"}, {"family": "Choudhury", "given": "Rajdeep", "initials": "R"}, {"family": "Avican", "given": "Kemal", "initials": "K"}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}], "type": "journal article", "published": "2020-11-10", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "5", "issue": "6", "pages": null, "issn-l": "2379-5077"}, "abstract": "RpoN, an alternative sigma factor commonly known as \u03c354, is implicated in persistent stages of Yersinia pseudotuberculosis infections in which genes associated with this regulator are upregulated. We here combined phenotypic and genomic assays to provide insight into its role and function in this pathogen. RpoN was found essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping genome-wide associations of Y. pseudotuberculosis RpoN using chromatin immunoprecipitation coupled with next-generation sequencing identified an RpoN binding motif located at 103 inter- and intragenic sites on both sense and antisense strands. Deletion of rpoN had a large impact on gene expression, including downregulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing. There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. Matching differential gene expression with locations of the binding sites implicated around 130 genes or operons potentially activated or repressed by RpoN. Mutagenesis of selected intergenic binding sites confirmed both positive and negative regulatory effects of RpoN binding. Corresponding mutations of intragenic sense sites had less impact on associated gene expression. Surprisingly, mutating intragenic sites on the antisense strand commonly reduced expression of genes carried by the corresponding sense strand.IMPORTANCE The alternative sigma factor RpoN (\u03c354), which is widely distributed in eubacteria, has been implicated in controlling gene expression of importance for numerous functions including virulence. Proper responses to host environments are crucial for bacteria to establish infection, and regulatory mechanisms involved are therefore of high interest for development of future therapeutics. Little is known about the function of RpoN in the intestinal pathogen Y. pseudotuberculosis, and we therefore investigated its regulatory role in this pathogen. This regulator was indeed found to be critical for establishment of infection in mice, likely involving its requirement for motility and biofilm formation. The RpoN regulon involved both activating and suppressive effects on gene expression which could be confirmed with mutagenesis of identified binding sites. This is the first study of its kind of RpoN in Y. pseudotuberculosis, revealing complex regulation of gene expression involving both productive and silent effects of its binding to DNA, providing important information about RpoN regulation in enterobacteria.", "doi": "10.1128/mSystems.01006-20", "pmid": "33172972", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "5/6/e01006-20"}, {"db": "pmc", "key": "PMC7657599"}], "notes": [], "created": "2020-11-21T09:21:23.391Z", "modified": "2024-01-16T13:48:41.377Z"}]}