{"entity": "researcher", "timestamp": "2026-07-17T08:47:33.555Z", "family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640"}}, "publications": [{"entity": "publication", "iuid": "e05c68328fed4b66bdae56b5a53a8183", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e05c68328fed4b66bdae56b5a53a8183.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e05c68328fed4b66bdae56b5a53a8183"}}, "title": "Enrichment of Neural Crest Cells by Antibody Labeling and Flow Cytometry for Single-Cell Transcriptomics in a Lizard.", "authors": [{"family": "Pranter", "given": "Robin", "initials": "R", "orcid": "0000-0003-3615-0281", "researcher": {"href": "https://publications.scilifelab.se/researcher/02c2a85e333a477597ff77429646a0a9.json"}}, {"family": "Patthey", "given": "Cedric", "initials": "C", "orcid": "0000-0002-2627-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7707e8bd3d4e029fb1e1f43df86ad4.json"}}, {"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Evol Dev", "issn": "1525-142X", "volume": "28", "issue": "1", "pages": "e70030", "issn-l": null}, "abstract": "Neural crest cells (NCCs) are a key component of the vertebrate body plan and contribute to a variety of different traits. Recent advances in single-cell transcriptomics (scRNA-seq) have significantly improved our understanding of NCC biology. However, their dynamic migratory behavior and spatiotemporal heterogeneity in the developing embryo pose significant challenges for their identification and isolation. Consequently, most studies of NCCs have been confined to model organisms with established transgenic tools or established methods for in ovo manipulation. To overcome this limitation, we present a novel approach that combines antibody labeling with fluorescence activated cell sorting to enrich for NCCs and we demonstrate the approach in the common wall lizard (Podarcis muralis). Through microscopy, reverse transcription quantitative polymerase chain reaction and single-cell RNA sequencing, we show that the method enriches for NCCs as efficiently as methods relying on transgenic animals. Using this technique, we successfully characterize transcriptional profiles of NCCs in wall lizard embryos. We anticipate that this method can be applied to a wide range of vertebrates that lack transgenic tools, enabling deeper insights into the diverse roles of neural crest cells in development and evolution.", "doi": "10.1111/ede.70030", "pmid": "41709476", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12917300"}], "notes": [], "created": "2026-02-26T15:21:38.415Z", "modified": "2026-03-24T09:08:52.661Z"}, {"entity": "publication", "iuid": "7d3c4336130e450099e81cfa741064ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d3c4336130e450099e81cfa741064ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d3c4336130e450099e81cfa741064ec"}}, "title": "Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.", "authors": [{"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}, {"family": "Yang", "given": "Weizhao", "initials": "W"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "While", "given": "Geoffrey M", "initials": "GM", "orcid": "0000-0001-8122-9322", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40ba32f8185473fa3543815e8a539fe.json"}}, {"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications.scilifelab.se/researcher/6346267a5c3e41c6a6825b7b20a53fa5.json"}}], "type": "journal article", "published": "2024-04-05", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "14", "pages": "eadk9315", "issn-l": "2375-2548"}, "abstract": "The joint expression of particular colors, morphologies, and behaviors is a common feature of adaptation, but the genetic basis for such \"phenotypic syndromes\" remains poorly understood. Here, we identified a complex genetic architecture associated with a sexually selected syndrome in common wall lizards, by capitalizing on the adaptive introgression of coloration and morphology into a distantly related lineage. Consistent with the hypothesis that the evolution of phenotypic syndromes in vertebrates is facilitated by developmental linkage through neural crest cells, most of the genes associated with the syndrome are involved in neural crest cell regulation. A major locus was a ~400-kb region, characterized by standing structural genetic variation and previously implied in the evolutionary innovation of coloration and beak size in birds. We conclude that features of the developmental and genetic architecture contribute to maintaining trait integration, facilitating the extensive and rapid introgressive spread of suites of sexually selected characters.", "doi": "10.1126/sciadv.adk9315", "pmid": "38569035", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10990284"}], "notes": [], "created": "2024-04-09T12:41:11.047Z", "modified": "2024-11-25T10:28:12.121Z"}, {"entity": "publication", "iuid": "6c5569285c5a4939ad2be97774b5939e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c5569285c5a4939ad2be97774b5939e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c5569285c5a4939ad2be97774b5939e"}}, "title": "The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype.", "authors": [{"family": "Earley", "given": "Timothy S", "initials": "TS", "orcid": "0000-0002-1549-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/7521826230264103acc78925ddb975cd.json"}}, {"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}, {"family": "Alvarez", "given": "Mariano F", "initials": "MF", "orcid": "0000-0002-9951-0013", "researcher": {"href": "https://publications.scilifelab.se/researcher/a99b8df8bf6f4f5f844f3d2025c02d06.json"}}, {"family": "Coolon", "given": "Joseph D", "initials": "JD", "orcid": "0000-0003-1591-9418", "researcher": {"href": "https://publications.scilifelab.se/researcher/f768f1de33f14431afa619b2d3299873.json"}}, {"family": "Sultan", "given": "Sonia E", "initials": "SE", "orcid": "0000-0001-8815-6437", "researcher": {"href": "https://publications.scilifelab.se/researcher/03c672c25b2a40609e638d4295b333ab.json"}}], "type": "journal article", "published": "2023-09-27", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "290", "issue": "2007", "pages": "20230824", "issn-l": "0962-8452"}, "abstract": "Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant Persicaria maculosa by varying two key resources-light and soil moisture-in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e. the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes, although the precise proportion of parental versus immediate DETs varied among genotypes. By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptomic level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.", "doi": "10.1098/rspb.2023.0824", "pmid": "37752834", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10523085"}, {"db": "Dryad", "key": "10.5061/dryad.jsxksn0fp"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.6834925"}], "notes": [], "created": "2023-11-24T08:25:14.399Z", "modified": "2024-01-16T13:48:32.052Z"}, {"entity": "publication", "iuid": "25a29e9b946b4f01b58409c5d20272c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25a29e9b946b4f01b58409c5d20272c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25a29e9b946b4f01b58409c5d20272c4"}}, "title": "Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.", "authors": [{"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}, {"family": "Radersma", "given": "Reinder", "initials": "R"}, {"family": "Vasquez", "given": "Louella", "initials": "L"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Tobi", "given": "Elmar W", "initials": "EW"}, {"family": "Heijmans", "given": "Bastiaan T", "initials": "BT"}, {"family": "Uller", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2022-05-20", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "25", "issue": "5", "pages": "104303"}, "abstract": "Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities.", "doi": "10.1016/j.isci.2022.104303", "pmid": "35573201", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2589-0042(22)00573-9"}, {"db": "pmc", "key": "PMC9097707"}, {"db": "Dryad", "key": "10.5061/dryad.f4qrfj6xq"}], "notes": [], "created": "2022-05-06T10:42:50.020Z", "modified": "2024-01-16T13:48:36.473Z"}]}