{"entity": "researcher", "timestamp": "2026-10-05T21:40:47.488Z", "family": "Ryd\u00e9n", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "affiliations": ["Department of Mathematics and Mathematical Statistics, Ume\u00e5 University, Ume\u00e5, SE, 90187, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef"}}, "publications": [{"entity": "publication", "iuid": "9ffabc46b92c4c76be483815e6bba9dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffabc46b92c4c76be483815e6bba9dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffabc46b92c4c76be483815e6bba9dc"}}, "title": "Epigenetic mediation may explain intergenerational associations between maternal obesogenic lifestyle and children's birth weight: findings from the NorthPop prospective birth cohort.", "authors": [{"family": "De Silva", "given": "Kushan", "initials": "K", "orcid": "0000-0003-0301-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fb44e3f1d204c2a996e747704e2e77f.json"}}, {"family": "Lundberg-Ulfsdotter", "given": "Richard", "initials": "R"}, {"family": "Bod\u00e9n", "given": "Stina", "initials": "S", "orcid": "0000-0002-8958-975X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dcfadb86b8040499a7af3c4a744d3b2.json"}}, {"family": "Vinnars", "given": "Marie-Therese", "initials": "MT"}, {"family": "Ryden", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}}, {"family": "West", "given": "Christina E", "initials": "CE", "orcid": "0000-0001-9599-2580", "researcher": {"href": "https://publications.scilifelab.se/researcher/be2972e4afa744e5aa0525a4c9d89348.json"}}, {"family": "Domell\u00f6f", "given": "Magnus", "initials": "M"}, {"family": "Harlid", "given": "Sophia", "initials": "S", "orcid": "0000-0001-8540-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a824f2687b460890ae6d9ef40d97c9.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "17", "issue": "1", "pages": "180", "issn-l": "1868-7075"}, "abstract": "Epigenetic alterations during fetal development have been proposed as key factors explaining associations between maternal lifestyle during pregnancy and later health outcomes in the offspring, pertaining to the developmental origin of health and disease hypothesis.\n\nTo assess the association of maternal lifestyle with offsprings' birth weight and underlying epigenetic mediatory mechanisms in the NorthPop prospective birth cohort.\n\nA three-step analytic pipeline was applied. In 722 mother-child pairs, overall associations between ten maternal lifestyle factors and the offspring's standardized birth weight were first evaluated by multiple linear regression. Three high-dimensional mediation methods, based on sure independence screening and penalized regression, were then applied on the beta methylation matrix to identify candidate CpG mediators in cord blood driving the significant overall associations. Finally, robust and ordinary least squares (OLS) regression-based classical mediation methods were used with candidate CpG probes to assess single- and multiple (parallel and serial)-mediator models on a low-dimensional space.\n\nGestational weight gain (GWG) (\u03b2-adj = 0.03; p = 2 \u00d7 10-5) and maternal BMI at the beginning of pregnancy (\u03b2-adj = 0.036; p = 1 \u00d7 10-4) were significantly associated with the offspring's standardized birth weight. High-dimensional mediation analyses identified pooled sets of four (cg19242268 [TCEA2]; cg08461903 [N/A]; cg14798382 [CHERP/C19orf44] and cg21516291 [SLC35C2]) and five (cg17040807 [CYGB]; cg19242268 [TCEA2]; cg26552621 [CIRBP]; cg04457572 [CDH23] and cg06457011 [PLCG1]) candidate CpG mediators related to GWG and BMI at the beginning of pregnancy, respectively. For both exposures, classical mediation analyses revealed a range of significant single- and multiple (both serial and parallel)-mediator models via both robust and OLS regression based approaches. These indicated the likely presence of individual, causally linked multiple, and causally independent multiple mediatory pathways underlying the two significant overall associations.\n\nOur findings support the hypothesis that neonatal health effects related to maternal lifestyle may be partly mediated by epigenetic alterations. Findings also suggest the possible involvement of multiple DNA methylation sites via various mediatory pathways.", "doi": "10.1186/s13148-025-02001-z", "pmid": "41163109", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12570728"}, {"db": "pii", "key": "10.1186/s13148-025-02001-z"}], "notes": [], "created": "2025-11-07T07:25:46.328Z", "modified": "2025-11-11T13:52:44.760Z"}, {"entity": "publication", "iuid": "c9468bade168413f9365ee51ab1da260", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260"}}, "title": "Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.", "authors": [{"family": "Kellgren", "given": "Therese", "initials": "T", "orcid": "0000-0002-4911-7037", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c7a5a8c5024d5186f1a4d7385778e2.json"}}, {"family": "Dwibedi", "given": "Chinmay", "initials": "C", "orcid": "0000-0001-6416-4440", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b0dbf807be449da1856c0c018f13a3.json"}}, {"family": "Widerstr\u00f6m", "given": "Micael", "initials": "M", "orcid": "0000-0002-1483-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/563f129fdb4e468395de5df2a7e80ee4.json"}}, {"family": "Sundell", "given": "David", "initials": "D", "orcid": "0000-0002-6269-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/084bd7876637499b929007562d5ac03a.json"}}, {"family": "\u00d6hrman", "given": "Caroline", "initials": "C", "orcid": "0000-0003-0516-7523", "researcher": {"href": "https://publications.scilifelab.se/researcher/a347bde191ef42a98a8aaba829adb553.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Monsen", "given": "Tor", "initials": "T", "orcid": "0000-0001-8489-757X", "researcher": {"href": "https://publications.scilifelab.se/researcher/804b654aa0be4d7a9ecdf113487fe443.json"}}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}}, {"family": "Johansson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0548-5943", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4cd5b852fab4d5da3231939f060e3f5.json"}}], "type": "journal article", "published": "2024-06-19", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "24", "issue": "1", "pages": "215", "issn-l": "1471-2180"}, "abstract": "A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings.\n\nWe completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2.\n\nThis study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.", "doi": "10.1186/s12866-024-03367-5", "pmid": "38890594", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11186124"}, {"db": "pii", "key": "10.1186/s12866-024-03367-5"}], "notes": [], "created": "2024-06-28T06:39:22.789Z", "modified": "2024-11-25T10:30:17.631Z"}]}